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Genes Jul 2023On a planet experiencing constant human population growth, it is necessary to explore the anthropogenic effects on the genetic diversity of species, and specifically...
On a planet experiencing constant human population growth, it is necessary to explore the anthropogenic effects on the genetic diversity of species, and specifically invasive species. Using an analysis that integrates comparative phylogeography, urban landscape genetics, macrogenetics and a systematic review, we explore the worldwide genetic diversity of the human commensal and anthropogenic species and . Based on metadata obtained considering 35 selected studies related to observed heterozygosity, measured by nuclear molecular markers (microsatellites, Single Nucleotide Polymorphisms-SNPs-, restrictition site-associated DNA sequencing -RAD-Seq-), socioeconomic and mobility anthropogenic factors were used as predictors of genetic diversity of and , using the Gini index, principal component analysis and Random Forest Regression as analysis methodology. Population density was on average the best predictor of genetic diversity in the species analyzed, indicating that the species respond in a particular way to the characteristics present in urban environments because of a combination of life history characteristics and human-mediated migration and colonization processes. To create better management and control strategies for these rodents and their associated diseases, it is necessary to fill the existing information gap in urban landscape genetics studies with more metadata repositories, with emphasis on tropical and subtropical regions of the world.
Topics: Humans; Rats; Animals; Population Density; Phylogeography; Introduced Species; Microsatellite Repeats; Polymorphism, Single Nucleotide
PubMed: 37510346
DOI: 10.3390/genes14071442 -
International Urogynecology Journal Nov 2023Bowel vaginoplasty is a surgical method for neovagina construction that, despite its advantages over other techniques, is still burdened by complications such as... (Review)
Review
BACKGROUND
Bowel vaginoplasty is a surgical method for neovagina construction that, despite its advantages over other techniques, is still burdened by complications such as prolapse. The incidence of sigmoid neovagina prolapse (SNP) is difficult to determine, and there are no evidence-based recommendations for treatment. We present a case of SNP and a systematic review of previous cases.
CASE
A 73-year-old woman presented with stage III prolapse of her sigmoid neovagina constructed 51 years prior. Dynamic pelvic MRI revealed that the majority of the prolapse was due to the mucosa's loss of support. Due to the presence of numerous pelvic adhesions, an alternative to the laparoscopic approach was evaluated by a multidisciplinary team which led to the patient being treated using a modification of Altemeier's procedure.
SYSTEMATIC REVIEW
After PROSPERO Registration (CRD42023400677), a systematic search of Medline and Scopus was performed using specific search terms. Study metadata including patient demographics, prolapse measurements, reconstruction techniques, recurrence rates, and timing were extracted. Fourteen studies comprising 17 cases of SNP were included. Vaginal resection of the redundant sigmoid, comprising Altemeier's procedure, was the most definitive surgery, but it was also associated with recurrences in three cases. Laparoscopic sacropexy was the second most definitive surgery with no recurrence reported.
CONCLUSION
Our review shows that the recurrence after correction of sigmoid neovagina prolapses is higher than previously reported. Laparoscopy colposacropexy appeared to be the best approach, but it's not always feasible. In these scenarios, a mucosal resection using the Altemeier's procedure is the most effective surgery.
Topics: Humans; Female; Pregnancy; Aged; Colon, Sigmoid; Prolapse; Vagina; Laparoscopy; Colpotomy; Mullerian Ducts; Congenital Abnormalities; 46, XX Disorders of Sex Development
PubMed: 37490063
DOI: 10.1007/s00192-023-05603-4 -
Frontiers in Genetics 2023Genetic variants cause a significant portion of developmental disorders and intellectual disabilities (DD/ID), but clinical and genetic heterogeneity makes...
Genetic variants cause a significant portion of developmental disorders and intellectual disabilities (DD/ID), but clinical and genetic heterogeneity makes identification challenging. Compounding the issue is a lack of ethnic diversity in studies into the genetic aetiology of DD/ID, with a dearth of data from Africa. This systematic review aimed to comprehensively describe the current knowledge from the African continent on this topic. Applicable literature published up until July 2021 was retrieved from PubMed, Scopus and Web of Science databases, following PRISMA guidelines, focusing on original research reports on DD/ID where African patients were the focus of the study. The quality of the dataset was assessed using appraisal tools from the Joanna Briggs Institute, whereafter metadata was extracted for analysis. A total of 3,803 publications were extracted and screened. After duplicate removal, title, abstract and full paper screening, 287 publications were deemed appropriate for inclusion. Of the papers analysed, a large disparity was seen between work emanating from North Africa compared to sub-Saharan Africa, with North Africa dominating the publications. Representation of African scientists on publications was poorly balanced, with most research being led by international researchers. There are very few systematic cohort studies, particularly using newer technologies, such as chromosomal microarray and next-generation sequencing. Most of the reports on new technology data were generated outside Africa. This review highlights how the molecular epidemiology of DD/ID in Africa is hampered by significant knowledge gaps. Efforts are needed to produce systematically obtained high quality data that can be used to inform appropriate strategies to implement genomic medicine for DD/ID on the African continent, and to successfully bridge healthcare inequalities.
PubMed: 37234869
DOI: 10.3389/fgene.2023.1137922 -
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 -
JPMA. the Journal of the Pakistan... May 2023To review the seroprevalence of toxoplasmosis in Pakistan.
OBJECTIVE
To review the seroprevalence of toxoplasmosis in Pakistan.
METHODS
The systematic review comprised search on Science Direct, Google Scholar, PubMed and Scopus databases for studies related to the seroprevalence of toxoplasmosis in Pakistan published between 2006 and 2020 which used serological diagnostic tests to detect Toxoplasma gondii. Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were used throughout the review and statistical analysis was done using forest plot and random effect model.
RESULTS
Of the 7093 human studies initially found, 20(0.28%) were reviewed. Of the 16,432 animal studies, 16(0.09%) were selected for detailed review. The pooled seroprevalence of toxoplasmosis in humans, calculated in this review was found as (76%) (95% confidence interval: 69-83%). Seroprevalence of human toxoplasmosis was higher in Khyber Pakhtunkhwa (31.7%) than Punjab (20.4%). Pooled seroprevalence in animals calculated in this review was found as (69%) (95% confidence interval: 64-74%). Seroprevalence in animals was higher in Khyber Pakhtunkhwa (44.7%) than Punjab (29.4%).
CONCLUSIONS
The seroprevalence of toxoplasmosis in both humans and animals should be studied it other parts of Pakistan as well.
Topics: Animals; Humans; Pakistan; Seroepidemiologic Studies; Metadata; Antibodies, Protozoan; Toxoplasmosis; Risk Factors
PubMed: 37218234
DOI: 10.47391/JPMA.5699 -
Studies in Health Technology and... May 2023The first step of a systematic review is the identification of publications related to a research question in different literature databases. The quality of the final...
The first step of a systematic review is the identification of publications related to a research question in different literature databases. The quality of the final review is mainly influenced by finding the best search query resulting in high precision and recall. Usually, this process is iterative and requires refining the initial query and comparing the different result sets. Furthermore, result sets of different literature databases must be compared as well. Objective of this work is to develop a command line interface, which supports the automated comparison of result sets of publications from literature databases. The tool should incorporate existing application programming interfaces of literature database and should be integrable into more complex analysis scripts. We present a command line interface written in Python and available as open-source application at https://imigitlab.uni-muenster.de/published/literature-cli under MIT license. The tool calculates the intersection and differences of the result sets of multiple queries on a single literature database or of the same query on different databases. These results and their configurable metadata can be exported as CSV-files or in Research Information System format for post-processing or as starting point for a systematic review. Due to the support of inline parameters, the tool can be integrated into existing analysis scripts. Currently, the literature databases PubMed and DBLP are supported, but the tool can easily be extended to support any literature database providing a web-based application programming interface.
Topics: Software; Databases, Factual; PubMed; User-Computer Interface
PubMed: 37203639
DOI: 10.3233/SHTI230095 -
Journal of Neuro-oncology May 2023Management of hydrocephalus symptoms in the setting of leptomeningeal disease (LMD) includes cerebrospinal fluid (CSF) diversion, which can in the form of... (Meta-Analysis)
Meta-Analysis Review
Postoperative course of cerebrospinal fluid diversion in the setting of leptomeningeal disease: a systematic review, meta-analysis, and meta-regression with an illustrative case.
BACKGROUND
Management of hydrocephalus symptoms in the setting of leptomeningeal disease (LMD) includes cerebrospinal fluid (CSF) diversion, which can in the form of ventriculoperitoneal shunting (VPS) and lumboperitoneal shunting (LPS). However, the quantifiable postoperative course following this intervention is poorly defined. Correspondingly the aim of our study was to quantitatively define and analyze the pooled metadata regarding this topic.
METHODS
Multiple electronic databases from inception to March 2023 were searched following PRISMA guidelines. Respective cohort-level outcomes were then abstracted and pooled by means of meta-analyses and analyzed by means meta-regression, both utilizing random-effects modeling. Post-hoc bias evaluation was then performed for all outcomes.
RESULTS
A total of 12 studies were identified for inclusion, describing 503 LMD patients managed by CSF diversion - 442 (88%) by VPS and 61 (12%) by LPS. Median male percentage and age at diversion were 32% and 58 years respectively, with lung and breast cancer the most common primary diagnoses. Meta-analysis demonstrated pooled incidence of symptom resolution in 79% (95% CI 68-88%) of patients after index shunt surgery, and shunt revision required in 10% (95% CI 6-15%) of cases. Pooled overall survival from index shunt surgery was 3.8 mo (95% CI 2.9-4.6 mo) across all studies. Meta-regression demonstrated that studies published later trended towards significantly shorter overall survival from index shunt surgery (co-efficient=-0.38, P = 0.023), whereas the proportion of VPS to LPS in each study did not impact survival (P = 0.89). When accounting for these biases, overall survival from index shunt surgery was re-estimated to be shorter 3.1 mo (95% CI 1.7-4.4 mo). We present an illustrative case demonstrating the course of symptom improvement, shunt revision and an overall survival of 2 weeks from index CSF diversion.
CONCLUSION
Although CSF diversion in the setting of LMD can improve hydrocephalus symptoms in the majority of patients, there is a non-negligible proportion that will require shunt revision. Postoperatively, the prognosis of LMD remains poor irrespective of shunt type, and despite possible biases within the current literature, the expected median overall survival after index surgery is a matter of months. These findings support CSF diversion as an effective palliative procedure when considering symptoms and quality of life. Further research is required to understand how postoperative expectations can be managed to respect the best wishes of patients, their family, and the treating clinical team.
Topics: Humans; Male; Cerebrospinal Fluid Shunts; Quality of Life; Lipopolysaccharides; Hydrocephalus; Ventriculoperitoneal Shunt; Retrospective Studies
PubMed: 37191912
DOI: 10.1007/s11060-023-04334-2 -
Journal of Neurosurgery. Pediatrics Jul 2023Neurosurgical outcomes are not well defined in the management of pediatric patients with cerebral venous sinus thrombosis (CVST) following acute mastoiditis. Specific... (Meta-Analysis)
Meta-Analysis
OBJECTIVE
Neurosurgical outcomes are not well defined in the management of pediatric patients with cerebral venous sinus thrombosis (CVST) following acute mastoiditis. Specific notable sequelae are otogenic (otitic) hydrocephalus and CVST management. Correspondingly, the aim of this study was to integrate the currently published metadata to summarize these outcomes.
METHODS
Electronic searches were performed using the Ovid Embase, PubMed, Scopus, and Cochrane databases from inception to November 2022 following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Cohort-level data were then abstracted for analysis for appropriate pediatric patients. Outcomes were pooled by random-effects meta-analyses of proportions where possible.
RESULTS
Twenty-three study cohorts describing 312 pediatric patients with otogenic CVST were included. At a cohort level, the median patient age was 6 years among 181 boys (58%) and 131 girls (42%). Modeling indicated papilledema at presentation in 46% of cases (95% CI 30%-62%). Regarding management, antibiotics were applied universally in all cases, mastoidectomy or other otologic surgery was performed in 91% (95% CI 82%-98%), and prophylactic anticoagulation was administered in 86% (95% CI 75%-95%). There was only 1 case (0.3%) of postprocedural intracranial hemorrhage, and there were no deaths reported among all studies. Although diagnostic lumbar puncture was performed in 14% (95% CI 3%-28%) at presentation, clinical otogenic hydrocephalus was ultimately suspected in 31% (95% CI 14%-49%), and acetazolamide was given in 65% (95% CI 35%-91%) overall. There were 10 cases (3%) that proceeded to permanent CSF diversion in the form of ventricular shunting. At a median follow-up of 8 months among all studies, the venous sinus was completely recanalized in 67% (95% CI 53%-79%).
CONCLUSIONS
Most CVSTs following acute mastoiditis will recanalize with the standard use of antibiotics, otologic surgery, and anticoagulation, with minimal symptomatic hemorrhage risk. However, an appreciable proportion of these patients will develop symptomatic otogenic hydrocephalus, and it is imperative that the appropriate surveillance and workup is performed to fully optimize patient outcomes long-term. The possible need for permanent CSF diversion should be recognized.
Topics: Male; Female; Child; Humans; Mastoiditis; Otitis Media; Anticoagulants; Hydrocephalus; Sinus Thrombosis, Intracranial; Anti-Bacterial Agents; Retrospective Studies
PubMed: 37060317
DOI: 10.3171/2023.2.PEDS2319 -
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 -
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