Quantitative Biology

An Exploration of Viral Evolution Following Zoonosis with Suggestions for Avoiding Future Pandemics

Authors: Patrick Douglas Shaw Stewart
Comments: 13 Pages.

The significant death toll from major viral outbreaks during the past century highlights the importance of understanding the factors that determine whether zoonotic spillovers escalate into full-blown human epidemics. Hundreds of thousands of humans are made sick by animal-derived viruses such as Lassa, Nipah, Marburg, and Ebola every year. This includes thousands of fatalities. Moreover, many viruses, including the four pathogens mentioned above, exhibit human-to-human spread. Given this information, an explanation is needed for why human viral pandemics caused by animal viruses are relatively rare. This review proposes that variations in the fidelity of viral replication play an important role and that low-fidelity replication creates a barrier to extended human-to-human transmission. After a zoonotic transfer to humans, a virus will be subject to unusually strong selection, and full adaptation to the new host would typically require multiple mutations. A rapid route for accumulating such mutations involves minor alterations to the virus's polymerase that increase its mutation frequency, allowing more rapid adaptation. I refer to this route as the mutation-induced enhanced mutability pathway (MIEMP). However, the cost of this route may be the loss of the virus’s long-term viability when harmful mutations accumulate. Recombination with a strain with a high-fidelity polymerase could, however, restore fidelity and longevity. This would typically require another virus jump from the original animal reservoir to an infected human. We might expect the MIEMP pathway to be active after zoonosis and also when a virus is subjected to strong selective pressures. There is some evidence from the COVID-19 pandemic to support this scenario: firstly, COVID-19 epidemics in several countries showed rapid rises followed by sudden collapses. Some lineages appeared to lose viability throughout large geographical areas very suddenly, which may have been a result of low fidelity. This is compatible with a MIEMP origin. Secondly, several SARS-CoV-2 variants, including the Omicron variants, appeared with a jump in the number of mutations compared to previous lineages, which is compatible with MIEMP followed by recombination. The same variants also had many mutations in the Spike gene but fewer in the rest of the genome. Moreover, an anomalously low proportion of the mutations in the Spike of Omicron (and other variants) were C-to-T nucleotide "transitions." Many coronaviruses have an excess of C-to-T transitions (often caused by host modifications of viral RNA). In contrast, low-fidelity polymerases are expected to generate all nucleotide exchanges randomly. This mutational pattern, which is otherwise difficult to explain, is therefore consistent with recombination events, where much of the right-hand-end "structural protein" sections of the genomes of these variants, including the Spike genes, came from error-prone partners, while much of the non-structural protein sections, including the polymerases, came from high-fidelity partners. These conclusions lead to recommendations for avoiding conditions that might allow dangerous recombination between well-adapted strains and high-fidelity spillovers.
Category: Quantitative Biology

Patterns of Transposable Element Distribution Around Chromatin Ligation Points Revealed by Micro-C Data Analysis

Authors: Alexandr V. Vikhorev, Michael M. Rempel, Oksana O. Polesskaya, Ivan V. Savelev, Max V. Myakishev-Rempel
Comments: 25 Pages.

Transposable elements (TEs) constitute a significant portion of eukaryotic genomes, yet their role in chromatin organization remains poorly understood. This study investigates the distribution patterns of TEs around chromatin ligation points (LPs) identified through Micro-C experiments in human cells. We analyzed the density of various TE families within a 100kb window centered on LPs, focusing on major families such as Alu and LINE-1 (L1) elements. Our findings reveal distinct, non-random distribution patterns that differ between TE families and exhibit consistent strand-specific biases. These patterns were reproducible across two independent datasets and showed marked differences from random genomic distributions. Notably, we observed family-specific variations in TE density near LPs, with some families showing depletion at LPs followed by periodic fluctuations in density. The consistency of these patterns across TE families and their orientation relative to chromosome arms suggest a fundamental relationship between TEs and higher-order chromatin structure. Our results provide new insights into the potential role of TEs in genome organization and challenge the notion of TEs as passive genomic components. This study lays the groundwork for future investigations into the functional implications of TE distribution in chromatin architecture and gene regulation.
Category: Quantitative Biology

Extraterrestrial Genetics

Authors: Max Myakishev-Rempel, Michael M. Rempel, Richard Alan Miller
Comments: 9 Pages. (Note by viXra Admin: An abstract and scientific references are required)

The Extraterrestrial Genetics Research Proposal (XG1) investigates the hypothesis that extraterrestrial beings have influenced human evolution through genetic engineering. By analyzing human and other species' genomes, the study seeks to uncover potential alien genetic contributions. Advanced bioinformatics and experimental sequencing techniques will be used to examine public genome data, DNA from self-identified abductees, starseeds, and hybrids, as well as ancient and modern skulls with unusual morphologies.The research will analyze genetic data for patterns indicative of alien manipulation, such as incomplete parental contributions and large genetic insertions, particularly in populations with alleged extraterrestrial connections. It will also investigate domesticated animals, plants, and cancer genomic data to identify artificial manipulation signatures. Additionally, the project will explore genetic markers in extraordinary individuals and starseeds using 23andMe data. Finally, stardust analysis aims to detect extraterrestrial spores in high orbit around Earth through collaboration with space industry leaders.
Category: Quantitative Biology

The Precision Oncology Approach to Molecular Cancer Therapeutics Targeting Oncogenic Signaling Pathways is a Means to an End

Authors: Manish Kumar
Comments: 53 Pages. Pictures and other related data have been taken from sources freely available for reuse or permission for the same can be obtained upon request. Pictures no. 1 and 2 have been added to the text with permission from Elsevier. (Order No. 5521991271884, date

Cancer is a deadly genetic disease with diverse aspects of complexity, including cancer immune evasion, treatment resistance, and recurrence requiring optimized treatment to be cured.Molecular studies have revealed that tumors are profoundly heterogeneous in nature, leading to the complexity of cancer progression that is ultimately linked to its genetic machinery. It is important to note that patients with the same types of cancer respond differently to cancer treatments, indicating the need for patient-specific treatment options. This requires an in-depth genomic study of the patient's tumors tofully understand the driving factors of cancer for effective targeted therapy. Precision oncology has evolved as a form of cancer therapy focused on genetic profiling of tumors to identify molecular alterations involved in cancer development for tailored individualized treatment of the disease. Whole genome sequencing, tumor and cell-free DNA profiling, transcriptomics, proteomics and exploration ofthe cancer immune system form the basis of this field of cancer research and treatment. This article aims to briefly explain the foundations and frontiers of precision oncology in the context of ongoing technological advancements in related fields of study in to assess its scope and importance in achieving effective cure against cancer.
Category: Quantitative Biology

Probabilistic Modeling in the Inference of Fungi Viability

Authors: Jorge Fernandez-de-Cossio, Ariadna Mendoza-Cuevas, Amanda Paz
Comments: 19 Pages.

Preservation of large volumes of documentary materials requires massive treatments to control fungal biodeterioration. Multi-inoculum in limited-dilution experiments is an economical format to provide informative data for fungal viability. Data gathering can be simpler and more precise, when the model for the assessment of viability depends on the number of colonized wells instead of the number of colonies, since the later vary in shape and definition. Probabilistic modeling for this kind of data led us to a truncated form of the Beta-exponential function, a variant from a family of generalized distributions, recently derived. We discuss performance from actual experimental data, and evaluate antifungal effect of biocide treatments in terms of viability.
Category: Quantitative Biology

Epigenetic Modeling as a Remedy for the Missing Heritability Problem

Authors: Stephen P. Smith
Comments: 15 Pages.

This paper argues that confounding between epigenetic and additive genetic effects explains the missing heritability problem, and offers two new epigenetic models describing transgenerational inheritance that may supplement the traditional mixed linear models used to make predictions of the additive genetic merit of animals. The new models utilize pedigree information and show the property of additivity, like the additive genetic models do. The combined predictions of both epigenetic and genetic effects may provide useful indexes that help farmers select replacement animals or breeding stock. The utility of these methods depends on data where both confounding and the parsimony of parameters come to bear on practical limits. The proposed epigenetic models are just a first step, and they may not win long-term favor when compared to future models that are still to be formulated.
Category: Quantitative Biology

Honey Bees Don`t Like it Hot Temperature Measurements in Beehives During High Sunlight

Authors: Marco Messelken, Julia Wurm, Claus Brell
Comments: 6 Pages. This paper is based on a contribution to the conference of the Entomologische Gesellschaft Düsseldorf e.V. in Düsseldorf, Germany, 2023

First measurements with the help of several temperature sensors in a beehive show that a high heat input through solar radiation in a beehive leads to stress in the bee colony. The bees show cooling behavior that can be observed directly and with sound analyses in order not to let the temperature in the hive rise above 38°C. A measurement without bees shows a difference in internal temperature of up to 7°C in a comparison between a shaded and an unshaded hive. The heat input can be reduced by simple measures such as shading by placing a rear-ventilated radiation shield. It is recommended to shade hives in summer.
Category: Quantitative Biology

COVID-19 Under Origin and Transmission: A Data-Driven Analysis for India and Bangladesh

Authors: Ajantha Devi, Hashnayne Ahmed
Comments: 17 Pages.

he coronavirus disease 2019 (COVID-19) is an exceptionally contagious and pathogenic viral disease brought about by the SARS-CoV-2 infection that was frst detailed at Wuhan, China, and later it spreads everywhere throughout the world. It was a severe acute respiratory syndrome (SARS)-like virus, and the primary host of this virus is bats, revealed through genome analysis. The intermediate medium between human and bats is still unknown, and it is quite contagious, resulting in rapid spreading of this disease. All things onsidered, there are no clinically endorsed medications or antibodies for this sickness, yet a few precautions and staying away from close contacts are suggested. The number of COVD-19 confrmed cases is rapidly increasing with higher mortality rates, more than other epidemics that occurred in the last century although it still fuctuates. We will analyze the COVID-19 outbreak situation considering confrmed cases, recoveries, mortality rate percentages, etc. India and Bangladesh are two geographically important countries, and we will also analyze the COVID-19 situation for these two countries either with similarities or differences.
Category: Quantitative Biology

Study Proposal: Towards Streptococcal Infections With Nonspecific Symptoms

Authors: Arturo Tozzi
Comments: (Note by viXra Admin: Future stub page/article will not be accepted)

In 2023, increases in scarlet fever's incidence have been detected throughout Europe. Based on general pediatricians' experience, we hypothesize that a shift has occurred in both group A streptococcus (GAS) clinical findings and age of onset. Therefore, we propose to evaluate whether the well-standardized signs and symptoms leading to GAS diagnosis still hold.
Category: Quantitative Biology

From Big Bang to Chaotic Complexity: A Theory of Big Evolution

Authors: Nicholas Hoggard
Comments: 29 Pages. (Correction made by viXra Admin to conform with scholarly norm)

One of the mainstays of modern evolutionary biology is that evolution is highly sensitive to initial conditions and that, according to the Butterfly Effect from Chaos Theory, it is impossible to predict evolution in any way. But Chaos Theory is more than the Butterfly Effect, and there are aspects of chaos that - in complete contradiction to the Butterfly Effect - are insensitive to initial conditions. Also known as Universality within Chaos Theory, there is a phenomenon known as a Period-Doubling Cascade, or Feigenbaum Cascade, which is ubiquitous in iterative non-linear dynamic processes with limited resources. And iterative non-linear dynamic processes with limited resources are not exactly uncommon in the universe. Evolution is just such a process.This study examines the spontaneous creation of innovations in Intentional Teaching among animals and early humans. Such innovations occurred during Cultural Evolution, which followed Physical and Biological Evolution. Each of the teaching innovations represents nothing less than a new form of evolution. If one accepts that transmission of cultural information is as legitimate a form of transmission of acquired information as transmission of DNA during biological reproduction, then the innovations in teaching methods are potentially highly significant. There are seven new teaching methods identified by cognitive archaeologists. Each of them transmits a new kind of information that is on a higher cognitive level than previous methods. The co-evolution of tool technology, teaching, and biology, led eventually to spoken language.Examination of the time intervals between these seven evolutionary stages shows that they are compatible with a Feigenbaum Cascade from Chaos Theory. Physical and Biological Evolution also converge to the time pattern of the Cascade, as do the development of information technology in the form of written language, the printing machine, and the computer. This forms the basis of a theory of Big Evolution, which - like Big History - covers the whole of time.
Category: Quantitative Biology

The H-Bond Breakdown Switch Allows DNA and Protein Transitions in the Brain to Control the Dynamics of Hormonal Communication and Learning Vocalization

Authors: Alfred Bennun
Comments: 37 Pages. 12 figures

The choroid plexus epithelium (CPE) generates cerebrospinal fluid (CSF) in a mutual exclusive vectorial kinetic according to a potential of hydrophilic-plasma 0mV -60mV to hydrophobic-CSF +4mV. Astrocytes are cells with actin filaments for pulsatile propulsion in the cell’s skeleton, bi-directional transport of ions gradient Na+, which impulses the CSF flux into the lumen along a glial network. Luminal K+ is required for sustained CSF secretion. At ventricular side, the Na+/K+-ATPase releases the Na+. Quantum mechanics microtubules nano scale (10-9m) flow a parallel transportation from the exterior to the nuclei of glucose, nascent Mg2+, O2, etc., and antiparallel of dimers. The microtubule diameter allows a very small number of molecules in a minimal volume to reach a saturation state for enzyme activity. An increasing in the number of random collisions allows to concatenate Na+/K+ translocation into nano space at minimal capacitance to operate at maximal voltage. Myelination discontinuity at the Ranvier nodes allows open systems exchanges with CSF to re-supply the optimal ion concentration to maintain rapid transmission of the propagation of the action potential. The Doppler shift could tune in with the spin-flip of electrons of a 21 cm line of hydrogen, operating as an antenna for the neuronal membrane action potential state of firing for vectorial networking. Thus, synchronizing the electric potential by a sequence of interneuronal crosstalk could avoid electromagnetic neuronal noises. At the nerve terminal, neurotransmitters are present within 35-50 nm synaptic vesicles that release neurotransmitters that dock and fuse at the base of specialized 10—15 nm cup-shaped lipoproteins. These porosomes range from 15 nm in neurons, astrocytes to 100—180 nm in endocrine and exocrine cells. In striatal neurons adenylyl cyclase (AC) coupled via 7TM receptors via stimulatory or inhibitory receptors (Rs and Ri) on G protein phosphorylation. A dopamine-(DA)-dependent cAMP/PKA interactions with acetylcholine and adenosine signals for DA transients to carry reward-related signals in learning reinforcement. The enthalpies of AC-H-bonds breakdown of intermediates coordinated by Mg2+ and bending and sliding when calmodulin release of Ca2+ to coordinative into hydrophobic box, and release of dimers in the up-hill thermodynamics cycling AMP into cAMP, creating molecular transitions capable to participate in meaningful encoding signals coordinative stages. The Mg-cAMP response element binding (CREB) protein by insertion for DNA H-bond breakdown unzipping into three strands and transcription cycle turnover by coupling to H-bond donor water cluster.
Category: Quantitative Biology

A Model and Genomic Evidence of Imprinting DNA Sequence on Water Structure Around Nucleosomes

Authors: Ivan Savelev, Aleksandr Vikhorev, Nelly Zyryanova, Oksana Polesskaya, Richard Alan, Miller, Inna Plastun, Pavel Zhylidin, Pavel Filin, Michael Rempel, Max Myakishev-Rempel
Comments: 4 Pages. (Corrections made by viXra Admin to conform with scholarly norm)

This paper presents a model where DNA imprints its structure on water, proposing a continuous and dynamic self-reorganization process of water clusters, called snowflake signaling. The model's hypothesis is that DNA structure affects water structure in the cell nucleus. Genomic evidence supports the model, revealing evolutionary genomic imprinting of DNA-DNA interactions through structured water.
Category: Quantitative Biology

Sex and Aging: The Theory of the "Prized Son"

Authors: Joao Carlos Holland Barcellos
Comments: 25 Pages. New theory of causes of senescence

After highlighting where some of the most well-known theories about aging and death fall short, we will propose a new theory that explains sexual reproduction and aging. In this theory, both sexual reproduction and senescence emerge as Darwinian adaptations. A mechanism that circumvents group selection is also suggested. We will then develop the "Equation of Death," which establishes species longevity as a function of parameters related to their prey and predators.
Category: Quantitative Biology

Can the Light be Used to Treat Obesity and Diabetes?

Authors: Rédoane Daoudi
Comments: 9 Pages.

The treatment of obesity and diabetes remains a challenge and the biological mechanisms of these diseases are still not fully understood. Diabetes and obesity are associated with increased risk of the development of cardiovascular complications and there is an urgent need to find novel therapeutic approaches for treating obesity and diabetes. Currently there are several approaches to treat these diseases. Among them chemical uncouplers could be used as an effectivetreatment for obesity but the dangerous side effects of these compounds has limited their use in vivo. Here we propose a novel theoretical model based on the mechanism of action of chemical uncouplers: the thermogenin-like system (TLS). The TLS may be used in vivo to reproduce the mechanism of action of chemical uncouplers but without their dangerous side effects.
Category: Quantitative Biology

Biological Relevance of Intestinal Gases in Healthy Humans

Authors: Arturo Tozzi, Raffaele Minella
Comments: 25 Pages.

Intestinal gases are usually discarded as physiologically inert, useless sub-products of colonic fermentation that must be expelled to prevent discomfort and meteorism. Starting from the observation that many living beings use exogenous and/or endogenous gases to attain evolutionary benefits, we question whether intestinal gases in healthy humans could have underestimated physiological effects, either intestinal or extra-intestinal. We examine gaseous volume, composition, source and local distribution in proximal as well as distal gut, providing extensive data that may serve as reference for future studies. We analyze each one of the most abundant intestinal gases and describe their diffusive patterns, active trans-barrier transport dynamics, chemical properties, intra-/extra-intestinal metabolic effects mediated by intracellular, extracellular, paracrine and distant actions. Discussing the physical properties of the whole intestinal gaseous mixture, we illustrate how changes in volume/pressure can be generated by two different mechanisms, namely, physical muscular gut contraction and biological colonic fermentation, with quite different metabolic outcomes. The experimental gas laws suggest that the gaseous exchanges between lumen and bloodstream are impaired by muscular contraction and improved by muscular relaxation. In turn, the surface-area-to-volume ratio suggests that the gaseous exchanges are impaired by microorganismal overproduction and improved by microorganismal reduction. Further, theoretical stochastic approaches from probability theory indicate that the non-turbulent, random paths of gas molecules inside colonic haustra do not homogenously spread over the whole mucosal surface. This means that the intestinal area available for lumen/blood metabolic exchanges is much less than expected not just in disease states, but also in healthy individuals.
Category: Quantitative Biology

Research Into Potential Therapies Against COVID-19, With Focus On Ivermectin

Authors: Reza Rezaie Khanghah
Comments: 73 Pages.

Purpose: Ivermectin is a broad-spectrum antiparasitic and an effective drug to treat COVID-19. In this article, we looked at the effects of ivermectin on coronavirus and its patients in three ways. We have discussed and organized other previously discovered potential therapies and reviewed them in Table 2 and in the last section. Methods: We searched for articles on MedRxiv, PubMed, Google Scholar, MEDLINE, EMBASE uses the appropriate search terms. ClinicalTrials.gov was searched for available clinical trials evaluating the effectiveness of ivermectin. We also use EU clinical trial registry data and ANZ registry data for clinical trials. Also, we performed our methods in 4 stages: Identifying studies, Selection of Studies, Collating Studies, Reporting results.Results: Results are variable. Some studies have shown the effectiveness of ivermectin, others have not. Furthermore, some studies show that a combination of ivermectin with other drugs is useful. Conclusion: Overall, we believe the reason ivermectin is useful is that it goes back to its origin, which is soil. Our theory and hypothesis is that if the coronavirus, created by man or by nature, can generally be treated with nature, that is, the soil. The interesting thing is that today we know that ivermectin is effective in the fight against the coronavirus. In fact, other drugs like teicoplanin, cyclosporine and rapamycin that are effective against the coronavirus have come from the soil. We hope that this article has been able to take a step in finding a corona drug, InshaAllah.
Category: Quantitative Biology

Covid-Period Mass Vaccination Campaign and Public Health Disaster in the Usa from Age/state-Resolved All-Cause Mortality by Time, Age-Resolved Vaccine Delivery by Time, and Socio-Geo-Economic Data

Authors: Denis Rancourt, Marine Baudin, Jeremie Mercier
Comments: 167 Pages.

All-cause mortality by time is the most reliable data for detecting and epidemiologically characterizing events causing death, and for gauging the population-level impact of any surge or collapse in deaths from any cause. Such data is not susceptible to reporting bias or to any bias in attributing causes of death. We compare USA all-cause mortality by time (month, week), by age group and by state to number of vaccinated individuals by time (week), by injection sequence, by age group and by state, using consolidated data up to week-5 of 2022 (week ending on February 5, 2022), in order to detect temporal associations, which would imply beneficial or deleterious effects from the vaccination campaign. We also quantify total excess all-cause mortality (relative to historic trends) for the entire covid period (WHO 11 March 2020 announcement of a pandemic through week-5 of 2022, corresponding to a total of 100 weeks), for the covid period prior to the bulk of vaccine delivery (first 50 weeks of the defined 100-week covid period), and for the covid period when the bulk of vaccine delivery is accomplished (last 50 weeks of the defined 100-week covid period); by age group and by state.We find that the COVID-19 vaccination campaign did not reduce all-cause mortality during the covid period. No deaths, within the resolution of all cause mortality, can be said to have been averted due to vaccination in the USA. The mass vaccination campaign was not justified in terms of reducing excess all-cause mortality. The large excess mortality of the covid period, far above the historic trend, was maintained throughout the entire covid period irrespective of the unprecedented vaccination campaign, and is very strongly correlated (r = +0.86) to poverty, by state; in fact, proportional to poverty. It is also correlated to several other socio-economic and health factors, by state, but not correlated to population fractions (65+, 75+, 85+ years) of elderly state residents.The excess all-cause mortality by age group (also expressed as percentage of pre-covid-period all-cause mortality for the age group) for the whole USA for the entire covid period through week-5 of 2022 is: all ages1.27M23%0-2413K12%25-44109K41%45-64274K27%65-74319K30%75-84316K24%85+240K14%

The corresponding fatality risk ratios are relatively uniform with age (non-exponential and non-near-exponential with age; and even skewed towards young adults), which holds essentially for all states, and for all examined periods within the covid period. This fundamental result implies that a dominant cause of excess mortality could not have been assigned COVID 19, which consistently has been measured to have a strong near-exponential infection fatality ratio with age. The implication is further corroborated by the absence of correlation between all-age-group-integrated excess mortality and age, by state. COVID-19 was not a dominant cause of excess mortality during the covid period in the USA.All of our observations can be coherently understood if we interpret that the covid-period socio-economic, regulatory and institutional conditions induced chronic stress and social isolation among members of large vulnerable groups (individuals afflicted and co-afflicted by poverty, obesity, diabetes, high susceptibility to bacterial respiratory infection [inferred from pre-covid-period antibiotic prescription rates], old age, societal exclusion, unemployment, drug and substance abuse, and mental disability or serious mental illness), which in turn caused many of these individuals to be more and fatally immunocompromised, allowing them to succumb to bacterial pneumonia, at a time when a documented national pneumonia epidemic raged and antibiotic prescriptions were systemically reduced; in addition to possible comorbidity from COVID-19 vaccine challenge against individuals thus made immunocompromised, under broad and hastily implemented "vaccine equity" programs.
Category: Quantitative Biology

Chaos Theory and Intentional Teaching in Evolution

Authors: Nicholas Hoggard
Comments: 20 Pages.

Gärdenfors and Hedberg have identified 6 levels of Intentional Teaching which have arisen in sequence, in synchrony with tool innovations during human evolution. Remarkably, these events appear at time intervals that decrease at a constant ratio equal to the Feigenbaum constant, 4.66920u2026 . This constant is the signature of period-doubling cascades, which can be found in many phenomena in nature and arise in iterative nonlinear processes in an environment of limited resources. Darwinian evolution is just such a process. Cherry picking is not an issue because the 6 levels of teaching were discovered by studying the evolution of human behaviour, without regard for when the behaviour arose. The pattern apparently extends both forwards in time from cultural evolution to information technology (movable-type printing, and computers), as well as backwards to physical and biological evolution (Big bang, life, sexual reproduction). All of these milestones mark new ways to transmit information to coming generations, first as DNA, then via teaching, and finally by information technology. If confirmed, this apparent pattern in evolution may have major consequences for evolution theory. Other studies showing that rates of genetic change and speciation are largely unaffected by climate support the idea that a regular pattern is possible.
Category: Quantitative Biology

The Psychophysical World of the Motile Diatom Bacillaria Paradoxa

Authors: Bradly Alicea, Richard Gordon, Jesse Parent
Comments: 43 Pages.

There are a large number of candidate hypotheses for the movement of diatoms, a taxonomic group of Algae. In particular, the genus Bacillaria exhibits highly interesting movement dynamics resembling a number of physical systems. None of these hypotheses account for the information processing that might result from the connection between environmental stimuli (e.g. photic, chemical, turbulence, and temperature gradients, and mechanical constraints) and motility. Even when there is no significant variation in terms of sensory input, the colonial structure is coordinated and mediated through information processing. Here, we propose a series of perspectives on how the concept of aneural cognition might explain the movement dynamics of individual colonies. More specifically, we can use analogies of neuronal mechanisms such as Collective Pattern Generators, Hebbian Learning, and predictive processing to understand and explore the potential for behavior generation. Quantitatively, these mechanisms can be summarized using psychophysical metrics, particularly the Weber-Fechner law. This analogy could be extended to out-of-equilibrium behaviors such as halting of oscillatory movement patterns, and further interpretations in terms of pseudo-intelligent behavior, which is simulated but not necessarily autonomous. Taken together, we can say that the psychophysical world can open up new avenues of exploration for understanding the regulation of diatom movement.
Category: Quantitative Biology

Frequentist and Bayesian Analysis Methods for Case Series Data and Application to Early Outpatient Covid-19 Treatment Case Series

Authors: Eleftherios Gkioulekas, Peter A McCullough, Vladimir Zelenko
Comments: 26 Pages. 26 pp, submitted to Reviews in Cardiovascular Medicine

When confronted with a public health emergency, significant innovative treatment protocols can sometimes be discovered by medical doctors at the front lines based on repurposed medications. We propose a very simple hybrid statistical framework for analyzing the case series of patients treated with such new protocols, that enables a comparison with our prior knowledge of expected outcomes, in the absence of treatment. The goal of the proposed methodology is not to provide a precise measurement of treatment efficacy, but to establish the existence of treatment efficacy, in order to facilitate the binary decision of whether the treatment protocol should be adopted on an emergency basis. The methodology consists of a frequentist component that compares a treatment group against the unknown probability of an adverse outcome in the absence of treatment, and calculates a lower bound for this unknown probability, that has to be exceeded, in order to control the corresponding $p$-value, and reject the null hypothesis. We explain the relationship of this method with the exact Fisher test and the binomial proportion confidence interval problem. The resulting lower bound (hereafter, efficacy threshold) is further adjusted with a Bayesian technique, in order to also control the false positive rate. The combined techniques are applied to case series of high-risk COVID-19 outpatients, that were treated using the early Zelenko protocol and the more enhanced McCullough protocol. The resulting efficacy thresholds are then compared against our prior knowledge of mortality and hospitalization rates of high-risk COVID-19 patients, as reported in the research literature.
Category: Quantitative Biology

The Fourth Wave of Covid-19 Breakout in Israel: Alternative Analysis: the Efficacy of Vaccination Protocols in Preventing Serious Disease and Death Vs. Increased Covid-19 Morbidity and Mortality Following Booster Vaccination

Authors: Yoram Oron
Comments: 15 Pages.

Background: During the months of August-October Israel has experienced the fourth wave of COVID-19 outbreak. This outbreak resulted in major increases in COVID-19 hospitalizations and mortality. At the beginning of this outbreak, Israel had one of the highest rates of two-dose Pfizer vaccination (2D protocol) and was beginning a vigorous campaign to promote a third-injection booster of the vaccine (3D protocol). Purpose: The official serious illness and deaths records were analyzed in order to assess the efficacy of the 2D and 3D protocols in preventing serious illness or death due to COVID-19 infection Methods: All raw data were obtained from the official Ministry of Health records (Data Dashboard). The same source was used to estimate the size of the relevant populations. The data for serious illness or mortality were normalized to sizes of the relevant populations on a daily basis.

Results and Conclusions: The 2D protocol alone, or followed by third-dose booster, significantly protected the relevant populations against serious illness (5 and 3-fold, respectively) and death (3.4 and 2.2-fold, respectively). However, this alternative analysis indicated that there was no protective advantage of the 3D over the 2D protocol. Actually, the protective effect of the 2D protocol against serious illness, and death in particular, appeared to exceed by a large factor that of the 3D protocol. Importantly, there was an unexpected early and prolonged rise in COVID-19 mortality in the 3D population. These results are discordant with the official statistics of the Ministry of Health and with some of the results presented in the scientific literature. Moreover, the kinetics of serious illness or mortality was spiking instead of the expected monotonous rise and decline, suggesting additional factors involved.
Category: Quantitative Biology

Novel Insights from Non-ultrametric Phylogenetic Trees: The Case of Neanderthal Introgression

Authors: Arturo Tozzi
Comments: 7 Pages.

Ultrametric spaces are widely used to depict evolutionary times in phylogenetic trees, since they assume that every population/species is located at the tips of divergent branches. The discrete branching of ultrametric trees permits the measurement of distances between pairs of individuals that are proportional to their divergence time. Here we overturn the traditional ultrametric concept of divergent phylogenetic tree and introduce a new type of non-ultrametric diagram to describe gene flows in terms of convergent branches. To provide an operational example, we examine the paleoanthropological issue of Neanderthal genome’s introgression in non-African humans. Neanderthals and ancient humans are not anymore two species that exchange chunks of DNA, rather become a novel cluster that must be considered by itself. Our converging, non-ultrametric phylogenetic trees permit the calibration of molecular clocks with a twofold benefit. When the date of the branching of two population/species from a common ancestor is known, our method allows to calculate the time of subsequent introgressions. On the contrary, when the date of the introgression between two population/species is known, our method allows to detect the time of their previous branching from a common ancestor.
Category: Quantitative Biology

The Effect of Artificial Amalgamates on Identifying Pathogenesis

Authors: Philip Naveen
Comments: 13 pages, associated with Godwin High School

The purpose of this research was to define acceleration in diagnostic procedures for airborne diseases. Airborne pathogenicity can be troublesome to diagnose due to intrinsic variation and overlapping symptoms. Coronavirus testing was an instance of a flawed diagnostic biomarker. The levels of independent variables (IV) were vanilla, sparse, and dense amalgamates formed from multilayer perceptrons and image processing algorithms. The dependent variable (DV) was the classification accuracy. It was hypothesized that if a dense amalgamate is trained to identify Coronavirus, the accuracy would be the highest. The amalgamates were trained to analyze the morphological patches within radiologist-verified medical imaging retrieved from online databanks. Using cross-validation simulations augmented with machine-learning, the DV was consulted for each amalgamate. Self-calculated t-tests supported the research hypothesis, with the dense amalgamate achieving 85.37% correct classification rate. The null hypothesis was rejected. Flaws within the databanks were possible sources of error. A new multivariate algorithm invented here performed better than the IV. It identified Coronavirus and other airborne diseases from 96-99% accuracy. The model was also adept in identifying heterogeneity and malignancy of lung cancer as well as differentiating viral and bacterial pathogenicity of infections. Future modifications would involve extending the algorithm to diseases in other anatomical structures such as osteopenia/osteoporosis in the vertebral column.
Category: Quantitative Biology

Recommendations for Improving the United States Centers for Disease Control (CDC) Data Practices for Pneumonia, Influenza, and COVID-19

Authors: John F. McGowan, Tam Hunt, Josh Mittledorf
Comments: 26 Pages.

During the pandemic, millions of Americans have become acquainted with the CDC because its reports and the data it collects affect their day-to-day lives. But the methodology used and even some of the data collected by CDC remain opaque to the public and to the community of academic epidemiology. In this paper, we highlight areas in which CDC methodology might be improved and where greater transparency might lead to broad collaboration. (1) "Excess" deaths are routinely reported, but not "years of life lost", an easily-computed datum that is important for public policy. (2) What counts as an "excess death"? The method for computing the number of excess deaths does not include error bars and we show a substantial range of estimates is possible. (3) Pneumonia and influenza death data on different CDC pages is grossly contradictory. (4) The methodology for computing influenza deaths is not described in sufficient detail that an outside analyst might pursue the source of the discrepancy. (5) Guidelines for filling out death certificates have changed during the COVID-19 pandemic, preventing the comparison of 2020-21 death profiles with any previous year. We conclude with a series of explicit recommendations for greater consistency and transparency, and ultimately to make CDC data more useful to outside epidemiologists.
Category: Quantitative Biology

Diversity of Aquatic Insects in Lake Pichhola of Udaipur, Rajasthan, India

Authors: Farha Naz, Sweety Nalwaya, Rahul Yadav, Kanan Saxena
Comments: 8 Pages. Published at online at: https://www.bpasjournals.com/zoology [Corrections made by viXra Admin to conform with the requirements on the Submission Form]

The present study conducted on Lake Pichhola with regard to its insect diversity revealed a total of 24 species during the period from October 2019 to March 2020 and these 24 species of insects belonged to 6 orders and 12 families. Maximum insect species were recorded from the littoral zone (vegetation rich site) and minimum insect species from limnetic zone and disturbed sites of the lake. A number of insect species and their immature stages from orders Odonata, Ephemeroptera, Diptera, Hemiptera, Coleoptera and Trichoptera were observed. The insect fauna from the order Odonata dominated over Ephemeroptera and the second most dominant order was Hemiptera. Aquatic insects are best known for their ability to indicate the water quality and monitoring of aquatic insect diversity and abundance can expedite the conservation of these lake ecosystems.
Category: Quantitative Biology

Application of Environmental DNA in the Investigation of Rare or Introduced Varieties with Carps, Bluegills, and Frogbits

Authors: Jung Choi
Comments: 10 Pages. 10 p, Korean, CC-BY-NC-ND 4.0

In this research project, I promote research for the application of environmental DNA to investigate rare or introduced varieties. In particular, I have focused on the development of estimating biomass by environmental DNA concentration in reservoirs and streams, the estimation of the exotic varieties’ distribution and biomass, application of environmental DNA technique on introduced or rare water plants. In study A, I measured biomass at the whole reservoir by collection when the reservoir is fully dehydrated and compared the biomass and environmental DNA amount. As a result, there are explicit correlation between eDNA amount and biomass, and its behaviour was not related to where samples were collected such as shore or buffer. In study B, I have done the development of real-time PCR primer probe and outdoor investigation on Hydrilla verticillate of and Egeria densa which are submerged plants of Hydrocharitaceae to confirm usefulness of eDNA analysis as aquatic plant distribution estimation method. As consequence, it was found that there is a correlation between biomass and eDNA amount and there are more plant eDNAs in some particles where animal eDNAs aren’t. The eDNA technique developed in this study is expected to be an effective mean to estimate biomass in various species, investigate organism distribution, determine the invasion scale of exotic genotype quickly.
Category: Quantitative Biology

The Equation of Life

Authors: Robert L. Jackson
Comments: 10 Pages. contact info: rljacksonmd@gmail.com

This study will first define the “equation of life” via the principle of least action. Then the paper will show how this “equation of life” can be used to derive smaller equations, involving transcription and translation, for [computer] modeling and simulation of a cell. The conclusion will provide a terse description of its uses in the realm of Systems Biology.
Category: Quantitative Biology

Asymptotic Analysis of the Sir Model: Applications to Covid-19 Modelling

Authors: Dimiter Prodanov
Comments: 14 Pages.

The SIR (Susceptible-Infected-Removed) model can be very useful in modelling epidemic outbreaks. The present paper derives the parametric solution of the model in terms of quadratures. The paper demonstrates a simple analytical asymptotic solution for the I-variable, which is valid on the entire real line. Moreover, the solution can be used successfully for parametric estimation either in stand-alone mode or as a preliminary step in the parametric estimation using numerical inversion of the parametric solution. The approach is applied to the ongoing coronavirus disease 2019 (COVID-19) pandemic in three European countries -- Belgium, Italy and Sweden.
Category: Quantitative Biology

Comments on "Analytical Features of the Sir Model and Their Applications to Covid-19"

Authors: Dimiter Prodanov
Comments: 5 Pages.

In their article, Kudryashov et al. (2021) try to establish the analytical solution of the SIR epidemiological model. One of the equations given there is wrong, which invalidates the presented solution, derived from this result. The objective of the present letter is to indicate this error and present the correct analytical solution to the SIR epidemiological model.
Category: Quantitative Biology

Prediction of Daily Contagions of CoViD-19 - SARS-CoV-2 from August 24 to July 31, 2021 in Sicily, a Region of Italy, by Using a New Epidemiologic Fractal Model

Authors: Calogero Rinzivillo, Sergio Conte, Francesco Casciaro, Renato Bernardini, Elena Benigni, Ines Paola Monte, Ferda Kaleagasioglu, Fang Wang, Cengiz Mordeniz, Giuseppe Liberti, Elio Conte
Comments: 3 Pages.

We study a new fractal model for prediction of contagions of CoViD-19 (SarbecoBetavirus SARSCoV- 2) from August 24, 2020 to July 31, 20201 in Sicily that is a region of Italy. We obtain that the time of the peak is estimated to be at December 7, 2020 and the number of contagions will be about 903 cases.
Category: Quantitative Biology

Prediction of Daily Contagions of CoViD-19 - SARS-CoV-2 from August 24 to October 20, 2020 in Italy by Using a New Epidemiologic Fractal Model

Authors: Calogero Rinzivillo, Sergio Conte, Francesco Casciaro, Elena Benigni, Ferda Kaleagasioglu, Cengiz Mordeniz, Fang Wang, Elio Conte
Comments: 3 Pages.

We study a new fractal model for prediction of contagions of CoViD-19 (SarbecoBetavirus SARSCoV- 2) from August 24, 2020 to October 20, 2020 in Italy. We obtain that the time of the peak is estimated to be at December 7, 2020 and the number of contagions will be about 20580 cases.
Category: Quantitative Biology

How Kenya Has Kept Its CoVID 19 Infection Figures Low

Authors: Nyagudi Musandu Nyagudi
Comments: 3 Pages.

Review of Paper: Revealing the extent of the COVID-19 pandemic in Kenya based on serological and PCR-test data (https://www.medrxiv.org/content/10.1101/2020.09.02.20186817v1.full.pdf ). On September 3, 2020 a paper was posted to Medrxiv, detailing the effort to control the CoVID 19 pandemic in Kenya, some aspects of that position cannot go unchallenged given the gravity of the decisions that would arise from what would effectively be a Government position backed by Researchers from the London School of Hygiene and Tropical Medicine in UK, The Zeeman’s Institute for Systems Biology and Infectious Diseases Epidemiology Research – Warwick University UK, School of Life Sciences – Warwick University UK, Centre for Tropical Medicine and Global Health – Nuffield Department of Medicine – Oxford University UK, Kenya Medical Research Institute – Wellcome Trust Kenya. Suffice it to say that some of the methods used to keep the CoVID 19 infection figures “low” in Kenya are Machiavellian
Category: Quantitative Biology

SARS-COV-2: Defferent Age, Different Virion

Authors: Arturo Tozzi
Comments: 5 Pages.

We suggest that the SARS-Cov-2 particles emerging from the cells of elder or pediatric hosts are phenotypically different, because they are equipped with a slightly different envelope. This might contribute to the well-documented variations of COVID-19 symptoms severity in populations of different ages.
Category: Quantitative Biology

A Study on the Treatment of Epididymis Obstructive Azoospermia Using Microsurgical Vessels

Authors: NamHyok KIM，GyuSol Han，UnChol Ri
Comments: 3 Pages.

From March 2010 to October 2015, microsurgical vas deferens epididymis anastomosis used to treat 25 cases of epididymis obstructive azoospermia. And postoperative recanalization and sperm motility were analyzed. The patients were routinely examined for semen at 1, 3, 6, 9, and 12 months after the operation, and the sperm density (82.6 ± 22.8) × 106 / ml when the sperm first discovered and the activity rate was (35.1 ± 8 .5) %, sperm motility a grade ratio is 16.0%, b grade ratio is 32.0%, c grade ratio is 40.0%, d grade ratio is 12.0%, surgical recanalization rate is 92. 0%. There were 16 cases of spouse pregnancy 1 year after surgery. Microsurgical vas deferens epididymal duct anastomosis is effective in treating epididymal obstructive azoospermia.
Category: Quantitative Biology

Analysis of Apobec and Adar Deaminase-Driven Riboswitch Haplotypes in Covid-19 Rna Strain Variants and the Implications for Mono-Strain Vaccine Design

Authors: Edward J. Steele, Robeyn A. Lindley
Comments: 34 Pages.

This paper reports the results of our initial analysis of APOBEC and ADAR deaminase-mediated mutation signa-ture patterns in complete COVID-19 genomes from informative locations and times in China, USA and Spain in the 2019-2020 pandemic. We have identified a unique set of 'new' putative coordinated Riboswitches in COVID-19 genomes not previously identified, and likely generating variants of the known common strain Haplotypes now in circulation. The results reveal that COVID-19 diversifies using switching of RNA Haplotypes with mini-mal alteration to protein structure (the normal targets for B and T cells in conventional vaccine development). The deaminase-driven RNA Haplotypes are most likely aligned with RNA secondary structures as several stud-ies already highlight how Riboswitches alter he ability of RNA to fold into intricate three-dimensional structures allowing them to execute their diverse cellular functions. The same functional outcomes are expected for viruses, particularly efficacy of RNA replication in new host cell environments. Thus, mono-strain vaccine designs that assume that the main viral protein antigens will be the only putative protective targets could fail to produce effec-tive and protective immunity. We conclude that understanding COVID-19 adaptation and survival strategy and identifying the host Haplotype, and which vaccine(s) is effective for each Haplotype group will be important for new vaccine design. Our study also has wider implications for the actual origins and spread of COVID-19 but these will be pursued in future publications.
Category: Quantitative Biology

Hydraulic Pressure Drives Urine Concentration Too

Authors: Johan Nygren
Comments: 4 Pages.

The kidney has connected filtration and reabsorption in series down a pressure gradient and both rely on pressure generated by the heart as a pump.
Category: Quantitative Biology

Kidney Filtration Pressure as a “single Effect” for Osmotic Gradient

Authors: Johan Nygren
Comments: 1 Page.

Consider the name of the renal pyramids, and that it points to them being pyramidal. This anatomy suggests the “urine compartment”, the nephrons and collecting ducts, narrows from the base of the renal pyramid (cortex) to the top (papilla), in the same way as a funnel. This anatomical arrangement likely has a role in the reabsorption of 99% of all filtrate produced per day, simply by providing resistance. If this architecture is able to contribute to reabsorption of water, and, by that, concentration of urine, and if this concentrated urine to some extent equilibrates with the surrounding medullary interstitium, then it would provide a “single effect” for an osmotic multiplier.
Category: Quantitative Biology

The Present Behavior of Linear Increasing of Cases of Covid-19

Authors: Valdir Monteiro dos Santos Godoi
Comments: 19 Pages.

We see in graphs the current approximately linear behavior of the advance in the number of confirmed cases, deaths and recovered cases by Covid-19.
Category: Quantitative Biology

When Will Brazil Overtake Other Countries in Numbers of Confirmed Cases and Deaths in This Pandemic?

Authors: Valdir Monteiro dos Santos Godoi
Comments: 7 Pages.

We calculated when Brazil, which today it is in the eighth position in the ranking of confirmed cases, but has the highest growth rate of this disease among the first 11 countries, will overtake the USA, today in first place in the ranking of confirmed cases and deaths by COVID-19. We did the same with the other 6 countries.
Category: Quantitative Biology

A New Forecast of Total Deaths by COVID-19 in the World, US and Countries of South America (May-04-2020)

Authors: Valdir Monteiro dos Santos Godoi
Comments: 5 Pages.

Based on datas of Johns Hopkins University we calculated an estimative of deaths by COVID-19 in the world, US and countries of South America.
Category: Quantitative Biology

Forecast of Total Deaths by COVID-19 in the World, US and South America (May-01-2020)

Authors: Valdir Monteiro dos Santos Godoi
Comments: 3 Pages.

We asked the following questions: 1) When an entire population will have been infected by the coronavirus, in this COVID-19 pandemic, assuming that no vaccination or other form of preventive (or curative) medication exists until that day, and the population remains constant (births and deaths are not accounted for)? We also assume that no change in social behavior occurs until that date, for simplicity. 2) What is the corresponding number of deaths by COVID-19 on that date?
Category: Quantitative Biology

Forecast of Complete Contamination by COVID-19 in the World, US and South America (April-28-2020)

Authors: Valdir Monteiro dos Santos Godoi
Comments: 2 Pages.

We asked the question of when an entire population will have been infected by the coronavirus, in this COVID-19 pandemic, assuming that no vaccination or other form of preventive (or curative) medication exists until that day.
Category: Quantitative Biology

Lethality, Velocity and Acceleration of COVID-19 Contamination in the World and 20 Selected Countries (April-24-2020)

Authors: Valdir Monteiro dos Santos Godoi
Comments: 3 Pages.

The objective of this paper is to introduce a study relative a mathematical modeling of coronavirus contamination, knowing some current numbers first, by COVID-19 pandemic.
Category: Quantitative Biology

Lethality of COVID-19 in the World and 20 Selected Countries (April-25-2020)

Authors: Valdir Monteiro dos Santos Godoi
Comments: 2 Pages.

The objective of this paper is to initiate a study relative a mathematical modeling of coronavirus contamination, knowing firstly some current numbers, given by COVID-19 pandemic.
Category: Quantitative Biology

New Prediction of Sars-Covid-19 in Italy

Authors: Calogero Rinzivillo, Sergio Conte, Ferda Kaleagasioglu, Fang Wang, Alberto Foletti, Cengiz Morderniz, Elio Conte
Comments: 4 Pages.

We estimate the contagions of Sars-Covid-19 in Italy until June 2020 and we compare the results with our previous estimations. We obtain that the fractal model we use, estimates the behavior of the experimental data and prediction with an r2 value of 0.95. We have that the time of peak is 37.80 days for the prediction 1 and 37.33 days for prediction 2 starting with February 20. The number of contagions will drop below 10 in June 28 for prediction 1 and July 14 for prediction 2 as explained in Figure 1.
Category: Quantitative Biology

Observer Repeatability and Interscan Reproducibility of 18F-Sodium Fluoride Coronary Microcalcification Activity

Authors: Piotr Slonka
Comments: 27 Pages.

Background (words 199/200) We aimed to establish the observer repeatability and interscan reproducibility of coronary 18F-sodium fluoride (18F-NaF) positron emission tomography (PET) uptake using a novel semi-automated approach, coronary microcalcification activity (CMA). Methods Patients with multivessel coronary artery disease underwent repeated hybrid PET and computed tomography angiography (CTA) imaging (PET/CTA). CMA was defined as the integrated standardized uptake values (SUV) in the entire coronary tree exceeding 2 standard deviations above the background SUV. Coefficients of repeatability between the same observer (intraobserver repeatability), between 2 observers (interobserver repeatability) and coefficient of reproducibility between 2 scans (interscan reproducibility), were determined at both vessel and patient level. Results In 19 patients, CMA was assessed twice in 43 coronary vessels on two PET/CT scans performed 12±5 days apart. There was excellent intraclass correlation on a per-vessel and per-patient level for intraobserver and interobserver repeatability as well as interscan reproducibility (≥0.991 for all). There was 100% intraobserver, interobserver and interscan agreement for the presence (CMA>0) or absence (CMA=0) of coronary18F-NaF uptake. Mean CMA was 3.12±0.62 with coefficients of repeatability of ≤10% for all measures: intraobserver 0.24 and 0.22, interobserver 0.30 and 0.29 and interscan 0.33 and 0.32 at a per-vessel and per-patient level respectively. Conclusions CMA is a repeatable and reproducible global measure of coronary atherosclerotic activity.
Category: Quantitative Biology

Respiration-Averaged CT Versus Standard CT Attenuation Maps for Correction of 18F-Naf Uptake on Hybrid Pet/ct

Authors: Piotr Slomka
Comments: 22 Pages.

Purpose To evaluate the impact of a respiratory averaged computed tomography attenuation correction (RACTAC) instead of a standard single-phase computed tomography (CT) attenuation correction (CTAC) map on the quantitative measures of coronary 18F-NaF uptake in PET/CT. Methods This study comprised 23 patients who underwent 18F-NaF coronary PET in a hybrid PET/CT system, employing 18F-NaF (250MBq). All patients had two CT scans, a standard single-phase CTAC obtained during free-breathing, and a 4D cine-CT scan. From the Cine-CT acquisition, RACTAC maps were obtained by averaging all images acquired over 5 seconds. Two PET reconstruction protocols, one employing CTAC and another employing RACTAC for attenuation correction were considered in this study. Following reconstruction, the quantitative impact of employing RACTAC was assessed using maximum target-to-background (TBRMAX) and coronary microcalcification activity (CMA). Statistical differences were analyzed using reproducibility coefficients and Bland-Altman plots. Results In 23 patients, we evaluated 34 coronary lesions using PET reconstructions utilizing CTAC and RACTAC. There was good agreement between CTAC and RACTAC PET reconstructions for TBRMAX (median [Interquartile range, IQR]: CTAC = 1.65[1.23-2.38], RACTAC = 1.63[1.23-2.33], p=0.55), with coefficient of reproducibility of 0.18. The CMA agreement was similar (median [IQR]: CTAC = 0.10 [0-1.0], RACTAC= 0.15[0-1.03], p=0.55 with coefficient of reproducibility of 0.17 Conclusion Employing RACTAC maps does not affect the quantification of the coronary 18F-NaF uptake on PET/CT.
Category: Quantitative Biology

Cardiovascular Disease in the Literature: a Selection of Recent Original Research Papers

Authors: AlJaroudi, Wael; Hage, Fadi
Comments: 6 Pages.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared a pandemic with devastating effects on the entire world. Madjid et al. from the University of Texas Health Science, Houston, Texas review current information on the virus and COVID-19 and its effects on the cardiovascular system. Coronaviruses, classified in 4 groups, were first identified in humans in the 1960s with 4 types (all from the α and β classes) are endemic in humans usually causing mild and self-limiting upper respiratory infections accounting for 15-30% of common colds. Both SARS (caused by SARS-CoV) and Middle East respiratory syndrome (MERS, caused by MERS-CoV) caused outbreaks (in 2002 and 2012, respectively) that had higher fatality rates but were much less widespread than COVID-19. SARS-CoV-2 is genetically more similar to SARS-CoV (82%) than MERS-CoV (50%). The virus has a mean incubation period of 5.2 days (95%CI, 4.1-7.0 days), with the 95th percentile of the distribution at 12.5 days according to one study and up to 14 days according to another. The World Health Organization reported a global mortality rate of 3.4% but importantly, this rate varies by location, intensity of transmission, variations of care, presence of comorbidities (including cardiovascular disease), advanced age, and likely other factors. The primary symptoms of COVID-19 are fever, cough, and shortness of breath. Acute cardiac injury determined by elevated high-sensitivity troponin levels is commonly observed in severe cases and is strongly associated with mortality, complications such as acute respiratory distress syndrome, arrhythmia, renal injury, and coagulopathy. There has been reported cases of viral infiltration of the myocardium causing myocarditis. Myocardial injury can also be caused by ischemia. It is important to note that COVID-19 in addition to inducing new cardiac pathologies (such as myocarditis) may also exacerbate pre-existing cardiovascular disease. Finally, some of the investigational therapies for COVID-19 may have cardiovascular effects. Current treatment, until investigational therapies have been shown to be effective, is supportive care and treatment of complications. The article offers a wonderful review of current knowledge on COVID-19 as well as a review of SARS and MERS which provide further insights on the effects of coronaviruses on the cardiovascular system.
Category: Quantitative Biology

Evaluation of the Diagnostic Value of Joint Pet Myocardial Perfusion and Metabolic Imaging for Vascular Stenosis in Patients with Obstructive Coronary Artery Disease

Authors: Fanghu Wang, Weiping Xu, Wenbing Lv, Dongyang Du, Hui Feng, Xiaochun Zhang, Shuxia Wang, Wufan Chen, Lijun Lu
Comments: 14 Pages.

Background. To investigate the diagnostic value of joint PET myocardial perfusion and metabolic imaging for vascular stenosis in patients with suspected obstructive coronary artery disease (CAD). Methods. Eighty-eight patients (53 and 35 applied for training and validation, respectively) with suspected obstructive CAD were referred to 13N-NH3 PET/CT myocardial perfusion imaging (MPI) and 18F-FDG PET/CT myocardial metabolic imaging (MMI) with available coronary angiography for analysis. One semi-quantitative indicator summed rest score (SRS) and five quantitative indicators, namely, perfusion defect extent (EXT), total perfusion deficit (TPD), myocardial blood flow (MBF), scar degree (SCR), and metabolism-perfusion mismatch (MIS), were extracted from the PET rest MPI and MMI scans. Different combinations of indicators and seven machine learning methods were used to construct diagnostic models. Diagnostic performance was evaluated using the sum of four metrics (noted as sumScore), namely, area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity. Results. In univariate analysis, MIS outperformed other individual indicators in terms of sumScore (2.816–3.042 vs. 2.138–2.908). In multivariate analysis, support vector machine (SVM) consisting of three indicators (MBF, SCR, and MIS) achieved the best performance (AUC 0.856, accuracy 0.810, sensitivity 0.838, specificity 0.757, and sumScore 3.261). This model consistently achieved significantly higher AUC compared with the SRS method for four specific subgroups (0.897, 0.833, 0.875, and 0.949 vs. 0.775, 0.606, 0.713, and 0.744; p=0.041, 0.005, 0.034 0.003, respectively). Conclusions. The joint evaluation of PET rest MPI and MMI could improve the diagnostic performance for obstructive CAD. The multivariate model (MBF, SCR, and MIS) combined with SVM outperformed other methods.
Category: Quantitative Biology

Rubidium-82 Generator Yield and Efficiency for PET Perfusion Imaging: Comparison of Two Clinical Systems

Authors: Ali Ahmadi, Ran Klein, Howard C Lewin, Rob S.B. Beanlands, Robert A. deKemp
Comments: 28 Pages.

Introduction. Strontium-82/Rubidium-82 (82Sr/82Rb) generators are used widely for positron emission tomography (PET) imaging of myocardial perfusion. In this study, the 82Rb isotope yield and production efficiency of two FDA-approved 82Sr/82Rb generators were compared. Methods. N=515 sequential daily quality assurance (QA) reports from 9 CardioGen-82® and 9 RUBY-FILL® generators were reviewed over a period of 2 years. A series of test elutions was performed at different flow-rates on the RUBY-FILL® system to determine an empirical correction-factor used to convert CardioGen-82® daily QA values of 82Rb activity (dose-calibrator ‘maximum’ of 50 mL elution at 50 mL/min) to RUBY-FILL® equivalent values (integrated ‘total’ of 35 mL elution at 20 mL/min). The generator yield (82Rb) and production efficiency (82Rb yield / 82Sr parent activity) were measured and compared after this conversion to a common scale. Results. At the start of clinical use, the system reported 82Rb activity from daily QA was lower for CardioGen-82® vs RUBY-FILL® (2.3 ± 0.2 vs 3.0 ± 0.2 GBq, p<0.001) despite having similar 82Sr activity. Dose-calibrator ‘maximum’ (CardioGen-82®) values were found to under-estimate the integrated ‘total’ (RUBY-FILL®) activity by ~24% at 50 mL/min. When these data were used to convert the CardioGen-82 values to a common measurement scale (integrated total activity) the CardioGen-82® efficiency remained slightly lower than the RUBY-FILL® system on average (88 ± 4% vs 95 ± 4%, p<0.001). The efficiency of 82Rb production improved for both systems over the respective periods of clinical use. Conclusions. 82Rb generator yield was significantly under-estimated using the CardioGen-82® vs RUBY-FILL® daily QA procedure. When generator yield was expressed as the integrated total activity for both systems, the estimated 82Rb production efficiency of the CardioGen-82® system was ~7% lower than RUBY-FILL® over the full period of clinical use.
Category: Quantitative Biology

Value of Sipm Pet in Myocardial Perfusion Imaging Using Rubidium-82

Authors: S.S. Koenders, J.A. van Dalen, P.L. Jager, S. Knollema, JR Timmer, M. Mouden, C.H. Slump, J.D. van Dijk
Comments: 22 Pages.

Background: PET scanners using silicon photomultipliers with digital readout (SiPM PET) have an improved temporal and spatial resolution compared to PET scanners using conventional photomultiplier tubes (PMT PET). However, the effect on image quality and visibility of perfusion defects in myocardial perfusion imaging (MPI) is unknown. Our aim was to determine the value of a SiPM PET scanner in MPI. Methods: We prospectively included 30 patients who underwent rest and regadenoson-induced stress Rubidium-82 (Rb-82) MPI on the D690 PMT PET (GE Healthcare) and within three weeks on the Vereos SiPM PET (Philips Healthcare). Two expert readers scored the image quality and assessed the existence of possible defects. In addition, interpreter’s confidence, myocardial blood flow (MBF) and myocardial flow reserve (MFR) values were compared. Results: Image quality improved (p=0.03) using the Vereos as compared to the D690. Image quality of the Vereos and the D690 was graded fair in 20% and 10%, good in 60% and 50%, and excellent in 20% and 40%, respectively. Defect interpretation and interpreter’s confidence did not differ between the D690 and the Vereos (p>0.50). There were no significant differences in rest MBF (p≥0.29), stress MBF (p≥0.11) and MFR (p≥0.51). Conclusion: SiPM PET provides an improved image quality in comparison to PMT PET. Defect interpretation, interpreter’s confidence and absolute blood flow measurements were comparable between both systems. SiPM PET is therefore a reliable technique for MPI using Rb-82.
Category: Quantitative Biology

Estimation of the R0 Factor of the Sir Model in Italy and Some Its Regions as Consequence of the Pandemic Sars Covid 19

Authors: Calogero Rinzivillo, Sergio Conte, Ferda Kaleagasioglu, Alberto Foletti, Cengiz Morderniz, Maria Pieralice, Elio Conte
Comments: 5 Pages.

We compute the factor R0(t) by using the SIR model in Italy and its some regional countries. We find that it is descending to a minimum value of 1.11 in Italy and respectively of 1.89, 1.86 and 3.13 for each region respectively
Category: Quantitative Biology

The SARS-CoV-2 is a Weekly Multifractal : the Basic Indications and the Clinical Implications

Authors: Calogero Rinzivillo, Sergio Conte, Ferda Kaleagasioglu, Fang Wang, Alberto Foletti, Elio Conte
Comments: 7 Pages.

We demonstrate that the SARS-CoV-2 is a multifractal and we study the implications of this discovery at the basic level as well as when this structure is intended for its function and when it could be used for test in the clinical applications depending the area of the singularity spectrum of the inspected virus and the other its characterizing parameters in each clinical case from the virulence of the virus.
Category: Quantitative Biology

Lower Bound for the Number of Asymptomatics in Infected by COVID-19

Authors: Vincenzo Nardozza
Comments: 3 Pages.

We propose a method for evaluating the number of asymptomatics in a COVID-19 Outbreak. The method will give only a lower bound for the real number.
Category: Quantitative Biology

Confirmation of Prediction of Daily Contagions of Covid-19 from February 20 to June 20 in Italy

Authors: Calogero Rinzivillo, Sergio Conte, Elio Conte
Comments: 3 Pages.

We study a fractal model for prediction of Covid-19 contagions from February 20 to June 20 in Italy . We obtain that the model confirms the experimental data obtained in the past seven days . The time of the peak is estimated to be at March 21-26 and the number of contagions will be about 240000 cases.
Category: Quantitative Biology

Prediction of Daily Contagions of Covid-19 from March 03 to June 01 in Sicily , a Region of Italy

Authors: Calogero Rinzivillo, Sergio Conte, Elio Conte
Comments: 2 Pages.

We study a fractal model for prediction of Covid-19 contagions from March 03 to June 01 in Sicily, a region of Italy . We obtain that the time of the peak is estimated to be at March 20-25 and the number of contagions will be about 3130 cases
Category: Quantitative Biology

The Predictions of the Growth of Covid19 (Part 2 for the Usa). v2

Authors: Dongchan Lee
Comments: 3 Pages.

This is the summary of Lee’s predictions about COVID-19’s infection population in the United States of America. It is the second part of the series. Unless the U.S. government and CDC take actions aggressively nationwide to cut the rampant growth of the virus, at least 0.1 Million Americans will catch COVID-19 by March and at least 10 million infected Americans by sometime April, and almost 100 Millions infected by sometime May 2020. We corrected the error for the prediction for the 10,000 infections from the version 1 (from the context, it is obvious to see the writing error.) In this second version, we included when the U.S. death tolls reach 1 thousand, 10 thousand, 100 thousand, and 1 Million.
Category: Quantitative Biology

The Predictions of the Growth of Covid19 (Part 3 for Italy)

Authors: Dongchan Lee
Comments: 1 Page.

In this part 4, I predicted the total global infections and the total death tolls of the COVID-19 , adding some more to those predicted in the part 1.
Category: Quantitative Biology

The Predictions of the Growth of Covid19 (Part 4 for the Global Explosions)

Authors: Dongchan Lee
Comments: 1 Page.

In this part 4, I predicted the total global infections and the total death tolls of the COVID-19 , adding some more to those predicted in the part 1.
Category: Quantitative Biology

Prediction of Daily Contagions of Covid-19 from March 01 to May 19 in Italy

Authors: Calogero Rinzivillo, Sergio Conte, Elio Conte
Comments: 3 Pages.

We study a fractal model for prediction of Covid-19 contagions from March 01 to May 19 in Italy . We obtain that the time of the peak is estimated to be at March 22-23 and the number of contagions will be about 110000 cases
Category: Quantitative Biology

The Predictions of the Growth of Covid-19 for the United States of America (Part 2)

Authors: Dongchan Lee
Comments: 2 Pages. version 1

This is the summary of Lee’s predictions about COVID-19’s infection population in the United States of America. It is the second part of the series. Unless the U.S. government and CDC take actions aggressively nationwide to cut the rampant growth of the virus, at least 0.1 Million Americans will catch COVID-19 by March and at least 10 million infected Americans by sometime April, and almost 100 Millions infected by sometime May 2020.
Category: Quantitative Biology

The Predictions of the Growth of Covid-19 (Part 1)

Authors: Dongchan Lee
Comments: 5 Pages.

This is the summary of Lee’s predictions about COVID-19’s infection population outside the mainland China. It is the first part of the series. The next ones will be the predictions of the virus in the U.S.A. and Mexico.
Category: Quantitative Biology

Estimation of the Size of the Corona Virus in Italy in the Next Ten Days Made by Nonparametric Time Series Prediction

Authors: Sergio Conte, Ferda Kaleagasioglu, Alberto Foletti, Elio Conte
Comments: 4 Pages.

By using the methods of the non parametric time series prediction we obtain that in the next ten days we will reach the size of 8000-9000 contagions in Italy.
Category: Quantitative Biology

Predicting Influenza Strains Based on Correlations Between Northern and Southern Hemispheres

Authors: Jonathan Harney, Michael Harney
Comments: 11 Pages.

There is research showing that influenza strains are correlated between the Northern and Southern hemispheres. If this data is corroborated, this may lead to a prediction algorithm that relies on the predominant influenza strain in one hemisphere that is coming out of its flu season in order to predict the strain in the opposing hemisphere that is going into its flu season. This may provide enough time to develop a vaccine that is more accurately targeting the correct strain than in previous years.
Category: Quantitative Biology

(PPB Sketch-V.1.0 27.01.2020 49 a6 Pages Without the Abbreviation Table Romanian Version) Pediatria PRACTICĂ DE Buzunar a DR. DRĂGOI (DR. DRAGOI’S Practical Pediatric Handbook) (Version in Romanian)

Authors: Andrei Lucian Dragoi
Comments: 49 Pages.

INTRODUCERE. Acest manual practic de pediatrie în format de buzunar (aflat deocamdată în stadiul de ...”morulă”) se adresează tuturor studenților la medicină, rezidenților, medicilor specialiști și chiar primari care doresc un instrument de uz zilnic în clinică, dar și o sursă rapidă de recapitulare pentru examene. Prezentul manual este atipic (similar unui dicționar/manual-dicționar) prin faptul că macro-verigile fiziopatologice (cele frecvent întâlnite în practica pediatrică), bolile și sindroamele pediatrice (dar și celelalte seturi de informații medicale relevante) sunt toate indexate în ordine alfabetică ca rubrici succesive într-un index unitar comun (pentru o accesare rapidă), iar bolile sunt prezentate în forma unui lanț cauzal orizontal compus din verigi fiziopatologice în “cascadă” (marcate prin subliniere orizontală și constituind de fapt “scheletul” etiopatogenic/fiziopatologic al unei boli anume) ce descriu în general afectări de țesut sau organ specifice ce au un tablou semiologic clinico-paraclinic (inclusiv imagistic) ȘI un tratament (curativ și/sau suportiv/simptomatic) comune. Note importante. (1) Bolile și sindroamele au fost marcate în index prin mici chenare, tocmai pentru a fi diferențiate de verigile fiziopatologice (listate în același index unitar comun). (2) Toți termenii subliniați în textul interior al oricărei rubrici (din indexul principal al acestui manual) reprezintă verigi fiziopatologice (sau alte seturi de informație medicală relevantă) ce au la rândul lor propria rubrică (ce poate fi accesată și separat, pentru citirea descrierii detaliate a acelei verigi) în indexul principal unitar al acestui manual-dicționar medical.
Category: Quantitative Biology

Studies on Protein Synthesis Within a Theoretical Model

Authors: Tumpa Saha, Biplab Chattopadhyay
Comments: 11 pages, 3 figures, published in IOSR Journal Of Pharmacy And Biological Sciences (IOSR-JPBS), Volume 14, Issue 5 Ser. II (2019), PP. 10-20

Synthesis of proteins through the phenomenological pathway of transcription and translation, that constitutes the central dogma, has been explored theoretically. Emphasizing the closed-cycle character of the phenomenon, a prototype of the same is framed in mathematical terms with the biological inputs from allied literature. The mathematical prototype is actually a set of three coupled time differential equations signifying time rate of change of DNA, RNA and protein densities occurring in the biological cells of eukaryotes. The prototype has been scrutinized by well-set mathematical tools in regard of its sustainability under detailed stability tests. To judge exact behavioural pattern of the prototype solutions, rigorous numerical simulations of the time differential equations are carried out. Analyses of numerical simulation results with various changing parameters lead to predictive conclusions about different regulatory mechanisms existing in the protein synthesis phenomenology. Some future research directions are indicated too.
Category: Quantitative Biology

Analogy Inspired Biology

Authors: Prashanth R. Rao
Comments: 1 Page.

In this hypothesis paper, we identify a potential biological principle purely inspired by real life analogy. It is most likely that real examples in biology, disease, and pharmacology exist for this principle and have already been identified. The principle suggests how in an attempt to restore the level of a biological processes at one location or one instance, organisms/living systems may unintentionally end up dysregulating the process at another location or instance.
Category: Quantitative Biology

Diet Effects on Sperm Quality

Authors: George Rajna
Comments: 37 Pages.

Sperm are influenced by diet, and the effects arise rapidly. This is the conclusion of a study by researchers at Linköping University, in which healthy young men were fed a diet rich in sugar. [24] Researchers analyzed semen from 49 men whose partners had lost three or more consecutive pregnancies before the 20-week mark. [23] Single-molecule fluorescent measurements provide fresh insights into a process for keeping errors out of our genomes. [22] Histones are proteins that regulate the unwinding of DNA in the cell nucleus and the expression of genes based on chemical modifications or "marks" that are placed on their tails. [21] Now, in a new paper published in Nature Structural & Molecular Biology, Mayo researchers have determined how one DNA repair protein gets to the site of DNA damage. [20] A microscopic thread of DNA evidence in a public genealogy database led California authorities to declare this spring they had caught the Golden State Killer, the rapist and murderer who had eluded authorities for decades. [19] Researchers at Delft University of Technology, in collaboration with colleagues at the Autonomous University of Madrid, have created an artificial DNA blueprint for the replication of DNA in a cell-like structure. [18] An LMU team now reveals the inner workings of a molecular motor made of proteins which packs and unpacks DNA. [17] Chemist Ivan Huc finds the inspiration for his work in the molecular principles that underlie biological systems. [16] What makes particles self-assemble into complex biological structures? [15] Scientists from Moscow State University (MSU) working with an international team of researchers have identified the structure of one of the key regions of telomerase-a so-called "cellular immortality" ribonucleoprotein. [14]
Category: Quantitative Biology

Seed Germination Events

Authors: George Rajna
Comments: 43 Pages.

Seed germination is controlled by several plant hormones, which are researched intensely. However, not much was known about the processes that need to take place to allow the hormones to function. [26] Since the tests are for vaccines that can save millions of animals, protect farmers' livelihoods and alleviate hunger, Beer said they were "justified". [25] Sperm are influenced by diet, and the effects arise rapidly. This is the conclusion of a study by researchers at Linköping University, in which healthy young men were fed a diet rich in sugar. [24] Researchers analyzed semen from 49 men whose partners had lost three or more consecutive pregnancies before the 20-week mark. [23] Single-molecule fluorescent measurements provide fresh insights into a process for keeping errors out of our genomes. [22] Histones are proteins that regulate the unwinding of DNA in the cell nucleus and the expression of genes based on chemical modifications or "marks" that are placed on their tails. [21] Now, in a new paper published in Nature Structural & Molecular Biology, Mayo researchers have determined how one DNA repair protein gets to the site of DNA damage. [20] A microscopic thread of DNA evidence in a public genealogy database led California authorities to declare this spring they had caught the Golden State Killer, the rapist and murderer who had eluded authorities for decades. [19] Researchers at Delft University of Technology, in collaboration with colleagues at the Autonomous University of Madrid, have created an artificial DNA blueprint for the replication of DNA in a cell-like structure. [18] An LMU team now reveals the inner workings of a molecular motor made of proteins which packs and unpacks DNA. [17] Chemist Ivan Huc finds the inspiration for his work in the molecular principles that underlie biological systems. [16]
Category: Quantitative Biology

A Proposed Diatom Stratospheric Life-form

Authors: Lincoln Stoller
Comments: 34 Pages.

We propose a species of diatom that conducts its full life cycle in the lower stratosphere by suggesting physical, chemical, and electrical mechanisms to maintain its location and metabolism. The life-form we propose exploits hydrogen sulfates to create water for hydration, hydrogen for buoyancy, and energy for metabolic processes. We detail a mechanism for harvesting negative ions by stable altitude cycling in the stratosphere's voltage gradient. This theoretical, predictive approach can be applied to terrestrial and extra-terrestrial atmospheric biomes. We suggest life-forms of this sort have been undetected residents in the stratosphere for the last 200 million years, and argue for new observations that preserve the in vivo conditions of the sampling environment, as is necessary to discover fragile, airborne life-forms.
Category: Quantitative Biology

Population Structure, Fecundity and Morphological Characteristics of M. Vollenhovenii (Herklots, 1857) on Lower Volta River Basin Channel, Ghana

Authors: Eniade Abiodun Adeyemi, Odedeyi Dominic Olabode, Bello-Olusoji A Oluayo, Adebayo Olabode Thomas, Agyakwah Seth Koranteng
Comments: 11 Pages.

Population structure, fecundity and morphological characteristics of M. vollenhovenii were studied around Lower Volta River, Ghana subject to dirt of information on this prawn species around the study location. The most prominent morphological characteristics already documented for identification of this species was rostrum bearing 13-15 continuous teeth dorsally and 4-5 teeth on its ventral part. These morphological traits formed the principal components for identification in this study. Results showed that morphological traits on second pereiopods such as presence of spines, spinules, teeth borne within the fingers, and dense projections of setae-like features on telson and uropod were observed relevant for identification purposes. Other results revealed that maximum total length recorded in this study (150-155mm) was higher than total length ranges (≤125mm) documented for this species in earlier studies. Consequently, two adult’s classes of prawns were identified (old adult class 81-120mm; and young adults 31-80mm) and older class was observed to be more in catches than the younger prawns. Absolute fecundity revealed that oocytes estimation varied with respect to seasons, ages of prawns and body sizes of specimens examined. In conclusion, this study observed that M. vollenhovenii fishery is operating in a sustainable manner at the time of this study around the study location.
Category: Quantitative Biology

Bacteriological Quality of Kunu-Zaki Sold on the Streets of Owerri Metropolis, Nigeria

Authors: Anumudu I. C., Anumudu C. K.
Comments: 5 Pages.

Kunu-zaki is a nourishing non-alcoholic beverage widely consumed in Nigeria. There is no standardized method for its preparation thus production practices differ amongst retailers. This study was undertaken to evaluate the bacteriological quality of kunu drink retailed in major markets of Owerri metropolis, Nigeria. Triplicate samples were obtained from four markets in Owerri and a control sample prepared in the laboratory. Kunu drink was analysed using the standard pour plate procedure. The results obtained showed that total heterotrophic bacteria count, total coliform count and total Salmonella Shigella count ranged from 1.4 x 103 – 4.5 x 104 cfu/ml, 1.2 x 103 – 3.8 x 104 cfu/ml to 0.6 x 103 – 3.1 x 104 respectively. A total of 9 bacteria genera including Staphylococcus specie, E. coli, Enterobacter specie, Proteus specie, Citrobacter specie, Serratia specie, Lactobacillus specie, Salmonella specie and Streptococcus specie were isolated with the highest percentage frequency of occurrence recorded for Staphylococcus sp. (16.66%) indicating possible low hygiene of the kunu zaki producers. The bacteria genera isolated from kunu zaki sold in Owerri and their number constitute main concerns for public health as these can cause a variety of infections or food intoxications. Thus, there is a need to establish a system of monitoring of street vended kunu zaki to make sure that it is safe for consumption.
Category: Quantitative Biology

Quantum Entanglement in Theoretical Physics as a New Insight Into Cancer Biology

Authors: Sorush Niknamian, Spmayeh Zaminpira, Sprephanie Seneff
Comments: 12 Pages.

Quantum entanglement is a phenomenon in theoretical physics that happens when pairs or groups of particles are generated in such a way that the quantum state of each particle cannot be described independently of the others, even when the particles are separated by a large distance. Instead, a quantum state must be described for the system as a whole. Based on the theory of cancer as an evolutionary metabolic disease (Evolutionary Metabolic Hypothesis of Cancer or EMHC), the cancerous cells are eukaryotic cells with different metabolic rate from healthy cells due to the damaged or shut down mitochondria in them. Assuming each human eukaryotic cell as a particle and the whole body as a Quantum Entangled System (QES), is a new perspective on the description of cancer disease, and this link between theoretical physics and biological sciences in the field of cancer therapies can be a new insight into the cause, prevention and treatment of cancer. Additionally, this perspective admits the Lamarckian evolution in the understanding of the mentioned disease. We have presented each human eukaryotic cell containing mitochondria as a QES, and the whole body containing healthy and normal cells as a QES as well. The difference between the entropy of the healthy cells and cancer cells has also been mentioned in this research.
Category: Quantitative Biology

Variations of Biomass and Carbon Contents in Different Traits and Components of Herbaceous Species from Tropical Grassland

Authors: Preeti Verma, R. Sagar, Hariom Verma, Abhishek Rai, Pratibha Chaturvedi, Prem Pratap Singh, Kuldeep Kumar, Sandeep Kumar Singh
Comments: 32 Pages.

Grasslands play a critical role in the global storage of atmospheric carbon (C). Precise estimation of C contents in different plant components is essential to formulate a strategy for mitigating the atmospheric C. Biomass (B) and C of different herbaceous plant components at species, functional group and site levels from tropical grassland locating on the campus of Banaras Hindu University, Varanasi, India were estimated. For this; 117 herbaceous species just-before flowering were harvested. B and C contents for each species and component were measured and statistically analyzed. The measured C (g plant-1) across the components varied from 0.08 to 31.12. On gm-2 basis; it varied between 29 (leaf) and 49 (root). Plant components, species and functional groups in isolation caused significant differences in the measured C. In the present study; the C content of stem was greater than the leaf and root. The perennial, erect, leguminous and native traits had greater C than the others. Therefore, this observation revealed that the perennial, erect, leguminous and native plants could be a better option for reducing the atmospheric CO2 by capturing it and then converting into B through photosynthesis. Further, the fitted regression equation between the root and shoot for B and C could be used for the extrapolation of B and C of the root component based on the shoot component. The conservative field measurement methods may give precise data on B and C but are destructive to grassland, difficult, time-consuming, and costly to cover at large scale. Hence, the present work could be substantial for the estimation of root C based on shoot component.
Category: Quantitative Biology

Explaining the Benefits of Human Genome Patent

Authors: Shahima Akter Topu
Comments: 5 Pages.

Gene patenting has been facing backlash for decades now. Even Michael Crichton, science fiction novelist, as joined the bandwagon speaking against gene patent.1 Such hostility towards patents, the professional interests of academics, researchers and inventors are under the threat of losing their rights over the work they have done. The biotech industry can never be out of discoveries. With constant biological changes, new diseases are appearing and they have to dig deeper. However, not all progress is free. Rewarding the inventors is not at all unfair. This paper will demonstrate that (i) patents are a foundation of the industry. They need to innovate further progress. The reason patent law exists to protect the inventions for a limited period of time. The paper will also demonstrate that (ii) the social myths about gene patent are not really manifested in reality. It will discuss the argument against gene patenting and then will present counter arguments with empirical evidence whether the myths are really true.
Category: Quantitative Biology

Genetic and Environmental Factors in Skin Color Determination

Authors: Callixte Yadufashije, Rebero Samuel
Comments: 4 Pages.

The origin of skin color has been significantly a discussion of importance among human biology scientists, anthropologists and others interested in evolution of human skin color. Experience was done to chimpanzee and other primates shared almost the same characters with mankind, and this impressed scientists to know what makes difference in skin color among people. Different researches conducted to know the real cause of dark skin and light skin among people of the same origin. There are no other results found out of permanent variation happened to our ancestors based on geographical location. Environmental factors played a huge role in skin color determination. High UVR has been led to dark skin color and low production of UVR led to lightly skin. By natural selection genes responded to environmental conditions for a human to survive in his own environment. Melanin production came as a response to UVR to protect against consequence of UVR in low latitude regions. Depigmentation happened due migration from low latitude to high latitude regions and led lightly skinned color for our ancestors. Everyone has skin color due to ancestry antique geographical location.
Category: Quantitative Biology

Dormancy and Germination in Two Australian Native Species (Acacia Aneura and Rhodanthe Floribunda)

Authors: Paul Theophile Epee Misse
Comments: 5 Pages.

In the laboratory of plant physiology of the University of Queensland (Gatton Campus), a seed germination experiment was undertaken on seeds of two Australian native plant species – Rhodanthe floribundato and Acacia aneura. Most Acacia, including A. aneura exhibit a physical dormancy due to the waxy coat covering the seed. Comparably, just a few species of Rhodanthe are studied as to their dormancy. However, they are also known to present different forms of dormancy. To understand and describe these dormancy mechanisms, a seed germination experiment was conducted on Acacia aneura and Rhodanthe floribunda. This experiment will either add to the existing knowledge regarding these species’ dormancy or corroborate them. It is expected that both species display some form(s) of dormancy.
Category: Quantitative Biology

Study of Chorioamnionitis Among Women with Preterm Birth at Ruhengeri Referral Hospital

Authors: Callixte Yadufashije, Jasmine Umugwaneza, Cedrick Izere, Emmanuel Munyeshyaka, Thierry Habyarimana
Comments: 8 Pages.

Background: Chorioamnionitis is the association of microorganisms infection in fetal membrane, placental membrane and amniotic fluid. About 2 to 4% of chorioamnionitis occurs in full-term deliveries, but higher than this prevalence in preterm birth. Objectives: The objective of this study was to detect the most dominant bacteria of chorioamnionitis and evaluate correlation of the presence of microorganisms infection in placental membrane, fetal membrane and amniotic fluids in women with preterm birth. Methods: It was cross section study where 20 women with preterm premature rupture of membrane, premature rupture of membrane or preterm birth. By caesarean section or without caesarean section with a group of control of 10 women with term delivery. After delivery immediately the samples swab of amniotic fluid, fetal membrane and placenta membrane sample were placed in separate sterile container (swabs Stuart plastic) in the hospital, where it was stored at temperatures ranging between 8oC-20oC. Culture technique, gram staining and biochemical test were used to identify the microorganisms in this study at INES-Ruhengeri Microbiology laboratory. At the Ruhengeri Referral Hospital and analyzed according to INES Microbiology Laboratory standard operating procedures. Results: in 20 women with preterm birth, the most dominant mircoroganism was yeast 28.4% and mould 28.4%, other infections were caused by Escherichia coli, with 9.3%, Klebsiella species with 3.7%, Streptococcus species with 9.3%, Staphylococcus species with 9.3%, Candida albican with 11.7%. Those microorganisms show the association in fetal membrane, placenta membrane and amniotic fluid, of all women suspected to have chorioamnionitis. In 10 samples of control group, for women with term birth, same microorganisms were found like in fetal membrane were (Staphylococcus species 11%, mould 33%, and Yeast 56%), in placenta membrane were (Staphylococcus species 20%, mould 30%, Yeast 50%) and Amniotic fluid were (Staphylococcus species 0%, mould 33%, Yeast 67%). Conclusion: Chorioamnionitis can be in women with preterm birth or with term birth, untreated microorganism infections will cause a big problem of chorioamnionitis in pregnant women this will conduct to preterm morbidity and mortality.
Category: Quantitative Biology

Artificial Neural Network (Ann) and Regression Model for Predicting the Albumin to Globulin (A/g) Ratio in a Serum Protein Electrophoresis Test

Authors: Akshansh Mishra
Comments: 10 Pages.

Multiple myeloma affects the several parts of bodies such as the spine, skull, pelvis and ribs. The cause of multiple myeloma is not known properly. The poor prognoses is associated with most cancers creates a sense of urgency for the brains behind healthcare Artificial Intelligence (AI) research. AI is able to detect cancer and other diseases earlier than possible through standard diagnostic methods, which could be lifesaving for future patients. The main objective of the research paper is to predict the Albumin to Globulin (A/G) ratio obtained by the electrophoresis test by developing regression model and Artificial Neural Network (ANN) model. The results obtained showed that the Mean Square Error (MSE) obtained by ANN model is less than the MSE obtained by the regression model.
Category: Quantitative Biology

Susceptibility of Common Weeds and Cultivated Crops in Major Maize Growing Agroecological Zones of Uganda to Viruses Causing Maize Lethal Necrosis Disease

Authors: Mudde, B., Miano D. W., Olubayo, F. M., Asea, G., Kilalo, D.c., Kwemoi, D. B., Adriko, J., Ssekiwoko, F., Male, A., Kiggundu, A.
Comments: 14 Pages.

Maize lethal necrosis (MLN) disease is caused when maize plants become coinfected with Maize chlorotic mottle virus (MCMV) and potyviruses notably Sugarcane Mosaic Virus (SCMV). Apart from maize, little is known about susceptibility of weed species and cultivated crop species usually growing in proximity with maize to MLN viruses in Uganda. The common weeds and crop plants were mechanically inoculated with combined sap from MCMV and SCMV infected maize plants. Samples were tested for MLN causing viruses by Double Antibody Sandwich Enzyme-Linked Immunosorbent Assay (DAS-ELISA) and Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR). The weeds that were susceptibility to MCMV were Digitaria abyssinica, Eleusine africana and Roetboellia cochinchinensis; while those susceptible to SCMV were Pennisetum purpureum, Panicum maximum and Roetboellia cochinchinensis. The cultivated crops were susceptible only to MCMV and included cassava (Manihot esculenta), groundnut (Arachis hypogaea) and bean (Phaseolus vulgaris). Common weeds and cultivated crops growing close to maize in Uganda have differential susceptibility to MLN causing viruses and can act as reservoirs of MLN causing viruses. It is critical to identify non MLN hosts in cultivated crops for crop rotation and early weeding to reduce on MLN virus inoculum in cropping systems.
Category: Quantitative Biology

Effect of Dietary Substitution of Maize Meal with Finger Millet Meal on Fat Deposition on Broiler Meat

Authors: Ndlovu, N., Usai, T., Usai, E., Manhokwe, S.
Comments: 9 Pages.

The aim of this study was to investigate the effect of a finger millet-based broiler feed on the meat quality of chicken. Proximate nutrient composition was analyzed on the finger millet meal and a feed formulated with finger millet as the main energy source. The feed was formulated on percent crude protein (CP) basis using Pearson square method. An experiment was designed and conducted on Ross Hybrid chickens to determine the effect of the feed on lean tissue development. A two-tailed t-test statistical analysis was conducted at a significance level of 5% to determine the effect of the feed on fat deposition and lean tissue development in broiler muscle. The finger millet feed increased mean lean tissue mass by 3.47%. This study showed that use of finger millet feed reduced the fat deposition and favored protein deposition in broiler muscle (increased leanness). This study also showed that finger millet feed significantly enhanced broiler growth performance. We concluded that finger millet has the potential to replace maize meal in broiler feed formulation in order to produce lean and healthier meat for consumers.
Category: Quantitative Biology

Phylogenetic and Morphological Diversity of Culturable Cyanobacteria from Lake Magadi in Kenya

Authors: Ngetha Edwin, Julia Khayeli Akhwale, Romano Mwirichia
Comments: 8 Pages.

Lake Magadi is an alkaline saline Lake in Kenya, which lies on the Great Eastern Rift valley. Although the lake is characterized by extremes of salt, pH and temperature, it supports diverse groups of cyanobacteria. In this study, we used different media to isolate novel groups of cyanobacteria. We recovered 11 isolates affiliated to the orders Chroococcales, Oscillatoriales, Pleurocapsales and Nostocales. Isolates affiliated to Chroococcidiopsis species had similarity values below 90% to currently characterized taxa indicating that these could be completely new phylotypes. This taxon has not been isolated before from the soda lake indicating the power of molecular techniques in identifying novel cyanobacterial taxa. Only two of the recovered isolates had 99% similarity to known organisms. Previous studies have mainly relied on microscopic examination and identification, which can lead to misidentification and subsequent assignment of an organism to the wrong taxon. The recovered isolates are a useful resource of more studies on taxonomy and secondary metabolite production.
Category: Quantitative Biology

Comparative Growth and Survival Performance of Sea Cucumber (Holothuria Scabra) in co-Cultured Pen System with Commercial Macroalgae

Authors: Muumin I. Hamad, Augustine W. Mwandya, Renalda S. Munubi, Sebastian Chenyambuga, Heiromin A. Lamtane.
Comments: 10 Pages.

Mariculture has recently been adopted in many parts of coastal East Africa as a source of income and employment to many women and heartbroken fishermen who are the main victim of dwindling wild stock of aquatic resources. The sea cucumber (Holothuria scabra) has for long time been collected and sold as export marine product. Macroalgae (Eucheuma denticulatum and Kappaphycus alvarezii) are the common cultured seaweed species that provide hope for future increase in mariculture production. An experiment was conducted along the intertidal lagoon of Unguja Ukuu village in Zanzibar to assess the survival and growth performance of sea cucumber (H. scabra) in two separate pens under co-cultured systems with E. denticulatum and K. alvarezii. Juvenile sea cucumber H. scabra with mean weight (± se) of 67.18 ± 2.06 were integrated with the two common commercial seaweed in pen system for 10 weeks. The results revealed that the growth rate and survival of H. scabra, E. denticulatum and K. alvarezii were better under integration system. The growth of H. scabra was higher (1.038 gd-1) in pen systems co-cultured with K. alvarezii compared to 0.898 gd-1 in pen systems co-culture with E. denticulatum. Survival rate of H. scabra was higher (76%) in the pen systems co-cultured with E. denticulatum compared to that (70%) observed in pen systems co-cultured with K. alvarezii. The results suggest that the best integration of sea cucumber and macroalgae is between H. scabra and K. alvarezii. However, reliable source of H. scabra juvenile is essential for the future expansion of pen co-culture system.
Category: Quantitative Biology

Influence of Mangrove Deforestation and Land Use Change on Trophic Organization of Fish Assemblages in Creek Systems

Authors: Augustine W. Mwandya
Comments: 15 Pages.

The impacts of human related activities on trophic structure of mangrove associated fish species, was investigated by sampling fish in mangrove creeks. Trophic organization and stable isotope signatures (δ13C and δ15N) of fish in undisturbed mangrove creeks were compared with clear-cut areas of mangrove and reservoirs for saltworks and fish farms constructed after mangrove clearing. Results showed significantly higher densities, species numbers, diversity (H’) and numbers of trophic groups in undisturbed sites compared to disturbed sites. Overall, omnivorous fish comprised the most abundant feeding guild, which dominated in the cleared sites followed in order by the uncleared sites and reservoirs. The zoobenthivores/piscivores was the most diverse group, with the highest species richness in the undisturbed areas. Multivariate analysis showed that assemblage structure of omnivores in the reservoirs was separated from those in uncleared and cleared sites, while zoobenthivores/piscivores differed between uncleared sites and disturbed areas. Stable isotope ratios of δ13C and δ15N values in fish muscles indicated significant diet shifts between undisturbed and disturbed mangrove creek systems, although the effects were species-specific. The findings suggest that mangrove deforestation combined with land-use changes, has a greater impact on the trophic structure of fish in mangrove creeks than mangrove deforestation only.
Category: Quantitative Biology

Determination Prevalence of Cymothoid Parasite Fish Families in Iwofe (Port Harcourt) Rivers State

Authors: Gloria Wonodi, Ugbomeh A.P., Gabriel U.U.
Comments: 10 Pages.

The aim of this study is to provide information on the morphology of the Cymothoid parasites of Haemulidae and Elopidae from Iwofe in Port Harcourt determine physico chemical parameter of study area. To determine the percentage prevalence of Cymothoid parasite of both fish families in the study area. To determine the species of the Cymothoid parasite in the study area. To compare the structure and morphology of the different life stages of the Cymothoids. A total of seventy six (76) fishes from Iwofe landing site were examined, forty six (46) fishes were infected with a prevalence of 68%, Pomadasys perotetei had (96.7%), Pomadasys jubelini had (57.1%), Clarias arius had (50%) and none was also isolated from Mugil curema. During the period of study no Elopidae was found in this station, samples were obtained only from Haemulidae. The fishermen said they do not always have that catch because of the kind of net they use in fishing the morphology of the Cymothoid parasites of Haemulidae and Elopidae and the sampling sites was Iwofe water side . The isolated parasite that was collected was Cymothoid parasites and they Cymothoid sodwana, Cymothoid pleibeia, Cymothoid spp1, Cymothoid spp2, Nerocila acuminata, Nerocila lomatia and Nerocila orbignyi. The physical chemical parameters of the water was analyzed and the result showed that there was a significant difference in salinity, Dissolved Oxygen (DO) and Electrical Conductivity (EC) across the sampling stations. Pomadasyidae had a higher prevalence of isopods than the other fish hosts and more than one type of parasite was found in the mouth while Elopidae had the parasite on their fins and body wall and none was recorded in the mouth. The cephalon, pereomeres, pleomeres, pleotelson, eyes and marsupium was different in the Cymothoids studied. The parasite also affected the condition of the fish.
Category: Quantitative Biology

Detection of Helicobacter Pylori Among Gastritis Patients Attending Nemba District Hospital

Authors: Callixte Yadufashije, Ange Yvette Uwitonze, Yvonne Manizabayo, Thierry Habyarimana
Comments: 8 Pages.

Background: Helicobacter pylori (H. pylori) is a small, spiral-shaped bacterium that lives in the surface of the stomach and duodenum. More than half of the world’s population is colonized with H. pylori in the gastric mucosa which is the major cause of chronic gastritis, peptic ulcer and also the most important etiological factor responsible for the duodenal and gastric ulcer and has an important role in the pathogenesis leading to gastric cancer. Objectives: The objectives of this study was to determine the prevalence of H. pylori among gastritis patients at Nemba district hospital, to compare sex prevalence level of H. pylori among gastritis patients and determine the prevalence of H. pylori among gastritis patients according to the age of gastritis patients. Methods: This study involved 140 patients with gastritis who attended Nemba district hospital from August to October 2018. The samples were collected and H. pylori rapid test strip was performed for all patients to diagnose H. pylori among gastritis patients. Results: Findings of the study showed that the prevalence of H. pylori infection was found to be significantly high among female participants than male participants. Despite high prevalence in females, the findings showed that there was no statistical significance of sex with H. pylori infection (χ2 = 0.6 and p > 0.05, p = 0.1). On basis of age, the prevalence of H. pylori infection was found to be high among participants and the prevalence increase between young age and old age. Results show that there was statistical significance between age and H. pylori infection with χ2 = 1.2 and p > 0.05, p = 0.04. the group of individuals with that ≥ 45 years old were more affected compared to other age groups and the prevalence of H. pylori infection was increased in older patients than younger patients. Our study showed an overall prevalence of H. pylori among gastritis patients was (45.7% n = 140). Conclusion: H. pylori infection is terrible burden of public health and affect people of all age and sex. H. pylori infection was significantly high in females and significance was found in age group of patients. Number of people are carrier of this terrible bacterium, thus hospitals are recommended to carry out early diagnosis to avoid later complication of infection.
Category: Quantitative Biology

(Asea in DMD Conferinta Ramnicu Sarat 2.11.2019) Efectele Remarcabile Ale Suplimentului Redox "Asea"® în 2 Cazuri de Distrofie Musculară Duchenne la Copil și Potențialul Terapeutic al Asea în Bolile Acute și Cronice cu O Importantă Componentă de Stres

Authors: Andrei Lucian Dragoi
Comments: 45 Pages. https://www.researchgate.net/publication/336990483

TITLE IN ENGLISH: The remarkable effects of " >® redox supplement" (ARS) in 2 cases of Duchenne muscular dystrophy in children and the therapeutic potential of Asea / ARS in acute and chronic diseases with a significant component of cellular oxidative stress) ABSTRACT IN ENGLISH: This research aims at discovering dietary supplements which may show comparable or even stronger beneficial effects (with less or none adverse effects) than corticosteroids in children with Duchenne Muscular Dystrophy (DMD). This paper presents a case report on the effects of an ionized “saline water” called “ASEA redox Supplement®” (ARS) oral solution in a ~2-year-old boy with DMD from Bucharest, Romania. In vitro studies showed that ARS is a very potent selective NRF2 activator, thus a very potent (indirect) antioxidant: the studies conducted in vivo also support this main pharmacological mechanism of ARS, with no toxicity up to high doses, in contrast with the much more toxic corticosteroids. From the first months of ARS treatment all the rhabdomyolysis markers (with very high initial serum levels) dropped significantly, with no found toxicity. The main conclusions of this paper are: (1) ARS has remarkable antioxidant and immunomodulatory effects and should be studied on larger groups of children with DMD under the age of 4 years old (but also on other age groups of children and even young adults), as an alternative to early corticosteroids; (2) Given its immunomodulatory effect (NRF2 selective activation and NF-kB inhibition), ARS deserves future cohort studies on its potential to replace corticosteroids and other non-steroidal immunosuppressants (at least partially) in many types of pulmonary/renal/hepatic/ articular/skin autoimmune and even malignant diseases of both children and adults; (3) Given its very strong antioxidant effects (by highly selective NRF2 potent activation), ARS deserves future cohort studies on acute/chronic diseases that imply high levels of tissular oxidative stress, especially some acute/chronic cardiovascular and respiratory diseases like acute myocardial infarction with acute/chronic heart failure, stroke, Chronic Obstructive Pulmonary Disease (COPD), asthma etc. of both children and adults (so that ARS may help millions and even billions worldwide). Keywords: ASEA redox supplement (ARS) oral solution, 3-year-old boy, Duchenne muscular dystrophy (DMD), NRF2 selective activation, corticosteroids --------------------------------- REZUMATUL LUCRARII/PREZENTARII (Rezumatul lucrării/prezentării) Această cercetare își propune să descopere suplimente alimentare care pot demonstra efecte benefice comparabile sau chiar mai puternice (cu efecte adverse mai mici sau deloc) decât corticosteroizii la copiii cu distrofie musculară Duchenne (DMD). Această prezentare conține 2 raporturi de caz (în premieră mondială) asupra efectelor unei soluții saline ionizate (de uz intern oral) numite "supliment redox < >”® (SRA) la doi băieței cu DMD de 4 respectiv 5 ani, ambii din București. Studiile in vitro au arătat că Asea este un foarte potent activator selectiv al factorului de transcripție nucleară NRF2 (ce guvernează răspunsul anti-stress celular de fază B), deci un antioxidant foarte puternic (indirect): studiile efectuate in vivo până în prezent susțin și ele acest principal mecanism farmacologic de acțiune al Asea, fără toxicitate demonstrată in vivo chiar până la doze relativ mari, în contrast cu toate tipurile de corticosteroizi, care au toxicitate demonstrată pe multe aparate și sisteme. Încă din primele luni de tratament cu Asea, toți markerii de rabdomioliză (cu niveluri serice inițiale foarte mari, tipice pentru DMD) au scăzut semnificativ, fără nici un semn clinic și/sau paraclinic de toxicitate. PRINCIPALELE CONCLUZII ALE ACESTUI ARTICOL (Principalele concluzii ale acestei lucrări) sunt: (1) Asea are efecte antioxidante și imunomodulatoare remarcabile și merită studiată pe grupuri mai mari de copii cu DMD cu vârsta sub 4 ani (dar și pe alte grupe de vârstă de copii și chiar adulți tineri), ca alternativă la corticosteroizii administrați precoce încă de la vârsta de 2-3 ani (cu cel puțin 1 an înainte de vârsta standard de 4 ani actualmente unanim acceptată ca moment de inițiere corticoizi în DMD); (2) Având în vedere efectul său imunomodulator (activarea selectivă a NRF2 și inhibarea factorului de transcripție NF-kB, ce guvernează răspunsul anti-stress celular de fază A), Asea merită studii viitoare de cohortă asupra potențialului său de a înlocui (cel puțin parțial!) corticosteroizii și alte imunosupresoare nesteroidiene în multe tipuri de boli pulmonare / renale / hepatice / boli autoimune articulare / cutanate și chiar maligne ale copiilor și adulților; (3) Având în vedere efectele antioxidante foarte puternice (prin hiper-activare înalt selectivă a NRF2), Asea merită studii viitoare de cohortă în bolile acute / cronice care implică niveluri ridicate de stres oxidativ tisular/celular, în special unele boli cardiovasculare și respiratorii acute / cronice precum infarctul miocardic acut cu insuficiență cardiacă acută / cronică, accident vascular cerebral, boală pulmonară obstructivă cronică (BPOC), astm bronșic etc. atât la copii cât și la adulți (astfel încât Asea poate ajuta milioane și chiar miliarde de bolnavi la nivel mondial). Cuvinte-cheie: supliment redox Asea (SRA) soluție orală, distrofie musculară Duchenne (DMD), factorii de transcripție nucleară NRF2 și NF-kB, activare selectivă de NRF2, corticosteroizi More Info: www.dragoii.com
Category: Quantitative Biology

Possible Traces of Resonance Signaling in the Genome

Authors: Ivan Savelyev, Max Myakishev-Rempel
Comments: 11 Pages.

Although theories regarding the role of sequence-specific DNA resonance in biology have abounded for over 40 years, the published evidence for it is lacking. Here, the authors reasoned that for sustained resonance signaling, the number of oscillating DNA sequences per genome should be exceptionally high and that, therefore, genomic repeats of various sizes are good candidates for serving as resonators. Moreover, it was suggested that for the two DNA sequences to resonate, they do not necessarily have to be identical. Therefore, the existence of sequences differing in the primary sequence but having similar resonating sub-structures was proposed. It was hypothesized that such sequences, named HIDERs, would be enriched in the genomes of multicellular species. Specifically, it was hypothesized that delocalized electron clouds of purine-pyrimidine sequences could serve as the basis of HIDERs. The consequent genomic analysis confirmed the enrichment of purine-pyrimidine HIDERs in a few selected genomes of mammals, an insect, and a plant, compared to randomized sequence controls. Similarly, it was suggested that hypothetical delocalized proton clouds of the hydrogen bonds of multiple stacked bases could serve as sequence-dependent hydrogen-bond-based HIDERs. Similarly, the enrichment of such HIDERs was observed. It is suggested that these enrichments are the first evidence in support of sequence-specific resonance signaling in the genome.
Category: Quantitative Biology

Estudo Taxonômico da Tribo Cassieae (Leguminosae – Caesalpinioideae) no Parque Ecológico Engenheiro Ávidos, Cajazeiras–PB

Authors: Flávio Sousa Souto, Aclébia Alves Quaresma, Rubens Teixeira de Queiroz, Maria do Socorro Pereira
Comments: 21 Pages.

This work consists in a taxonomic study of the Tribe Cassieae in the Engenheiro Ávidos Ecological Park, Cajazeiras - Paraíba, carried out between February/2017 an April/2018. Twelve species were recorded in the area, distributed in two genera: Chamaecrista (6) and Senna (6). Among the species found, we highlight Chamaecrista pilosa, here cited as a new registry for the state of Paraíba and the occurrences of C. amiciella and C. duckeana, endemic species of the Caatinga. Analytical key for species identification, morphological descriptions and complementary information are presented. In this context, the relevant contribution of this study to the knowledge of the flora in the region is evidenced.
Category: Quantitative Biology

Lista Atualizada da Flora Vascular do Parque Nacional (Parna) Serra de Itabaiana, Sergipe, Brasil

Authors: Ana Cecília da Cruz Silva, Eduardo Vinícius da Silva Oliveira, Marccus Alves, Marta Cristina Vieira Farias, Aline da Costa Mota, Christopher Anderson Santos Souza, Ana Paula do Nascimento Prata
Comments: 28 Pages.

The Serra de Itabaiana National Park is located in an ecotone between Atlantic Rainforest and Caatinga biomes. It is one of the main areas of scientific studies in Sergipe. There are works approaching botanical families and listings of vascular flora. However, there is a need to update and compile the lists to better knowledge of the diversity of local flora. Therefore, a checklist was prepared from previous publications and Herbarium database of the Federal University of Sergipe (ASE). In total 124 families and 830 species of vascular plants were recorded distributed between Angiosperm (803 species), Ferns and Lycophytes (26) and Gymnosperms (1). The families of greater richness were: Fabaceae (73 species), Poaceae (65), Cyperaceae (59), Rubiaceae (40) and Asteraceae (36). The most representative habits were herbs (41.2%), shrubs (24.7%) and tree (17.6%). One hundred and seventy species are new occurrences for Sergipe, there is a new species for science, six rare species, three endangered species, nine almost endangered and three vulnerable, in addition there are 80 endemic species of the Atlantic Forest and 13 endemic to the Caatinga.
Category: Quantitative Biology

Estudo Taxonômico Das Subfamílias Cercidoideae e Detarioideae (Leguminosae) no Parque Ecológico Engenheiro Ávidos, Sertão Paraibano

Authors: Flávio Sousa Souto, Aclébia Alves Quaresma, Anaine Batista Araruna, Rubens Teixeira de Queiroz, Maria do Socorro Pereira
Comments: 7 Pages.

The subfamilies Cercidoideae and Detarioideae represent the basal lineages among the Leguminosae. In this work it is reported the occurrence of three species in the Engenheiro Ávidos Ecological Park, being two members of Cercidoideae, Bauhinia cheilantha (Bong.) Steud. and B. pentandra (Bong.) D. Dietr. and one of Detarioideae, Tamarindus indica L. It is worth mentioning that B. pentandra occurs in Paraíba only in the municipalities that comprise the Sertão mesoregion, while B. cheilantha is distributed in all geographic regions of the state. Tamarindus indica is an exotic species, widely cultivated, due to its food potential. These floristic data are relevant because they contribute to the increase of the knowledge of the vegetal cover in the semiarid.
Category: Quantitative Biology

Fragmentação Florestal na Área de Proteção Ambiental de Tambaba, Paraíba, Brasil

Authors: Saara Souza Rodrigues, Cleber Salimon, Saulo Roberto de Oliveira Vital
Comments: 8 Pages.

One of the most fragmented ecosystems in Brazil is the Atlantic Rain Forest, due to centuries of deforestation along the coast which holds one of the world’s greatest biodiversity. Landscape metrics and shape can impact on border effect on patterns and processes of a forested ecosystem. In this paper, we map and characterize the forest fragmentation of the Tambaba Environmental Protection Area (APA), on the coast of Paraíba State, Brazil, using landscape metrics to verify the effectiveness of this protected area. We conducted a land cover classification (supervised classification by maximum likelyhood, RapidEye imagery) into two categories (1) forest and (2) non forest. Landscape metrics (number of fragments, total core area, proportion of core area, among others) were calculated using ArcGis extension Patch Analyst. From the APA’s total 11.550 ha, 2.200 ha were classified as forest (19%), distributed in 1.364 fragments of different sizes. Total core area varied from 1.470 (10 m border effect) to 370 ha (50 m border effect), dependending on edge effect distance, which provides a true conservation of only 13 to 3% of the total APA. These results point to the necessity of an intense and rigorous surveillance of the compliance with laws, as well as a rational and participatory management, through the APA’s management council and public agencies, in order to protect the remnant fragments.
Category: Quantitative Biology

Predation of Dermatonotus Muelleri (Anura, Microhylidae) by Guira Guira (Cuculiformes, Cuculidae) in the Coastline of the Sergipe State, Northeastern Brazil

Authors: Francis Luiz Santos Caldas, Bruno Jackson Melo de Almeida, Rafael Alves dos Santos
Comments: 4 Pages.

Predation can drive significant effect upon the community structure. However, the observation and documentation of this ecological interaction is occasional and yet scarce for many groups. Our goal here is to report the predation of Dermatonotus muelleri (Boettger, 1885) by Guira guira (Gmelin, JF, 1788). Because G. guira diet frequently includes small vertebrates we believe that this species may act as an important regulator of D. muelleri population. This predation report can input insights about the knowledge of interactions of Microhylidae Günther, 1858 (1843) members and others species.
Category: Quantitative Biology

Occurrence of Amblyomma Sp. (Acari: Ixodidae) in Tropidurus Hispidus (Spix, 1825) (Squamata: Tropiduridae) in Parque Nacional Serra de Itabaiana, Sergipe, Brazil

Authors: Daniel Oliveira Santana, Francis Luiz Santos Caldas, Lucas Barbosa de Queiroga Cavalcanti, Fabíola Fonseca Almeida Gomes, Bruno Duarte da Silva, Rafael Alves dos Santos, Renato Gomes Faria
Comments: 5 Pages.

Lizards are often parasitized by Acari species (mites and ticks). In this study we report the occurrence of a specimen of tick (Amblyomma sp.) parasitizing a juvenile individual of Tropidurus hispidus (Spix, 1825) in Parque Nacional Serra de Itabaiana (PNSI) in the state of Sergipe, northeastern Brazil.
Category: Quantitative Biology

Aranhas Epígeas de um Fragmento de Mata em área Urbana em Fortaleza, Ceará, Brasil

Authors: Raul Azevedo, Kamilla Gonçalves Menezes, Raissa Aguiar Barbosa, Joaquin Deusdedit Rocha Matos Neto, José Onofre Nascimento Monteiro, Alysson Guedes Coutinho, Luis Gonzaga Sales Júnior
Comments: 10 Pages.

Spiders are indicators of environment quality due fact of been sensible to environment changes. Their adaptions among the environment and their relations between vegetal communities make them have a special role in forest ecosystems. However, this relation makes spiders susceptible to effects of urban process and to defloration and ecosystem fragmentation process. A spider fauna survey was developed using 50 “pitfall traps”, annual sample process begun in 2010 and finished in 2011 (total samples = 600) in an urbanized patch. A total of 1238 individuals were collected, constituting 51 species belonged to 18 families which Zodariidae and Lycosidae were most abundant, and Salticidae and Theridiidae were the richest families. It´s also observed many rare species (Singletons and Doubletons). The richness estimators didn´t exhibit a trend do exhibit an asymptote and the relation between collected species and estimated species, suggesting more samples process also suggests a necessity of develop politics to preserve the local biodiversity.
Category: Quantitative Biology

Críticas ao “Tree Thinking”: Elucidando O Significado Das Relações Filogenéticas

Authors: Rafael Gomes de Souza
Comments: 15 Pages.

The “Tree Thinking” is regarded as the dominant methodology in current Systematic Biology. However, criticisms of the procedures carried out by it are diverse. Here the criticisms made by Fitzhugh regarding its philosophical basis and the consequences of such modifications are presented and defended. Thus, the present work aims to demonstrate that “Tree Thinking”, as it has been used, is incomplete because it does not recognize that phylogenetic relationships are of the causal type previously summarized in an explanatory sketch (cladogram). In addition, to support such an argument, a discussion on the definition and objectives of Systematic Biology and “Tree Thinking” is provided. As a result, it is possible to observe confusion between classifying and systematizing the knowledge by those who follow "Tree Thinking". In addition, “Tree Thinking” fails to provide causal explanations regarding the origin and fixation of the characteristics studied. In this way, “Tree Thinking” can be considered an incomplete practice within Systematic Biology and, therefore, the application of the proposals of Fitzhugh are recommended.
Category: Quantitative Biology

New Records and Geographic Distribution Map of Pseudopaludicola Pocoto (Anura: Leptodactylidae: Leiuperinae) in Northeastern Brazil

Authors: Charles de Sousa Silva, Igor Joventino Roberto, Robson Waldemar Ávila, Drausio Honorio Morais
Comments: 5 Pages.

We provide new records and an updated geographic distribution map of Pseudopaludicola pocoto Magalhães, Loebmann, Kokubum, Haddad & Garda, 2014 for the Brazilian states of Ceará, Rio Grande do Norte and Pernambuco. The present work helps to fill gaps in distribution of this recently described species in Caatinga Biome, which can be useful in future conservation plans.
Category: Quantitative Biology

O Status Ecológico Das Comunidades de Fungos Coprófilos

Authors: Francisco J. Simões Calaça, Jéssica Conceição Araújo, Solange Xavier-Santos
Comments: 7 Pages.

We discuss the ecological status of coprophilous fungi communities lato sensu, presenting key points to the definition of scientific hypothesis and future studies aiming to understand the ecological factors that modulate the coprophilous lifestyle’s choice by these fungi. We present a new scientific term (copromycodiversity) that better describes the magnitude of this group, considering the comprehensiveness of this fungal group, including the morphological, physiological and ecological diversities to a coprophilous fungi population recorded to a specific geographical region. Furthermore, we raised some questions related to the life cycle of these fungi, taking into account recent studies as well as the traditionally accepted assumption that supports the spore passage through animals’s gut to its growth and development on dung. We expect that future research would best define these communities, avoiding uncertainties about the definition of the coprophilous lifestyle, even that some species would growth on others substrates (fimicolous fungi), but still displaying some connection with its animal host (coprophilia). While we are waiting for future directions, new hypothesis must be planned and tested aiming the predictors that truly modulates the occurrence of coprophilous fungi in different environments.
Category: Quantitative Biology

Acidentes Causados Por Aranhas e Escorpiões no Estado do Ceará, Nordeste do Brasil: Casos Subnotificados e Superestimados Baseados na Distribuição Geográfica Das Espécies

Authors: Raul Azevedo, Francisco Roberto de Azevedo, Relrison Dias Ramalho, Paulo André Margonari Goldoni, Antonio Domingos Brescovit
Comments: 14 Pages.

The accidents caused by arachnids have increased its frequency along the years and the majority of accidents reports do not contain species identification, contributing to underreporting of data. In Ceará state, specific information about accidents with full notifications or accident description are scarce. In this present study, data about accidents involving spiders and scorpions in Ceará state from 2010 to 2015 period were correlated with geographic distribution based on data from main Brazilian scientific collections of arachnids. An increased number of accidents caused by spiders and scorpions was observed, mainly in 2013 for scorpions, and a constant number of municipalities reported scorpionic accidents to this period. According to Sistema de Informação de Agravos de Notificação - SINAN, in Ceará state, many cases were credited to Phoneutria sp., Loxosceles sp., and Latrodectus sp., whoever this occurrence is not correlated with their geographic distribution supported on arachnid collections data. Therefore, knowledge on species geographic distribution with public health significance combined with properly notified records can contribute to reduction of accidents numbers and development of politics aimed to public health.
Category: Quantitative Biology

Bats (Mammalia, Chiroptera) from an Area of Caatinga in Southwestern Bahia, Brazil

Authors: Fábio Soares, Patrício Adriano da Rocha, Stephen Ferrari, Thiago Acioli, James Prado Pinto-Sobrinho
Comments: 9 Pages.

The present study provides an inventory of the bat species recorded in the municipality of Caetité, in southwestern Bahia, Brazil. Sixty-eight individuals were captured, belonging to nine species and three families. The Jackknife 1 procedure estimated a species richness of 9.9. The phyllostomid bats were the most abundant, and Carollia perspicillata (Linnaeus, 1758) was captured most frequently. Our results are consistent with previous studies conducted in Bahia and the Caatinga, providing data on the local bat community structure. It also highlights the importance of rapid inventories for the understanding of the diversity and distribution of the bat fauna.
Category: Quantitative Biology

Note on bats (Mammalia, Chiroptera) in a Restinga area of Rio Grande do Norte, Brazil

Authors: Fábio Soares, Marcela Daher, Raul Perrelli, José Armando Torres Moreno, Stephen Ferrari
Comments: 5 Pages.

Currently, forty-one species of bats are known to occur in the restingas of Brazil. However, most studies on restingas’ bats are limited to the south and southeastern regions of Brazil, leaving the northeastern region with a gap of knowledge. The present article presents data on bats captured in three areas of restinga of the municipality of Tibau do Sul, Rio Grande do Norte, collected from a short-term sampling. Mist nets were used to capture bats near the ground and the water bodies. Were captured 38 individuals of six species and two families: five Phyllostomidae and one Molossidae. The bat Carollia perspicillata (Linnaeus, 1758) was the most abundant species. We present here the first list of bats captured in the restinga area for the Rio Grande do Norte State.
Category: Quantitative Biology

New Records of Albardia Furcata Van Der Weele, 1903 (Neuroptera, Ascalaphidae, Albardiinae) from Paraíba, with Notes on a Predator Species

Authors: Alessandre Pereira-Colavite, Izabela Souza Braga, Wellington Emanuel dos Santos
Comments: 5 Pages.

New records of the rare owlfly Albardia furcata van der Weele, 1903 are provided from the state of Paraiba, in the Caatinga and Atlantic Forest, including four new localities. A referential map is included to the recorded specimens. The first report of the predator fly Peckia (Sarcodexia) lambens (Wiedemann, 1830) on dead body of A. furcata is registered.
Category: Quantitative Biology

Papel Das Moscas (Insecta, Diptera) na Entomologia Forense

Authors: Wellington Emanuel dos Santos
Comments: 8 Pages.

This paper presents a brief review of the role of flies (Insecta, Diptera) in Forensic Entomology. Discussions on presence in human cadavers and vertebrate carcasses, Postmortem Interval (PMI) estimations, studies carried out in Brazil and other countries, families of forensic importance and biological, ecological and distribution aspects of the main species are presented.
Category: Quantitative Biology

Invasão Biológica Por Cryptostegia Madagascariensis: Uma Abordagem Voltada Para Estresses Abióticos

Authors: Jailma dos Santos de Medeiros, Francisco de Oliveira Mesquita, Leonaldo Alves de Andrade, Cleiton José de Oliveira, Edlânia Maria de Souza, Jânio Kleiber Camelo de Souza
Comments: 11 Pages.

The introduction, accidental or deliberate, of exotic species by different vectors is currently a major global changes, resulting in a number of local and global problems. Although not all introductions of non-native species have negative effects, many of the non-native species can have undesirable effects on biodiversity from the genetic level to the landscape. This work aimed to present the current knowledge on biological invasions by species and particularly on invasive Cryptostegia madagascariensis Bojer ex Decne. New introductions are made every year around the world and only a small part of these taxa become invasive, yet cause serious damage to ecosystems invaded. The success of weed plants is due to the intrinsic characteristics of these species that ensures the same competitive advantages with native species and the level of disruption in new niches which makes them totally supportive environments to establish new species and the emergence of monodominadas areas. In this context is C. madagascariensis, origin of climbing on the island of Madagascar in Africa, which was introduced in Brazil with ornamental purposes, becoming invasive in natural ecosystems, especially in riparian environments and humid lowlands, in the field of savanna and associated ecosystems.
Category: Quantitative Biology

Diversity and Community Composition of Marine Mollusks Fauna on a Mainland Island of the Coast of Paraná, Southern Brazil

Authors: Marcos de Vasconcellos Gernet, Eduardo Colley, Elizângela da Veiga Santos, Carlos João Birckolz
Comments: 11 Pages.

Farol Island is a continental island in the state of Paraná, southern Brazil. Due to its position in relation to the continent, three distinct environmental areas are observed: rocky shore area with open exposure to the sea (A); estuarine area (B); sandy beach area (C). Considering that the continental islands are excellent study models that reproduce the environmental conditions of the coastal zone in a smaller scale, the study aimed at surveying and researching the marine malacofauna on the Farol Island and comparing the diversity and shellfish composition. The sampling method was based on a monthly collection in three locations for two years (2011-2012). The survey found 91 species: 47 Gastropoda, 41 Bivalvia and three Scaphopoda. The highest abundance and species richness prevailed in environmental area A. The greatest equitability was observed in B and the highest dominance in C. There was a predominance of Gastropoda and Bivalvia in A, while the frequency of Scaphopoda did not vary among environments. The species composition of the three classes varied among the three areas. The variation of diversity and species composition in the three environments may be related to the natural characteristics of each side of the island, as salinity and wave action.
Category: Quantitative Biology

New Records of Two Species of Acanthocarpus Stimpson, 1871 (Crustacea: Decapoda: Calappidae) in Northeastern Brazil

Authors: Flavio de Almeida Alves-Jr., Ângela Ferreira Pereira, Marina de Sá Leitão Câmara de Araújo
Comments: 7 Pages.

The gladiator box crab of the genus Acanthocarpus Stimpson, 1871 has benthonic habits, occurring in continental shelf on gravel or muddy substrates with occurrence in all oceans, especially between 20-522 m depth. In this paper we report the occurrence of Acanthocarpus alexandri Stimpson, 1871 and A. bispinosus A. Milne-Edwards, 1880 from the Potiguar Basin (Rio Grande do Norte), located in the Brazilian northeast and increase the knowledge about the distributional aspects of this species from Brazilian coast.
Category: Quantitative Biology

Predation of Hemidactylus Mabouia (Sauria: Gekkonidae) by a Vine Snake Oxybelis Aeneus (Serpentes: Colubridae) in an Atlantic Forest Fragment, Northeastern Brazil

Authors: Lissa Dellefrate Franzini, Carmem Karime Bacalháo Pedro, Lucas Barbosa de Queiroga Cavalcanti, Daniel Oliveira Mesquita
Comments: 4 Pages.

Oxybelis aeneus (Wagler, 1824) is an arboreal snake species that is widely distributed in the American continent whose diet is composed mainly by vertebrates, such as lizards. Several lizard species have already been reported as prey of this snake, including the alien species Hemidactylus mabouia (Moreau de Jonnès, 1818). Herein we describe in details a predation event of H. mabouia by O. aeneus, widening our knowledge regarding the natural history of both species to scientific literature.
Category: Quantitative Biology

Efeito de Técnicas de Enriquecimento Ambiental no Comportamento de Leontopithecus Chrysomelas (Kuhl, 1820) (Primates: Callitrichidae)

Authors: Denise Costa Rebouças Lauton, Antônio de Oliveira Costa Neto
Comments: 8 Pages.

Environmental enrichment consists in techniques that modify the captive environment, in order to make it more dynamic. The adoption of the method, often, results in the reduction of abnormal behavior (stereotypies) and expression of a more typical behavioral repertoire. Believing in the effectiveness of environmental enrichment techniques and that it is possible to improve the condition of captives individuals, this work was proposed. There were applied techniques of Physical and Feed enrichment to groups and solitary individuals captives of Leontopithecus chrysomelas (Kuhl, 1820) kept in Tropical Laboratory of Primatology (TLP), of the Universidade Federal da Paraíba (UFPB). The observations were made in three phases: Control; Enrichment of the Physical; and Nutritional. Individuals presented frequent abnormal behaviors during Control phase, such as pacing and excessive watching, especially the lonely individuals. During the experimental phase, only the act to guard presented significant difference for the family groups (Fr2 = 7.58; gl = 2; p = 0.023). The results show that L. chrysomelas of the TLP seem to be more resistant to change, possibly due to the long period of exposition of these to a conditioned environment to a routine and without stimuli. Aimed to modify this scenario, it is suggested to adopt methods of “routine break” concomitant to the techniques of environmental enrichment.
Category: Quantitative Biology

Population Structure and Fecundity of Upogebia Omissa (Decapoda: Gebiidea: Upogebiidae) in an Estuarine Region in Sergipe, Northeastern Brazil

Authors: Rafael de Carvalho Santos, Luiz Filipe Santos Silva, Bruna dos Santos, Juliana Menezes Motta, Douglas Fernandes Rodrigues Alves
Comments: 9 Pages.

Upogebiidae mud shrimps are important organisms in soft-bottom communities, where they dig burrows acting as ecosystem engineers. The present study describes some parameters of the population structure and the reproductive biology of the mud shrimp Upogebia omissa. The mud shrimps were sampled in the Vaza-Barris estuarine river, Sergipe State, northeastern Brazil. In laboratory, specimens were sexed and measured for carapace length (CL). Ovigerous females had their total eggs counted. The body size ranged between 3.0 and 12.9 mm CL. Males were significantly smaller than females. The overall sex ratio was 0.34, female-biased (binomial test, P = 0.001). Fecundity ranged from 240 to 2339 eggs per female, and it was significantly affected by the bodysize. The sexual dimorphism evidenced by the mean size of each sex is a common pattern in decapods that incubate eggs, and in that case, fecundity normally varies in function of body size. Finally, we suggest that additional studies are needed, given the ecological importance of these mud shrimps and the scarcity of studies about them.
Category: Quantitative Biology

Some Pycnogonida (Arthropoda: Chelicerata) from the “Paulo Young” Invertebrate Collection (CIPY) of the Federal University of Paraíba (UFPB), Brazil

Authors: Rudá Amorim Lucena, Martin Lindsey Christoffersen
Comments: 13 Pages.

Biodiversity studies are increasingly urgent, due mainly to the speed with which anthropic degredation is affecting the environment, marine localities in particular. Due to these human impacts, part of the marine biota is becoming increasingly unavailable in natural environments. Biological collections thus are of key importance, functioning as data bases for studies in Taxonomy, Systematics and Biogeography, as well as for several applied areas of research. Biological collections in Brazil suffer from lack of financial support, lack of human resources (both technical and scientific) and are difficult to access by the scientific cummunity. The Invertebrate Collection “Paulo Young” (CIPY) contains more than 18.000 identified and numbered samples of several marine invertebrates, from sponges to tunicates. The pycnogonid section, although less numerous than many other animal groups, has been the focus of attention in recent years. Several new species and new records have been reported from Brazil. The aim of the present paper is to disclose the CIPY reference collection, recording the Pycnogonida collection that was not the subject of previous publications.
Category: Quantitative Biology

Relação Entre Massa Corporal e Taxa Respiratória em Arthropoda de Floresta Atlântica (Paraíba, Brasil)

Authors: Idalio Amaranto, Cleber Ibraim Salimon, Douglas Zeppelini
Comments: 10 Pages.

Respiratory rate studies in arthropods refer to important physiological data, since these animals perform important ecosystem functions and because they are the greatest diversity and abundance of animals present on Earth. This study measures and describes respiratory rates through the emission of CO2, and relates them to the body mass of arthropods. The study was carried out in remnant fragments of coastal Atlantic Forest of Paraíba, Brazil. The research encompasses all living subphyla of arthropods (Crustacea, Chelicerata, Myriapoda and Hexapoda) represented by 705 specimens actively collected and tested through respirometry and measured by Infrared Gas Analyzer (IRGA). As a result, we observed that among the studied arthropods, Hexapoda and Chelicerata showed higher rates of carbon dioxide emission, while Crustacea and Myriapoda had the lowest rates. Regarding its relationship with body mass, Hexapoda and Crustacea showed higher respiration by specific mass and, in general, all Arthropoda corroborated the pattern described by animal physiology, where body mass and animal respiratory rate are inversely correlated.
Category: Quantitative Biology

Breve História da Sistemática de Agaricaceae (Fungi) e Distribuição no Brasil

Authors: Felipe Wartchow
Comments: 17 Pages.

The family Agaricaceae belongs to order Agaricales. In general the agaricoid species of this group are characterized by having squamulose pileus. This revision presents a brief history of the systematic of this group and distribution of their agaricoid species in Brazil since from early 19th Century to present days.
Category: Quantitative Biology

Registro de Olivancillaria Vesica (Gastropoda, Olividae) Sinistrógira no Litoral do Estado do Paraná, Brasil

Authors: Marcos de Vasconcellos Gernet, Carlos Eduardo Belz, Carlos João Birckolz, Elizângela da Veiga Santos
Comments: 4 Pages.

Olivancillaria vesica (Gmelin, 1791) commonly inhabitant beaches in southern and southeastern Brazil, living semi-buried in sandy substrates from the intertidal zone to deeper areas in the sub-littoral. In this work, we report the meeting of a sinistral shell of O. vesica, characteristic that is rare for this species. Its main measurements are: 10.6 mm in height, 5.1 mm in width, 8.1 mm in height of the aperture and 2.1 mm in width of the aperture. It was collected in the municipality of Matinhos, coast of Paraná state, southernern Brazil, in biodetritic gravel.
Category: Quantitative Biology

First Record of Calycuoniscus Goeldii (Lemos de Castro, 1967) (Oniscidea: Dubioniscidae) for the State of Piauí, Northeastern Brazil

Authors: Vanderley Ferreira Silva Costa, Daniela Correia Grangeiro, Carlos Anderson Soares Bezerra Pereira
Comments: 6 Pages.

The present work provides the first record of Calycuoniscus goeldii (Lemos de Castro, 1967) from the municipality of Picos, state of Piauí, northeastern Brazil. In addition, this paper contributes to increase the knowledge about the biodiversity of terrestrial isopods of the state of Piauí and distribution of the family Dubioniscidae in northeastern Brazil.
Category: Quantitative Biology

Exploração e Utilização do Potencial Madeireiro da Caatinga no Município de Aurora – Estado do Ceará

Authors: Amanda Pereira de Souza, Francisco Carlos Pinheiro da Costa, Rosana Ferreira de Alencar, Silvio Felipe Barbosa Lima
Comments: 10 Pages.

Plant species of the Caatinga have considerable logging and economic potential. This paper addresses the extraction and use of Caatinga wood in the municipality of Aurora (state of Ceará, Brazil) as well as residents’ conceptions regarding the origins and environmental impacts of the exploitation of this resource. A semi-structured questionnaire was used to obtain information on the origin and the forms of wood used. The data showed that, even when recognizing the risks of these actions, the interviewees extract wood from the Caatinga in a destructive manner, which is used for making furniture, doors, sculptures, instruments and fences as well as for fuel in cooking activities in homes, bakeries and pizzerias. The following species were more cited: Mimosa tenuiflora (jurema-preta), Croton sonderianus (marmeleiro), Mimosa caesalpiniifolia (sabiá), Amburana cearensis (cumaru), Combretum leprosum (mufumbo), Myracrodruon urundeuva (aroeira) and Handroanthus impetiginosus (pau-d’arco). The results point to the need for implementation of actions for the supervision and control of the exploitation of the Caatinga vegetation as well as adequate management guidelines for this important natural resource.
Category: Quantitative Biology

Guia Ilustrado Dos Echinodermata da Porção Sul do Embaiamento Sul Brasileiro

Authors: Maristela de Lima Bueno, Renata Aparecida dos Santos Alitto, Pablo Damian Borges Guilherme, Maikon Di Domenico, Michela Borges
Comments: 68 Pages.

The present guide describes 57 species of Echinodermata Bruguière, 1791 [ex Klein, 1734] from the southern portion of the Brazilian South Estuary (BSE), which includes the following coasts: the Southern of the State of São Paulo, entire of the State of Paraná and Northern of the State of Santa Catarina. We designed this guide for students and researchers providing a valuable resource for the identification and appreciation of shallow-water echinoderms. The guide describes the general features of the phylum Echinodermata, has a brief presentation of the study area and the techniques of collection and preservation of the specimens. For each class, the main morphological structures are illustrated, followed by the diagnoses of the species recorded in the BSE. Within each class, the species are organized by family, then alphabetically according to genus and species. For each species, we provide diagnoses, photos, geographic distribution and habitat when available in the literature. This work is the first illustrated guide of echinoderms in Brazil and complements the knowledge of biodiversity this group and provide support for future interventions, management and maintenance of the diversity of this wonderful group of marine animals.
Category: Quantitative Biology

Ocorrência de Dentes Fossilizados de Tubarões em Cascalhos Biodetríticos na Praia Dos Amores, Matinhos, Paraná, Brasil

Authors: Marcos de Vasconcellos Gernet, Elizângela da Veiga Santos, Esther Valentina da Veiga de V. Gernet
Comments: 4 Pages.

The coastal plain of Paraná originated in the Quaternary Period from cyclical movements of transgression and marine regression from the Holocene climatic oscillations. The sediments of the coastal plain present dates that vary from Pleistocene to Holocene. Along the coast of Paraná, several points are found that present deposits of biodetritic gravel, with great accumulation of fossiliferous material coming from this geologic period, among them shark teeth. The site chosen for collecting the fossilized teeth was in the gravel bank located in front of the Farol Island, located in the Amores Beach, in the municipality of Matinhos, Paraná. In total, 563 fossilized shark teeth were found, from six different species of two families. These data are very important to better understand this past biodiversity.
Category: Quantitative Biology

O Gênero Amanita (Fungi): Sistemática e Distribuição no Brasil

Authors: Felipe Wartchow
Comments: 16 Pages.

This revision presents topic related to the iconic mushrooms belonging to fungal genus Amanita. A brief story regarding to the Systematic and Taxonomy and the distribution of the species in Brazil are also presented.
Category: Quantitative Biology

Checklist of the Holothuroidea (Echinodermata) from the State of Paraíba, Brazil

Authors: Jéssica Prata, Martin Lindsey Christoffersen
Comments: 14 Pages.

The study presents the first species list for holothurians from the coast of the State of Paraíba, northeastern Brazil. The list was made based on the study of specimens deposited in the Invertebrate Collection Paulo Young, Federal University of Paraíba. A total of 16 species from seven families of Holothuroidea were recorded. This paper contributes to the biodiversity studies from the northeast coast of Brazil.
Category: Quantitative Biology

Lizard Predation Tropidurus Hispidus (Squamata, Tropiduridae) by False Coral Snake Oxyrhopus Trigeminus (Squamata, Dipsadidae) in the Caatinga, in Northeastern Brazil

Authors: Jefferson Simanas Mikalauskas, Daniel Oliveira Santana, Stephen Francis Ferrari
Comments: 8 Pages.

The predation of lizards is rarely observed in the wild, and events involving snakes are scarcer still. Here we document in detail the predation of a lizard (Tropidurus hispidus (Spix, 1825)) by a snake (Oxyrhopus trigeminus Duméril, Bibron & Duméril, 1854). Many studies have identified Tropidurus Wied-Neuwied, 1825 lizards as prey for Brazilian snakes. Thus, this record provides important insights into the natural history of both species, especially O. trigeminus, which are essential for the understanding of their ecology.
Category: Quantitative Biology

Physical, Biological and Human-Induced Effects on the Reef Fishes of Fernando de Noronha Archipelago, Brazil

Authors: Paulo Roberto de Medeiros, Ana Maria Alves de Medeiros
Comments: 15 Pages.

Several factors have the potential to influence the distribution and composition of reef fish communities. Amongst the most important are rugosity, wave exposure, substrate cover and human activities. The present study evaluated the influence of these factors on reef fishes from sites following a gradient of human-induced effects on the Fernando de Noronha archipelago, northeast Brazil and determined their relative importance to reef fish ecology. Rugosity did not influence fish richness, but had a positive influence on number of individuals, juveniles and endemic species, whereas benthic cover did not seem to be an important determinant for any fish variable evaluated. These results suggest that availability of shelter (physical protection) is more limiting than availability of food (i.e. benthic cover). Furthermore, water flow showed somewhat low values, but even so, had negative effects on fish numbers. Recreational activities, albeit seemingly non-impacting, had a negative effect on fish abundance with the partially protected site (Atalaia) showing a similar community structure to the unrestricted site (Porto). These results suggest that human presence, even when supervised, may interfere on reef fish structure. Low-impact tourism practices are required especially in partially protected and unprotected areas.
Category: Quantitative Biology

Thresholding for Population-Level Polygenic Scores to Maximize Predictive Accuracy: iq and Educational Abilities.

Authors: Davide Piffer
Comments: 16 Pages.

Polygenic scores (PGS) are being used to predict group-level traits across time and space, hence proving useful to detect recent selection. The aim of this study is to investigate the impact of different p value thresholds on signal to noise ratio and predictive validity of polygenic scores, using the largest GWAS of educational attainment and cognition to date. Signal to noise ratio linearly decreases with p value, but this phenomenon is limited to Eurasians. There is a linear degradation of validity and population differentiation in allele frequencies with higher p values. However, compounded polygenic scores have a quadratic relationship with p value. A thresholding at or below the conventional GWAS significance (p<5*10-8) seems to maximize validity, corroborating earlier results. The highest correlation with population IQ is achieved by the Highest Math Class completed and the EDU MTAG PGS (r= 0.90 and 0.89, respectively). Using random SNPs, it is shown that correlations of this magnitude occur only once out of 46k trials. A table provides an empirical estimate of the rarity of the correlation coefficients and it is shown that they are a function of PGS size. Finally, an analogy between the noise contained in polygenic scores and physical instruments is put forward.
Category: Quantitative Biology

The Contributions of the Gallo Team and the Montagnier Team to the Discovery of the AIDS Virus

Authors: Rainer W. Kühne
Comments: 4 Pages.

In this paper I review the main works of the teams headed by Robert Gallo and Luc Montagnier which led to the discovery of the HIV retrovirus and to the blood test with which one can prove HIV infection. I show that this discovery which saved millions of human lifes (and perhaps the survival of mankind) was made possible only (i) because Gallo's team discovered the T-cell lymphocyte growth factor with which they were able to discover the first retrovirus that infects humans (HTLV-I) and their hypothesis that AIDS is caused by a retrovirus, and (ii) because Montagnier's team detected an antibody against alpha interferon in order to enhance retrovirus production with which they were able to discover the HIV retrovirus and their examination and blood test that gave evidence that HIV causes AIDS. Their examination was improved by the Gallo team who proved without doubt that HIV is the cause of AIDS. I leave the question open whether Gallo deserved the Nobel Prize or whether the Nobel committee's decision to award the prize only to Montagnier and Barre-Sinoussi was correct.
Category: Quantitative Biology

Arguments that Prehistorical and Modern Humans Belong to the Same Species

Authors: Rainer W. Kühne
Comments: 3 Pages.

I argue that the evidence of the Out-of-Africa hypothesis and the evidence of multiregional evolution of prehistorical humans can be understood if there has been interbreeding between Homo erectus, Homo neanderthalensis, and Homo sapiens at least during the preceding 700,000 years. These interbreedings require descendants who are capable of reproduction and therefore parents who belong to the same species. I suggest that a number of prehistorical humans who are at present regarded as belonging to different species belong in fact to one single species.
Category: Quantitative Biology

Why Recessive Lethal Alleles Have not Disappeared?

Authors: Jorma Jormakka
Comments: 11 Pages. I have several times tried to submit this paper, please delete the earlier versions.

The article derives the probability for lethal recessive alleles in the case of recessive disadvantage or advantage and discusses why lethal recessive alleles have not disappeared. It is shown that recessive advantage of a lethal gene can be detected by the ratio of heterozygotes and homozygotes. This demonstrates that higher IQ of certain ethnic groups cannot be explained by recessive advantage of lethal genes.
Category: Quantitative Biology

Failure of Complex Systems, Cascading Disasters, and the Onset of Disease

Authors: Anthony J Webster
Comments: 18 Pages.

Complex systems can fail through different routes, often progressing through a series of (rate-limiting) steps and modified by environmental exposures. The onset of disease, cancer in particular, is no different. A simple but very general mathematical framework is described for studying the failure of complex systems, or equivalently, the onset of disease. It includes the Armitage-Doll multi-stage cancer model as a particular case, and has potential to provide new insights into how diseases arise and progress. A method described by E.T. Jaynes is developed to provide an analytical solution for the models, and highlights connections between the convolution of Laplace transforms, sums of random samples, and Schwinger/Feynmann parameterisations. Examples include: exact solutions to the Armitage-Doll model, the sum of Gamma-distributed variables with integer-valued shape parameters, a clonal-growth cancer model, and a model for cascading disasters. The approach is sufficiently general to be used in many contexts, such as engineering, project management, disease progression, and disaster risk for example, allowing the estimation of failure rates in complex systems and projects. The intended result is a mathematical toolkit for the study of failure rates in complex systems and the onset of disease, cancer in particular.
Category: Quantitative Biology

A Geometric Pattern that Distinguishes the “Iron Sulfur” Group of Cytochrome P450 Enzymes

Authors: James A Studier
Comments: 4 Pages.

Given a phylogenetic tree of the P450 enzymes we describe a geometric pattern that distinguishes a major subtree.
Category: Quantitative Biology

Introgression from Gorilla Caused the Human-Chimpanzee Split

Authors: Johan Nygren
Comments: 4 Pages.

ABSTRACT: The Gorilla Genome Project (Scally, 2012) showed that 30% of the gorilla genome introgressed into the ancestor of humans and chimpanzees, and that the two species diverged through lineage sorting with 15% ending up in Pan and another 15% in Homo. That introgression is the Pan-Homo split, hybridization, which led to speciation as the new hybrid lineages became reproductively isolated from one another.

The NUMT on chromosome 5 fits perfectly with the introgression speciation model, it was formed from mtDNA that had diverged as much as ~4.5 Myr at the time of introgression, perfect fit with the Gorilla/Pan-Homo split, and the mtDNA fragments that formed it were inserted at the time of the Homo/Pan split, and ended up in both the Gorilla, Pan and Homo lineages around the same time period, 6 million years ago. (Popadin, 2017)

The Speciation of Australopithecus and Paranthropus Was Caused by Introgression from the Gorilla Lineage

Authors: Johan Nygren
Comments: 6 Pages.

ABSTRACT: The discovery of Paranthropus deyiremeda in 3.3–3.5 million year old fossil sites in Afar (Haile-Selassie, 2015), together with 30% of the gorilla genome showing lineage sorting between humans and chimpanzees (Scally, 2012), and a NUMT (“nuclear mitochondrial DNA segment”) that is shared by both gorillas, humans and chimpanzees, and that dates back to 6 million years ago (Popadin, 2017), is conclusive evidence that introgression from the gorilla lineage caused the speciation of both the Australopithecus lineage and the Paranthropus lineage, providing a lens into the gorilla-like features within Paranthropus, as well as traits within Homo that originate from the gorilla branch, such as a high opposable thumb index (Almécija, 2015), an adducted great toe (Tocheri, 2011; McHenry, 2006), and large deposits of subcutaneous fat.
Category: Quantitative Biology

Data Integration at Single-Cell

Authors: George Rajna
Comments: 28 Pages.

A team of computational biologists has developed an algorithm that can 'align' multiple sequencing datasets with single-cell resolution. [17] Chemist Ivan Huc finds the inspiration for his work in the molecular principles that underlie biological systems. [16] What makes particles self-assemble into complex biological structures? [15] Scientists from Moscow State University (MSU) working with an international team of researchers have identified the structure of one of the key regions of telomerase—a so-called "cellular immortality" ribonucleoprotein. [14] Researchers from Tokyo Metropolitan University used a light-sensitive iridium-palladium catalyst to make "sequential" polymers, using visible light to change how building blocks are combined into polymer chains. [13] Researchers have fused living and non-living cells for the first time in a way that allows them to work together, paving the way for new applications. [12] UZH researchers have discovered a previously unknown way in which proteins interact with one another and cells organize themselves. [11] Dr Martin Sweatman from the University of Edinburgh's School of Engineering has discovered a simple physical principle that might explain how life started on Earth. [10] Nearly 75 years ago, Nobel Prize-winning physicist Erwin Schrödinger wondered if the mysterious world of quantum mechanics played a role in biology. A recent finding by Northwestern University's Prem Kumar adds further evidence that the answer might be yes. [9] A UNSW Australia-led team of researchers has discovered how algae that survive in very low levels of light are able to switch on and off a weird quantum phenomenon that occurs during photosynthesis. [8] This paper contains the review of quantum entanglement investigations in living systems, and in the quantum mechanically modeled photoactive prebiotic kernel systems. [7] The human body is a constant flux of thousands of chemical/biological interactions and processes connecting molecules, cells, organs, and fluids, throughout the brain, body, and nervous system. Up until recently it was thought that all these interactions operated in a linear sequence, passing on information much like a runner passing the baton to the next runner. However, the latest findings in quantum biology and biophysics have discovered that there is in fact a tremendous degree of coherence within all living systems. The accelerating electrons explain not only the Maxwell Equations and the Special Relativity, but the Heisenberg Uncertainty Relation, the Wave-Particle Duality and the electron's spin also, building the Bridge between the Classical and Quantum Theories. The Planck Distribution Law of the electromagnetic oscillators explains the electron/proton mass rate and the Weak and Strong Interactions by the diffraction patterns. The Weak Interaction changes the diffraction patterns by moving the electric charge from one side to the other side of the diffraction pattern, which violates the CP and Time reversal symmetry. The diffraction patterns and the locality of the self-maintaining electromagnetic potential explains also the Quantum Entanglement, giving it as a natural part of the Relativistic Quantum Theory and making possible to understand the Quantum Biology.
Category: Quantitative Biology

Could Answer to Russian Poison Novichok Come from Holistic Medicine?

Authors: Edgars Alksnis
Comments: 1 Page.

Some experiments show, that replacement of fragments of neural system could in principle be possible. This requires deep rethinking of what we know about human body.
Category: Quantitative Biology

Estimating Genetic Parameters in a Dominance Model that Includes Inbreeding

Authors: Stephen P. Smith, Asko Mäki-Tanila
Comments: 21 Pages.

A dominance model is described coming with inbreeding, and five genetic parameter plus the environmental variance. The linear model is specified by the phenotypic equations and the mid-parent equations. They are placed in an indefinite system that is highly sparse, not the mixed model equations. From this system the augmented matrix K is built that is symmetric and indefinite, leading to restricted maximum likelihood. Likelihood evaluation follows from the factorization of K, and various sparse matrix tools are described for maximizing the likelihood. The method is used to estimate the six parameters for 2706 egg-laying hens that were part of a selection experiment.
Category: Quantitative Biology

Inverting the Extended Genomic Table: a Case Study

Authors: Stephen P. Smith, Asko Mäki-Tanila
Comments: 12 Pages.

A series of programs are described which calculate the inverse of the extended genomic table. These programs are demonstrated using a pedigree taken from a selection experiment involving egg-laying hens. The calculations are feasible and the inverse matrix was found to be sparse.
Category: Quantitative Biology

Six Fractal Codes of Biological Life: Perspectives in Astrobiology and Emergence of Binary Logics

Authors: Jean claude Perez
Comments: 50 Pages. none

The discovery of a simple numerical formula for the projection of all the atomic mass of life-sustaining CONHSP bioatoms leads to the emergence of a set of Nested CODES unifying all the biological, genetic and genomic components by unifying them from bioatoms up to whole genomes. In particular, we demonstrate the existence of a digital meta-code common to the three languages ​​of biology that are RNA, DNA and amino acid sequences. Through this meta-code, genomic and proteomic images appear almost analogous and correlated. The analysis of the textures of these images then reveals a binary code as well as an undulatory code whose analysis on the human genome makes it possible to predict the alternating bands constituting the karyotypes of the chromosomes. The application of these codes to perspectives in astrobiology and the emergence of binary codes and regions of local stability (voting process), whose fractal nature we demonstrate is illustrated.
Category: Quantitative Biology

The Brain is Processing Information, not Data: Does Anybody Knows About That?

Authors: Emanuel Diamant
Comments: 10 Pages. A preliminary version presented at The ISIS Summit “The Information Society at the Crossroads”, Vienna, Austria, 3–7 June 2015

Discriminating and opposing “data” and “information” (as it is emphasized in the paper’s title) for most of the scientific community sounds like something odd and unnatural. Raised in the spirit of Shannon’s Information Theory, most of the scientific community is convinced that data and information are inseparable. Nevertheless, over the last decade we witness a growing recognition that Shannon’s Information Theory is wrong, or speaking more politely, is limited only to data communication issues. Today, distinguishing data and information processing is gradually becoming a popular and widespread trend. However, because this trend is missing a firm theoretical underpinning, it looks a bit messy and inconsistent. Despite of this, the paradigm shift in contemporary science is clearly evident – from a data processing (computational) approach we are firstly moving to an information processing (cognitive) approach. (“Cognitive” here implies “capable of information processing”). Undeniably, Computational biology, Computational neuroscience, Computational linguistics (and so on) are being replaced today by Cognitive biology, Cognitive neuroscience, Cognitive linguistics, and so on. However, this tendency is hampered by a lack of understanding about what is “information processing”. Subsequently, a question “what is information?” immediately rise up. A consensus answer to it does not exist. I believe I have the answer. But instead of repetitive explanations about what is information, I prefer to bring an informational perspective to the everyday practice of scientific exploration, especially biological and neuroscience explorations. Maybe this will be more advantageous.
Category: Quantitative Biology

On the Importance of the Dynamic Measurement of the Pupil Size

Authors: Vicent Sanchis-Jurado, Álvaro Pons, Santiago García-Lázaro
Comments: 8 Pages.

In this pilot study we analyse the pupil fluctuations of the right eye of two subjects during forty-five seconds while keeping constant the viewing distance and the room illumination. Measurements were taken with an infrared eye-tracker working at 250 Hz. The results were for subject A a median diameter of 2.913 mm with a maximum diameter of 3.313 mm and a minimum diameter of 2.66 mm, for subject B the median diameter was 4.39 mm with a maximum of 5.23 mm and a minimum of 3.26 mm. For both subjects the distribution of the pupil diameter did not follow a normal distribution, this was determined with the Lilliefors test, the p-values were 0.0251 for subject A and 0.001 for subject B. In conclusion, even in constant conditions of illumination and viewing distance the pupil cannot be considered to remain constant and its diameter varies not following a normal distribution.
Category: Quantitative Biology

Effect of Fixation Target on the Contrast Sensitivity in the Foveal and Parafoveal Area

Authors: Vicent Sanchis-Jurado, Sophie Triantaphillidou, Edward Fry, Álvaro Pons
Comments: 12 pages, 4 figures, 1 table

Purpose To determine the influence on the contrast sensitivity when the stimulus contains a fixation target in two retinal locations, foveal and parafoveal. Methods Four young adults with 0.0 logMar acuity participated in this study. The stimulus was based on vertical sinusoidal gratings masked by a circular (for foveal area) or a ring (for parafoveal area). To increase the luminance resolution of the display a bit-stealing technique was used. Four different sets of stimuli were generated, two for exploring the foveal sensitivity and two for the parafoveal area. The difference between the sets designed for the same area was the presence, or absence, of a fixation target (a white cross) in the centre of the stimulus. A modified staircase method was implemented. Results The results show a drop in the contrast sensitivity when the fixation target was present on the stimulus for frequencies smaller than 4 cycles per degree. Conclusions The presence of fixation targets diminishes the contrast sensitivity for low to mid frequencies over different concentric areas of the retina. This could be due to the fixational eye movements, different patterns of eye movements were found using an eyetracker. The relationship between the sensitivity in the foveal area and the parafoveal agrees with those reported by other authors using different designs confirming that the new stimulus design is suitable to measure the contrast sensitivity outside the foveal area.
Category: Quantitative Biology

Rotationally Symmetric Structures of the C-ring of Escherichia Coli

Authors: Herbert Weidner
Comments: 5 Pages.

The C-ring of a motor contains either 34 or 44 copies of FliM but only about 26 copies of FliG. In addition, the amount of FliMs is influenced both by the direction of rotation and by the number of CheY-P signal molecules in the cytoplasm. The rotationally symmetrical model described here combines all known properties.
Category: Quantitative Biology

Color Perception: Controlled Excitation of Opponent Channels

Authors: Prashanth Alluvada
Comments: 15 Pages. Describes monochromatic spectra that cause controlled opponent channel excitation

We describe controlled excitation of opponent color channels. For monochromatic impingement of spectral energy, the wavelength sequences we develop cause a channel to attain a preset excitation level, causing thereby a controlled excitation of color channels.
Category: Quantitative Biology

The Existence of God: An Application of the Poisson Distribution

Authors: Charles M. Byrne
Comments: 13 pages, Keywords: God, evolution, mutation, recombination, genetics, molecular biology, naturalism, Poisson distribution

In his theory of evolution by natural selection, Charles Darwin provided a plausible alternative to Christianity's creation account of human origins. In response, the Christian botanist Asa Gray suggested to Darwin that the variation that drives evolution might be generated by God. Darwin rejected Gray’s hypothesis, invoking philosophical naturalism, a hallmark scientific paradigm. Darwin's conclusion was reached on ideological grounds rather than empirical ones. Biological evidence that emerged subsequent to Darwin’s time yields a different conclusion. A means to assess the question of the source of genetic variation is provided by fitting the Poisson distribution to counts of mutation and chromosome crossover events at the DNA sites where they occur. A general failure of fit between observational data and the Poisson distribution confirms an exception to the naturalistic paradigm, and thereby provides epistemic access to the existence of God.
Category: Quantitative Biology

On Richard III's Y-DNA and Time-Asymmetric Mutation Rates

Authors: John Smith
Comments: 20 Pages.

A skeleton excavated in 2012 is almost certainly that of the English king, Richard III (1452 -1485), and mtDNA (which is passed from mother to child) extracted from the skeleton matches mtDNA taken from descendants of Richard's sister Anne of York. However Y-DNA (which is passed from father to son) extracted from the skeleton apparently doesn't match Y-DNA taken from descendants of Henry Somerset the 5th Duke of Beaufort, who according to history descended from Richard's 2nd great grand father Edward III (1312 - 1377). The implication according to geneticists, and the media, is that there is a "false paternity event" somewhere between Edward and the Somersets. In this note, a formula for calculating the time of the most recent common ancestor is introduced, and some of its consequences outlined. This formula is attached to a mathematical framework within which it is possible that the traditional genealogy is correct. If this framework is the right framework for understanding of genetic inheritance, then it has been wrongly assumed that Y-DNA mutation rates are like-line, constant and smooth - in reality they are wave-like and decrease erratically in the direction of the future, and the contrary impression is is an illusion created by an over-focus on the relatively constant and smooth nature of genetic change in the present and the near-present.
Category: Quantitative Biology

Principal Directon Divising Partitioning Initialisation of K-Means Clustering Allows to Identify the Most Salient Genes in Discriminating Among Leukemias

Authors: Diego Liberati
Comments: 35 Pages.

This paper attempts to cluster leukemia patients described by gene expression data, and to discover the most discriminating genes that are responsible for the clustering. A combined approach of Principal Direction Divisive Partitioning and bisect K-means algorithms is applied to the clustering of the investigated leukemia dataset. Both unsupervised and supervised methods are considered in order to get optimal result. The combination of PDDP and bisect K-means successfully clusters leukemia patients, and efficiently discovers salient genes able to the discriminate the clusters. The combined approach works well on the automatic clustering of leukemia patients depending merely on the gene expression information, and it has great potential on solving similar problems, like classifying pancreatic tumors. The salient identified genes may thus enhance relevant information for discriminating among leukemias.
Category: Quantitative Biology

Simulating the Idling Behavior of Escherichia Coli

Authors: Herbert Weidner
Comments: 10 Pages.

Until now, it is not known how the motors of E. coli reverse the direction of rotation, mostly simultaneously. If the C-ring is bistable and if the number of bound CheY-P depends on the direction of rotation, there is a strong variation in the concentration of CheY-P in the cytoplasm. Then, the synchronous changeover can be explained without further additional assumptions.
Category: Quantitative Biology

Nylonase Genes and Proteins - Distribution, Conservation, and Possible Origins

Authors: S.T. Cordova, J.C. Sanford
Comments: 78 Pages.

Nylon comprises a family of man-made substances that were first manufactured in 1935. Nylonases are biological enzymes that can break down nylon oligomers. Although the most prominent nylonases are within the family of enzymes classified as 6-aminohexanoate hydrolases, some enzymes not formally classified as 6-aminohexanoate hydrolases also have the ability to breakdown nylons, and so can also be classified as nylonases. Organisms that encode a nylonase enzyme do not necessarily have the ability to actually survive on a nylon substrate as their sole carbon source. Among the first documented organisms that did have this ability was the soil bacterium Arthrobacter KI72. It has long been thought that nylonase genes and proteins were essentially absent from the biosphere prior to 1935. This belief led to the widespread assumption that any nylonase gene observed in the present must have emerged since 1935. Several authors developed hypothetical models of how a specific nylonase gene (the nylB gene found within Arthrobacter KI72), might have arisen very recently as a de novo gene. In this paper we show that the widely-held assumption that all nylonase genes must have evolved very recently is no longer credible. This is in light of the wide-spread distribution of diverse nylonases throughout the biosphere. Likewise, we show that the early speculations regarding the possible de novo origin of the nylB nylonase gene are no longer credible. Our review of the literature shows that a variety of nylonase-digesting bacteria have been found in extremely diverse natural environments – far removed from any synthetic nylon sources. In addition, we show there are over 1800 organisms with computationally predicted (provisional) 6-aminohexanoate hydrolase/nylonase genes in the NIH-funded UNIPROT database. These 1800 predicted nylonases are not yet experimentally confirmed to cleave nylons, but have significant homology to the experimentally confirmed nylonases. In addition to 6-aminohexanoate hydrolases, proteases like trypsin and certain lipases have been experimentally demonstrated to have nylonase activity. If we include all proteases and lipases that may have nylonase activity, the number of organisms with nylonase activity may exceed ten thousand. The widespread distribution of nylonases and their homologs strongly suggests that nylonases were already widespread prior to 1935. Lastly, we have carefully examined the claims that the nylB gene arose as a de novo gene very recently. The theories of Ohno (the frame shift hypothesis) and Okada (the gene duplication hypothesis), were speculative in nature, and yet were uncritically accepted. In light of new data, these early speculations no longer appear tenable.
Category: Quantitative Biology

Brain Stimulation with Neutrinos

Authors: Evgeny A Novikov
Comments: 2 Pages.

A possibility of brain stimulation with neutrinos is discussed.
Category: Quantitative Biology

Crispr Technology Challenge Facing the Numerical Integrity of Whole Human Genome DNA

Authors: Jean Claude Perez
Comments: 10 Pages.

Background : Global analysis of 3 human genomes of increasing levels of evolution (Neanderthal / Sapiens Build34 / Sapiens hg38) reveals 2 levels of numerical constraints controlling, structuring and optimizing these genome's DNA sequences. A global constraint - called "HGO" for "Human Genome Optimum" - optimizes the genome at its global scale. The same operator applied to each of the 24 individual chromosomes reveals a hierarchical structure of these 24 chromosomes. Results : Then analysing the single strand DNA CG / TA proportions at whole chromosomes and genome scale reveals strong fine-tuned numerical ratios evidencing the "closure" nature (Varela's autopoiesis theory) of whole human genome.
Category: Quantitative Biology

Programa Analizador de Retrovirus

Authors: Roberto Reinosa
Comments: 3 Pages. Spanish

En el presente artículo se va a mostrar un programa, que sirve para realizar una serie de análisis a partir de secuencias provirales de retrovirus.
Category: Quantitative Biology

Combining Genetic Similarities Among Known Relatives that Connect to an Unknown Relative

Authors: Stephen P. Smith, Cambrian Lopez, Nicole Lam
Comments: 15 Pages.

Various DNA testing companies promise their customers a collection of genetic matches to facilitate finding family members. The matches are in centimorgans (cM), where the higher the cM value the closer the relationship to a customer (R). Unless the relationship is close, such as parent-offspring or among 1st cousins, a single cM value is not that informative if the goal is to locate family. This paper describes a statistical method that combines a collection cM values from a cluster of unknown relatives of R, but where the cluster members are known among themselves being for example 2rd and 3th cousins. A presumed envoy is attached to the cluster, where R is a descendant of the envoy, and the various cM values are combined to provide an overall cM value between R and the envoy. The envoy’s cM comes with a statistical error to judge significance. Unlike a single cM value on a typical unknown relative, the envoy’s cM can be quite large and indicative of a real genetic path to R that has previously been undiscovered. This paper describes the method for two sisters, where the path from the envoy led to their lost father, a father that was later discovered.
Category: Quantitative Biology

Tracking the Diffusion of Signal Proteins in Escherichia Coli

Authors: Herbert Weidner
Comments: 6 Pages.

We describe a fast computational model to study the signal transduction in E. coli chemo­taxis. It allows to trace the places and chemical reactions of individual molecules in a cell as a function of time. From the spatial resolution of the model and the known diffusion constant of the proteins, a time step of 3 µs is calculated for the simulation.
Category: Quantitative Biology

Reproductive Cloning

Authors: Ian von Hegner
Comments: 20 Pages.

Progressiv forkortelse af telomere ved DNA replikation er blevet sat i forbindelse med cellulær ældning. Hvad vil der ske med dyr, fremkommet ved somatisk kerneoverførsel, hvis differentierede celler fra voksne dyr med forkortede teleomerelængde benyttes til at starte embryo udvikling? Vil de forkortede telomere påvirke deres livslængde eller udvikling, eller er de forkortede telomere fra donerceller blevet rekonstrueret til fuld længde i klonede dyr?
Category: Quantitative Biology

Recognition from Description Through Synthesis and Reduction to Theory and Model

Authors: Andrzej Gecow
Comments: 9 Pages. in Polish

The half a century attempts to transmit the results of the theoretical work on the biological issues which used the methodology of physics, gave an insight into the methodological limitations resulting from the stereotypes of thinking in biology. It is primarily a lack of interest in the pursuit to deductive theory. Abstraction and deduction - the basis of physics, is despised and omitted as speculation, which creates a blockade in the development of theory in biology. The process of this development stops at an analysis that should (and does not do) reduce the sufficient conditions noted in the description to the necessary and sufficient conditions, ie. to determine the reasons for the phenomena being considered. Determination of the necessary conditions is the basis of reduction, which in the applied reductionism is not noticed. This chapter is not a recognized knowledge imparted authoritatively to use, nor fight against the official position of biology, but a collection of arguments against conservative stereotypes, to compare with other more elaborate sources on the reader's own responsibility to work out his own view rather than uncontrolled take over of the defective tradition.
Category: Quantitative Biology

Materials for Discussion of Methodological Limitations Resulting from the Stereotypes of Biologists Thinking

Authors: Andrzej Gecow
Comments: 18 Pages. in Polish

Attempts to communicate the results of theoretical works on the evolutionary biology using the methodology of physics have not yielded results for half a century, but have led to the recognition of methodological limitations stemming from the stereotypes of thinking in biology. It is primarily a lack of interest in the pursuit of deductive theory. Abstraction and deduction - the basis of physics, are despised and omitted as speculation, which creates a blockade in the development of theory in biology. As a basis for this diagnosis, five reviews of the text addressed to “KOSMOS” have been analyzed, which led to the conclusion that the text, because of the thesis contained therein, is unreadable to biologists. This study is the basis for a wider discussion in a separate publication.
Category: Quantitative Biology

Current Return to Lamarck in Agreement with Darwin

Authors: Andrzej Gecow
Comments: 11 Pages. in Polish

The terms ‘Darwinism’ and ‘Lamarckism’ mean different things to different people. Nowadays, they are rarely used in a historically correct way – clime Jablonka and Lamb, the scientists that mainly contribute to proving than not only genes can curry hereditary information and new hereditary channels show characteristic of Lamarckian mechanisms. Especially Lamarckism was seen in false and superficial way in lot of aspects. The inheritance of acquired characters was connected to Lamarck. It was rejected too radically. Today it revives but mainly not basing on epigenetic inheritance. Generally Lamarckian mechanisms increase in the complex and diverse ways the chances of accurate adaptive changes, so they no longer look like a random, appear as ‘effects of instructions’ or ‘directed variations’ but these ‘instructions’ have been previously acquired through Darwinian natural selection. The richness of these phenomena causes great difficulty of their brief describtion. Lamarckian dimension of evolution is now known better. This phenomena cannot be explained in the range of Modern Synthesis assumptions. It does not mean, that MS is false and should be rejected. Lamarckian mechanisms are created by Darwinian natural selection, but their explanations need wider assumptions, than are a basis of MS, means Extended Evolutionary Synthesis is necessary. This theme is one of the main in current discussion.
Category: Quantitative Biology

Programa Para Análisis de Secuencias Biológicas

Authors: Roberto Reinosa
Comments: 2 Pages. Spanish

Programa para el análisis de secuencias de ADN, ARN y proteínas.
Category: Quantitative Biology

Information as the Evolution Driving Force

Authors: Igor Krichtafovitch
Comments: 17 Pages.

The article presents third alternative for the biological evolution, first two being Darwinism and Intelligent Design (ID). The main hypothesis postulates that Biosphere is a single living organism with all parts and cells interconnected. As such it acts as a gigantic bio-computer capable to generate new life forms. The evolution is driven by recursive growth of total biological memory volume and accelerated complexity of living organisms. Intelligent Design is a natural phenomenon inherent into living matter from pre-biotic RNA to modern complex organisms.
Category: Quantitative Biology

On Richard III, the Livingstons of Callendar, and the Conflict Between Genealogy and Genetics 1.0.0

Authors: John Smith
Comments: 31 Pages.

A skeleton excavated at the presumed site of the Grey Friars friary in Leicester in 2012 is almost certainly that of the English king, Richard III (1452 -1485), and mtDNA (which is passed from mother to child) extracted from the skeleton matches mtDNA taken from descendants of Richard's sister Anne of York. However Y-DNA (which is passed from father to son) extracted from the skeleton apparently doesn't match Y-DNA taken from descendants of Henry Somerset the 5th Duke Of Beaufort, who according to history descended from Richard's 2nd great grand father Edward III (1312 - 1377). The implication according to geneticists, and the media, is that there is a 'false paternity event' somewhere between Edward and the Somersets. Also, the false paternity events don't end there, for only 4 of these 5 Somerset descendants match each other. And it may be worse even than this: the patrilineal line of a Frenchman named Patrice de Warren apparently traces back to Richard III through the illegitimate son of Edward III's 4th great grandfather, Geoffrey Plantagenet, Count of Anjou (1113 - 1151). But de Warren's Y-DNA doesn't match that of either Richard III or any of the Somersets. In this note, a formula for calculating the time of the most recent common ancestor is introduced, and some of its consequences outlined. This formula arises from a mathematical framework within which it is possible that the traditional genealogy is correct, and that Geoffrey Plantaganet was the father of a male line incorporating Richard III, all 5 Somersets, and Patrice de Warren.
Category: Quantitative Biology

Golden and Harmonic Mean in the Genetic Code

Authors: Miloje M. Rakocevic
Comments: 6 Pages. From Proceedings of the 2nd International Conference “Theoretical Approaches to BioInformation Systems” (TABIS.2013), September 17 – 22, 2013, Belgrade, Serbia.

In previous two works [1], [2] we have shown the determination of genetic code by golden and harmonic mean within standard Genetic Code Table (GCT), i.e. nucleotide triplet table, whereas in this paper we show the same determination through a specific connection between two tables – of nucleotide doublets Table (DT) and triplets Table (TT), over polarity of amino acids, measured by Cloister energy. (Miloje M. Rakočević) (Belgrade, 6.01.2017) (www.rakocevcode.rs) (mirkovmiloje@gmail.com)
Category: Quantitative Biology

Harmony of Genetic Code (Volume 1)

Authors: Miloje M. Rakocevic
Comments: 255 Pages.

This book contains my works published in the period 2005-2013 on my website (also in arXiv). The concept of "harmony" in the title refers to the determination of the genetic code by golden mean, generalized golden mean and harmonic mean. Some parts of the contents, in the meantime are published in some of the official journals, but most are not, and this was the reason for my decision to publish all papers here in their entirety. Miloje M. Rakočević) (Belgrade, 31.12.2016) (www.rakocevcode.rs) (mirkovmiloje@gmail.com)
Category: Quantitative Biology

Enigmas of the Genetic Code, Enigma 3: a Third Hidden Arithmetical Algorithm

Authors: Miloje M. Rakocevic
Comments: 6 Pages.

This third enigma is standing in relation to enigmas 1 & 2, given in our previous two communications. It is relating to total number of atoms (239) in side chains of 23 protein amino acids, within standard genetic code. By this three amino acids (L, S, R) are included twice each.
Category: Quantitative Biology

Enigmas of the Genetic Code, Enigma 2: a Second Hidden Arithmetical Algorithm

Authors: Miloje M. Rakocevic
Comments: 7 Pages.

This second Enigma is standing in relation to Enigma 1 in our previous communication. It is relating to total number of atoms (204) in side chains of 20 protein amino acids, within standard genetic code.
Category: Quantitative Biology

Enigmas of the Genetic Code, Enigma 1: a Hidden Arithmetical Algorithm

Authors: Miloje M. Rakocevic
Comments: 3 Pages.

In a certain way, this enigma is standing in relation to so-called Gaussian arithmetical algorithm, valid for the genetic code (Rakocevic, 2006). However, the difference is, among other things, that there (in the article on the Gaussian algorithm), I said and showed all openly - what is the enigma [classes of AAs (2 x 2), or (4 x 5), or (2 x 4) with 11, 21, 31, 41, – , 61, 71, 81, 91 of atoms within their side chains, respectively]; and here the hidden algorithm is hidden twice: once by the very Nature, the other way from myself. I make here, namely, only a hint of the solution. Certainly, in coming a few weeks (or months), I will present the solution, if someone else, in meantime, offers (or doesn’t offer) the solution.
Category: Quantitative Biology

Notes About Genetic Code, Note 2: the Relations Between Four Diversity Types of Protein Amino Acids

Authors: Miloje M. Rakocevic
Comments: 5 Pages.

This Note follows from Note 1(viXra:1612.0127, submitted on 2016-12-08 07:01:10) and it shows further distinctions and splittings within four diversity types of protein amino acids (AAs). First type as in Note 1 (G, P) and second one, also as in Note 1 (A, L; V, I). Within third type there is a chemicaly directed splitting into 4 + 2 AAs [(F, Y, H, W) + (C, M)]. Forth type consists of two halves in form of 4 + 4 AAs; four AAs with nitrogen, and four without: [(N, Q; K, R) + ( S, T, D, E)]. All these distinctions are followed through specific arithmetical regularities.
Category: Quantitative Biology

Notes about Genetic Code, Note 1: Four Diversity Types of Protein Amino Acids

Authors: Miloje M. Rakocevic
Comments: 7 Pages.

In this Note is presented the existence of four diversity types of protein amino acids (AAs). Fist type with two AAs (G; P); second with four AAs (A, L; V, I); third with six AAs (F, Y, H, W; C, M); and fourth type with eight AAs (S, T, D, E; N, Q; K, R).
Category: Quantitative Biology

Atomic-Scale MRI

Authors: George Rajna
Comments: 22 Pages.

Researchers at the University of Melbourne have developed a way to radically miniaturise a Magnetic Resonance Imaging (MRI) machine using atomic-scale quantum computer technology. [12] With one in two Australian children reported to have tooth decay in their permanent teeth by age 12, researchers from the University of Sydney believe they have identified some nanoscale elements that govern the behaviour of our teeth. [11] When cryoEM images are obtained from protein nanocrystals the images themselves can appear to be devoid of any contrast. A group of scientists from the Netherlands have now demonstrated that lattice information can be revealed and enhanced by a specialized filter. [10] There is also connection between statistical physics and evolutionary biology, since the arrow of time is working in the biological evolution also. From the standpoint of physics, there is one essential difference between living things and inanimate clumps of carbon atoms: The former tend to be much better at capturing energy from their environment and dissipating that energy as heat. [8] This paper contains the review of quantum entanglement investigations in living systems, and in the quantum mechanically modeled photoactive prebiotic kernel systems. [7] The human body is a constant flux of thousands of chemical/biological interactions and processes connecting molecules, cells, organs, and fluids, throughout the brain, body, and nervous system. Up until recently it was thought that all these interactions operated in a linear sequence, passing on information much like a runner passing the baton to the next runner. However, the latest findings in quantum biology and biophysics have discovered that there is in fact a tremendous degree of coherence within all living systems. The accelerating electrons explain not only the Maxwell Equations and the Special Relativity, but the Heisenberg Uncertainty Relation, the Wave-Particle Duality and the electron's spin also, building the Bridge between the Classical and Quantum Theories. The Planck Distribution Law of the electromagnetic oscillators explains the electron/proton mass rate and the Weak and Strong Interactions by the diffraction patterns. The Weak Interaction changes the diffraction patterns by moving the electric charge from one side to the other side of the diffraction pattern, which violates the CP and Time reversal symmetry. The diffraction patterns and the locality of the self-maintaining electromagnetic potential explains also the Quantum Entanglement, giving it as a natural part of the Relativistic Quantum Theory and making possible to understand the Quantum Biology.
Category: Quantitative Biology

A Surgical Simulator for Training Surgeons in a Few Tasks Related to Minimally Invasive Surgery

Authors: Kirana Kumara P
Comments: 8 Pages. This is the complete specification for the application filed for Indian patent (the patent application filed on September 17, 2016; application number: 201641031739).

The present invention relates to a surgical simulator that may be used to train surgeons for minimally invasive surgery. The simulator makes use of the Boundary Element Method together with a simulation approach that was proposed in an academic paper authored by this inventor. Moreover, the simulator makes use of the boundary element codes developed by this inventor. The simulator consists of a computer screen, a keyboard, a mouse, a haptic device, and a multicore CPU. The simulator would include the geometry of representative human kidney and human liver. The simulator has provisions for moving and changing the orientation of the liver and the kidney, and detecting the collision between the liver or the kidney and the mouse pointer. The simulator also has provisions for interactively displaying the deformed shape of the liver or the kidney, depending on the position of the mouse pointer (mouse cursor (pointer) represents the tip of surgical tools). The simulator can be used to train surgeons in the following tasks: eye-hand coordination, manipulating 3D objects while deformation of the objects is observed on 2D screens.
Category: Quantitative Biology

Phenotypic and Biotypic Characterization of Klebsiella Oxytoca: an Impact of Biofield Treatment

Authors: Mahendra Kumar Trivedi
Comments: 4 Pages.

Klebsiella oxytoca (K. oxytoca) is a Gram-negative microbe generally associated with community and hospitalacquired infections. Due to its clinical significance, we evaluated the effect of biofield treatment on phenotype and biotype characteristics of K. oxytoca (ATCC 43165). The study was performed into three groups i.e. C (control), T1 (treatment, revived); and T2 (treatment, lyophilized). Subsequently, groups T1 and T2 were received biofield treatment and control group was remained as untreated. The antimicrobial sensitivity results showed 3.33% and 6.67% alteration in antimicrobials susceptibility in group T1 cells on day 5 and 10, respectively, and 3.33% alteration in antimicrobials susceptibility was observed in group T2 cells on day 10 as compared to control. The sensitivity patterns of cefazolin were changed from resistant (R) to intermediate (I) on day 5, and resistance (R) to susceptible (S) on day 10, in T1 cells of K. oxytoca. The MIC value of cefazolin was decreased by 2-fold in group T1 on day 10 as compared to control. The biofield treated K. oxytoca exhibited the changes in biochemical reactions about 3.03% and 15.15% of total tested biochemicals in group T1 cells on day 5 and 10, respectively as compared to control. The biotype number of K. oxytoca was altered in biofield treated group and organism identified as Raoultella ornithinolytica in T1 on day 10 as compared to control, which is the prominent finding of this study. These changes were found in treated bacteria that might be due to some alteration happened in metabolic/enzymatic pathway and/ or at genetic level of K. oxytoca. Based on these data, it is speculated that biofiled treatment could be an alternative approach that can improve the effectiveness of the existing antimicrobials against the resistant pathogens.
Category: Quantitative Biology

Antibiogram Typing and Biochemical Characterization of Klebsiella Pneumoniae After Biofield Treatment

Authors: Mahendra Kumar Trivedi
Comments: 6 Pages.

Klebsiella pneumoniae (K. pneumoniae) is a common nosocomial pathogen causing respiratory tract (pneumoniae) and blood stream infections. Multidrug-resistant (MDR) isolates of K. pneumoniae infections are difficult to treat in patients in health care settings. Aim of the present study was to determine the impact of Mr. Trivedi’s biofield treatment on four MDR clinical lab isolates (LS) of K. pneumoniae (LS 2, LS 6, LS 7, and LS 14). Samples were divided into two groups i.e. control and biofield treated. Control and treated groups were analyzed for antimicrobial susceptibility pattern, minimum inhibitory concentration (MIC), biochemical study and biotype number using MicroScan Walk-Away® system. The analysis was done on day 10 after biofield treatment as compared with control group. Antimicrobial sensitivity assay showed that there was 46.42% alteration in sensitivity of tested antimicrobials in treated group of MDR K. pneumonia isolates. MIC results showed an alteration in 30% of tested antimicrobials out of thirty after biofield treatment in clinical isolates of K. pneumoniae. An increase in antimicrobial sensitivity and decrease in MIC value was reported (in LS 6) in case of piperacillin/tazobactam and piperacillin. Biochemical study showed a 15.15% change in biochemical reactions as compared to control. A significant change in biotype numbers were reported in all four clinical isolates of MDR K. pneumoniae after biofield treatment as compared to control group. On the basis of changed biotype number after biofield treatment, new organism was identified as Enterobacter aerogenes in LS 2 and LS 14. These results suggest that biofield treatment has a significant effect on altering the antimicrobial sensitivity, MIC values, biochemical reactions and biotype number of multidrug-resistant isolates of K. pneumoniae.
Category: Quantitative Biology

Spectroscopic Characterization of Disodium Hydrogen Orthophosphate and Sodium Nitrate After Biofield Treatment

Authors: Mahendra Kumar Trivedi, Alice Branton, Dahryn Trivedi, Gopal Nayak
Comments: 5 Pages.

Disodium hydrogen orthophosphate is a water soluble white powder widely used as pH regulator and saline laxative. The sodium nitrate is a highly water soluble white solid, used in high blood pressure, dentinal hypersensitivity, and production of fertilizers. The present study was aimed to investigate the impact of biofield treatment on spectral properties of disodium hydrogen orthophosphate and sodium nitrate. The study was performed in two groups i.e., control and treatment of each compound. The treatment groups were subjected to Mr. Trivedi’s biofield treatment. The spectral properties of control and treated groups of both compounds were studied using Fourier transform infrared (FT-IR) and Ultraviolet-Visible (UV-Vis) spectroscopic techniques. FT-IR spectrum of biofield treated disodium hydrogen orthophosphate showed the shifting in wavenumber of vibrational peaks (with respect to control) corresponding to O-H stretching from 2975 to 3357 cm-1, PO-H symmetrical stretching from 2359 to 2350 cm-1, O=P-OH deformation from 1717-1796 cm-1 to 1701-1735 cm-1, P=O asymmetric stretching from 1356 to 1260 cm-1 and P=O symmetric stretching from 1159 to 1132 cm-1, etc. Likewise, the FT-IR spectrum of sodium nitrate exhibited the shifting of vibrational frequency of N=O stretching from 1788 to 1648 cm-1 and NO3 asymmetric and symmetric stretchings from 1369 to 1381 cm-1 and 1340 to 1267 cm-1. UV spectrum of treated disodium hydrogen orthophosphate revealed a negative absorbance; it may be due to decrease in UV absorbance as compared to control. UV spectrum of control sodium nitrate exhibited two absorbance maxima (λmax) at 239.4 nm and 341.4 nm, which were altered to one absorbance maxima (λmax) at 209.2 nm after biofield treatment. Overall, the FT-IR and UV spectroscopic data of both compounds suggest an impact of biofield treatment on spectral properties with respect to force constant, bond strength, dipole moments and transition energy between two orbitals (ground state and excited state) as compared to respective control.
Category: Quantitative Biology

An Evaluation of Biofield Treatment on Susceptibility Pattern of Multidrug Resistant Stenotrophomonas Maltophilia: an Emerging Global Opportunistic Pathogen

Authors: Mahendra Kumar Trivedi, Mayank Gangwar, Snehasis Jana
Comments: 5 Pages.

Stenotrophomonas maltophilia (S. maltophilia) is a Gram-negative bacillus, an opportunistic pathogen, particularly among nosocomial infections. Multi-drug resistant strains are associated with very high rate of morbidity and mortality in severely immunocompromised patients. Present study was designed to evaluate the effect of biofield treatment against multidrug resistant S. maltophilia. Clinical sample of S. maltophilia was collected and divided into two groups i.e. control and biofield treated which were analyzed after 10 days with respect to control. The following parameters viz. susceptibility pattern, minimum inhibitory concentration (MIC), biochemical studies and biotype number of both control and treated samples were measured by MicroScan Walk-Away® system. The results showed an overall change of 37.5% in susceptibility pattern and 39.4% in biochemical study while 33.3% changes in MIC values of tested antimicrobials after biofield treatment. Further, the treated group of S. maltophilia has also shown a significant change in biochemical reactions followed by its biotype number as compared to control group. Biochemical reactions of treated group showed negative reaction to acetamide and positive reactions to colistin, glucose, adonitol, melibiose, arabinose, nitrate, oxidation-fermentation, raffinose, rhaminose, sorbitol, sucrose, and Voges-Proskauer as compared with control. The biofield treatment showed an alteration in MIC values of amikacin, amoxicillin/K-clavulanate, chloramphenicol, gatifloxacin, levofloxacin, moxifloxacin, ceftazidime, cefotetan, ticarcillin/K-clavulanate, trimethoprim/sulfamethoxazole. Altogether, data suggest that biofield treatment has significant effect to alter the sensitivity pattern of antimicrobials and biotype number against multidrug resistant strain of S. maltophilia.
Category: Quantitative Biology

Biopsy-Implantable Chemical Sensor for Monitoring and Adjusting Cancer Treatments

Authors: Ahmed El Demerdash - Hassan Sameh
Comments: 20 Pages.

“In the battle against cancer, which kills nearly 8 million people worldwide each year, doctors have in their arsenal myriads of powerful weapons, including various forms of Chemotherapy and Radiation. What they lack, however, is good reconnaissance — a reliable way to obtain realtime data about how well a particular therapy is working for any given patient. That’s why, a tiny biochemical sensor that is implanted in the cancerous tissue will be made; the sensor then wirelessly sends chemical measurements to an external “reader” device, allowing doctors to better monitor a patient’s progress and switch therapies accordingly. This device boosts treatments’ efficacy while reducing patients’ exposure to serious side effects. “ Design requirements are critical for the success of any project. And so, accuracy and cost are considered the main design requirements of our project. A simple prototype has been crafted in order to test the mechanism of our idea. Dissolved Oxygen (DO) and pH levels are measured, and a simulation has been made in order to mimic the environment of the tumor. In conclusion, our smart device offers an opportunity to accurately monitor the state of the cancerous tissues with a quite low cost.
Category: Quantitative Biology

The Everest Hypothesis: Sexual Reproduction as a Conserver of Replicative Fidelity and an Adaptation to Unstable Environments

Authors: Patrick Douglas Shaw Stewart
Comments: 14 Pages. I wanted to change the title back to Everest Hypothesis because I think the previous title was confusing

AbstractThis review examines three critical questions in evolutionary biology: (1) why do virtually allmulticellular and many unicellular organisms reproduce sexually? (2) Why have some animalsevolved extravagant ornaments and complex mating rituals that appear detrimental? (3) How does natural selection maintain high-fidelity genetic replication? I present a simple "Everest hypothesis" to answer these questions. First, I note that the genes that specify the proteinsthat replicate DNA are subject to mutation, so replicative fidelity must vary between individuals. Moreover, many organisms choose their mates by responding to various complex biochemical mechanisms, physical displays, and behaviors, generated by many gene products acting together. I propose that natural selection consistently adds unnecessary complexity to the mechanisms that transfer genetic material between individuals, and since most mutations are either harmful or neutral, mutator mutations are likely to disrupt these mechanisms. Sex may, therefore, provide a filter to reduce the dissemination of mutator mutations. Sex may also have allowed ancient organisms to colonize unstable environments where strong selective pressures would apply. This can explain many puzzling biological phenomena. For example, the migration and spawning of Atlantic salmon and the complex displays of birds of paradise may be bestunderstood as "tests" to show that potential mates possess genes for high-fidelity geneticreplication. Animals that have developed ornaments that appear harmful, such as peacocks,and animals that undertake remarkable migrations, such as monarch butterflies, may provide conspicuous examples of such tests. I also make suggestions for experiments to test the hypothesis.
Category: Quantitative Biology

Accelerating Information Transmission in the Evolution of Intelligent Life

Authors: Nicholas Hoggard
Comments: 42 Pages.

If making tools by hand was important in human evolution, was the use of tools to make tools just as important, or less so? As it happens, these two innovations each needed their own new method of teaching in order to pass them on to new generations. We could say that — from the teaching point of view — they are equal. We know of seven teaching methods from cultural evolution, all still in use, and each one associated with an evolutionary milestone (namely: cumulative culture, tool use, toolmaking, tool-made tools, composite tools, new inventions and new livelihoods).But there is something more that connects these teaching events. Together they form a simple geometric time sequence in which the time interval between successive events is shorter than the previous interval by the same factor, 4.6692... (the "Feigenbaum Constant δ"). The phenomenon of events accelerating by the Feigenbaum Constant δ is known in Chaos Theory as a "Feigenbaum Cascade" and is found in various non-linear dynamic systems, such as dripping taps, population dynamics, and various kinds of oscillator.Cherry-picking of data to fit the time-pattern is avoided because the teaching levels were identified without reference to date other than in which order they appeared.Teaching is cultural transmission of information. Extrapolating the Feigenbaum Cascade backwards in time indicates two events of genetic transmission of information (namely, self- replicating cells, and sexual reproduction). Extrapolating forwards in time indicates events involving writing-based transmission of information (in the form of written language, printing machines, and the computer).The sequence suggests that there will be future events, due to reach a conclusion around the year 2200.The hypothesis presented here is:u2022 that these information transmission events form a Feigenbaum Cascade. u2022 that each event is associated with a new means of adaptation.It follows that the timing of the levels of evolution is predictable. I suggest a mechanism for the Feigenbaum Cascade and a tentative description of the evolution levels.
Category: Quantitative Biology

Frequentist and Bayesian Analysis Methods for Case Series Data and Application to Early Outpatient Covid-19 Treatment Case Series of High Risk Patients

Authors: Eleftherios Gkioulekas
Comments: 27 Pages. resubmitted to Reviews in Cardiovascular Medicine

When confronted with a public health emergency, significant innovative treatment protocols can sometimes be discovered by medical doctors at the front lines based on repurposed medications. We propose a very simple hybrid statistical framework for analyzing the case series of patients treated with such new protocols, that enables a comparison with our prior knowledge of expected outcomes, in the absence of treatment. The goal of the proposed methodology is not to provide a precise measurement of treatment efficacy, but to establish the existence of treatment efficacy, in order to facilitate the binary decision of whether the treatment protocol should be adopted on an emergency basis. The methodology consists of a frequentist component that compares a treatment group against the probability of an adverse outcome in the absence of treatment, and calculates an efficacy threshold that has to be exceeded by this probability, in order to control the corresponding $p$-value, and reject the null hypothesis. The efficacy threshold is further adjusted with a Bayesian technique, in order to also control the false positive rate. A selection bias threshold is then calculated from the efficacy threshold to control for random selection bias. Exceeding the efficacy threshold establishes efficacy by the preponderance of evidence, and exceeding the more demanding selection bias threshold establishes efficacy by the clear and convincing evidentiary standard. The combined techniques are applied to case series of high-risk COVID-19 outpatients, that were treated using the early Zelenko protocol and the more enhanced McCullough protocol. The resulting efficacy thresholds are then compared against our prior knowledge of mortality and hospitalization rates of untreated high-risk COVID-19 patients, as reported in the research literature.
Category: Quantitative Biology

The Equations of Life

Authors: Robert L. Jackson
Comments: 8 Pages. contact rljacksonmd@gmail

This study will first define the "equation of life" via the principle of least action. Then the paper will show how this "equation of life" can be used to derive smaller equations, involving transcription and translation, for [computer] modeling and simulation of a cell. The conclusion will provide a terse description of its uses in the realm of Systems Biology.
Category: Quantitative Biology

The Equation of Life

Authors: Robert L. Jackson
Comments: 10 Pages. contact at rljacksonmd@gmail.com

This study will first define the “equation of life” via the principle of least action. Then the paper will show how this “equation of life” can be used to derive smaller equations, involving transcription and translation, for [computer] modeling and simulation of a cell. The conclusion will provide a terse description of its uses in the realm of Systems Biology.
Category: Quantitative Biology

The Equation of Life

Authors: Robert L. Jackson
Comments: 11 Pages. email rljacksonmd@gmail.com

This study will first define the “equation of life” via the principle of least action. Then the paper will show how this “equation of life” can be used to derive smaller equations, involving transcription and translation, for [computer] modeling and simulation of a cell. The conclusion will provide a terse description of its uses in the realm of Systems Biology.
Category: Quantitative Biology

The Equation of Life

Authors: Robert L. Jackson
Comments: 11 Pages. contact at rljacksonmd@gmail.com

This study will first define the “equation of life” via the principle of least action. Then the paper will show how this “equation of life” can be used to derive smaller equations, involving transcription and translation, for [computer] modeling and simulation of a cell. The conclusion will provide a terse description of its uses in the realm of Systems Biology.
Category: Quantitative Biology

Chaos Theory and Information Transmission in Evolution

Authors: Nicholas Hoggard
Comments: 37 Pages.

There have been twelve occasions in the history of life on Earth when new ways of transmitting information to future generations have arisen. There are 2 biological mechanisms: Asexual Reproduction, and Sexual Reproduction. These are followed by no less than 7 cultural methods, all of them forms of intentional teaching of skills and/or language. Finally there are (so far) 3 information technology methods: Written language, Movable-type Printing, and Computers. Remarkably, when dates are assigned to these events, they are consistent with the pattern of a period-doubling cascade described by Chaos Theory, the time between each event getting shorter by a factor which converges to 4.66920… a number known as the Universal Feigenbaum constant Delta. Cherry-picking of data is not applicable because the 2 biological events are well known, and the 7 levels of teaching have been arrived at by studying the development of tools by early humans and without regard for dates. The information technology events reinforce the pattern. Period-doubling cascades can be found in many phenomena in nature and apply to nonlinear iterative processes with limited resources. The period-doubling pattern in the evolution of intelligent life on Earth can be explained if the bifurcations are interpreted as population size, and if the bifurcation parameter is Darwinian fitness, and if fitness increases with complexity which in turn increases with time. Nonlinearities in these relationships do not necessarily affect the result. Also, studies showing that rates of genetic change and speciation are largely unaffected by climate support the idea that a regular pattern is possible. Darwinian evolution fits the definition of a nonlinear iterated process, which explains why evolution can behave as a period-doubling system, generating self-similar structures – in this case, new information channels – in a predetermined time sequence. The bifurcations (population instabilities) can be explained by each new information channel increasing the organism’s speed of adaptation, which gives a fitness advantage, but also causes overconsumption of ecosystem resources, destabilizing the population level. There have been 12 new information channels so far, but the pattern implies that more will appear, until the intervals approach zero in the relatively near future. The process governing the evolution of Life on Earth may be the same process that governed the physical evolution of the universe.
Category: Quantitative Biology

Analysis of Apobec and Adar Deaminase-Driven Riboswitch Haplotypes in Covid-19 Rna Strain Variants and the Implications for Vaccine Design

Authors: Edward J Steele, Robyn A Lindley
Comments: 35 Pages. Accepted for publication

This paper reports the results of our initial analysis of APOBEC and ADAR deaminase-mediated mutation signa-ture patterns in complete COVID-19 genomes from informative locations and times in China, USA and Spain in the 2019-2020 pandemic. We have identified a unique set of 'new' putative coordinated Riboswitches in COVID-19 genomes not previously identified, and likely generating variants of the known common strain Haplotypes now in circulation. The results reveal that COVID-19 diversifies using switching of RNA Haplotypes with mini-mal alteration to protein structure (the normal targets for B and T cells in conventional vaccine development). The deaminase-driven RNA Haplotypes are most likely aligned with RNA secondary structures. Several stud-ies already highlight how Riboswitches alter the ability of RNA to fold into intricate three-dimensional structures allowing them to execute their diverse cellular functions. The same functional outcomes are expected for viruses, particularly efficacy of RNA replication in new host cell environments. Thus, vaccine designs that assume that the main viral protein antigens will be the only putative protective targets could fail to produce effective and protective immunity. We conclude that understanding COVID-19 adaptation and survival strategy and identifying the host Haplotype, and which vaccine(s) is effective for each Haplotype group will be important for new vaccine design.
Category: Quantitative Biology

Analysis of Apobec and Adar Deaminase-Driven Riboswitch Haplotypes in Covid-19 Rna Strain Variants and the Implications for Vaccine Design

Authors: Edward J Steele, Robyn A Lindley
Comments: 35 Pages.

This paper reports the results of our initial analysis of APOBEC and ADAR deaminase-mediated mutation signa-ture patterns in complete COVID-19 genomes from informative locations and times in China, USA and Spain in the 2019-2020 pandemic. We have identified a unique set of 'new' putative coordinated Riboswitches in COVID-19 genomes not previously identified, and likely generating variants of the known common strain Haplotypes now in circulation. The results reveal that COVID-19 diversifies using switching of RNA Haplotypes with mini-mal alteration to protein structure (the normal targets for B and T cells in conventional vaccine development). The deaminase-driven RNA Haplotypes are most likely aligned with RNA secondary structures. Several stud-ies already highlight how Riboswitches alter the ability of RNA to fold into intricate three-dimensional structures allowing them to execute their diverse cellular functions. The same functional outcomes are expected for viruses, particularly efficacy of RNA replication in new host cell environments. Thus, vaccine designs that assume that the main viral protein antigens will be the only putative protective targets could fail to produce effective and protective immunity. We conclude that understanding COVID-19 adaptation and survival strategy and identifying the host Haplotype, and which vaccine(s) is effective for each Haplotype group will be important for new vaccine design.
Category: Quantitative Biology

Analysis of Apobec and Adar Deaminase-Driven Riboswitch Haplotypes in Covid-19 Rna Strain Variants and the Implications for Vaccine Design

Authors: Edward J Steele, Robyn A Lindley
Comments: 35 Pages.

This paper reports the results of our initial analysis of APOBEC and ADAR deaminase-mediated mutation signa-ture patterns in complete COVID-19 genomes from informative locations and times in China, USA and Spain in the 2019-2020 pandemic. We have identified a unique set of 'new' putative coordinated Riboswitches in COVID-19 genomes not previously identified, and likely generating variants of the known common strain Haplotypes now in circulation. The results reveal that COVID-19 diversifies using switching of RNA Haplotypes with mini-mal alteration to protein structure (the normal targets for B and T cells in conventional vaccine development). The deaminase-driven RNA Haplotypes are most likely aligned with RNA secondary structures as several stud-ies already highlight how Riboswitches alter the ability of RNA to fold into intricate three-dimensional structures allowing them to execute their diverse cellular functions. The same functional outcomes are expected for viruses, particularly efficacy of RNA replication in new host cell environments. Thus, vaccine designs that assume that the main viral protein antigens will be the only putative protective targets could fail to produce effective and protective immunity. We conclude that understanding COVID-19 adaptation and survival strategy and identifying the host Haplotype, and which vaccine(s) is effective for each Haplotype group will be important for new vaccine design. Our study also has wider implications for the actual origins and spread of COVID-19 but these will be pursued in future publications.
Category: Quantitative Biology

A New Forecast of Total Deaths by COVID-19 in the World, US and Countries of South America (May-04-2020)

Authors: Valdir Monteiro dos Santos Godoi
Comments: 5 Pages.

Based on datas of Johns Hopkins University we calculated an estimative of deaths by COVID-19 in the world, US and countries of South America.
Category: Quantitative Biology

A New Forecast of Total Deaths by COVID-19 in the World, US and Countries of South America (May-04-2020)

Authors: Valdir Monteiro dos Santos Godoi
Comments: 5 Pages.

Based on datas of Johns Hopkins University we calculated an estimative of deaths by COVID-19 in the world, US and countries of South America.
Category: Quantitative Biology

Forecast of Complete Contamination by COVID-19 in the World, US and South America (April-28-2020)

Authors: Valdir Monteiro dos Santos Godoi
Comments: 2 Pages.

We asked the question of when an entire population will have been infected by the coronavirus, in this COVID-19 pandemic, assuming that no vaccination or other form of preventive (or curative) medication exists until that day, and the population remains constant (births and deaths are not accounted for). We also assume that no change in social behavior occurs until that date.
Category: Quantitative Biology

Forecast of Complete Contamination by COVID-19 in the World, US and South America (April-28-2020)

Authors: Valdir Monteiro dos Santos Godoi
Comments: 2 Pages.

We asked the question of when an entire population will have been infected by the coronavirus, in this COVID-19 pandemic, assuming that no vaccination or other form of preventive (or curative) medication exists until that day, and the population remains constant (births and deaths are not accounted for). We also assume that no change in social behavior changes until that date.
Category: Quantitative Biology

Lethality, Velocity and Acceleration of COVID-19 Contamination in the World and 20 Selected Countries (April-24-2020)

Authors: Valdir Monteiro dos Santos Godoi
Comments: 3 Pages.

The objective of this paper is to introduce a study relative a mathematical modeling of coronavirus contamination, knowing some current numbers first, by COVID-19 pandemic.
Category: Quantitative Biology

Lethality of COVID-19 in the World and 20 Selected Countries (April-25-2020)

Authors: Valdir Monteiro dos Santos Godoi
Comments: 2 Pages.

The objective of this paper is to initiate a study relative a mathematical modeling of coronavirus contamination, knowing firstly some current numbers, given by COVID-19 pandemic.
Category: Quantitative Biology

Early Evaluation and Effectiveness of Social Distancing Measures for Controlling COVID-19 Outbreaks

Authors: Vincenzo Nardozza
Comments: 8 Pages.

Based on real data, we study the effectiveness and we propose an early evaluation method for COVID-19 social distancing measures. Version v2 posted on 26/03/20. Version v3 posted on 26/04/20. In version v3 sections 7 and 8 have been added leaving unchanged previous sections.
Category: Quantitative Biology

Genetic Groups and the Feasibility of Reference Sire Schemes

Authors: Stephen P. Smith, Robert D. Scarth, Bruce Tier
Comments: 8 Pages.

A method of measuring linkage in sire reference schemes is described. The method consists of determining estimability and prediction error variance for linear contrasts when the assumed animal model includes genetic groups. Base animals in a herd are assigned a common genetic group and different herds correspond to different genetic groups. The set of linear contrasts used to determine linkage is the set of group differences. Groups differences can be scrutinized using a simplified lease-squares analysis.
Category: Quantitative Biology

The Existence of God: An Application of the Poisson Distribution

Authors: Charles M. Byrne
Comments: 14 pages, Keywords: God, evolution, mutation, recombination, genetics, molecular biology, naturalism, Poisson distribution

In his theory of evolution by natural selection, Charles Darwin provided a plausible alternative to Christianity's creation account of human origins. In response, the Christian botanist Asa Gray suggested to Darwin that the variation that drives evolution might be generated by God. Darwin rejected Gray’s hypothesis, invoking philosophical naturalism, a hallmark scientific paradigm. Darwin's conclusion was reached on ideological grounds rather than empirical ones. Biological evidence that emerged subsequent to Darwin’s time yields a different conclusion. A means to assess the question of the source of genetic variation is provided by fitting the Poisson distribution to counts of point mutation and chromosome crossover events at the DNA sites where they occur. A general failure of fit between observational data and the Poisson distribution constitutes an exception to the naturalistic paradigm, and thereby provides epistemic access to the existence of God.
Category: Quantitative Biology

Crispr Technology Challenge Facing the Numerical Integrity of Whole Human Genome DNA

Authors: Jean Claude Perez
Comments: 10 Pages. updated release

Background : Global analysis of 3 human genomes of increasing levels of evolution (Neanderthal / Sapiens Build34 / Sapiens hg38) reveals 2 levels of numerical constraints controlling, structuring and optimizing these genome's DNA sequences. A global constraint - called "HGO" for "Human Genome Optimum" - optimizes the genome at its global scale. The same operator applied to each of the 24 individual chromosomes reveals a hierarchical structure of these 24 chromosomes. Results : Then analysing the single strand DNA CG / TA proportions at whole chromosomes and genome scale reveals strong fine-tuned numerical ratios evidencing the "closure" nature (Varela's autopoiesis theory) of whole human genome.
Category: Quantitative Biology

Combining Genetic Similarities Among Known Relatives that Connect to a Pair of Unknown Relatives

Authors: Stephen P. Smith, Cambrian Lopez, Nicole Lam
Comments: 12 Pages.

Smith, Lopez and Lam described how to combine genetic similarities, measured in centimorgans (cM), among declared relatives in an outside pedigree, and to concentrate those cM values into a single cM measurement for an envoy that is a representative of the outside pedigree. An unknown relative is presumed to be a descendant of the envoy, but has the cM values with relatives in the outside pedigree. That prior effort was a univariate analysis, where there is only one unknown relative with matches with others in the outside pedigree. The present paper presents a bivariate analysis, where there are two sisters that have matches with others in the outside pedigree. The cM values are now paired, where any DNA tested member of the pedigree has two cM values that match to both sisters. The bivariate analysis offers more efficient use of information, compared to two univariate analyses done for each sister in turn. This advantage comes with an increase in model complexity, in that a model is developed for treating three mutually exclusive categories representing genes found in the sisters: for genes in the first sister but not in the second sister; genes common to both sisters; or genes in the second sister but not in the first. The model is applied to the inheritance of the cM values in the pedigree. Even though the number of random effects is increased by a factor of three, the number of fixed effects that actually spend two degrees of freedom is unchanged from the univariate analysis. This is on top of the doubling of the number of observations for the bivariate analysis compared to one univariate analysis.
Category: Quantitative Biology

Current Return to Lamarck in Agreement with Darwin

Authors: Andrzej Gecow
Comments: 12 Pages. in Polish

The terms ‘Darwinism’ and ‘Lamarckism’ mean different things to different people. Nowadays, they are rarely used in a historically correct way – clime Jablonka and Lamb, the scientists that mainly contribute to proving than not only genes can curry hereditary information and new hereditary channels show characteristic of Lamarckian mechanisms. Especially Lamarckism was seen in false and superficial way in lot of aspects. The inheritance of acquired characters was connected to Lamarck. It was rejected too radically. Today it revives but mainly not basing on epigenetic inheritance. Generally Lamarckian mechanisms increase in the complex and diverse ways the chances of accurate adaptive changes, so they no longer look like a random, appear as ‘effects of instructions’ or ‘directed variations’ but these ‘instructions’ have been previously acquired through Darwinian natural selection. The richness of these phenomena causes great difficulty of their brief describtion. Lamarckian dimension of evolution is now known better. This phenomena cannot be explained in the range of Modern Synthesis assumptions. It does not mean, that MS is false and should be rejected. Lamarckian mechanisms are created by Darwinian natural selection, but their explanations need wider assumptions, than are a basis of MS, means Extended Evolutionary Synthesis is necessary. This theme is one of the main in current discussion.
Category: Quantitative Biology

On Richard III, The Livingstons of Callendar, and the Conflict Between Genealogy and Genetics

Authors: John Smith
Comments: 31 Pages.

A skeleton excavated at the presumed site of the Grey Friars friary in Leicester in 2012 is almost certainly that of the English king, Richard III (1452 -1485), and mtDNA (which is passed from mother to child) extracted from the skeleton matches mtDNA taken from descendants of Richard's sister Anne of York. However Y-DNA (which is passed from father to son) extracted from the skeleton apparently doesn't match Y-DNA taken from descendants of Henry Somerset the 5th Duke of Beaufort, who according to history descended from Richard's 2nd great grand father Edward III (1312 - 1377). The implication according to geneticists, and the media, is that there is a 'false paternity event' somewhere between Edward and the Somersets. Also, the false paternity events don't end there, for only 4 of these 5 Somerset descendants match each other. And it may be worse even than this: the patrilineal line of a Frenchman named Patrice de Warren apparently traces back to Richard III through the illegitimate son of Edward III's 4th great grandfather, Geoffrey Plantagenet, Count of Anjou (1113 - 1151), but de Warren's Y-DNA doesn't match that of either Richard III or any of the Somersets. In this note, a formula for calculating the time of the most recent common ancestor is introduced, and some of its consequences outlined. This formula arises from a mathematical framework within which it is possible that the traditional genealogy is correct, and that Geoffrey Plantaganet was the father of a male line incorporating Richard III, all 5 Somersets, and Patrice de Warren.
Category: Quantitative Biology

Golden and Harmonic Mean in the Genetic Code

Authors: Miloje M. Rakočević
Comments: 8 Pages. From Proceedings of the 2nd International Conference “Theoretical Approaches to BioInformation Systems” (TABIS.2013), September 17 – 22, 2013, pp. 205-2014, Belgrade, Serbia.

In previous two works [1], [2] we have shown the determination of genetic code by golden and harmonic mean within standard Genetic Code Table (GCT), i.e. nucleotide triplet table, whereas in this paper we show the same determination through a specific connection between two tables – of nucleotide doublets Table (DT) and triplets Table (TT), over polarity of amino acids, measured by Cloister energy. (Miloje M. Rakočević) (Belgrade, 6.01.2017) (www.rakocevcode.rs) (mirkovmiloje@gmail.com)
Category: Quantitative Biology