The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.
This study analyses the effectiveness of teaching an undergraduate process control course in a flipped mode, with a constraint that the students do not have to do more work than in a conventional class. Video lectures delivered by the instructor in the past were used as study material. It was supplemented by classroom and LMS based discussions, a virtual lab, and tutorial sessions. To enforce the watching of video lectures, a weekly quiz was conducted. Assessments were also carried out through three longer forms of quiz, a mid-semester examination and an end-semester examination. The performance of the students was evaluated using the following metrics: (1) Perception analysis of the flipped class students. (2) A limited comparison of the performance of the flipped class students (experimental group) with a similar set of students who underwent a conventional course simultaneously (control group) (3) Studying the consistency of the flipped class students' performance over different evaluation criteria and correlations between them. The results are consistent with each other and the performance is good. An overwhelming majority of the flipped class students (about 80%) also perceive the flipped method to be as effective as or better than the conventional method of teaching. As it helps achieve the benefits of a flipped method, simultaneously with high satisfaction levels, this method can be considered as successful and hence is easily implementable, even in large scale.
Abstract The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.
ABSTRACT Background: A difficult airway is anticipated with cervical spine injuries (CSIs) as immobilization techniques such as manual in-line stabilization (MILS) are used, which distort the oro-pharyngeal-laryngeal axis. Video laryngoscopes (VLs) make difficult airway management easy, as they do not require axis alignment. The present study aimed to compare the total time taken by Macintosh laryngoscope (ML), conventional blade, and D-blade ™ of C-MAC ® VL in simulated CSI scenarios using MILS. Methods: Ninety patients were randomly allocated into three groups: Group M (ML), Group C (conventional blade of C-MAC ® ), and Group D (D-blade ™ of C-MAC ® ) with MILS applied before intubation. Primary outcome was the total time taken for successful intubation, while secondary outcomes were to assess Cormack–Lehane (CL) grade, number of attempts, hemodynamic response, and associated complications. Results: Total time for intubation in Group C was 23.40 ± 7.06 sec compared to 35.27 ± 6.53 and 47.27 ± 2.53 sec in groups D and M, respectively ( P < 0.001). CL-grade I was observed in 15/30 (50%) in Group M, 25/30 (83.3%) in Group C, and 29/30 (96.7%) in Group D. Group M reported 7/30 (23.3%) failed intubations, while none were observed in other groups. Hemodynamic parameters were significantly higher at 3 and 5 min in Group M. Postoperative sore throat was recorded in 12/30 (40%) in Group M compared to 3/30 (10%) in groups C and D each ( P value 0.037). Conclusion: C-MAC ® VL requires less time for intubation, provides better glottic view, and has higher success, with better attenuation of hemodynamic response and fewer complications compared to ML.
The Ensembl project (https://www ensembl org) annotates genomes and disseminates genomic data for vertebrate species We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces Here, we present recent Ensembl developments including two new website portals Ensembl Rapid Release (http://rapid ensembl org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects Our SARS-CoV-2 genome browser (https://covid-19 ensembl org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic We also report on other updates to our annotation resources, tools and services All Ensembl data and software are freely available without restriction
Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.
We present a collaborative attempt to build select toolboxes of Scilab using external Free and Open Source Software (FOSS) libraries. A C/C++ interface is written for each library. Scilab variables are transferred to C/C++ variables, computations carried out through one or more function calls and variables returned to Scilab. State of the art libraries, such as Octave, COIN-OR, OpenCV and IT++ have been used to build Scilab toolboxes. Scilab is selected as the frontend as it has a block based GUI to build models, called Xcos. Optimization, Signal Processing, Communication, Image Processing, Computer Vision, Signal Processing and Identification toolboxes are in advanced stages of development and use. Control Systems and Scilab to C toolboxes are in early stages of development.
We validated the CREST model, a 5 variable score for stratifying the risk of circulatory aetiology death (CED) following out-of-hospital cardiac arrest (OHCA) and compared its discrimination with the SCAI shock classification. Circulatory aetiology death occurs in approximately a third of patients admitted after resuscitated OHCA. There is an urgent need for improved stratification of the patient with OHCA on arrival to a cardiac arrest centre to improve patient selection for invasive interventions.
The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation and comparative genomics across the vertebrate subphylum and key model organisms. The Ensembl annotation pipeline is capable of integrating experimental and reference data from multiple providers into a single integrated resource. Here, we present 94 newly annotated and re-annotated genomes, bringing the total number of genomes offered by Ensembl to 227. This represents the single largest expansion of the resource since its inception. We also detail our continued efforts to improve human annotation, developments in our epigenome analysis and display, a new tool for imputing causal genes from genome-wide association studies and visualisation of variation within a 3D protein model. Finally, we present information on our new website. Both software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license) and data updates made available four times a year.
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