Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data

The investigation of the interconnections between the molecular and genetic events that govern biological systems is essential if we are to understand the development of disease and design effective novel treatments. Microarray and next-generation sequencing technologies have the potential to provide this information. However, taking full advantage of these approaches requires that biological connections be made across large quantities of highly heterogeneous genomic datasets. Leveraging the increasingly huge quantities of genomic data in the public domain is fast becoming one of the key challenges in the research community today.We have developed a novel data mining framework that enables researchers to use this growing collection of public high-throughput data to investigate any set of genes or proteins. The connectivity between molecular states across thousands of heterogeneous datasets from microarrays and other genomic platforms is determined through a combination of rank-based enrichment statistics, meta-analyses, and biomedical ontologies. We address data quality concerns through dataset replication and meta-analysis and ensure that the majority of the findings are derived using multiple lines of evidence. As an example of our strategy and the utility of this framework, we apply our data mining approach to explore the biology of brown fat within the context of the thousands of publicly available gene expression datasets.Our work presents a practical strategy for organizing, mining, and correlating global collections of large-scale genomic data to explore normal and disease biology. Using a hypothesis-free approach, we demonstrate how a data-driven analysis across very large collections of genomic data can reveal novel discoveries and evidence to support existing hypothesis

” There is a difference, because gender” En kvalitativ studie om hur kön görs på ett barnhem i Moshi, Tanzania

Syfte: Syftet med vår undersökning är att studera hur man konstruerar kön på ett barnhem i Moshi, Tanzania utifrån att titta på aktiviteter och platser. Vi vill titta på hur barnen och personalen talar om och gestaltar kön på barnhemmet. Frågeställningar: 1. Finns det könade, respektive könsneutrala aktiviteter för barnen på barnhemmet och hur ser i så fall dessa ut (det vill säga hur gestaltas kön i relation till aktiviteter)? 2. Finns det platser som är könade respektive könsneutrala för barnen på barnhemmet och hur ser i så fall dessa ut (det vill säga hur gestaltas kön i relation till platser)? 3. Hur talar barnen om och hur iscensätter de kön, samt hur talar personalen på barnhemmet kring barnens sätt att vara flicka respektive pojke? Metod: Materialet till denna kvalitativa studie har inhämtats med hjälp av strukturerade intervjuer och direktobservationer för att skapa en bild av hur man på detta specifika barnhem gör kön. Vi har en socialkonstruktionistiskt utgångspunkt där vi ser på kön som en social konstruktion. Resultat: Det vi fann mest framträdande i resultaten från denna studie var att flickor och pojkar separerades i könsspecifikagrupper när det kom till viktiga frågor och att detta var ett sätt att göra kön på barnhemmet. De fick i en tidig ålder lära sig om vilka beteenden, aktiviteter och platser som var lämpliga för en flicka respektive pojke. Ett sätt att köna aktivt var att begränsa samt utöka möjligheterna för barnen att delta i viss aktivitet och vistas på en viss plats. Vi såg att barnen tidigt skolades in i det rätta sättet att förhålla sig till dessa aktiviteter och platser, utifrån sitt kön

Understanding the structure and function of GDSL-type esterase/lipase genes in pigeon pea for their role under moisture stress conditions

The SGNH hydrolase superfamily's GDSL-type esterase/lipase proteins (GELPs) play a crucial role in plant growth and stress tolerance. However, limited knowledge exists regarding the molecular role of GELP genes under drought conditions, especially in pigeon pea. In this study, 112 GDSL genes were found, distributed over the 11 pigeon pea chromosomes, and classified into 5 clades based on the phylogenetic analysis. The pigeon pea GDSL gene family seems to have grown significantly as a result of tandem duplications (48 %). Five exons and four introns represent the coding areas of more than 71.4 % of the CcGDSL genes, according to our analysis. According to the cis-elements study, CcGDSL gene expression was observed to be mostly influenced by fluctuating stressful situations and also by light and plant hormones. We could narrow down to 14 stress-responsive CcGDSL genes in order to assess their expression levels under seedling-stage drought stress conditions. Our data indicates that among these 112 genes, CcGDSL21, CcGDSL63, CcGDSL64 and CcGDSL92 could be involved in regulating the primary response under drought stress. This preliminary study will add to our understanding of GDSL genes in pigeon pea and help in elucidating their role in drought tolerance in pigeon pea

Association of postoperative nausea/vomiting and pain with breastfeeding success

Abstract Background Successful breastfeeding is a goal set forth by the World Health Organization to improve neonatal care. Increasingly, patients express the desire to breastfeed, and clinicians should facilitate successful breastfeeding. The primary aim of this study is to determine if postoperative nausea and vomiting (PONV) or postoperative pain are associated with decreased breastfeeding success after cesarean delivery. Methods This is a historical cohort study using the Stony Brook Elective Cesarean Delivery Database. Self-reported breastfeeding success at 4 weeks postoperative was analyzed for associations with postoperative antiemetic use and postoperative pain scores. Breastfeeding success was also analyzed for associations with patient factors and anesthetic medications. Results Overall, 86% of patients (n = 81) who intended on breastfeeding reported breastfeeding success. Breastfeeding success was not associated with postoperative nausea or vomiting as measured by post anesthesia care unit antiemetic use (15% use in successful vs. 18% use in unsuccessful, p = 0.67) or 48-h antiemetic use (28% use in successful group vs 36% use in unsuccessful group, p = 0.732). Pain visual analog scale scores at 6, 12 and 24 h postoperatively were not significantly different between patients with or without breastfeeding success. Breastfeeding success was associated with having had at least 1 previous child (86% vs 36%, p < 0.001). Patients with asthma were less likely to have breastfeeding success (45% vs 4%, p = 0.002). Conclusions Efforts to improve PONV and pain after cesarean delivery may not be effective in improving breastfeeding success. To possibly improve breastfeeding rates, resources should be directed toward patients with no previous children and patients with asthma

Multisystem inflammatory syndrome in children and Kawasaki disease: a critical comparison

International audienceChildren and adolescents infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are predominantly asymptomatic or have mild symptoms compared with the more severe coronavirus disease 2019 (COVID-19) described in adults. However, SARS-CoV-2 is also associated with a widely reported but poorly understood paediatric systemic vasculitis. This multisystem inflammatory syndrome in children (MIS-C) has features that overlap with myocarditis, toxic-shock syndrome and Kawasaki disease. Current evidence indicates that MIS-C is the result of an exaggerated innate and adaptive immune response, characterized by a cytokine storm, and that it is triggered by prior SARS-CoV-2 exposure. Epidemiological, clinical and immunological differences classify MIS-C as being distinct from Kawasaki disease. Differences include the age range, and the geographical and ethnic distribution of patients. MIS-C is associated with prominent gastrointestinal and cardiovascular system involvement, admission to intensive care unit, neutrophilia, lymphopenia, high levels of IFNγ and low counts of naive CD4+ T cells, with a high proportion of activated memory T cells. Further investigation of MIS-C will continue to enhance our understanding of similar conditions associated with a cytokine storm

Longitudinal microbiome analysis of single donor fecal microbiota transplantation in patients with recurrent Clostridium difficile infection and/or ulcerative colitis.

Studies of colonoscopic fecal microbiota transplant (FMT) in patients with recurrent CDI, indicate that this is a very effective treatment for preventing further relapses. In order to provide this service at Stony Brook University Hospital, we initiated an open-label prospective study of single colonoscopic FMT among patients with ≥ 2 recurrences of CDI, with the intention of monitoring microbial composition in the recipient before and after FMT, as compared with their respective donor. We also initiated a concurrent open label prospective trial of single colonoscopic FMT of patients with ulcerative colitis (UC) not responsive to therapy, after obtaining an IND permit (IND 15642). To characterize how FMT alters the fecal microbiota in patients with recurrent Clostridia difficile infections (CDI) and/or UC, we report the results of a pilot microbiome analysis of 11 recipients with a history of 2 or more recurrences of C. difficile infections without inflammatory bowel disease (CDI-only), 3 UC recipients with recurrent C. difficile infections (CDI + UC), and 5 UC recipients without a history of C. difficile infections (UC-only).V3V4 Illumina 16S ribosomal RNA (rRNA) gene sequencing was performed on the pre-FMT, 1-week post-FMT, and 3-months post-FMT recipient fecal samples along with those collected from the healthy donors. Fitted linear mixed models were used to examine the effects of Group (CDI-only, CDI + UC, UC-only), timing of FMT (Donor, pre-FMT, 1-week post-FMT, 3-months post-FMT) and first order Group*FMT interactions on the diversity and composition of fecal microbiota. Pairwise comparisons were then carried out on the recipient vs. donor and between the pre-FMT, 1-week post-FMT, and 3-months post-FMT recipient samples within each group.Significant effects of FMT on overall microbiota composition (e.g., beta diversity) were observed for the CDI-only and CDI + UC groups. Marked decreases in the relative abundances of the strictly anaerobic Bacteroidetes phylum, and two Firmicutes sub-phyla associated with butyrate production (Ruminococcaceae and Lachnospiraceae) were observed between the CDI-only and CDI + UC recipient groups. There were corresponding increases in the microaerophilic Proteobacteria phylum and the Firmicutes/Bacilli group in the CDI-only and CDI + UC recipient groups. At a more granular level, significant effects of FMT were observed for 81 genus-level operational taxonomic units (OTUs) in at least one of the three recipient groups (p<0.00016 with Bonferroni correction). Pairwise comparisons of the estimated pre-FMT recipient/donor relative abundance ratios identified 6 Gammaproteobacteria OTUs, including the Escherichia-Shigella genus, and 2 Fusobacteria OTUs with significantly increased relative abundance in the pre-FMT samples of all three recipient groups (FDR < 0.05), however the magnitude of the fold change was much larger in the CDI-only and CDI + UC recipients than in the UC-only recipients. Depletion of butyrate producing OTUs, such as Faecalibacterium, in the CDI-only and CDI + UC recipients, were restored after FMT.The results from this pilot study suggest that the microbial imbalances in the CDI + UC recipients more closely resemble those of the CDI-only recipients than the UC-only recipients