bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical and mental health impacts of COVID-19 on healthcare workers: a scoping review
Authors: Shaukat Natasha , Ali Daniyal Mansoor , Razzak Junaid 
Published: July 2020

Abstract
Background
Coronavirus disease (COVID-19) pandemic has spread to 198 countries, with approximately 2.4 million confirmed cases and 150,000 deaths globally as of April 18. Frontline healthcare workers (HCWs) face a substantially higher risk of infection and death due to excessive COVID-19 exposure. This review aimed at summarizing the evidence of the physical and mental health impacts of COVID-19 pandemic on health-care workers (HCWs).

Methods
We used the Arksey O’Malley framework to conduct a scoping review. A systematic literature search was conducted using two databases: PubMed and Google Scholar. We found 154 studies, and out of which 10 met our criteria. We collected information on the date of publication, first author’s country, the title of the article, study design, study population, intervention and outcome, and key findings, and divided all research articles into two domains: physical and mental health impact.

Results
We reviewed a total of 154 articles from PubMed (126) and Google Scholar (28), of which 58 were found to be duplicate articles and were excluded. Of the remaining 96 articles, 82 were excluded after screening for eligibility, and 4 articles did not have available full texts. Ten full-text articles were reviewed and included in this study.
Our findings identified the following risk factors for COVID-19-related health impact: working in a high-risk department, diagnosed family member, inadequate hand hygiene, suboptimal hand hygiene before and after contact with patients, improper PPE use, close contact with patients (≥ 12 times/day), long daily contact hours (≥ 15 h), and unprotected exposure. The most common symptoms identified amongst HCWs were fever (85%), cough (70%), and weakness (70%). Prolonged PPE usage led to cutaneous manifestations and skin damage (97%), with the nasal bridge (83%) most commonly affected site. HCWs experienced high levels of depression, anxiety, insomnia, and distress. Female HCWs and nurses were disproportionately affected.

Conclusion
The frontline healthcare workers are at risk of physical and mental consequences directly as the result of providing care to patients with COVID-19. Even though there are few intervention studies, early data suggest implementation strategies to reduce the chances of infections, shorter shift lengths, and mechanisms for mental health support could reduce the morbidity and mortality amongst HCWs.
Predicting DNA binding protein-drug interactions based on network similarity
Authors: Wang Wei , Lv Hehe , Zhao Yuan 
Published: July 2020

Abstract
Background
The study of DNA binding protein (DBP)-drug interactions can open a breakthrough for the treatment of genetic diseases and cancers. Currently, network-based methods are widely used for protein-drug interaction prediction, and many hidden relationships can be found through network analysis. We proposed a DCA (drug-cluster association) model for predicting DBP-drug interactions. The clusters are some similarities in the drug-binding site trimmers with their physicochemical properties. First, DBPs-drug binding sites are extracted from scPDB database. Second, each binding site is represented as a trimer which is obtained by sliding the window in the binding sites. Third, the trimers are clustered based on the physicochemical properties. Fourth, we build the network by generating the interaction matrix for representing the DCA network. Fifth, three link prediction methods are detected in the network. Finally, the common neighbor (CN) method is selected to predict drug-cluster associations in the DBP-drug network model.

Result
This network shows that drugs tend to bind to positively charged sites and the binding process is more likely to occur inside the DBPs. The results of the link prediction indicate that the CN method has better prediction performance than the PA and JA methods. The DBP-drug network prediction model is generated by using the CN method which predicted more accurately drug-trimer interactions and DBP-drug interactions. Such as, we found that Erythromycin (ERY) can establish an interaction relationship with HTH-type transcriptional repressor, which is fitted well with silico DBP-drug prediction.

Conclusion
The drug and protein bindings are local events. The binding of the drug-DBPs binding site represents this local binding event, which helps to understand the mechanism of DBP-drug interactions.
Clonal evolution driven by superdriver mutations
Authors: Grossmann Patrick , Cristea Simona , Beerenwinkel Niko 
Published: July 2020

Abstract
Background
Tumors are widely recognized to progress through clonal evolution by sequentially acquiring selectively advantageous genetic alterations that significantly contribute to tumorigenesis and thus are termned drivers. Some cancer drivers, such as TP53 point mutation or EGFR copy number gain, provide exceptional fitness gains, which, in time, can be sufficient to trigger the onset of cancer with little or no contribution from additional genetic alterations. These key alterations are called superdrivers.

Results
In this study, we employ a Wright-Fisher model to study the interplay between drivers and superdrivers in tumor progression. We demonstrate that the resulting evolutionary dynamics follow global clonal expansions of superdrivers with periodic clonal expansions of drivers. We find that the waiting time to the accumulation of a set of superdrivers and drivers in the tumor cell population can be approximated by the sum of the individual waiting times.

Conclusions
Our results suggest that superdriver dynamics dominate over driver dynamics in tumorigenesis. Furthermore, our model allows studying the interplay between superdriver and driver mutations both empirically and theoretically.
Effects of HTR1B 3′ region polymorphisms and functional regions on gene expression regulation
Authors: Xia Xi , Ding Mei , Xuan Jin-feng , Xing Jia-xin , Pang Hao , Yao Jun , Wu Xue , Wang Bao-jie 
Published: July 2020

Abstract
Background
The HTR1B gene encodes the 5-hydroxytryptamine (5-HT1B) receptor, which is involved in a variety of brain activities and mental disorders. The regulatory effects of non-coding regions on genomic DNA are one of many reasons for the cause of genetic-related diseases. Post-transcriptional regulation that depends on the function of 3′ regulatory regions plays a particularly important role. This study investigated the effects, on reporter gene expression, of several haplotypes of the HTR1B gene (rs6297, rs3827804, rs140792648, rs9361234, rs76194807, rs58138557, and rs13212041) and truncated fragments in order to analyze the function of the 3′ region of HTR1B.

Results
We found that the haplotype, A-G-Del-C-T-Ins-A, enhanced the expression level compared to the main haplotype; A-G-Del-C-G-Ins-A; G-G-Del-C-G-Ins-G decreased the expression level. Two alleles, rs76194807T and rs6297G, exhibited different relative luciferase intensities compared to their counterparts at each locus. We also found that + 2440 ~ + 2769 bp and + 1953 ~ + 2311 bp regions both had negative effects on gene expression.

Conclusions
The 3′ region of HTR1B has a regulatory effect on gene expression, which is likely closely associated with the interpretation of HTR1B-related disorders. In addition, the HTR1B 3′ region includes several effector binding sites that induce an inhibitory effect on gene expression.
Genomics of sex allocation in the parasitoid wasp Nasonia vitripennis
Authors: Pannebakker Bart A. , Cook Nicola , van den Heuvel Joost , van de Zande Louis , Shuker David M. 
Published: July 2020

Abstract
Background
Whilst adaptive facultative sex allocation has been widely studied at the phenotypic level across a broad range of organisms, we still know remarkably little about its genetic architecture. Here, we explore the genome-wide basis of sex ratio variation in the parasitoid wasp Nasonia vitripennis, perhaps the best studied organism in terms of sex allocation, and well known for its response to local mate competition.

Results
We performed a genome-wide association study (GWAS) for single foundress sex ratios using iso-female lines derived from the recently developed outbred N. vitripennis laboratory strain HVRx. The iso-female lines capture a sample of the genetic variation in HVRx and we present them as the first iteration of the Nasonia vitripennis Genome Reference Panel (NVGRP 1.0). This panel provides an assessment of the standing genetic variation for sex ratio in the study population. Using the NVGRP, we discovered a cluster of 18 linked SNPs, encompassing 9 annotated loci associated with sex ratio variation. Furthermore, we found evidence that sex ratio has a shared genetic basis with clutch size on three different chromosomes.

Conclusions
Our approach provides a thorough description of the quantitative genetic basis of sex ratio variation in Nasonia at the genome level and reveals a number of inter-related candidate loci underlying sex allocation regulation.
Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome
Authors: Le Vuong , Quinn Thomas P. , Tran Truyen , Venkatesh Svetha 
Published: July 2020

AbstractBackgroundTechnological advances in next-generation sequencing (NGS) and chromatographic assays [e.g., liquid chromatography mass spectrometry (LC-MS)] have made it possible to identify thousands of microbe and metabolite species, and to measure their relative abundance. In this paper, we propose a sparse neural encoder-decoder network to predict metabolite abundances from microbe abundances.ResultsUsing paired data from a cohort of inflammatory bowel disease (IBD) patients, we show that our neural encoder-decoder model outperforms linear univariate and multivariate methods in terms of accuracy, sparsity, and stability. Importantly, we show that our neural encoder-decoder model is not simply a black box designed to maximize predictive accuracy. Rather, the network’s hidden layer (i.e., the latent space, comprised only of sparsely weighted microbe counts) actually captures key microbe-metabolite relationships that are themselves clinically meaningful. Although this hidden layer is learned without any knowledge of the patient’s diagnosis, we show that the learned latent features are structured in a way that predicts IBD and treatment status with high accuracy.ConclusionsBy imposing a non-negative weights constraint, the network becomes a directed graph where each downstream node is interpretable as the additive combination of the upstream nodes. Here, the middle layer comprises distinct microbe-metabolite axes that relate key microbial biomarkers with metabolite biomarkers. By pre-processing the microbiome and metabolome data using compositional data analysis methods, we ensure that our proposed multi-omics workflow will generalize to any pair of -omics data. To the best of our knowledge, this work is the first application of neural encoder-decoders for the interpretable integration of multi-omics biological data.
Diversity and evolution of cytochrome P450s of Jacobaea vulgaris and Jacobaea aquatica
Authors: Chen Yangan , Klinkhamer Peter G. L. , Memelink Johan , Vrieling Klaas 
Published: July 2020

Abstract
Background
Collectively, plants produce a huge variety of secondary metabolites (SMs) which are involved in the adaptation of plants to biotic and abiotic stresses. The most characteristic feature of SMs is their striking inter- and intraspecific chemical diversity. Cytochrome P450 monooxygenases (CYPs) often play an important role in the biosynthesis of SMs and thus in the evolution of chemical diversity. Here we studied the diversity and evolution of CYPs of two Jacobaea species which contain a characteristic group of SMs namely the pyrrolizidine alkaloids (PAs).

Results
We retrieved CYPs from RNA-seq data of J. vulgaris and J. aquatica, resulting in 221 and 157 full-length CYP genes, respectively. The analyses of conserved motifs confirmed that Jacobaea CYP proteins share conserved motifs including the heme-binding signature, the PERF motif, the K-helix and the I-helix. KEGG annotation revealed that the CYPs assigned as being SM metabolic pathway genes were all from the CYP71 clan but no CYPs were assigned as being involved in alkaloid pathways. Phylogenetic analyses of full-length CYPs were conducted for the six largest CYP families of Jacobaea (CYP71, CYP76, CYP706, CYP82, CYP93 and CYP72) and were compared with CYPs of two other members of the Asteraceae, Helianthus annuus and Lactuca sativa, and with Arabidopsis thaliana. The phylogenetic trees showed strong lineage specific diversification of CYPs, implying that the evolution of CYPs has been very fast even within the Asteraceae family. Only in the closely related species J. vulgaris and J. aquatica, CYPs were found often in pairs, confirming a close relationship in the evolutionary history.

Conclusions
This study discovered 378 full-length CYPs in Jacobaea species, which can be used for future exploration of their functions, including possible involvement in PA biosynthesis and PA diversity.
The kinematics and strategies of recovery steps during lateral losses of balance in standing at different perturbation magnitudes in older adults with varying history of falls
Authors: Batcir Shani , Shani Guy , Shapiro Amir , Alexander Neil , Melzer Itshak 
Published: July 2020

Abstract
Background
Step-recovery responses are critical in preventing falls when balance is lost unexpectedly. We investigated the kinematics and strategies of balance recovery in older adults with a varying history of falls.

Methods
In a laboratory study, 51 non-fallers (NFs), 20 one-time fallers (OFs), and 12 recurrent-fallers (RFs) were exposed to random right/left unannounced underfoot perturbations in standing of increasing magnitude. The stepping strategies and kinematics across an increasing magnitude of perturbations and the single- and multiple-step threshold trials, i.e., the lowest perturbation magnitude to evoke single step and multiple steps, respectively, were analyzed. Fall efficacy (FES) and self-reported lower-extremity function were also assessed.

Results
OFs had significantly lower single- and multiple-step threshold levels than NFs; the recovery-step kinematics were similar. Surprisingly, RFs did not differ from NFs in either threshold. The kinematics in the single-step threshold trial in RFs, however, showed a significant delay in step initiation duration, longer step duration, and larger center of mass (CoM) displacement compared with NFs and OFs. In the multiple-step threshold trial, the RFs exhibited larger CoM displacements and longer time to fully recover from balance loss. Interestingly, in the single-stepping trials, 45% of the step-recovery strategies used by RFs were the loaded-leg strategy, about two times more than OFs and NFs (22.5 and 24.2%, respectively). During the multiple-stepping trials, 27.3% of the first-step recovery strategies used by RFs were the loaded-leg strategy about two times more than OFs and NFs (11.9 and 16.4%, respectively), the crossover stepping strategy was the dominated response in all 3 groups (about 50%). In addition, RFs reported a lower low-extremity function compared with NFs, and higher FES in the OFs.

Conclusions
RFs had impaired kinematics during both single-step and multiple-step recovery responses which was associated with greater leg dysfunction. OFs and NFs had similar recovery-step kinematics, but OFs were more likely to step at lower perturbation magnitudes suggesting a more “responsive” over-reactive step response related from their higher fear of falling and not due to impaired balance abilities. These data provide insight into how a varying history of falls might affect balance recovery to a lateral postural perturbation.

Trial registration
This study was registered prospectively on November 9th, 2011 at clinicaltrials.gov (NCT01439451).
Satisfaction in parturients receiving epidural analgesia after prenatal shared decision-making intervention: a prospective, before-and-after cohort study
Authors: Cheng Wan-Jung , Hung Kuo-Chuan , Ho Chung-Han , Yu Chia-Hung , Chen Yi-Chen , Wu Ming-Ping , Chu Chin-Chen , Chang Ying-Jen 
Published: July 2020

AbstractBackgroundThe explanation of epidural analgesia by anesthesiologist would often begin after the parturient is admitted to the hospital. Because of labor pain, the decision of receiving epidural analgesia would often be made by the family members, instead of the parturient herself. We aimed to test whether earlier prenatal shared decision-making (SDM) interventions increase parturient’s comprehension and satisfaction of epidural labor analgesia, compared to conventional explanation after labor pain begun.MethodsDuring the 28th week of gestation, we provided the SDM parturient health education as well as a leaflet with quick response codes. Scanning the code would link to education videoclips which explained what epidural analgesia is and its advantages and disadvantages. Original routine practice group parturients received explanation of analgesia after admission for delivery. To measure the satisfaction of labor pain service, the accessibility of information, and the communication with medical staff, we designed a questionnaire with reference to (1) Pregnancy and Maternity Care Patients’ Experiences Questionnaire (PreMaPEQ), (2) Preterm Birth Experience and Satisfaction Scale (P-BESS), and (3) Women’s Views of Birth Labor Satisfaction Questionnaire (WOMBLSQ). The questionnaire was amended after a pretest involving 30 parturients who had received epidural analgesia. Scree test analysis and exploratory factor analysis were performed; then, the questionnaire was revised again. A total of 200 valid questionnaires were collected—100 each from the original routine practice group and the SDM group.ResultsThe SDM group reported significantly higher satisfaction with and understanding of epidural analgesia, and a significantly higher satisfaction with the information received, and the quality of pain relief. After SDM intervention, significant increasement of the average satisfaction scores in question “my epidural is effective” (9.10%; mean difference: 0.38; 95% confidence interval, 0.17 ~ 0.59;p < 0.001) and “The effect of epidural is just as what I have expected” (10.41%; mean difference: 0.41; 95% confidence interval, 0.18 ~ 0.64;p < 0.001) was demonstrated.ConclusionsAn earlier prenatal SDM intervention with sufficient information through videoclips increased parturients’ comprehensions and satisfaction of epidural analgesia service.Trial registrationISRCTNregistry, 14,256,563. Registered April 1st, 2020 (10.1186/ISRCTN14256563).
Vitamin D toxicity in a pediatric toxicological referral center; a cross-sectional study from Iran
Authors: Farnaghi Fariba , Hassanian-Moghaddam Hossein , Zamani Nasim , Gholami Narges , Gachkar Latif , Hosseini Yazdi Maryam 
Published: July 2020

Abstract
Background
Vitamin D is an essential element for body health with its supplements generally administered to prevent vitamin D deficiency. Since these supplements are available in domestic settings, vitamin D toxicity may happen in children.

Methods
All children younger than 12 years who presented to the pediatric emergency department of Loghman Hakim Hospital, Tehran, Iran with history of ingestion of more than 1500 IU/day of vitamin D supplements were enrolled. Patients’ demographic data, on-presentation signs and symptoms, laboratory findings, treatments given, and outcome were evaluated.

Result
Fifteen patients presented during the study period. Their mean age was 46.53 ± 10.14 months and 12 (80%) were girls. All of them had unintentionally ingested vitamin D. Mean ingested dose was 406700.7 ± 227400.1 IU. In eight patients (53.3%), 25 hydroxy vitamin D level was more than 100 ng/mL. One patient experienced hypercalcemia while all of them were asymptomatic and discharged without complications. There was no significant difference between patients with and without high levels of 25 OH vitamin D regarding lab tests, toxicity course, and outcome.

Conclusions
It seems that acute vitamin D toxicity is a benign condition in our pediatric population which may be due to high prevalence of vitamin D deficiency in Iran.
Housing as a social determinant of health and wellbeing: developing an empirically-informed realist theoretical framework
Authors: Rolfe Steve , Garnham Lisa , Godwin Jon , Anderson Isobel , Seaman Pete , Donaldson Cam 
Published: July 2020

Abstract
Background
The role of housing as a social determinant of health is well-established, but the causal pathways are poorly understood beyond the direct effects of physical housing defects. For low-income, vulnerable households there are particular challenges in creating a sense of home in a new tenancy which may have substantial effects on health and wellbeing. This study examines the role of these less tangible aspects of the housing experience for tenants in the social and private rented sectors in west central Scotland.

Methods
The paper analyses quantitative data from a mixed methods, longitudinal study of tenants from three housing organisations, collected across the first year of their tenancy. The paper postulates causal hypotheses on the basis of staff interviews and then uses a Realist Research approach to test and refine these into a theoretical framework for the connections between tenants’ broader experience of housing and their health and wellbeing.

Results
Housing service provision, tenants’ experience of property quality and aspects of neighbourhood are all demonstrated to be significantly correlated with measures of of health and wellbeing. Analysis of contextual factors provides additional detail within the theoretical framework, offering a basis for further empirical work.

Conclusions
The findings provide an empirically-informed realist theoretical framework for causal pathways connecting less tangible aspects of the housing experience to health and wellbeing. Applying this within housing policy and practice would facilitate a focus on housing as a public health intervention, with potential for significant impacts on the lives of low-income and vulnerable tenants. The framework also offers a basis for further research to refine our understanding of housing as a social determinant of health.