- Istituto Superiore di Sanità Viale Regina Elena 299
00161, Roma, Italia - +390649902579
Alessandro Giuliani
Istituto Superiore di Sanità, Dipartimento Ambiente e Salute, Department Member
- Istituto Superiore di Sanità, Ambiente E Connessa Prevenzione Primaria, Department Memberadd
- Alessandro Giuliani took his Laurea in Biological Sciences at Universita' di Roma "La Sapienza" score 110/110 cum l... moreAlessandro Giuliani took his Laurea in Biological Sciences at Universita' di Roma "La Sapienza" score 110/110 cum laude (Anno Accademico 81/82).He served as Junior Scientist at Sigma-Tau Biological Laboratories as data analyst for both clinical and biological experimentation (1985-1988), then became Responsible of Mathematical Modeling Unit at Istituto Ricerca sulla Senescenza Sigma-Tau, (1988-1997). He served as Senior Scientist at Environment and Health Dept. Istituto Superiore di Sanita’ , (1997- ) and now is Research Director in the same Institute.
He was Visiting Scientist at University of California Los Angeles (UCLA), Brain Research Institute, 1990, at Pomona College Los Angeles, Department of Organic Chemistry, 1991, , Rush University of Chicago, Dept. of Molecular Biophysics and Physiology, (2003), Bioinformatics Institute , Singapore (2003 and 2004), Keio University (Tsuruoka, Japan) 2005 and 2013, Kerala Bioinformatics Institute (2010), Caltech Pasadena (LA, USA) (2011) .Professor on contract basis of Biophysics at Universita' degli Studi di Roma "La Sapienza", Medical school prof. Alfredo Colosimo (Head of Dept.) . Academic Years: 1994/1995, 1995/1996, 1996/1997. Professor on Contract Basis: Philosophy of Science, Pontificia Università Urbaniana, Roma: 2014-2016,Faculty member: Doctorate in Biophysics University ‘La Sapienza’, Roma, Italy.Dr. Alessandro Giuliani is involved in the generation and testing of soft physical and statistical models for life sciences. He puts a a special emphasis on the elucidation of mesoscopic complex systems like protein sequence/structure prediction, complex network approaches, QSAR, Systems Biology and, together with prof. Webber and prof. Zbilut developed Recurrence Quantification Analysis (RQA) an innovative non-linear data analysis tool.edit
In this work, we face the time-honored problem of the contraposition/integration of analytical and intuitive knowledge, and the impact of such interconnection on the onset of awareness resulting from human decision-making processes.... more
In this work, we face the time-honored problem of the contraposition/integration of analytical and intuitive knowledge, and the impact of such interconnection on the onset of awareness resulting from human decision-making processes. Borrowing the definitions of concepts like intuition, tacit knowledge, uncertainty, metacognition, and emotions from the philosophical, psychological, decision theory, and economic points of view, we propose a skeletonized mathematical model grounded on Markov Decision Processes of these multifaceted concepts. Behavioral patterns that emerged from the solutions of the model enabled us to understand some relevant properties of the interaction between explicit (mainly analytical) and implicit (mainly holistic) knowledge. The impact of the roles played by the same factors for both styles of reasoning and different stages of the decision process has been evaluated. We have found that awareness emerges as a dynamic process allowing the decision-maker to switc...
Research Interests:
Research Interests:
The environment impacts human health in profound ways, yet few theories define the form of the relationship between human physiology and the environment. It is conjectured that such complex systems cannot interact directly, but rather... more
The environment impacts human health in profound ways, yet few theories define the form of the relationship between human physiology and the environment. It is conjectured that such complex systems cannot interact directly, but rather their interaction requires the formation of an intermediary “interface.” This position contrasts with current epidemiological constructs of causation, which implicitly assume that two complex systems transfer information directly while remaining separate entities. Further, it is contended that dynamic, process‐based interfaces incorporate components from all the interacting systems but exhibit operational independence. This property has many consequences, the foremost being that characteristics of the interface cannot be fully resolved by only studying the systems involved in the interaction. The interface itself must be the subject of inquiry. Without refocusing the attention on biodynamic interfaces, how the environment impacts health cannot be disce...
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
This book features 13 papers presented at the Fifth International Symposium on Recurrence Plots, held August 2013 in Chicago, IL. It examines recent applications and developments in recurrence plots and recurrence quantification analysis... more
This book features 13 papers presented at the Fifth International Symposium on Recurrence Plots, held August 2013 in Chicago, IL. It examines recent applications and developments in recurrence plots and recurrence quantification analysis (RQA) with special emphasis on biological and cognitive systems and the analysis of coupled systems using cross-recurrence methods. Readers will discover new applications and insights into a range of systems provided by recurrence plot analysis and new theoretical and mathematical developments in recurrence plots. Recurrence plot based analysis is a powerful tool that operates on real-world complex systems that are nonlinear, non-stationary, noisy, of any statistical distribution, free of any particular model type and not particularly long. Quantitative analyses promote the detection of system state changes, synchronized dynamical regimes or classification of system states. The book will be of interest to an interdisciplinary audience of recurrence plot users and researchers interested in time series analysis of complex systems in general.
Research Interests:
Commentary on: Transtrum M.K. et al., 2015, Perspective: Sloppiness and emergent theories in physics, biology and beyond, The Journal of Chemical Physics. Vol. 143: 01091.
Research Interests:
Candida gut colonization and yeast biofilm production capacity were investigated, by means of XTT reduction assay, in Clostridioides difficile infected (CDI) patients, in non-CDI diarrheic patients, and in healthy donors in two different... more
Candida gut colonization and yeast biofilm production capacity were investigated, by means of XTT reduction assay, in Clostridioides difficile infected (CDI) patients, in non-CDI diarrheic patients, and in healthy donors in two different time periods (2013–2015 and 2018–2019 respectively). Candida gut colonization was significantly (p < 0.001) associated to C. difficile infection, and to patients infected with hypervirulent C. difficile strains bearing the tcdC deletion at nucleotide 117 (p = 0.0003). Although there was not a prevalent yeast species in CDI patients, C. albicans was the species significantly (p < 0.001) associated to both the infections sustained by the non-hypervirulent C. difficile strains and those caused by the hypervirulent strain (p = 0.001). The biofilm production by the yeasts isolated from the CDI patients and from non-CDI diarrheic patients did not differ significantly. However, a significantly (p = 0.007) higher biofilm production was observed in the...
Research Interests:
Research Interests:
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Research Interests:
Research Interests:
Some relevant emerging properties of intelligent systems are “adaptation to a changing environment,” “reaction to unexpected situations,” “capacity of problem solving,” and “ability to communicate.” Single cells have remarkable abilities... more
Some relevant emerging properties of intelligent systems are “adaptation to a changing environment,” “reaction to unexpected situations,” “capacity of problem solving,” and “ability to communicate.” Single cells have remarkable abilities to adapt, make adequate context-dependent decision, take constructive actions, and communicate, thus theoretically meeting all the above-mentioned requirements. From a biological point of view, cancer can be viewed as an invasive species, composed of cells that move from primary to distant sites, being continuously exposed to changes in the environmental conditions. Blood represents the first hostile habitat that a cancer cell encounters once detached from the primary site, so that cancer cells must rapidly carry out multiple adaptation strategies to survive. The aim of this review was to deepen the adaptation mechanisms of cancer cells in the blood microenvironment, particularly referring to four adaptation strategies typical of animal species (phe...
Research Interests:
Herein, we provide a brief overview of complex systems theory approaches to investigate the genomic mechanism of cell-fate changes. Cell trajectories across the epigenetic landscape, whether in development, environmental responses, or... more
Herein, we provide a brief overview of complex systems theory approaches to investigate the genomic mechanism of cell-fate changes. Cell trajectories across the epigenetic landscape, whether in development, environmental responses, or disease progression, are controlled by extensively coordinated genome-wide gene expression changes. The elucidation of the mechanisms underlying these coherent expression changes is of fundamental importance in cell biology and for paving the road to new therapeutic approaches. In previous studies, we pointed at dynamic criticality as a plausible characteristic of genome-wide transition dynamics guiding cell fate. Whole-genome expression develops an engine-like organization (genome engine) in order to establish an autonomous dynamical system, capable of both homeostasis and transition behaviors. A critical set of genes behaves as a critical point (CP) that serves as the organizing center of cell-fate change. When the system is pushed away from homeosta...
Research Interests:
The Mediterranean Sea hosts a population of fin whale (Balaenoptera physalus), the only species of Mysticete regularly occurring in the basin. Observed and inferred mortality suggests that the population is likely declining. Accordingly,... more
The Mediterranean Sea hosts a population of fin whale (Balaenoptera physalus), the only species of Mysticete regularly occurring in the basin. Observed and inferred mortality suggests that the population is likely declining. Accordingly, understanding the causes of mortality and assessing the health status is pivotal to the survival of this endangered population. While such studies are inherently difficult for a highly roaming species with a pelagic distribution, mortality events provide the opportunity to investigate biological and epidemiological traits linked to these events, and evaluate the footprint of human activity, especially when long-term data series exist. We present a comprehensive spatial–temporal overview of fin whale mortality events along the Italian coast encompassing four centuries (1624–2021). Time series analysis was used to highlight structural changes in the evolution of mortality through time, while spatial–temporal patterns in the distribution of mortality e...
Research Interests:
Research Interests:
The multi-level organization of nature is self-evident: proteins do interact among them to give rise to an organized metabolism, while in the same time each protein (a single node of such interaction network) is itself a network of... more
The multi-level organization of nature is self-evident: proteins do interact among them to give rise to an organized metabolism, while in the same time each protein (a single node of such interaction network) is itself a network of interacting amino-acid residues allowing coordinated motion of the macromolecule and systemic effect as allosteric behavior. Similar pictures can be drawn for structure and function of cells, organs, tissues, and ecological systems. The majority of biologists are used to think that causally relevant events originate from the lower level (the molecular one) in the form of perturbations, that “climb up” the hierarchy reaching the ultimate layer of macroscopic behavior (e.g., causing a specific disease). Such causative model, stemming from the usual genotype-phenotype distinction, is not the only one. As a matter of fact, one can observe top-down, bottom-up, as well as middle-out perturbation/control trajectories. The recent complex network studies allow to ...
Research Interests:
Hepatitis B virus (HBV) infection is one of the major infectious hazards for health-care workers (HCWs) because of the frequency of percutaneous exposures to blood or body fluids. For this reason, all HCWs should be vaccinated, including... more
Hepatitis B virus (HBV) infection is one of the major infectious hazards for health-care workers (HCWs) because of the frequency of percutaneous exposures to blood or body fluids. For this reason, all HCWs should be vaccinated, including students in medicine and health professional degree programs. The aim of this study was to assess the immune coverage to anti-HBV vaccine and long-lasting protective titres of anti-HBs antibodies in female and male students to evaluate gender-related differences in response to HBV vaccination. Data relative to anti-HBs antibody titre, sex, age, and age at vaccination were collected and analyzed from 5291 Italian students (1812 males and 3479 females) of the graduate courses at the School of Medicine, who underwent the mandatory health surveillance of workers exposed to biological risk. The results indicated that gender affects the immune response to HBV vaccine, particularly evident in the case of females vaccinated after one year of age who exhibit...
Research Interests:
Research Interests:
The aim of this report is to unveil specific prognostic factors for retroperitoneal sarcoma (RPS) patients by univariate and multivariate statistical techniques. A phase I-II study on localized RPS treated with high-dose ifosfamide and... more
The aim of this report is to unveil specific prognostic factors for retroperitoneal sarcoma (RPS) patients by univariate and multivariate statistical techniques. A phase I-II study on localized RPS treated with high-dose ifosfamide and radiotherapy followed by surgery (ISG-STS 0303 protocol) demonstrated that chemo/radiotherapy was safe and increased the 3-year relapse-free survival (RFS) with respect to historical controls. Of 70 patients, twenty-six developed local, 10 distant, and 5 combined relapse. Median disease-free interval (DFI) was 29.47 months. According to a discriminant function analysis, DFI, histology, relapse pattern, and the first treatment approach at relapse had a statistically significant prognostic impact. Based on scientific literature and clinical expertise, clinicopathological data were analyzed using both a supervised and an unsupervised classification method to predict the prognosis, with similar sample sizes (66 and 65, resp., in casewise approach and 70 i...
Research Interests: Multivariate Statistics, Machine Learning, Data Mining, Biomarkers, Cancer Research, and 15 moreMedicine, Multivariate Analysis, Humans, Linear Discriminant Analysis, Female, Male, Cluster Analysis, Biomed, Aged, Middle Aged, Adult, Cohort Studies, Clinical Trials as Topic, Disease Free Survival, and Mahalanobis distance
This study explored the effects of the EMDR Integrative Group Treatment Protocol (EMDR-IGTP) on child survivors of the earthquakes that struck Umbria, a region of central Italy, on August 24th and on October 26th 2016. Three hundred and... more
This study explored the effects of the EMDR Integrative Group Treatment Protocol (EMDR-IGTP) on child survivors of the earthquakes that struck Umbria, a region of central Italy, on August 24th and on October 26th 2016. Three hundred and thirty-two children from the town of Norcia and nearby severely disrupted villages received 3 cycles of EMDR-IGTP. The Emotion Thermometers (ET-5) and the Children's Revised Impact of Event Scale (CRIES-13) were administered before (T0) and about 1 week after the conclusion of the third cycle (T3) of EMDR-IGTP. At T3, older children showed a reduction of distress and anger, whereas younger children reported an increase on these domains; moreover, older children reported a greater reduction of anxiety than younger ones. A greater reduction of distress, anxiety, and need for help was evidenced in females, whereas a greater improvement in depressive symptoms was evidenced in males. The effects of the EMDR-IGTP treatment on post-traumatic symptoms we...
Research Interests:
Selective serotonin reuptake inhibitors (SSRIs), the most commonly prescribed antidepressant drugs, have a variable and incomplete efficacy. In order to better understand SSRI action, we explored the hypothesis that SSRIs do not affect... more
Selective serotonin reuptake inhibitors (SSRIs), the most commonly prescribed antidepressant drugs, have a variable and incomplete efficacy. In order to better understand SSRI action, we explored the hypothesis that SSRIs do not affect mood per se but amplify the influence of the living conditions on mood. To this aim, we exploited the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) data set, selected a subpopulation of 591 patients with an overlapping clinical history and analyzed treatment outcome according to dosage −20 or 40 mg per day of citalopram. We found that sociodemographic characteristics affected treatment response in the same direction in the two dose groups, but these effects reached statistical significance only in the 40 mg per day dose group. In the latter, higher improvement rate was associated with having a working employment status (P=0.0219), longer education (P=0.0053), high income (P=0.01) or a private insurance (P=0.0031), and the higher remi...
Research Interests:
Apathy is a very common symptom in the institutionalized elderly and represents a condition of both clinical and public health importance. The Apathy Evaluation Scale (AES) has been shown to be a valid and reliable tool for... more
Apathy is a very common symptom in the institutionalized elderly and represents a condition of both clinical and public health importance. The Apathy Evaluation Scale (AES) has been shown to be a valid and reliable tool for characterizing, quantifying and differentiating apathy in various health conditions. The aims of this study were to establish the validity and reliability of the Italian version of the AES, and to assess the severity of apathy in a sample of Italian institutionalized geriatric patients. Data were collected from clinical interviews using the AES informant version (AES-I). Associations between measures of apathy and depression, cognitive functioning and perceived quality of life were evaluated, as well as the effects of the living environment on apathetic symptoms. Multiple forms of reliability and validity (i.e. test-retest, internal consistency, discriminability of apathy rating from a standard measure of depression) were satisfied. Our results also show that the...
Research Interests: Psychology, Clinical Psychology, Quality of life, Medicine, Italy, and 15 moreHumans, Nursing Homes, Female, Pubmed, Male, Apathy, Rating Scale, Aged, Geriatric Depression Scale, Institutionalization, Public health systems and services research, Reproducibility of Results, Geriatric Assessment, Psychiatric Status Rating Scales, and Neuropsychological Tests
Benign mammary lumps and mastalgia are the most common breast disorders; yet, there is no clear-cut consensus about the best strategy for their treatment. We hypothesized that a combination, including boswellic acid, betaine, and... more
Benign mammary lumps and mastalgia are the most common breast disorders; yet, there is no clear-cut consensus about the best strategy for their treatment. We hypothesized that a combination, including boswellic acid, betaine, and myoinositol, would be beneficial in breast disorders by exerting a pleiotropic effect on multiple pathways. Indeed, myoinositol has already been proven to modulate some factors involved in the genesis of breast diseases, such as fibrosis and metabolic and endocrine cues. In our study, 76 women were randomly assigned to either the experimental or the placebo arm. After six months of treatment, statistically significant differences between the two groups were recorded for pain relief (56% vs 17%) and breast density reduction (60% vs 9%). Furthermore, benign breast mass dimension showed a reduction in the experimental group (40% vs 16%). The combination of boswellic acid, betaine, and myoinositol has been demonstrated to be effective in the treatment of breast...
Research Interests:
Some relevant emerging properties of intelligent systems are "adaptation to a changing environment," "reaction to unexpected situations," "capacity of problem solving," and "ability to communicate." Single cells have remarkable abilities... more
Some relevant emerging properties of intelligent systems are "adaptation to a changing environment," "reaction to unexpected situations," "capacity of problem solving," and "ability to communicate." Single cells have remarkable abilities to adapt, make adequate context-dependent decision, take constructive actions, and communicate, thus theoretically meeting all the above-mentioned requirements. From a biological point of view, cancer can be viewed as an invasive species, composed of cells that move from primary to distant sites, being continuously exposed to changes in the environmental conditions. Blood represents the first hostile habitat that a cancer cell encounters once detached from the primary site, so that cancer cells must rapidly carry out multiple adaptation strategies to survive. The aim of this review was to deepen the adaptation mechanisms of cancer cells in the blood microenvironment, particularly referring to four adaptation strategies typical of animal species (phenotypic adaptation, metabolic adaptation, niche adaptation, and collective adaptation), which together define the broad concept of biological intelligence. We provided evidence that the required adaptations (either structural, metabolic, and related to metastatic niche formation) and "social" behavior are useful principles allowing putting into a coherent frame many features of circulating cancer cells. This interpretative frame is described by the comparison with analog behavioral traits typical of various animal models.
Research Interests:
Modeling systems at multiple interacting scales is probably the most relevant task for pursuing a physically motivated explanation of biological regulation. In a new study, Smart and Zilman develop a convincing, albeit preliminary, model... more
Modeling systems at multiple interacting scales is probably the most relevant task for pursuing a physically motivated explanation of biological regulation. In a new study, Smart and Zilman develop a convincing, albeit preliminary, model of the interplay between the cell microscale and the macroscopic tissue organization in biological systems.
Research Interests:
The structure of proteins impacts directly on the function they perform.Mutations in the primary sequence can provoke structural changes with consequent modification of functional properties. SARS-CoV-2 viral proteins have been... more
The structure of proteins impacts directly on the function they perform.Mutations in the primary sequence can provoke structural changes with consequent modification of functional properties. SARS-CoV-2 viral proteins have been extensively studied during the pandemic. Thus, a considerable body of data related to sequence and structure is available, enabling joint sequence-structure analysis. In this work, we focus on the SARS-CoV-2 S (Spike) protein and therelations between sequence mutations and structure variations, in order toshed light on the structural changes stemming from the position ofmutated amino acid residues in three different SARS-CoV-2 strains. We propose the use of Protein Contact Network (PCN) formalism able to: (i) get aglobal structural metric space and to compare various molecular entities and (ii) givea mechanistic explanation of the observed phenotype.PCNs have been used to compare sequence and structure of the α, δ and Omicron SARS-COV2 variants, and we found ...
Research Interests:
Biomedical sciences are traversing a ``reproducibility crisis'': it is estimated that more than 85% of basic research results in cancer research [25] are not replicable, and similar figures hold for other investigation fields. The... more
Biomedical sciences are traversing a ``reproducibility crisis'': it is estimated that more than 85% of basic research results in cancer research [25] are not replicable, and similar figures hold for other investigation fields. The urgent need of rethinking the quantitative approach to biology is evident, here I try to enucleate the roots of the problem and sketch some possible solutions with a particular emphasis on complex network approaches
Research Interests:
Research Interests:
Commentary on: Curtin, P, Austin, C, Curtin, A, Gennings, C, Figueroa-Romero, C, Mikhail, KA et al. 2020, Dysregulated biodynamics in metabolic attractor systems precede the emergence of amyotrophic lateral sclerosis, PLoS Comput Biol,... more
Commentary on: Curtin, P, Austin, C, Curtin, A, Gennings, C, Figueroa-Romero, C, Mikhail, KA et al. 2020, Dysregulated biodynamics in metabolic attractor systems precede the emergence of amyotrophic lateral sclerosis, PLoS Comput Biol, vol. 16, no. 4. e1007773. https://doi.org/10.1371/journal.pcbi.1007773. Citation: Giuliani, A, 2020, “The Claude Bernard and Conrad Waddington Legacy: Homeostasis, When Observed for a Very Long Time, is Homeoresis”, Organisms: Journal of Biological Sciences, vol. 4, no. 1 pp. 15-16. DOI: 10.13133/2532-5876/16958.
Research Interests: Philosophy and Citation
The data deluge (generally referred as "Big Data") biomedical scientists are facing in these years asks for a serious epistemological thinking in order to avoid both "data bases idolatry" and "preconceived... more
The data deluge (generally referred as "Big Data") biomedical scientists are facing in these years asks for a serious epistemological thinking in order to avoid both "data bases idolatry" and "preconceived refusal". Starting from the evident reproducibility crisis of biomedical sciences here we sketch some hopefully useful indications for a sensible use of data mining approaches.
Research Interests:
Inefficient response to oxidative stress has been associated with ageing and health risk. Metals are known to inhibit DNA repair and may modify the antioxidant response. How genetic variability and lifestyle factors modulate the response... more
Inefficient response to oxidative stress has been associated with ageing and health risk. Metals are known to inhibit DNA repair and may modify the antioxidant response. How genetic variability and lifestyle factors modulate the response to oxidative stress is poorly explored. Our study aims to disentangle the contribution of genetics and environmental exposures to oxidative stress response using data from twin pairs. The non-enzymatic antioxidant capacity (NEAC), the repair capacity of 8-oxo-7,8-dihydroguanine (OGG activity) and the levels of twelve metals were measured in blood of 64 monozygotic and 31 dizygotic twin pairs. The contributions of genetic and environmental effects were assessed using standard univariate twin modelling. NEAC and OGG activity significantly decreased with age. Gender-, age- and body mass index-associated differences were identified for some metals. Principal Component Analysis identified two groups of metals whose levels in blood were highly correlated:...
Research Interests: Biomarkers, Biology, Oxidative Stress, DNA damage, DNA repair, and 15 moreMedicine, Twins, Antioxidants, Heavy metals, Humans, Female, Antioxidant, Male, Metals, Oxidative stress and free radical biology and medicine, Adult, Environmental Pollutants, Environmental Exposure, Antioxidant Capacity, and Biochemistry and cell biology
Research Interests:
Research Interests:
For many years, there has been general interest in developing virtual cells or digital twin models [...]
Research Interests:
Cancer is widely considered a genetic disease. Notably, recent works have highlighted that every human gene may possibly be associated with cancer. Thus, the distinction between genes that drive oncogenesis and those that are associated... more
Cancer is widely considered a genetic disease. Notably, recent works have highlighted that every human gene may possibly be associated with cancer. Thus, the distinction between genes that drive oncogenesis and those that are associated to the disease, but do not play a role, requires attention. Here we investigated single cells and bulk (cell-population) datasets of several cancer transcriptomes and proteomes in relation to their healthy counterparts. When analyzed by machine learning and statistical approaches in bulk datasets, both general and cancer-specific oncogenes, as defined by the Cancer Genes Census, show invariant behavior to randomly selected gene sets of the same size for all cancers. However, when protein–protein interaction analyses were performed, the oncogenes-derived networks show higher connectivity than those relative to random genes. Moreover, at single-cell scale, we observe variant behavior in a subset of oncogenes for each considered cancer type. Moving forw...
Research Interests:
We consider a class of non-integrable 2D Ising models whose Hamiltonian, in addition to the standard nearest neighbor couplings, includes additional weak multi-spin interactions which are even under spin flip. We study the model in... more
We consider a class of non-integrable 2D Ising models whose Hamiltonian, in addition to the standard nearest neighbor couplings, includes additional weak multi-spin interactions which are even under spin flip. We study the model in cylindrical domains of arbitrary aspect ratio and compute the multipoint energy correlations at the critical temperature via a multiscale expansion, uniformly convergent in the domain size and in the lattice spacing. We prove that, in the scaling limit, the multipoint energy correlations converge to the same limiting correlations as those of the nearest neighbor Ising model in a finite cylinder with renormalized horizontal and vertical couplings, up to an overall multiplicative constant independent of the shape of the domain. The proof is based on a representation of the generating function of correlations in terms of a non-Gaussian Grassmann integral, and a constructive Renormalization Group (RG) analysis thereof. A key technical novelty compared with pr...
Research Interests:
In this paper, meant as a companion to Antinucci et al. (Energy correlations of non-integrable Ising models: the scaling limit in the cylinder, 2020. arXiv: 1701.05356), we consider a class of non-integrable 2D Ising models in cylindrical... more
In this paper, meant as a companion to Antinucci et al. (Energy correlations of non-integrable Ising models: the scaling limit in the cylinder, 2020. arXiv: 1701.05356), we consider a class of non-integrable 2D Ising models in cylindrical domains, and we discuss two key aspects of the multiscale construction of their scaling limit. In particular, we provide a detailed derivation of the Grassmann representation of the model, including a self-contained presentation of the exact solution of the nearest neighbor model in the cylinder. Moreover, we prove precise asymptotic estimates of the fermionic Green’s function in the cylinder, required for the multiscale analysis of the model. We also review the multiscale construction of the effective potentials in the infinite volume limit, in a form suitable for the generalization to finite cylinders. Compared to previous works, we introduce a few important simplifications in the localization procedure and in the iterative bounds on the kernels ...
Research Interests:
The potential of targeting the Renin-Angiotensin-Aldosterone System (RAAS) as a treatment for the coronavirus disease 2019 (COVID-19) is currently under investigation. One way to combat this disease involves the repurposing of angiotensin... more
The potential of targeting the Renin-Angiotensin-Aldosterone System (RAAS) as a treatment for the coronavirus disease 2019 (COVID-19) is currently under investigation. One way to combat this disease involves the repurposing of angiotensin receptor blockers (ARBs), which are antihypertensive drugs, because they bind to angiotensin-converting enzyme 2 (ACE2), which in turn interacts with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. However, there has been no in silico analysis of the potential toxicity risks associated with the use of these drugs for the treatment of COVID-19. To address this, a network-based bioinformatics methodology was used to investigate the potential side effects of known Food and Drug Administration (FDA)-approved antihypertensive drugs, Sartans. This involved identifying the human proteins targeted by these drugs, their first neighbors, and any drugs that bind to them using publicly available experimentally supported data, an...
Research Interests:
Herein, we provide a brief overview of complex systems theory approaches to investigate the genomic mechanism of cell-fate changes. Cell trajectories across the epigenetic landscape, whether in development, environmental responses, or... more
Herein, we provide a brief overview of complex systems theory approaches to investigate the genomic mechanism of cell-fate changes. Cell trajectories across the epigenetic landscape, whether in development, environmental responses, or disease progression, are controlled by extensively coordinated genome-wide gene expression changes. The elucidation of the mechanisms underlying these coherent expression changes is of fundamental importance in cell biology and for paving the road to new therapeutic approaches. In previous studies, we pointed at dynamic criticality as a plausible characteristic of genome-wide transition dynamics guiding cell fate. Whole-genome expression develops
an engine-like organization (genome engine) in order to establish an autonomous dynamical system, capable of both homeostasis and transition behaviors. A critical set of genes behaves as a critical
point (CP) that serves as the organizing center of cell-fate change. When the system is pushed away from homeostasis, the state change that occurs at the CP makes local perturbation spread over the
genome, demonstrating self-organized critical (SOC) control of genome expression. Oscillating-Mode genes (which normally keep genome expression on pace with microenvironment fluctuations), when
in the presence of an effective perturbative stimulus, drive the dynamics of synchronization, and thus guide the cell-fate transition.
an engine-like organization (genome engine) in order to establish an autonomous dynamical system, capable of both homeostasis and transition behaviors. A critical set of genes behaves as a critical
point (CP) that serves as the organizing center of cell-fate change. When the system is pushed away from homeostasis, the state change that occurs at the CP makes local perturbation spread over the
genome, demonstrating self-organized critical (SOC) control of genome expression. Oscillating-Mode genes (which normally keep genome expression on pace with microenvironment fluctuations), when
in the presence of an effective perturbative stimulus, drive the dynamics of synchronization, and thus guide the cell-fate transition.
Research Interests:
Cancer is widely considered a genetic disease. Notably, recent works have highlighted that every human gene may possibly be associated with cancer. Thus, the distinction between genes that drive oncogenesis and those that are associated... more
Cancer is widely considered a genetic disease. Notably, recent works have highlighted that every human gene may possibly be associated with cancer. Thus, the distinction between genes that drive oncogenesis and those that are associated to the disease, but do not play a role, requires attention. Here we investigated single cells and bulk (cell-population) datasets of several cancer transcriptomes and proteomes in relation to their healthy counterparts. When analyzed by machine learning and statistical approaches in bulk datasets, both general and cancer-specific oncogenes, as defined by the Cancer Genes Census, show invariant behavior to randomly selected gene sets of the same size for all cancers. However, when protein-protein interaction analyses were performed, the oncogenes-derived networks show higher connectivity than those relative to random genes. Moreover, at singlecell scale, we observe variant behavior in a subset of oncogenes for each considered cancer type. Moving forward, we concur that the role of oncogenes needs to be further scrutinized by adopting protein causality and higher-resolution single-cell analyses.
Research Interests:
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Research Interests:
The urban overheating phenomenon in Mediterranean cities is a societal challenge with vast implications for the protection of public health. An additional analysis of the pilot TEMP randomized 2 × 2 cross-over trial was set up, using... more
The urban overheating phenomenon in Mediterranean cities is a societal challenge with vast implications for the protection of public health. An additional analysis of the pilot TEMP randomized 2 × 2 cross-over trial was set up, using wearable sensor-based skin temperature measurements (n = 14). The study objectives were to: (i) assess the recurrence patterns of skin temperature measurements in individuals spending time in two climatologically contrasting settings (urban versus mountainous), and (ii) evaluate the association between the diurnal nonlinear recurrence quantification analysis (RQA) metrics and metabolic hormone levels. The intervention was a short-term stay (5–7 days) in a mountainous, climate-cooler setting (range 600–900 m altitude), which is about a 1 h drive from the main urban centres of Cyprus. The RQA analysis showed a blunting phenomenon on the nonlinear temporal dynamics of skin temperature time series observed in the urban setting. Compared with the mountainous...
Research Interests:
8-Oxoguanine, a common mutagenic DNA lesion, generates G:C>T:A transversions via mispairing with adenine during DNA replication. When operating normally, the MUTYH DNA glycosylase prevents 8-oxoguanine-related mutagenesis by excising... more
8-Oxoguanine, a common mutagenic DNA lesion, generates G:C>T:A transversions via mispairing with adenine during DNA replication. When operating normally, the MUTYH DNA glycosylase prevents 8-oxoguanine-related mutagenesis by excising the incorporated adenine. Biallelic MUTYH mutations impair this enzymatic function and are associated with colorectal cancer (CRC) in MUTYH-Associated Polyposis (MAP) syndrome. Here, we perform whole-exome sequencing that reveals a modest mutator phenotype in MAP CRCs compared to sporadic CRC stem cell lines or bulk tumours. The excess G:C>T:A transversion mutations in MAP CRCs exhibits a novel mutational signature, termed Signature 36, with a strong sequence dependence. The MUTYH mutational signature reflecting persistent 8-oxoG:A mismatches occurs frequently in the APC, KRAS, PIK3CA, FAT4, TP53, FAT1, AMER1, KDM6A, SMAD4 and SMAD2 genes that are associated with CRC. The occurrence of Signature 36 in other types of human cancer indicates that DNA...
Research Interests: Genetics, Biology, DNA damage, DNA repair, Medicine, and 15 moreColorectal cancer, Humans, Mutation, Genetic Association Studies, Exome Sequencing, Oncogenes, KRAS, Mutation Rate, Base Excision Repair, Mutational Signatures, Colorectal Neoplasms, DNA mutational analysis, alleles, Microsatellite instability, and Gene frequency
Un libro che raccoglie le opinioni di diversi autori di formazione filosofica. teologica e scientifica sul rapporto tra conoscenza scientifica e verità.
Research Interests:
Breve introduzione alla complessità che parte dal suo (solo apparente) contrario: la semplicità, correttamente intesa non come semplificazione arbitraria ma come ordine emergente.
Research Interests:
This book is dedicated to the consolidation and to the expansion of theoretic systems thinking as a necessary integration of the general reductionist and analytical attitude dominant in our culture. Reductionism and analytical approaches... more
This book is dedicated to the consolidation and to the expansion of theoretic systems thinking
as a necessary integration of the general reductionist and analytical attitude dominant in our
culture. Reductionism and analytical approaches have produced significant results in many
fields of contemporary knowledge giving a great contribution to relevant scientific discoveries
and to their technological application, but their validity has been improperly universalized as
the only and best methods of knowledge in every domain. It is nowadays clear that analytical
or mereological approaches are inadequate to solve many problems and that we should
introduce – or support the diffusion of - new concepts and different research attitudes. A good
candidate to support such a shift is the well known theoretical approach based on the concept
of “system” that no more considers the elementary constituents of an object, but the entity
emerging from the relations and interactions among its elementary parts. It becomes possible
to reconstruct several domains, both philosophical and scientific, from the systemic point of
view, introducing fresh ideas in the research in view of a general rational vision of the world on
more comprehensive basis.
as a necessary integration of the general reductionist and analytical attitude dominant in our
culture. Reductionism and analytical approaches have produced significant results in many
fields of contemporary knowledge giving a great contribution to relevant scientific discoveries
and to their technological application, but their validity has been improperly universalized as
the only and best methods of knowledge in every domain. It is nowadays clear that analytical
or mereological approaches are inadequate to solve many problems and that we should
introduce – or support the diffusion of - new concepts and different research attitudes. A good
candidate to support such a shift is the well known theoretical approach based on the concept
of “system” that no more considers the elementary constituents of an object, but the entity
emerging from the relations and interactions among its elementary parts. It becomes possible
to reconstruct several domains, both philosophical and scientific, from the systemic point of
view, introducing fresh ideas in the research in view of a general rational vision of the world on
more comprehensive basis.
Research Interests:
The dream of a manmade living creature dates back to the dawn of civilization [1]: the Jewish legend of Golem and the late‐romantic Mary Shelley’s character of Frankenstein’s Monster are just two of the most famous archetypes of synthetic... more
The dream of a manmade living creature dates back to the dawn of civilization [1]: the Jewish legend of Golem and the late‐romantic Mary Shelley’s character of Frankenstein’s Monster are just two of the most famous archetypes of synthetic (human) biology. The passage from myth and metaphor to science and technology has been continuous and, since the eighteenth century mechanic automata up until today, the basic view of synthetic biology research has basically been the same [2].
The emphasis shifted from the eighteenth‐century “organism as a clockwork” metaphor to the nineteenth‐century organism as a “thermal machine,” ending up with the organism as a “computer” of the twentieth and twenty‐first centuries (with a more marked emphasis on network systems in these days with respect to the logical flux of information of the second half of the previous century).
Notwithstanding that, both the fiction and technological ideas edounded
about the idea of the existence of a “basic mechanism of life” that, albeit
complex, could, be replicated in a laboratory (at least in principle).
Thus, it is not without interest to have a closer look at the concept of synthesis.
Not all the projects of artificial life are properly “synthetic.” We do not use
the word synthesis (characterized by the Greek prefix “syn” pointing to the emergence of new features by the organic fusion of different elements) for cars or computer programs. On the other hand, we currently speak of organic synthesis, referring to the production of new organic molecules not present in nature and “synthesizer” is the name given machines devoted to the fusion of different sounds in electronic musical composition.
The emphasis shifted from the eighteenth‐century “organism as a clockwork” metaphor to the nineteenth‐century organism as a “thermal machine,” ending up with the organism as a “computer” of the twentieth and twenty‐first centuries (with a more marked emphasis on network systems in these days with respect to the logical flux of information of the second half of the previous century).
Notwithstanding that, both the fiction and technological ideas edounded
about the idea of the existence of a “basic mechanism of life” that, albeit
complex, could, be replicated in a laboratory (at least in principle).
Thus, it is not without interest to have a closer look at the concept of synthesis.
Not all the projects of artificial life are properly “synthetic.” We do not use
the word synthesis (characterized by the Greek prefix “syn” pointing to the emergence of new features by the organic fusion of different elements) for cars or computer programs. On the other hand, we currently speak of organic synthesis, referring to the production of new organic molecules not present in nature and “synthesizer” is the name given machines devoted to the fusion of different sounds in electronic musical composition.
Research Interests:
Un libro sullo stato della scienza tra artigianato e idolatria
Research Interests:
Il problema dell'interpretazione delle notizie scientifiche che appaiono nei media da parte di chi scienziato non è è qui trattato in una serie di brevi capitoli che cercano di far comprendere il senso profondo dell'agire scientifico e... more
Il problema dell'interpretazione delle notizie scientifiche che appaiono nei media da parte di chi scienziato non è è qui trattato in una serie di brevi capitoli che cercano di far comprendere il senso profondo dell'agire scientifico e così fornire anticorpi per difendersi dalla superstizione scientista.
Research Interests:
Research Interests:
Presentation at Riga conference (COST Action CA15214 Workshop) on Nuclear Lamins, Nuclear Organization and Transcription. The presentation deals with basic concepts linking structures (with a particualr emphasis on networks) and... more
Presentation at Riga conference (COST Action CA15214 Workshop) on Nuclear Lamins, Nuclear Organization and Transcription. The presentation deals with basic concepts linking structures (with a particualr emphasis on networks) and dynamics. The emphasis is on biological structures and signal spreading in heterogeneous reticular media like cell nucleus, proteins, brain.