2,396 results match your criteria open license


Asthma Phenotypes and COVID-19 Risk: A Population-based Observational Study.

Am J Respir Crit Care Med 2021 Oct 20. Epub 2021 Oct 20.

Imperial College London, National Heart and Lung Institute, London, United Kingdom of Great Britain and Northern Ireland.

Rationale: Studies have suggested some asthma patients are at risk of severe COVID-19, but they have had limited data on asthma phenotype and have not considered if risks are specific to COVID-19.

Objectives: Determine the effect of asthma phenotype on three levels of COVID-19 outcomes. Compare hospitalisation rates to influenza and pneumonia. Read More

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October 2021

Profeel-An open source dosimetry data visualization and analysis software.

Comput Methods Programs Biomed 2021 Oct 8;212:106457. Epub 2021 Oct 8.

Department of Medical Physics and Department of Oncology, Tampere University Hospital, Tampere, Finland.

Background And Objectives: This article presents Profeel, a Matlab (MathWorks Inc., MA) based open source dosimetry data visualization and analysis software. Profeel aims to support quality assurance, dosimetry and research in the field of radiotherapy by providing an environment to visualize, process and analyse measured and simulated dosimetry data from several data sources used in radiotherapy practice and research. Read More

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October 2021

Resources and Geographical Access to Care for Severe Pediatric Pneumonia in Four Resource-Limited Settings.

Am J Respir Crit Care Med 2021 Oct 18. Epub 2021 Oct 18.

Johns Hopkins University, 1466, Division of Pulmonary and Critical Care, School of Medicine, Baltimore, Maryland, United States;

Rationale: Pneumonia is the leading cause of death in children worldwide. Identifying and appropriately managing severe pneumonia in a timely manner improves outcomes. Little is known about the readiness of healthcare facilities to manage severe pediatric pneumonia in low-resource settings. Read More

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October 2021

Genome Assembly and Transcriptome of CsGL1, a New Resource to Study Anthracnose Disease in Sorghum.

Mol Plant Microbe Interact 2021 Oct 18:MPMI04210094A. Epub 2021 Oct 18.

Donald Danforth Plant Science Center, St. Louis, MO 63132, U.S.A.

species are globally distributed and well known as members of a destructive phytopathogenic genus, causing the anthracnose disease in a wide variety of crops and fruits. is the causal agent of the anthracnose disease in sorghum, causing losses of up to 50% in yield. Here, we used PacBio sequencing combined with RNA-seq to generate a chromosome-level assembly and annotation of the strain CsGL1. Read More

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October 2021

The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction.

J Cheminform 2021 Oct 16;13(1):81. Epub 2021 Oct 16.

Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China.

Structure-based drug design depends on the detailed knowledge of the three-dimensional (3D) structures of protein-ligand binding complexes, but accurate prediction of ligand-binding poses is still a major challenge for molecular docking due to deficiency of scoring functions (SFs) and ignorance of protein flexibility upon ligand binding. In this study, based on a cross-docking dataset dedicatedly constructed from the PDBbind database, we developed several XGBoost-trained classifiers to discriminate the near-native binding poses from decoys, and systematically assessed their performance with/without the involvement of the cross-docked poses in the training/test sets. The calculation results illustrate that using Extended Connectivity Interaction Features (ECIF), Vina energy terms and docking pose ranks as the features can achieve the best performance, according to the validation through the random splitting or refined-core splitting and the testing on the re-docked or cross-docked poses. Read More

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October 2021

Disciplinary complaints concerning transgressive behaviour by healthcare professionals: an analysis of 5 years jurisprudence in the Netherlands.

BMJ Open 2021 Oct 12;11(10):e053401. Epub 2021 Oct 12.

Centre for Education Development and Research in Health Professions (CEDAR), University Medical Centre Groningen, Groningen, The Netherlands

Objectives: To study the frequency of observed cases of disciplinary law complaints concerning transgressive behaviour in Dutch healthcare by analysing disciplinary cases handled in Dutch disciplinary law.

Design: Retrospective review of complaints in the Dutch disciplinary law tribunals from the period 1 January 2015 to 1 January 2020.

Setting: Dutch healthcare. Read More

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October 2021

Constructing Japanese MeSH term dictionaries related to the COVID-19 literature.

Genomics Inform 2021 Sep 30;19(3):e25. Epub 2021 Sep 30.

Computer Science Department, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK.

The coronavirus disease 2019 (COVID-19) pandemic has led to a flood of research papers and the information has been updated with considerable frequency. For society to derive benefits from this research, it is necessary to promote sharing up-to-date knowledge from these papers. However, because most research papers are written in English, it is difficult for people who are not familiar with English medical terms to obtain knowledge from them. Read More

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September 2021

A Novel Homozygous Variant is Associated with a Neurodevelopmental Disorder and Movement Abnormalities.

Mov Disord Clin Pract 2021 Oct 31;8(7):1140-1143. Epub 2021 Jul 31.

Department of Neuromuscular Disorders University College London, Institute of Neurology London United Kingdom.

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October 2021

Fast parallel construction of variable-length Markov chains.

BMC Bioinformatics 2021 Oct 9;22(1):487. Epub 2021 Oct 9.

Department of Computer Science and Engineering, University of Gothenburg - Chalmers University of Technology, Gothenburg, Sweden.

Background: Alignment-free methods are a popular approach for comparing biological sequences, including complete genomes. The methods range from probability distributions of sequence composition to first and higher-order Markov chains, where a k-th order Markov chain over DNA has [Formula: see text] formal parameters. To circumvent this exponential growth in parameters, variable-length Markov chains (VLMCs) have gained popularity for applications in molecular biology and other areas. Read More

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October 2021

Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data.

mSystems 2021 Oct 5:e0069121. Epub 2021 Oct 5.

Department of Pediatrics, School of Medicine, University of California, San Diegogrid.266100.3, California, USA.

Microbiome data are sparse and high dimensional, so effective visualization of these data requires dimensionality reduction. To date, the most commonly used method for dimensionality reduction in the microbiome is calculation of between-sample microbial differences (beta diversity), followed by principal-coordinate analysis (PCoA). Uniform Manifold Approximation and Projection (UMAP) is an alternative method that can reduce the dimensionality of beta diversity distance matrices. Read More

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October 2021

A Humane Approach To Caring For New Mothers In Psychiatric Crisis.

Authors:
April Dembosky

Health Aff (Millwood) 2021 Oct;40(10):1528-1533

This article is part of a series on transforming health systems published with support from The Robert Wood Johnson Foundation. This is an open access article distributed in accordance with the terms of the Creative Commons Attribution (CC BY 4.0) license, which permits others to distribute, remix, adapt, and build upon this work, for commercial use, provided the original work is properly cited. See https://creativecommons.org/licenses/by/4.0/. April Dembosky is the health correspondent at KQED public radio, the NPR station in San Francisco, California. Her travel for this article was supported by the Association of Health Care Journalists' International Health Study Fellowship, which is funded by The Commonwealth Fund.

In England, Mother and Baby Units allow for joint inpatient admissions-the standard of care for women requiring treatment. Read More

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October 2021

Pharmacological Modulation of Neurite Outgrowth in Human Neural Progenitor Cells by Inhibiting Non-muscle Myosin II.

Front Cell Dev Biol 2021 17;9:719636. Epub 2021 Sep 17.

Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.

Studies on neural development and neuronal regeneration after injury are mainly based on animal models. The establishment of pluripotent stem cell (PSC) technology, however, opened new perspectives for better understanding these processes in human models by providing unlimited cell source for hard-to-obtain human tissues. Here, we aimed at identifying the molecular factors that confine and modulate an early step of neural regeneration, the formation of neurites in human neural progenitor cells (NPCs). Read More

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September 2021

SamQL: a structured query language and filtering tool for the SAM/BAM file format.

BMC Bioinformatics 2021 Oct 2;22(1):474. Epub 2021 Oct 2.

Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA.

Background: The Sequence Alignment/Map Format Specification (SAM) is one of the most widely adopted file formats in bioinformatics and many researchers use it daily. Several tools, including most high-throughput sequencing read aligners, use it as their primary output and many more tools have been developed to process it. However, despite its flexibility, SAM encoded files can often be difficult to query and understand even for experienced bioinformaticians. Read More

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October 2021

PLoS Computational Biology Issue Image | Vol. 17(9) October 2021.

Authors:

PLoS Comput Biol 2021 Oct 1;17(9):ev17.i09. Epub 2021 Oct 1.

The tomato flowers are characterized by possessing poricidal anthers, which restrict the exit of the pollen to a tiny opening on the apex of the anther. To extract pollen efficiently, some visiting bees grasp the anthers and quickly contracting their flight muscles, producing vibrations and an audible sound. The vibrations are transferred to the anthers, shaking and stimulating the pollen inside them to leave by the pores, a phenomenon known as floral sonication or buzz-pollination. Read More

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October 2021

PLoS Computational Biology Issue Image | Vol. 1(9) October 2021.

Authors:

PLoS Comput Biol 2021 Oct 1;1(9):ev01.i09. Epub 2021 Oct 1.

The tomato flowers are characterized by possessing poricidal anthers, which restrict the exit of the pollen to a tiny opening on the apex of the anther. To extract pollen efficiently, some visiting bees grasp the anthers and quickly contracting their flight muscles, producing vibrations and an audible sound. The vibrations are transferred to the anthers, shaking and stimulating the pollen inside them to leave by the pores, a phenomenon known as floral sonication or buzz-pollination. Read More

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October 2021

GENETEX-a GENomics Report TEXt mining R package and Shiny application designed to capture real-world clinico-genomic data.

JAMIA Open 2021 Jul 28;4(3):ooab082. Epub 2021 Sep 28.

Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.

Objectives: Clinico-genomic data (CGD) acquired through routine clinical practice has the potential to improve our understanding of clinical oncology. However, these data often reside in heterogeneous and semistructured data, resulting in prolonged time-to-analyses.

Materials And Methods: We created GENETEX: an R package and Shiny application for text mining genomic reports from electronic health record (EHR) and direct import into Research Electronic Data Capture (REDCap). Read More

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Development of an Online General Biology Open Educational Resource (OER) Laboratory Manual.

J Microbiol Biol Educ 2021 30;22(2). Epub 2021 Jul 30.

Department of Biological Sciences, Kingsborough Community College, The City University of New York, Brooklyn, New York, USA.

Currently, many academic institutions are using one or more variations of online modalities due to the COVID-19 pandemic, and science educators face a unique challenge with distance-learning laboratories. Many resources to engage students in virtual, interactive laboratory activities exist, but we found that high costs and/or overlooked content left gaps for several topics typically taught in a general, introductory biology course for undergraduate biology majors (e.g. Read More

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Cobiveco: Consistent biventricular coordinates for precise and intuitive description of position in the heart - with MATLAB implementation.

Med Image Anal 2021 Sep 20;74:102247. Epub 2021 Sep 20.

Institute of Biomedical Engineering, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 1, Karlsruhe 76131, Germany.

Ventricular coordinates are widely used as a versatile tool for various applications that benefit from a description of local position within the heart. However, the practical usefulness of ventricular coordinates is determined by their ability to meet application-specific requirements. For regression-based estimation of biventricular position, for example, a symmetric definition of coordinate directions in both ventricles is important. Read More

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September 2021

AlphaMap: an open-source python package for the visual annotation of proteomics data with sequence specific knowledge.

Bioinformatics 2021 Sep 29. Epub 2021 Sep 29.

Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.

Summary: Integrating experimental information across proteomic datasets with the wealth of publicly available sequence annotations is a crucial part in many proteomic studies that currently lacks an automated analysis platform. Here we present AlphaMap, a Python package that facilitates the visual exploration of peptide-level proteomics data. Identified peptides and post-translational modifications in proteomic datasets are mapped to their corresponding protein sequence and visualized together with prior knowledge from UniProt and with expected proteolytic cleavage sites. Read More

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September 2021

Analysis of Single Board Architectures Integrating Sensors Technologies.

Sensors (Basel) 2021 Sep 21;21(18). Epub 2021 Sep 21.

Centro Científico Tecnológico de Huelva (CCTH), University of Huelva, 21007 Huelva, Spain.

Development boards, Single-Board Computers (SBCs) and Single-Board Microcontrollers (SBMs) integrating sensors and communication technologies have become a very popular and interesting solution in the last decade. They are of interest for their simplicity, versatility, adaptability, ease of use and prototyping, which allow them to serve as a starting point for projects and as reference for all kinds of designs. In this sense, there are innumerable applications integrating sensors and communication technologies where they are increasingly used, including robotics, domotics, testing and measurement, Do-It-Yourself (DIY) projects, Internet of Things (IoT) devices in the home or workplace and science, technology, engineering, educational and also academic world for STEAM (Science, Technology, Engineering and Mathematics) skills. Read More

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September 2021

An Updated Definition and Severity Classification of COPD Exacerbations: The Rome Proposal.

Am J Respir Crit Care Med 2021 Sep 27. Epub 2021 Sep 27.

Imperial College London, National Heart and Lung Institute, London, United Kingdom of Great Britain and Northern Ireland.

The current definition of a chronic obstructive pulmonary disease (COPD) exacerbation (ECOPD) is based solely on worsening respiratory symptoms, with severity classified post hoc by the healthcare resource used to treat the event, which may vary among practitioners and healthcare systems. These shortcomings support a need to revise the ECOPD definition and severity classification to one that is useful at time of patient contact. To achieve this, an expert panel used a modified Delphi method of five rounds of questions generated by a thorough review of the literature, supplemented by virtual discussions. Read More

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September 2021

GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.

PLoS Comput Biol 2021 Sep 27;17(9):e1009444. Epub 2021 Sep 27.

Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital Charlestown, Massachusetts, United States of America.

Transcription factors (TFs) are proteins that promote or reduce the expression of genes by binding short genomic DNA sequences known as transcription factor binding sites (TFBS). While several tools have been developed to scan for potential occurrences of TFBS in linear DNA sequences or reference genomes, no tool exists to find them in pangenome variation graphs (VGs). VGs are sequence-labelled graphs that can efficiently encode collections of genomes and their variants in a single, compact data structure. Read More

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September 2021

Tiara: Deep learning-based classification system for eukaryotic sequences.

Bioinformatics 2021 Sep 27. Epub 2021 Sep 27.

Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland.

Motivation: With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step towards a better understanding of eukaryotic diversity.

Results: We developed Tiara, a deep-learning-based approach for the identification of eukaryotic sequences in the metagenomic datasets. Read More

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September 2021

Developing a dashboard for faculty development in competency-based training programs: a design-based research project.

Can Med Educ J 2021 Sep 14;12(4):48-64. Epub 2021 Sep 14.

Department of Emergency Medicine, University of Saskatchewan, Saskatchewan, Canada.

Background: Canadian specialist residency training programs are implementing a form of competency-based medical education (CBME) that requires frequent assessments of entrustable professional activities (EPAs). Faculty struggle to provide helpful feedback and assign appropriate entrustment scores. CBME faculty development initiatives rarely incorporate teaching metrics. Read More

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September 2021

miRkit: R framework analyzing miRNA PCR array data.

BMC Res Notes 2021 Sep 26;14(1):376. Epub 2021 Sep 26.

Institute of Applied Biosciences, Centre of Research and Technology Hellas, 57001, Thessaloniki, Greece.

Objective: The characterization of microRNAs (miRNA) in recent years is an important advance in the field of gene regulation. To this end, several approaches for miRNA expression analysis and various bioinformatics tools have been developed over the last few years. It is a common practice to analyze miRNA PCR Array data using the commercially available software, mostly due to its convenience and ease-of-use. Read More

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September 2021

Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment.

Gigascience 2021 Sep;10(9)

Department of Computer Science, Rice University, Houston, TX 77251-1892, USA.

Background: Long-read sequencing has enabled unprecedented surveys of structural variation across the entire human genome. To maximize the potential of long-read sequencing in this context, novel mapping methods have emerged that have primarily focused on either speed or accuracy. Various heuristics and scoring schemas have been implemented in widely used read mappers (minimap2 and NGMLR) to optimize for speed or accuracy, which have variable performance across different genomic regions and for specific structural variants. Read More

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September 2021

ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram.

Front Genet 2021 7;12:706907. Epub 2021 Sep 7.

State Key Laboratory of Agricultural Microbiology, State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.

Venn diagrams are widely used diagrams to show the set relationships in biomedical studies. In this study, we developed ggVennDiagram, an R package that could automatically generate high-quality Venn diagrams with two to seven sets. The ggVennDiagram is built based on ggplot2, and it integrates the advantages of existing packages, such as venn, RVenn, VennDiagram, and sf. Read More

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September 2021

Towards the characterization of neutron carcinogenesis through direct action simulations of clustered DNA damage.

Phys Med Biol 2021 Oct 12;66(20). Epub 2021 Oct 12.

Medical Physics Unit, McGill University, Montreal, QC, H4A3J1, Canada.

Neutron exposure poses a unique radiation protection concern because neutrons have a large, energy-dependent relative biological effectiveness (RBE) for stochastic effects. Recent computational studies on the microdosimetric properties of neutron dose deposition have implicated clustered DNA damage as a likely contributor to this marked energy dependence. So far, publications have focused solely on neutron RBE for inducing clusters of DNA damage containing two or more DNA double strand breaks (DSBs). Read More

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October 2021

De Novo Powered Air-Purifying Respirator Design and Fabrication for Pandemic Response.

Front Bioeng Biotechnol 2021 6;9:690905. Epub 2021 Sep 6.

Greater Boston Pandemic Fabrication Team (PanFab) c/o Harvard-MIT Center for Regulatory Science, Harvard Medical School, Boston, MA, United States.

The rapid spread of COVID-19 and disruption of normal supply chains has resulted in severe shortages of personal protective equipment (PPE), particularly devices with few suppliers such as powered air-purifying respirators (PAPRs). A scarcity of information describing design and performance criteria for PAPRs represents a substantial barrier to mitigating shortages. We sought to apply open-source product development (OSPD) to PAPRs to enable alternative sources of supply and further innovation. Read More

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September 2021

Deeper Understanding of Appearance in Orofacial Clefts: A Structural Equation Model of the CLEFT-Q Appearance Scales.

Plast Reconstr Surg Glob Open 2021 Sep 17;9(9):e3806. Epub 2021 Sep 17.

Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.

Background: The CLEFT-Q is a patient-reported outcome measure with seven scales measuring elements of facial appearance in cleft lip and/or palate. We built on the validated CLEFT-Q structural model to describe conceptual relationships between these scales, and tested our hypothesis through structural equation modeling (SEM). In our hypothesized model, the appearance of the nose, nostrils, teeth, jaw, lips, and cleft lip scar all contribute to overall facial appearance. Read More

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September 2021