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https://www.readbyqxmd.com/read/30545485/provcare-characterizing-scientific-reproducibility-of-biomedical-research-studies-using-semantic-provenance-metadata
#1
Satya S Sahoo, Joshua Valdez, Matthew Kim, Michael Rueschman, Susan Redline
OBJECTIVE: Reproducibility of research studies is key to advancing biomedical science by building on sound results and reducing inconsistencies between published results and study data. We propose that the available data from research studies combined with provenance metadata provide a framework for evaluating scientific reproducibility. We developed the ProvCaRe platform to model, extract, and query semantic provenance information from 435, 248 published articles. METHODS: The ProvCaRe platform consists of: (1) the S3 model and a formal ontology; (2) a provenance-focused text processing workflow to generate provenance triples consisting of subject, predicate, and object using metadata extracted from articles; and (3) the ProvCaRe knowledge repository that supports "provenance-aware" hypothesis-driven search queries...
January 2019: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/30535518/correction-to-ultrasound-guided-renal-transplant-biopsy-practical-and-pragmatic-considerations
#2
Maitray D Patel, Scott W Young, J Scott Kriegshauser, Nirvikar Dahiya
The original version of this article unfortunately contained an error. Though one of the coauthor names correctly appeared in the published version, it is incorrectly displayed in indexing sites due to a tagging error in metadata.
December 7, 2018: Abdominal Radiology
https://www.readbyqxmd.com/read/30535239/pdx-finder-a-portal-for-patient-derived-tumor-xenograft-model-discovery
#3
Nathalie Conte, Jeremy C Mason, Csaba Halmagyi, Steven Neuhauser, Abayomi Mosaku, Galabina Yordanova, Aikaterini Chatzipli, Dale A Begley, Debra M Krupke, Helen Parkinson, Terrence F Meehan, Carol C Bult
Patient-derived tumor xenograft (PDX) mouse models are a versatile oncology research platform for studying tumor biology and for testing chemotherapeutic approaches tailored to genomic characteristics of individual patients' tumors. PDX models are generated and distributed by a diverse group of academic labs, multi-institution consortia and contract research organizations. The distributed nature of PDX repositories and the use of different metadata standards for describing model characteristics presents a significant challenge to identifying PDX models relevant to specific cancer research questions...
December 7, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30533276/implementing-the-dicom-standard-for-digital-pathology
#4
Markus D Herrmann, David A Clunie, Andriy Fedorov, Sean W Doyle, Steven Pieper, Veronica Klepeis, Long P Le, George L Mutter, David S Milstone, Thomas J Schultz, Ron Kikinis, Gopal K Kotecha, David H Hwang, Katherine P Andriole, A John Iafrate, James A Brink, Giles W Boland, Keith J Dreyer, Mark Michalski, Jeffrey A Golden, David N Louis, Jochen K Lennerz
Background: Digital Imaging and Communications in Medicine (DICOM® ) is the standard for the representation, storage, and communication of medical images and related information. A DICOM file format and communication protocol for pathology have been defined; however, adoption by vendors and in the field is pending. Here, we implemented the essential aspects of the standard and assessed its capabilities and limitations in a multisite, multivendor healthcare network. Methods: We selected relevant DICOM attributes, developed a program that extracts pixel data and pixel-related metadata, integrated patient and specimen-related metadata, populated and encoded DICOM attributes, and stored DICOM files...
2018: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/30527585/partitioning-of-poly-and-perfluoroalkyl-substances-from-soil-to-groundwater-within-aqueous-film-forming-foam-source-zones
#5
R Hunter Anderson, Dave T Adamson, Hans F Stroo
Metadata from on-going site investigations at U.S. Air Force sites impacted by Aqueous Film-Forming Foam (AFFF) were used to evaluate primary factors that affect transport of poly- and perfluoroalkyl substances (PFAS) within source zones. Soil-to-groundwater ratios (γSoil-GW ) were calculated for each site and PFAS as an empirical transport metric and regressed against select soil chemical and physical properties, as well as relevant interactions thereof, using analysis of covariance (ANCOVA). Total organic carbon and percent total clay content were significant covariates and best fit log-transformed Kd with a parallel lines model...
November 27, 2018: Journal of Contaminant Hydrology
https://www.readbyqxmd.com/read/30521609/porcine-circovirus-2-pcv-2-genotype-update-and-proposal-of-a-new-genotyping-methodology
#6
Giovanni Franzo, Joaquim Segalés
Porcine circovirus 2 (PCV-2) is one of the most widespread viral infections of swine, causing a remarkable economic impact because of direct losses and indirect costs for its control. As other ssDNA viruses, PCV-2 is characterized by a high evolutionary rate, leading to the emergence of a plethora of variants with different biological and epidemiological features. Over time, several attempts have been made to organize PCV-2 genetic heterogeneity in recognized genotypes. This categorization has clearly simplified the epidemiological investigations, allowing to identify different spatial and temporal patterns among genotypes...
2018: PloS One
https://www.readbyqxmd.com/read/30514831/smartphone-app-for-non-invasive-detection-of-anemia-using-only-patient-sourced-photos
#7
Robert G Mannino, David R Myers, Erika A Tyburski, Christina Caruso, Jeanne Boudreaux, Traci Leong, G D Clifford, Wilbur A Lam
We introduce a paradigm of completely non-invasive, on-demand diagnostics that may replace common blood-based laboratory tests using only a smartphone app and photos. We initially targeted anemia, a blood condition characterized by low blood hemoglobin levels that afflicts >2 billion people. Our app estimates hemoglobin levels by analyzing color and metadata of fingernail bed smartphone photos and detects anemia (hemoglobin levels <12.5 g dL-1 ) with an accuracy of ±2.4 g dL-1 and a sensitivity of 97% (95% CI, 89-100%) when compared with CBC hemoglobin levels (n = 100 subjects), indicating its viability to serve as a non-invasive anemia screening tool...
December 4, 2018: Nature Communications
https://www.readbyqxmd.com/read/30510545/high-throughput-sequencing-facilitates-characterization-of-a-forgotten-plant-virus-the-case-of-a-henbane-mosaic-virus-infecting-tomato
#8
Anja Pecman, Denis Kutnjak, Nataša Mehle, Magda Tušek Žnidarič, Ion Gutiérrez-Aguirre, Patricija Pirnat, Ian Adams, Neil Boonham, Maja Ravnikar
High-throughput sequencing has dramatically broadened the possibilities for plant virus research and diagnostics, enabling discovery of new or obscure viruses, and virus strains and rapid sequencing of their genomes. In this research, we employed high-throughput sequencing to discover a new virus infecting tomato, Henbane mosaic virus (Potyvirus , Potyviridae ), which was first discovered at the beginning of 20th century in the United Kingdom in cultivated henbane. A field tomato plant with severe necrotic symptoms of unknown etiology was sampled in Slovenia and high-throughput sequencing analysis using small RNA and ribosomal RNA depleted total RNA approaches revealed a mixed infection with Potato virus M ( Carlavirus , Betaflexiviridae ), Southern tomato virus ( Amalgavirus , Amalgamaviridae ) and henbane mosaic virus in the sample...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30505982/an-inventory-of-ready-to-use-and-publicly-available-tools-for-the-safety-assessment-of-nanomaterials
#9
A Paula K Jantunen, Stefania Gottardo, Kirsten Rasmussen, Hugues P Crutzen
Legislation addressing environmental, health and safety aspects of nanomaterials in consumer products and ensuring their safe use is being continuously updated in the European Union and globally. This leads to a growing need for tools to implement this developing legislation. A freely accessible inventory of ready-to-use and publicly available tools that together cover the tasks within a nanomaterial safety assessment process was built in the presented work. This inventory is a unique metadata set in Excel® format: the 'NANoREG Toolbox', which assembles information needed for selecting and accessing instruments that meet specific goals...
October 2018: NanoImpact
https://www.readbyqxmd.com/read/30502161/iso-food-ontology-a-formal-representation-of-the-knowledge-within-the-domain-of-isotopes-for-food-science
#10
Tome Eftimov, Gordana Ispirova, Doris Potočnik, Nives Ogrinc, Barbara Koroušić Seljak
To link and harmonize different knowledge repositories with respect to isotopic data, we propose an ISO-FOOD ontology as a domain ontology for describing isotopic data within Food Science. The ISO-FOOD ontology consists of metadata and provenance data that needs to be stored together with data elements in order to describe isotopic measurements with all necessary information required for future analysis. The new domain has been linked with existing ontologies, such as Units of Measurements Ontology, Food, Nutrient and the Bibliographic Ontology...
March 30, 2019: Food Chemistry
https://www.readbyqxmd.com/read/30497362/glossary-the-global-ocean-16s-subunit-web-accessible-resource
#11
M Tangherlini, M Miralto, C Colantuono, M Sangiovanni, A Dell' Anno, C Corinaldesi, R Danovaro, M L Chiusano
BACKGROUND: Environmental metagenomics is a challenging approach that is exponentially spreading in the scientific community to investigate taxonomic diversity and possible functions of the biological components. The massive amount of sequence data produced, often endowed with rich environmental metadata, needs suitable computational tools to fully explore the embedded information. Bioinformatics plays a key role in providing methodologies to manage, process and mine molecular data, integrated with environmental metagenomics collections...
November 30, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/30470627/artificial-intelligence-and-medical-imaging-2018-french-radiology-community-white-paper
#12
(no author information available yet)
The rapid development of information technology and data processing capabilities has led to the creation of new tools known as artificial intelligence (AI). Medical applications of AI are emerging, and the French radiology community felt it was therefore timely to issue a position paper on AI as part of its role as a leader in the development of digital projects. Essential information about the application of AI to radiology includes a description of the available algorithms with a glossary; a review of the issues raised by healthcare data, notably those pertaining to imaging (imaging data and co-variables, metadata); a look at research and innovation; an overview of current and future applications; a discussion of AI education; and a scrutiny of ethical issues...
November 2018: Diagnostic and Interventional Imaging
https://www.readbyqxmd.com/read/30465646/tetyper-a-bioinformatic-pipeline-for-classifying-variation-and-genetic-contexts-of-transposable-elements-from-short-read-whole-genome-sequencing-data
#13
Anna E Sheppard, Nicole Stoesser, Ian German-Mesner, Kasi Vegesana, A Sarah Walker, Derrick W Crook, Amy J Mathers
Much of the worldwide dissemination of antibiotic resistance has been driven by resistance gene associations with mobile genetic elements (MGEs), such as plasmids and transposons. Although increasing, our understanding of resistance spread remains relatively limited, as methods for tracking mobile resistance genes through multiple species, strains and plasmids are lacking. We have developed a bioinformatic pipeline for tracking variation within, and mobility of, specific transposable elements (TEs), such as transposons carrying antibiotic-resistance genes...
November 22, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/30465642/panini-pangenome-neighbour-identification-for-bacterial-populations
#14
Khalil Abudahab, Joaquín M Prada, Zhirong Yang, Stephen D Bentley, Nicholas J Croucher, Jukka Corander, David M Aanensen
The standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here, we introduce panini (Pangenome Neighbour Identification for Bacterial Populations), a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding based on the t-SNE (t-distributed stochastic neighbour embedding) algorithm...
November 22, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/30461598/establishment-of-a-gonococcal-antimicrobial-surveillance-programme-gasp-in-accordance-with-who-standards-in-c%C3%A3-te-d-ivoire-western-africa-2014-2017
#15
Alain Yéo, Belinda Kouamé-Blavo, Clarisse E Kouamé, Abdoulaye Ouattara, Ahou C Yao, Brigitte D Gbedé, Francis Bazan, Hortense Faye-Ketté, Mireille Dosso, Teodora Wi, Magnus Unemo
BACKGROUND: Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is compromising the treatment of gonorrhea globally. Recent AMR data are extremely limited in Africa, and mainly totally lacking in Western Africa including Côte d'Ivoire. This study i) established a quality-assured gonococcal antimicrobial surveillance programme (GASP), according to WHO quality criteria, ii) investigated the AMR to eight therapeutic antimicrobials in gonococcal isolates from 2014 to 2017, and iii) provided evidence for updating the national STD syndromic management guidelines in Côte d'Ivoire...
November 19, 2018: Sexually Transmitted Diseases
https://www.readbyqxmd.com/read/30459140/description-of-cardiological-apps-from-the-german-app-store-semiautomated-retrospective-app-store-analysis
#16
Urs-Vito Albrecht, Gerd Hasenfuß, Ute von Jan
BACKGROUND: In the app stores of mobile platforms, consumers are confronted with an enormous number of mobile apps. Over the past few years, considerable research has been undertaken into to identifying, characterizing, and evaluating apps, be it in health-related or other contexts. However, many of these projects are restricted to specific areas of application and offer little flexibility in adapting the applied criteria. OBJECTIVE: This paper presents an adaptable method for selecting and characterizing mobile apps listed in a mobile App Store (the Apple App Store)...
November 20, 2018: JMIR MHealth and UHealth
https://www.readbyqxmd.com/read/30457569/a-reference-set-of-curated-biomedical-data-and-metadata-from-clinical-case-reports
#17
J Harry Caufield, Yijiang Zhou, Anders O Garlid, Shaun P Setty, David A Liem, Quan Cao, Jessica M Lee, Sanjana Murali, Sarah Spendlove, Wei Wang, Li Zhang, Yizhou Sun, Alex Bui, Henning Hermjakob, Karol E Watson, Peipei Ping
Clinical case reports (CCRs) provide an important means of sharing clinical experiences about atypical disease phenotypes and new therapies. However, published case reports contain largely unstructured and heterogeneous clinical data, posing a challenge to mining relevant information. Current indexing approaches generally concern document-level features and have not been specifically designed for CCRs. To address this disparity, we developed a standardized metadata template and identified text corresponding to medical concepts within 3,100 curated CCRs spanning 15 disease groups and more than 750 reports of rare diseases...
November 20, 2018: Scientific Data
https://www.readbyqxmd.com/read/30457533/ctx-m-65-extended-spectrum-%C3%AE-lactamase-producing-salmonella-enterica-serotype-infantis-united-states-1
#18
Allison C Brown, Jessica C Chen, Louise K Francois Watkins, Davina Campbell, Jason P Folster, Heather Tate, Jamie Wasilenko, Christine Van Tubbergen, Cindy R Friedman
Extended-spectrum β-lactamases (ESBLs) confer resistance to clinically important third-generation cephalosporins, which are often used to treat invasive salmonellosis. In the United States, ESBLs are rarely found in Salmonella. However, in 2014, the US Food and Drug Administration found blaCTX-M-65 ESBL-producing Salmonella enterica serotype Infantis in retail chicken meat. The isolate had a rare pulsed-field gel electrophoresis pattern. To clarify the sources and potential effects on human health, we examined isolates with this pattern obtained from human surveillance and associated metadata...
December 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/30455210/fungarium-specimens-a-largely-untapped-source-in-global-change-biology-and-beyond
#19
REVIEW
Carrie Andrew, Jeffrey Diez, Timothy Y James, Håvard Kauserud
For several hundred years, millions of fungal sporocarps have been collected and deposited in worldwide collections (fungaria) to support fungal taxonomy. Owing to large-scale digitization programs, metadata associated with the records are now becoming publicly available, including information on taxonomy, sampling location, collection date and habitat/substrate information. This metadata, as well as data extracted from the physical fungarium specimens themselves, such as DNA sequences and biochemical characteristics, provide a rich source of information not only for taxonomy but also for other lines of biological inquiry...
November 19, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30453940/developing-a-healthcare-dataset-information-resource-dir-based-on-semantic-web
#20
Jingyi Shi, Mingna Zheng, Lixia Yao, Yaorong Ge
BACKGROUND: The right dataset is essential to obtain the right insights in data science; therefore, it is important for data scientists to have a good understanding of the availability of relevant datasets as well as the content, structure, and existing analyses of these datasets. While a number of efforts are underway to integrate the large amount and variety of datasets, the lack of an information resource that focuses on specific needs of target users of datasets has existed as a problem for years...
November 20, 2018: BMC Medical Genomics
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