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Reproduction (Cambridge, England) Jun 2023Adverse trends in reproductive function are a concern in humans, companion, livestock, and wildlife species. This study indicates that equine populations are at risk of...
IN BRIEF
Adverse trends in reproductive function are a concern in humans, companion, livestock, and wildlife species. This study indicates that equine populations are at risk of a comparable decline in sperm progressive motility.
ABSTRACT
There is increasing evidence reporting geographically sensitive adverse trends in human semen quality, with parallel trends observed in the dog sentinel. Despite significant economic and welfare complications associated with poor testicular function, trends in current equine populations are undetermined. Given the predictive value of sperm progressive motility (PMOT) in male factor infertility and fertilisation potential, research determining trends in this parameter is warranted. This research analysed trends in stallion sperm PMOT through systematic review and meta-regression. Using a comprehensive search strategy, Scopus, Embase (Ovid), Medline (Ovid), and VetMed (CAB direct) were scoped for eligible data. Using best practices, 230 meta-data points from 229 articles published from 1991 to 2021 were collated for meta-regression analysis. Sperm PMOT declined significantly between 1984 and 2019 (simple linear regression: b -0.340, P = 0.017; meta-regression: b -0.610, P ≤ 0.001). Overall and yearly PMOT declines were predicted at 33.51 and 0.96%, respectively (1984: 63.69 ± 5.07%; 2019: 42.35 ± 3.69%). Trends remained consistent irrespective of sensitivity analyses. Yearly and overall declines were stronger in western (yearly: 0.75%, overall: 26.29%) compared to non-western (yearly: 0.46%, overall: 10.65%) populations. Adverse trends contribute vital data to the debate surrounding declining semen quality, supporting the use of equines as novel comparative models for human reproduction. Results could have significant economic, health, and welfare consequences for equine breeding sectors. A comparable decline in human, dog, and horse sperm quality is indicative of a common environmental aetiology, indicating the need for a holistic One Health approach in determining causes and developing preventative strategies.
Topics: Male; Horses; Animals; Humans; Dogs; Semen Analysis; Semen; Sperm Motility; Spermatozoa; Infertility, Male; Sperm Count
PubMed: 37000597
DOI: 10.1530/REP-22-0490 -
Comprehensive Reviews in Food Science... Jul 2021Essential oils (EOs) are commercially important products, sources of compounds with antioxidant and antimicrobial activities considered indispensable for several fields,... (Meta-Analysis)
Meta-Analysis
Essential oils (EOs) are commercially important products, sources of compounds with antioxidant and antimicrobial activities considered indispensable for several fields, such as the food industry, cosmetics, perfumes, pharmaceuticals, sanitary and agricultural industries. In this context, this systematic review and meta-analysis, a novel approach will be presented using chemometric tools to verify and recognize patterns of antioxidant, antibacterial, and antifungal activities of EOs according to their geographic, botanical, chemical, and microbiological distribution. Scientific papers were selected following the Preferred Reporting Items for Systematic Review and Meta-Analyses statement flow diagram, and the data were evaluated by the self-organizing map and hierarchical cluster analysis. Overall, this novel approach allowed us to draw an overview of antioxidants and antimicrobials activities of EOs reported in 2019, through 585 articles evaluated, obtaining a dataset with more than 10,000 data, distributed in more than 80 countries, 290 plant genera, 150 chemical compounds, 30 genera of bacteria, and 10 genera of fungi. The networks for geographic, botanical, chemical, and microbiological distribution indicated that Brazil, Asia, the botanical genus Thymus, species Thymus vulgaris L. "thyme," the Lamiaceae family, limonene, and the oxygenated monoterpene class were the most representative in the dataset, while the species Escherichia coli and Candida albicans were the most used to assess the antimicrobial activity of EOs. This work can be seen as a guide for the processing of metadata using a novel approach with non-conventional statistical methods. However, this preliminary approach with EOs can be extended to other sources or areas of food science.
Topics: Candida albicans; Lamiaceae; Microbial Sensitivity Tests; Oils, Volatile; Thymus Plant
PubMed: 34125485
DOI: 10.1111/1541-4337.12773 -
PLOS Global Public Health 2023Enteric and parasitic infections such as soil-transmitted helminths cause considerable mortality and morbidity in low- and middle-income settings. Earthen household...
Enteric and parasitic infections such as soil-transmitted helminths cause considerable mortality and morbidity in low- and middle-income settings. Earthen household floors are common in many of these settings and could serve as a reservoir for enteric and parasitic pathogens, which can easily be transmitted to new hosts through direct or indirect contact. We conducted a systematic review and meta-analysis to establish whether and to what extent improved household floors decrease the odds of enteric and parasitic infections among occupants compared with occupants living in households with unimproved floors. Following the PRISMA guidelines, we comprehensively searched four electronic databases for studies in low- and middle-income settings measuring household flooring as an exposure and self-reported diarrhoea or any type of enteric or intestinal-parasitic infection as an outcome. Metadata from eligible studies were extracted and transposed on to a study database before being imported into the R software platform for analysis. Study quality was assessed using an adapted version of the Newcastle-Ottawa Quality Assessment Scale. In total 110 studies were eligible for inclusion in the systematic review, of which 65 were eligible for inclusion in the meta-analysis after applying study quality cut-offs. Random-effects meta-analysis suggested that households with improved floors had 0.75 times (95CI: 0.67-0.83) the odds of infection with any type of enteric or parasitic infection compared with household with unimproved floors. Improved floors gave a pooled protective OR of 0.68 (95CI: 0.58-0.8) for helminthic infections and 0.82 OR (95CI: 0.75-0.9) for bacterial or protozoan infections. Overall study quality was poor and there is an urgent need for high-quality experimental studies investigating this relationship. Nevertheless, this study indicates that household flooring may meaningfully contribute towards a substantial portion of the burden of disease for enteric and parasitic infections in low- and middle-income settings.
PubMed: 38039279
DOI: 10.1371/journal.pgph.0002631 -
BMJ Open Jan 2023Various studies have been published to better understand the underlying spatial and temporal dynamics of COVID-19. This review sought to identify different spatial and...
OBJECTIVE
Various studies have been published to better understand the underlying spatial and temporal dynamics of COVID-19. This review sought to identify different spatial and spatio-temporal modelling methods that have been applied to COVID-19 and examine influential covariates that have been reportedly associated with its risk in Africa.
DESIGN
Systematic review using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.
DATA SOURCES
Thematically mined keywords were used to identify refereed studies conducted between January 2020 and February 2022 from the following databases: PubMed, Scopus, MEDLINE via Proquest, CINHAL via EBSCOhost and Coronavirus Research Database via ProQuest. A manual search through the reference list of studies was also conducted.
ELIGIBILITY CRITERIA FOR SELECTING STUDIES
Peer-reviewed studies that demonstrated the application of spatial and temporal approaches to COVID-19 outcomes.
DATA EXTRACTION AND SYNTHESIS
A standardised extraction form based on critical appraisal and data extraction for systematic reviews of prediction modelling studies checklist was used to extract the meta-data of the included studies. A validated scoring criterion was used to assess studies based on their methodological relevance and quality.
RESULTS
Among 2065 hits in five databases, title and abstract screening yielded 827 studies of which 22 were synthesised and qualitatively analysed. The most common socioeconomic variable was population density. HIV prevalence was the most common epidemiological indicator, while temperature was the most common environmental indicator. Thirteen studies (59%) implemented diverse formulations of spatial and spatio-temporal models incorporating unmeasured factors of COVID-19 and the subtle influence of time and space. Cluster analyses were used across seven studies (32%) to explore COVID-19 variation and determine whether observed patterns were random.
CONCLUSION
COVID-19 modelling in Africa is still in its infancy, and a range of spatial and spatio-temporal methods have been employed across diverse settings. Strengthening routine data systems remains critical for generating estimates and understanding factors that drive spatial variation in vulnerable populations and temporal variation in pandemic progression.
PROSPERO REGISTRATION NUMBER
CRD42021279767.
Topics: Humans; COVID-19; Africa; Cluster Analysis
PubMed: 36697047
DOI: 10.1136/bmjopen-2022-067134 -
Journal of Affective Disorders Dec 2021Bias-prone psychiatric interviews remain the mainstay of bipolar disorder (BD) assessment. The development of digital phenotyping promises to improve BD management. We... (Review)
Review
BACKGROUND
Bias-prone psychiatric interviews remain the mainstay of bipolar disorder (BD) assessment. The development of digital phenotyping promises to improve BD management. We present a systematic review of the evidence about the use of portable digital devices for the identification of BD, BD types and BD mood states and for symptom assessment.
METHODS
We searched Web of Knowledge, Scopus ®, IEEE Xplore, and ACM Digital Library databases (until 5/1/2021) for articles evaluating the use of portable/wearable digital devices, such as smartphone apps, wearable sensors, audio and/or visual recordings, and multimodal tools. The protocol is registered in PROSPERO (CRD42020200086).
RESULTS
We included 62 studies (2325 BD; 724 healthy controls, HC): 27 using smartphone apps, either for recording self-assessments (n = 10) or for passively gathering metadata (n = 7) or both (n = 10); 15 using wearable sensors for physiological parameters; 17 analysing audio and/or video recordings; 3 using multiple technologies. Two thirds of the included studies applied artificial intelligence (AI)-based approaches. They achieved fair to excellent classification performances.
LIMITATIONS
The included studies had small sample sizes and marked heterogeneity. Evidence of overfitting emerged, limiting generalizability. The absence of clear guidelines about reporting classification performances, with no shared standard metrics, makes results hardly interpretable and comparable.
CONCLUSIONS
New technologies offer a noteworthy opportunity to BD digital phenotyping with objectivity and high granularity. AI-based models could deliver important support in clinical decision-making. Further research and cooperation between different stakeholders are needed for addressing methodological, ethical and socio-economic considerations.
Topics: Artificial Intelligence; Bipolar Disorder; Humans; Self-Assessment; Wearable Electronic Devices
PubMed: 34488086
DOI: 10.1016/j.jad.2021.08.052 -
PloS One 2023Several studies applying Machine Learning to deception detection have been published in the last decade. A rich and complex set of settings, approaches, theories, and...
Several studies applying Machine Learning to deception detection have been published in the last decade. A rich and complex set of settings, approaches, theories, and results is now available. Therefore, one may find it difficult to identify trends, successful paths, gaps, and opportunities for contribution. The present literature review aims to provide the state of research regarding deception detection with Machine Learning. We followed the PRISMA protocol and retrieved 648 articles from ACM Digital Library, IEEE Xplore, Scopus, and Web of Science. 540 of them were screened (108 were duplicates). A final corpus of 81 documents has been summarized as mind maps. Metadata was extracted and has been encoded as Python dictionaries to support a statistical analysis scripted in Python programming language, and available as a collection of Jupyter Lab Notebooks in a GitHub repository. All are available as Jupyter Lab Notebooks. Neural Networks, Support Vector Machines, Random Forest, Decision Tree and K-nearest Neighbor are the five most explored techniques. The studies report a detection performance ranging from 51% to 100%, with 19 works reaching accuracy rate above 0.9. Monomodal, Bimodal, and Multimodal approaches were exploited and achieved various accuracy levels for detection. Bimodal and Multimodal approaches have become a trend over Monomodal ones, although there are high-performance examples of the latter. Studies that exploit language and linguistic features, 75% are dedicated to English. The findings include observations of the following: language and culture, emotional features, psychological traits, cognitive load, facial cues, complexity, performance, and Machine Learning topics. We also present a dataset benchmark. Main conclusions are that labeled datasets from real-life data are scarce. Also, there is still room for new approaches for deception detection with Machine Learning, especially if focused on languages and cultures other than English-based. Further research would greatly contribute by providing new labeled and multimodal datasets for deception detection, both for English and other languages.
Topics: Neural Networks, Computer; Research Design; Publications; Machine Learning; Deception
PubMed: 36757928
DOI: 10.1371/journal.pone.0281323 -
Malaria Journal Jan 2021Malaria and HIV are two important public health issues. However, evidence on HIV-Plasmodium vivax co-infection (HIV/PvCo) is scarce, with most of the available...
BACKGROUND
Malaria and HIV are two important public health issues. However, evidence on HIV-Plasmodium vivax co-infection (HIV/PvCo) is scarce, with most of the available information related to Plasmodium falciparum on the African continent. It is unclear whether HIV can change the clinical course of vivax malaria and increase the risk of complications. In this study, a systematic review of HIV/PvCo studies was performed, and recent cases from the Brazilian Amazon were included.
METHODS
Medical records from a tertiary care centre in the Western Brazilian Amazon (2009-2018) were reviewed to identify HIV/PvCo hospitalized patients. Demographic, clinical and laboratory characteristics and outcomes are reported. Also, a systematic review of published studies on HIV/PvCo was conducted. Metadata, number of HIV/PvCo cases, demographic, clinical, and outcome data were extracted.
RESULTS
A total of 1,048 vivax malaria patients were hospitalized in the 10-year period; 21 (2.0%) were HIV/PvCo cases, of which 9 (42.9%) had AIDS-defining illnesses. This was the first malaria episode in 11 (52.4%) patients. Seven (33.3%) patients were unaware of their HIV status and were diagnosed on hospitalization. Severe malaria was diagnosed in 5 (23.8%) patients. One patient died. The systematic review search provided 17 articles (12 cross-sectional or longitudinal studies and 5 case report studies). A higher prevalence of studies involved cases in African and Asian countries (35.3 and 29.4%, respectively), and the prevalence of reported co-infections ranged from 0.1 to 60%.
CONCLUSION
Reports of HIV/PvCo are scarce in the literature, with only a few studies describing clinical and laboratory outcomes. Systematic screening for both co-infections is not routinely performed, and therefore the real prevalence of HIV/PvCo is unknown. This study showed a low prevalence of HIV/PvCo despite the high prevalence of malaria and HIV locally. Even though relatively small, this is the largest case series to describe HIV/PvCo.
Topics: Adolescent; Adult; Aged; Brazil; Child; Coinfection; Female; HIV Infections; HIV-1; Humans; Incidence; Malaria, Vivax; Male; Middle Aged; Plasmodium vivax; Prevalence; Young Adult
PubMed: 33407474
DOI: 10.1186/s12936-020-03518-9 -
MBio Dec 2021High-throughput 16S rRNA sequencing has allowed the characterization of helminth-uninfected (HU) and helminth-infected (HI) gut microbiomes, revealing distinct profiles.... (Meta-Analysis)
Meta-Analysis
High-throughput 16S rRNA sequencing has allowed the characterization of helminth-uninfected (HU) and helminth-infected (HI) gut microbiomes, revealing distinct profiles. However, there have been no qualitative or quantitative syntheses of these studies, which show marked variation in participant age, diet, pathogen of interest, and study location. A predefined minimally biased search strategy identified 23 studies in humans. For each of these studies, we qualitatively addressed the effects of helminth infection on within-individual (alpha) and between-individual (beta) fecal microbiome diversity, infection-associated microbial taxa, the effect of helminth clearance on microbiome composition, microbiome composition as a predictor of infection status or treatment outcome, and treatment-specific effects on the fecal microbiome. Concomitantly, we performed a meta-analysis on a subset of 7 of these studies containing raw, paired-end 16S reads and individual-level metadata, comprising 424 pretreatment or untreated HI individuals and 497 HU controls. After reducing the batch effect and adjusting for age, our data demonstrated that intestinal helminth parasites can alter the host gut microbiome by increasing alpha diversity and promoting taxonomic reassortment and gradient collapse. Most strongly influencing the microbiome composition were the helminths found in the large intestine, Enterobius vermicularis and Trichuris trichiura, suggesting that this influence appears to be specific to soil-transmitted helminths (STH) species and host anatomical niche. In summary, using a large and diverse sample set captured in the meta-analysis, we were able to evaluate the influence of individual helminth species as well as species-species interactions, each of which explained a significant portion of the variation in the microbiome. The gut microbiome has established importance in regulating many aspects of human health, including nutrition and immunity. While many internal and environmental factors are known to influence the microbiome, less is known about the effects of intestinal helminth parasites (worms), which together affect one-sixth of the world's population. Through a comprehensive qualitative systematic review and quantitative meta-analysis of existing literature, we provide strong evidence that helminth infection dynamically shifts the intestinal microbiome structure. Moreover, we demonstrated that such influence seems to be specific to helminth species and host anatomical niche. Our findings suggest that the gut microbiome may underlie some of the pathology associated with intestinal worm infection and support future work to understand the precise nature of the helminth-microbiome relationship.
Topics: Adolescent; Adult; Aged; Animals; Bacteria; Child; Child, Preschool; Dysbiosis; Feces; Female; Gastrointestinal Microbiome; Helminthiasis; Helminths; Humans; Infant; Male; Middle Aged; Phylogeny; Young Adult
PubMed: 34933444
DOI: 10.1128/mBio.02890-21 -
Frontiers in Cellular Neuroscience 2023We performed a systematic review that identified at least 9,000 scientific papers on PubMed that include immunofluorescent images of cells from the central nervous...
BACKGROUND
We performed a systematic review that identified at least 9,000 scientific papers on PubMed that include immunofluorescent images of cells from the central nervous system (CNS). These CNS papers contain tens of thousands of immunofluorescent neural images supporting the findings of over 50,000 associated researchers. While many existing reviews discuss different aspects of immunofluorescent microscopy, such as image acquisition and staining protocols, few papers discuss immunofluorescent imaging from an image-processing perspective. We analyzed the literature to determine the image processing methods that were commonly published alongside the associated CNS cell, microscopy technique, and animal model, and highlight gaps in image processing documentation and reporting in the CNS research field.
METHODS
We completed a comprehensive search of PubMed publications using Medical Subject Headings (MeSH) terms and other general search terms for CNS cells and common fluorescent microscopy techniques. Publications were found on PubMed using a combination of column description terms and row description terms. We manually tagged the comma-separated values file (CSV) metadata of each publication with the following categories: animal or cell model, quantified features, threshold techniques, segmentation techniques, and image processing software.
RESULTS
Of the almost 9,000 immunofluorescent imaging papers identified in our search, only 856 explicitly include image processing information. Moreover, hundreds of the 856 papers are missing thresholding, segmentation, and morphological feature details necessary for explainable, unbiased, and reproducible results. In our assessment of the literature, we visualized current image processing practices, compiled the image processing options from the top twelve software programs, and designed a road map to enhance image processing. We determined that thresholding and segmentation methods were often left out of publications and underreported or underutilized for quantifying CNS cell research.
DISCUSSION
Less than 10% of papers with immunofluorescent images include image processing in their methods. A few authors are implementing advanced methods in image analysis to quantify over 40 different CNS cell features, which can provide quantitative insights in CNS cell features that will advance CNS research. However, our review puts forward that image analysis methods will remain limited in rigor and reproducibility without more rigorous and detailed reporting of image processing methods.
CONCLUSION
Image processing is a critical part of CNS research that must be improved to increase scientific insight, explainability, reproducibility, and rigor.
PubMed: 37545881
DOI: 10.3389/fncel.2023.1188858 -
Photodiagnosis and Photodynamic Therapy Jun 2022Oral potentially malignant disorders (OPMD) represent a group of lesions with increased risk for malignant transformation. The management of such injuries is based on... (Meta-Analysis)
Meta-Analysis Review
Oral potentially malignant disorders (OPMD) represent a group of lesions with increased risk for malignant transformation. The management of such injuries is based on surgical treatment or detailed follow-up throughout the patient's lifetime. This systematic review and meta-analysis investigated and critically evaluated the use of autofluorescence and fluorescent probes as potential techniques for the early detection of OPMD. A comprehensive search was performed on Pubmed, Scopus, Web of Science and LIVIVO databases. The gray literature was also consulted and included Google Scholar, Proquest and Open gray databases. 2715 articles were retrieved, and after the different stages of critical evaluation, were reduced to 25 articles that fully met the inclusion criteria. VELscope® was the most used equipment for autofluorescence, while aminolevulinic acid (5-ALA) was the main representative of the probes. The meta-analysis performed included 10 articles that used VELscope® as a method to detect oral disorders. A 95% confidence interval (CI) with a p value significance <0.05 was considered as a criterion for the statistical analysis. The combined sensitivity was 74% (CI95 60-76%, p = 0.0001) and the specificity was 57% (CI95 52-60%, p = 0.0000). The inclusion of these adjunct methods in clinical practice is very promising, since they are able to help both the clinician and the specialist in the early detection of potentially malignant oral disorders, favoring a better prognosis. However, it is still necessary to carry out further studies, with the aim of establishing a protocol for use and qualification of results.
Topics: Data Analysis; Early Detection of Cancer; Fluorescent Dyes; Humans; Mouth Diseases; Mouth Neoplasms; Photochemotherapy; Precancerous Conditions
PubMed: 35192945
DOI: 10.1016/j.pdpdt.2022.102764