Upper gastrointestinal endoscopy findings in patient presenting with dyspepsia

ntroductions: The objective of this study was to evaluate the upper gastrointestinal endoscopy findings in patients presenting with dyspepsia. Methods: This retrospective observational study was conducted in Department of internal medicine, Patan Hospital from April 2013 to March 2014. Adult patients who underwent upper gastrointestinal endoscopy for dyspepsia were included in the study. Results: There were 2141 endoscopies (out of total 3195) performed for dyspepsia, male 996 (46.52 %), female 1145 (53.48%), mean age 39.37 years (SD ±18.16). A single endoscopic diagnosis was made in 1991 (93%) and in rest combinations of lesions were seen. Gastritis 892 (41.66%), Oesophagitis 215 (10.04%), Duodenal Ulcer 100 (4.67%), Gastro-duodenitis 85 (3.97%), Hiatus hernia 82 (3.82%), Gastric Ulcer 46 (2.14%) and no lesions in 594 (27.74%) were seen. Conclusion: Gastritis followed by oesophagitis was seen half of the dyspeptic, while a quarter had functional dyspepsia with normal findings. Keywords: duodenal ulcer, gastritis, gastric ulcer, hiatus hernia, oesophagitis, upper gastrointestinal (UGI) endoscopyÂ

Implications of TGFβ on Transcriptome and Cellular Biofunctions of Palatal Mesenchyme

Development of the palate comprises sequential stages of growth, elevation, and fusion of the palatal shelves. The mesenchymal component of palates plays a major role in early phases of palatogenesis, such as growth and elevation. Failure in these steps may result in cleft palate, the second most common birth defect in the world. These early stages of palatogenesis require precise and chronological orchestration of key physiological processes, such as growth, proliferation, differentiation, migration, and apoptosis. There is compelling evidence for the vital role of TGFβ-mediated regulation of palate development. We hypothesized that the isoforms of TGFβ regulate different cellular biofunctions of the palatal mesenchyme to various extents. Human embryonic palatal mesenchyme (HEPM) cells were treated with TGFβ1, β2, and β3 for microarray-based gene expression studies in order to identify the roles of TGFβ in the transcriptome of the palatal mesenchyme. Following normalization and modeling of 28,869 human genes, 566 transcripts were detected as differentially expressed in TGFβ-treated HEPM cells. Out of these altered transcripts, 234 of them were clustered in cellular biofunctions, including growth and proliferation, development, morphology, movement, cell cycle, and apoptosis. Biological interpretation and network analysis of the genes active in cellular biofunctions were performed using IPA. Among the differentially expressed genes, 11 of them are known to be crucial for palatogenesis (EDN1, INHBA, LHX8, PDGFC, PIGA, RUNX1, SNAI1, SMAD3, TGFβ1, TGFβ2, and TGFβR1). These genes were used for a merged interaction network with cellular behaviors. Overall, we have determined that more than 2% of human transcripts were differentially expressed in response to TGFβ treatment in HEPM cells. Our results suggest that both TGFβ1 and TGFβ2 orchestrate major cellular biofunctions within the palatal mesenchyme in vitro by regulating expression of 234 genes

FGDB: Database of Follicle Stimulating Hormone Glycans

Glycomics, the study of the entire complement of sugars of an organism has received significant attention in the recent past due to the advances made in high throughput mass spectrometry technologies. These analytical advancements have facilitated the characterization of glycans associated with the follicle-stimulating hormones (FSH), which play a central role in the human reproductive system both in males and females utilizing regulating gonadal (testicular and ovarian) functions. The irregularities in FSH activity are also directly linked with osteoporosis. The glycoanalytical studies have been tremendously helpful in understanding the biological roles of FSH. Subsequently, the increasing number of characterized FSH glycan structures and related glycoform data has thrown a challenge to the glycoinformatics community in terms of data organization, storage and access. Also, a user-friendly platform is needed for providing easy access to the database and performing integrated analysis using a high volume of experimental data to accelerate FSH-focused research. FSH Glycans DataBase (FGDB) serves as a comprehensive and unique repository of structures, features, and related information of glycans associated with FSH. Apart from providing multiple search options, the database also facilitates an integrated user-friendly interface to perform the glycan abundance and comparative analyses using experimental data. The automated integrated pipelines present the possible structures of glycans and variants of FSH based on the input data, and allow the user to perform various analyses. The potential application of FGDB will significantly help both glycoinformaticians as well as wet-lab researchers to stimulate the research in this area. FGDB web access: https://fgdb.unmc.edu/

Prevalence of long covid-19 syndrome among health care workers of Patan Academy of Health Sciences

Introduction: Any symptoms acquired after COVID-19 infection that persists beyond 12 weeks period and not explained by any other disease either already present or acquired after COVID-19 infection is termed as long COVID 19 by World Health Organisation. We tried to find out the prevalence of long COVID 19 in healthcare workers. Method: Questionnaire was made in google form based on COVID-19 Yorkshire Rehabilitation Screening Tool (COVID YRS Tool). Ethical approval was taken from IRC-PAHS. Data collected from all health care workers of PAHS from 2022/05/20 to 2022/07/20. Difference in Precovid and Postcovid status in different domains were compared by statistical tests. Result: The median age of our participants was 29 years. Prevalence of Long COVID 19 was 68.1%. 19 55.3% ha mild, 10.4% had moderate, 2.4% had severe symptoms. The most common symptom was fatigue (44%), anxiety (41%) and shortness of breath (36%). The COVID YRS Tool overall score was statically significant with p value <0.001. Pre COVID 19 and Post COVID 19, patients had statically significant in breathlessness, fatigue, nutrition, anxiety, usual activity, pain, anxiety and depression. Only 6% of our patients had severe COVID 19.   Conclusion: People are still experiencing various symptoms after COVID 19 infection. Long COVID 19 has now been a health care problem.  Long COVID 19 patients have multisystem involvement and multi speciality team is needed for their management and rehabilitation

Histopathological findings of renal biopsy in systemic lupus erythematousus

Introductions: Classifying morphological pattern of renal involvement is important in systemic lupus erythematosus (SLE) for definitive treatment and prognosis. This study aim to analyse the histopathological pattern of glomerular in SLE patients.Methods: This was a retrospective chart review of patients diagnosed with SLE who had renal biopsy during October 2013 to September 2015 at Patan Hospital.Results: There were 38 patients of SLE.  Antinuclear antibody (ANA) was positive in all patients 38 (100 %), Anti-dsDNA seen in 18 (47.4%). Active urinary sediment & proteinuria was seen 25 (65.8%) patients and proteinuria in 13 (34.2%) patients. Histopathological patterns were of glomerular involvement was, ISN Class II in 2 (5.3%), Class III in 2 (5.3%), class IV 20 (52.5%), class V in 6 (15.8%) and mixed IV –V in 8 (21.1%).Conclusions: The diffuse proliferative lupus nephritis (ISN Class IV) was the most com­mon pattern of lupus nephritis encountered in our study followed by mixed pattern (ISN class IV&V) and membranous lupus nephritis (ISN class IV). Keywords: histopathology, lupus nephritis, renal biopsy, systemic lupus erythematosu

Kidney biopsy in glomerular disease: a hospital based study

Introductions: Kidney biopsy is the standard tool to diagnose glomerular disease (GD). There is lack of national registry of kidney biopsy for the type, incidence and prevalence of GD. We aim to review kidney biopsy at Patan Hospital for profile of GD in local scenario. Methods: This was a chart review of patients who underwent kidney biopsy at Patan Hospital, Nepal, from October 2013 to September 2015. We analyzed the data for indication of kidney biopsy, types of GD and complication of biopsy. Results: There were 117 patients who had kidney biopsies. Immunoglobulin A Nephropathy was seen in 42 (35.8%) and Lupus Nephritis in 38 (32.5%). Sub nephrotic range proteinuria with or without active urinary sediments was found in 75 (64%). Blood transfusion was required in 3 (2.5%) patients after biopsy. There was no surgical intervention or mortality related to biopsy. Conclusions: IgA Nephropathy was the commonest glomerular disease. Kidney biopsy was a safe and effective procedure. Keywords: glomerular disease, kidney biopsy, nephropath

Pacti: Scaling Assume-Guarantee Reasoning for System Analysis and Design

Contract-based design is a method to facilitate modular system design. While there has been substantial progress on the theory of contracts, there has been less progress on scalable algorithms for the algebraic operations in this theory. In this paper, we present: 1) principles to implement a contract-based design tool at scale and 2) Pacti, a tool that can efficiently compute these operations. We then illustrate the use of Pacti in a variety of case studies

Mammalian alteration/deficiency in activation 3 (Ada3) is essential for embryonic development and cell cycle progression.

Ada3 protein is an essential component of histone acetyl transferase containing coactivator complexes conserved from yeast to human. We show here that germline deletion of Ada3 in mouse is embryonic lethal, and adenovirus-Cre mediated conditional deletion of Ada3 in Ada3(FL/FL) mouse embryonic fibroblasts leads to a severe proliferation defect which was rescued by ectopic expression of human Ada3. A delay in G(1) to S phase of cell cycle was also seen that was due to accumulation of Cdk inhibitor p27 which was an indirect effect of c-myc gene transcription control by Ada3. We further showed that this defect could be partially reverted by knocking down p27. Additionally, drastic changes in global histone acetylation and changes in global gene expression were observed in microarray analyses upon loss of Ada3. Lastly, formation of abnormal nuclei, mitotic defects and delay in G(2)/M to G(1) transition was seen in Ada3 deleted cells. Taken together, we provide evidence for a critical role of Ada3 in embryogenesis and cell cycle progression as an essential component of HAT complex

Red Cabbage Juice-Mediated Gut Microbiota Modulation Improves Intestinal Epithelial Homeostasis and Ameliorates Colitis

Gut microbiota plays a crucial role in inflammatory bowel diseases (IBD) and can potentially prevent IBD through microbial-derived metabolites, making it a promising therapeutic avenue. Recent evidence suggests that despite an unclear underlying mechanism, red cabbage juice (RCJ) alleviates Dextran Sodium Sulfate (DSS)-induced colitis in mice. Thus, the study aims to unravel the molecular mechanism by which RCJ modulates the gut microbiota to alleviate DSS-induced colitis in mice. Using C57BL/6J mice, we evaluated RCJ’s protective role in DSS-induced colitis through two cycles of 3% DSS. Mice were daily gavaged with PBS or RCJ until the endpoint, and gut microbiota composition was analyzed via shotgun metagenomics. RCJ treatment significantly improved body weight (p ≤ 0.001), survival in mice (p \u3c 0.001) and reduced disease activity index (DAI) scores. Further, RCJ improved colonic barrier integrity by enhancing the expression of protective colonic mucins (p \u3c 0.001) and tight junction proteins (p ≤ 0.01) in RCJ + DSS-treated mice compared to the DSS group. Shotgun metagenomic analysis revealed an enrichment of short-chain fatty acids (SCFAs)-producing bacteria (p \u3c 0.05), leading to increased Peroxisome Proliferator-Activated Receptor Gamma (PPAR-ү ) activation (p ≤ 0.001). This, in turn, resulted in repression of the nuclear factor кB (NFкB) signaling pathway, causing decreased production of inflammatory cytokines and chemokines. Our study demonstrates colitis remission in a DSS-induced mouse model, showcasing RCJ as a potential modulator for gut microbiota and metabolites, with promising implications for IBD prevention and treatment

A New Rhesus Macaque Assembly and Annotation for Next-Generation Sequencing Analyses

BACKGROUND: The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another rhesus macaque assembly, CR_1.0, is also available but is substantially more fragmented than rheMac2 with smaller contigs and scaffolds. Annotations for these two assemblies are limited in completeness and accuracy. High quality assembly and annotation files are required for a wide range of studies including expression, genetic and evolutionary analyses. RESULTS: We report a new de novo assembly of the rhesus macaque genome (MacaM) that incorporates both the original Sanger sequences used to assemble rheMac2 and new Illumina sequences from the same animal. MacaM has a weighted average (N50) contig size of 64 kilobases, more than twice the size of the rheMac2 assembly and almost five times the size of the CR_1.0 assembly. The MacaM chromosome assembly incorporates information from previously unutilized mapping data and preliminary annotation of scaffolds. Independent assessment of the assemblies using Ion Torrent read alignments indicates that MacaM is more complete and accurate than rheMac2 and CR_1.0. We assembled messenger RNA sequences from several rhesus tissues into transcripts which allowed us to identify a total of 11,712 complete proteins representing 9,524 distinct genes. Using a combination of our assembled rhesus macaque transcripts and human transcripts, we annotated 18,757 transcripts and 16,050 genes with complete coding sequences in the MacaM assembly. Further, we demonstrate that the new annotations provide greatly improved accuracy as compared to the current annotations of rheMac2. Finally, we show that the MacaM genome provides an accurate resource for alignment of reads produced by RNA sequence expression studies. CONCLUSIONS: The MacaM assembly and annotation files provide a substantially more complete and accurate representation of the rhesus macaque genome than rheMac2 or CR_1.0 and will serve as an important resource for investigators conducting next-generation sequencing studies with nonhuman primates. REVIEWERS: This article was reviewed by Dr. Lutz Walter, Dr. Soojin Yi and Dr. Kateryna Makova