Search results for "Bases"
showing 10 items of 1240 documents
Expression profiling of uniparental mouse embryos is inefficient in identifying novel imprinted genes
2006
AbstractImprinted genes are expressed from only one allele in a parent-of-origin-specific manner. We here describe a systematic approach to identify novel imprinted genes using quantification of allele-specific expression by Pyrosequencing, a highly accurate method to detect allele-specific expression differences. Sixty-eight candidate imprinted transcripts mapping to known imprinted chromosomal regions were selected from a recent expression profiling study of uniparental mouse embryos and analyzed. Three novel imprinted transcripts encoding putative non-protein-coding RNAs were identified on the basis of parent-of-origin-specific monoallelic expression in E11.5 (C57BL/6 × Cast/Ei)F1 and in…
gcType : a high-quality type strain genome database for microbial phylogenetic and functional research
2020
Abstract Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This …
Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics
2019
Abstract Background Distributed approaches based on the MapReduce programming paradigm have started to be proposed in the Bioinformatics domain, due to the large amount of data produced by the next-generation sequencing techniques. However, the use of MapReduce and related Big Data technologies and frameworks (e.g., Apache Hadoop and Spark) does not necessarily produce satisfactory results, in terms of both efficiency and effectiveness. We discuss how the development of distributed and Big Data management technologies has affected the analysis of large datasets of biological sequences. Moreover, we show how the choice of different parameter configurations and the careful engineering of the …
Preventive strategies and factors associated with surgically treated necrotising enterocolitis in extremely preterm infants: an international unit su…
2019
ObjectivesTo compare necrotising enterocolitis (NEC) prevention practices and NEC associated factors between units from eight countries of the International Network for Evaluation of Outcomes of Neonates, and to assess their association with surgical NEC rates.DesignProspective unit-level survey combined with retrospective cohort study.SettingNeonatal intensive care units in Australia/New Zealand, Canada, Finland, Israel, Spain, Sweden, Switzerland and Tuscany (Italy).PatientsExtremely preterm infants born between 240to 286weeks’ gestation, with birth weights<1500 g, and admitted between 2014–2015.ExposuresNEC prevention practices (probiotics, feeding, donor milk) using responses of an o…
IMI – Oral biopharmaceutics tools project – Evaluation of bottom-up PBPK prediction success part 4: Prediction accuracy and software comparisons with…
2020
Oral drug absorption is a complex process depending on many factors, including the physicochemical properties of the drug, formulation characteristics and their interplay with gastrointestinal physiology and biology. Physiological-based pharmacokinetic (PBPK) models integrate all available information on gastro-intestinal system with drug and formulation data to predict oral drug absorption. The latter together with in vitro-in vivo extrapolation and other preclinical data on drug disposition can be used to predict plasma concentration-time profiles in silico. Despite recent successes of PBPK in many areas of drug development, an improvement in their utility for evaluating oral absorption i…
BioTIME: A database of biodiversity time series for the Anthropocene
2018
Abstract Motivation The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. Main types of variables included The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, th…
Controlling false match rates in record linkage using extreme value theory
2011
AbstractCleansing data from synonyms and homonyms is a relevant task in fields where high quality of data is crucial, for example in disease registries and medical research networks. Record linkage provides methods for minimizing synonym and homonym errors thereby improving data quality. We focus our attention to the case of homonym errors (in the following denoted as ‘false matches’), in which records belonging to different entities are wrongly classified as equal. Synonym errors (‘false non-matches’) occur when a single entity maps to multiple records in the linkage result. They are not considered in this study because in our application domain they are not as crucial as false matches. Fa…
Spatio-temporal Schema Integration with Validation: A Practical Approach
2005
We propose to enhance a schema integration process with a validation phase employing logic-based data models. In our methodology, we validate the source schemas against the data model; the inter-schema mappings are validated against the semantics of the data model and the syntax of the correspondence language. In this paper, we focus on how to employ a reasoning engine to validate spatio-temporal schemas and describe where the reasoning engine is plugged into our integration methodology. The validation phase distinguishes our integration methodology from other approaches. We shift the emphasis on automation from the a priori discovery to the a posteriori checking of the inter-schema mapping…
Population geocoding for healthcare management. Technical challenges and quality issues
2015
The present work aims at describing the main issues related with population geocoding for healthcare management. Some of the available procedures for geocoding multiple addresses are described and an indicator of quality of the geocoded addresses is proposed. As a case study, the geocoding of population addresses of a set of 9 Sicilian Municipalities is described and results deriving from the use of two different methods are compared in terms of quality. Some potential applications of population geocoding in healthcare management are finally discussed.
Nationwide evaluation of day-to-day clinical pharmacists' interventions in German hospitals.
2015
tudy Objective To describe and evaluate the extent and diversity of nationwide data from clinical pharmacists’ interventions (PIs) in German hospitals. Design Retrospective analysis. Data Source The ADKA-DokuPIK German database, a national anonymous self-reported Internet-based documentation system for routine PIs as well as for medication errors reported by German hospital pharmacists. Measurements and Main Results Data sets from ADKA-DokuPIK entered between January 2009 and December 2012 were analyzed descriptively. A total of 27,610 PIs were entered, mainly by ward-based clinical pharmacists (82.5%). Most of the PIs were performed on surgical wards (37.8%), followed by anesthesiology/int…