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Microbiome Mar 2017Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the microbiome in NEC and preterm infants lack power and have reported inconsistent results.
METHODS AND RESULTS
Our objectives were to perform a systematic review and meta-analyses of stool microbiome profiles in preterm infants to discern and describe microbial dysbiosis prior to the onset of NEC and to explore heterogeneity among studies. We searched MEDLINE, PubMed, CINAHL, and conference abstracts from the proceedings of Pediatric Academic Societies and reference lists of relevant identified articles in April 2016. Studies comparing the intestinal microbiome in preterm infants who developed NEC to those of controls, using culture-independent molecular techniques and reported α and β-diversity metrics, and microbial profiles were included. In addition, 16S ribosomal ribonucleic acid (rRNA) sequence data with clinical meta-data were requested from the authors of included studies or searched in public data repositories. We reprocessed the 16S rRNA sequence data through a uniform analysis pipeline, which were then synthesized by meta-analysis. We included 14 studies in this review, and data from eight studies were available for quantitative synthesis (106 NEC cases, 278 controls, 2944 samples). The age of NEC onset was at a mean ± SD of 30.1 ± 2.4 weeks post-conception (n = 61). Fecal microbiome from preterm infants with NEC had increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes prior to NEC onset. Alpha- or beta-diversity indices in preterm infants with NEC were not consistently different from controls, but we found differences in taxonomic profiles related to antibiotic exposure, formula feeding, and mode of delivery. Exploring heterogeneity revealed differences in microbial profiles by study and the target region of the 16S rRNA gene (V1-V3 or V3-V5).
CONCLUSIONS
Microbial dysbiosis preceding NEC in preterm infants is characterized by increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes. Microbiome optimization may provide a novel strategy for preventing NEC.
Topics: Bacteria; Bacteroides; Dysbiosis; Enterocolitis, Necrotizing; Feces; Firmicutes; Gastrointestinal Microbiome; Humans; Infant, Newborn; Infant, Premature; Infant, Premature, Diseases; Intestines; Proteobacteria; RNA, Ribosomal, 16S
PubMed: 28274256
DOI: 10.1186/s40168-017-0248-8 -
Journal of Medical Internet Research Jan 2022Metadata are created to describe the corresponding data in a detailed and unambiguous way and is used for various applications in different research areas, for example,... (Review)
Review
BACKGROUND
Metadata are created to describe the corresponding data in a detailed and unambiguous way and is used for various applications in different research areas, for example, data identification and classification. However, a clear definition of metadata is crucial for further use. Unfortunately, extensive experience with the processing and management of metadata has shown that the term "metadata" and its use is not always unambiguous.
OBJECTIVE
This study aimed to understand the definition of metadata and the challenges resulting from metadata reuse.
METHODS
A systematic literature search was performed in this study following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines for reporting on systematic reviews. Five research questions were identified to streamline the review process, addressing metadata characteristics, metadata standards, use cases, and problems encountered. This review was preceded by a harmonization process to achieve a general understanding of the terms used.
RESULTS
The harmonization process resulted in a clear set of definitions for metadata processing focusing on data integration. The following literature review was conducted by 10 reviewers with different backgrounds and using the harmonized definitions. This study included 81 peer-reviewed papers from the last decade after applying various filtering steps to identify the most relevant papers. The 5 research questions could be answered, resulting in a broad overview of the standards, use cases, problems, and corresponding solutions for the application of metadata in different research areas.
CONCLUSIONS
Metadata can be a powerful tool for identifying, describing, and processing information, but its meaningful creation is costly and challenging. This review process uncovered many standards, use cases, problems, and solutions for dealing with metadata. The presented harmonized definitions and the new schema have the potential to improve the classification and generation of metadata by creating a shared understanding of metadata and its context.
Topics: Humans; Metadata; Publications; Reference Standards
PubMed: 35014967
DOI: 10.2196/25440 -
Coronavirus sampling and surveillance in bats from 1996-2019: a systematic review and meta-analysis.Nature Microbiology Jun 2023The emergence of SARS-CoV-2 highlights a need for evidence-based strategies to monitor bat viruses. We performed a systematic review of coronavirus sampling (testing for... (Meta-Analysis)
Meta-Analysis
The emergence of SARS-CoV-2 highlights a need for evidence-based strategies to monitor bat viruses. We performed a systematic review of coronavirus sampling (testing for RNA positivity) in bats globally. We identified 110 studies published between 2005 and 2020 that collectively reported positivity from 89,752 bat samples. We compiled 2,274 records of infection prevalence at the finest methodological, spatiotemporal and phylogenetic level of detail possible from public records into an open, static database named datacov, together with metadata on sampling and diagnostic methods. We found substantial heterogeneity in viral prevalence across studies, reflecting spatiotemporal variation in viral dynamics and methodological differences. Meta-analysis identified sample type and sampling design as the best predictors of prevalence, with virus detection maximized in rectal and faecal samples and by repeat sampling of the same site. Fewer than one in five studies collected and reported longitudinal data, and euthanasia did not improve virus detection. We show that bat sampling before the SARS-CoV-2 pandemic was concentrated in China, with research gaps in South Asia, the Americas and sub-Saharan Africa, and in subfamilies of phyllostomid bats. We propose that surveillance strategies should address these gaps to improve global health security and enable the origins of zoonotic coronaviruses to be identified.
Topics: Animals; Humans; Chiroptera; Phylogeny; SARS-CoV-2; COVID-19; China
PubMed: 37231088
DOI: 10.1038/s41564-023-01375-1 -
Infection Apr 2021The coronavirus outbreak emerged as a severe pandemic, claiming more than 0.8 million lives across the world and raised a major global health concern. We survey the...
PURPOSE
The coronavirus outbreak emerged as a severe pandemic, claiming more than 0.8 million lives across the world and raised a major global health concern. We survey the history and mechanism of coronaviruses, and the structural characteristics of the spike protein and its key residues responsible for human transmissions.
METHODS
We have carried out a systematic review to summarize the origin, transmission and etiology of COVID-19. The structural analysis of the spike protein and its disordered residues explains the mechanism of the viral transmission. A meta-data analysis of the therapeutic compounds targeting the SARS-CoV-2 is also included.
RESULTS
Coronaviruses can cross the species barrier and infect humans with unexpected consequences for public health. The transmission rate of SARS-CoV-2 infection is higher compared to that of the closely related SARS-CoV infections. In SARS-CoV-2 infection, intrinsically disordered regions are observed at the interface of the spike protein and ACE2 receptor, providing a shape complementarity to the complex. The key residues of the spike protein have stronger binding affinity with ACE2. These can be probable reasons for the higher transmission rate of SARS-CoV-2. In addition, we have also discussed the therapeutic compounds and the vaccines to target SARS-CoV-2, which can help researchers to develop effective drugs/vaccines for COVID-19. The overall history and mechanism of entry of SARS-CoV-2 along with structural study of spike-ACE2 complex provide insights to understand disease pathogenesis and development of vaccines and drugs.
Topics: Amino Acid Sequence; Animals; COVID-19; Coronavirus Infections; Humans; Protein Binding; Protein Folding; SARS-CoV-2; Spike Glycoprotein, Coronavirus; Virus Internalization; COVID-19 Drug Treatment
PubMed: 32886331
DOI: 10.1007/s15010-020-01516-2 -
BMJ Open Nov 2022To support the Zika virus (ZIKV) Individual Participant Data (IPD) Consortium's efforts to harmonise and analyse IPD from ZIKV-related prospective cohort studies and...
OBJECTIVES
To support the Zika virus (ZIKV) Individual Participant Data (IPD) Consortium's efforts to harmonise and analyse IPD from ZIKV-related prospective cohort studies and surveillance-based studies of pregnant women and their infants and children; we developed and disseminated a metadata survey among ZIKV-IPD Meta-Analysis (MA) study participants to identify and provide a comprehensive overview of study-level heterogeneity in exposure, outcome and covariate ascertainment and definitions.
SETTING
Cohort and surveillance studies that measured ZIKV infection during pregnancy or at birth and measured fetal, infant, or child outcomes were identified through a systematic search and consultations with ZIKV researchers and Ministries of Health from 20 countries or territories.
PARTICIPANTS
Fifty-four cohort or active surveillance studies shared deidentified data for the IPD-MA and completed the metadata survey, representing 33 061 women (11 020 with ZIKV) and 18 281 children.
PRIMARY AND SECONDARY OUTCOME MEASURES
Study-level heterogeneity in exposure, outcome and covariate ascertainment and definitions.
RESULTS
Median study sample size was 268 (IQR=100, 698). Inclusion criteria, follow-up procedures and exposure and outcome ascertainment were highly heterogenous, differing meaningfully across regions and multisite studies. Enrolment duration and follow-up for children after birth varied before and after the declaration of the Public Health Emergency of International Concern (PHEIC) and according to the type of funding received.
CONCLUSION
This work highlights the logistic and statistical challenges that must be addressed to account for the multiple sources of within-study and between-study heterogeneity when conducting IPD-MAs of data collected in the research response to emergent pathogens like ZIKV.
Topics: Child; Female; Humans; Infant; Infant, Newborn; Pregnancy; Metadata; Parturition; Pregnancy Complications, Infectious; Pregnant Women; Prospective Studies; Zika Virus; Zika Virus Infection; Meta-Analysis as Topic
PubMed: 36414312
DOI: 10.1136/bmjopen-2022-064362 -
Environmental Health Perspectives May 2022Per- and polyfluoroalkyl substances (PFAS) are a large class of synthetic (man-made) chemicals widely used in consumer products and industrial processes. Thousands of... (Review)
Review
BACKGROUND
Per- and polyfluoroalkyl substances (PFAS) are a large class of synthetic (man-made) chemicals widely used in consumer products and industrial processes. Thousands of distinct PFAS exist in commerce. The 2019 U.S. Environmental Protection Agency (U.S. EPA) Per- and Polyfluoroalkyl Substances (PFAS) Action Plan outlines a multiprogram national research plan to address the challenge of PFAS. One component of this strategy involves the use of systematic evidence map (SEM) approaches to characterize the evidence base for hundreds of PFAS.
OBJECTIVE
SEM methods were used to summarize available epidemiological and animal bioassay evidence for a set of PFAS that were prioritized in 2019 by the U.S. EPA's Center for Computational Toxicology and Exposure (CCTE) for toxicity and toxicokinetic assay testing.
METHODS
Systematic review methods were used to identify and screen literature using manual review and machine-learning software. The Populations, Exposures, Comparators, and Outcomes (PECO) criteria were kept broad to identify mammalian animal bioassay and epidemiological studies that could inform human hazard identification. A variety of supplemental content was also tracked, including information on model systems; exposure measurement-only studies in humans; and absorption, distribution, metabolism, and excretion (ADME). Animal bioassay and epidemiology studies meeting PECO criteria were summarized with respect to study design, and health system(s) were assessed. Because animal bioassay studies with exposure duration (or reproductive/developmental study design) were most useful to CCTE analyses, these studies underwent study evaluation and detailed data extraction. All data extraction is publicly available online as interactive visuals with downloadable metadata.
RESULTS
More than 40,000 studies were identified from scientific databases. Screening processes identified 44 animal and 148 epidemiology studies from the peer-reviewed literature and 95 animal and 50 epidemiology studies from gray literature that met PECO criteria. Epidemiological evidence (available for 15 PFAS) mostly assessed the reproductive, endocrine, developmental, metabolic, cardiovascular, and immune systems. Animal evidence (available for 40 PFAS) commonly assessed effects in the reproductive, developmental, urinary, immunological, and hepatic systems. Overall, 45 PFAS had evidence across animal and epidemiology data streams.
DISCUSSION
Many of the PFAS were data poor. Epidemiological and animal evidence were lacking for most of the PFAS included in our search. By disseminating this information, we hope to facilitate additional assessment work by providing the initial scoping literature survey and identifying key research needs. Future research on data-poor PFAS will help support a more complete understanding of the potential health effects from PFAS exposures. https://doi.org/10.1289/EHP10343.
Topics: Animals; Databases, Factual; Epidemiologic Studies; Fluorocarbons; Humans; Mammals; Reproduction; United States; United States Environmental Protection Agency
PubMed: 35580034
DOI: 10.1289/EHP10343 -
Journal of Global Antimicrobial... Mar 2024Mycoplasma and Ureaplasma spp. especially M. hominis, U. parvum, and U. urealyticum recognized as an important cause of urogenital infections. Sake of the presence of... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Mycoplasma and Ureaplasma spp. especially M. hominis, U. parvum, and U. urealyticum recognized as an important cause of urogenital infections. Sake of the presence of antibiotic resistance and a continuous rise in resistance, the treatment options are limited, and treatment has become more challenging and costlier.
OBJECTIVES
Therefore, this meta-analysis aimed to estimate worldwide resistance rates of genital Mycoplasmas and Ureaplasma to fluoroquinolones (ciprofloxacin, ofloxacin, moxifloxacin, and levofloxacin) agents.
METHODS
We searched the relevant published studies in PubMed, Scopus, and Embase from until 3, March 2022. All statistical analyses were carried out using the statistical package R.
RESULTS
The 30 studies included in the analysis were performed in 16 countries. In the metadata, the proportions of ciprofloxacin, ofloxacin, moxifloxacin, and levofloxacin resistance in Mycoplasma and Ureaplasma urogenital isolates were reported 59.8% (95% CI 49.6, 69.1), 31.2% (95% CI 23, 40), 7.3% (95% CI 1, 31), and 5.3% (95% CI 1, 2), respectively. According to the meta-regression, the ciprofloxacin, ofloxacin, moxifloxacin, and levofloxacin rate increased over time. There was a statistically significant difference in the fluoroquinolones resistance rates between different continents/countries (P < 0.05).
CONCLUSIONS
Based on the results obtained in this systematic review and meta-analysis we recommend the use of the newer group of fluoroquinolones especially levofloxacin as the first choice for the treatment of genital mycoplasmosis, as well as ofloxacin for the treatment of genital infections caused by U. parvum.
Topics: Humans; Ureaplasma; Mycoplasma; Fluoroquinolones; Levofloxacin; Ureaplasma urealyticum; Moxifloxacin; Mycoplasma hominis; Microbial Sensitivity Tests; Ureaplasma Infections; Urinary Tract Infections; Ciprofloxacin
PubMed: 38016593
DOI: 10.1016/j.jgar.2023.11.007 -
Vascular Pharmacology Nov 2018A systematic review and meta-analysis was performed to test candidate therapeutic approaches in pulmonary hypertension (PH). The efficacy of 522 interventions with >200... (Meta-Analysis)
Meta-Analysis Review
A systematic review and meta-analysis was performed to test candidate therapeutic approaches in pulmonary hypertension (PH). The efficacy of 522 interventions with >200 unregistered drugs was tested on 7254 animals. We propose a modified formula to assess meta-data that concerns the contribution of PH animal model to the denoted efficacy of tested agents. The measure of efficacy expressed as a response ratio for right ventricle systolic pressure was 0.48 (95% CI, 0.46-0.50; P < 0.00001), mean pulmonary artery pressure was 0.54 (0.52-0.56; P < 0.00001), right ventricle hypertrophy was 0.49 (0.48-0.51; P < 0.00001) and pulmonary artery wall thickness was 0.58 (0.56-0.61; P < 0.00001). Only 41 out of 522 interventions were ineffective. The most potent agents to improve both haemodynamic and hypertrophic parameters were ATP-sensitive potassium channel openers with iptakalim, Rho/ROCK inhibitors with fasudil, RAAS regulators with adenosine and ACE2 activators, and anti-inflammatories with n-3 polyunsaturated fatty acids and NF-кB inhibitors.
Topics: Animals; Antihypertensive Agents; Arterial Pressure; Disease Models, Animal; Hypertension, Pulmonary; Hypertrophy, Right Ventricular; Molecular Targeted Therapy; Pulmonary Artery; Signal Transduction; Vascular Remodeling; Ventricular Function, Right; Ventricular Remodeling
PubMed: 30145225
DOI: 10.1016/j.vph.2018.08.004 -
Annals of Vascular Surgery Sep 2022Artificial intelligence (AI) and machine learning (ML) have seen increasingly intimate integration with medicine and healthcare in the last 2 decades. The objective of... (Review)
Review
BACKGROUND
Artificial intelligence (AI) and machine learning (ML) have seen increasingly intimate integration with medicine and healthcare in the last 2 decades. The objective of this study was to summarize all current applications of AI and ML in the vascular surgery literature and to conduct a bibliometric analysis of published studies.
METHODS
A comprehensive literature search was conducted through Embase, MEDLINE, and Ovid HealthStar from inception until February 19, 2021. Reporting of this study was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Title and abstract screening, full-text screening, and data extraction were conducted in duplicate. Data extracted included study metadata, the clinical area of study within vascular surgery, type of AI/ML method used, dataset, and the application of AI/ML. Publishing journals were classified as having either a clinical scope or technical scope. The author academic background was classified as clinical, nonclinical (e.g., engineering), or both, depending on author affiliation.
RESULTS
The initial search identified 7,434 studies, of which 249 were included for a final analysis. The rate of publications is exponentially increasing, with 158 (63%) studies being published in the last 5 years alone. Studies were most commonly related to carotid artery disease (118, 47%), abdominal aortic aneurysms (51, 20%), and peripheral arterial disease (26, 10%). Study authors employed an average of 1.50 (range: 1-6) distinct AI methods in their studies. The application of AI/ML methods broadly related to predictive models (54, 22%), image segmentation (49, 19.4%), diagnostic methods (46, 18%), or multiple combined applications (91, 37%). The most commonly used AI/ML methods were artificial neural networks (155/378 use cases, 41%), support vector machines (64, 17%), k-nearest neighbors algorithm (26, 7%), and random forests (23, 6%). Datasets to which these AI/ML methods were applied frequently involved ultrasound images (87, 35%), computed tomography (CT) images (42, 17%), clinical data (34, 14%), or multiple datasets (36, 14%). Overall, 22 (9%) studies were published in journals specific to vascular surgery, with the majority (147/249, 59%) being published in journals with a scope related to computer science or engineering. Among 1,576 publishing authors, 46% had exclusively a clinical background, 48% a nonclinical background, and 5% had both a clinical and nonclinical background.
CONCLUSIONS
There is an exponentially growing body of literature describing the use of AI and ML in vascular surgery. There is a focus on carotid artery disease and abdominal aortic disease, with many other areas of vascular surgery under-represented. Neural networks and support vector machines composed most AI methods in the literature. As AI/ML continue to see expanded applications in the field, it is important that vascular surgeons appreciate its potential and limitations. In addition, as it sees increasing use, there is a need for clinicians with expertise in AI/ML methods who can optimize its transition into daily practice.
Topics: Artificial Intelligence; Bibliometrics; Carotid Artery Diseases; Humans; Machine Learning; Treatment Outcome; Vascular Surgical Procedures
PubMed: 35339595
DOI: 10.1016/j.avsg.2022.03.019 -
Human Reproduction (Oxford, England) May 2017Are boys who are born to mothers who use analgesics during pregnancy at increased risk of cryptorchidism compared to those born to mothers who do not take analgesia? (Meta-Analysis)
Meta-Analysis Review
STUDY QUESTION
Are boys who are born to mothers who use analgesics during pregnancy at increased risk of cryptorchidism compared to those born to mothers who do not take analgesia?
SUMMARY ANSWER
In this systematic review and meta-analysis of 10 published studies, we observed only weak evidence of an association between analgesia use during pregnancy and risk of cryptorchidism in the son.
WHAT IS KNOWN ALREADY
Concentrations of analgesia relevant to human exposure have been implicated as causing endocrine disturbances in the developing foetal testis. However, when viewed collectively there appears to be conflicting evidence regarding an association between maternal use of analgesics and development of cryptorchidism.
STUDY DESIGN, SIZE, DURATION
A systematic review and meta-analysis of studies on analgesia use during pregnancy and risk of cryptorchidism was performed. The search terms used were (analges* OR paracetamol OR acetaminophen) AND (cryptorchidism OR cryptorchism OR undescended test* OR non-descended test* OR non descended test*) for the databases Ovid Medline, Embase, Scopus and Web of Science. The search included all published articles up until 23 May 2016 and no limits were set in terms of language.
PARTICIPANTS/MATERIALS, SETTING, METHODS
Abstracts were screened by one reviewer to remove irrelevant studies, with a 10% random sample of these verified by a second reviewer. The full text of all remaining papers was assessed by two reviewers. Abstracts included in the final analysis were studies which reported associations between the exposure (analgesia) and the outcome (cryptorchidism). Studies were only included if data were provided from which summary associations (odds ratios (ORs) or relative risks) and their 95% CIs could be calculated, or if summary associations were provided by the authors themselves. For each included study, two reviewers independently extracted study meta-data in line with PRISMA recommendations. We assessed study quality and potential for bias using the criteria outlined in the Newcastle-Ottawa Quality Assessment Scale, but did not determine a quality score. Two reviewers independently assessed study quality against these criteria.
MAIN RESULTS AND THE ROLE OF CHANCE
After screening 350 manuscripts, 10 were included in our review (5 case-control studies, 5 cohort studies). We observed weak evidence of an association between ever use of analgesia and risk of cryptorchidism (pooled crude OR: 1.11, 95% CI: 1.00-1.23), with case-control studies revealing a marginally stronger association (1.23, 95% CI: 0.85-1.78) than cohort studies (1.09, 95% CI: 0.97-1.22). We observed weak evidence of a dose-response relationship between increasing weeks of analgesia exposure and risk of cryptorchidism, as well as weak evidence of an effect of timing on analgesia exposure and risk of cryptorchidism. Assessment of study quality via the Newcastle-Ottawa criteria revealed little (if any) evidence of substantial bias that may have meaningfully affected a given study's results.
LIMITATIONS, REASONS FOR CAUTION
While confounding does not appear to be important, misclassification of the exposure is possibly an important source of measurement error in this context. The systematic review is open to reporting bias. Owing to scant data, no meta-analyses for two key questions (relating to dose-response and timing of exposure) could be performed. Medications were grouped based on their common effect and this offers little insight into the relation between specific types of analgesia and cryptorchidism. Finally, there are limitations in assuming that analgesia use reported by mothers is synonymous with actual intrauterine exposure.
WIDER IMPLICATIONS OF THE FINDINGS
The ubiquity of analgesia use during pregnancy makes this exposure particularly important from a population health perspective. About 9 of the 10 studies were conducted in Europe or USA, limiting generalizability of our observations. While the observations from our systematic review and meta-analysis suggest that analgesia use during pregnancy is not strongly associated with cryptorchidism development in the son, they also highlight the need for further detailed assessments of this relationship.
STUDY FUNDING/COMPETING INTEREST(S)
This study was funded by the Health Research Council of New Zealand (reference #: 14/052). The authors have no conflict of interest to declare.
REGISTRATION NUMBER
CRD42016041414.
Topics: Analgesia; Analgesics; Cryptorchidism; Female; Humans; Male; Pain Management; Pregnancy; Risk
PubMed: 28333256
DOI: 10.1093/humrep/dex047