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World Journal of Experimental Medicine Jun 2024Hepatitis E virus (HEV), responsible for widespread viral hepatitis, infects approximately 2.3 billion individuals globally, with a significant mortality burden in Asia....
Hepatitis E virus (HEV), responsible for widespread viral hepatitis, infects approximately 2.3 billion individuals globally, with a significant mortality burden in Asia. The virus, primarily transmitted through contaminated water and undercooked meat, is often underdiagnosed, particularly in immunocompromised patients. Current HEV treatments, while effective, are limited by adverse effects, necessitating research into safer alternatives. Moreover, HEV's extrahepatic manifestations, impacting the nervous and renal systems, remain poorly understood. This study underscores the imperative for enhanced HEV research, improved diagnostic methods, and more effective treatments, coupled with increased public health awareness and preventive strategies.
PubMed: 38948414
DOI: 10.5493/wjem.v14.i2.90481 -
Data in Brief Aug 2024This article presents data collected through Computer-Assisted Web Interviewing (CAWI), conducted in Italy with the aim of exploring the Italian population's reaction to...
This article presents data collected through Computer-Assisted Web Interviewing (CAWI), conducted in Italy with the aim of exploring the Italian population's reaction to the Russian invasion of Ukraine in February 2022 and monitoring this reaction for the first six months of the attack through a six-round survey. Each round involved a representative sample of approximately 1010 (1007-1015) Italian adult citizens. Participants were asked questions about emotional reactions to the Russian invasion, coping strategies used, solidarity behaviour toward Ukrainian refugees, perceptions of refugees as a threat to the country, trust in national and international authorities to manage the international situation, and prospects for the future. Demographic data on the respondents were also collected. The survey design was developed by a research group from two universities (the University of Salento and the University of Foggia) and a European research centre, EICAP (European Institute of Cultural Analysis for Policy). The data provided in this article is a resource for researchers, public authorities, and other parties interested in surveying and studying public opinion. This dataset can be used to explore a wide range of topics, including prosocial behaviour and attitudes towards refugees in humanitarian emergencies.
PubMed: 38948411
DOI: 10.1016/j.dib.2024.110579 -
Journal of Multidisciplinary Healthcare 2024Despite over 30 years of microbiome and skeletal muscle research, no quantitative analysis of sarcopenia and the microbiome literature had been conducted. Our... (Review)
Review
Despite over 30 years of microbiome and skeletal muscle research, no quantitative analysis of sarcopenia and the microbiome literature had been conducted. Our bibliometric study examined research status, hotspots, and future trends. We utilized bibliometric techniques to search the Science Citation Index Extended Database on February 27, 2023, using the Bibliometrix package in R to create a map displaying scientific production and subject categories. Collaborative network maps between countries/regions were visualized using Scimago Graphica, while VOSviewer explored collaboration modes among individuals and institutions. We analyzed the top 25 emerging keywords, top co-occurring keyword networks, and co-occurring keyword clusters using CiteSpace. A total of 997 articles were retrieved for sarcopenia and microbiome, of which 633 papers were analyzed. Both the number of publications and total citation frequency had been continuously increasing. The United States had the highest total citation frequency, while China had the highest number of publications. Research on the impact of the microbiome on sarcopenia was in its nascent stage and spans multiple disciplines, including nutrition, microbiology, geriatrics, immunology, endocrinology and metabolism, molecular biology, and sports medicine. The University of Copenhagen contributed the most to the number of publications (n=16), with Tibbett M (n=7) and Hulver MW (n=7) among the top authors. The most published journal was "Nutrients" (n=24). Analysis of keywords and clusters revealed new research hotspots in microbes and sarcopenia, such as malnutrition, dietary fiber, signaling pathways, frailty, and intestinal permeability. Research on the impact of the microbiome on sarcopenia is in its infancy and spans multiple disciplines. Malnutrition, dietary fiber, signaling pathways, frailty, and intestinal microbes are currently research hotspots. Furthermore, the visual atlas analysis of research on microbes and sarcopenia helps to track the knowledge structure in research fields related to sarcopenia and microbes, providing direction for future research.
PubMed: 38948393
DOI: 10.2147/JMDH.S469747 -
Journal of Pediatrics. Clinical Practice Sep 2024To evaluate the association between shift-level organizational data (unit occupancy, nursing overtime ratios [OTRs], and nursing provision ratios [NPRs]) with nosocomial...
OBJECTIVE
To evaluate the association between shift-level organizational data (unit occupancy, nursing overtime ratios [OTRs], and nursing provision ratios [NPRs]) with nosocomial infection (NI) among infants born very preterm in the neonatal intensive care unit (NICU).
STUDY DESIGN
This was a multicenter, retrospective cohort study, including 1921 infants 23-32 weeks of gestation admitted to 3 tertiary-level NICUs in Quebec between 2014 and 2018. Patient characteristics and outcomes (NIs) were obtained from the Canadian Neonatal Network database and linked to administrative data. For each shift, unit occupancy (occupied/total beds), OTR (nursing overtime hours/total nursing hours), and NPR (number of actual/number of recommended nurses) were calculated. Mixed-effect logistic regression models were used to calculate aOR for the association of organizational factors (mean over 3 days) with the risk of NI on the following day for each infant.
RESULTS
Rate of NI was 11.5% (220/1921). Overall, median occupancy was 88.7% [IQR 81.0-94.6], OTR 4.4% [IQR 1.5-7.6], and NPR 101.1% [IQR 85.5-125.1]. A greater 3-day mean OTR was associated with greater odds of NI (aOR 1.08, 95% CI 1.02-1.15), a greater 3-day mean NPR was associated lower odds of NI (aOR 0.96, 95% CI 0.95-0.98), and occupancy was not associated with NI (aOR, 0.99, 95% CI 0.96-1.02). These findings were consistent across multiple sensitivity analyses.
CONCLUSIONS
Nursing overtime and nursing provision are associated with the adjusted odds of NI among infants born very preterm in the NICU. Further interventional research is needed to infer causality.
PubMed: 38948384
DOI: 10.1016/j.jpedcp.2024.200112 -
Frontiers in Genetics 2024The DNA damage repair (DDR) system in human genome is pivotal in maintaining genomic integrity. Pathogenic variation (PV) in DDR genes impairs their function, leading to...
INTRODUCTION
The DNA damage repair (DDR) system in human genome is pivotal in maintaining genomic integrity. Pathogenic variation (PV) in DDR genes impairs their function, leading to genome instability and increased susceptibility to diseases, especially cancer. Understanding the evolution origin and arising time of DDR PV is crucial for comprehending disease susceptibility in modern humans.
METHODS
We used big data approach to identify the PVs in DDR genes in modern humans. We mined multiple genomic databases derived from 251,214 modern humans of African and non-Africans. We compared the DDR PVs between African and non-African. We also mined the DDR PVs in the genomic data derived from 5,031 ancient humans. We used the DDR PVs from ancient humans as the intermediate to further the DDR PVs between African and non-African.
RESULTS AND DISCUSSION
We identified 1,060 single-base DDR PVs across 77 DDR genes in modern humans of African and non-African. Direct comparison of the DDR PVs between African and non-African showed that 82.1% of the non-African PVs were not present in African. We further identified 397 single-base DDR PVs in 56 DDR genes in the 5,031 ancient humans dated between 45,045 and 100 years before present (BP) lived in Eurasian continent therefore the descendants of the latest out-of-Africa human migrants occurred 50,000-60,000 years ago. By referring to the ancient DDR PVs, we observed that 276 of the 397 (70.3%) ancient DDR PVs were exclusive in non-African, 106 (26.7%) were shared between non-African and African, and only 15 (3.8%) were exclusive in African. We further validated the distribution pattern by testing the PVs in and , two of the important genes in genome stability maintenance, in African, non-African, and Ancient humans. Our study revealed that DDR PVs in modern humans mostly emerged after the latest out-of-Africa migration. The data provides a foundation to understand the evolutionary basis of disease susceptibility, in particular cancer, in modern humans.
PubMed: 38948361
DOI: 10.3389/fgene.2024.1408952 -
Clinical Ophthalmology (Auckland, N.Z.) 2024An estimated 13 million Australians live with one or more chronic eye conditions, with prevalence increasing. Eye care services today and in the future rely on effective...
PURPOSE
An estimated 13 million Australians live with one or more chronic eye conditions, with prevalence increasing. Eye care services today and in the future rely on effective workforces, in which nurses play a pivotal role. Despite nurse involvement in eye care, there is no information describing their engagement, deployment, training, and opinion. This paper offers the first review of nurse engagement in eye care in Australia.
METHODS
We conducted an e-survey on Australian nurse engagement in eye care. Quantitative questions were analysed by descriptive, chi-square and bivariate correlation coefficients with assumed power of 0.80, and significance of =0.05. Grounded theory, sentiment and saturation analysis extracted key themes, meaning and opinion from the qualitative questions.
RESULTS
There were n=238 Australian nurse participants. Results indicated they were satisfied with their role, engaged in a wide range of healthcare and eye care setting and organisations, and adapted to their employer. Task-shifting "to" and "from" nurses was not universally supported but recognised by participants as necessary. Of concern, the results suggested that 68.6% of our participants would exit eye care over the next ten years, with insufficient entry pathways into the field for graduate and early-career nurses.
CONCLUSION
For Australia to meet and sustain eye care services for its population, steps must be taken to improve exposure and entry to the field for students, graduates, and early-career nurses. Strategies to train and prepare nurses for task-shifting are urgently required and the eye care nursing sector must professionalise to achieve positive change.
PubMed: 38948343
DOI: 10.2147/OPTH.S463743 -
Bio-protocol Jun 2024Human babesiosis is a tick-borne disease caused by pathogens. The disease, which presents with malaria-like symptoms, can be life-threatening, especially in individuals...
Human babesiosis is a tick-borne disease caused by pathogens. The disease, which presents with malaria-like symptoms, can be life-threatening, especially in individuals with weakened immune systems and the elderly. The worldwide prevalence of human babesiosis has been gradually rising, prompting alarm among public health experts. In other pathogens, genetic techniques have proven to be valuable tools for conducting functional studies to understand the importance of specific genes in development and pathogenesis as well as to validate novel cellular targets for drug discovery. Genetic manipulation methods have been established for several non-human and species and, more recently, have begun to be developed for human Babesia parasites. We have previously reported the development of a method for genetic manipulation of the human pathogen . This method is based on positive selection using the hDHFR gene as a selectable marker, whose expression is regulated by the ef-1aB promoter, along with homology regions that facilitate integration into the gene of interest through homologous recombination. Herein, we provide a detailed description of the steps needed to implement this strategy in to study gene function. It is anticipated that the implementation of this method will significantly improve our understanding of babesiosis and facilitate the development of novel and more effective therapeutic strategies for the treatment of human babesiosis. Key features This protocol provides an effective means of transfection of , enabling genetic manipulation and editing to gain further insights into its biology and pathogenesis. The protocol outlined here for the electroporation of represents an advancement over previous methods used for [1]. Improvements include higher volume of culture used during the electroporation step and an enhancement in the number of electroporation pulses. These modifications likely enhance the efficiency of gene editing in , allowing for quicker and more effective selection of transgenic parasites.
PubMed: 38948263
DOI: 10.21769/BioProtoc.5016 -
PeerJ 2024TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is...
TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org. TIN-X uses natural language processing to identify disease and protein mentions within PubMed content using previously published tools for named entity recognition (NER) of gene/protein and disease names. Target data is obtained from the Target Central Resource Database (TCRD). Two important metrics, novelty and importance, are computed from this data and when plotted as log(importance) . log(novelty), aid the user in visually exploring the novelty of drug targets and their associated importance to diseases. TIN-X Version 3.0 has been significantly improved with an expanded dataset, modernized architecture including a REST API, and an improved user interface (UI). The dataset has been expanded to include not only PubMed publication titles and abstracts, but also full-text articles when available. This results in approximately 9-fold more target/disease associations compared to previous versions of TIN-X. Additionally, the TIN-X database containing this expanded dataset is now hosted in the cloud Amazon RDS. Recent enhancements to the UI focuses on making it more intuitive for users to find diseases or drug targets of interest while providing a new, sortable table-view mode to accompany the existing plot-view mode. UI improvements also help the user browse the associated PubMed publications to explore and understand the basis of TIN-X's predicted association between a specific disease and a target of interest. While implementing these upgrades, computational resources are balanced between the webserver and the user's web browser to achieve adequate performance while accommodating the expanded dataset. Together, these advances aim to extend the duration that users can benefit from TIN-X while providing both an expanded dataset and new features that researchers can use to better illuminate understudied proteins.
Topics: Humans; User-Computer Interface; Natural Language Processing; PubMed; Software
PubMed: 38948230
DOI: 10.7717/peerj.17470 -
PeerJ 2024Reviewers rarely comment on the same aspects of a manuscript, making it difficult to properly assess manuscripts' quality and the quality of the peer review process. The...
BACKGROUND
Reviewers rarely comment on the same aspects of a manuscript, making it difficult to properly assess manuscripts' quality and the quality of the peer review process. The goal of this pilot study was to evaluate structured peer review implementation by: 1) exploring whether and how reviewers answered structured peer review questions, 2) analysing reviewer agreement, 3) comparing that agreement to agreement before implementation of structured peer review, and 4) further enhancing the piloted set of structured peer review questions.
METHODS
Structured peer review consisting of nine questions was piloted in August 2022 in 220 Elsevier journals. We randomly selected 10% of these journals across all fields and IF quartiles and included manuscripts that received two review reports in the first 2 months of the pilot, leaving us with 107 manuscripts belonging to 23 journals. Eight questions had open-ended fields, while the ninth question (on language editing) had only a yes/no option. The reviews could also leave and . Answers were independently analysed by two raters, using qualitative methods.
RESULTS
Almost all the reviewers ( = 196, 92%) provided answers to all questions even though these questions were not mandatory in the system. The longest answer (Md 27 words, IQR 11 to 68) was for reporting methods with sufficient details for replicability or reproducibility. The reviewers had the highest (partial) agreement (of 72%) for assessing the flow and structure of the manuscript, and the lowest (of 53%) for assessing whether interpretation of the results was supported by data, and for assessing whether the statistical analyses were appropriate and reported in sufficient detail (52%). Two thirds of the reviewers ( = 145, 68%) filled out the section, of which 105 (49%) resembled traditional peer review reports. These reports contained a Md of 4 (IQR 3 to 5) topics covered by the structured questions. Absolute agreement regarding final recommendations (exact match of recommendation choice) was 41%, which was higher than what those journals had in the period from 2019 to 2021 (31% agreement, = 0.0275).
CONCLUSIONS
Our preliminary results indicate that reviewers successfully adapted to the new review format, and that they covered more topics than in their traditional reports. Individual question analysis indicated the greatest disagreement regarding the interpretation of the results and the conducting and the reporting of statistical analyses. While structured peer review did lead to improvement in reviewer final recommendation agreements, this was not a randomized trial, and further studies should be performed to corroborate this. Further research is also needed to determine whether structured peer review leads to greater knowledge transfer or better improvement of manuscripts.
Topics: Pilot Projects; Peer Review, Research; Periodicals as Topic; Humans; Editorial Policies; Peer Review
PubMed: 38948202
DOI: 10.7717/peerj.17514 -
PeerJ 2024Good sleep quality is crucial for dental students as they must have optimal cognitive function, memory, and decision-making to accomplish their learning requirements....
BACKGROUND
Good sleep quality is crucial for dental students as they must have optimal cognitive function, memory, and decision-making to accomplish their learning requirements. This study aims to determine sleep quality, its associated factors, and the association between sleep quality and academic performance among dental students in Malaysia.
METHODS
This cross-sectional study involved dental students at four public universities in Malaysia. A validated Pittsburgh Sleep Quality Index (PSQI) questionnaire was used to assess their sleep quality. An additional self-administered questionnaire was employed to obtain the students' sociodemographic profile, lifestyle, and academic performance. The data were analysed using descriptive, chi-square, and multiple logistic regression.
RESULTS
Three hundred eighty-four dental students participated in this study. About half of the dental students (51.6%) have poor sleep quality. The mean of sleep hours per night was 5.72 (SD 1.06). The sleep quality was significantly poor among Malay students ( = 0.023), students who stayed at hostel ( = 0.002), and those who consumed caffeinated drinks ( = 0.028). Multiple logistic regression analysis revealed that the poor sleep quality was significantly associated with self-perceived poor academic performance (Adjusted Odds Ratio (AOR) 2.95, 95% CI [1.25-6.96], -value = 0.013) and students skipping class (AOR 1.70, 95% CI [1.00-2.91], -value = 0.046).
CONCLUSIONS
Most of the dental students in Malaysia have poor sleep quality. Ethnicity, accommodation, and caffeine consumption were significantly associated with sleep quality. Awareness to sleep quality among dental students is needed to ensure they are able to cope with the challenging dental school learning environment.
Topics: Humans; Malaysia; Students, Dental; Male; Female; Cross-Sectional Studies; Surveys and Questionnaires; Sleep Quality; Young Adult; Adult; Academic Performance
PubMed: 38948199
DOI: 10.7717/peerj.17522