bluuebunny/crossref_metadata_2025_split huggingface dataset:
Would large dataset sample size unveil the potential of deep neural networks for improved genome-enabled prediction of complex traits? The case for body weight in broilers.
Authors: Passafaro Tiago Luciano , Lopes Fernando B. , Dórea João R. R. , Craven Mark , Breen Vivian , Hawken Rachel J. , Rosa Guilherme J. M. 
Published: June 2020

Abstract
Background: Deep neural networks (DNN) are a particular case of artificial neural networks (ANN) composed by multiple hidden layers, and have recently gained attention in genome-enabled prediction of complex traits. Yet, few studies in genome-enabled prediction have assessed the performance of DNN compared to traditional regression models. Strikingly, no clear superiority of DNN has been reported so far, and results seem highly dependent on the species and traits of application. Nevertheless, the relatively small datasets used in previous studies, most with fewer than 5,000 observations may have precluded the full potential of DNN. Therefore, the objective of this study was to investigate the impact of the dataset sample size on the performance of DNN compared to Bayesian regression models for genome-enable prediction of body weight in broilers by sub-sampling 63,526 observations of the training set.Results: Predictive performance of DNN improved as sample size increased, reaching a plateau at about 0.32 of prediction correlation when 60% of the entire training set size was used (i.e., 39,510 observations). Interestingly, DNN showed superior prediction correlation using up to 3% of training set, but poorer prediction correlation after that compared to Bayesian Ridge Regression (BRR) and Bayes Cπ. Regardless the amount of data used to train the predictive machines, DNN displayed the lowest mean square error of prediction compared to all other approaches. The predictive bias was lower for DNN compared to Bayesian models regardless the amount of data used with estimates closed to one with larger sample sizes. Conclusions: DNN had worse prediction correlation compared to BRR and Bayes Cπ, but improved mean square error of prediction and bias relative to both Bayesian models for genome-enabled prediction of body weight in broilers. Such findings, highlights advantages and disadvantages between predictive approaches depending on the criterion used for comparison. Nonetheless, further analysis is necessary to detect scenarios where DNN can clearly outperform Bayesian benchmark models.
Assessment of exercise-induced stress by automated measurement of salivary cortisol concentrations within the circadian rhythm in Japanese female long-distance runners
Authors: Ushiki Kazumi , Tsunekawa Katsuhiko , Shoho Yoshifumi , Martha Larasati , Ishigaki Hirotaka , Matsumoto Ryutaro , Yanagawa Yoshimaro , Nakazawa Asuka , Yoshida Akihiro , Nakajima Kiyomi , Araki Osamu , Kimura Takao , Murakami Masami 
Published: June 2020

Abstract
Background: Overtraining syndrome, caused by prolonged excessive stress, results in reduced performance and cortisol responsiveness in athletes. It is necessary to collect saliva samples sequentially within circadian rhythm for assessing exercise stress by measuring cortisol concentrations, and automated cortisol measurements using electrochemiluminescence immunoassay (ECLIA) may be useful for measuring a large number of saliva samples. In this study, we evaluated the appropriate use of cortisol-based exercise stress assessment within the circadian rhythm, which may diagnose and prevent overtraining syndrome in athletes. Methods: We collected saliva and sera from 54 healthy participants and analyzed the correlation between salivary cortisol concentrations measured by ECLIA and enzyme-linked immunosorbent assay (ELISA) or serum cortisol analysis. We also collected saliva continuously from 12 female long-distance runners on 2 consecutive days involving different intensities and types of exercise early in the morning and in the afternoon and measured salivary cortisol concentrations using ECLIA. Each exercise intensity of runners was measured by running velocities, Borg Scale score, and rate of change in the pulse rate by exercise. Results: ECLIA-based salivary cortisol concentrations correlated positively with those detected by ELISA (ρ = 0.924, p < 0.001) and serum cortisol (ρ = 0.591, p = 0.001). In long-distance runners, circadian rhythm of salivary cortisol including peak after waking and decrease promptly thereafter were detected on both days by continuous saliva sampling. The rates of change in salivary cortisol concentrations were significantly lower after an early morning exercise than after an afternoon exercise on both days (day 1, p = 0.002 and day 2, p = 0.003). In the early morning exercise, the rate of change in salivary cortisol concentration was significantly higher on day 1 than on day 2 ( p = 0.034), similar to significant difference in running velocities ( p = 0.001).Conclusions: Our results suggest that automated ECLIA-based salivary cortisol measurements are able to detect the athletes' circadian rhythm and compare the exercise stress intensities at the same times on different days, even in the early morning, possibly leading to prevention of overtraining syndrome.
Rates, predictors and mortality of sepsis-associated acute kidney injury: systematic review and meta-analysis
Authors: Liu Jie feng , Xie Hebin , ye ziwei , Wang Lesan 
Published: June 2020

Abstract
Objective:The incidence and mortality of sepsis-induced acute kidney injury is high. Many studies have explored the causes of sepsis-induced acute kidney injury (AKI). However, its predictors are still uncertain; additionally, a complete overview is missing. A systematic review and a meta-analysis were performed to determine the predisposing factors for sepsis-induced AKI. Method: A systematic literature search was performed in the Medline, Embase, Cochrane Library, PubMed and Web of Science databases, with an end date parameter of May 25, 2019. Valid data were retrieved in compliance with the inclusion and exclusion criteria. Result: Forty-seven observational studies were included for analysis. A cumulative number of 55911sepsis patients were evaluated. The incidence of AKI caused by septic shock is the highest. 30 possible risk factors were included in the meta-analysis. The results showed that 20 factors were found to be significant. The odds ratio(OR),95% confidence interval (CI) and Prevalence of the most prevalent predisposing factors for sepsis-induced AKI were as the following: Septic shock[2.88(2.36-3.52), 60.47%], Hypertension[1.43(1.20-1.70),38.39%), Diabetes mellitus[1.59(1.47-1.71),27.57%],Abdominal infection[1.44(1.32-1.58),30.87%], Vasopressors use[2.95(1.67-5.22),64.61%],vasoactive drugs use [3.85(1.89-7.87),63.22%], Mechanical ventilation[1.64(1.24-2.16),68.00%), Positive blood culture[1.60(1.35-1.89), 41.19%], Smoke history[1.60(1.09-2.36),43.09%]. Other risk factors include cardiovascular, coronary artery disease, liver disease, unknow infection, diuretics use, ACEI or ARB, gram-negative bacteria and organ transplant. Conclusion: A large number of factors are associated with AKI development in sepsis patients. Our review can guide risk-reducing interventions, clinical prediction rules, and patient-specific treatment and management strategies for sepsis-induced acute kidney injury.
Principles of “Humanistic Environment” in Dental Education: Design, Validation, and Standardization of a Questionnaire
Authors: Mehrnia Nika , Sadeghipour Maryam , Zafarmand A. Hamid 
Published: June 2020

Abstract
Background

Health science education for students should comply with the principles of the Humanistic Environment. Adhering to these principles, along with other didactic and clinical training courses, will make treatment more successful and brings more satisfaction for patients.
Methods

Six completely related researches were found in the literature (Pubmed, Google Scholar). A questionnaire consisting of 67 questions was collected for evaluation. The questionnaire was submitted to 9 members of a panel of experts for a survey. Using statistical methods, Content Validity Index (CVI) and Content Validity Ratio (CVR) were determined and its reliability was evaluated. According to the relevant formula and Lawshe table questions with a score higher than 0.79 and 0.78 were included in the questionnaire, respectively. The questionnaire was also administered to 8 students for determining the Face Validity. Cronbach's Alpha was calculated 0.808, using SPSS (v.#22) software. The Reliability Analysis was determined based upon 15 students’ opinions.
Results

Eventually, a questionnaire containing 39 questions was finalized and categorized in 7 eminent humanistic fields. These are: Internal Feelings, Rules and Regulations, Interpersonal Relations, Behavior Change, Administration, Commitment & Satisfaction, Professional Ethics.
Conclusions

The principles of Humanistic Environment provide favorable interaction between students and teachers, satisfy the welfare of patient, and succeed the outcome of treatment along with regular scientific courses. Due to cultural and social differences, a specific questionnaire should be designed for each community to reflect their interests.
Effect of bendiocarb based (Ficam® 80% WP) Indoor Residual Spraying on feeding patterns from malaria vectors in Burkina Faso, West Africa.
Authors: HIEN Sawdetuo Aristide , Soma Dieudonné Diloma , Sawadogo Simon Pengwende , Poda Serge Bèwadéyir , Namountougou Moussa , Ouédraogo Georges Anicet , Diabaté Abdoulaye , Dabiré Roch Kounbobr 
Published: June 2020

Abstract
Background: The fight against vector is essential in malaria prevention strategies in several endemic countries in Africa. In Burkina Faso, malaria transmission is seasonal in most parts of country, so a single round of spraying should provide effective protection against malaria, provided the insecticide remains effective over the entire malaria transmission season. The outcomes of indoor residual spraying towards curtailing malaria transmission are firstly to decrease the life span of vector mosquitoes and also to reduce the malaria vectors density.Methods : CDC light trap and early morning collections by pyrethrum spray catches were performed monthly to determine the change in malaria vector indices in sprayed (Diebougou) and unsprayed sites (Dano). The female’s malaria vectors collected by both methods were used to determine their blood feeding, biting and sporozoites rate and malaria transmission risk estimated by entomological inoculation rate.Results: Anopheles gambiae complex composed to Anopheles gambiae, Anopheles coluzzii and Anopheles arabiensis were present throughout the transmission season, but An. gambiae was the predominant species collected (P =0.0005), comprising 88% of the total collected and the most infected species. Malaria vectors densities were significantly lower in sprayed villages (n=4,303) compared with unsprayed villages (n=12,569) during post-spraying period (P = 0.0012). In addition, mean human biting rate of An. gambiae sl and An. funestus sl were significantly lower in sprayed areas compared to unsprayed areas (P<0.05). Overall, malaria vector transmission risk was significant lower in villages which received IRS (P=0.0001) whatever the malaria vectors species (An. gambiae sl and An. An. funestus sl).Conclusions: The results showed that in the sprayed area (Diebougou), vector densities, human biting rates and malaria transmission risks were very lower than unsprayed areas (Dano). The findings also showed a change in vector behavior especially within An. funestus which became more zoophagic following IRS. The indoor residual spraying could be recommanded as control tool in areas where malaria transmission occured a given period of year.
Therapeutic effects of Zuojin Pill on Helicobacter pylori-induced chronic atrophic gastritis through JMJD2B/COX-2/VEGF signaling axis
Authors: Wu Shihua , Bao Chunmei , Wang Ruilin , Zhang Xiaomei , Gao Sijia , Qin Weihan , Zhang Jianzhong , Zhang Juling , Li Ruisheng , Chen Xing , Wen Jianxia , Yang Tao , Wei Shizhang , Li Haotian , Wei Ying , Ren Sichen , Xia Houlin , Zhao Yanling 
Published: June 2020

Abstract
Background: Zuojin Pill (ZJP), a famous Chinese medicinal formula, widely accepted for treatment of chronic atrophic gastritis (CAG) in China. This study aimed to explore the therapeutic effects and mechanisms of ZJP in Helicobacter pylori (H. pylori) - induced chronic atrophic gastritis (CAG) in vivo and in vitro. Methods: CAG rat model was induced by H. pylori. ZJP (0.63, 1.26, and 2.52 g/kg, respectively) was administered orally for four weeks. Therapeutic effects of ZJP were identified by H&E staining and serum indices. In addition, cell viability, morphology and proliferation were detected by cell counting kit-8 (CCK8) and high-content screening assay (HCS), respectively. Moreover, relative mRNA expression and protein expression related to JMJD2B/COX-2/VEGF axis was detected to investigate the potential mechanisms of ZJP in CAG. Results: Results showed the symptoms (weight loss and gastric mucosa damage) of CAG were alleviated, and the contents of TNF-α in serum was markedly decreased after treating with ZJP. Moreover, cell viability, proliferation and morphology changes of GES-1 cells were ameliorated by ZJP intervention. In addition, proinflammatory genes and JMJD2B/COX-2/VEGF axis related genes were suppressed by ZJP administration in vitro and in vivo. Meanwhile, immunohistochemistry (IHC) and western blot confirmed down-regulation of these genes by ZJP intervention. Conclusion: ZJP treatment can alleviate gastric mucosal damage induced by H. pylori via JMJD2B/COX-2/VEGF axis.
Frequent horizontal and mother-to-child transmission may contribute to high prevalence of STLV-1 infection in Japanese macaques
Authors: Murata Megumi , Yasunaga Jun-ichirou , Washizaki Ayaka , Seki Yohei , Kuramitsu Madoka , Keat Tan Wei , Hu Anna , Okuma Kazu , Hamaguchi Isao , Mizukami Takuo , Matsuoka Masao , Akari Hirofumi 
Published: June 2020

Abstract
Background: Simian T-cell leukemia virus type-1 (STLV-1) is disseminated among various non-human primate species and is closely related to human T-cell leukemia virus type-1 (HTLV-1), the causative agent of adult T-cell leukemia and HTLV-1-associated myelopathy/ tropical spastic paraparesis. Notably, t he prevalence of STLV-1 infection in Japanese macaques (JMs) is estimated to be >60%, much greater than that in other non-human primates; however, the mechanism and mode of STLV-1 transmission remain unknown. The aim of this study is to examine the epidemiological background by which STLV-1 infection is highly prevalent in JMs. Results: The prevalence of STLV-1 in the JMs rearing in our free-range facility reached up to 64% (180/280 JMs) with variation from 55 to 77% among five independent troops. Anti-STLV-1 antibody titers (ABTs) and STLV-1 proviral loads ( PVLs) were normally distributed with mean values of 4076 and 0.62%, respectively, which were mostly comparable to those of HTLV-1-infected humans. Our initial hypothesis that some of the macaques might contribute to frequent horizontal STLV-1 transmission as viral super-spreaders was unlikely because of the absence of the macaques exhibiting abnormally high PVLs but poor ABTs. Rather, ABTs and PVLs were statically corelated (p < 0.0001), indicating that the increasing PVLs led to the greater humoral immune response. Further analyses demonstrated that the STLV-1 prevalence as determined by detection of the proviral DNA was dramatically increased with age; 11%, 31%, and 58% at 0, 1, and 2 years of age, which was generally consistent with the result of seroprevalence and suggested the frequent incidence of mother-to-child transmission (MTCT). Moreover, our longitudinal follow-up study indicated that 24 of 28 seronegative JMs during the periods from 2011 to 2012 converted to seropositive (86%) four years later; among them, the seroconversion rates of sexually matured (4 years of age and older) macaques and immature macaques (3 years of age and younger) at the beginning of study were comparably high (80% and 89%, respectively), suggesting the frequent incidence of horizontal transmission. Conclusions: Together with the fact that almost all of the full-adult JMs older than 9 years old were infected with STLV-1, our results of this study demonstrated for the first time that frequent horizontal and mother-to-child transmission may contribute to high prevalence of STLV-1 infection in JMs
Efficacy of Corticosteroids Treatment on Reducing the Risk of Post-Extubation Stridor: Study Protocol for a Randomized Controlled Trial
Authors: Wang Jingyi , Walline Joseph , Dai Yili , Yin Lu , Dai Jiayuan , Zhu Huadong , Yu Xuezhong , Xu Jun 
Published: June 2020

Abstract
Background: Laryngotracheal injury is one of common complications of airway intubation, with severe cases leading to stridor or even extubation failure (need for reintubation within 48 hours after extubation). As corticosteroids have anti-inflammatory effects, they may play an important role in reducing the risk of post-extubation stridor and extubation failure among adult patients.Aim: To investigate the efficacy of corticosteroids on reducing the risk of post-extubation stridor. Methods: A multicenter, randomized, placebo-controlled trial will be performed. The trial will enroll 232 patients undergoing extubation from mechanical ventilation. The patients will be randomly assigned to treatment four hours prior to extubation either with intravenous methylprednisolone 40mg or placebo. The primary endpoint is the occurrence of laryngeal stridor within 48 hours, and the secondary endpoints are the need for respiratory support or reintubation secondary to post-extubation stridor within 48 hours after extubation, side effects or corticosteroids, hospital length of stay, and 30-day mortality.Discussion: The trial will examine if corticosteroid therapy before extubation is effective at reducing the risk of post-extubation stridor-related complications among adult patients. Trial registration: Chictr.org.cn, ChiCTR2000030349. Registered on 29 Feb 2020.
Effect of Hypertension on Outcomes of Adult Inpatients with COVID-19 in Wuhan, China: A Propensity Score–matching Analysis
Authors: Yang Qing , Zhou Ying , Wang Xinrong , Gao Shan , Xiao Yang , Zhang Weimin , Hu Yi , Wang Yafei 
Published: June 2020

Abstract
Background: Previous studies have shown that Coronavirus Disease 2019 (COVID-19) patients with underlying comorbidities can have worse outcomes. However, the effect of hypertension on outcomes of COVID-19 patients remains unclear.Research Question: The aim of this study was to explore the effect of hypertension on the outcomes of patients with COVID-19 by using propensity score–matching (PSM) analysis.Study Design and Methods: Participants enrolled in this study were patients with COVID-19 who had been hospitalized at the Central Hospital of Wuhan, China. Chronic comorbidities and laboratory and radiological data were reviewed; patient outcomes and lengths of stay were obtained from discharge records. We used the Cox proportional-hazard model (CPHM) to analyze the effect of hypertension on these patients’ outcomes and PSM analysis to further validate the abovementioned effect.Results: A total of 226 patients with COVID-19 were enrolled in this study, of whom 176 survived and 50 died. The proportion of patients with hypertension among non-survivors was higher than that among survivors (26.70% vs. 74.00%; P < 0.001). Results obtained via CPHM showed that hypertension could increase risk of mortality in COVID-19 patients (hazard ratio 3.317; 95% CI [1.709–6.440]; P < 0.001). Increased D-dimer levels and higher ratio of neutrophils to lymphocytes (N/L) were also found to increase these patients’ mortality risk. After matching on propensity score, we still came to similar conclusions. After we applied the same method in critically ill patients, we found that hypertension also increased risk of death in patients with severe COVID-19.Conclusion: Hypertension, increased D-dimer and the ratio of neutrophil to lymphocyte increased mortality in patients with COVID-19, with hypertension in particular.
A model for survival rate projection of Covid19 patients
Authors: Madalli Devika P. , Gajbe Sagar Bhimrao , Gopalji  , Kumar Akhilesh Ajith 
Published: June 2020

Abstract
The novel coronavirus has been declared a worldwide pandemic. The pandemic has unleashed health as well as economic devastation across the world. In view of this, various governments, researchers and agencies are trying to work towards solutions to control the spread of the virus. There are many studies that have been initiated that consider the various parameters that contribute to the spread of the virus. We present a model to predict the survival rate of Covid19 infected patients. The study takes into consideration death rate (normal) and Covid infection death rate in India. Other factors considered are the number of infections and active infection numbers. We also incorporate a ‘learning module’ to learn from the observed error rate. We compute the moving average of error which is then deployed to minimise projection error in the model. The factor obtained from the learning is deployed into the survival rate computation to achieve best results.
A Metadata Driven Module for Managing and Interpreting HDSS Verbal Autopsy Datasets using Interva-4 Model
Authors: KOMBASSERE KOULIGA , Nimako Gideon , Mare Irma 
Published: June 2020

Abstract
Background: The World Health Organisation provides a standardised survey-based questionnaire for collecting cause of death data. This standardised tool is undergoing iterative changes almost every 3 to 5 years resulting in the redesign of in-use re-adapted questionnaires and their database schemes. Given the size of this questionnaire, its redesign process requiring a lot of time and resources does not allow research centres to update their questionnaire. In addition, the heaviness and the expensive cost of the Physician Certified Verbal Autopsy method used for collected data interpretation, led the emergence of new methods with which data are usually managed in ad hoc fashion by using spreadsheets and Comma Separated Value files. Therefore, these tools not allow preservation of the contextual metadata and also not support recovery and building relationship among data object. While the absence of data object relationships does not facilitate the use of relational database management systems and data preservation over time in longitudinal studies contexts such Health and Demographic surveillance systems.Results: This research used Microsoft Visual studio based on model-driven and metadata architectures associated with R.NET Package,R InterVA function, Google Maps API, eXtensible Mark-up Language and Microsoft SQL Server 2012 to develop a Verbal Autopsy data management platform. This platform assists INDEPTH Network HDSS fields sites to quickly follow the iterative changes of WHO questionnaire through questionnaire generation, data collection and entry, and a mapping layer that translates verbal autopsy CRF to ODK XML data dictionary enabling cause of death data collection in offline mode using handheld devices. In addition, being a R InterVA function aided tool for the interpretation of cause of death data, this web application has an interface for visualising cause of death patterns using Google Maps API.Conclusions: Verbal autopsy data management interpretation over time in the longitudinal studies context such Health and Demographic Surveillance System is feasible. Thereby, possibilities given by metadata-driven to build reliable software architecture for verbal autopsy data collection, interpretation and cause of death patterns visualisation and particularly compliance with regulatory relational database management requirements are achievable.