Zebrafish information network,the knowledgebase for Danio rerio research

The Zebrafish Information Network (zfin.org) is the central repository for Danio rerio genetic and genomic data. The Zebrafish Information Network has served the zebrafish research community since 1994, expertly curating, integrating, and displaying zebrafish data. Key data types available at the Zebrafish Information Network include, but are not limited to, genes, alleles, human disease models, gene expression, phenotype, and gene function. The Zebrafish Information Network makes zebrafish research data Findable, Accessible, Interoperable, and Reusable through nomenclature, curatorial and annotation activities, web interfaces, and data downloads. Recently, the Zebrafish Information Network and 6 other model organism knowledgebases have collaborated to form the Alliance of Genome Resources, aiming to develop sustainable genome information resources that enable the use of model organisms to understand the genetic and genomic basis of human biology and disease. Here, we provide an overview of the data available at the Zebrafish Information Network including recent updates to the gene page to provide access to single-cell RNA sequencing data, links to Alliance web pages, ribbon diagrams to summarize the biological systems and Gene Ontology terms that have annotations, and data integration with the Alliance of Genome Resources.     

A Large Number of Reviews on Physician Rating Websites May Reflect Reputation Management

BackgroundPhysicians with a large number of reviews and a high rating may be employing reputation management strategies. Specialists may be more likely than non-specialists to employ such strategies. This should be apparent in a study of online physician reviews on physician rating websites (PRW).MethodsUsing one physician rating website, we gathered orthopedic surgeon and family physician reviews. We measured Spearman correlations between the number of reviews and average numerical rating and used chi-squared to test threshold relationships.ResultsThere were very small negative Spear-man correlations between the number of online reviews and the average numerical rating for orthopedic surgeons (p= -0.097, p-value=<0.001) family medicine physicians (p= -0.170, p-value=<0.001; Figure 2). Physicians with more than 100 reviews had a greater average numerical rating than physicians with fewer than 50 reviews. Orthopedic surgeons are more likely than family medicine physicians to have a large number of reviews and average numerical rating greater than 3.Open in a separate windowFigure 2.Family medicine physicians average rating plotted against number of reviews.ConclusionThe small fraction of physician with a high number of reviews may be utilizing reputation management strategies, and this seems relatively specific to specialists rather than non-specialists. Level of Evidence: III     

Chemotherapeutic potential of Cayratia trifolia L nhexane extract on A2780 cells

It is of interest to report the chemotherapeutic (drug target based) potential of n-hexane Cayratia trifolia L. (C.trifolia) extract on A2780 cell lines. mRNA and protein expression analysis of the human chemokine receptor (CXCR4) and human epidermal growth factor receptors-2 (HER2) were studied using RT-PCR analysis and western blot analysis. The results show significant cell growth inhibition with minimal IC50 values of 46.25 ± 0.42 micro g/mL against A2780 cell lines. mRNA and protein expression were considerably reduced in C. trifoliatreated A2780 cell lines for further consideration as a chemotherapeutic agents.     

Ionic polymeric amphiphiles with cholesterol mesogen: adsorption and organization characteristics at the air/water interface from Langmuir film balance studies

Ionic polymeric amphiphiles consisting of cholesterol mesogen were investigated for the interfacial adsorption characteristics at the air/water interface using a Langmuir film balance with an aim to understand the influence of ionic segment from 2-acrylamido-2-methyl-1-propane sulfonic acid (AMPS) on the packing behavior of cholesterol at the interface. From surface pressure (pi)-area (A) isotherm characteristics, it is demonstrated that the homopolymer and the copolymer C consisting of 0.15 mol fraction CAB segments exhibit the most expanded structures contributing to surface area of about 84 A(2)/molecule. It is shown that the copolymer B with 0.1 mol fraction CAB provides optimum hydrophilic liphophilic balance to form the most compact structures contributing to a surface area of 35.75 A(2)/molecule. The high surface pressure, >40 mN/m, in contrast to that of PAMPS demonstrates significant adsorption of the copolymers at the interface. An interesting correlation among interfacial packing characteristics, thermal behavior, and solution structures is demonstrated. From molecular models developed for CAB, it is shown that the horizontal orientation of the linker group with respect to cholesterol chain in CAB underlies the expanded structures observed in PCAB and copolymer C.     

BMI vs. waist circumference for identifying vascular risk

Objective: Current guidelines recommend measurement of both BMI and waist circumference (WC) in individuals with BMI between 25.0 and 34.9 kg/m². We investigated the relative contributions of BMI and WC toward identifying risk of adverse vascular events in a community‐based sample. Methods and Procedures: We evaluated Framingham Study participants (n = 4,195 person‐examinations, 53% women) using pooled logistic regression to assess the incremental prognostic utility of WC in predicting risk of a first cardiovascular disease (CVD) event in the three BMI categories (normal, <25 kg/m²; overweight, 25 to <30 kg/m²; obese, ≥ 30 kg/m²) and to assess the incremental prognostic utility of BMI and WC separately for predicting risk of a first cardiovascular event. Results: On follow‐up (16 years), 430 participants (158 women) had experienced a first CVD event. In overweight women, but not in overweight men, larger WC was found to be an independent predictor of CVD incidence, longitudinally (in women, multivariable‐adjusted odds ratio (OR) per s.d. increment in WC 1.86, 95% confidence interval (CI) = 1.03–3.36, P = 0.04; in men adjusted OR per s.d. increment in WC 0.91, 95% CI 0.60–1.38, P = 0.66). In obese individuals and in those with normal BMI, WC was not associated independently with incident CVD. When BMI and WC were analyzed separately for predicting risk of a first cardiovascular event, the c statistics associated with the multivariable CVD models incorporating BMI vs. WC were nearly identical in men and women. Discussion: Knowledge of WC aids identification of vascular risk among overweight women. Among normal weight or obese women and men (regardless of BMI category) WC did not appear to substantially add to prediction of risk of vascular events.     

Isolation and characterization of the prokaryotic proteasome homolog HslVU (ClpQY) from Thermotoga maritima and the crystal structure of HslV

Heat-shock locus VU (HslVU) is an ATP-dependent proteolytic system and a prokaryotic homolog of the proteasome. It consists of HslV, the protease, and HslU, the ATPase and chaperone. We have cloned, sequenced and expressed both protein components from the hyperthermophile Thermotoga maritima. T. maritima HslU hydrolyzes a variety of nucleotides in a temperature-dependent manner, with the optimum lying between 75 and 80 °C. It is also nucleotide-unspecific for activation of HslV against amidolytic and caseinolytic activity. The Escherichia coli and T. maritima HslU proteins mutually stimulate HslV proteins from both sources, suggesting a conserved activation mechanism. The crystal structure of T. maritima HslV was determined and refined to 2.1-Å resolution. The structure of the dodecameric enzyme is well conserved compared to those from E. coli and Haemophilus influenzae. A comparison of known HslV structures confirms the presence of a cation-binding site, although its exact role in the proteolytic mechanism of HslV remains unclear. Amongst factors responsible for the thermostability of T. maritima HslV, extensive ionic interactions/salt-bridge networks, which occur specifically in the T. maritima enzyme in comparison to its mesophilic counterparts, seem to play an important role.     

Multi-scale inference of genetic trait architecture using biologically annotated neural networks

In this article, we present Biologically Annotated Neural Networks (BANNs), a nonlinear probabilistic framework for association mapping in genome-wide association (GWA) studies. BANNs are feedforward models with partially connected architectures that are based on biological annotations. This setup yields a fully interpretable neural network where the input layer encodes SNP-level effects, and the hidden layer models the aggregated effects among SNP-sets. We treat the weights and connections of the network as random variables with prior distributions that reflect how genetic effects manifest at different genomic scales. The BANNs software uses variational inference to provide posterior summaries which allow researchers to simultaneously perform (i) mapping with SNPs and (ii) enrichment analyses with SNP-sets on complex traits. Through simulations, we show that our method improves upon state-of-the-art association mapping and enrichment approaches across a wide range of genetic architectures. We then further illustrate the benefits of BANNs by analyzing real GWA data assayed in approximately 2,000 heterogenous stock of mice from the Wellcome Trust Centre for Human Genetics and approximately 7,000 individuals from the Framingham Heart Study. Lastly, using a random subset of individuals of European ancestry from the UK Biobank, we show that BANNs is able to replicate known associations in high and low-density lipoprotein cholesterol content.