bluuebunny/crossref_metadata_2025_split huggingface dataset:
A single-model quality assessment method for poor quality protein structure
Authors: Ouyang Jianquan , Huang Ningqiao , Jiang Yunqi 
Published: April 2020

Abstract
Background: Quality assessment of protein tertiary structure prediction models, in which structures of the best quality are selected from decoys, is a major challenge in protein structure prediction, and is crucial to determine a model’s utility and potential applications. Estimating the quality of a single model predicts the model’s quality based on the single model itself. In general, the Pearson correlation value of the quality assessment method increases in tandem with an increase in the quality of the model pool. However, there is no consensus regarding the best method to select a few good models from the poor quality model pool.Results: We introduce a novel single-model quality assessment method for poor quality models that uses simple linear combinations of six features. We perform weighted search and linear regression on a large dataset of models from the 12th Critical Assessment of Protein Structure Prediction (CASP12) and benchmark the results on CASP13 models. We demonstrate that our method achieves outstanding performance on poor quality models.Conclusions: According to results of poor protein structure assessment based on six features, contact prediction and relying on fewer prediction features can improve selection accuracy.
Prevalence Of Irritable Bowel Syndrome, Celiac Disease And Their Manifestations Among Muhimbili University Of Health And Allied Sciences Staff And Students: A Cross Sectional Study
Authors: Gembe Adam Miraj 
Published: April 2020

Abstract
Background: Global prevalence of irritable bowel syndrome is high among medical students and health care professionals with significant morbidity. Similarly, the prevalence of celiac disease in irritable bowel syndrome is higher than the general population. These conditions impair quality of life and contribute to social-economic burden. In Tanzania, little is known about irritable bowel syndrome and celiac disease among medical students and health care professionals. Methods: A cross sectional study was conducted to MUHAS and Mloganzila Academic Medical Center (MAMC) staff and students who fulfilled the online shared Rome IV criteria of irritable bowel syndrome from August to November 2018. A structured questionnaire was used to collect socio-demographic data, anthropometric measurements and clinical manifestations. Blood samples for full blood picture, liver enzymes and Erythrocyte Sedimentation Rate were taken. Celiac disease was tested using anti-tissue transglutaminase antibody test. Qualitative and quantitative data were summarized using frequency distribution tables. Chi-square and fishers exact test were used to study comparison between groups. Logistic regression was used to study associations. Data was analyzed using SPSS version 20.0 and a P value of ≤0.05 was considered significant.Results: Out of 1,321 participants, 192 (14.5%) had irritable bowel syndrome in which 77 (40.1%) were males and 115 (59.9%) were females. Among the 192 participants with irritable bowel syndrome, 3 (1.6%) were positive for celiac disease, 2 (66.7%) were females and 1 (33.3%) was a male. Of the 3 patients with CD, 2 had elevated ALAT and 1 had anaemia. Age (AOR 2.53, 95% C.I 1.57-4.09), sex (AOR 1.67, 95% C.I 1.16-2.41), marital status (AOR 4.95 C.I 2.07-11.82), alcohol intake (AOR 2.47, 95% C.I 1.16-5.23), year of study (AOR 8.49, 95% C.I 5.71-12.64) and sleep duration (AOR 2.24, 95% C.I 1.23-4.06) were found to be independently associated with IBS. Conclusion: Prevalence of IBS and its associated factors in our study population was similar to findings from studies done elsewhere. Also, our study revealed a low prevalence of celiac disease among IBS participants.
Clinical characteristics of 194 cases of COVID-19 in Huanggang and Taian, China
Authors: Zhang Hong , Shang Wenli , Liu Qinghua , Zhang Xuejing , Zheng Maochuan , Yue Maokui 
Published: April 2020

Abstract
Purpose We aimed to report the clinical characteristics of 194 cases coronavirus disease-19 (COVID-19) in Huanggang, Hubei and Taian, Shandong. Methods We retrospectively investigated the clinical, laboratory characteristics and CT imaging of confirmed cases of COVID-19 from Jan 22 to Feb 28, 2020 in Huanggang Central Hospital and The Second Affiliated Hospital of Shandong First Medical University. Real time PCR was used to detect the new coronavirus in respiratory samples. Immunohistochemical staining was used to detect the expressions of ACE2 in tissues. Results Among the 194 patients infected with COVID-19, 108 patients were male, with a median age of 48.3 years. The average preclinical period was 7.44 day. Except for 37 severe or critically ill patients, the rest of the 157 patients exhibited mild or moderate symptoms. 190 (97.94%) patients were confirmed during the three times nucleic acid test. The main clinical symptom of the patients were fever, sore throat and cough, which accounted for 146 cases (75.26%), 98 (50.52%) and 86 cases (44.33%%), respectively. 30 patients (15.46%) showed liver dysfunction. Imaging examination showed that 141 patients (72.68%) showed abnormal, 53 cases (27.32%) had no obvious abnormal density shadow in the parenchyma of both lungs. Up to now, 109 cases were discharged from the hospital, and 9 patients died. The ACE2 expression levels were up-regulated in patients of severe type and critically ill type. Conclusion Clinical symptoms, laboratory tests and CT imaging should be combined for comprehensive analysis to diagnose COVID-19. ACE2 may be the receptor of COVID-19.
Introducing an Efficient Sampling Method for National Surveys with Limited Sample Sizes: Application to a National Study to Determine Quality and Cost of Healthcare.
Authors: Parsaeian Mahboubeh , Mahdavi Mahdi , Saadati Mojdeh , Mehdipour Parinaz , Sheidaei Ali , Khatibzadeh Shahab , Farzadfar Farshad , Shahraz Saeid 
Published: April 2020

Abstract
Background: Due to budget constraints, many national studies are only affordable with small sample sizes. Facing a similar constraint, the national study of “Iran Quality of Care in Medicine Program” (IQCAMP), aims to evaluate the quality and costs of medical care in the country for 8 selected high-cost high-volume diseases by only recruiting 300 participants per disease under study. We proposed and tested a data mining method to efficiently design such national studies with small sample sizes.Methods: We developed a sampling design based on hierarchical clustering method (HCM) and model-based clustering method (MCM). Based on these methods, we used healthcare structure and outcome data to define the optimum clusters of districts and provinces of Iran. An expert group checked the face validity of the defined clusters. We subsequently compared the internal validity of HCM with MCM by within clusters sum of square, average silhouette width, and Dunn index. The stability validity was also examined by statistical indices. We selected the optimum clusters based on the results of these measures. Per cluster, one province was systematically selected for data collection. The features of selected clusters were delineated by the Decision Tree Learning and the most important distinguishing indicators were identified. The efficiency of the selected sampling method was compared with a simple random sampling through simulation.Results: MCM and HCM divided the districts into eight and two clusters, respectively. The measures of internal and stability validity showed that clusters created by MCM were more separated, compact, and stable, thus forming our optimum clusters. The probability of death from stroke, chronic obstructive pulmonary disease, and in-hospital mortality rate were the most important indicators that distinguished the eight clusters. Based on the simulation results, MCM increased the efficiency of the sampling design up to 70% compared to simple random sampling.Conclusions: By using this sampling method we selected 300 participants per health condition across the country only from eight provinces rather than all 31 provinces. Our sampling method benefits studies with small sample sizes by decreasing the level of sampling variability and the overall cost of studies.
Possible protective effects of trans-resveratrol against 1,4-dioxane induced toxicity in meristematic cells of plant bioassays
Authors: Kurt Deniz , Yalçın Emine , Çavuşoğlu Kültiğin 
Published: April 2020

Abstract
Background In this study, the protective effects of trans-resveratrol against 1,4-dioxane induced toxicity in meristematic cells were investigated. For this purpose, Allium test which is a reliable test was used and the alterations in all experimental groups were examined by using physiological, cytogenetic, biochemical and anatomical parameters.Results As a result of the analysis, it has been determined that 1,4-dioxane causes serious abnormalities in Allium cepa meristematic cells. It was determined that in 1,4-dioxane treated group germination percentage regressed 1.6-times, root length reduced 12.7-times and weight gain decreased 7.7-times compared to control group. It has been observed that trans-resveratrol administration with 1,4-dioxane causes improvement in physiological parameters and reduces the damage rate from 0.4 to 0.16. Mitotic index, micronucleus and chromosomal abnormality frequency were investigated as cytogenetic parameters. It was determined that mitotic index decreased, chromosomal abnormalities and micronucleus frequency increased in 1,4-dioxane treated group. Trans-resveratrol treatment was found to cause a dose dependent improvement in genotoxic effects induced by 1,4-dioxane. Changes in the antioxidant system in all experimental groups were determined by measuring malondialdehyde, glutathione, superoxide dismutase and catalase enzyme levels. It was determined that 1,4-dioxane administration caused an increase in malondialdehyde level, decreased glutathion rate and induced antioxidant enzyme activity. Trans-resveratrol application was found to cause improvement in these alterations induced by 1,4-dioxane. It was observed that the 200 mg/mL trans-resveratrol+1,4-dioxane treatment caused a 1.9-fold decrease in malondialdehyde level which is indicator of lipid peroxidation compared to only 1,4-dioxane treated group. The abnormalities caused by 1,4-dioxane application in the meristematic cells are also found in the anatomical structure. In 1,4-dioxane treatment group, anatomical changes such as cell deformation and cortex wall thickening were observed. The frequency of these changes decreased with trans-resveratrol administration.Conclusions As a result, it was determined that 1,4-dioxane caused a versatile toxicity in Allium cepa meristematic cells, while trans-resveratrol was found to have a dose-dependent protective feature against 1,4-dioxane-induced toxicity.
Bioactive Diterpenoids Impact the Composition of the Root-Associated Microbiome in Maize (Zea mays)
Authors: Murphy Katherine M. , Ewards Joseph , Louie Katherine B. , Bowen Benjamin P. , Sundaresan Venkatesan , Northen Trent R. , Zerbe Philipp 
Published: April 2020

Abstract
Background : Plants deploy both primary and species-specific, specialized metabolites to communicate with other organisms and adapt to environmental challenges. This includes interactions with soil-dwelling microbial communities, where plants may exchange sugars for important nutrients and protection against environmental perturbations, directly benefitting plant fitness. However, the molecular mechanisms underlying these plant-microbe interactions often remain elusive. Results : In this study, we report that maize ( Zea mays ) specialized diterpenoid metabolites with known antifungal bioactivities also influence rhizosphere bacterial communities. Metabolite profiling showed that dolabralexins, antibiotic diterpenoids that are highly abundant in roots of some maize varieties, can be exuded from the roots. Comparative 16S rRNA gene sequencing determined the bacterial community composition of the maize mutant Zman2 ( anther ear 2 ), which is deficient in dolabralexins and closely related bioactive kauralexin diterpenoids. Under well-watered conditions, the Zman2 rhizosphere microbiome differed significantly from the wild-type sibling with the most significant changes observed for Alphaproteobacteria of the order Sphingomonadales. By contrast, there was no difference in the microbiome composition between the mutant and wild-type was observed under drought stress. Metabolomics analyses support that these differences are attributed to the diterpenoid deficiency of the Zman2 mutant, rather than other metabolome alterations. Conclusions : Together, these findings support physiological functions of maize diterpenoids beyond known chemical defenses, including the assembly of the rhizosphere microbiome.
Isolation and evaluation of the probiotic potential of lactic acid strains from healthy equines for potential use in salmonellosis diarrhea
Authors: Pei Lulu , Hao Yang , Yan Ziyin , Zhang Hui , Lan Yanfang , Li Aoyun , Iqba Mudassar , Shen Yaoqin 
Published: April 2020

Abstract
The objective of the present study was to evaluate the probiotic properties, security and antibacterial ability in vivo of isolated strains from healthy equine. In the present study, two Pediococcus acidilactici (P1 and P2) and two Lactobacillus equi (L1 and L2) were isolated. All isolates died when exposed to pH 2.0 for 3h but survived at pH 3.0 with differential survival. The viable bacteria count was sustained at high levels in a tolerance test with artificial gastrointestinal fluid. The isolates survived and grew at temperatures between 37 and 55 ℃ but died at 65 ℃. Four strains exhibited inhibitory activity against pathogens, including Salmonella typhimurium (CVCC542), Escherichia coli (C83902), Staphylococcus aureus (BNCC186335) and Pasteurella multocida (clinical isolate). These isolates exhibited differential antibiotic susceptibility. In safety trials, all isolates were γ-hemolytic, and the oral toxicity of strains P1 (gavaged with 1×109 CFU/day) and L1 (gavaged with 1×109 CFU/day) were analyzed in vivo. There were no effects on overall health status in mice. There were no significant differences in the incidence of bacteria translocation to blood, liver and spleen. Mice gavaged with Pediococcus acidilactici P1 (1×108 CFU/day) or Lactobacillus equi L1 (1×108 CFU/day) as prevention showed lower rates of diarrhea and mortality after challenged with Salmonella Typhimurium (4×106 CFU signal dose, 0.1 ml by intragastric gavage). The results indicate that the isolated strains could act as potential probiotics, providing a new way to reduce salmonella infection, which merit future application studies.
Preoperative assessment of cognitive function and risk assessment of cognitive impairment in elderly patients with orthopedics: A cross-sectional study.
Authors: Gan Shuyuan , Yu Yang , Wu Jiateng , Tang Xiaodong , Zheng Yueying , Wang Mingcang , Zhu Shengmei 
Published: April 2020

Abstract
Background Preexisting cognitive impairment is emerging as a predictor of poor postoperative outcomes in seniors. Nevertheless, cognitive impairment in a large proportion of geriatric patients has not been well identified and diagnosed.Methods This is a cross-sectional study. Mini-mental state examination scale was used to assess cognitive function of elderly patients aged ≥ 65 years undergoing orthopedic surgery preoperatively. The baseline, living habits and laboratory examination results of the two groups were compared, and multivariate Logistic regression model was used to identify independent predictors of preoperative cognitive impairment.Results A total of 374 elderly patients with orthopedics met the inclusion criteria, and 28.61% with preoperative cognitive impairment. Multivariate Logistic regression analysis showed that age (OR=1.089, P<0.001), subjective sleep disorders (OR=1.996, P=0.021), atherosclerosis (OR=2.367, P=0.017), high cholesterol level (OR=1.373, P=0.028) were independent risk factors for preoperative cognitive impairment, while high education level performed as a protective factor (Compared with illiterate group, primary school group: OR=-0.885, P=0.009; middle school or above group: OR=-2.118, P<0.001).Conclusions The prevalence of preoperative cognitive dysfunction in geriatric elective orthopedic surgical patients was high. Our study identified venerable age, low level of education, subjective sleep disorders, atherosclerosis, high cholesterol level as risk factors for preoperative cognitive impairment in these patients. Understanding these risk factors contribute to assist in prevention and directed interventions for the high-risk population.
Establishing seasonal and alert influenza thresholds in Morocco
Authors: Rguig Ahmed , Cherkaoui Imad , McCarron Margaret , Oumzil Hicham , Triki Soumia , Elmbarki Houria , Bimouhen Abderrahman , Falaki Fatima El , Regragui Zakia , Ihazmad Hassan , Nejjari Chakib , Youbi Mohammed 
Published: April 2020

Abstract
Background: Several statistical methods of variable complexity have been developed to establish thresholds for influenza activity to inform public health guidance. We compared the results of two methods and explored how they worked to characterize the 2017-2018 season.Methods: Historical data from the 2005/2006 to 2016/2017 seasons were provided by a network of 412 primary health centers in charge of influenza like illness (ILI) sentinel surveillance. We used the WHO averages and the moving epidemic method (MEM) to evaluate the proportion of ILI visits among all outpatient consultations (ILI%) as a proxy for influenza activity. We also used the MEM method to evaluate three seasons of composite data (ILI% multiplied by percent of ILI with laboratory-confirmed influenza) as recommended by WHO.Results: The WHO method estimated the seasonal ILI% threshold at 0.9%. The annual epidemic period begins on average at week 46 and lasts an average of 18 weeks. The MEM model estimated the epidemic threshold (corresponding to the WHO seasonal threshold) at 1.5% of ILI visits among all consultations. The annual epidemic period began on week 49 and lasted on average 14 weeks. Intensity thresholds were similar using both methods. When using the composite measure, the MEM method showed a clearer estimate of the beginning of the influenza epidemic, which was coincident with a sharp increase in confirmed ILI cases.Conclusions: We found that the threshold methodology presented in the WHO manual is simple to implement and easy to adopt for use by the Moroccan influenza surveillance system. The MEM method is more statistically sophisticated and may allow a better detection of the start of seasonal epidemics. Incorporation of virologic data into the composite parameter as recommended by WHO has the potential to increase the accuracy of seasonal threshold estimation.
Influence of culture conditions on the production of extracellular polymeric substances (EPS) by Arthrospira platensis
Authors: Silva Mariana Barbalho , Azero Edwin G. , Teixeira Cláudia M. L. L. , Andrade Cristina T. 
Published: April 2020

Abstract
Arthrospira platensis is a cyanobacterium that exhibits a large biotechnological interest at food industry because its high protein content, pigments, lipids and carbohydrates. The extracellular polymeric substances (EPS) are co-products of secondary metabolism that present thickening or gelling property. A 3-level factorial design was used to study the combined effect of different nitrate concentrations and photon flux density (PFD) to evaluate the biomass and EPS production by Arthrospira platensis. Characterization of the EPS produced the rheological behavior were also evaluated. The best result for biomass production was obtained at condition 6 (2 g.L-1 NaNO3 and 600 µE.m-2s-1) leading a biomass concentration of 1.292 mg.L-1. Condition 1 (0.25 g.L-1NaNO3 and 200 µE.m-2s-1) produce the major EPS content (111 mg.g-1) followed by condition 9 (2 g.L-1NaNO3 and 1000 µE.m-2s-1). Rheological studies performed for the product at 5 and 10g.L-1 concentrations revealed a dilute solution behavior.
Security Assurance Modelling of Security Incident in Healthcare using the Generic Security Template (GST)
Authors: He Ying , Luo Cunjin 
Published: April 2020

Abstract
Background: The recent industry reports show that the number of security incidents in healthcare sector is still increasing, especially the high severity incident, such as data leakage incident and ransomware, which can lead to significant impact on healthcare services. It is imperative for the organizations to learn lessons from those incidents. Traditional ways to disseminate lessons learned are based on text approach, the linear format of which can obscure relationships among concepts and discourage readers from integrating information across ideas. Graphical diagrams can serve this purpose, as it can communicate both individual elements of information and relationships between them. Methods: The Generic Security Template (GST) has been proposed to support the exchange of lessons learned from security incidents. It utilises graphical notations to communicate both individual elements of information and relationships between them. This paper conducts a case study by adopting the GST to capture and structure the incident information of a data leakage incident in a UK healthcare organization in order to facilitate incident exchange. Results: The results show that, the GST was able to visualise and depict the key elements, including lessons learned, the associated security requirements and organizational contextual information identified from the selected data leakage incident case study from NHS. GST provides a unified way to communicate incident information. Conclusions: This research has significance for the healthcare organizations to improve their incident learning practices. It fosters an environment where different stakeholders can speak the same language while exchanging the lessons learned from the security incidents. Future work will consider apply the GST to analyse other complex security incidents such as the advanced persistent threats (APTs) in healthcare organizations and extend the use of the GST in other industries. Keywords: Security Assurance Modelling, Generic Security Template (GST), Security Incident, Healthcare Organization.