bluuebunny/crossref_metadata_2025_split huggingface dataset:
Attribution of country level foodborne disease to food group and food types in three African countries: Conclusions from a structured expert judgment study
Authors: Sapp Amanda C. , Amaya Mirna P. , Havelaar Arie H. , Nane Gabriela F. 
Published: September 2022

Background
According to the World Health Organization, 600 million cases of foodborne disease occurred in 2010. To inform risk management strategies aimed at reducing this burden, attribution to specific foods is necessary.

Objective
We present attribution estimates for foodborne pathogens (Campylobacter spp., enterotoxigenic Escherichia coli (ETEC), Shiga-toxin producing E. coli, nontyphoidal Salmonella enterica, Cryptosporidium spp., Brucella spp., and Mycobacterium bovis) in three African countries (Burkina Faso, Ethiopia, Rwanda) to support risk assessment and cost-benefit analysis in three projects aimed at increasing safety of beef, dairy, poultry meat and vegetables in these countries.

Methods
We used the same methodology as the World Health Organization, i.e., Structured Expert Judgment according to Cooke’s Classical Model, using three different panels for the three countries. Experts were interviewed remotely and completed calibration questions during the interview without access to any resources. They then completed target questions after the interview, using resources as considered necessary. Expert data were validated using two objective measures, calibration score or statistical accuracy, and information score. Performance-based weights were derived from the two measures to aggregate experts’ distributions into a so-called decision maker. The analysis was made using Excalibur software, and resulting distributions were normalized using Monte Carlo simulation.

Results
Individual experts’ uncertainty assessments resulted in modest statistical accuracy and high information scores, suggesting overconfident assessments. Nevertheless, the optimized item-weighted decision maker was statistically accurate and informative. While there is no evidence that animal pathogenic ETEC strains are infectious to humans, a sizeable proportion of ETEC illness was attributed to animal source foods as experts considered contamination of food products by infected food handlers can occur at any step in the food chain. For all pathogens, a major share of the burden was attributed to food groups of interest. Within food groups, the highest attribution was to products consumed raw, but processed products were also considered important sources of infection.

Conclusions
Cooke’s Classical Model with performance-based weighting provided robust uncertainty estimates of the attribution of foodborne disease in three African countries. Attribution estimates will be combined with country-level estimates of the burden of foodborne disease to inform decision making by national authorities.
Epidemiology of infection by pulmonary non-tuberculous mycobacteria in French Guiana 2008–2018
Authors: Chaptal Milène , Andrejak Claire , Bonifay Timothée , Beillard Emmanuel , Guillot Geneviève , Guyomard-Rabenirina Stéphanie , Demar Magalie , Trombert-Paolantoni Sabine , Jacomo Veronique , Mosnier Emilie , Veziris Nicolas , Djossou Felix , Epelboin Loïc ,   French Guiana PNTM working group
Published: September 2022

Introduction
Unlike diseases caused by Mycobacterium tuberculosis, M. leprae and M. ulcerans, the epidemiology of pulmonary non-tuberculous mycobacteria (PNTM) has not received due attention in French Guiana. The main objective of the current study was to define the incidence of these PNTM infections: NTM pulmonary diseases (NTM-PD) and casual PNTM isolation (responsible of latent infection or simple colonization). The secondary objectives were to determine species diversity and geographic distribution of these atypical mycobacteria.

Methods
A retrospective observational study (2008–2018) of French Guiana patients with at least one PNTM positive respiratory sample in culture was conducted. Patients were then classified into two groups: casual PNTM isolation or pulmonary disease (NTM-PD), according to clinical, radiological and microbiological criteria defined by the American Thoracic Society / Infectious Disease Society of America (ATS / IDSA) in 2007.

Results
178 patients were included, out of which 147 had casual PNTM isolation and 31 had NTM-PD. Estimated annual incidence rate of respiratory isolates was 6.17 / 100,000 inhabitants per year while that of NTM-PD was 1.07 / 100,000 inhabitants per year. Among the 178 patients, M. avium complex (MAC) was the most frequently isolated pathogen (38%), followed by M. fortuitum then M. abscessus (19% and 6% of cases respectively), the latter two mycobacteria being mainly found in the coastal center region. Concerning NTM-PD, two species were mainly involved: MAC (81%) and M. abscessus (16%).

Discussion/Conclusion
This is the first study on the epidemiology of PNTM infections in French Guiana. PNTM’s incidence looks similar to other contries and metropolitan France and NTM-PD is mostly due to MAC and M.abscessus. Although French Guiana is the French territory with the highest tuberculosis incidence, NTM should not be overlooked.
Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea
Authors: Lee Jingyeong , Park Kyungmin , Kim Jongwoo , Lee Seung-Ho , Lee Geum-Young , Cho Seungchan , Kim Heung-Chul , Klein Terry A. , Kim Jeong-Ah , Choi Jeewan , Park Juwan , Song Dong-Hyun , Gu Se Hun , Yun Hyeongseok , Kim Jung-Eun , Lee Daesang , Hur Gyeung Haeng , Jeong Seong Tae , Hwang Il-Ung , Kim Won-Keun , Song Jin-Won 
Published: September 2022

Background
Whole-genome sequencing plays a critical role in the genomic epidemiology intended to improve understanding the spread of emerging viruses. Dabie bandavirus, causing severe fever with thrombocytopenia syndrome (SFTS), is a zoonotic tick-borne virus that poses a significant public health threat. We aimed to evaluate a novel amplicon-based nanopore sequencing tool to obtain whole-genome sequences of Dabie bandavirus, also known as SFTS virus (SFTSV), and investigate the molecular prevalence in wild ticks, Republic of Korea (ROK).

Principal findings
A total of 6,593 ticks were collected from Gyeonggi and Gangwon Provinces, ROK in 2019 and 2020. Quantitative polymerase chain reaction revealed the presence of SFSTV RNA in three Haemaphysalis longicornis ticks. Two SFTSV strains were isolated from H. longicornis captured from Pocheon and Cheorwon. Multiplex polymerase chain reaction-based nanopore sequencing provided nearly full-length tripartite genome sequences of SFTSV within one hour running. Phylogenetic and reassortment analyses were performed to infer evolutionary relationships among SFTSVs. Phylogenetic analysis grouped SFTSV Hl19-31-4 and Hl19-31-13 from Pocheon with sub-genotype B-1 in all segments. SFTSV Hl20-8 was found to be a genomic organization compatible with B-1 (for L segment) and B-2 (for M and S segments) sub-genotypes, indicating a natural reassortment between sub-genotypes.

Conclusion/Significance
Amplicon-based next-generation sequencing is a robust tool for whole-genome sequencing of SFTSV using the nanopore platform. The molecular prevalence and geographical distribution of SFTSV enhanced the phylogeographic map at high resolution for sophisticated prevention of emerging SFTS in endemic areas. Our findings provide important insights into the rapid whole-genome sequencing and genetic diversity for the genome-based diagnosis of SFTSV in the endemic outbreak.
Reproductive health needs of Human papillomavirus (HPV) positive women: A systematic review
Authors: Galeshi Mina , Shirafkan Hoda , Yazdani Shahla , Motaghi Zahra 
Published: September 2022

Objectives
Human papillomavirus is one of the most important causes of cervical cancer. Participating in an HPV test and receiving an HPV diagnosis can create questions about the needs and preferences. The present systematic review was conducted to determine the reproductive health needs of women with HPV.

Methods
We searched PubMed, Scopus, Web of Science, Google Scholar and Magiran, SID and Iranmedex. Without language restrictions and time constraints. We also searched the grey literature and carried out forward/backward citation searches.

Results
In the first, 1056 articles were retrieved, and, after removing them, 13 articles published were entered. The studies were qualitative (N = 9), quantitative (N = 3), and one was unclear. Most qualitative studies collected data using individual interviews (N = 7), two qualitative studies, narratives of HPV patients from a website of patient experiences and questions. Women wanted further information on different HPV viral types, transmission, implications for sexual partners, prevalence, latency and regression of HPV, their management options and the implications of infection for cancer risk and fertility. Women’s experience of searching the Internet for further information about HPV was reported as difficult, anxiety provoking and contributing to the stigma of the infection because information was often located in the context of other sexually transmitted infections, with multiple sexual partners highlighted as a risk factor for infection.

Conclusion
Surveys showed that the majority of women had unanswered questions about their HPV test results. The information that women thought was helpful in interpreting their test results included having a high-risk type of HPV, and cancer survival statistics for the virus. Women also needed information about sexual transmission, how HPV tested positive in a long-term relationship, and the potential consequences for their partners and the risk of re-infection. Younger women had questions about whether HPV could affect fertility.
The concordance of signals based on irregular incremental lines in the human tooth cementum with documented pregnancies: Results from a systematic approach
Authors: Mani-Caplazi Gabriela , Vach Werner , Wittwer-Backofen Ursula , Hotz Gerhard 
Published: September 2022

Background and objectiveThere is evidence from previous studies that pregnancies and diseases are recorded in the tooth cementum. This study aims to assess the degree of concordance between signals based on irregular incremental lines (ILs) and reported pregnancies.Material and methods23 recent and 24 archaeological human teeth with known birth history were included in this investigation. 129 histological sections of tooth roots were assessed for irregularities in appearance and width using a standardized protocol. Similarity of observed irregularities at the section level allowed us to define signals at the tooth level. The sensitivity of signals to detect pregnancies was determined and related to the signal prevalence.ResultsPregnancy signals were frequently visually observed. However, applying a standardized process we could only reach signal sensitivities to identify pregnancies up to 20 percentage points above chance level.ConclusionsBased on a standardized and reproducible method it could be confirmed that some pregnancies leave visible signals in the tooth cementum. The results show the potential of the tooth cementum to support reconstruction of life courses in paleopathology. However, it seems that not all pregnancies affect the cementogenesis in such a way that irregular ILs are identifiable. Further research is needed to better understand which type of pregnancies and other conditions are recorded in the tooth cementum.
COVID-19 pandemic and food security in different contexts: A systematic review protocol
Authors: Doustmohammadian Azam , Mohammadi-Nasrabadi Fatemeh , Fadavi Ghasem 
Published: September 2022

Background
Given the unprecedented nature of the COVID-19 crisis and the importance of early implementation of prevention programs, it is essential to understand better its potential impacts on various food security dimensions and indicators.

Methods
Research databases, including Cochrane Central Register of Controlled Trials (CENTRAL), Cochrane Public Health Register, PubMed/MEDLINE, SCOPUS, EMBASE, CINAHL, Web of science, and Google Scholar, will be searched using a search strategy and keywords developed in collaboration with librarians. The review will include all field and community trials and observational studies in all population groups. Searching electronic databases, study selection, and data extraction will be conducted by two researchers independently. Four critical appraisal tools will be used to assess the quality of included studies according to the study design: The Joanna Briggs Institute (JBI) Prevalence Critical Appraisal tool, the JBI critical appraisal checklist for randomized control/pseudo-randomized trial, descriptive/case series, and comparable cohort/case-control. These tools were initially designed for use in systematic reviews. A narrative synthesis will be implemented to summarize findings if meta-analyses are not appropriate.

Discussion
The current systematic review results can be used to predict the effect of COVID-19 on the individuals’ and households’ food security, especially in vulnerable populations, and develop effective interventions. This review can provide information for policymakers to better understand the factors influencing the implementation of these interventions and inform decision-making to improve food security.

Systematic review registration
The present study registration number in the international prospective register of systematic reviews (PROSPERO) is CRD42020185843.
COVID-19 contact tracing app reviews reveal concerns and motivations around adoption
Authors: Dixon Erica L. , Joshi Sukanya M. , Ferrell William , Volpp Kevin G. , Merchant Raina M. , Guntuku Sharath Chandra 
Published: September 2022

Background
Google and Apple’s Exposure Notifications System (ENS) was developed early in the COVID-19 pandemic to complement existing contact tracing efforts while protecting user privacy. An analysis by the Associated Press released in December 2020 estimated approximately 1 in 14 people had downloaded apps in states one was available. In this study, we assessed the motivation and experience of individuals who downloaded ENS apps from the Google Play and Apple App Stores.

Methods
We collected review text, star rating, and date of rating for all the reviews on ENS apps in the Google Play and Apple App stores. We extracted the relative frequency of single words and phrases from reviews and created an open vocabulary language, with themes categorized by the research team, to study the salient themes around reviews with high (3–5 stars), neutral (3 stars), and negative (1–2 stars) ratings using logistic regression.

Results
Of 7622 reviews obtained from 26 states between 04/07/2020 to 03/31/2021, 6364 were from Google Play Store, and 1258 were from Apple App Store. We obtained reviews for a total of 38 apps, with 25 apps from the Google Play Store and 13 apps from the Apple Play Store. 78% of the reviews are either 1 star or 5 stars. Positive reviews were driven by ease of use, support for the state government in creating the app, and encouragement for others to download, as well as engage in other COVID-19 precautions. Negative and neutral reviews focused on issues with app functionality (i.e., installation and tracking errors).

Conclusions
Uptake was the largest barrier to success for ENS apps, but states can use insight from app store reviews to better position themselves if they choose to develop further public health apps.
Network pharmacology study of Yishen capsules in the treatment of diabetic nephropathy
Authors: Fang Jingai , Wang Chendan , Zheng Jie , Liu Yuxiang 
Published: September 2022

ObjectiveIn this study, we used network pharmacology to explore the possible therapeutic mechanism underlying the treatment of diabetic nephropathy with Yishen capsules.MethodsThe active chemical constituents of Yishen capsules were acquired using the Traditional Chinese Medicine Systems Pharmacology platform and the Encyclopedia of Traditional Chinese Medicine. Component target proteins were then searched and screened in the BATMAN database. Target proteins were cross-validated using the Comparative Toxicogenomics Database, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of the target proteins were performed. Then, protein–protein interaction (PPI) analysis was performed using the STRING database. Finally, a pharmacological network was constructed to show the component-target-pathway relationships. Molecular docking was used to analyse the interaction between drug components and target proteins.ResultsIn total, 285 active chemical components were found, including 85 intersection targets against DN. In the pharmacological network, 5 key herbs (A.membranaceus,A.sinensis,E.ferox,A.orientale, andR.rosea) and their corresponding 12 key components (beta-sitosterol, beta-carotene, stigmasterol, alisol B, mairin, quercetin, caffeic acid, 1-monolinolein, kaempferol, jaranol, formononetin, and calycosin) were screened. Furthermore, the 12 key components were related to 24 target protein nodes (e.g., AGT, AKT1, AKT2, BCL2, NFKB1, and SIRT1) and enriched in 24 pathway nodes (such as the NF-kappa B, AGE-RAGE, toll-like receptor, and relaxin signaling pathways). Molecular docking revealed that hydrogen bond was formed between drug components and target proteins.ConclusionIn conclusion, the active constituents of Yishen capsules modulate targets or signaling pathways in DN pathogenesis.
Fact boxes that inform individual decisions may contribute to a more positive evaluation of COVID-19 vaccinations at the population level
Authors: Rebitschek Felix G. , Ellermann Christin , Jenny Mirjam A. , Siegel Nico A. , Spinner Christian , Wagner Gert G. 
Published: September 2022

Objective
For an effective control of the SARS-CoV-2 pandemic with vaccines, most people in a population need to be vaccinated. It is thus important to know how to inform the public with reference to individual preferences–while also acknowledging the societal preference to encourage vaccinations. According to the health care standard of informed decision-making, a comparison of the benefits and harms of (not) having the vaccination would be required to inform undecided and skeptical people. To test evidence-based fact boxes, an established risk communication format, and to inform their development, we investigated their contribution to knowledge and evaluations of COVID-19 vaccines.

Methods
We conducted four studies (1, 2, and 4 were population-wide surveys with N = 1,942 to N = 6,056): Study 1 assessed the relationship between vaccination knowledge and intentions in Germany over three months. Study 2 assessed respective information gaps and needs of the population in Germany. In parallel, an experiment (Study 3) with a mixed design (presentation formats; pre-post-comparison) assessed the effect of fact boxes on risk perceptions and fear, using a convenience sample (N = 719). Study 4 examined how effective two fact box formats are for informing vaccination intentions, with a mixed experimental design: between-subjects (presentation formats) and within-subjects (pre-post-comparison).

Results
Study 1 showed that vaccination knowledge and vaccination intentions increased between November 2020 and February 2021. Study 2 revealed objective information requirements and subjective information needs. Study 3 showed that the fact box format is effective in adjusting risk perceptions concerning COVID-19. Based on those results, fact boxes were revised and implemented with the help of a national health authority in Germany. Study 4 showed that simple fact boxes increase vaccination knowledge and positive evaluations in skeptics and undecideds.

Conclusion
Fact boxes can inform COVID-19 vaccination intentions of undecided and skeptical people without threatening societal vaccination goals of the population.
Death-coping self-efficacy and its influencing factors among Chinese nurses: A cross-sectional study
Authors: Lin Xi , Li Xiaoqin , Bai Yongqi , Liu Qin , Xiang Weilan 
Published: September 2022

BackgroundNurses are the main caregivers of dying patients. Facing or dealing with death-related events is inevitable. Death-coping self-efficacy (DCS) is very important, as it can reduce the risk of nursing staff to adverse emotional distress, help them participate in end-of-life care and improve the quality of care of patients.MethodsUsing the convenient sampling method, this study included a total of 572 nurses from a tertiary hospital in Hangzhou, China. The status and influencing factors of the DCS of nurses were explored using a general information questionnaire and DCS scale.ResultsThe scores of each parameter, ranging from low to high, were in the order of coping with grief, preparation for death and hospice care. Factors influencing nurses’ DCS included attendance in hospice care education courses within the previous year, experience of accompanying the family members of the deceased and attitude towards death.ConclusionsThe overall self-efficacy of nurses in palliative care was at a medium level. Moreover, their self-efficacy in coping with grief and preparation for death should be strengthened. Managers of medical institutions can assess the death-coping ability of nurses, which helps provide corresponding support and training for nurses at an early stage. Nurses should receive guidance in grief adjustment and emotion regulation. Medical units should provide nurses with a platform for continuous training and education, use of death-related theoretical models and frameworks to guide nurses in dealing with death-related events, reduce nurses’ negative mood and jointly promote their mental health.
Microbial Associations with Microscopic Colitis
Authors: Sun Shan , Blakley Ivory C. , Fodor Anthony A. , Keku Temitope O. , Woosley John T. , Peery Anne F. , Sandler Robert S. 
Published: September 2022

ABSTRACT

BACKGROUND AND OBJECTIVE:
Microscopic colitis is a relatively common cause of chronic diarrhea and may be linked to luminal factors. Given the essential role of the microbiome in human gut health, analysis of microbiome changes associated with microscopic colitis could provide insights into the development of the disease.

METHODS:
We enrolled patients who underwent colonoscopy for diarrhea. An experienced pathologist classified patients as having microscopic colitis (n=52) or controls (n=153). Research biopsies were taken from the ascending and descending colon, and the microbiome was characterized with Illumina sequencing. We analyzed the associations between microscopic colitis and microbiome with a series of increasingly complex models adjusted for a range of demographic and health factors.

RESULTS:
We found that alpha-diversity was significantly lower in microscopic colitis cases compared to controls in the descending colon microbiome. In the descending colon, a series of models that adjusted for an increasing number of co-variates found taxa significantly associated with microscopic colitis, including Proteobacteria that was enriched in cases and Collinsella enriched in controls. While the alpha-diversity and taxa were not significantly associated with microscopic colitis in the ascending colon microbiome, the inference p-values based on ascending and descending microbiomes were highly correlated.

CONCLUSION:
Our study demonstrates an altered microbiome in microscopic colitis cases compared to controls. Because both the cases and controls had diarrhea, we have identified candidate taxa that could be mechanistically responsible for the development of microscopic colitis independent of changes to the microbial community caused by diarrhea.