scholarly journals Graphing Ecotoxicology: The MAGIC Graph for Linking Environmental Data on Chemicals

Data ◽  
2019 ◽  
Vol 4 (1) ◽  
pp. 34 ◽  
Author(s):  
Sascha Bub ◽  
Jakob Wolfram ◽  
Sebastian Stehle ◽  
Lara Petschick ◽  
Ralf Schulz
Keyword(s):  
Large Scale ◽  
Meta Analysis ◽  
Environmental Data ◽  
Relational Data ◽  
Chemical Information ◽  
Graph Database ◽  
Data Systems ◽  
Large Scale Analysis ◽  
Multiple Data ◽  
The Impact

Assessing the impact of chemicals on the environment and addressing subsequent issues are two central challenges to their safe use. Environmental data are continuously expanding, requiring flexible, scalable, and extendable data management solutions that can harmonize multiple data sources with potentially differing nomenclatures or levels of specificity. Here, we present the methodological steps taken to construct a rule-based labeled property graph database, the “Meta-analysis of the Global Impact of Chemicals” (MAGIC) graph, for potential environmental impact chemicals (PEIC) and its subsequent application harmonizing multiple large-scale databases. The resulting data encompass 16,739 unique PEICs attributed to their corresponding chemical class, stereo-chemical information, valid synonyms, use types, unique identifiers (e.g., Chemical Abstract Service registry number CAS RN), and others. These data provide researchers with additional chemical information for a large amount of PEICs and can also be publicly accessed using a web interface. Our analysis has shown that data harmonization can increase up to 98% when using the MAGIC graph approach compared to relational data systems for datasets with different nomenclatures. The graph database system and its data appear more suitable for large-scale analysis where traditional (i.e., relational) data systems are reaching conceptional limitations.

The Association between COMT Val158Met Polymorphism and the Post-Traumatic Stress Disorder Risk: A Meta-Analysis

2021 ◽  
pp. 1-14
Author(s):  
Mi Su ◽  
Yongyan Song
Keyword(s):  
Post Traumatic Stress Disorder ◽  
Traumatic Stress ◽  
Large Scale ◽  
Stress Disorder ◽  
Meta Analysis ◽  
Cochrane Library ◽  
Post Traumatic Stress ◽  
Val158met Polymorphism ◽  
Post Traumatic ◽  
The Impact

<b><i>Background:</i></b> Genetic factors were suggested to have influence on the development of post-traumatic stress disorder (PTSD). The possible association between catechol-O-methyltransferase (<i>COMT</i>) Val158Met polymorphism and PTSD has been evaluated in several studies. But the results were still controversial. Therefore, we conduct this meta-analysis to address these issues. <b><i>Methods:</i></b> The PubMed, EMBASE, Cochrane Library, and Web of Science databases were searched for eligible studies. The pooled odds ratio (OR) with 95% confidence interval (CI) was calculated to estimate the association between <i>COMT</i> Val158Met polymorphism and PTSD. <b><i>Results:</i></b> Five articles including 6 studies with 893 cases and 968 controls were finally included in the present meta-analysis. The pooled analyses did not demonstrate a significant association between the <i>COMT</i> Val158Met polymorphism and PTSD in any of the selected genetic models: allele model (OR = 1.13, 95% CI: 0.97–1.31), dominant model (OR = 1.17, 95% CI: 0.93–1.46), recessive model (OR = 1.44, 95% CI: 0.78–2.66), and additive model (OR = 1.54, 95% CI: 0.85–2.80). Subgroup analyses suggested that the Hardy-Weinberg equilibrium status of genotype distributions could influence the relationship of <i>COMT</i> Val158Met polymorphism and PTSD. <b><i>Conclusions:</i></b> The present meta-analysis suggested that the <i>COMT</i> Val158Met polymorphism may not be associated with the PTSD risk. Further large-scale and population-representative studies are warranted to evaluate the impact of the <i>COMT</i> Val158Met polymorphism on the risk of PTSD.

scholarly journals Towards Best Practice in Hair Metabolomic Studies: Systematic Investigation on the Impact of Hair Length and Color

Metabolites ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 381
Author(s):  
Lisa Eisenbeiss ◽  
Tina M. Binz ◽  
Markus R. Baumgartner ◽  
Thomas Kraemer ◽  
Andrea E. Steuer
Keyword(s):  
Large Scale ◽  
Best Practice ◽  
Data Interpretation ◽  
Systematic Investigation ◽  
Hair Color ◽  
Large Scale Analysis ◽  
Retrospective Monitoring ◽  
Hair Samples ◽  
Endogenous Metabolites ◽  
The Impact

Untargeted metabolomic studies are used for large-scale analysis of endogenous compounds. Due to exceptional long detection windows of incorporated substances in hair, analysis of hair samples for retrospective monitoring of metabolome changes has recently been introduced. However, information on the general behavior of metabolites in hair samples is scarce, hampering correct data interpretation so far. The presented study aimed to investigate endogenous metabolites depending on hair color and along the hair strand and to propose recommendations for best practice in hair metabolomic studies. A metabolite selection was analyzed using untargeted data acquisition in genuine hair samples from different hair colors and after segmentation in 3 cm segments. Significant differences in metabolites among hair colors and segments were found. In conclusion, consideration of hair color and hair segments is necessary for hair metabolomic studies and, subsequently, recommendations for best practice in hair metabolomic studies were proposed.

scholarly journals Simulation-Based Evaluation of the Performance of Broadband over Power Lines with Multiple Repeaters in Linear Topology of Distribution Substations

2020 ◽  
Vol 10 (19) ◽  
pp. 6879
Author(s):  
Petr Musil ◽  
Petr Mlynek ◽  
Jan Slacik ◽  
Jiri Pokorny
Keyword(s):  
Smart Grids ◽  
Large Scale ◽  
Field Measurements ◽  
Lessons Learned ◽  
Power Lines ◽  
Multiple Streams ◽  
Linear Topology ◽  
Performance Improvements ◽  
Multiple Data ◽  
The Impact

Broadband over Power Lines (BPL) is considered a promising communication technology in the concept of Smart Grids. This paper evaluates networks based on BPL, with a focus on the impact of repeaters in the linear topology of distribution substations. In large-scale Smart Grids network planning, positions of repeaters have to be carefully chosen. This article should help to determine such positions and limitations of BPL linear topology networks. Laboratory and on-field measurements and their results are presented in this article. Results show the impact of repeater’s deployment for different testing methodologies also with regard to other already presented studies. Measured values and the determined impacts of repeaters are later used as input data for simulation of the linear BPL topology in terms of network throughput with multiple streams and bottlenecks. These occur especially on lines shared by multiple communicating nodes. Furthermore, the simulation investigates the balancing time of multiple data streams throughput. The simulation shows that the throughput balancing can occupy a significant time slot, up to tens of seconds before the throughput of different streams balances. Also, the more data is generated, the more time the balancing time takes. Additionally, the throughput drop caused by a repeater is determined into the range of 35–60%. Based on the measurement and simulation results, lessons learned are presented, and possible performance improvements are discussed.

scholarly journals Informal nature experience on the school playground

2015 ◽  
Vol 2 (1) ◽  
pp. 18-25 ◽  
Author(s):  
Andreas Raith
Keyword(s):  
Primary Schools ◽  
Large Scale ◽  
School Teacher ◽  
Meta Analysis ◽  
Educational Institutions ◽  
Primary School Teacher ◽  
School Playgrounds ◽  
First Results ◽  
The Impact ◽  
Nature Experience

Abstract In Germany, all-day care and all-day schooling are currently increasing on a large-scale. The extended time children spend in educational institutions could potentially result in limited access to nature experience for children. On the other hand, it could equally create opportunities for informal nature experience if school playgrounds have a specific nature-oriented design. This article is written from the perspective of a primary school teacher and presents the findings of a meta-analysis which looks at the impact nature experience has on the development of children. Furthermore, the first results of a research study on green playgrounds in primary schools is discussed. The results so far seem to indicate that green school playgrounds have the potential of providing nature experience particularly for primary students

scholarly journals Meta-analysis and profiling of cardiac expression modules

2008 ◽  
Vol 35 (3) ◽  
pp. 305-315 ◽  
Author(s):  
Uri David Akavia ◽  
Dafna Benayahu
Keyword(s):  
Heart Failure ◽  
Large Scale ◽  
Meta Analysis ◽  
Gene Expression Omnibus ◽  
Biological Knowledge ◽  
Map Algorithm ◽  
Large Scale Analysis ◽  
Expression Of Genes ◽  
Prior Biological Knowledge ◽  
Clinical Conditions

Heart failure is a complex, complicated disease that is not yet fully understood. We used the Module Map algorithm to uncover groups of genes that have a similar pattern of expression under various conditions of heart stress. These groups of genes are called modules and may serve as computational predictions of biological pathways for the various clinical situations. The Module Map algorithm allows a large-scale analysis of genes expressed. We applied this algorithm to 700 different mouse experiments downloaded from the Gene Expression Omnibus database, which identified 884 modules. The analysis reconstructed partially known principles that play a role in governing the response of heart to stress, thus demonstrating the strength of the method. We have shown a role of genes related to the immune system in conditions of heart remodeling and failure. We have also shown changes in the expression of genes involved with energy metabolism and changes in the expression of contractile proteins of the heart following myocardial infarction. When focusing on another module we noted a new correlation between genes related to osteogenesis and heart failure, including Runx2 and Ahsg, whose role in heart failure was unknown so far. Despite a lack of prior biological knowledge, the Module Map algorithm has reconstructed known pathways, which demonstrates the strength of this new method for analyzing gene profiles related to clinical phenomenon. The method and the analysis presented are a new avenue to uncover the correlation of clinical conditions to the molecular level.

scholarly journals Association Analysis and Meta-Analysis of Multi-allelic Variants for Large Scale Sequence Data

2017 ◽  
Author(s):  
Xiaowei Zhan ◽  
Sai Chen ◽  
Yu Jiang ◽  
Mengzhen Liu ◽  
William G. Iacono ◽  
...  
Keyword(s):  
Large Scale ◽  
Rare Variants ◽  
Sequence Data ◽  
Meta Analysis ◽  
Joint Modeling ◽  
Allelic Variants ◽  
Association Analyses ◽  
Link Type ◽  
Gene Level ◽  
The Impact

AbstractMotivation:There is great interest to understand the impact of rare variants in human diseases using large sequence datasets. In deep sequences datasets of >10,000 samples, ∼10% of the variant sites are observed to be multi-allelic. Many of the multi-allelic variants have been shown to be functional and disease relevant. Proper analysis of multi-allelic variants is critical to the success of a sequencing study, but existing methods do not properly handle multi-allelic variants and can produce highly misleading association results.Results:We propose novel methods to encode multi-allelic sites, conduct single variant and gene-level association analyses, and perform meta-analysis for multi-allelic variants. We evaluated these methods through extensive simulations and the study of a large meta-analysis of ∼18,000 samples on the cigarettes-per-day phenotype. We showed that our joint modeling approach provided an unbiased estimate of genetic effects, greatly improved the power of single variant association tests, and enhanced gene-level tests over existing approaches.Availability:Software packages implementing these methods are available at (https://github.com/zhanxw/rvtestshttp://genome.sph.umich.edu/wiki/RareMETAL).Contact:[email protected]; [email protected]

scholarly journals Cortical Thickness Trajectories across the Lifespan: Data from 17,075 healthy individuals aged 3-90 years

2020 ◽  
Author(s):  
Sophia Frangou ◽  
Amirhossein Modabbernia ◽  
Gaelle E Doucet ◽  
Efstathios Papachristou ◽  
Steven CR Williams ◽  
...  
Keyword(s):  
Cortical Thickness ◽  
Large Scale ◽  
Meta Analysis ◽  
General Pattern ◽  
Individual Variability ◽  
Anterior Cingulate ◽  
Healthy Individuals ◽  
Large Scale Analysis ◽  
Age Related ◽  
Steep Decrease

AbstractDelineating age-related cortical trajectories in healthy individuals is critical given the association of cortical thickness with cognition and behaviour. Previous research has shown that deriving robust estimates of age-related brain morphometric changes requires large-scale studies. In response, we conducted a large-scale analysis of cortical thickness in 17,075 individuals aged 3-90 years by pooling data through the Lifespan Working group of the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) Consortium. We used fractional polynomial (FP) regression to characterize age-related trajectories in cortical thickness, and we computed normalized growth centiles using the parametric Lambda, Mu, and Sigma (LMS) method. Inter-individual variability was estimated using meta-analysis and one-way analysis of variance. Overall, cortical thickness peaked in childhood and had a steep decrease during the first 2-3 decades of life; thereafter, it showed a gradual monotonic decrease which was steeper in men than in women particularly in middle-life. Notable exceptions to this general pattern were entorhinal, temporopolar and anterior cingulate cortices. Inter-individual variability was largest in temporal and frontal regions across the lifespan. Age and its FP combinations explained up to 59% variance in cortical thickness. These results reconcile uncertainties about age-related trajectories of cortical thickness; the centile values provide estimates of normative variance in cortical thickness, and may assist in detecting abnormal deviations in cortical thickness, and associated behavioural, cognitive and clinical outcomes.

scholarly journals TDD Dynamics: Understanding the Impact of Test-Driven Development on Software Quality and Productivity

2021 ◽  
Author(s):  
Yahha Rafique
Keyword(s):  
Empirical Research ◽  
Large Scale ◽  
Meta Analysis ◽  
Empirical Studies ◽  
Extreme Programming ◽  
Second Phase ◽  
Moderator Variables ◽  
Empirical Measures ◽  
Test Driven Development ◽  
The Impact

Test-Driven Development (TDD) is one of the cornerstone practices of the Extreme Programming agile methodology. Today, despite the large scale adoption of TDD in industry, including large software firms such as Microsoft and IBM, its usefulness with regard to the quality and productivity constructs it still under question. Empirical Research has failed to produce conclusive results; all possible results have been reported for both constructs. This research adopts non-empirical measures to gain a deeper understanding of TDD. A two-phased approach has been undertaken towards the goal. The first phase involves conducting a meta-analysis of past empirical research. The meta-analysis quantitatively combines the results of individual empirical studies and identifies moderator variables that could potentially govern the performance of TDD. The second phase of the approach involves the construction of a simulation model of a TDD-based development process. The presented model further analyzes the impact of changes in moderator variables.

scholarly journals Efficacy and safety profile of doxofylline compared to theophylline in asthma: a meta-analysis

2019 ◽  
Vol 14 ◽  
Author(s):  
Paola Rogliani ◽  
Luigino Calzetta ◽  
Josuel Ora ◽  
Mario Cazzola ◽  
Maria Gabriella Matera
Keyword(s):  
Safety Profile ◽  
Large Scale ◽  
Meta Analysis ◽  
Forced Expiratory Volume ◽  
Chronic Obstructive ◽  
Efficacy And Safety ◽  
Major Drawback ◽  
Asthmatic Patients ◽  
Quantitative Synthesis ◽  
The Impact

Background: Oral methylxanthines are effective drugs for the treatment of chronic obstructive respiratory disorders. The novel methylxanthine doxofylline, that has bronchodilator and anti-inflammatory activities, is not affected by the major drawback of theophylline. Nowadays large-scale quantitative synthesis comparing the efficacy and safety profile of doxofylline vs. theophylline in the treatment of asthma is still lacking. Therefore, we performed a quantitative synthesis to compare the efficacy/safety profile of doxofylline and theophylline in asthma. Methods: A pairwise and network meta-analyses were performed to assess the impact of doxofylline vs. theophylline and placebo on the change in asthma events, risk of adverse events (AEs), forced expiratory volume in 1 s (FEV1), and salbutamol use. Results: Data obtained from 696 asthmatic patients were extracted from 4 randomized controlled trials published between 2015 and 2018. Doxofylline was significantly (P < 0.05) more effective than theophylline in reducing the daily asthma events (mean difference − 0.14, 95%CI -0.27 – 0.00) and risk of AEs (relative risk 0.76, 95%CI 0.59–0.99). Doxofylline was as effective as theophylline in improving FEV1, and a trend of superiority (P = 0.058) was detected for doxofylline over theophylline with respect to the reduction in the use of salbutamol as rescue medication. The rank of effectiveness was doxofylline>theophylline> > placebo, and the rank of safety was placebo>doxofylline> > theophylline. Conclusions: Doxofylline is an effective and safe methylxanthine for the treatment of asthma, with an efficacy/ safety profile greater than that of theophylline. Trial registration: Meta-analysis registration: CRD42019119849.

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