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Sum-Based Meta-Analytical Enrichment of Gene Expression Data to Identify Pathway Signatures of Cancers

Journal of Cancer Therapy 2010年第1期1卷 36-42页

作者： Kavishwar Wagholikar Prasanna Venkatraman Sundararajan Vijayraghavan chandan kumar-sinha Advanced Centre for Treatment Research and Education in Cancer Navi Mumbai India Interdisciplinary School of Scientific Computing University of Pune Pune India Michigan Center for Translational Pathology Department of Pathology University of Michigan Ann Arbor MI USA

A new method for analysis of microarray gene expression experiments referred to as Sum-based Meta-analytical Enrichment?(SME) is proposed in this manuscript. SME is a combined enrichment and meta-analytical approach to infer?on the association of gene sets with particular phenotypes. SME allows enrichment to be performed across datasets,?which to our knowledge was not earlier possible. As a proof of concept study, this technique is applied to datasets from?Oncomine, a publicly available cancer microarray database. The genes that are significantly up-/down-regulated?(p-value ≤ 10-4) in various cancer types in Oncomine were listed. These genes were assigned to biological processes?using GO annotations. The SME algorithm was applied to identify a list of GO processes most deregulated in 4 major?cancer types. For validation we examined whether the processes predicted by SME were already documented in *** method identified several known processes for the 4 cancer types and identified several novel processes?which are biologically plausible. Nearly all the pathways identified by SME as common to the 4 cancers were found to?contribute to processes which are widely regarded as cancer hallmarks. SME provides an intuitive yet objective ‘process-centric’ interpretation of the ‘gene-centric’ output of individual microarray comparison studies. The methods described?here should be applicable in the next-generation sequencing based gene expression analysis as well.

关键词： Gene Expression Microarray Enrichment Meta-Analysis

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Masseter Vestibular evoked myogenic potentials: A new tool to assess the vestibulomasseteric reflex pathway

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Journal of Otology 2024年第1期19卷 46-54页

作者： Aishwarya Nagarajan Sujeet kumar sinha Department of Audiology AIISHMysore06India

Purpose: This review article provides the readers with an in-depth insight in understanding and interpreting various research literatures on the masseter vestibular evoked myogenic potentials(mVEMP). The article also reviews the contemporary researches involving the clinical applications of the mVEMP. Conclusions: Masseter VEMP is an evolving yet clinically promising neuro-otology test tool that has recently gained more research interest and is considered an additional tool to diagnose various vestibular disorders. Masseter VEMP assesses the functional integrity of the acoustic-masseteric and vestibulo-masseteric reflex pathways. The mVEMP could be used as a complementary test to evaluate the same peripheral generator as the cervical VEMP but a different central pathway i.e., vestibulo-trigeminal pathway. Various research studies that have experimented on parameters such as the effect of different electrode montages(zygomatic vs mandibular configurations), stimulation rates, filter settings and stimuli used to evoke mVEMP have been discussed in this article that could assist in the optimization of a comprehensive clinical protocol. The latency and the amplitude of mVEMP waveforms serve as significant parameters in differentiating normals from those of the clinical populations. Along with the cVEMPs and oVEMPs, mVEMP might help diagnose brainstem lesions in REM Sleep behaviour disorders, Multiple Sclerosis and Parkinson's disease. However, further studies are required to probe in this area of research.

关键词： Masseter vestibular evoked myogenic potentials(mVEMP) Vestibulo-masseteric pathway Acoustic-masseteric pathway

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Bidirectional link between periodontitis and systemic inflammation in diabetic retinopathy

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World Journal of Diabetes 2024年第7期15卷 1651-1653页

作者： Prateek Nishant Sony sinha Ranjeet kumar sinha Arvind kumar Morya Department of Ophthalmology ESIC Medical CollegePatna 801103BiharIndia Department of Ophthalmology-Vitreo-Retina Neuro-Ophthalmology and OculoplastyAll India Institute of Medical SciencesPatna 801507BiharIndia Department of Community Medicine Patna Medical CollegePatna 800004BiharIndia Department of Ophthalmology All India Institute of Medical SciencesHyderabad 508126TelanganaIndia

Periodontitis is independently associated with numerous lifestyle *** patients have approximately threefold increased odds of periodontitis,which in turn increases the risk of systemic *** study by Thazhe Poyil et al is an effort to establish the inflammatory link between diabetic retinopathy(DR)and periodontitis based on the periodontal inflamed surface area in diabetic patients with and without *** further advance the study,we suggest refining the eligibility criteria to explicitly state the clinical correlates of periodontitis and DR,larger sample size and improved sampling methodology,matching of baseline characteristics of the two groups,as well as improved statistical approach and interpretation of the study *** of hemoglobin A1c(HbA1c)in studies comparing type 2 diabetes mellitus patients with DR of matched severity with and without periodontitis could provide a clearer picture of whether HbA1c level is indeed influenced by periodontitis.

关键词： Glucose intolerance Hyperglycemia Inflammation Research methodology Vision

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Nutrition interventions and clinical outcomes of pregnant women with gestational diabetes mellitus: More than meets the eye

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World Journal of Diabetes 2024年第1期15卷 126-128页

作者： Sony sinha Prateek Nishant Ranjeet kumar sinha Arvind kumar Morya Ripunjay Prasad Department of Ophthalmology-Vitreo-Retina Neuro-Ophthalmology and OculoplastyAll India Institute of Medical SciencesPatnaPatna 801507BiharIndia Department of Ophthalmology ESIC Medical CollegePatnaPatna 801103BiharIndia Department of Community Medicine Patna Medical CollegePatna 800004BiharIndia Department of Ophthalmology All India Institute of Medical SciencesHyderabad 508126TelanganaIndia Department of Ophthalmology RP Eye InstituteDelhi 110001DelhiIndia

In the retrospective study by Luo et al regarding clinical outcomes in gestational diabetes mellitus(GDM),the results are statistically significant in favour of the benefits of individualized nutrition interventions enumerated *** study has provided important evidence to improve maternal and child health in the Asian *** methods,however,appear to have considerable limi-tations,wherein the time point of diagnosis of GDM,severity of GDM,selection bias,compliance to therapy,important maternal covariates,observable microvascular abnormalities and the confounding effect of added insulin have not been *** have provided suggestions to improve the external validity of the study,including the use of Equator Network reporting guidelines and inclusion of overweight and obese patients in future studies.

关键词： Glucose intolerance Hyperglycemia Obesity Pregnancy Research methodology

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Radiative heat transfer analysis of a concave porous fin under the local thermal non-equilibrium condition:application of the clique polynomial method and physics-informed neural networks

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Applied Mathematics and Mechanics(English Edition) 2024年第9期45卷 1613-1632页

作者： K.chandan K.KARTHIK K.V.NAGARAJA B.C.PRASANNAkumarA R.S.VARUN kumar T.MUHAMMAD Amrita School of Artificial Intelligence Amrita Vishwa VidyapeethamBengaluru 560035KarnatakaIndia Department of Studies in Mathematics Davangere UniversityDavangere 577002KarnatakaIndia Computational Science Lab Amrita School of EngineeringAmrita Vishwa VidyapeethamBengaluru 560035KarnatakaIndia Department of Pure and Applied Mathematics School of Mathematical SciencesSunway UniversityPetaling Jaya 47500Malaysia Department of Mathematics College of ScienceKing Khalid UniversityAbha 61413Saudi Arabia

The heat transfer through a concave permeable fin is analyzed by the local thermal non-equilibrium(LTNE)*** governing dimensional temperature equations for the solid and fluid phases of the porous extended surface are modeled,and then are nondimensionalized by suitable dimensionless ***,the obtained nondimensional equations are solved by the clique polynomial method(CPM).The effects of several dimensionless parameters on the fin's thermal profiles are shown by graphical ***,the current study implements deep neural structures to solve physics-governed coupled equations,and the best-suited hyperparameters are attained by comparison with various network *** results of the CPM and physicsinformed neural network(PINN)exhibit good agreement,signifying that both methods effectively solve the thermal modeling problem.

关键词： heat transfer fin porous fin local thermal non-equilibrium(LTNE)model physics-informed neural network(PINN)

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Nitrosamines crisis in pharmaceuticals-Insights on toxicological implications,root causes and risk assessment:A systematic review

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Journal of Pharmaceutical Analysis 2024年第5期14卷 639-652页

作者： Hemanth P.R.Vikram Tegginamath Pramod kumar Gunjan kumar Narasimha M.Beeraka Rajashree Deka Sheik Mohammed Suhail Sandeep Jat Namitha Bannimath Gayatiri Padmanabhan Ravandur S.chandan Pramod kumar Bannimath Gurupadayya Department of Pharmaceutical Chemistry JSS College of Pharmacy MysuruJSS Academy of Higher Education and Research(JSSAHER)Mysuru570015India Xenone Healthcare Pvt.Ltd. New Delhi110076India Department of Pharmaceutics JSS College of Pharmacy MysuruJSS Academy of Higher Education and Research(JSSAHER)Mysuru570015India Department of Human Anatomy I.M.Sechenov First Moscow State Medical University(Sechenov University)Moscow119991Russian Federation Department of Pharmacology Raghavendra Institute of Pharmaceutical Education and Research(RIPER)Ananthapuramu515721India Herman B.Wells Center for Pediatric Research Department of PediatricsIndiana University School of MedicineIndianapolisIN46202USA Animal Physiology and Biochemistry Laboratory Department of ZoologyGauhati UniversityGuwahati781014India Department of Pharmacology JSS College of Pharmacy MysuruJSS Academy of Higher Education and Research(JSSAHER)Mysuru570015India Department of Pharmaceutical Analysis National Institute of Pharmaceutical Education and Research(NIPER)-GuwahatiChangsari781101India Department of Pharmacology University of GalwayGalwayH91 TK33Ireland

The presence of N-nitroso compounds,particularly N-nitrosamines,in pharmaceutical products has raised global safety concerns due to their significant genotoxic and mutagenic *** systematic review investigates their toxicity in active pharmaceutical ingredients(APIs),drug products,and pharmaceutical excipients,along with novel analytical strategies for detection,root cause analysis,reformulation strategies,and regulatory guidelines for *** review emphasizes the molecular toxicity of N-nitroso compounds,focusing on genotoxic,mutagenic,carcinogenic,and other physiological ***,it addresses the ongoing nitrosamine crisis,the development of nitrosamine-free products,and the importance of sensitive detection methods and precise risk *** comprehensive overview will aid molecular biologists,analytical scientists,formulation scientists in research and development sector,and researchers involved in management of nitrosamine-induced toxicity and promoting safer pharmaceutical products.

关键词： Carcinogenicity Genotoxicity Mutagenicity Molecular toxicity Nitrosamine impurities Nitrosamine drug substance-related impurities

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Tubularized incised plateurethroplasty and grafted tubularized incised plate urethroplasty: systematic review, metaanalysis and trial sequential analysis

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World Journal of Pediatric Surgery 2024年第1期7卷 10-19页

作者： Nitinkumar Borkar Charu Tiwari Abhijit Nair Debajyoti Mohanty C K sinha Jai kumar Mahajan Paediatric Surgery All India Institute of Medical Sciences-RaipurRaipurChhattisgardhIndia Department of Anaesthesiology Ibra HospitalbraOman General Surgery All India Institute of Medical Sciences-RaipurRaipurChhattisgardhIndia Paediatric Surgery St George's University Hospitals NHS Foundation TrustLondonUK Pediatric Surgery PGIMERChandigarhIndia

Background Hypospadias is one of the most common genital birth *** are around 300 various techniques available for the repair of *** study aims to compare the reported outcomes of Tubularized incised plate urethroplasty(TIP)and Grafted TIP(GTIP)repair in children undergoing primary *** This meta-analysisadhered to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines,and we framed our research question using the population,intervention,control and outcomes *** conducted comprehensive electronic searches across various databases,employing a Boolean search strategy with predefined search *** randomized controlled trials(RCTs)were included for quantitative *** Totally,10 RCTs met our inclusion criteria for quantitative *** results indicated that urethrocutaneous fistula,glans dehiscence,and stricture rates were comparable between the two *** incidence of meatal stenosis was found to be significantly lower in the GTIP group with a relative risk(RR)of 0.32(95%confidence interval(Cl)0.15 to 0.67).Conclusion The coucomes UCF,glans dehiscence,and stricture rates were comparable between the two ***,the incidence of meatal stenosis was found to be significantly lower in the grafted TIP *** terms of operative time,our quantitative synthesis demonstrated that the TIP group had a shorter operative time than the GTIP group with significant heterogeneity.

关键词： plate grafted analysis

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Intraocular lens selection in diabetic patients:How to increase the odds for success

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World Journal of Diabetes 2024年第6期15卷 1199-1211页

作者： Arvind kumar Morya Prateek Nishant Prasanna Venkatesh Ramesh Sony sinha Aarti Heda Sarika Salodia Ripunjay Prasad Department of Ophthalmology All India Institute of Medical SciencesHyderabad 508126TelanganaIndia Department of Ophthalmology ESIC Medical CollegePatna 801113BiharIndia Department of Glaucoma and Research Mahathma Eye Hospital Private LimitedTrichy 620017Tamil NaduIndia Department of Ophthalmology-Vitreo-Retina Neuro-Ophthalmology and OculoplastyAll India Institute of Medical SciencesPatnaPatna 801507BiharIndia Department of Ophthalmology National Institute of OphthalmologyPune 411000MaharashtraIndia Department of Safety Global Medical SafetyLundbeckSingapore 307591Singapore Department of Ophthalmology RP Eye InstituteDelhi 110001India

The incidence of cataracts is significantly higher in diabetic individuals,particularly in younger age groups,with rates quadrupled in those under 65 and doubled in those over 65 compared to *** surgery in diabetic patients poses many challenges:Poor epithelial healing,decreased corneal sensitivity,increased central corneal thickness,decreased endothelial cell count,variable topography,poor pupillary dilatation,anterior capsular phimosis,posterior capsular opacification(PCO),chances of progression of diabetic retinopathy(DR),zonular weakness,and vitreous prolapse and diabetic macular *** of an appropriate intraocular lens(IOL)is crucial for visual rehabilitation and monitoring *** choice of IOL in diabetic cataract patients is a challenging ***-edge IOLs are favored for their capacity to mitigate PCO,whereas hydrophilic counterparts may incur calcification in the setting of proliferative *** advisability of premium IOLs for achieving spectacle independence warrants judicious evaluation,particularly in the presence of advanced *** IOL placement within the capsular bag is advocated to minimize postoperative *** preoperative assessment and informed patient counseling regarding IOL options are indispensable for optimizing surgical *** review article covers various aspects regarding the choice of IOLs in different case scenarios and complications in the diabetic population.

关键词： Diabetics Cataract Intraocular lens Diabetic retinopathy Diabetes mellitus

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Ophthalmic complications of injectable facial fillers

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World Journal of Clinical Cases 2024年第34期12卷 6736-6739页

作者： Prateek Nishant Arvind kumar Morya Sony sinha Ranjeet kumar sinha Department of Ophthalmology ESIC Medical CollegePatna 801103BiharIndia Department of Ophthalmology All India Institute of Medical SciencesHyderabad 508126TelanganaIndia Department of Ophthalmology-Vitreo-Retina Neuro-Ophthalmology and OculoplastyAll India Institute of Medical SciencesPatna 801507BiharIndia Department of Community Medicine Patna Medical CollegePatna 800004BiharIndia

The recently published mini-review article by Miotti et al is an effort to clarify various aspects regarding the choice between fat grafts and fillers in facial aesthetic *** of the complications associated with the administration of fillers is the possibility of vascular injury and spread of the dermal filler into the orbit,causing unexpected effects at a site distant from that of the initial injection,including ophthalmoplegia,ptosis and even visual *** vision loss following filler injection is a devastating complication,occurring in up to 0.0008%of *** greatest risk of this complication occurs with nasal augmentation,followed by glabellar wrinkle *** injected autologous fat predominantly occludes the proximal portion of the ophthalmic artery,hyaluronic acid fillers obstruct the ophthalmic artery comparatively *** interventions include thrombolysis,hyperbaric oxygen therapy,oral aspirin,cobamamide and acetazolamide and administration of ***,most studies show a poor prognosis in the form of partial or no recovery of ***,prevention is of paramount importance.A high index of suspicion is also warranted on the part of both those administering as well as receiving injections of facial fillers to prevent potentially vision-threatening complications of this seemingly innocuous procedure.

关键词： Adverse effects Blindness Cosmetic techniques Dermal drug administration Hyaluronic acid Iatrogenic disease

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Intensive care unit-acquired weakness and mechanical ventilation:A reciprocal relationship

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World Journal of Clinical Cases 2024年第18期12卷 3644-3647页

作者： Ranjeet kumar sinha Sony sinha Prateek Nishant Arvind kumar Morya Department of Community Medicine Patna Medical CollegeBiharPatna 800004India Department of Ophthalmology-Vitreo-Retina Neuro-Ophthalmology and OculoplastyAll India Institute of Medical SciencesBiharPatna 801507India Department of Ophthalmology ESIC Medical CollegeBiharPatna 801113India Department of Ophthalmology All India Institute of Medical SciencesTelanganaHyderabad 508126India

Intensive care unit-acquired weakness(ICU-AW;ICD-10 Code:G72.81)is a syndrome of generalized weakness described as clinically detectable weakness in critically ill patients with no other credible *** risk factors for ICU-AW include hyperglycemia,parenteral nutrition,vasoactive drugs,neuromuscular blocking agents,corticosteroids,sedatives,some antibiotics,immobilization,the disease severity,septicemia and systemic inflammatory response syndrome,multiorgan failure,prolonged mechanical ventilation(MV),high lactate levels,older age,female sex,and pre-existing systemic *** is a definite association between the duration of ICU stay and MV with ***,the interpretation that these are modifiable risk factors influencing ICU-AW,appears to be flawed,because the relationship between longer ICU stays and MV with ICU-AW is reciprocal and cannot yield clinically meaningful strategies for the prevention of *** strategies must be based on other risk *** multicentric randomized controlled trials as well as meta-analysis of such studies can be a more useful approach towards determining the influence of these risk factors on the occurrence of ICU-AW in different populations.

关键词： Critical illness Meta-analysis Morbidity Myopathy Polyneuropathy Risk factors

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