Search results for "Database and Informatics Methods"
showing 10 items of 62 documents
Big Data in metagenomics: Apache Spark vs MPI.
2020
The progress of next-generation sequencing has lead to the availability of massive data sets used by a wide range of applications in biology and medicine. This has sparked significant interest in using modern Big Data technologies to process this large amount of information in distributed memory clusters of commodity hardware. Several approaches based on solutions such as Apache Hadoop or Apache Spark, have been proposed. These solutions allow developers to focus on the problem while the need to deal with low level details, such as data distribution schemes or communication patterns among processing nodes, can be ignored. However, performance and scalability are also of high importance when…
The rise of the middle author: Investigating collaboration and division of labor in biomedical research using partial alphabetical authorship
2017
Contemporary biomedical research is performed by increasingly large teams. Consequently, an increasingly large number of individuals are being listed as authors in the bylines, which complicates the proper attribution of credit and responsibility to individual authors. Typically, more importance is given to the first and last authors, while it is assumed that the others (the middle authors) have made smaller contributions. However, this may not properly reflect the actual division of labor because some authors other than the first and last may have made major contributions. In practice, research teams may differentiate the main contributors from the rest by using partial alphabetical author…
Effects of seniority, gender and geography on the bibliometric output and collaboration networks of European Research Council (ERC) grant recipients.
2019
Assessing the success and performance of researchers is a difficult task, as their grant output is influenced by a series of factors, including seniority, gender and geographical location of their host institution. In order to assess the effects of these factors, we analysed the publication and citation outputs, using Scopus and Web of Science, and the collaboration networks of European Research Council (ERC) starting (junior) and advanced (senior) grantees. For this study, we used a cohort of 355 grantees from the Life Sciences domain of years 2007-09. While senior grantees had overall greater publication output, junior grantees had a significantly greater pre-post grant award increase in …
Diagnostic accuracy of adding copeptin to cardiac troponin for non-ST-elevation myocardial infarction: A systematic review and meta-analysis.
2018
Introduction This study aimed to determine the diagnostic accuracy of adding copeptin to cardiac troponin (cTn) on admission to the emergency department (ED) for non-ST elevation myocardial infarction (NSTEMI) compared to cTn alone. Materials and methods A literature search of MEDLINE, EMBASE, and the Cochrane Library was performed (search date: April 13, 2018). Primary studies were included if they accurately reported on patients with symptoms suggestive of acute myocardial infarction and measured both cTn alone and cTn with copeptin upon admission to the ED. The patients with evidence of ST elevation myocardial infarction were excluded. To assess the risk of bias for the included studies,…
Assessing the format and content of journal published and non-journal published rapid review reports: A comparative study
2020
Background As production of rapid reviews (RRs) increases in healthcare, knowing how to efficiently convey RR evidence to various end-users is important given they are often intended to directly inform decision-making. Little is known about how often RRs are produced in the published or unpublished domains, and what and how information is structured. Objectives To compare and contrast report format and content features of journal-published (JP) and non-journal published (NJP) RRs. Methods JP RRs were identified from key databases, and NJP RRs were identified from a grey literature search of 148 RR producing organizations and were sampled proportionate to cluster size by organization and pro…
The short-term efficacy and safety of artificial total disc replacement for selected patients with lumbar degenerative disc disease compared with ant…
2018
PurposeTo systematically compare the efficacy and safety of lumbar total disc replacement (TDR) with the efficacy and safety of anterior lumbar interbody fusion (ALIF) for the treatment of lumbar degenerative disc disease (LDDD).MethodsThe electronic databases PubMed, Web of Science and the Cochrane Library were searched for the period from the establishment of the databases to March 2018. The peer-reviewed articles that investigate the safety and efficacy of TDR and ALIF were retrieved under the given search terms. Quality assessment must be done independently by two authors according to each item of criterion. The statistical analyses were performed using RevMan (version 5.3) and Stata (v…
Human exome and mouse embryonic expression data implicate ZFHX3, TRPS1, and CHD7 in human esophageal atresia
2020
Introduction Esophageal atresia with or without tracheoesophageal fistula (EA/TEF) occurs approximately 1 in 3.500 live births representing the most common malformation of the upper digestive tract. Only half a century ago, EA/TEF was fatal among affected newborns suggesting that the steady birth prevalence might in parts be due to mutational de novo events in genes involved in foregut development. Methods To identify mutational de novo events in EA/TEF patients, we surveyed the exome of 30 case-parent trios. Identified and confirmed de novo variants were prioritized using in silico prediction tools. To investigate the embryonic role of genes harboring prioritized de novo variants we perfor…
A systematic review of maternal smoking during pregnancy and fetal measurements with meta-analysis
2017
Maternal smoking during pregnancy is linked to reduced birth weight but the gestation at onset of this relationship is not certain. We present a systematic review of the literature describing associations between maternal smoking during pregnancy and ultrasound measurements of fetal size, together with an accompanying meta-analysis. Studies were selected from electronic databases (OVID, EMBASE and Google Scholar) that examined associations between maternal smoking or smoke exposure and antenatal fetal ultrasound measurements. Outcome measures were first, second or third trimester fetal measurements. There were 284 abstracts identified, 16 papers were included in the review and the meta-anal…
Spatial Distribution of Fungal Communities in an Arable Soil.
2015
Fungi are prominent drivers of ecological processes in soils, so that fungal communities across different soil ecosystems have been well investigated. However, for arable soils taxonomically resolved fine-scale studies including vertical itemization of fungal communities are still missing. Here, we combined a cloning/Sanger sequencing approach of the ITS/LSU region as marker for general fungi and of the partial SSU region for arbuscular mycorrhizal fungi (AMF) to characterize the microbiome in different maize soil habitats. Four compartments were analyzed over two annual cycles 2009 and 2010: a) ploughed soil in 0-10 cm, b) rooted soil in 40-50 cm, c) root-free soil in 60-70 cm soil depth a…
In silico identification and experimental validation of hits active against KPC-2 β-lactamase
2018
Bacterial resistance has become a worldwide concern, particularly after the emergence of resistant strains overproducing carbapenemases. Among these, the KPC-2 carbapenemase represents a significant clinical challenge, being characterized by a broad substrate spectrum that includes aminothiazoleoxime and cephalosporins such as cefotaxime. Moreover, strains harboring KPC-type β-lactamases are often reported as resistant to available β-lactamase inhibitors (clavulanic acid, tazobactam and sulbactam). Therefore, the identification of novel non β-lactam KPC-2 inhibitors is strongly necessary to maintain treatment options. This study explored novel, non-covalent inhibitors active against KPC-2, …