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 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 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.

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 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 Association study of RS535296987 in TEX14 gene in azoospermiamen: RFLP and DNA sequencing

Genetika ◽  
2021 ◽  
Vol 53 (2) ◽  
pp. 729-737
Author(s):  
Mohammad Vahedi ◽  
Masoud Sheidai
Keyword(s):  
Dna Sequencing ◽  
Dna Sequences ◽  
Chromosome 17 ◽  
Protein Coding ◽  
Nucleotide Variability ◽  
Functional Studies ◽  
Low Degree ◽  
Different Populations ◽  
Human Chromosome 17 ◽  
And Control

Azoospermia is one of the kinds of male infertility, with clinically the most severe phenotype as the natural conception cannot occur. It has been estimated to affect 0.1 to 1% of all men and 10-15% of men in infertile couples. TEX14 (Testis expressed 14, intercellular bridge forming factor) is a protein coding gene, which is located in human chromosome 17, (17q22). Tex14 gene appears to be crucial for perfect spermatogenesis and functional studies indicate the role of TEX14 in the intercellular bridges between developing male germ cells. The gene contains 32 exons and spans 137 kb. A heterogeneousresultis available on the association TEX14 gene and azoospermia. Therefore, it is suggested to investigate this gene in different populations. We analyzed about 200 men in two categories of azoospermia and healthy persons by RFLP as well as DNA sequencing to indicate an association between rs535296987 in TEX14 and its adjacent nucleotides to azoospermia. We found no significant association based on RFLP data and also by clustering of case and control specimens based on DNA sequencing. In general, a low level of nucleotide variability was observed in DNA sequences. Therefore, both eternity in the studied samples and low degree of mutations in this genetic region, may be the reason for heterogeneous reports on association of TEX14 and azoospermia.

scholarly journals A review of methods for addressing components of interventions in meta-analysis

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246631
Author(s):  
Maria Petropoulou ◽  
Orestis Efthimiou ◽  
Gerta Rücker ◽  
Guido Schwarzer ◽  
Toshi A. Furukawa ◽  
...  
Keyword(s):  
Panic Disorder ◽  
Analytical Methods ◽  
Meta Analysis ◽  
Complex Interventions ◽  
Software Tools ◽  
Analytical Models ◽  
New Developments ◽  
Healthcare Interventions ◽  
Multicomponent Interventions ◽  
Interacting Components

Many healthcare interventions are complex, consisting of multiple, possibly interacting, components. Several methodological articles addressing complex interventions in the meta-analytical context have been published. We hereby provide an overview of methods used to evaluate the effects of complex interventions with meta-analytical models. We summarized the methodology, highlighted new developments, and described the benefits, drawbacks, and potential challenges of each identified method. We expect meta-analytical methods focusing on components of several multicomponent interventions to become increasingly popular due to recently developed, easy-to-use, software tools that can be used to conduct the relevant analyses. The different meta-analytical methods are illustrated through two examples comparing psychotherapies for panic disorder.

Analysis of the last 10 years of articles and theses on authentic learning: A meta-analysis study

2020 ◽  
Vol 8 (3) ◽  
pp. 78-91
Author(s):  
Ezgi Pelin Yildiz
Keyword(s):  
Sampling Method ◽  
Meta Analysis ◽  
Authentic Learning ◽  
Nursing Curriculum ◽  
Learning Technology ◽  
Learning Approaches ◽  
Analysis Method ◽  
Network Learning ◽  
Purposeful Sampling ◽  
The World

The aim of this research is to examine articles and thesis studies in the field of authentic learning approaches and applications in education in the last 10 years and to reveal the trends in this context. In the methodology part of the research, the meta-analysis method was used. Meta-analysis studies refers to the critical review and integration of the findings of separate studies. For the purpose of the study, a total of 111 pieces of research, published between 2010 and 2021 and selected by purposeful sampling method were analyzed. Databases used in research are Eric, IEEE Xplore, Ebsco, Springer, Science Direct, Scopus, Web of Sciences. Authentic learning approaches and applications in education throughout the world were examined under 16 criteria. These data were interpreted based on percentage and frequency. As a result, authentic learning approaches and applicationare integrated in many fields such as ICT, engineering, network learning technology, nursing, curriculum & instruction, geography, medicine and more.   Keywords: Learning Approaches, Meta-Analysis, Publication Classification, Authenic, Analysis

3. Making sense of genes and genomes

2018 ◽  
pp. 28-43
Author(s):  
John Archibald
Keyword(s):  
Dna Sequencing ◽  
Computational Methods ◽  
Genome Assembly ◽  
Physical Nature ◽  
Living Cells ◽  
Shotgun Sequencing ◽  
Significant Challenge ◽  
Making Sense ◽  
Problems And Solutions ◽  
Balancing Efficiency

While DNA sequencing is faster and cheaper than ever before, genome assembly remains a significant challenge. ‘Making sense of genes and genomes’ explores how laboratory and computational methods are used in combination to elucidate the true physical nature of DNA molecules inside living cells, and how genes are identified among the vast quantities of chemical letters making up an organism’s genome. It begins with shotgun sequencing—a method that has stood the test of time in balancing efficiency and accuracy. It then considers the problems and solutions of genome assembly; gene finding with transcriptomics; the BLAST algorithm; how to find where proteins carry out their functions; and genome re-sequencing.

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