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Deepak Patil

    Deepak Patil

    Due to the failure of virus isolation of the Omicron variant in Vero CCL-81 from the clinical specimens of COVID-19 cases, an initial in vivo and subsequent in vitro approach was utilized for the isolation of the virus. A total of 74... more
    Due to the failure of virus isolation of the Omicron variant in Vero CCL-81 from the clinical specimens of COVID-19 cases, an initial in vivo and subsequent in vitro approach was utilized for the isolation of the virus. A total of 74 oropharyngeal/nasopharyngeal specimens were collected from SARS-CoV-2 positive international travellers and a contact case at Delhi and Mumbai, India. All the specimens were sequenced using next-generation sequencing and simultaneously inoculated onto Vero CCL-81 cells for virus isolation. Subsequently, two omicron positive specimens were inoculated into Syrian hamsters for two passages. The initial passage of the positive hamster specimens was inoculated onto Vero CCL-81 cells. The clinical specimens, hamster specimens, and Vero CCL-81 passages were sequenced to assess the mutational changes in different host species. The replication of the Omicron variant in hamsters was confirmed with the presence of a high viral load in nasal turbinate and lung spec...
    Granular media continue to be among the most manipulated materials found in various industries. Particle interactions in granular flow has fundamental importance in analyzing the performance of a wide range of key engineering applications... more
    Granular media continue to be among the most manipulated materials found in various industries. Particle interactions in granular flow has fundamental importance in analyzing the performance of a wide range of key engineering applications such as hoppers, tumblers, and mixers etc. In spite of such ubiquitous presence, till date, our understanding of the granular flow is very limited. This restricts our ability to design efficient and optimal granular processing equipment. Additionally, the existing design abilities are also constrained by the number of particles to be analyzed, where, a typical industrial application involves millions of particles. This motivated the current research where investigations on the above limitations are pursued from three different angles: experimental, theoretical, and simulation. More specifically, this work aims to study particle-wall interaction and developing a computationally efficient cellular automata simulation framework for industrial granular...
    Background: National Tuberculosis Control Programme (RNTCP) of India, based on the DOTS strategy, patients are treated with an intermittent short-course regimen with drugs administered thrice weekly on alternate days. Aims and Objectives:... more
    Background: National Tuberculosis Control Programme (RNTCP) of India, based on the DOTS strategy, patients are treated with an intermittent short-course regimen with drugs administered thrice weekly on alternate days. Aims and Objectives: To study treatment outcomes of sputum smear positive pulmonary tuberculosis re-treatment cases at tertiary health care center. Methodology: After approval from institutional ethical committee this cross-sectional study was carried out in the department of the pulmonary medicine (TB Chest) at tertiary health care center during the year January 2016 to January 2017 in all re-treatment TB case. So, during one year period total 97 patients included into study after written explained consent. All the necessary information like age, sex etc. was noted. The statistical analysis done of Z-test (Standard error of difference between two proportions) Result : In our study we have found that the majority of the patients were in the age group of 50-60 were 29.9...
    Triangulation in Pivot-Based Statistical Machine Translation(SMT) is a very effective method for building Machine Translation(MT) systems in case of scarcity of the parallel corpus. Phrase Table Triangulation helps in such a resource... more
    Triangulation in Pivot-Based Statistical Machine Translation(SMT) is a very effective method for building Machine Translation(MT) systems in case of scarcity of the parallel corpus. Phrase Table Triangulation helps in such a resource constrained setting by inducing new phrase pairs with the help of a pivot. However, it does not explore the possibility of extracting reordering information through the use of pivot. This paper presents a novel method for triangulation of reordering tables in Pivot Based SMT. We show that the use of a pivot can help in extracting better reordering information and can assist in improving the quality of the translation. With a detailed example, we show that triangulation of reordering tables also improves the lexical choices a system makes during translation. We observe a BLEU score improvement of 1.06 for Marathi to English MT system with Hindi as a pivot, and also significant improvements in 8 other translation systems by using this method.
    An investigation was conducted on farmer’s field with an objective to study the “Residual effect of post spent wash on properties of soil solum and yield of Pearl millet” in the jurisdiction of Padmashri Vitthalrao Vikhe Patil Sahakari... more
    An investigation was conducted on farmer’s field with an objective to study the “Residual effect of post spent wash on properties of soil solum and yield of Pearl millet” in the jurisdiction of Padmashri Vitthalrao Vikhe Patil Sahakari Sakhar Karkhana, Pravaranagar, Taluka area of Pravaranagar and Gogalgaon village were selected, where spent wash was applied @ 70 season. Soil profiles were dug in the treated farms at harvest of the crop to study the residual effect of post biomethanated spent wash application on soil profile characteristics. The untreated fields were selected, adjacent to treated fields, where no spent wash was applied and were treated as control check to assess the effect of spent wash treated profiles in comparison to untreated soil profiles. The effect as test crop. The result revealed that post biomethanated spent wash was neutral in reaction with high concentration of soluble salt. The application of post biomethanated spent wash conductivity and water retentio...
    Related Article: Christian A. Juillerat, Vancho Kocevski, Gregory Morrison, Stavros G. Karakalos, Deepak Patil, Scott T. Misture, Theodore M. Besmann, Hans-Conrad zur Loye|2019|Inorg.Chem.Front.|6|3203|doi:10.1039/C9QI00537D
    Background: Embryo quality is of paramount importance in an in vitro fertilization and embryo transfer (IVF-ET) cycle. A healthy embryo leads to a robust pregnancy. Incubation in an ideal atmosphere is essential requirement in an IVF-ET... more
    Background: Embryo quality is of paramount importance in an in vitro fertilization and embryo transfer (IVF-ET) cycle. A healthy embryo leads to a robust pregnancy. Incubation in an ideal atmosphere is essential requirement in an IVF-ET cycle.Methods: Traditionally carbon dioxide incubator with sensors for carbon dioxide levels and temperature has been used widely. We compared the quality of these embryos to incubation in hypoxic condition by addition of nitrogen. Oxygen levels were brought to 5% as compared to 21% in room air.Results: Ladies with high body mass index (BMI) and advanced age had more embryos available for transfer. More embryos reached day 3 and day 5, thus increasing availability for cryopreservation. The fragmentation rate and fertilization failure were less. Pregnancy rate was definitely improved as compared to traditional incubation.Conclusions: Hypoxic incubation condition leads to better embryo health. This translates into improved and efficient cycle outcome.
    BackgroundMUC1 is a highly glycosylated protein that is expressed at the apical border of mucosal epithelium where it plays a protective role. MUC1 is comprised of an N-terminal subunit (MUC1N) tethered to a C-terminal subunit (MUC1C),... more
    BackgroundMUC1 is a highly glycosylated protein that is expressed at the apical border of mucosal epithelium where it plays a protective role. MUC1 is comprised of an N-terminal subunit (MUC1N) tethered to a C-terminal subunit (MUC1C), forming a stable complex on the cell surface. A proteolytic ‘stump’ of MUC1C that may be aberrantly glycosylated is over-represented in cancer, making it an attractive therapeutic target. Here we report generation of allogeneic MUC1C-specific CAR T cells, P-MUC1C-ALLO1, that are designed to leverage the learnings of our P-BCMA-ALLO1 program. P-MUC1C-ALLO1 targets a MUC1C epitope and has the potential for efficacy against a wide range of solid tumors, without targeting normal epithelial cells.Methods mRNA-generated MUC1C CAR-T cells were evaluated for specificity and function by degranulation assay against various solid tumor and normal cells and cell lines. Autologous and allogeneic MUC1C CAR-T cells were produced using the piggyBac® DNA Modification ...
    Background & objectives: Chikungunya (CHIK) is a neglected, re-emerging arboviral disease. Limited information on CHIK-confirmed cases during interepidemic period is available from India. This surveillance study was conducted in... more
    Background & objectives: Chikungunya (CHIK) is a neglected, re-emerging arboviral disease. Limited information on CHIK-confirmed cases during interepidemic period is available from India. This surveillance study was conducted in Madhya Pradesh (MP), India, during the years 2016-2017, to provide information about CHIK cases. Methods: Blood samples collected from patients suspected having CHIK were tested by immunoglobulin (Ig) IgM ELISA or real time reverse transcription-polymerase chain reaction (rRT-PCR) for the detection of CHIK virus (CHIKV)-specific IgM antibodies or viral RNA, respectively. Partial envelope-1 gene sequencing was done. Clinical and demographic data were collected and analyzed. Results: Of the 4019 samples tested, 494 (12.2%) were found positive for CHIKV infection. The positivity was detected in both rural and urban areas. The mean age of CHIK-positive cases was 33.12±18.25 yr. Headache and joint pain were the most prominent symptoms, 34.6 per cent (171/494) of the CHIK cases required hospitalization and six patients with CHIKV infection died. The East/Central/South African genotype of CHIKV was found to be circulating in the study area. Interpretation & conclusions: Our study recorded a higher CHIK positivity during 2016-2017 in comparison to earlier reports from MP, India. A high proportion of CHIK cases required hospitalization and deaths were also reported, which indicated the severity of the disease in the study area. In-depth molecular analysis of the virus and other risk factors is essential to understand the trends in disease severity.
    Bipolar disorder is psychological illness with periodic episodes of mania and depression. Schizophrenia is a complex mental disorder identified by delusions, hallucinations, disorganized behavior, impaired cognitive ability, disorganized... more
    Bipolar disorder is psychological illness with periodic episodes of mania and depression. Schizophrenia is a complex mental disorder identified by delusions, hallucinations, disorganized behavior, impaired cognitive ability, disorganized speech and sudden change in personality. In both the diseases quetiapine fumarate (QF) drug is worth important in today’s scenario. This review gives complete QF drug profile along with mechanism of action. Quetiapine alone is successful for acute bipolar depression and the prevention of mania/hypomania switching. Literature survey section of this review gives information about quetiapine in different dosage form. By this review one can explore the scale up of quetiapine fumarate not only with immediate release and sustained release dosage form but also with novel drug delivery system like solid lipid nanoparticle and nanostructured lipid carrier.
    In 1954, a virus named Wad Medani virus (WMV) was isolated from Hyalomma marginatum ticks from Maharashtra State, India. In 1963, another virus was isolated from Sturnia pagodarum birds in Tamil Nadu, India, and named Kammavanpettai virus... more
    In 1954, a virus named Wad Medani virus (WMV) was isolated from Hyalomma marginatum ticks from Maharashtra State, India. In 1963, another virus was isolated from Sturnia pagodarum birds in Tamil Nadu, India, and named Kammavanpettai virus (KVPTV) based on the site of its isolation. Originally these virus isolates could not be identified with conventional methods. Here we describe next-generation sequencing studies leading to the determination of their complete genome sequences, and identification of both virus isolates as orbiviruses (family Reoviridae). Sequencing data showed that KVPTV has an AT-rich genome, whereas the genome of WMV is GC-rich. The size of the KVPTV genome is 18 234 nucleotides encoding proteins ranging 238-1290 amino acids (aa) in length. Similarly, the size of the WMV genome is 16 941 nucleotides encoding proteins ranging 214-1305 amino acids in length. Phylogenetic analysis of the VP1 gene, along with the capsid genes VP5 and VP7, revealed that KVPTV is likely...
    Ticks are distributed worldwide and can harbourand transmit a range of pathogenic microorganisms that affect livestock and humans. Most tick-borne diseases are caused by tick-borne viruses. Two major tick-borne virus zoonotic diseases,... more
    Ticks are distributed worldwide and can harbourand transmit a range of pathogenic microorganisms that affect livestock and humans. Most tick-borne diseases are caused by tick-borne viruses. Two major tick-borne virus zoonotic diseases, Kyasanur forest disease (KFD) and Crimean-Congo haemorrhagic fever (CCHF), are notifiable in India and are associated with highmortality rates. KFD virus was first identified in 1957 in Karnataka state; the tick Haemaphysalis spinigera is the main vector. During 2012-2013, cases were reported from previouslyunaffected areas in Karnataka, and newer areas of Kerala and Tamil Nadu states. These reports may be the result of improved active surveillance or may reflect altered virus transmission because of environmental change. CCHF is distributed in Asia, Africa and some part of Europe; Hyalomma spp. ticks are the main vectors. The existence of CCHF in India was first confirmed in 2011 in Gujaratstate. In 2013, a non-nosocomial CCHF outbreak in Amreli dist...
    Solid processing storage and conveying units (e.g., hoppers, silos, tumblers, etc.) often involve the collision of granular media with relatively thin walls. Therefore, the impact of a sphere with a thin plate is a problem with both... more
    Solid processing storage and conveying units (e.g., hoppers, silos, tumblers, etc.) often involve the collision of granular media with relatively thin walls. Therefore, the impact of a sphere with a thin plate is a problem with both fundamental and practical importance. In the present work, the normal elastoplastic impact between a sphere and a thin plate is analyzed using an explicit finite element method (FEM). The impact involves plastic deformation and flexural vibrations, which when combined results in significant energy dissipation. One way to quantify the energy dissipation is to employ the coefficient of restitution (COR), which is also a key input parameter needed in various granular flow models. The results were validated against the available experimental data. It is observed that, in addition to material properties and impact parameters, the energy dissipation is strongly dependent on the ratio of plate thickness to sphere diameter. A comprehensive parametric study is co...
    ABSTRACT Nitinol 60 (NiTi60) is a nickel–titanium alloy that has a unique combination of properties such as high hardness, low elastic modulus, and superelasticity. Recent studies of static indentation tests on prestressed samples... more
    ABSTRACT Nitinol 60 (NiTi60) is a nickel–titanium alloy that has a unique combination of properties such as high hardness, low elastic modulus, and superelasticity. Recent studies of static indentation tests on prestressed samples demonstrated a considerable load capacity increase, which led to the current experimental work. The coefficient of restitution (COR) is measured for two NiTi60 spheres of different diameters (0.635 and 1.270 cm). This work shows that mechanically stressing NiTi60 spheres enables them to achieve a normal COR greater than 0.9 when colliding with NiTi60 landing. This is one of the highest ever reported COR values for self-mated crystalline metal alloys at moderate impact velocities. Consequently, it is believed that this material may be a potential candidate for use in applications requiring highly resilient and wear-resistant metallic materials. A well-known analytical formulation for the coefficient of restitution is used to gain insight and to elucidate some of the COR results presented.
    A total of 30 endophytic fungi (AAP-PS 1–30) were isolated from the medicinal herb Phyllanthus amarus and screened for the production of Trichothecinol-A. Out of all the endophytic strains screened for Trichothecinol-A production, the... more
    A total of 30 endophytic fungi (AAP-PS 1–30) were isolated from the medicinal herb Phyllanthus amarus and screened for the production of Trichothecinol-A. Out of all the endophytic strains screened for Trichothecinol-A production, the culture filtrate of AAP-PS-1 extracted with ethyl acetate yielded Trichothecinol-A extracellularly in appreciable amounts. Trichothecinol-A was purified, quantified and completely characterized by different standard chromatographic and spectroscopic techniques including reverse phase HPLC, 1D and 2D NMR spectroscopy, etc. The compound was tested for antifungal activity against filamentous fungi and yeast, apoptotic activity against B16F10 cells, anticancer activity against MDA-MB-231, HeLa and B16F10 cells as well as antimetastatic activity against MDA-MB-231 cell line. Results: The endophyte producing Trichothecinol-A was identified as Trichothecium sp. by morphological, cultural and molecular methods. RP-HPLC analyses performed on a Waters model usin...
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    Introduction: Influenza viruses are known to cause global outbreak with massive morbidity and mortality. Information on the activity and prevalence of influenza virus in our country is limited. Haffkine Institute is a WHO Influenza... more
    Introduction: Influenza viruses are known to cause global outbreak with massive morbidity and mortality. Information on the activity and prevalence of influenza virus in our country is limited. Haffkine Institute is a WHO Influenza Surveillance centre, engaged in surveillance of Influenza Virus in Mumbai region. Objective: To monitor influenza viruses in Mumbai and further isolate and type the virus. Material and Methods: During July 2007 to July 2009, a total of 193 clinical respiratory samples (Nasal and Throat swab) were collected from patients having acute respiratory symptoms. Samples were collected in Viral Transport Medium and processed by molecular (rRT-PCR) and tissue culture methods using MDCK cell line. Haemagglutination Assay was performed and isolates obtained were sub-typed by Haemagglutination Inhibition Assay. Results: Out of 193 clinical samples processed by rRT-PCR, 24(12.43%) samples tested positive for influenza virus, out of which 13(6.73%) were influenza type A...
    INTRODUCTION: The 2009 Influenza Pandemic (‘Swine Flu’) caused by a novel H1N1 Influenza Virus (Swine Origin Influenza A; SOIA) has waved panic world-over since April 2009. Haffkine Institute is the regional centre for molecular diagnosis... more
    INTRODUCTION: The 2009 Influenza Pandemic (‘Swine Flu’) caused by a novel H1N1 Influenza Virus (Swine Origin Influenza A; SOIA) has waved panic world-over since April 2009. Haffkine Institute is the regional centre for molecular diagnosis of Influenza Virus in and around Mumbai. We present here some important findings from our testing. MATERIALS: 3750 throat/nasal swab samples from patients suspected of Influenza were obtained during August–September 2009. Since viral safety has not been completely established, P2 level biosafety cabinets with P3 level safety practices were followed. METHODS: Molecular diagnosis was performed according to WHO/CDC recommended protocols. RNA extraction using spin-column-based kits and One-Step Real-Time Reverse-Transcriptase PCR (rRT-PCR) were used to diagnose SOIA along with Seasonal Influenza A. RESULTS: The percent positivity of SOIA is approximately 20%, while that of Seasonal Influenza A is approximately 16%. Analysis of partial epidemiological d...
    INTRODUCTION: The first confirmed case of ‘Swine Flu’ Novel H1N1 Influenza A (Swine Origin Influenza A; SOIA) reported in India on 16 May 2009 heralded an alarming increase in positive cases. Haffkine Institute is a regional center for... more
    INTRODUCTION: The first confirmed case of ‘Swine Flu’ Novel H1N1 Influenza A (Swine Origin Influenza A; SOIA) reported in India on 16 May 2009 heralded an alarming increase in positive cases. Haffkine Institute is a regional center for the molecular diagnosis of Influenza in the Mumbai region. Here we present an analysis of the co-existence of the SOIA virus vis-à-vis the Seasonal Influenza A Virus in the community during August–September 2009. MATERIALS: 3750 throat/nasal swab samples from patients suspected of Influenza were obtained during August–September 2009. Since viral safety has not been completely established, P2 level biosafety cabinets with P3 level safety practices were followed. METHODS: Molecular diagnosis was carried out according to WHO/CDC recommended protocols. RNA extraction using spin-column-based kits and One-Step Real-Time Reverse-Transcriptase PCR (rRT-PCR) were used to diagnose SOIA along with Seasonal Influenza A. RESULTS: The overall percent positivity of ...
    Kyasanur Forest disease virus (KFDV) was first identified in 1957, when it was isolated from a sick monkey from the Kyasanur Forest in Karnataka State, India. Since then it has been reported to be enzootic in five districts of Karnataka... more
    Kyasanur Forest disease virus (KFDV) was first identified in 1957, when it was isolated from a sick monkey from the Kyasanur Forest in Karnataka State, India. Since then it has been reported to be enzootic in five districts of Karnataka State, India. Recent reports of human infections have reached an alarming level, in spite of the availability of a vaccine. This disease has also been reported from new areas, such as Tamil Nadu and Kerala State. During January-March 2014, KFDV-positive cases were detected in Thirthahalli taluk, Shimoga District, Karnataka State, India. Here, we report an outbreak of Kyasanur Forest disease occurring in the Kannangi and Konandur area, Thirthahalli taluk in Karnataka State, India, with sporadic cases from eight other areas.
    Cotton is an important source of natural fibre used in the textile industry and the productivity of the crop is adversely affected by drought stress. High throughput transcriptomic analyses were used to identify genes involved in fibre... more
    Cotton is an important source of natural fibre used in the textile industry and the productivity of the crop is adversely affected by drought stress. High throughput transcriptomic analyses were used to identify genes involved in fibre development. However, not much information is available on cotton genome response in developing fibres under drought stress. In the present study a genome wide transcriptome analysis was carried out to identify differentially expressed genes at various stages of fibre growth under drought stress. Our study identified a number of genes differentially expressed during fibre elongation as compared to other stages. High level up-regulation of genes encoding for enzymes involved in pectin modification and cytoskeleton proteins was observed at fibre initiation stage. While a large number of genes encoding transcription factors (AP2-EREBP, WRKY, NAC and C2H2), osmoprotectants, ion transporters and heat shock proteins and pathways involved in hormone (ABA, ethylene and JA) biosynthesis and signal transduction were up-regulated and genes involved in phenylpropanoid and flavonoid biosynthesis, pentose and glucuronate interconversions and starch and sucrose metabolism pathways were down-regulated during fibre elongation. This study showed that drought has relatively less impact on fibre initiation but has profound effect on fibre elongation by down-regulating important genes involved in cell wall loosening and expansion process. The comprehensive transcriptome analysis under drought stress has provided valuable information on differentially expressed genes and pathways during fibre development that will be useful in developing drought tolerant cotton cultivars without compromising fibre quality.
    Background: Group B Streptococcus (GBS) is the cause of severe early-onset infection in newborns. The CDC's 2002 guidelines recommended culture-based screening for vagino-rectal GBS colonization at 35–37 weeks of gestation to identify... more
    Background: Group B Streptococcus (GBS) is the cause of severe early-onset infection in newborns. The CDC's 2002 guidelines recommended culture-based screening for vagino-rectal GBS colonization at 35–37 weeks of gestation to identify candidates for the intrapartum antibiotic prophylaxis. Some studies reported a poor correlation between screening results and intrapartum GBS colonization. Nevertheless maternal GBS status is sometimes unknown at labour. Design and population: Intrapartum rapid methods as Real Time Protein Chain Reaction (RT-PCR) and rapid tests for the GBS-antigen detection were developed. The aim of this study was to compare GBS selective culture versus PCR and two rapid methods in 230 pregnant women admitted for delivery at Imola Hospital. Material and methods: 230 intrapartum vaginal swab specimens were tested by culture and RT-PCR, 115 out of 230 by an immunocromatographic assay (TEST ULTIMED StrepB, Promesan) and 115 out of 230 by StrepB-OIA (Biostar, Promesan). Results: Positive and negative concordance with cultures were respectively 43% and 99% for RT-PCR, 46% and 94% for StrepB-OIA and 66% and 90% for TEST ULTIMED StrepB. Conclusions: RT-PCR had higher concordance with culture than StrepB-OIA but it requires more time to be performed and more complex equipment. StrepB-OIA is a rapid test of easy execution with a fairly good concordance with culture. We suggest that OIA could be an effective method to identify women actually GBS-colonized at delivery.
    Background Fuzzless-lintless cotton mutants are considered to be the ideal material to understand the molecular mechanisms involved in fibre cell development. Although there are few reports on transcriptome and proteome analyses in cotton... more
    Background Fuzzless-lintless cotton mutants are considered to be the ideal material to understand the molecular mechanisms involved in fibre cell development. Although there are few reports on transcriptome and proteome analyses in cotton at fibre initiation and elongation stages, there is no comprehensive comparative transcriptome analysis of fibre-bearing and fuzzless-lintless cotton ovules covering fibre initiation to secondary cell wall (SCW) synthesis stages. In the present study, a comparative transcriptome analysis was carried out using G. hirsutum L. cv. MCU5 wild-type (WT) and it’s near isogenic fuzzless-lintless (fl) mutant at fibre initiation (0 dpa/days post anthesis), elongation (5, 10 and 15 dpa) and SCW synthesis (20 dpa) stages. Results Scanning electron microscopy study revealed the delay in the initiation of fibre cells and lack of any further development after 2 dpa in the fl mutant. Transcriptome analysis showed major down regulation of transcripts (90%) at fibre...

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