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Genomics, Proteomics & Bioinformatics 2010年第1期8卷 42-56页

作者： shriparna Dutt V.K. singh soma s.marla Anil Kumar Department of Molecular Biology and Genetic Engineering G.B.Pant University of Agriculture and Technology

Phytocystatins constitute a multigene family that regulates the activity of endogenous and/or exogenous cysteine proteinases. Cereal crops like wheat are continuously threatened by a multitude of pathogens, therefore cystatins offer to play a pivotal role in deciding the plant response. In order to study the need of having diverse specificities and activities of various cystatins, we conducted comparative analysis of six wheat cystatins （WCs） with twelve rice, seven barley, one sorghum and ten corn cystatin sequences employing different bioinformatics tools. The obtained results identified highly conserved signature sequences in all the cystatins considered. several other motifs were also identified, based on which the sequences could be categorized into groups in congruence with the phylogenetic clustering. Homology modeling of WCs revealed 3D structural topology so well shared by other cystatins. Protein-protein interaction of WCs with papain supported the notion that functional diversity is a con- sequence of existing differences in amino acid residues in highly conserved as well as relatively less conserved motifs. Thus there is a significant conservation at the sequential and structural levels; however, concomitant variations maintain the functional diversity in this protein family, which constantly modulates itself to reciprocate the diversity while counteracting the cysteine proteinases.

关键词： wheat cystatins structural diversity functional diversity comparative analysis

A Novel Technique for Detecting Various Thyroid Diseases Using Deep Learning

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Intelligent Automation & soft Computing 2023年第1期35卷 199-214页

作者： soma Prathibha Deepak Dahiya C.R.Rene Robin Cherukuru Venkata Nishkala s.swedha Department of Information Technology Sri Sai Ram Engineering CollegeChennai600044India College of Computer and Information sciences(CCIs) Majmaah UniversityMajmaah11952Kingdom of Saudi Arabia Department of Computer science and Engineering Sri Sai Ram Engineering CollegeChennai602109India Associate solutions Engineer PegasystemsChennai600044India systems Engineer Infosys Ltd.Chennai600119India

Thyroid disease is a medical condition caused due to the excess release of thyroid hormone.It is released by the thyroid gland which is in front of the neck just below the larynx.Medical pictures such as X-rays and CT scans can,however,be used to diagnose it.In this proposed model,Deep Learning technology is used to detect thyroid diseases.A Convolution Neural Network(CNN)based modified ResNet architecture is employed to detectfive different types of thyroid diseases namely 1.Hypothyroid 2.Hyperthyroid 3.Thyroid cancer 4.Thyroiditis 5.Thyroid nodules.In the proposed work,the training method is enhanced using dual optimizers for better accuracy and results.Keras,a Python library that is high level runs as the main part of the Tensor Flow framework.It is used in the proposed work to implement deep learning techniques.The comparative analysis of the proposed model and the existing work helps to show that there is a great improvement in the performance metrics in classifying the type of thyroid disease.By applying Adam and sGD(stochastic Gradient Descent)optimizers in the training phase of the proposed model it was identified that these increase the operational efficiency of the modified ResNet model.After retraining the model with sGD,the modified ResNet provides more accuracy of about 97%whereas the basic ResNet architecture attains 94%accuracy.A web-based frame-work is also developed which yields the type of thyroid disease as the output for a given input scanned image of the system.

关键词： Thyroid deep learning convolution neural network modified ResNet dual optimizer

Forensic Identification of Four Indian snake species Using single Multiplex Polymerase Chain Reaction

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Journal of Forensic science and Medicine 2022年第3期8卷 81-87页

作者： Ishani Mitra soma Roy Ikramul Haque Division of Biology Central Forensic Science LaboratoryKolkataWest BengalIndia Office of Director Central Forensic Science LaboratoryChandigarhIndia

Among different endangered animal species,snakes are the most neglected creature looked at with apathy and therefore,are ruthlessly killed,illegally trafficked,and poached for their venom,lucrative skin,meat,and bones for manufacturing of medicines,accessories,and food items.Establishing the identity of the endangered snake species is important for punishing the offenders under Wildlife Protection Act(WPA)(1972)but morphological characters fail to establish identity as they are often altered.The technique of identification of snake species at molecular level holds very effective conclusion in punishing offender.Here,we have constructed and demonstrated a novel multiplexing polymerase chain reaction technique,using 16s rRNA and C-mos gene for identification of four Indian snake species,namely Ptyas mucosa,Daboia russellii,Naja naja,and Xenochrophis piscator.They are listed in Appendix-II and III of convention on international trade in endangered species of wild fauna and flora and schedule II;Part II of Indian WPA,1972.Therefore,it may be considered a functional tool for establishing species-specific identity of four Indian snake species and promising to be useful for their conservation.

关键词： 16s rRNA C-mos forensic identification Indian snakes multiplex polymerase chain reaction amplification Wildlife Protection Act(1972)

Low-dose lipopolysaccharide as an immune regulator for homeostasis maintenance in the central nervous system through transformation to neuroprotective microglia

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Neural Regeneration Research 2021年第10期16卷 1928-1934页

作者： Haruka Mizobuchi Gen-Ichiro soma Control of Innate Immunity Technology Research AssociationKagawaJapan Macrophi Inc. KagawaJapan Research Institute for Healthy Living Niigata University of Pharmacy and Applied Life SciencesNiigataJapan

Microglia,which are tissue-resident macrophages in the brain,play a central role in the brain innate immunity and contribute to the maintenance of brain homeostasis.Lipopolysaccharide is a component of the outer membrane of gram-negative bacteria,and activates immune cells including microglia via Toll-like receptor 4 signaling.Lipopolysaccharide is generally known as an endotoxin,as administration of highdose lipopolysaccharide induces potent systemic inflammation.Also,it has long been recognized that lipopolysaccharide exacerbates neuroinflammation.In contrast,our study revealed that oral administration of lipopolysaccharide ameliorates Alzheimer’s disease pathology and suggested that neuroprotective microglia are involved in this phenomenon.Additionally,other recent studies have accumulated evidence demonstrating that controlled immune training with low-dose lipopolysaccharide prevents neuronal damage by transforming the microglia into a neuroprotective phenotype.Therefore,lipopolysaccharide may not a mere inflammatory inducer,but an immunomodulator that can lead to neuroprotective effects in the brain.In this review,we summarized current studies regarding neuroprotective microglia transformed by immune training with lipopolysaccharide.We state that microglia transformed by lipopolysaccharide preconditioning cannot simply be characterized by their general suppression of proinflammatory mediators and general promotion of anti-inflammatory mediators,but instead must be described by their complex profile comprising various molecules related to inflammatory regulation,phagocytosis,neuroprotection,anti-apoptosis,and antioxidation.In addition,microglial transformation seems to depend on the dose of lipopolysaccharide used during immune training.Immune training of neuroprotective microglia using lowdose lipopolysaccharide,especially through oral lipopolysaccharide administration,may represent an innovative prevention or treatment for neurological diseases;however more vigorous studies are still required to properly mo

关键词： cognitive impairment endotoxin lipopolysaccharide low-dose microglia neuroprotection oral administration preconditioning tolerance trained innate immunity

Competition between axial anomaly and ferromagnetic ordering in Bi_(2-x)Fe_(x)se_(3-x)s_(x) topological insulator:A study of magnetic and magnetotransport properties

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Journal of Materiomics 2022年第3期8卷 669-677页

作者： Rahul singh shiv Kumar A.Jain Mahima singh Labanya Ghosh A.singh soma Banik A.Lakhani s.Patil E.F.schwier K.shimada s.M.Yusuf sandip Chatterjee solid state Physics Division Bhabha Atomic Research CenterTrombayMumbai400085India Hiroshima synchrotron Radiation Center HiroshimaJapan Homi Bhabha National Institute AnushaktinagarMumbai400094India Department of Physics Indian Institute of Technology(BHU)Varanasi221005India synchrotrons Utilization section Raja Ramanna Centre for Advanced TechnologyIndore452013India UGC-DAE Consortium for scientific Research IndoreMadhya Pradesh452017India Department of CMP&Ms Tata Institute of Fundamental ResearchMumbai400005India

The topological insulators Bi_(2-x)Fe_(x)se_(3-x)s_(x) have been investigated by the dc-magnetization,magnetotransport and angle resolved photoemission spectroscopy(ARPEs)techniques.With doping of Fe and s,a negative giant magneto-resistance(MR)is observed for parallel electric and magnetic fields(H||E).The MR behavior at lower magnetic field can be explained with the semi-classical theory whereas the MR behavior at higher field has been attributed to the axial anomaly.Interestingly,the system reached to the quantum limit at low magnetic field(~4.5T).The magnetic ordering can be explained with the presence of both the RKKY(surface)and van-Vleck(bulk)interaction.The ARPEs study reveals that a surface gap is suppressed when the magnetic ordering changes from ferromagnetic to anti-ferromagnetic ordering.The ARPEs study and the appearance of quantum oscillations(sdH)in the resistivity pattern reveal that the topological surface property is preserved with the co-doping of Fe and s.

关键词： spintronics Magnetoresistance Magnetism Topological insulators RKKY interaction ARPEs study

Cryopreserved ovine spermatogonial stem cells maintain stemness and colony forming ability in vitro

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Asian pacific Journal of Reproduction 2023年第6期12卷 273-280页

作者： R.Kumar Pramod Deepthi Varughese A.Javed Jameel Bhisma Narayan Panda soma Goswami Abhijit Mitra ICMR-National Animal Resource Facility for Biomedical Research HyderabadTelangana500101India Inter University Centre for Biomedical Research&super speciality Hospital Kerala686009India College of Veterinary and Animal sciences MannuthyKerala680651India Translational Health science and Technology Institute FaridabadHaryana121001India G V Research Platform HyderabadTelangana500101India Department of Animal Husbandry&Dairying MoFAHDKrishi BhavanNew Delhi110001India

Objective:To assess the effect of cryopreservation on stemness and proliferation potential of sheep spermatogonial stem cells(ssCs)in vitro.Methods:sheep testicular cells were isolated and putative ssCs were enriched by the laminin-based differential plating method.Putative ssCs were co-cultured with the sertoli cell feeder prepared by the Datura stramonium Agglutinin(DsA-lectin)-based method.The cultured putative ssCs were cryopreserved in Dulbecco's Modified Eagle Medium-10%fetal bovine serum mixture(DMEM-10%FBs)media containing 10%dimethyl sulfoxide(DMsO)alone or 10%DMsO plus 200 mM trehalose.Cryopreserved putative ssCs were evaluated for their proliferation potential using in vitro culture and stemness by immunocytochemistry.Finally,the transfection ability of cryopreserved putative ssCs was analyzed.Results:We isolated 91%viable testicular cells from sheep testes.The majority of the laminin enriched cells expressed the ssC related marker,ITGA6.Co-culture of sheep putative ssCs with sertoli cell feeder resulted in the generation of stable colonies,and the expression of ssC marker was maintained after several passages.A significantly higher number of viable putative ssCs was recovered from ssCs cryopreserved in media containing 10%DMsO and 200 mM trehalose compared to 10%DMsO alone(Pserved putative ssCs formed colonies and showed ssC marker expression similar to the non-cryopreserved putative ssCs.The appearance of green fluorescent colonies over the sertoli cell feeder indicated that cryopreserved sheep ssCs were successfully transfected.Conclusions:Cryopreserved putative ssCs can retain their stemness,colony forming ability,and transfection efficiency in vitro.Our research may help in the effective preservation of germplasm and the generation of transgenic ovine species.

关键词： spermatogonial stem cell sheep stemness Cryopreservation Transfection

Age Estimation Using single-Rooted Teeth of Indian Residents by Modified Kvaal’s Method:A Pilot study

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Journal of Forensic science and Medicine 2023年第1期9卷 53-56页

作者： Deepa Jose Deepa R Mane soma susan Varghese Pramod Philip Mathews Joseph sebastian Department of Oral Pathology and Microbiology Mar Baselios Dental CollegeErnakulamKeralaIndia Department of Oral Pathology KLE VK Institute of Dental SciencesJNMC CampusBelagaviKarnatakaIndia

Background:This study aimed to create an age estimation formula with high sensitivity and specificity using the modified Kvaal’s dental radiographic method.The parameters for age estimation were assessed by measuring the length and width of tooth,root,and pulp with the help of a stereomicroscope and digital image analysis.Materials and Methods:Only single-rooted noncarious teeth were included.A total of 203 samples of teeth,with an age ranging from 15 to 85 years,were collected,of which only 123 samples were included in the study.Images of vertically sectioned teeth specimens were captured under a stereomicroscope(version sZ-790,×10 mm eyepiece),and parameters were measured using Adobe Photoshop.Results:Karl Pearson’s correlation coefficient was used to correlate age with the dental parameters,and step-wise regression analysis was used to derive the age estimation formula.A significant correlation of age with pulp length and root and pulp width having Ps observed,and an age estimation formula with a standard estimation error of 14 could be derived.Conclusion:Kvaal’s parameter in extracted single-rooted tooth showed a better reliability and reproducibility in age estimation.Further studies with a larger sample size and tooth-specific formula using principal component analysis should be considered to validate the accuracy of the present result.

关键词： Computer assisted regression analysis tooth root

synthesis of carbon nanosheet from barley and its use as non-enzymatic glucose biosensor

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Journal of Pharmaceutical Analysis 2014年第6期4卷 351-359页

作者： soma Das Mitali saha Department of Chemistry National Institute of TechnologyAgartala 799046TripuraIndia

In this work,carbon nanosheet（CNs） based electrode was designed for electrochemical biosensing of glucose.CNs has been obtained by the pyrolysis of barley at 600-750℃ in a muffle furnace：it was then purified and functionalized.The CNs has been characterized by scanning electron microscopy（sEM）.X-ray diffraction（XRD） and Raman spectroscopic techniques.The electrochemical activity of CNs-based electrode was investigated by linear sweep vollammetry（LsV） and square wave voltammetry（sWV）,for the oxidation of glucose in 0.001 M H2sO4（pH 6.0）.The linear range of the sensor was found to be 10-4-10-6M（1-100 μM） within the response time of 4 s.Interestingly,its sensitivity reached as high as 26.002±0.01 μA/μM cm2.Electrochemical experiments revealed that the proposed electrode offered an excellent electrochemical activity towards the oxidation of glucose and could be applied for the construction of non-enzymatic glucose biosensors.

关键词： Carbon nanosheet β-D glucose Linear sweep voltammetry square wave voltammetry Pharmaceutical analysis

state of machine and deep learning in histopathological applications in digestive diseases

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World Journal of Gastroenterology 2021年第20期27卷 2545-2575页

作者： soma Kobayashi Joel H saltz Vincent W Yang Department of Biomedical Informatics Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Medicine Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Physiology and Biophysics Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States

Machine learning(ML)-and deep learning(DL)-based imaging modalities have exhibited the capacity to handle extremely high dimensional data for a number of computer vision tasks.While these approaches have been applied to numerous data types,this capacity can be especially leveraged by application on histopathological images,which capture cellular and structural features with their highresolution,microscopic perspectives.Already,these methodologies have demonstrated promising performance in a variety of applications like disease classification,cancer grading,structure and cellular localizations,and prognostic predictions.A wide range of pathologies requiring histopathological evaluation exist in gastroenterology and hepatology,indicating these as disciplines highly targetable for integration of these technologies.Gastroenterologists have also already been primed to consider the impact of these algorithms,as development of real-time endoscopic video analysis software has been an active and popular field of research.This heightened clinical awareness will likely be important for future integration of these methods and to drive interdisciplinary collaborations on emerging studies.To provide an overview on the application of these methodologies for gastrointestinal and hepatological histopathological slides,this review will discuss general ML and DL concepts,introduce recent and emerging literature using these methods,and cover challenges moving forward to further advance the field.

关键词： Artificial intelligence Machine learning Deep learning Gastroenterology Hepatology Histopathology

Rainfall and Temperature Variations over Burkina Faso: Possible Influence of Geomagnetic Activity, solar Activity and Associated Energies from 1975 to 2020

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Atmospheric and Climate sciences 2022年第4期12卷 603-612页

作者： Yacouba sawadogo somaïla Koala Jean Louis Zerbo Laboratoire de Matériaux d’Héliophysique et Environnement (La.M.H.E) Université Nazi Boni Bobo-Dioulasso Burkina Faso Unité de Formation et de Recherche en sciences Exactes et Appliquées (UFR/sEA) Université Nazi Boni Bobo-Dioulasso Burkina Faso

This study investigates climatic parameters (rainfall, and temperature) over Burkina Faso and the possible role of solar activity and its induced energies. Through morphological investigations, we analyzed solar activity indices (sunspot number, IMF, PC index, Cosmic rays) over the last three solar cycles (1975-2020). Results about interplanetary heating show that joule heating is well correlated with the dynamic pressure of the solar plasma. Climate parameters (rainfall, Temperature) variabilities are modulated by disturbances in solar activity: 1) quiet solar characterized by a drop in solar plasma’s parameters is associated with important cloud cover and consequently bring important rainfall which chills terrestrial atmosphere, 2) active solar characterized by important input energy is associated with weak incident cosmic ray consequently with low cloudiness which brings warming. Thus, the possible natural link can be suggested between solar activity and climatic parameters even if it is not the only factor of global warming.

关键词： Temperature Rainfall solar Activity Geomagnetic Activity Climate Burkina Faso