HARMONY: a server for the assessment of protein structures

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (φ,ψ) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located a

Does exposure of male Drosophila melanogaster to acute gamma radiation influence egg to adult development time and longevity of F1–F3 offspring?

Two- to three-day-old male Drosophila melanogaster flies were irradiated with 1, 2, 4, 6, 8, 10, 20, 25, 30, 40 and 50 Gy doses of gamma radiation. The longevity and rate of development were observed for three successive generations to assess the impact of irradiation. The mean lifespan of irradiated flies was significantly increased at 1, 2 and 8 Gy, while it was vice versa for high doses at 30, 40 and 50 Gy. Paternal irradiation had an impact on F1 generation, with significantly increased mean longevity at 2 (female), 4, 6, 8 and 10 and decreased mean longevity at 40 and 50 Gy (male and female). Significant increase in the longevity was observed in the F2 generation of the 8 (male and female) and 10 Gy (male) irradiated groups, while decreased longevity was observed in F2 female progeny at 40 Gy. In the case of F3 progeny of irradiated flies, longevity did not show significant difference with the control. Paternal exposure to radiation had a significant impact on the mean egg to adult developmental time of the F1 generation; it was shortened at 2 Gy and extended at 25, 30, 40 and 50 Gy compared to the control. Mean development time at 30, 40 and 50 Gy was significantly increased in the F2 generation, while there were no significant changes in the F3 generation. The present study concludes that the effect of acute gamma irradiation on longevity and “egg to adult” development time of D. melanogaster may persist to following generations

STIFDB—Arabidopsis Stress Responsive Transcription Factor DataBase

Elucidating the key players of molecular mechanism that mediate the complex stress-responses in plants system is an important step to develop improved variety of stress tolerant crops. Understanding the effects of different types of biotic and abiotic stress is a rapidly emerging domain in the area of plant research to develop better, stress tolerant plants. Information about the transcription factors, transcription factor binding sites, function annotation of proteins coded by genes expressed during abiotic stress (for example: drought, cold, salinity, excess light, abscisic acid, and oxidative stress) response will provide better understanding of this phenomenon. STIFDB is a database of abiotic stress responsive genes and their predicted abiotic transcription factor binding sites in Arabidopsis thaliana. We integrated 2269 genes upregulated in different stress related microarray experiments and surveyed their 1000 bp and 100 bp upstream regions and 5′UTR regions using the STIF algorithm and identified putative abiotic stress responsive transcription factor binding sites, which are compiled in the STIFDB database. STIFDB provides extensive information about various stress responsive genes and stress inducible transcription factors of Arabidopsis thaliana. STIFDB will be a useful resource for researchers to understand the abiotic stress regulome and transcriptome of this important model plant system

Adult hypertrophic pyloric stenosis due to peptic ulcer disease: a rare presentation

Primary adult hypertrophic stenosis is uncommon with an uncertain etiopathogenesis and associated gastric outlet obstruction mimics gastric carcinoma. We present a case of AHPS as sequel of peptic ulcer disease in a 72 year old male. With the advent of proton pump inhibitors as a mainstay of medical therapy, complication into gastric outlet obstruction is a rare disease today. Upper GI endoscopy revealed a distended stomach, residual food and a hyperemic bulky pylorus not accommodating the endoscope. Barium meal follow-through revealed a dilated stomach and minimal barium passing through the pylorus. Histological analysis revealed mild dysplasia at the focus with dense inflammatory infiltrates composed of lymphocytes and eosinophils in the lamina propria. No evidence of malignancy was noted, favouring chronic gastritis. The condition mimics other forms of proliferative disorders like carcinoma, gastrointestinal stromal tumors. We present the clinical findings, imaging analysis and discuss etiopathogenesis and management

Generation of a Compendium of Transcription Factor Cascades and Identification of Potential Therapeutic Targets using Graph Machine Learning

Transcription factors (TFs) play a vital role in the regulation of gene expression thereby making them critical to many cellular processes. In this study, we used graph machine learning methods to create a compendium of TF cascades using data extracted from the STRING database. A TF cascade is a sequence of TFs that regulate each other, forming a directed path in the TF network. We constructed a knowledge graph of 81,488 unique TF cascades, with the longest cascade consisting of 62 TFs. Our results highlight the complex and intricate nature of TF interactions, where multiple TFs work together to regulate gene expression. We also identified 10 TFs with the highest regulatory influence based on centrality measurements, providing valuable information for researchers interested in studying specific TFs. Furthermore, our pathway enrichment analysis revealed significant enrichment of various pathways and functional categories, including those involved in cancer and other diseases, as well as those involved in development, differentiation, and cell signaling. The enriched pathways identified in this study may have potential as targets for therapeutic intervention in diseases associated with dysregulation of transcription factors. We have released the dataset, knowledge graph, and graphML methods for the TF cascades, and created a website to display the results, which can be accessed by researchers interested in using this dataset. Our study provides a valuable resource for understanding the complex network of interactions between TFs and their regulatory roles in cellular processes

DESIGN OF AIR CONDITIONING SYSTEM IN AUTOMOBILE

Abstract: Transportation is one the need of human being, which is existing since the evolution of mankind. Today, the field of air conditioning design is more technologically challenging than ever before. In the present the design of air conditioning is done for a Volvo bus, a fully equipped automotive air-conditioning system consists of five main components: a compressor, a condenser, an orifice tube, an evaporator and an accumulator. R-134a is used as refrigerant by considering the various parameters

BioStar: An Online Question & Answer Resource for the Bioinformatics Community

Parnell, Laurence D. et al.Although the era of big data has produced many bioinformatics tools and databases, using them effectively often requires specialized knowledge. Many groups lack bioinformatics expertise, and frequently find that software documentation is inadequate while local colleagues may be overburdened or unfamiliar with specific applications. Too often, such problems create data analysis bottlenecks that hinder the progress of biological research. In order to help address this deficiency, we present BioStar, a forum based on the Stack Exchange platform where experts and those seeking solutions to problems of computational biology exchange ideas. The main strengths of BioStar are its large and active group of knowledgeable users, rapid response times, clear organization of questions and responses that limit discussion to the topic at hand, and ranking of questions and answers that help identify their usefulness. These rankings, based on community votes, also contribute to a reputation score for each user, which serves to keep expert contributors engaged. The BioStar community has helped to answer over 2,300 questions from over 1,400 users (as of June 10, 2011), and has played a critical role in enabling and expediting many research projects. BioStar can be accessed at http://www.biostars.org/.This work was partially supported by NSF grants MCB-0618402 and CCF-0643529 (CAREER), NIH grants 1R55AI065507 – 01A2 and 1 R01 GM083113-01, NIH/NCRR grant number UL1RR033184, and FPI fellowship SAF-2007-63171/BES-2009-017731 from the Ministerio de Educación y Ciencia, Spain. These funders had no role in the design of BioStar, decision to publish, or preparation of the manuscript.Peer reviewe

Correction to: Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits

Erratum for Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits. [BMC Med Genomics. 2019

Original article title: "Comparison of therapeutic efficacy of topical corticosteroid and oral zinc sulfate-topical corticosteroid combination in the treatment of vitiligo patients: a clinical trial"

<p>Abstract</p> <p>Background</p> <p>Vitiligo is the most prevalent pigmentary disorder which occurs worldwide, with an incidence rate between 0.1-4 percent. It is anticipated that the discovery of biological pathways of vitiligo pathogenesis will provide novel therapeutic and prophylactic targets for future approaches to the treatment and prevention of vitiligo. The purposes of this study were evaluating the efficacy of supplemental zinc on the treatment of vitiligo.</p> <p>Methods</p> <p>This randomized clinical trial was conducted for a period of one year. Thirty five patients among 86 participants were eligible to entrance to the study. The patients in two equal randomized groups took topical corticosteroid and combination of oral zinc sulfate-topical corticosteroid.</p> <p>Results</p> <p>The mean of responses in the corticosteroid group and the zinc sulfate-corticosteroid combination group were 21.43% and 24.7%, respectively.</p> <p>Conclusion</p> <p>Although, the response to corticosteroid plus zinc sulfate was more than corticosteroid, there was no statistically significant difference between them. It appeared that more robust long-term randomized controlled trials on more patients, maybe with higher doses of zinc sulfate, are needed to fully establish the efficacy of oral zinc in management of vitiligo.</p> <p>Trial Registration</p> <p>chiCTRTRC10000930</p