bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Quality Genome Sequence Assembly of R.A73 Enterococcus faecium Isolated from Freshwater fish mucus
Authors: Jeni Rim El , Ghedira Kais , Bour Monia El , Abdelhak Sonia , Kahla Alia Ben , Bouhaouala-Zahar Balkiss 
Published: September 2020

Abstract
Background: Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs) have been extensively used in fermentation and more recently as probiotics in food products that promote health. Genome sequencing and functional genomics investigations of LABs varieties provide rapid and important information about their diversity and their evolution, revealing a significant molecular basis.This study investigated the whole genome sequences of the Enterococcus faecium strain (HG937697), isolated from the mucus of freshwater fish in Tunisian dams. Genomic DNA was extracted using the Quick-GDNA kit and sequenced using the Illumina HiSeq2500 system. Sequences quality assessment was performed using FastQC software. The complete genome annotation was carried out with the Rapid Annotation using Subsystem Technology (RAST) web server then NCBI PGAAP. Results: The Enterococcus faecium R.A73 assembled in 28 contigs consisting of 2,935,283 bps. The genome annotation revealed 2,884 genes in total including 2,834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16s, one rRNA 23s and one rRNA 5s) and 47 tRNAs. Twenty-two genes implicated in bacteriocin production are identified within the Enterococcus faecium R.A73 strain. Conclusion: Data obtained provide insights to further investigate the effective strategy for testing this Enterococcus faecium R.A73 strain in the industrial manufacturing process. Studying their metabolism with bioinformatics tools represents the future challenge and contribution to improving the utilization of the multi-purpose bacteria in food.
Evaluating the effectiveness of countermeasures to control the novel coronavirus disease 2019 in Jilin Province, China
Authors: Zhao Qinglong , Wang Yao , Yang Meng , Li Meina , Zhao Zeyu , Lu Xinrong , Shen Bo , Luan Bo , Zhao Yifei , Cao Bonan , Yao Laishun , Zhao Benhua , Su Yanhua , Chen Tianmu 
Published: September 2020

Abstract
Objective: Based on differences in populations and prevention and control measures, the spread of new coronary pneumonia in different countries and regions also differs. This study aimed to calculate the transmissibility of coronavirus disease 2019 (COVID-19), and to evaluate the effectiveness of countermeasures to control the disease in Jilin Province, China.
Methods: The data of reported COVID-19 cases were collected, including imported and local cases from Jilin Province as of March 14, 2019. A Susceptible–Exposed–Infectious–Asymptomatic–Recovered (SEIAR) model was developed to fit the data, and the effective reproduction number ( R eff ) was calculated at different stages in the province. Finally, the effectiveness of the countermeasures was assessed.
Results: A total of 97 COVID-19 infections were reported in Jilin Province, among which 45 were imported infections (including one asymptomatic infection) and 52 were local infections (including three asymptomatic infections). The model fit well with the reported data ( R 2 = 0.593, P < 0.001). The R eff of COVID-19 before and after February 1, 2020 was 1.64 and 0.05, respectively. Without the intervention taken on February 1, 2020, the predicted cases would reach a peak of 177,011 on October 22, 2020 (284 days from the first case). The projected number of cases until the end of the outbreak (on October 9, 2021) would be 17,129,367, with a total attack rate of 63.66%. Based on the comparison between the predicted incidence of the model and the actual incidence, the comprehensive intervention measures implemented in Jilin Province on February 1 reduced the incidence of cases by 99.99%. Therefore, according to the current measures and implementation efforts, Jilin Province can achieve good control of the virus’s spread.
Conclusions: COVID-19 has a moderate transmissibility in Jilin Province, China. The interventions implemented in the province had proved effective, increasing social distancing and a rapid response by the prevention and control system will help control the spread of the disease.
Kernel principal components based cascade forest towards disease identification with human microbiota
Authors: Zhou Jiayu , Wang Xuwen , Ye Yanqing , Jiang Jiang 
Published: September 2020

Abstract
Numerous pieces of clinical evidence have shown that many phenotypic traits of human disease are related to their gut microbiome. Through supervised classification, it is feasible to determine the human disease states by revealing the intestinal microbiota compositional information. However, the abundance matrix of microbiome data is so sparse, an interpretable deep model is crucial to further represent and mine the data for expansion, such as the deep forest. What's more, overfitting can still exist in the original deep forest model when dealing with such “large p, small n” biology data. Feature reduction is considered to improve the ensemble forest model especially towards the disease identification in the human microbiota. In this work, we propose the kernel principal components based cascade forest method, so-called KPCCF, to classify the disease states of patients by using taxonomic profiles of the microbiome at the family level. In detail, the kernel principal components analysis method is first used to reduce the original dimension of human microbiota datasets. Besides, the processed data is fed into the cascade forest to preliminarily discriminate the disease state of the samples. Thus, the proposed KPCCF algorithm can represent the small-scale and high-dimension human microbiota datasets with the sparse feature matrix. Systematic comparison experiments demonstrate that our method consistently outperforms the state-of-the-art methods with the comparative study on 4 datasets. Additionally, compared to other dimensionality reduction methods, the kernel principal components analysis method is more suitable for microbiota datasets.
Impact of Patron Saint Festivities on Cholera in Three Communes in Haiti
Authors: Moise Kenny , Achille Aude Mélody , Batumbo Doudou , Bourdeau Bertiny , Rebaudet Stanislas , Lerebours Gérald , Henrys Jean Hugues , Raccurt Christian 
Published: September 2020

Abstract
Background: Religious pilgrimages are among the anthropogenic factors known to be associated with the transmission of diarrheal diseases, such as cholera. This ecological study aimed to describe the evolution of cholera and assess the relationship between the implementation of the ‘coup de poing’ strategy during the patron saint festivities and the incidence of cholera in the three communes of Cabaret, Carrefour, and Croix-des-Bouquets in Haiti in 2017.Methods: An epidemiological curve was produced to illustrate the evolution of cholera at the communal level. Generalized linear models assuming a Poisson distribution were used to weight the annual cholera incidence of communal sections against variables such as the number of patronal festivities, population density and annual precipitation rates. The number of cases in the week of the festivity as well as one and two weeks later was weighted against patronal festivities and weekly precipitation rates.Results: In total, 3 633 suspected cholera cases were continuously reported in three communes in Haiti (Cabaret, Carrefour, Croix-des-bouquets) during the 52-epidemiological week period in 2017. After controlling for rainfall and population density, the implementation of the ‘coup de poing’ strategy during the patron saint festivities was associated with a significant reduction in cholera incidence of 57.23% [PR=0.4277 (97.5% CI: 0.2798-0.6193), p=0.0000244]. The implementation of the strategy was associated with a reduction in cholera incidence of 25.41% one week following patronal festivities.Conclusion: This study showed a continuous presence of cholera in three communes in Haiti in 2017 and an association between the implementation of the ‘coup de poing’ strategy during patronal festivities and a reduction in cholera incidence. The findings imply that the multi-partner ‘coup de poing’ strategy may have contributed to the reduced cholera incidence following patron saint festivities and in Ouest department in Haiti in 2017.
Stakeholders’ Perceptions of the Nutrition and Dietetics Needs and the Requisite Professional Competencies in Uganda: A Cross-Sectional Mixed Methods Study
Authors: Kikomeko Peterson Kato , Ochola Sophie , Kaaya Archileo N. , Ogada Irene , Birungi Tracy Lukiya , Nakitto Peace 
Published: September 2020

Abstract
Background: Effective implementation of nutrition and dietetics interventions necessitates professionals in these fields to possess the requisite competencies for health systems performance. This study explored the stakeholders’ perceptions of the community nutrition and dietetics needs, the nature of work done by graduates of the Bachelor’s degree in Human Nutrition/Human Nutrition and Dietetics (HN/HND), and the competencies required of Nutrition and Dietetics professionals in Uganda. Methods: A cross-sectional mixed methods design was used. Respondents included 132 graduates of the Bachelor’s degrees in HN/HND obtained from the Makerere and Kyambogo Universities during the period 2005-2016; 14 academic staff that train HN/HND in the two universities; and 10 HN/HND work/internship supervisors. Data from the graduates was collected through an email-based survey while that from other participants was through face to face interviews using a structured key informant interview guide. Results: Most HN/HND respondents (84.8%) obtained their Bachelor's degrees from Kyambogo University and 61.4% graduated in the years 2013-2016. Most (64.3%) academic staff that responded were females and the majority (57.1%) had doctorate training. All stakeholders viewed communities as facing a variety of nutrition and dietetics challenges some of which fall across different Sustainable Development Goals. The nutrition and dietetics interventions requested, provided, and considered a priority to provide to communities were both nutrition-specific and nutrition-sensitive. Work done by HN/HND graduates encompassed seven main domains; the dominant being organizational leadership and management; management of nutrition-related disease conditions; nutrition and health promotion; research and documentation; and advocacy, communication, and awareness. Conclusions: This study shows that nutrition and dietetics challenges in Uganda are multifaceted. HN/HND graduates are employed in different sectors; provide nutrition-specific and sensitive interventions in a multisectoral environment; are expected to possess a variety of knowledge and skills. However, graduates have knowledge and skills gaps even in some of the key areas they are expected to exhibit competency. We recommend using these findings to develop a HN/HND competency-based education model suitable for Uganda; develop a national HN/HND training and practice standards; and undertake further research to understand the quality and relevancy of HN/HND curricula to the job market requirements.
Views of advanced cancer patients, families, and oncologists on initiating and engaging in advance care planning: a qualitative study
Authors: Toguri James Thomas , Grant-Nunn Lindsay , Urquhart Robin 
Published: September 2020

Abstract
Background: Advance care planning (ACP) is a process by which patients reflect upon their goals, values and beliefs to allow them to make decisions about their future medical treatment that align with their goals and values, improving patient-centered care. Despite this, ACP is underutilized and is reported as one of the most difficult processes of oncology. We sought to: 1) explore patients’ and families’ understanding, experience and reflections on ACP, as well as what they need from their physicians during the process; 2) explore physicians’ views of ACP, including their experiences with initiating ACP and views on ACP training. Methods: This was a qualitative descriptive study in Nova Scotia, Canada with oncologists, advanced cancer out-patients and their family members. Semi-structured interviews with advanced cancer out-patients and their family members (n=4 patients, 4 family members) and oncologists (n=10) were conducted; each participant was recruited separately. Data were analyzed using constant comparative analysis, which entailed coding, categorizing, and identifying themes recurrent across the datasets. Results: Themes were identified from the patient / family and oncologist groups, four and five respectively. Themes from patients / families included: 1) positive attitudes towards ACP; 2) healthcare professionals (HCPs) lack an understanding of patients’ and families’ informational needs during the ACP process; 3) limited access to services and supports; and 4) poor communication between HCPs. Themes from oncologists included: 1) initiation of ACP discussions; 2) navigating patient-family dynamics; 3) limited formal training in ACP; 4) ACP requires a team approach; and 5) lack of coordinated systems hinders ACP. Conclusions: Stakeholders believe ACP for advanced cancer patients is important. Patients and families desire earlier and more in-depth discussion of ACP, additional services and supports, and improved communication between their HCPs. In the absence of formal training or guidance, oncologists have used clinical acumen to initiate ACP and a collaborative healthcare team approach.
Mild behavioral impairment is related to frailty in non-dementia older adults: a cross-sectional study
Authors: Fan Shaoyi , Liang Ximin , Yun Tianchan , Pei Zhong , Hu Bin , Ismail Zahinoor , Yang Zhimin , Xu Fuping 
Published: September 2020

Abstract
Background: Frailty and cognitive decline are highly prevalent among older adults. However, the relationship between frailty and mild behavioral impairment (MBI), a neurobehavioral syndrome characterized by later-life emergence of sustained neuropsychiatric symptoms, has yet to be elucidated.We aimed to evaluate the associations between mild behavioral impairment and frailty in non-dementia older adults.Methods: This is a cross-sectional study. A consecutive series of 137 non-dementia older adults in the Anti-Aging Study, recruited from primary care clinics, were enrolled. Frailty was estimated using the Fried phenotype. MBI was evaluated by the Mild Behavioral Impairment Checklist at a cut-off point of >8 (optimizing sensitivity and specificity), which was developed to assess emergent neuropsychiatric symptoms in accordance with the MBI criteria. Cognition was assessed with the Chinese versions of the Montreal Cognitive Assessment (MoCA-BC) and Mini-mental State Examination (MMSE). Multivariate logistic regression was performed to estimate the relationship between MBI and objective cognition with frailty status.Results: At baseline, 30.7% of the older adults had frailty and 18.2% had MBI (MBI+ status). Multivariate logistic regression analysis demonstrated that compared to MBI- status (without MBI), MBI+ was more likely to have frailty (odds ratio [OR] = 7.44, 95% CI = 1.49-37.21, p = 0.02).Conclusions: MBI is significantly associated with an increased risk of having frailty before the presence of overt dementia. This association merits further study to identify strategies for the early detection, prevention and therapeutic intervention of frailty.
A Multi-Method Exploratory Study of Health Professional Students’ Experiences with Compliance Behaviours
Authors: Violato Efrem , King Sharla , Bulut Okan 
Published: September 2020

Abstract
Background: Research in healthcare, including students as participants, has begun to document experiences with negative compliance, specifically conformity and obedience. There is a growing body of experimental and survey literature, however, currently lacking is a direct measure of the frequency at which health professional students have negative experiences with conformity and obedience integrated with psychological factors, the outcomes of negative compliance, and students’ perceptions. Methods: To develop empirical knowledge about the frequency of negative compliance and student perceptions during health professional education a multi-methods survey approach was used. The survey was administered to health professional students across ten disciplines at four institutions. Results: The results indicated students regularly experience obedience and conformity and are influenced by impression management and displacement of responsibility. Moral distress was identified as a consistent negative outcome. Student self-reported experiences aligned with the empirical findings. Conclusions: The findings of the present study demonstrate the pervasiveness of experiences with negative compliance during health professional’s education along with some attendant psychological factors. The findings have educational and practical implications, as well as pointing to the need for further integration of social and cognitive psychology in explaining compliance in healthcare. The results are likely generalizable to a population level however replication is encouraged to better understand the true frequency of negative compliance at a health professional population level.
Spatio-temporal mapping of breast and prostate cancers in South Iran from 2014-2017
Authors: Montazeri Mahdieh , Hoseini Benyamin , Firouraghi Neda , Kiani Fatemeh , Raouf-Mobini Hosein , Biabangard Adele , Dadashi Ali , Zolfaghari Vahideh , Ahmadian Leila , Eslami Saeid , Bergquist Robert , Bagheri Nasser , Kiani Behzad 
Published: September 2020

Abstract
Background: The most common gender-specific malignancies are cancer of the breast and the prostate. In developing countries, cancer screening of all at risk is impractical because of healthcare resource limitations. Thus, determining high-risk areas might be an important first screening step. This study explores potential high-risk clusters in the incidence pattern of breast and prostate cancers in southern Iran.Methods:This cross-sectional study was conducted in the province of Kerman, South Iran. Patient data were aggregated at the county and district levels and the incidence rate per 100,000 people both for cancer of the breast and the prostate were calculated. We used the natural-break classification with five classes to produce descriptive maps. A spatial clustering analysis (Anselin Local Moran’s I) was used to identify potential clusters and outliers in the pattern of these cancers from 2014 to 2017.Results:The age-standardised incidence rate of breast cancer showed an increase from 29.93 to 32.27 cases per 100,000 people and that of prostate cancer from 13.93 to 15.47 cases per 100,000 during 2014-2017. Cluster analysis at the county level identified high-high clusters of breast cancer in the North-West of the province for all years, but the analysis at the district level showed high-high clusters for only two of the years. Furthermore, cluster analysis at the county and district levels of prostate cancer also identified high-high clusters in the North-West of the province for two of the years.Conclusions:North-western Kerman had a significantly higher incidence rate of both breast and prostate cancer, which should help in designing tailored screening and surveillance systems. Furthermore, this study generates new hypotheses to test potential relationships between environmental risk factors and incidence of cancers in areas with higher cancer risk than the average.
Generating Real-world Evidence from Unstructured Clinical Notes to Examine Clinical Utility of Genetic Tests: Use Case in BRCAness
Authors: ZHAO Yiqing , Weroha Saravut J , Goode Ellen , Liu Hongfang , Wang Chen 
Published: September 2020

Abstract
Background : Next- generation sequencing provides comprehensive information about individuals’ genetic makeup and is commonplace in oncology clinical practice. However, the utility of genetic information in clinical decision-making process has not been examined extensively from a real-world, data-driven perspective. Through mining real-world data (RWD) from clinical notes, we could extract patients’ genetic information and further associate treatment decisions with genetic information. Methods : We proposed a real-world evidence (RWE) study framework that incorporates context-based natural language processing (NLP) methods and data quality examination before final association analysis. The framework was demonstrated in a Foundation-tested women cancer cohort (N=196). Upon retrieval of patients’ genetic information using NLP system, we assessed the completeness of genetic data captured in unstructured clinical notes according to a genetic data-model. We examined the distribution of different topics regarding BRCA1/2 throughout patients’ treatment process, and then analyzed the association between BRCA1/2 mutation status and the discussion/prescription of targeted therapy . Results: We identified seven topics in clinical context of genetic mentions including: Information, Evaluation, Insurance, Order, Negative, Positive, and Variants of unknown significance (VUS) . O ur rule-based system achieved a precision of 0.87, recall of 0.93 and F- measure of 0.91. Our machine learning system achieved a precision of 0.901, recall of 0.899 and F- measure of 0.9 for four-topic classification and a precision of 0.833, recall of 0.823 and F- measure of 0.82 for seven-topic classification. We found in result-containing sentences, capture of BRCA1/2 mutation information was 75%, but detailed variant information (e.g. variant types) is largely missing. Using cleaned RWD, significant associations were found between BRCA1/2 positive mutation and targeted therapies. Conclusions : In conclusion, we demonstrated a framework to generate RWE using RWD from different clinical sources. Rule-based NLP system achieved the best performance for resolving contextual variability when extracting RWD from unstructured clinical notes . Data quality issues such as incompleteness and discrepancies exist thus manual data cleaning is needed before further analysis can be performed. Finally, we were able to use cleaned RWD to evaluate real-world utility of genetic information to initiate a prescription of targeted therapy.