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Environmental Research Mar 2023Assessing health outcomes associated with exposure to polychlorinated biphenyls (PCBs) is important given their persistent and ubiquitous nature. PCBs are classified as... (Review)
Review
Assessing health outcomes associated with exposure to polychlorinated biphenyls (PCBs) is important given their persistent and ubiquitous nature. PCBs are classified as a Group 1 carcinogen, but the full range of potential noncancer health effects from exposure to PCBs has not been systematically summarized and evaluated. We used systematic review methods to identify and screen the literature using combined manual review and machine learning approaches. A protocol was developed that describes the literature search strategy and Populations, Exposures, Comparators, and Outcomes (PECO) criteria used to facilitate subsequent screening and categorization of literature into a systematic evidence map of PCB exposure and noncancer health endpoints across 15 organs/systems. A comprehensive literature search yielded 62,599 records. After electronic prioritization steps, 17,037 studies were manually screened at the title and abstract level. An additional 900 studies identified by experts or supplemental searches were also included. After full-text screening of 3889 references, 1586 studies met the PECO criteria. Relevant study details such as the endpoints assessed, exposure duration, and species were extracted into literature summary tables. This review compiles and organizes the human and mammalian studies from these tables into an evidence map for noncancer health endpoints and PCB mixture exposure to identify areas of robust research as well as areas of uncertainty that would benefit from future investigation. Summary data are available online as interactive visuals with downloadable metadata. Sufficient research is available to inform PCB hazard assessments for most organs/systems, but the amount of data to inform associations with specific endpoints differs. Furthermore, despite many years of research, sparse data exist for inhalation and dermal exposures, which are highly relevant human exposure routes. This evidence map provides a foundation for future systematic reviews and noncancer hazard assessments of PCB mixtures and for strategic planning of research to inform areas of greater uncertainty.
Topics: Animals; Humans; Carcinogens; Mammals; Polychlorinated Biphenyls; Uncertainty
PubMed: 36580985
DOI: 10.1016/j.envres.2022.115148 -
Seizure Oct 2022Multiple hippocampal transection (MHT) is a surgical technique that offers adequate seizure control with minimal perioperative morbidity. However, there is little... (Review)
Review
PURPOSE
Multiple hippocampal transection (MHT) is a surgical technique that offers adequate seizure control with minimal perioperative morbidity. However, there is little evidence available to guide neurosurgeons in selecting this technique for use in appropriate patients. This systematic review analyzes patient-level data associated with MHT for intractable epilepsy, focusing on postoperative seizure control and memory outcomes.
METHODS
The systematic review was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Relevant articles were identified from 3 databases (PubMed, Medline, Embase) up to August 1, 2021. Inclusion criteria were that the majority of patients had received a diagnosis of intractable epilepsy, the article was written in English, MHT was the primary procedure, and patient-level metadata were included.
RESULTS
Fifty-nine unique patients who underwent MHT were identified across 11 studies. Ten (17%) of 59 patients underwent MHT alone. Forty-three (75%) of 57 patients who had a follow-up 12 months or longer were seizure free at last follow-up. With respect to postoperative verbal memory retention, 9 of 38 (24%) patient test scores did not change, 14 (37%) decreased, and 16 (42%) increased. With respect to postoperative nonverbal memory retention, 12 of 38 (34%) patient test scores did not change, 13 (34%) decreased, and 13 (33%) increased.
CONCLUSION
There are few reported patients analyzed after MHT. Although the neurocognitive benefits of MHT are unproven, this relatively novel technique has shown promise in the management of seizures in patients with intractable epilepsy. However, structured trials assessing MHT in isolation are warranted.
Topics: Drug Resistant Epilepsy; Epilepsy, Temporal Lobe; Hippocampus; Humans; Memory; Postoperative Complications; Seizures; Treatment Outcome
PubMed: 36041364
DOI: 10.1016/j.seizure.2022.08.007 -
Frontiers in Microbiology 2022Third generation cephalosporins and carbapenems are considered critically important antimicrobials in human medicine. Food animals such as swine can act as reservoirs of... (Review)
Review
Global Distribution of Extended Spectrum Cephalosporin and Carbapenem Resistance and Associated Resistance Markers in of Swine Origin - A Systematic Review and Meta-Analysis.
Third generation cephalosporins and carbapenems are considered critically important antimicrobials in human medicine. Food animals such as swine can act as reservoirs of antimicrobial resistance (AMR) genes/bacteria resistant to these antimicrobial classes, and potential dissemination of AMR genes or resistant bacteria from pigs to humans is an ongoing public health threat. The objectives of this systematic review and meta-analysis were to: (1) estimate global proportion and animal-level prevalence of swine phenotypically resistant to third generation cephalosporins (3GCs) and carbapenems at a country level; and (2) measure abundances and global distribution of the genetic mechanisms that confer resistance to these antimicrobial classes in these isolates. Articles from four databases (CAB Abstracts, PubMed/MEDLINE, PubAg, and Web of Science) were screened to extract relevant data. Overall, proportion of resistant to 3GCs was lower in Australia, Europe, and North America compared to Asian countries. Globally, <5% of all were carbapenem-resistant. Fecal carriage rates (animal-level prevalence) were consistently manifold higher as compared to pooled proportion of resistance in isolates. were the most common 3GC resistance genes globally, with the exception of North America where were the predominant 3GC resistance genes. There was not a single dominant gene subtype globally and several subtypes were dominant depending on the continent. A wide variety of carbapenem-resistance genes ( , ) were identified to be circulating in pig populations globally, albeit at very-low frequencies. However, great statistical heterogeneity and a critical lack of metadata hinders the true estimation of prevalence of phenotypic and genotypic resistance to these antimicrobials. Comparatively frequent occurrence of 3GC resistance and emergence of carbapenem resistance in certain countries underline the urgent need for improved AMR surveillance in swine production systems in these countries.
PubMed: 35620091
DOI: 10.3389/fmicb.2022.853810 -
Birth Defects Research Oct 2022The dynamics and complexities of in utero fetal development create significant challenges in transitioning from lab animal-centric developmental toxicity testing methods...
BACKGROUND
The dynamics and complexities of in utero fetal development create significant challenges in transitioning from lab animal-centric developmental toxicity testing methods to assessment strategies based on new approach methodologies (NAMs). Nevertheless, considerable progress is being made, stimulated by increased research investments and scientific advances, such as induced pluripotent stem cell-derived models. To help identify developmental toxicity NAMs for toxicity screening and potential funding through the American Chemistry Council's Long-Range Research Initiative, a systematic literature review was conducted to better understand the current landscape of developmental toxicity NAMs.
METHODS
Scoping review tools were used to systematically survey the literature (2010-2021; ~18,000 references identified), results and metadata were then extracted, and a user-friendly interactive dashboard was created.
RESULTS
The data visualization dashboard, developed using Tableau® software, is provided as a free, open-access web tool. This dashboard enables straightforward interactive queries and visualizations to identify trends and to distinguish and understand areas or NAMs where research has been most, or least focused.
CONCLUSIONS
Herein, we describe the approach and methods used, summarize the benefits and challenges of applying the systematic-review techniques, and highlight the types of questions and answers for which the dashboard can be used to explore the many different facets of developmental toxicity NAMs.
Topics: Animals; Software; Toxicity Tests; United States
PubMed: 36205106
DOI: 10.1002/bdr2.2075 -
The Lancet. Digital Health Jan 2022Publicly available skin image datasets are increasingly used to develop machine learning algorithms for skin cancer diagnosis. However, the total number of datasets and...
Publicly available skin image datasets are increasingly used to develop machine learning algorithms for skin cancer diagnosis. However, the total number of datasets and their respective content is currently unclear. This systematic review aimed to identify and evaluate all publicly available skin image datasets used for skin cancer diagnosis by exploring their characteristics, data access requirements, and associated image metadata. A combined MEDLINE, Google, and Google Dataset search identified 21 open access datasets containing 106 950 skin lesion images, 17 open access atlases, eight regulated access datasets, and three regulated access atlases. Images and accompanying data from open access datasets were evaluated by two independent reviewers. Among the 14 datasets that reported country of origin, most (11 [79%]) originated from Europe, North America, and Oceania exclusively. Most datasets (19 [91%]) contained dermoscopic images or macroscopic photographs only. Clinical information was available regarding age for 81 662 images (76·4%), sex for 82 848 (77·5%), and body site for 79 561 (74·4%). Subject ethnicity data were available for 1415 images (1·3%), and Fitzpatrick skin type data for 2236 (2·1%). There was limited and variable reporting of characteristics and metadata among datasets, with substantial under-representation of darker skin types. This is the first systematic review to characterise publicly available skin image datasets, highlighting limited applicability to real-life clinical settings and restricted population representation, precluding generalisability. Quality standards for characteristics and metadata reporting for skin image datasets are needed.
Topics: Datasets as Topic; Dermoscopy; Humans; Machine Learning; Skin Neoplasms
PubMed: 34772649
DOI: 10.1016/S2589-7500(21)00252-1 -
Therapeutic Advances in Infectious... 2021Chagas disease (CD) is caused by . When acquired, the disease develops in stages. For diagnosis, laboratory confirmation is required, and an extensive assessment of the... (Review)
Review
INTRODUCTION
Chagas disease (CD) is caused by . When acquired, the disease develops in stages. For diagnosis, laboratory confirmation is required, and an extensive assessment of the patient's health should be performed. Treatment consists of the administration of trypanocidal drugs, which may cause severe adverse effects. The objective of our systematic review was to analyze data contained in the CD published case reports to understand the challenges that patients and clinicians face worldwide.
MATERIALS AND METHODS
We performed a systematic review following the PRISMA guidance. PubMed database was explored using the terms 'American trypanosomiasis' or 'Chagas disease'. Results were limited to human case reports written in English or Spanish. A total of 258 reports (322 patients) were included in the analysis. Metadata was obtained from each article. Following this, it was analyzed to obtain descriptive measures.
RESULTS
From the sample, 56.2% were males and 43.8% were females. Most cases were from endemic countries (85.4%). The most common clinical manifestations were fever during the acute stage (70.0%), dyspnea during the chronic stage in its cardiac form (53.7%), and constipation during the chronic stage in its digestive form (73.7%). Most patients were diagnosed in the chronic stage (72.0%). Treatment was administered in 56.2% of cases. The mortality rate for the acute stage cases was 24.4%, while for the chronic stage this was 28.4%.
DISCUSSION
CD is a parasitic disease endemic to Latin America, with increasing importance due to human and vector migration. In this review, we report reasons for delays in diagnosis and treatment, and trends in medical practices. Community awareness must be increased to improve CD's diagnoses; health professionals should be appropriately trained to detect and treat infected individuals. Furthermore, public health policies are needed to increase the availability of screening and diagnostic tools, trypanocidal drugs, and, eventually, vaccines.
PubMed: 34408874
DOI: 10.1177/20499361211033715 -
Journal of Biomedical Informatics Jan 2023Publicly accessible benchmarks that allow for assessing and comparing model performances are important drivers of progress in artificial intelligence (AI). While recent... (Review)
Review
Publicly accessible benchmarks that allow for assessing and comparing model performances are important drivers of progress in artificial intelligence (AI). While recent advances in AI capabilities hold the potential to transform medical practice by assisting and augmenting the cognitive processes of healthcare professionals, the coverage of clinically relevant tasks by AI benchmarks is largely unclear. Furthermore, there is a lack of systematized meta-information that allows clinical AI researchers to quickly determine accessibility, scope, content and other characteristics of datasets and benchmark datasets relevant to the clinical domain. To address these issues, we curated and released a comprehensive catalogue of datasets and benchmarks pertaining to the broad domain of clinical and biomedical natural language processing (NLP), based on a systematic review of literature and. A total of 450 NLP datasets were manually systematized and annotated with rich metadata, such as targeted tasks, clinical applicability, data types, performance metrics, accessibility and licensing information, and availability of data splits. We then compared tasks covered by AI benchmark datasets with relevant tasks that medical practitioners reported as highly desirable targets for automation in a previous empirical study. Our analysis indicates that AI benchmarks of direct clinical relevance are scarce and fail to cover most work activities that clinicians want to see addressed. In particular, tasks associated with routine documentation and patient data administration workflows are not represented despite significant associated workloads. Thus, currently available AI benchmarks are improperly aligned with desired targets for AI automation in clinical settings, and novel benchmarks should be created to fill these gaps.
Topics: Humans; Artificial Intelligence; Benchmarking; Natural Language Processing
PubMed: 36539106
DOI: 10.1016/j.jbi.2022.104274 -
BMJ Open Science 2021Preclinical research is a vital step in the drug discovery pipeline and more generally in helping to better understand human disease aetiology and its management....
Preclinical research is a vital step in the drug discovery pipeline and more generally in helping to better understand human disease aetiology and its management. Systematic reviews (SRs) can be powerful in summarising and appraising this evidence concerning a specific research question, to highlight areas of improvements, areas for further research and areas where evidence may be sufficient to take forward to other research domains, for instance clinical trial. Guidance and tools for preclinical research synthesis remain limited despite their clear utility. We aimed to create an online end-to-end platform primarily for conducting SRs of preclinical studies, that was flexible enough to support a wide variety of experimental designs, was adaptable to different research questions, would allow users to adopt emerging automated tools and support them during their review process using best practice. In this article, we introduce the Systematic Review Facility (https://syrf.org.uk), which was launched in 2016 and designed to support primarily preclinical SRs from small independent projects to large, crowdsourced projects. We discuss the architecture of the app and its features, including the opportunity to collaborate easily, to efficiently manage projects, to screen and annotate studies for important features (metadata), to extract outcome data into a secure database, and tailor these steps to each project. We introduce how we are working to leverage the use of automation tools and allow the integration of these services to accelerate and automate steps in the systematic review workflow.
PubMed: 35047698
DOI: 10.1136/bmjos-2020-100103 -
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 -
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