239 research outputs found
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A Hippo-like Signaling Pathway Controls Tracheal Morphogenesis in Drosophila melanogaster
Hippo-like pathways are ancient signaling modules first identified in yeasts. The best-defined metazoan module forms the core of the Hippo pathway, which regulates organ size and cell fate. Hippo-like kinase modules consist of a Sterile 20-like kinase, an NDR kinase, and non-catalytic protein scaffolds. In the Hippo pathway, the upstream kinase Hippo can be activated by another kinase, Tao-1. Here, we delineate a related Hippo-like signaling module that Tao-1 regulates to control tracheal morphogenesis in Drosophila melanogaster. Tao-1 activates the Sterile 20-like kinase GckIII by phosphorylating its activation loop, a mode of regulation that is conserved in humans. Tao-1 and GckIII act upstream of the NDR kinase Tricornered to ensure proper tube formation in trachea. Our study reveals that Tao-1 activates two related kinase modules to control both growth and morphogenesis. The Hippo-like signaling pathway we have delineated has a potential role in the human vascular disease cerebral cavernous malformation
Adherence of SARSâCoVâ2 Seroepidemiologic Studies to the ROSESâS Reporting Guideline During the COVIDâ19 Pandemic
Background: Complete reporting of seroepidemiologic studies is critical to their utility in evidence synthesis and public health decision making. The Reporting of Seroepidemiologic studiesâSARSâCoVâ2 (ROSESâS) guideline is a checklist that aims to improve reporting in SARSâCoVâ2 seroepidemiologic studies. Adherence to the ROSESâS guideline has not yet been evaluated. Objectives: This study aims to evaluate the completeness of SARSâCoVâ2 seroepidemiologic study reporting by the ROSESâS guideline during the COVIDâ19 pandemic, determine whether guideline publication was associated with reporting completeness, and identify study characteristics associated with reporting completeness. Methods: A random sample from the SeroTracker living systematic review database was evaluated. For each reporting item in the guideline, the percentage of studies that were adherent was calculated, as well as median and interquartile range (IQR) adherence across all items and by item domain. Beta regression analyses were used to evaluate predictors of adherence to ROSESâS. Results: One hundred and ninetyânine studies were analyzed. Median adherence was 48.1% (IQR 40.0%â55.2%) per study, with overall adherence ranging from 8.8% to 72.7%. The laboratory methods domain had the lowest median adherence (33.3% [IQR 25.0%â41.7%]). The discussion domain had the highest median adherence (75.0% [IQR 50.0%â100.0%]). Reporting adherence to ROSESâS before and after guideline publication did not significantly change. Publication source (p < 0.001), study risk of bias (p = 0.001), and sampling method (p = 0.004) were significantly associated with adherence. Conclusions: Completeness of reporting in SARSâCoVâ2 seroepidemiologic studies was suboptimal. Publication of the ROSESâS guideline was not associated with changes in reporting practices. Authors should improve adherence to the ROSESâS guideline with support from stakeholders
A novel approach to phylogenetic tree construction using stochastic optimization and clustering
BACKGROUND: The problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational biology. RESULTS: A new phylogenetic tree construction method from a given set of objects (proteins, species, etc.) is presented. As an extension of ant colony optimization, this method proposes an adaptive phylogenetic clustering algorithm based on a digraph to find a tree structure that defines the ancestral relationships among the given objects. CONCLUSION: Our phylogenetic tree construction method is tested to compare its results with that of the genetic algorithm (GA). Experimental results show that our algorithm converges much faster and also achieves higher quality than GA
Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genomescale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.Fil: Hughes, Lily C.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: OrtĂ, Guillermo. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Huang, Yu. Beijing Genomics Institute; China. Chinese Academy of Sciences; RepĂșblica de ChinaFil: Sun, Ying. China National Genebank; China. Beijing Genomics Institute; ChinaFil: Baldwin, Carole C.. National Museum of Natural History; Estados UnidosFil: Thompson, Andrew W.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Arcila, Dahiana. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Betancur, Ricardo. National Museum of Natural History; Estados Unidos. Universidad de Puerto Rico, Recinto de Rio Piedras; Puerto RicoFil: Li, Chenhong. Shanghai Ocean University; ChinaFil: Becker, Leandro Anibal. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Centro CientĂfico TecnolĂłgico Conicet - Patagonia Norte. Instituto Andino PatagĂłnico de TecnologĂas BiolĂłgicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino PatagĂłnico de TecnologĂas BiolĂłgicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Bellora, NicolĂĄs. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Centro CientĂfico TecnolĂłgico Conicet - Patagonia Norte. Instituto Andino PatagĂłnico de TecnologĂas BiolĂłgicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino PatagĂłnico de TecnologĂas BiolĂłgicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Zhao, Xiaomeng. Chinese Academy of Sciences; RepĂșblica de China. Beijing Genomics Institute; ChinaFil: Li, Xiaofeng. Chinese Academy of Sciences; RepĂșblica de China. Beijing Genomics Institute; ChinaFil: Wang, Min. Beijing Genomics Institute; ChinaFil: Fang, Chao. Chinese Academy of Sciences; RepĂșblica de ChinaFil: Xie, Bing. Bgi-shenzhen; ChinaFil: Zhoui, Zhuocheng. China Fisheries Association; ChinaFil: Huang, Hai. Hainan Tropical Ocean University; ChinaFil: Chen, Songlin. Yellow Sea Fisheries Research Institute Chinese Academy Of Fishery Science; ChinaFil: Venkatesh, Byrappa. A-star, Institute Of Molecular And Cell Biology;Fil: Shi, Qiong. Chinese Academy of Sciences; RepĂșblica de Chin
Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-Scale Transcriptome Data for Fish Evolution Studies
Ray-finned fishes (Actinopterygii) represent more than 50 % of extant vertebrates and are of great evolutionary, ecologic and economic significance, but they are relatively underrepresented in âomics studies. Increased availability of transcriptome data for these species will allow researchers to better understand changes in gene expression, and to carry out functional analyses. An international project known as the âTranscriptomes of 1,000 Fishesâ (Fish-T1K) project has been established to generate RNA-seq transcriptome sequences for 1,000 diverse species of ray-finned fishes. The first phase of this project has produced transcriptomes from more than 180 ray-finned fishes, representing 142 species and covering 51 orders and 109 families. Here we provide an overview of the goals of this project and the work done so far
Substantial Progress Yet Significant Opportunity for Improvement in Stroke Care in China
BACKGROUND AND PURPOSE: Stroke is a leading cause of death in China. Yet the adherence to guideline-recommended ischemic stroke performance metrics in the past decade has been previously shown to be suboptimal. Since then, several nationwide stroke quality management initiatives have been conducted in China. We sought to determine whether adherence had improved since then.
METHODS: Data were obtained from the 2 phases of China National Stroke Registries, which included 131 hospitals (12â173 patients with acute ischemic stroke) in China National Stroke Registries phase 1 from 2007 to 2008 versus 219 hospitals (19â604 patients) in China National Stroke Registries phase 2 from 2012 to 2013. Multiple regression models were developed to evaluate the difference in adherence to performance measure between the 2 study periods.
RESULTS: The overall quality of care has improved over time, as reflected by the higher composite score of 0.76 in 2012 to 2013 versus 0.63 in 2007 to 2008. Nine of 13 individual performance metrics improved. However, there were no significant improvements in the rates of intravenous thrombolytic therapy and anticoagulation for atrial fibrillation. After multivariate analysis, there remained a significant 1.17-fold (95% confidence interval, 1.14-1.21) increase in the odds of delivering evidence-based performance metrics in the more recent time periods versus older data. The performance metrics with the most significantly increased odds included stroke education, dysphagia screening, smoking cessation, and antithrombotics at discharge.
CONCLUSIONS: Adherence to stroke performance metrics has increased over time, but significant opportunities remain for further improvement. Continuous stroke quality improvement program should be developed as a national priority in China
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