-
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 -
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 -
A systematic review with meta-analysis of Yoga's contributions to neuropsychiatric aspects of aging.Behavioural Brain Research Oct 2023Yoga is one of the most common Complementary and Alternative Medicines (CAM) for mind-body approaches to psychological and stress-related conditions in aging. Such wide... (Meta-Analysis)
Meta-Analysis Review
UNLABELLED
Yoga is one of the most common Complementary and Alternative Medicines (CAM) for mind-body approaches to psychological and stress-related conditions in aging. Such wide usage demands the review and systematization of the scientific literature, searching for accumulated evidence of its effectiveness. We reviewed the literature to assess whether Yoga would offer significant improvements to neuropsychiatric aspects of the elderly: anxiety, depression, stress, memory and executive functions.
METHODS
This systematic review with meta-analyses organized the results from all analyzed articles, comparing them between the experimental and either the control or waiting groups, calculating the effect size (Cohen-d) and the p-value of a two-tailed T-test. We presented the transformed metadata in forest graphs.
RESULTS AND DISCUSSION
Given the heterogeneity of methods, results, and effect sizes of each study and due to the number of articles found, this meta-analysis indicates that it is not possible to state that Yoga reduces anxiety and stress in the elderly or improves cognition. However, this meta-analysis found significant results of Yoga in reducing depression with small to medium effect sizes.
CONCLUSION
According to the currently available literature on Yoga and aspects of aging, we concluded that yoga was effective in most studies on reducing depression.
Topics: Aged; Humans; Yoga; Aging; Anxiety; Anxiety Disorders; Cognition
PubMed: 37598905
DOI: 10.1016/j.bbr.2023.114636 -
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 -
PeerJ. Computer Science 2022Microservices is an emerging paradigm for developing distributed systems. With their widespread adoption, more and more work investigated the relation between...
Microservices is an emerging paradigm for developing distributed systems. With their widespread adoption, more and more work investigated the relation between microservices and security. Alas, the literature on this subject does not form a well-defined : it is spread over many venues and composed of contributions mainly addressing specific scenarios or needs. In this work, we conduct a systematic review of the field, gathering 290 relevant publications-at the time of writing, the largest curated dataset on the topic. We analyse our dataset along two lines: (a) quantitatively, through publication metadata, which allows us to chart publication outlets, communities, approaches, and tackled issues; (b) qualitatively, through 20 research questions used to provide an aggregated overview of the literature and to spot gaps left open. We summarise our analyses in the conclusion in the form of a call for action to address the main open challenges.
PubMed: 35111904
DOI: 10.7717/peerj-cs.779 -
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 -
Frontiers in Immunology 2023The surge in the number of publications on psoriasis has posed significant challenges for researchers in effectively managing the vast amount of information. However,...
BACKGROUND
The surge in the number of publications on psoriasis has posed significant challenges for researchers in effectively managing the vast amount of information. However, due to the lack of tools to process metadata, no comprehensive bibliometric analysis has been conducted.
OBJECTIVES
This study is to evaluate the trends and current hotspots of psoriatic research from a macroscopic perspective through a bibliometric analysis assisted by machine learning based semantic analysis.
METHODS
Publications indexed under the Medical Subject Headings (MeSH) term "Psoriasis" from 2003 to 2022 were extracted from PubMed. The generative statistical algorithm latent Dirichlet allocation (LDA) was applied to identify specific topics and trends based on abstracts. The unsupervised Louvain algorithm was used to establish a network identifying relationships between topics.
RESULTS
A total of 28,178 publications were identified. The publications were derived from 176 countries, with United States, China, and Italy being the top three countries. For the term "psoriasis", 9,183 MeSH terms appeared 337,545 times. Among them, MeSH term "Severity of illness index", "Treatment outcome", "Dermatologic agents" occur most frequently. A total of 21,928 publications were included in LDA algorithm, which identified three main areas and 50 branched topics, with "Molecular pathogenesis", "Clinical trials", and "Skin inflammation" being the most increased topics. LDA networks identified "Skin inflammation" was tightly associated with "Molecular pathogenesis" and "Biological agents". "Nail psoriasis" and "Epidemiological study" have presented as new research hotspots, and attention on topics of comorbidities, including "Cardiovascular comorbidities", "Psoriatic arthritis", "Obesity" and "Psychological disorders" have increased gradually.
CONCLUSIONS
Research on psoriasis is flourishing, with molecular pathogenesis, skin inflammation, and clinical trials being the current hotspots. The strong association between skin inflammation and biologic agents indicated the effective translation between basic research and clinical application in psoriasis. Besides, nail psoriasis, epidemiological study and comorbidities of psoriasis also draw increased attention.
Topics: Humans; United States; Psoriasis; Arthritis, Psoriatic; Bibliometrics; Dermatitis; Machine Learning; Inflammation
PubMed: 37954610
DOI: 10.3389/fimmu.2023.1272080 -
Toxins Sep 2023The aim of this systematic review is to provide an update on the occurrence and co-occurrence of selected non-regulated mycotoxins and provide an overview of current... (Review)
Review
The aim of this systematic review is to provide an update on the occurrence and co-occurrence of selected non-regulated mycotoxins and provide an overview of current regulations. Fifteen non-regulated mycotoxins were found in 19 food categories worldwide. On top of that, 38 different combinations of non-regulated mycotoxins were found, with mixtures varying from binary combinations up to 12 mycotoxins. Taking into consideration the amount of evidence regarding the prevalence and co-occurrence of non-regulated mycotoxins, future steps should be taken considering continuous monitoring, scientific exchange, and generation of high-quality data. To enhance data quality, guidelines outlining the minimum quality criteria for both occurrence data and metadata are needed. By doing so, we can effectively address concerns related to the toxicity of non-regulated mycotoxins. Furthermore, obtaining more data concerning the co-occurrence of both regulated and non-regulated mycotoxins could aid in supporting multiple chemical risk assessment methodologies. Implementing these steps could bolster food safety measures, promote evidence-based regulations, and ultimately safeguard public health from the potential adverse effects of non-regulated mycotoxins.
Topics: Data Accuracy; Fenbendazole; Food; Food Safety; Mycotoxins
PubMed: 37756008
DOI: 10.3390/toxins15090583 -
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