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PeerJ 2023The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR-findable, accessible, interoperable, and...
The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR-findable, accessible, interoperable, and reusable-despite growing awareness of the importance of such practices. In order to better understand these data usability challenges, we systematically reviewed 60 peer reviewed articles conducting a specific subset of eDNA research: metabarcoding studies in marine environments. For each article, we characterized approximately 90 features across several categories: general article attributes and topics, methodological choices, types of metadata included, and availability and storage of sequence data. Analyzing these characteristics, we identified several barriers to data accessibility, including a lack of common context and vocabulary across the articles, missing metadata, supplementary information limitations, and a concentration of both sample collection and analysis in the United States. While some of these barriers require significant effort to address, we also found many instances where small choices made by authors and journals could have an outsized influence on the discoverability and reusability of data. Promisingly, articles also showed consistency and creativity in data storage choices as well as a strong trend toward open access publishing. Our analysis underscores the need to think critically about data accessibility and usability as marine eDNA metabarcoding studies, and eDNA projects more broadly, continue to proliferate.
Topics: DNA, Environmental; Biodiversity; DNA Barcoding, Taxonomic
PubMed: 36992947
DOI: 10.7717/peerj.14993 -
BMC Medical Informatics and Decision... Jun 2021Natural language processing (NLP) has a significant role in advancing healthcare and has been found to be key in extracting structured information from radiology...
BACKGROUND
Natural language processing (NLP) has a significant role in advancing healthcare and has been found to be key in extracting structured information from radiology reports. Understanding recent developments in NLP application to radiology is of significance but recent reviews on this are limited. This study systematically assesses and quantifies recent literature in NLP applied to radiology reports.
METHODS
We conduct an automated literature search yielding 4836 results using automated filtering, metadata enriching steps and citation search combined with manual review. Our analysis is based on 21 variables including radiology characteristics, NLP methodology, performance, study, and clinical application characteristics.
RESULTS
We present a comprehensive analysis of the 164 publications retrieved with publications in 2019 almost triple those in 2015. Each publication is categorised into one of 6 clinical application categories. Deep learning use increases in the period but conventional machine learning approaches are still prevalent. Deep learning remains challenged when data is scarce and there is little evidence of adoption into clinical practice. Despite 17% of studies reporting greater than 0.85 F1 scores, it is hard to comparatively evaluate these approaches given that most of them use different datasets. Only 14 studies made their data and 15 their code available with 10 externally validating results.
CONCLUSIONS
Automated understanding of clinical narratives of the radiology reports has the potential to enhance the healthcare process and we show that research in this field continues to grow. Reproducibility and explainability of models are important if the domain is to move applications into clinical use. More could be done to share code enabling validation of methods on different institutional data and to reduce heterogeneity in reporting of study properties allowing inter-study comparisons. Our results have significance for researchers in the field providing a systematic synthesis of existing work to build on, identify gaps, opportunities for collaboration and avoid duplication.
Topics: Humans; Machine Learning; Natural Language Processing; Radiology; Radiology Information Systems; Reproducibility of Results
PubMed: 34082729
DOI: 10.1186/s12911-021-01533-7 -
Virulence Dec 2021is an emerging zoonotic pathogen. Over 100 putative virulence factors have been described, but it is unclear to what extent these virulence factors could contribute to... (Meta-Analysis)
Meta-Analysis
is an emerging zoonotic pathogen. Over 100 putative virulence factors have been described, but it is unclear to what extent these virulence factors could contribute to zoonotic potential of . We identified all virulence factors studied in experimental models of human origin in a systematic review and assessed their contribution to zoonotic potential in a subsequent genomic meta-analysis. PubMed and Scopus were searched for English-language articles that studied virulence published until 31 March 2021. Articles that analyzed a virulence factor by knockout mutation, purified protein, and/or recombinant protein in a model of human origin, were included. Data on virulence factor, strain characteristics, used human models and experimental outcomes were extracted. All publicly available genomes with available metadata on host, disease status and country of origin, were included in a genomic meta-analysis. We calculated the ratio of the prevalence of each virulence factor in human and pig isolates. We included 130 articles and 1703 genomes in the analysis. We identified 53 putative virulence factors that were encoded by genes which are part of the core genome and 26 factors that were at least twice as prevalent in human isolates as in pig isolates. Hhly3 and NisK/R were particularly enriched in human isolates, after stratification by genetic lineage and country of isolation. This systematic review and genomic meta-analysis have identified virulence factors that are likely to contribute to the zoonotic potential of .
Topics: Animals; Genomics; Streptococcal Infections; Streptococcus suis; Swine; Swine Diseases; Virulence; Virulence Factors
PubMed: 34666617
DOI: 10.1080/21505594.2021.1985760 -
Journal of Family Medicine and Primary... Mar 2020Common Data Elements (CDEs) are data-metadata descriptors used to collect research study data. CDEs facilitate the collection, processing, and sharing of breast cancer... (Review)
Review
BACKGROUND
Common Data Elements (CDEs) are data-metadata descriptors used to collect research study data. CDEs facilitate the collection, processing, and sharing of breast cancer data. This study intended to explore the CDEs of breast cancer for research databases and primary care systems.
METHODS
This study was conducted using systematic search and review. This systematic literature review covered PubMed, Scopus, Science Direct, SID, ISC, Web of Science, and Google Scholar search engine. It included studies in English language with accessible full-text from the beginning of 2007 to September 2019.
RESULTS
Reviewing 25 studies revealed that 52 percent of studies were carried out in the US and most studies were conducted between 2013 and 2015. The most domains for using CDEs were: Pathology Report and Registry. The CDEs of breast cancer for research databases were categorized into three categories namely clinical, research, and non-clinical and indicate the importance of these data elements. Most of the studies focused on creating and deploying clinical CDEs as physical examination, clinical history and pathology data.
CONCLUSION
The integration of biomedical and clinical data relevant to breast cancer enhances the power of research variable analysis and statistical analysis, thereby facilitating improved knowledge of effective therapeutic interventions. Also CDEs used to collect, store, and retrieve patient data in various health setting such as primary care and research databases.
PubMed: 32509607
DOI: 10.4103/jfmpc.jfmpc_931_19 -
Value in Health : the Journal of the... Mar 2023Real-world evidence (RWE) studies are increasingly being used to support healthcare decisions. Various frameworks, tools, and checklists exist for ensuring quality of... (Review)
Review
Use of Structured Template and Reporting Tool for Real-World Evidence for Critical Appraisal of the Quality of Reporting of Real-World Evidence Studies: A Systematic Review.
OBJECTIVES
Real-world evidence (RWE) studies are increasingly being used to support healthcare decisions. Various frameworks, tools, and checklists exist for ensuring quality of real-world data, designing robust studies, and assessing potential for bias. In January 2021, Structured Template and Reporting Tool for RWE (STaRT-RWE) was released to further reduce ambiguity, assumptions, and misinterpretation while planning, implementing, and reporting RWE studies of the safety and effectiveness of treatments. The objective of this study was to identify gaps in the reporting quality of published RWE studies by using this template for critical appraisal.
METHODS
Two reviewers conducted a keyword search on PubMed for free-full-text research articles using real-world data, RWE design, and safety with or without effectiveness outcomes of a medicinal product or intervention in humans of any age or gender, published in English between January 13, 2021, and January 13, 2022. Assessment of risk of bias was done using Assessment of Real-World Observational Studies critical appraisal tool. Deficiencies in methods and findings as per STaRT-RWE template were reported as frequencies.
RESULTS
A total of 54 of 2374 retrieved studies were included in the review. Based on the STaRT-RWE template, the studies inadequately reported empirically defined covariates, power and sample size calculation, attrition, sensitivity analyses, index date (day 0) defining criterion, predefined covariates, outcome, metadata about data source and software, objective, inclusion and exclusion criteria, analysis specifications, and follow-up.
CONCLUSIONS
The use of STaRT-RWE template along with its tables, design diagram, and library of published studies has a potential of improving robustness of RWE studies.
Topics: Humans; Bias; Checklist
PubMed: 36210293
DOI: 10.1016/j.jval.2022.09.003 -
International Journal of Qualitative... 2014To synthesize and interpret qualitative research findings focusing on parental experiences of skin-to-skin care (SSC) for newborn infants. (Meta-Analysis)
Meta-Analysis Review
AIM
To synthesize and interpret qualitative research findings focusing on parental experiences of skin-to-skin care (SSC) for newborn infants.
BACKGROUND
SSC induces many benefits for newborn infants and their parents. Three meta-analyses have been conducted on physiological outcomes, but no previous qualitative meta-synthesis on parental experiences of SSC has been identified.
DESIGN
The present meta-synthesis was guided by the methodology described by Paterson and co-workers.
DATA SOURCES
Four databases were searched, without year or language limitations, up until December 2013. Manual searches were also performed. The searches and subsequent quality appraisal resulted in the inclusion of 29 original qualitative papers from 9 countries, reporting experiences from 401 mothers and 94 fathers.
REVIEW METHODS
The meta-synthesis entails a meta-data analysis, analysis of meta-method, and meta-theory in the included primary studies. Based on the three analyses, the meta-synthesis represents a new interpretation of a phenomenon. The results of the meta-data analysis have been presented as a qualitative systematic review in a separate paper.
RESULTS
When synthesizing and interpreting the findings from the included analyses, a theoretical model of Becoming a parent under unfamiliar circumstances emerged. Providing SSC seems to be a restorative as well as an energy-draining experience. A supportive environment has been described as facilitating the restorative experience, whereas obstacles in the environment seem to make the provision of SSC energy-draining for parents. When the process is experienced as positive, it facilitates the growth of parental self-esteem and makes the parents ready to assume full responsibility for their child.
CONCLUSION
The results show that SSC can be interpreted not only as a family-including and important health care intervention but also in terms of actually becoming a parent. The process of becoming a parent in this specific situation is influenced by external factors in three different levels; family and friends, community, and society at large. The descriptions of providing SSC are similar to what has previously been described as the natural process of becoming a mother or a father.
Topics: Humans; Kangaroo-Mother Care Method; Mother-Child Relations; Object Attachment; Parents; Qualitative Research; Touch
PubMed: 25319747
DOI: 10.3402/qhw.v9.24907 -
Heliyon Aug 2023This study aims to comprehensively review the literature on human resource outsourcing (HRO) published from 2001 to 2021. The study begins with metadata analysis on 69... (Review)
Review
This study aims to comprehensively review the literature on human resource outsourcing (HRO) published from 2001 to 2021. The study begins with metadata analysis on 69 papers and presents insights into 32 papers on HRO identified from the Scopus and ISI Web of Science databases. The literature is classified based on content analysis, which comprises conceptual understanding, drivers and barriers, functions outsourced, and firm performance. The study reveals that cost advantage, organisational learning, and the opportunity to concentrate on core business functions motivate the organisation to practice HRO. However, the lack of psychological contact among current employees, the risk of opportunism in the freelancing organisation, lack of management legislation, and prior experience are the common barriers to HRO adoption. Despite thesedrawbacks and barriers, recruitment, payroll processing, and technology-centric human resource (HR) activities are standard HR functions outsourced by organisations. The contributions of this study are to offer an integrated and conclusive definition of HRO and provide a simple, easy-to-understand, yet comprehensive framework for understanding HRO practices in any organisation. Researchers and academicians can utilize this paper to explore future research directions while gaining a thorough understanding of the HRO concept.
PubMed: 37600375
DOI: 10.1016/j.heliyon.2023.e19018 -
PloS One 2023The use of cannabis for medicinal purposes has increased globally over the past decade since patient access to medicinal cannabis has been legislated across...
The use of cannabis for medicinal purposes has increased globally over the past decade since patient access to medicinal cannabis has been legislated across jurisdictions in Europe, the United Kingdom, the United States, Canada, and Australia. Yet, evidence relating to the effect of medical cannabis on the management of symptoms for a suite of conditions is only just emerging. Although there is considerable engagement from many stakeholders to add to the evidence base through randomized controlled trials, many gaps in the literature remain. Data from real-world and patient reported sources can provide opportunities to address this evidence deficit. This real-world data can be captured from a variety of sources such as found in routinely collected health care and health services records that include but are not limited to patient generated data from medical, administrative and claims data, patient reported data from surveys, wearable trackers, patient registries, and social media. In this systematic scoping review, we seek to understand the utility of online user generated text into the use of cannabis as a medicine. In this scoping review, we aimed to systematically search published literature to examine the extent, range, and nature of research that utilises user-generated content to examine to cannabis as a medicine. The objective of this methodological review is to synthesise primary research that uses social media discourse and internet search engine queries to answer the following questions: (i) In what way, is online user-generated text used as a data source in the investigation of cannabis as a medicine? (ii) What are the aims, data sources, methods, and research themes of studies using online user-generated text to discuss the medicinal use of cannabis. We conducted a manual search of primary research studies which used online user-generated text as a data source using the MEDLINE, Embase, Web of Science, and Scopus databases in October 2022. Editorials, letters, commentaries, surveys, protocols, and book chapters were excluded from the review. Forty-two studies were included in this review, twenty-two studies used manually labelled data, four studies used existing meta-data (Google trends/geo-location data), two studies used data that was manually coded using crowdsourcing services, and two used automated coding supplied by a social media analytics company, fifteen used computational methods for annotating data. Our review reflects a growing interest in the use of user-generated content for public health surveillance. It also demonstrates the need for the development of a systematic approach for evaluating the quality of social media studies and highlights the utility of automatic processing and computational methods (machine learning technologies) for large social media datasets. This systematic scoping review has shown that user-generated content as a data source for studying cannabis as a medicine provides another means to understand how cannabis is perceived and used in the community. As such, it provides another potential 'tool' with which to engage in pharmacovigilance of, not only cannabis as a medicine, but also other novel therapeutics as they enter the market.
Topics: Humans; Social Media; Cannabis; Medicine; Delivery of Health Care; United Kingdom
PubMed: 36662832
DOI: 10.1371/journal.pone.0269143 -
Clinical Infectious Diseases : An... Feb 2020Whether human immunodeficiency virus (HIV) infection impacts gut microbial α-diversity is controversial. We reanalyzed raw 16S ribosomal RNA (rRNA) gene sequences and... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Whether human immunodeficiency virus (HIV) infection impacts gut microbial α-diversity is controversial. We reanalyzed raw 16S ribosomal RNA (rRNA) gene sequences and metadata from published studies to examine α-diversity measures between HIV-uninfected (HIV-) and HIV-infected (HIV+) individuals.
METHODS
We conducted a systematic review and individual level meta-analysis by searching Embase, Medline, and Scopus for original research studies (inception to 31 December 2017). Included studies reported 16S rRNA gene sequences of fecal samples from HIV+ patients. Raw sequence reads and metadata were obtained from public databases or from study authors. Raw reads were processed through standardized pipelines with use of a high-resolution taxonomic classifier. The χ2 test, paired t tests, and generalized linear mixed models were used to relate α-diversity measures and clinical metadata.
RESULTS
Twenty-two studies were identified with 17 datasets available for analysis, yielding 1032 samples (311 HIV-, 721 HIV+). HIV status was associated with a decrease in measures of α-diversity (P < .001). However, in stratified analysis, HIV status was associated with decreased α-diversity only in women and in men who have sex with women (MSW) but not in men who have sex with men (MSM). In analyses limited to women and MSW, controlling for HIV status, women displayed increased α-diversity compared with MSW.
CONCLUSIONS
Our study suggests that HIV status, sexual risk category, and gender impact gut microbial community α-diversity. Future studies should consider MSM status in gut microbiome analyses.
Topics: Female; Gastrointestinal Microbiome; HIV Infections; Homosexuality, Male; Humans; Male; RNA, Ribosomal, 16S; Sexual and Gender Minorities
PubMed: 30921452
DOI: 10.1093/cid/ciz258 -
Environment International Jun 2021Conservation activities and natural resource management interventions have often aimed to tackle the dual challenge of improving nature conservation and human... (Review)
Review
What is the evidence documenting the effects of marine or coastal nature conservation or natural resource management activities on human well-being in South East Asia? A systematic map.
BACKGROUND
Conservation activities and natural resource management interventions have often aimed to tackle the dual challenge of improving nature conservation and human well-being. However, there is concern over the extent to which this dual goal has been achieved, and an increasing recognition of trade-offs and synergies within and between aspects of each of the goals. The amount and scope of the available evidence on the success of conservation and management interventions in both arenas has lacked documentation, for a number of reasons, including limited resources for monitoring and evaluation and the difficulty in bringing together a disparate evidence base. This systematic map focuses on the interaction between marine conservation management and the health and well-being of coastal communities in South East Asia.
METHOD
We searched bibliographic databases to find published literature, and identified grey literature through institutional and organisational website searches and key stakeholders. Eligibility criteria were applied in two stages, title and abstract and full text, with consistency checks. We extracted meta-data on the design and characteristics of each study, from which we produced an interactive database and map, and a narrative summary.
RESULTS
We assessed 42,894 records at title and abstract from the main searches. 1,331 articles were assessed at full text (30 articles were not retrievable). 287 articles (281 studies) were included in the systematic map. Most studies were peer-reviewed publications (90%), and from the Philippines and Indonesia (72%). 31% of studies were solely qualitative, 45% were solely quantitative and 24% included both qualitative and quantitative research. Only 24% (31/127) of quantitative studies included a comparator. We identified knowledge clusters where studies investigated the links between the marine conservation interventions: Site Protection, Economic or Livelihood Incentives or Alternatives, or Habitat Management, and the human health and well-being outcomes: Economic Living Standards, Governance and Empowerment, or Social Relations. In addition, qualitative research clusters were identified exploring the links between the intervention Habitat Management, and the outcome Governance and Empowerment, and between the intervention Economic or Livelihood Incentives or Alternatives, and the outcomes of Governance and Empowerment, and Social Relations. We identified major knowledge gaps in evidence for the effect of marine conservation interventions on the outcomes Freedom of Choice and Action, Security and Safety, Subjective Well-being, Health, and Culture and Spirituality. There was a lack of studies involving Education, Awareness and Activism interventions that reported any human health and well-being outcomes.
CONCLUSION
We present the first updatable, interrogable and comprehensive evidence map on this topic for South East Asia. Our work supports further, detailed investigation of knowledge clusters using systematic review and also serves to identify understudied topic areas. The lack of comparative, quantitative studies suggests that future research should include counterfactuals to strengthen the robustness of evidence base. Users of this systematic map should recognise that much evidence may be national or locally specific, and that we did not undertake an assessment of study quality. Thus, when considering implications for policy and decision-making, users should carefully consider the heterogeneity of available evidence and refer to original research articles to gain a full depth of understanding and context.
Topics: Conservation of Natural Resources; Asia, Eastern; Humans; Natural Resources; Philippines; Socioeconomic Factors
PubMed: 33713939
DOI: 10.1016/j.envint.2021.106397