bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of microbial interaction network: zero-inflated latent Ising model based approach
Authors: Zhou Jie , Viles Weston D. , Lu Boran , Li Zhigang , Madan Juliette C. , Karagas Margaret R. , Gui Jiang , Hoen Anne G. 
Published: October 2020

AbstractBackgroundThroughout their lifespans, humans continually interact with the microbial world, including those organisms which live in and on the human body. Research in this domain has revealed the extensive links between the human-associated microbiota and health. In particular, the microbiota of the human gut plays essential roles in digestion, nutrient metabolism, immune maturation and homeostasis, neurological signaling, and endocrine regulation. Microbial interaction networks are frequently estimated from data and are an indispensable tool for representing and understanding the conditional correlation between the microbes. In this high-dimensional setting, zero-inflation and unit-sum constraint for relative abundance data pose challenges to the reliable estimation of microbial interaction networks.Methods and ResultsTo identify the microbial interaction network, thezero-inflated latent Ising(ZILI) model is proposed which assumes the distribution of relative abundance relies only on finite latent states and provides a novel way to solve issues induced by the unit-sum and zero-inflation constrains. A two-step algorithm is proposed for the model selection of ZILI. ZILI is evaluated through simulated data and subsequently applied to an infant gut microbiota dataset from New Hampshire Birth Cohort Study. The results are compared with results from Gaussian graphical model (GGM) and dichotomous Ising model (DIS). Providing ZILI is the true data-generating model, the simulation studies show that the two-step algorithm can identify the graphical structure effectively and is robust to a range of parameter settings. For the infant gut microbiota dataset, the final estimated networks from GGM and ZILI turn out to have significant overlap in which the ZILI tends to select the sparser network than those from GGM. From the shared subnetwork, a hub taxon Lachnospiraceae is identified whose involvement in human disease development has been discovered recently in literature.ConclusionsConstrains induced by relative abundance of microbiota such as zero inflation and unit sum render the conditional correlation analysis unreliable for conventional methods such as GGM. The proposed optimal categoricalization based ZILI model provides an alternative yet elegant way to deal with these difficulties. The results from ZILI have reasonable biological interpretation. This model can also be used to study the microbial interaction in other body parts.
Hydroxymethylbilane synthase (HMBS) gene-based endogenous internal control for avian species
Authors: Wang Yaoyao , Zhang Jilei , Patrick Kelly , Li Min , Gong Jiansen , Xu Bu , Shen Qiuping , Yang Yi , Wei Lanjing , Zhang Yuanyuan , Peng Daxin , Ye Jianqiang , Poudel Anil , Wang Chengming 
Published: October 2020

AbstractWith PCR becoming one of the most important and widely-used diagnostic tools for infectious diseases of poultry, an urgent need has developed for an endogenous internal control (EIC) that monitors the quality and quantity of poultry DNA in test samples. In this study we developed a SYBR-qPCR to target the poultry homolog of the hydroxymethylbilane synthase (HMBS) gene as an EIC for avian species. The avian HMBS-based qPCR was very sensitive, detecting one HMBS gene copy in a 20 µL reaction, and is highly specific for avian species. It amplified DNA from 11 organs and tissues of chickens showing it can be used as an EIC on a large variety of samples. The application of the established EIC on clinically and experimentally infected samples demonstrated that false negativity and result variations could result from samples being collected using different operators, techniques, preservatives, and storage times. The high sensitivity and specificity of the avian HMBS-based qPCR, its ability to quantify DNAs extracted from a wide range of tissues and poultry species along with its usefulness in reducing false negativity in PCR results associated with inadequate sampling and storage degradation makes it an ideal EIC for poultry DNA and RNA PCR diagnostics. The study also highlights the importance of appropriate sampling and storage of samples in ensuring accuracy of molecular diagnostic testing.
Differences in substance use by sexual orientation and gender among Jewish young adults in Israel
Authors: Bonny-Noach Hagit , Shechory-Bitton Mally 
Published: October 2020

AbstractBackgroundThis study focuses on sexual orientation and gender-based differences among Israeli young adult substance use behaviors. In addition, it evaluates young adult perception of substance use and acceptance of substances use by close friends.MethodsWe conducted a cross-sectional study. A self-reported anonymous questionnaire was distributed to a convenience sample of 496 young-adults (age: M = 23.14, SD = 2.48), which included 126 heterosexual males, 128 heterosexual females, 131 gay men, and 111 lesbians.ResultsThis study revealed significant sexual orientation and gender differences in all outcomes examined. Significant substance usage differences were found for same-sex orientation as 52% reported cannabis use and 24% reported using other illegal substances during the past 12 months compared to 34 and 6% (respectively) among heterosexuals. Significant gender differences were found, as male participants reported 50% cannabis use and 19% reported other illegal substance use in the past 12 months compared to 35 and 11% (respectively) among females.Additionally, compared with heterosexuals, gay men and lesbians perceived/assessed significantly higher substance usage rates among their close friends and higher levels of substance use acceptance by close friends. Regression models indicated the important role of respondent perceived and acceptance of substance use among close friends.Binge drinking, cannabis use, and other illegal substance use were positively associated with participants’ perceived substance use and substance use acceptance level by close friends, after controlling for gender, sexual orientation, age, and level of education.ConclusionsClose friends and community norms can play an important role in shaping substance usage among young adults, especially among gay men and lesbians. The results of the current study highlight the need for developing prevention and harm reduction drug policies for Israeli young adults, especially for gay men and lesbians. Interventions should also focus on young adult peers and community norms related to substance use by professionals in educational, policy-making, and therapeutic contexts.
Current transition management of adolescents and young adults with allergy and asthma: a European survey
Authors: Khaleva Ekaterina , Vazquez-Ortiz Marta , Comberiati Pasquale , DunnGalvin Audrey , Pite Helena , Blumchen Katharina , Garriga-Baraut Teresa , Hox Valerie , Santos Alexandra F. , Gore Claudia , Knibb Rebecca C. , Alviani Cherry , Mortz Charlotte G. , Angier Elizabeth , Duca Bettina , Jensen Britt , Sanchez-Garcia Silvia , Gowland M. Hazel , Timmermans Frans , Pfaar Oliver , Roberts Graham 
Published: October 2020

AbstractBackgroundTransition from parent-delivered to self-management is a vulnerable time for adolescents and young adults (AYA) with allergy and asthma. There is currently no European guideline available for healthcare professionals (HCPs) on transition of these patients and local/national protocols are also mostly lacking.MethodsEuropean HCPs working with AYA with allergy and asthma were invited to complete an online survey assessing challenges of working with these patients, current transition practices and access to specific healthcare resources.ResultsA total of 1179 responses from 41 European countries were collected. Most HCPs (86%) reported a lack of a transition guideline and a lack of a transition process (20% paediatric HCPs, 50% of adult HCPs, 56% HCP seeing all ages). Nearly half (48%) acknowledged a lack of an established feedback system between paediatric and adult medical services. Many respondents never routinely asked about mental health issues such as self-harm or depression and are not confident in asking about self-harm (66.6%), sexuality (64%) and depression (43.6%). The majority of HCPs (76%) had not received specific training in the care of AYA although 87% agreed that transition was important for AYA with allergy and asthma.ConclusionAlthough there was agreement that transition is important for AYA with allergy and asthma, there are crucial limitations and variations in the current provision of transition services across Europe. Standardisation of AYA management and specific training are required. This should improve management and continuity of care during adolescence and into adulthood to achieve the best healthcare outcomes.
The risk of cardiovascular disease in women after miscarriage, stillbirth, and therapeutic abortion: a protocol for a systematic review and meta-analysis
Authors: Muehlschlegel Charlotte , Kyriacou Harry , Al-Mohammad Abdulrahman , Foster-Davies Lowri A. , Simmons-Jones Fiona , Oliver-Williams Clare 
Published: October 2020

Abstract
Background
Cardiovascular disease (CVD) is the leading cause of death in women, responsible for approximately a third of all female deaths. Pregnancy complications are known to be associated with a greater risk of incident CVD in mothers. However, the relationships between pregnancy loss due to miscarriage, stillbirth, or therapeutic abortion, and future maternal cardiovascular health are under-researched. This study seeks to provide an up-to-date systematic review and meta-analysis of the relationship between these three forms of pregnancy loss and the subsequent development of CVD.

Methods
This systematic review will follow the Preferred Reporting Items for Systematic Review and Meta-Analysis checklist (PRISMA) and the Meta-analyses Of Observational Studies in Epidemiology (MOOSE) Checklist. A systematic search will be undertaken using publications identified in MEDLINE (PubMed), Scopus, Web of Knowledge, the CINAHL Nursing Database, and the Cochrane Library. The eligibility of each publication will be determined by predefined selection criteria. The quality of the included studies will be rated using the Newcastle-Ottawa Scale. Pooled measures of association will be computed using random-effects model meta-analyses. Between-study heterogeneity will be assessed using the I2 statistic and the Cochrane χ2 statistic. Small study effects will be evaluated for meta-analyses with sufficient studies through the use of funnel plots and Egger’s test.

Discussion
The results of this systematic review will discuss the long-term risks of multiple types of cardiovascular disease in women who have experienced miscarriage, stillbirth, and/or therapeutic abortion. It will contribute to the growing field of cardio-obstetrics as the first to consider the full breadth of literature regarding the association between all forms of pregnancy loss and future maternal cardiovascular disease.

Systematic review registration
PROSPERO registration number [CRD42020167587]
Prevalence of multimorbid degenerative lumbar spinal stenosis with knee and/or hip osteoarthritis: protocol for a systematic review and meta-analysis
Authors: Young James J. , Hartvigsen Jan , Jensen Rikke K. , Roos Ewa M. , Ammendolia Carlo , Juhl Carsten Bogh 
Published: October 2020

Abstract
Background
Lumbar spinal stenosis (LSS) and knee and hip osteoarthritis (OA) are prevalent conditions in the aging population and published literature suggests they share many symptoms and often are present at the same time in patients. However, no prevalence estimates of multimorbid LSS and knee and/or hip OA are currently available. The primary objective of this systematic review is therefore to estimate the prevalence of multimorbid LSS with knee and/or hip OA using radiological, clinical, and combined case definitions.

Methods
This systematic review protocol has been designed according to the guidelines from the Cochrane Collaboration and is reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols. A comprehensive search will be performed in the following databases: MEDLINE, EMBASE, CENTRAL, and CINAHL. Forward citation tracking will be performed in Web of Science. No restriction for publication date and language will be applied in the literature search, but only articles in English will be included. The search strategy will include the following domains: LSS, knee OA, and hip OA. Retrieved citations will be screened by two authors independently. Disagreements will be discussed until consensus, and a third reviewer will be consulted if consensus cannot be reached. Data extraction and assessment of risk of bias assessment will be done by two authors independently, using a standardized data extraction form and a modified risk of bias tool for prevalence studies. Meta-analysis estimating prevalence with 95% CI will be performed using a random effects model. Meta-regression analyses will be performed to investigate the impact of the following covariates: LSS clinical presentations, sample population, healthcare setting, risk of bias, and other patient characteristics on prevalence estimates for multimorbid LSS and knee and/or hip OA.

Discussion
The results of this review will provide the first estimates of the prevalence of multimorbid LSS and hip and knee OA based on various case definitions. The impact of covariates such as LSS clinical presentations, sample population, healthcare setting, risk of bias, and patient characteristics on prevalence estimates will also be presented.

Systematic review registration
PROSPERO, awaiting registration
Assessing the nature of asthma in African epidemiological studies: a scoping review protocol
Authors: Ndlovu Vuyelwa , Chimbari Moses John , Sibanda Elopy 
Published: October 2020

AbstractBackgroundAsthma is one of the most common chronic respiratory conditions in the world and is increasing in prevalence, particularly in Africa and other low-income countries. The disproportionately high numbers of premature deaths and severe or uncontrolled cases in many African countries are indicative of their inability to cope with a costly disease like asthma. Progress has, however, been made in understanding the complex and heterogeneous nature of the disease. The objective of this study will be to summarise the epidemiological literature on the nature of asthma in African countries.MethodsWe registered a study protocol for a scoping review. The review was designed following the Arksey and O’Malley framework. We will search PubMed/MEDLINE, African Journals Online (AJOL) and relevant grey literature (e.g. Google Scholar, EBSCOhost) from January 1990 onwards. Only primary epidemiological studies of asthma (e.g. frequency, disease mechanisms, associated risk factors and comorbidities) written in English and conducted in Africa will be included. Two reviewers will independently screen all citations, full-text articles and abstract data. Potential conflicts will be resolved through discussion. Findings will be reported using narrative synthesis and tabulation of the summaries.DiscussionThis scoping review will capture the state of the current epidemiological literature on asthma in African countries. Results will be published in a peer-reviewed journal. We anticipate this review will identify gaps and make recommendations for future areas of study.Scoping review registrationOpen Science Frameworkhttp://osf.io/n2p87/
A hybrid recommendation model in social media based on deep emotion analysis and multi-source view fusion
Authors: Jiang Liang , Liu Lu , Yao Jingjing , Shi Leilei 
Published: October 2020

AbstractThe recommendation system is an effective means to solve the information overload problem that exists in social networks, which is also one of the most common applications of big data technology. Thus, the matrix decomposition recommendation model based on scoring data has been extensively studied and applied in recent years, but the data sparsity problem affects the recommendation quality of the model. To this end, this paper proposes a hybrid recommendation model based on deep emotion analysis and multi-source view fusion which makes a personalized recommendation with user-post interaction ratings, implicit feedback and auxiliary information in a hybrid recommendation system. Specifically, the HITS algorithm is used to process the data set, which can filter out the users and posts with high influence and eliminate most of the low-quality users and posts. Secondly, the calculation method of measuring the similarity of candidate posts and the method of calculatingKnearest neighbors are designed, which solves the problem that the text description information of post content in the recommendation system is difficult to mine and utilize. Then, the cooperative training strategy is used to achieve the fusion of two recommended views, which eliminates the data distribution deviation added to the training data pool in the iterative training. Finally, the performance of the DMHR algorithm proposed in this paper is compared with other state-of-art algorithms based on the Twitter dataset. The experimental results show that the DMHR algorithm has significant improvements in score prediction and recommendation performance.
The burden of legionnaires’ disease in Belgium, 2013 to 2017
Authors: Fastl Christina , Devleesschauwer Brecht , van Cauteren Dieter , Lajot Adrien , Leroy Mathias , Laisnez Valeska , Schirvel Carole , Mahieu Romain , Pierard Denis , Michel Charlotte , Jacquinet Stéphanie 
Published: October 2020

Abstract
Background
Legionnaires’ disease (LD) is a severe bacterial infection causing pneumonia. Surveillance commonly underestimates the true incidence as not all cases are laboratory confirmed and reported to public health authorities. The aim of this study was to present indicators for the impact of LD in Belgium between 2013 and 2017 and to estimate its true burden in the Belgian population in 2017, the most recent year for which the necessary data were available.

Methods
Belgian hospital discharge data, data from three infectious disease surveillance systems (mandatory notification, sentinel laboratories and the national reference center), information on reimbursed diagnostic tests from the Belgian National Institute for Health and Disability Insurance and mortality data from the Belgian statistical office were used. To arrive at an estimate of the total number of symptomatic cases in Belgium, we defined a surveillance pyramid and estimated a multiplication factor to account for LD cases not captured by surveillance. The multiplication factor was then applied to the pooled number of LD cases reported by the three surveillance systems. This estimate was the basis for our hazard- and incidence-based Disability-Adjusted Life Years (DALYs) calculation. To account for uncertainty in the estimations of the DALYs and the true incidence, we used Monte Carlo simulations with 10,000 iterations.

Results
We found an average of 184 LD cases reported by Belgian hospitals annually (2013–2017), the majority of which were male (72%). The surveillance databases reported 215 LD cases per year on average, 11% of which were fatal within 90 days after diagnosis. The estimation of the true incidence in the community yielded 2674 (95% Uncertainty Interval [UI]: 2425–2965) cases in 2017. LD caused 3.05 DALYs per case (95%UI: 1.67–4.65) and 8147 (95%UI: 4453–12,426) total DALYs in Belgium in 2017, which corresponds to 71.96 (95%UI: 39.33–109.75) DALYs per 100,000 persons.

Conclusions
This analysis revealed a considerable burden of LD in Belgium that is vastly underestimated by surveillance data. Comparison with other European DALY estimates underlines the impact of the used data sources and methodological approaches on burden estimates, illustrating that national burden of disease studies remain essential.
Bidirectional information sharing between Nagoya Memorial Hospital and health insurance pharmacies using a communication sheet for pharmaceutical cooperation
Authors: Kabeya Megumi , Hibi Satoshi , Yuasa Shu , Kayukawa Satoshi , Ina Kenji 
Published: October 2020

Abstract
Background
We collaborated with the regional pharmaceutical associations near Nagoya Memorial Hospital and created a communication sheet for pharmaceutical cooperation between the hospital and health insurance pharmacies.

Methods
The communication sheet for pharmaceutical cooperation was issued in October 2014. We conducted a questionnaire survey of both cancer patients and community pharmacists 1 year after the implementation of the use of this sheet. Based on the results of the survey, we modified our communication sheet and added a unified reply form in October 2016. We examined the number of replies from community pharmacists from October 2014 to April 2019. We then analyzed how community pharmacists instructed and communicated with cancer patients using the results of both the questionnaire survey and the reply form, which were compared before and after introducing the modified version of the communication sheet.

Results
During the 5 years of observation, 743 communication sheets were sent from Nagoya Memorial Hospital to community pharmacists. As a result of pharmaceutical cooperation in using the communication sheet, 96.4% of prescribed medication were immediately prepared in health insurance pharmacies on that day. The communication sheet also enhanced the conversations between cancer patients and pharmacists. The introduction of the unified reply form increased the response rate of community pharmacists from 1.7 to 69.5% (p < 0.001). The communication between community pharmacists and cancer patients was significantly hindered by prescriptions without an oral cancer drug and patient age < 65 years old (p < 0.05). However, this hindrance was reduced by the use of the modified form.

Conclusions
The communication sheet for pharmaceutical cooperation is useful for bidirectional information sharing between hospitals and health insurance pharmacies, which may enable pharmacists to provide cancer patients with medication instructions in coordination with hospitals and increase the quality of outpatient pharmacy services.