scholarly journals Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies

2017 ◽  
Author(s):  
Paul P. Gardner ◽  
Renee J. Watson ◽  
Xochitl C. Morgan ◽  
Jenny L. Draper ◽  
Robert D. Finn ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Environmental Monitoring ◽  
Dna Sequences ◽  
Meta Analysis ◽  
Environmental Dna ◽  
Z Score ◽  
Analysis Method ◽  
Bioinformatic Tools ◽  
Significant Challenge ◽  
Ranking Procedure

AbstractEnvironmental DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. We have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are generally accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.

scholarly journals Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6160 ◽  
Author(s):  
Paul P. Gardner ◽  
Renee J. Watson ◽  
Xochitl C. Morgan ◽  
Jenny L. Draper ◽  
Robert D. Finn ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Environmental Monitoring ◽  
Dna Sequences ◽  
Meta Analysis ◽  
Software Tools ◽  
Analysis Method ◽  
Bioinformatic Tools ◽  
Significant Challenge ◽  
Ranking Procedure ◽  
Barcode Dna

Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robustZ-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.

scholarly journals Gray Matter alterations in MS and CIS: a Coordinate based Meta-analysis and regression

2020 ◽  
Author(s):  
Sonika Singh ◽  
Christopher Tench ◽  
Radu Tanasescu ◽  
Cris Constantinescu
Keyword(s):  
Grey Matter ◽  
Disease Duration ◽  
Type I Error ◽  
Meta Analysis ◽  
Random Effect ◽  
Clinically Isolated Syndrome ◽  
Type I ◽  
Z Score ◽  
Analysis Method ◽  
Voxel Based Morphometry

AbstractThe purpose of this coordinate based meta-analysis (CBMA) was to summarise the available evidence related to regional grey matter (GM) changes in patients with multiple sclerosis (MS) and clinically isolated syndrome (CIS). CBMA is a way to find the consistent results across multiple independent studies that are otherwise not easily comparable due to methodological differences. The coordinate based random effect size (CBRES) meta-analysis method utilizes the reported coordinates (foci of the clusters of GM loss) and Z score standardised by number of subjects, controlling type I error rate by false cluster discovery rate (FCDR). Thirty-four published articles reporting forty-five independent studies using voxel-based morphometry (VBM) for the assessment of GM atrophy between MS or CIS patients and healthy controls were identified from electronic databases. The primary meta-analysis identified clusters of spatially consistent cross-study reporting of GM atrophy; subgroup analyses and meta-regression were also performed. This meta-analysis demonstrates consistent areas of GM loss in MS or CIS, in the form of significant clusters. Some clusters also demonstrate correlation with disease duration.

scholarly journals Effectiveness of Community Nutrition-Specific Interventions on Improving Malnutrition of Children under 5 Years of Age in the Eastern Mediterranean Region: A Systematic Review and Meta-Analysis

2021 ◽  
Vol 18 (15) ◽  
pp. 7844
Author(s):  
Delaram Ghodsi ◽  
Nasrin Omidvar ◽  
Bahareh Nikooyeh ◽  
Roshanak Roustaee ◽  
Elham Shakibazadeh ◽  
...  
Keyword(s):  
Cost Effectiveness ◽  
Mediterranean Region ◽  
Eastern Mediterranean ◽  
Meta Analysis ◽  
Eastern Mediterranean Region ◽  
Child Malnutrition ◽  
Z Score ◽  
Community Based ◽  
Nutritional Status Of Children ◽  
Children Under 5

Childhood malnutrition remains an important public health and development problem in low- and middle-income countries. This study aimed to systematically review the community-based nutrition-specific interventions and their effectiveness and/or cost-effectiveness on the nutritional status of children under 5 years of age in the Eastern Mediterranean Region (EMR). A systematic literature search of the English electronic databases, including PubMed, Scopus, ISI Web of Knowledge, Ovid, EMBASE, as well as Persian databases (SID and Magiran) was performed up to May 2019. Studies regarding the effectiveness/cost-effectiveness of the community-based nutrition-specific programs and interventions targeted at under-five-year children in EMR countries were selected. The primary outcomes were mean of Weight-for-age z-score (WAZ), Height-for-Age z-score (HAZ), and Weight-for-Height z-score (WHZ) of children or prevalence of wasting, stunting, and/or underweight among the children. Meta-analysis was also performed on the selected articles and intervention effects (mean differences) were calculated for each outcome for each study and pooled using a weighted random effects model. Risk of bias (ROB) of each included study was assessed based on the Cochrane Handbook for Systematic Reviews. The study protocol was registered in PROSPERO (CRD42020172643). Of 1036 identified studies, eight met the inclusion criteria. Amongst these, seven were from Pakistan and one from Iran. Only one study conducted in Pakistan reported the cost-effectiveness of nutrition-specific interventions in the region. Nutrition education/consultation and cash-based interventions were the most common nutrition-specific strategies used for management of child malnutrition in the EMR countries. Out of these eight studies, four were included in the meta-analysis. When different interventions were pooled, they had resulted in a significant improvement in WHZ of children (MD: 0.26; 95% CI: 0.07 to 0.46, three studies, I2 82.40%). Considering the high prevalence of child malnutrition in a number of countries in the region, capacity building and investigation regarding the implementation of new approaches to improve nutritional status of children and their effect(s) and cost-effectiveness assessment are highly recommended.

scholarly journals The value of travel time savings in freight transport: a meta-analysis

2021 ◽  
Author(s):  
Jawaher Binsuwadan ◽  
Gerard De Jong ◽  
Richard Batley ◽  
Phill Wheat
Keyword(s):  
Travel Time ◽  
Cost Benefit Analysis ◽  
Meta Analysis ◽  
Cost Benefit ◽  
Freight Transport ◽  
Survey Respondent ◽  
Analysis Method ◽  
Marginal Rate ◽  
Travel Time Savings ◽  
Time Savings

AbstractThe value of freight travel time savings (VFTTS) is a monetary value that is considered an important input into cost–benefit analysis and traffic forecasting. The VFTTS is defined as the marginal rate of substitution between travel time and cost and may therefore differ across firms, time and countries. The paper aims to explain variations in the VFTTS by using the meta-analysis method. The analysis covers 106 monetary valuations extracted from 56 studies conducted from 1988 to 2018 in countries across the globe. The meta-analysis method determines the factors that have an impact on these VFTTS variations. The paper briefly introduces the VFTTS concept and describes the adopted meta-analysis methodology, wherein different meta-models are used in VFTTS estimations. The results highlight the necessity of including multiple explanatory variables to ensure adequate explanation of the VFTTS variations. The findings also show that GDP per capita, transport mode and type of survey respondent are statistically significant variables. The paper sheds some light on the variations, thereby advancing the understanding of each factor’s effects on the VFTTS. Furthermore, meta-model outcomes are used to generate new values of travel time savings for different transport modes in freight transport, for several countries. These implied VFTTS can be used as benchmarks to assess existing evidence or provide new evidence to countries where no such values exist.

scholarly journals The Effectiveness of School-Based Interventions on Obesity-Related Behaviours in Primary School Children: A Systematic Review and Meta-Analysis of Randomised Controlled Trials

Children ◽  
2021 ◽  
Vol 8 (6) ◽  
pp. 489
Author(s):  
Sarah Nally ◽  
Angela Carlin ◽  
Nicole E. Blackburn ◽  
Judith S. Baird ◽  
Jo Salmon ◽  
...  
Keyword(s):  
Sedentary Behaviour ◽  
Vegetable Intake ◽  
Data Extraction ◽  
Meta Analysis ◽  
Primary School Children ◽  
Control Group ◽  
Z Score ◽  
School Based ◽  
Positive Treatment ◽  
School Based Interventions

School-based interventions are promising for targeting a change in obesity-related behaviours in children. However, the efficacy of school-based interventions to prevent obesity remains unclear. This review examined the effectiveness of school-based interventions at changing obesity-related behaviours (increased physical activity, decreased sedentary behaviour and improved nutrition behaviour) and/or a change in BMI/BMI z-score. Following PRISMA guidelines, seven databases were systematically searched from 1 January 2009 to 31 December 2020. Two review authors independently screened studies for eligibility, completed data extraction and assessed the risk of bias of each of the included studies. Forty-eight studies met the inclusion criteria and were included in a narrative synthesis. Thirty-eight studies were eligible for inclusion in a meta-analysis. The findings demonstrate that interventions in children when compared to controls resulted in a small positive treatment effect in the control group (2.14; 95% CI = 0.77, 3.50). There was no significant effect on sedentary behaviour, energy intake and fruit and vegetable intake. Significant reductions were found between groups in BMI kg/m2 (−0.39; 95% CI = −0.47, −0.30) and BMI z-score (−0.05; 95% CI = −0.08, −0.02) in favour of the intervention. The findings have important implications for future intervention research in terms of the effectiveness of intervention components and characteristics.

META ANALYSIS METHOD OVERVIEW OF MODELS USED IN OCCUPATIONAL SAFETY TRAININGS

2021 ◽  
Vol 6 (15) ◽  
pp. 482-490
Author(s):  
Filiz ARICAK ◽  
Evren ÇAĞLARER
Keyword(s):  
Work Environment ◽  
Occupational Safety ◽  
Meta Analysis ◽  
Health And Safety ◽  
Safety Training ◽  
Working Environment ◽  
Future Generations ◽  
Analysis Method ◽  
Training Models ◽  
Safety Procedures

In this study, an analysis of independent studies dealing with occupational safety training in different learning environments, in which various learning materials are used, was carried out. As a method, meta-analysis method was used. For this purpose, databases were used to collect national and international articles and papers suitable for the purpose of the study. Studies that did not mention the tools, equipment and environment used in education in the collected studies were excluded from the research, and 18 studies were included in the meta-analysis. The data obtained studies are categorized according to the education models, the sectors in which the education is applied and the characteristics of the participants in the education. As it is known, occupational health and safety procedures aim at a healthy and reliable working environment for its employees. However, the ultimate goal is to raise not only employees but also future generations with this awareness. The most important instrument of this is undoubtedly education. For this reason, it is necessary to develop training models suitable for the work environment, age, gender and every conceivable situation.

An updated look at the uneven distribution of cryptic diversity among parasitic helminths

2017 ◽  
Vol 92 (2) ◽  
pp. 197-202 ◽  
Author(s):  
G. Pérez-Ponce de León ◽  
R. Poulin
Keyword(s):  
Cryptic Species ◽  
Dna Sequences ◽  
Meta Analysis ◽  
Parasitic Nematodes ◽  
Trematode Species ◽  
Sampling Effort ◽  
Separate Analysis ◽  
Cryptic Diversity ◽  
Parasite Diversity ◽  
Parasitic Helminths

AbstractCryptic parasite diversity is a major issue for taxonomy and systematics, and for attempts to control diseases of humans, domestic animals and wildlife. Here, we re-examine an earlier report that, after correcting for sampling effort, more cryptic species of trematodes are found per published study than for other helminth taxa. We performed a meta-analysis of 110 studies that used DNA sequences to search for cryptic species in parasitic helminth taxa. After correcting for study effort and accounting for the biogeographical region of origins, we found that more cryptic species tend to be uncovered among trematodes, and fewer among cestodes and animal-parasitic nematodes, than in other helminth groups. However, this pattern was only apparent when we included only studies using nuclear markers in the analysis; it was not seen in a separate analysis based only on mitochondrial markers. We propose that the greater occurrence of cryptic diversity among trematodes may be due to some of their unique features, such as their mode of reproduction or frequent lack of hard morphological structures, or to the way in which trematode species are described. Whatever the reason, the high frequency of cryptic species among trematodes has huge implications for estimates of parasite diversity and for future taxonomic research.

scholarly journals Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Reference Database ◽  
Chloroplast Gene ◽  
Coastal Plants ◽  
Reference Databases ◽  
Targeted Capture ◽  
Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

scholarly journals META-ANALYSIS: TYPES OF MEDIA AND CHARACTERISTICS OF PHYSICAL MATERIALS SUITABLE FOR PHYSICS LEARNING MEDIA BASED ON ADOBE FLASH SOFTWARE

2020 ◽  
Vol 8 (1) ◽  
pp. 24
Author(s):  
Hasbi Azis ◽  
Mutia Risma ◽  
Sinta Yolanda ◽  
Desnita Desnita ◽  
Usmeldi Usmeldi
Keyword(s):  
Meta Analysis ◽  
Secondary Data ◽  
Analysis Method ◽  
Physics Learning ◽  
Computer Based Learning ◽  
Adobe Flash ◽  
Temperature Heat ◽  
Computer Based ◽  
The Media ◽  
Physical Materials

This research aimed to analyze the types of media and the characteristics of physics materials that are suitable for use in the development of physics learning media, using Adobe Flash software. The research uses a meta-analysis method, which is a method for analyzing many of the research that has been done. This research uses secondary data obtained from previous research in the form of journals related to the media using Adobe Flash software for senior high school physics subjects. The journals examined in this research consisted of 20 research articles that developed an adobe flash-based interactive learning media for physics learning in senior high schools. The number of articles reviewed consisted of 3 articles from international journals and 17 articles from national journals. Based on the results of the analysis that has been done, found 13 physics materials obtained from 20 journals analyzed, where the concepts of temperature, heat, and transfer are the most widely used material as content in the development of physics learning media based on Adobe Flash software. While the type of media that is widely used in computer-based learning media.

scholarly journals Estimation accuracy of species abundance based on environmental DNA with relation to its production source, state, and assay methodology suggested by meta-analyses

2021 ◽  
Author(s):  
Toshiaki Jo ◽  
Hiroki Yamanaka
Keyword(s):  
Meta Analysis ◽  
Empirical Studies ◽  
Species Abundance ◽  
Environmental Dna ◽  
Efficient Estimation ◽  
Estimation Accuracy ◽  
Accurate Estimation ◽  
Abundance Estimation ◽  
Natural Environments ◽  
Promising Tool

Environmental DNA (eDNA) analysis is a promising tool for non-disruptive and cost-efficient estimation of species abundance. However, its practical applicability in natural environments is limited because it is unclear whether eDNA concentrations actually represent species abundance in the field. Although the importance of accounting for eDNA dynamics, such as transport and degradation, has been discussed, the influences of eDNA characteristics, including production source and state, and methodology, including collection and quantification strategy and abundance metrics, on the accuracy of eDNA-based abundance estimation were entirely overlooked. We conducted a meta-analysis using 56 previous eDNA literature and investigated the relationships between the accuracy (R2) of eDNA-based abundance estimation and eDNA characteristics and methodology. Our meta-regression analysis found that R2 values were significantly lower for crustaceans than fish, suggesting that less frequent eDNA production owing to their external morphology and physiology may impede accurate estimation of their abundance via eDNA. Moreover, R2 values were positively associated with filter pore size, indicating that selective collection of larger-sized eDNA, which is typically fresher, could improve the estimation accuracy of species abundance. Furthermore, R2 values were significantly lower for natural than laboratory conditions, while there was no difference in the estimation accuracy among natural environments. Our findings shed a new light on the importance of what characteristics of eDNA should be targeted for more accurate estimation of species abundance. Further empirical studies are required to validate our findings and fully elucidate the relationship between eDNA characteristics and eDNA-based abundance estimation.

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