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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

Deep learning for peptide identification from metaproteomics datasets.

J Proteomics 2021 09 8;247:104316. Epub 2021 Jul 8.

Department of Computer Science and Engineering, University of North Texas, TX, USA. Electronic address:

Metaproteomics is becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS) coupled with liquid chromatography. In this paper, we proposed a deep-learning-based algorithm, named DeepFilter, for improving peptide identifications from a collection of tandem mass spectra. Read More

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September 2021

S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types.

Bioinformatics 2021 Mar 3. Epub 2021 Mar 3.

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.

Summary: Epigenetic modifications reflect key aspects of transcriptional regulation, and many epigenomic data sets have been generated under different biological contexts to provide insights into regulatory processes. However, the technical noise in epigenomic data sets and the many dimensions (features) examined make it challenging to effectively extract biologically meaningful inferences from these data sets. We developed a package that reduces noise while normalizing the epigenomic data by a novel normalization method, followed by integrative dimensional reduction by learning and assigning epigenetic states. Read More

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Standardization of T1-mapping in cardiovascular magnetic resonance using clustered structuring for benchmarking normal ranges.

Int J Cardiol 2021 03 21;326:220-225. Epub 2020 Oct 21.

Oxford Centre for Clinical Magnetic Resonance Research (OCMR), Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.

Background: Cardiovascular magnetic resonance T1-mapping is increasingly used for tissue characterization, commonly based on Modified Look-Locker Inversion recovery (MOLLI). However, there are numerous MOLLI variants with differing normal ranges. This lack of standardization presents confusion and difficulty in inter-center comparisons, hindering widespread adoption of T1-mapping. Read More

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open-japanese-mesh: assigning MeSH UIDs to Japanese medical terms via open Japanese-English glossaries.

Genomics Inform 2020 Jun 16;18(2):e22. Epub 2020 Jun 16.

National Bioscience Database Center, Japan Science and Technology Agency, Tokyo 102-8666, Japan.

The Medical Subject Headings (MeSH) system is a controlled vocabulary for indexing biomedical documents that is used for document retrieval and other natural language processing purposes. However, although the original English MeSH is freely available, its Japanese translation has a restricted license. We attempted to create an open alternative, and for this purpose we made a script for assigning MeSH UIDs to Japanese medical terms using Japanese-English glossaries. Read More

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Focus on the spectra that matter by clustering of quantification data in shotgun proteomics.

Nat Commun 2020 06 26;11(1):3234. Epub 2020 Jun 26.

Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, 17121, Solna, Sweden.

In shotgun proteomics, the analysis of label-free quantification experiments is typically limited by the identification rate and the noise level in the quantitative data. This generally causes a low sensitivity in differential expression analysis. Here, we propose a quantification-first approach for peptides that reverses the classical identification-first workflow, thereby preventing valuable information from being discarded in the identification stage. Read More

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CAMITAX: Taxon labels for microbial genomes.

Gigascience 2020 01;9(1)

Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.

Background: The number of microbial genome sequences is increasing exponentially, especially thanks to recent advances in recovering complete or near-complete genomes from metagenomes and single cells. Assigning reliable taxon labels to genomes is key and often a prerequisite for downstream analyses.

Findings: We introduce CAMITAX, a scalable and reproducible workflow for the taxonomic labelling of microbial genomes recovered from isolates, single cells, and metagenomes. Read More

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January 2020

Resources for assigning MeSH IDs to Japanese medical terms.

Authors:
Yuka Tateisi

Genomics Inform 2019 Jun 27;17(2):e16. Epub 2019 Jun 27.

National Bioscience Database Center, Japan Science and Technology Agency, Tokyo 102-8666, Japan.

Medical Subject Headings (MeSH), a medical thesaurus created by the National Library of Medicine (NLM), is a useful resource for natural language processing (NLP). In this article, the current status of the Japanese version of Medical Subject Headings (MeSH) is reviewed. Online investigation found that Japanese-English dictionaries, which assign MeSH information to applicable terms, but use them for NLP, were found to be difficult to access, due to license restrictions. Read More

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masstodon: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry.

Anal Chem 2019 02 28;91(3):1801-1807. Epub 2019 Jan 28.

Department of Mathematics, Informatics, and Mechanics , University of Warsaw , Warsaw 02-097 , Poland.

Top-down mass spectrometry methods are becoming continuously more popular in the effort to describe the proteome. They rely on the fragmentation of intact protein ions inside the mass spectrometer. Among the existing fragmentation methods, electron transfer dissociation is known for its precision and wide coverage of different cleavage sites. Read More

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February 2019

HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads.

BMC Bioinformatics 2018 07 3;19(1):252. Epub 2018 Jul 3.

Department of Informatics, Systems, and Communication, University of Milano-Bicocca, Milan, Italy.

Background: Haplotype assembly is the process of assigning the different alleles of the variants covered by mapped sequencing reads to the two haplotypes of the genome of a human individual. Long reads, which are nowadays cheaper to produce and more widely available than ever before, have been used to reduce the fragmentation of the assembled haplotypes since their ability to span several variants along the genome. These long reads are also characterized by a high error rate, an issue which may be mitigated, however, with larger sets of reads, when this error rate is uniform across genome positions. Read More

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Usefulness of the DETECT program for assessing the internal structure of dimensionality in simulated data and results of the Korean nursing licensing examination.

J Educ Eval Health Prof 2017 27;14:32. Epub 2017 Dec 27.

Department of Parasitology and Institute of Medical Education, College of Medicine, Hallym University, Chuncheon, Korea.

Purpose: The dimensionality of examinations provides empirical evidence of the internal test structure underlying the responses to a set of items. In turn, the internal structure is an important piece of evidence of the validity of an examination. Thus, the aim of this study was to investigate the performance of the DETECT program and to use it to examine the internal structure of the Korean nursing licensing examination. Read More

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Continuing education requirements among State Occupational Therapy Regulatory Boards in the United States of America.

J Educ Eval Health Prof 2016 27;13:37. Epub 2016 Oct 27.

Department of Occupational Therapy, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL, USA.

Purpose: The purpose of this study is to compare and contrast the contents of each state's occupational therapy (OT) regulatory board requirements regarding licensees' acquisition of continuing education units in the United States of America.

Methods: Data related to continuing education requirements from each OT regulatory board of all 50 states and the District of Columbia in the United States were reviewed and categorized by two reviewers. Analysis was conducted based on the categorization of the continuing education requirements and activities required, allowed, and not allowed/not mentioned for continuing education units. Read More

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IDGenerator: unique identifier generator for epidemiologic or clinical studies.

BMC Med Res Methodol 2016 09 15;16:120. Epub 2016 Sep 15.

Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany.

Background: Creating study identifiers and assigning them to study participants is an important feature in epidemiologic studies, ensuring the consistency and privacy of the study data. The numbering system for identifiers needs to be random within certain number constraints, to carry extensions coding for organizational information, or to contain multiple layers of numbers per participant to diversify data access. Available software can generate globally-unique identifiers, but identifier-creating tools meeting the special needs of epidemiological studies are lacking. Read More

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September 2016

CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data.

Bioinformatics 2016 Feb 26;32(3):388-97. Epub 2015 Sep 26.

Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, UK.

Motivation: Simple bioinformatic tools are frequently used to analyse time-series datasets regardless of their ability to deal with transient phenomena, limiting the meaningful information that may be extracted from them. This situation requires the development and exploitation of tailor-made, easy-to-use and flexible tools designed specifically for the analysis of time-series datasets.

Results: We present a novel statistical application called CLUSTERnGO, which uses a model-based clustering algorithm that fulfils this need. Read More

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February 2016

Assigning Israeli medical graduates to internships.

Isr J Health Policy Res 2015 20;4. Epub 2015 Mar 20.

Schneider Children's Medical Center, Petach-Tikvah, Israel.

Background: Physicians in Israel are required to do an internship in an accredited hospital upon completion of the medical studies, and prior to receiving the medical license. For most students, the assignment is determined by a lottery, which takes into consideration the preferences of these students.

Objectives: We propose a novel way to perform this lottery, in which (on average) a larger number of students gets one of their top choices. Read More

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Bayesian genome assembly and assessment by markov chain monte carlo sampling.

PLoS One 2014 26;9(6):e99497. Epub 2014 Jun 26.

Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America.

Most genome assemblers construct point estimates, choosing only a single genome sequence from among many alternative hypotheses that are supported by the data. We present a Markov chain Monte Carlo approach to sequence assembly that instead generates distributions of assembly hypotheses with posterior probabilities, providing an explicit statistical framework for evaluating alternative hypotheses and assessing assembly uncertainty. We implement this approach in a prototype assembler, called Genome Assembly by Bayesian Inference (GABI), and illustrate its application to the bacteriophage [Formula: see text]X174. Read More

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October 2015

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.

Bioinformatics 2014 Apr 13;30(7):923-30. Epub 2013 Nov 13.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Department of Computing and Information Systems and Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia.

Motivation: Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read More

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Automated quality assessment of autonomously acquired microscopic images of fluorescently stained bacteria.

Cytometry A 2010 Jan;77(1):76-85

Department of Limnology, Institute of Plant Biology, University of Zürich, Kilchberg CH-8802, Switzerland.

Quality assessment of autonomously acquired microscopic images is an important issue in high-throughput imaging systems. For example, the presence of low quality images (>or=10%) in a dataset significantly influences the counting precision of fluorescently stained bacterial cells. We present an approach based on an artificial neural network (ANN) to assess the quality of such images. Read More

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January 2010

The glucocorticoid hormone: from pedestal to dust and back.

Authors:
L Angelucci

Eur J Pharmacol 2000 Sep;405(1-3):139-47

Dipartimento di Fisiologia Umana e Farmacologia, Università degli Studi "La Sapienza", Piazzale A. Moro, 5 00185, Rome, Italy.

A potential injury to the hippocampus has been postulated by the "glucocorticoid cascade hypothesis" as deriving from the life-long exposure to the stress glucocorticoid hormone. This hypothesis has been extensively resorted to in the search of a physio-pathological basis of the cognitive and behavioural impairments of old age, as well as for assigning to the hormone a not-irrelevant pathogenic role in brain degenerative diseases. Here I discuss the experimental evidences that have credited to stress a killing-licence, and pose, on the contrary, that the modest degrees of hypercortisolemia present in the above conditions could be interpreted as a beneficial occurrence. Read More

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September 2000

The development of technical and spectrum requirements for meeting federal, state and local public safety agency communication requirements through the year 2010, establishment of rules and requirements for priority access service--FCC. Final rule.

Authors:

Fed Regist 1998 Nov;63(211):58645-58

The Federal Communications Commission (Commission) adopted a First Report and Order ("First Report") contemporaneously with a Third Notice of Proposed Rulemaking that is summarized elsewhere in this edition of the Federal Register. In the First Report, the Commission amends its rules relating to public safety communications in the 764-806 MHz band ("700 MHz band") that the Commission previously reallocated for public safety services and in general. This action commences the process of assigning licenses for frequencies in the 700 MHz band and addresses an urgent need for additional public safety radio spectrum and the need for nationwide interoperability among local, state, and federal entities. Read More

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November 1998
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