bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of sample size on the stability of risk scores from clinical prediction models: a case study in cardiovascular disease
Authors: Pate Alexander , Emsley Richard , Sperrin Matthew , Martin Glen P. , Staa Tjeerd van 
Published: February 2020

Abstract
Background Stability of risk estimates from prediction models may be highly dependent on the sample size of the dataset available for model derivation. In this paper, we evaluate the stability of cardiovascular disease risk scores for individual patients when using different sample sizes for model derivation; such sample sizes include those similar to models recommended in national guidelines, and those based on recently published sample size formula for prediction models. Methods We mimicked the process of sampling N patients from a population to develop a risk prediction model by sampling patients from the Clinical Practice Research Datalink. A cardiovascular disease risk prediction model was developed on this sample and used to generate risk scores for an independent cohort of patients. This process was repeated 1000 times, giving a distribution of risks for each patient. N = 100 000, 50 000, 10 000 and N min (derived from sample size formula) were considered. The 2.5 – 97.5 percentile range of risks across these models was used to evaluate instability. Patients were grouped by a risk derived from a model developed on the entire population (population derived risk) to summarise results. Results For a sample size of 10 000, the median 2.5 – 97.5 percentile range of risks for patients across the 1000 models was approximately 60% of their population derived risk. For example, for patients with a population derived risk of 9 - 10% or 19 - 20%, the median percentile range was 6.25% and 12.59% respectively. Using the formula derived sample size, the range was approximately 170% of their average risk score. Restricting this analysis to models with high discrimination or good calibration reduced the percentile range, but high levels of instability remained. Conclusions Widely used cardiovascular disease risk prediction models suffer from high levels of instability induced by sampling variation. Stability of risk estimates should be a criterion when determining the minimum sample size to develop models.
Molecular Characteristics and Antimicrobial Susceptibility Profile of Pseudomonas aeruginosa isolated from patients attending Healthcare Facilities in Mthatha, South Africa
Authors: Hosu Mojisola C. , Vasaikar Sandeep D. , Okuthe Grace E. , apalata teke 
Published: February 2020

Abstract
Background Pseudomonas aeruginosa is a common pathogen causing healthcare-associated infections most especially in critically ill and immunocompromised patients. This pathogen poses a public health threat due to its innate resistance to many antimicrobial agents and its ability to acquire new resistance mechanisms under pressure. Infections with Extended spectrum β-lactamases (ESBL)-producing isolates result into outbreaks that lead to serious antibiotic management concerns with higher mortality and morbidity and significant economic causatives. In this study, we evaluated the antimicrobial resistance patterns and characterized genetically the ESBLs and Metallo- β-lactamases (MBL) produced by this pathogen. Methods Isolates of P. aeruginosa cultured from patients who attended Nelson Mandela Academic Hospital and other clinics in the four district municipalities of the Eastern Cape between August 2017 and May 2019 were identified; and their antibiotic resistance patterns were tested against amikacin, aztreonam, cefepime, ceftazidime, ciprofloxacin, doripenem, gentamicin, imipenem, levofloxacin, meropenem, piperacillin, piperacillin/tazobactam and tobramycin using the bioMérieux VITEK® 2 and confirmed by Beckman autoSCAN-4 System. Real-time PCR was done using Roche Light Cycler 2.0 to detect the presence of ESBLs; blaSHV, blaTEM and blaCTX-M genes; and MBLs; blaIMP, blaVIM. Results High antibiotic resistance in decreasing order was observed in piperacillin (64.2%), aztreonam (57.8%), cefepime (51.5%), ceftazidime (51.0%), piperacillin/tazobactam (50.5%), and imipenem (46.6%). A total of 75 (36.8%) multidrug resistant (MDR) isolates were observed of the total pool of isolates. The blaTEM, blaSHV and blaCTX-M was detected in 79.3%, 69.5% and 31.7% isolates (n=82), respectively. The blaIMP was detected in 1.25% while no blaVIM was detected in any of the isolates tested. Conclusions The study showed a high rate of MDR P. aeruginosa in our setting. The vast majority of these resistant isolates carried blaTEM and blaSHV genes. Continuous monitoring of antimicrobial resistance and strict compliance towards infection prevention and control practices are the best defence against spread of MDR P. aeruginosa.
Prediction key genes and the potential molecular mechanism for early recurrent pregnancy loss by Multi-Omics analysis
Authors: Huang Le , Wei Changqiang , Zhang Zhao , Cen Jiao , Zhu Zhiwei , Deng Lingjie , Pang Lihong 
Published: February 2020

Abstract
Background: The potential mechanism of early recurrent pregnancy loss (ERPL) has not been fully elucidated, a multi-omics analysis can help us find key genes.Results: We download data from Gene Expression Omnibus (GEO), 90 hypermethylation-down regulated genes and 49 hypomethylation-up regulated genes were identified by intersection. Compared with the normal early pregnancy group, the expression of ERCC2 and MLH1 was lower in ERPL group, but the expression of PLEK and FOS was higher, and the expression of MLH1 was statistically significant (p<0.05). Compared with the anembryonic (empty sac) miscarriage group, the expression of MLH1, PLEK, FOS decreased, and that of ERCC2 increased in the embryonic miscarriage group. TF-MDEGs networks predicted SP1, POLR2A, YY1, CREM and CREB1 were involved in methylation regulation of DNA promoter with MDEGs. Among them, YY1, FOXP3 and p53 may be related to the mechanism of MLH1 in ERPL.Conclusions: Our study identified possible aberrant MDEGs, and TF- MDEGs regulatory networks may be related to its mechanism. MLH1 may play an important role in early embryonic development.
A single mutation in ACTR8 gene results in lineage-specific expression in primates
Authors: Choe Se-Hee , Park Sang-je , Cho Hyeon-Mu , Park Hye-Ri , Lee Ja-Rang , Kim Young-Hyun , Huh Jae-Won 
Published: February 2020

Abstract
Background: Alternative splicing (AS) generate various transcripts from a single gene and thus plays a significant role in transcriptomic diversity and proteomic complexity. Alu elements are primate-specific transposable elements (TEs) and can provide a donor or acceptor site for AS. In a study on TE-mediated AS, we recently identified a novel Alu Sz6-exonized ACTR8 transcript of a crab-eating monkey ( Macaca fascicularis ). In the present study, we sought to analyse the molecular mechanism of Alu Sz6-derived exonization in ACTR8 gene.Results: We performed RT-PCR and genomic PCR using the tissue RNA and DNA samples from the crab-eating monkey and various other primates, including humans, to study Alu Sz6-derived exonization in ACTR8 gene and transcript variants expression. Alu Sz6 integration was estimated to have occurred before the divergence of simians and prosimians. The novel transcript was expressed only in Old world monkeys and apes, and humans. Lineage-specific expression of ACTR8 gene was due to a ‘G’ duplication in the Alu Sz6 sequences of Old world monkey and ape lineages. Six alternative transcripts (TV1-TV6) generated by various AS mechanisms were newly identified. Based on in-silico analysis, the alternative transcripts were transcribed into new isoforms with C-terminus deletion.Conclusion: ‘G’ duplication together with TE exonization and AS via various mechanisms resulted in a different fate of ACTR8 gene expression during primate evolution.
Is the Fibula High in Children and Adolescents with Discoid Lateral Meniscus?
Authors: Jang Woo Young , Lim Chaemoon , Shin Chang Ho , Cho Tae-Joon , Choi In Ho , Yoo Won Joon 
Published: February 2020

Abstract
Background A high fibular location on plain radiographs has been considered suggestive of a discoid lateral meniscus (DLM). We sought to determine whether the high location of the fibular head observed in DLM patients represents a true pathologic finding. Methods Eighty-two patients with symptomatic DLM who underwent arthroscopic treatment constituted the study group (DLM group). The same number of age-matched patients without DLM (control group) were recruited. The DLM group was further divided according to the presence or absence of a knee extension block (EB) of more than 10 degrees into EB(+) and EB(-) subgroups. We defined the compensated distance to the fibular head (CDF) as the distance from the lateral joint line to the tip of the fibular head divided by the femoral condylar width. CDF values measured on anteroposterior (AP) plain radiographs and sagittal MR images were compared between the DLM and control groups and between the EB(+) and EB(-) subgroups. Results There was no significant difference in the mean preoperative CDF value on either AP plain radiographs or sagittal MR images between the DLM and control groups. However, the mean CDF value on AP plain radiographs was significantly lower in the EB(+) subgroup than in the EB(-) subgroup ( p =0.011). The knee EB disappeared in all patients after arthroscopic treatment when the CDF on AP plain radiographs showed no significant difference between subgroups ( p >0.05). Linear regression analysis revealed that the CDF on AP plain radiographs decreased significantly when knee flexion was increased from 0 to 30 degrees ( p =0.003). Conclusions The high fibular location observed on AP plain radiography in DLM patients was associated with limited knee extension. Altered X-ray beam projection to the flexed knee creates the false appearance of a high fibular location on AP plain radiography.
Cancer risk after total hip replacements. A prospective study of 41,402 patients in the Norwegian Arthroplasty Register linked to the Cancer Registry of Norway
Authors: Dybvik Eva , Furnes Ove , Havelin Leif I. , Fosså Sophie D. , Trovik Clement , Lie Stein Atle 
Published: February 2020

Abstract
Background Concerns have been raised that implants used in total hip replacements (THR) could lead to a future increased cancer risk. Several different materials and metals are used in joint prosthesis, as well as different fixation techniques and types of articulation for the surface of the joint can lead to an increased escape of particles or ions into the human body. Methods Patients with THR registered in the Norwegian Arthroplasty Register during 1987-2009 were linked to the Cancer registry of Norway. Patients with THR due to osteoarthritis, under the age of 75 at time of surgery, were included. Standardized incidence ratios (SIR) were applied to compare cancer risk for THR patients to the general population. Types of THR were divided into cemented (both components), uncemented (both components), and hybrid (cemented femoral and uncemented acetabular component). To account for selection mechanisms, time dependent covariates were applied in Cox-regression, adjusting for cancer risk the first 10 years after surgery. The analyses were adjusted for age, gender, and if the patient had additional THR-surgery in the same or the opposite hip. The study is according to the STROBE guidelines.Results When comparing patients with THR to the general population in Norway we found no differences in the risk. The overall SIR for the THR-patients after 10 years of follow-up was 1.02 (95% CI: 0.97-1.07). For cemented THR, the SIR after 10 years of follow-up was 0.99 (95% CI: 0.94-1.05), while it was 1.16 (95% CI: 1.02-1.30) for uncemented THRs, and 1.12 (95% CI: 0.91-1.33) for hybrid THRs. Adjusted Cox analyses showed that patients with uncemented THRs had an elevated risk of cancer (hazard ratio: HR=1.24, 95% CI: 1.05-1.46, p=0.009) when compared to patients with cemented THRs after 10 years of follow-up. The risk for patients with hybrid THRs was not significantly increased (HR=1.07, 95% CI: 0.85-1.35, p=0.55) compared to patients with cemented THRs. Conclusions We found that receiving an uncemented THR was associated with a small increased risk of cancer, in particular prostate cancer for younger men.
Ecological differentiation in Rumex crispus L. natural populations in metal mining areas
Authors: Zhang Yajing , Yang Huaju , Wang Yue , Tang Chundong , Liu Chang'e , Zhao Yonggui , Li Shiyu , Duan Changqun 
Published: February 2020

Abstract
Background: Variations in phenotypic traits of various plants living in either normal or stressed environments have been well studied, but ecological responses of plants to long-term persistent toxic metal pollution have little been reported. In this study, in order to explore the effects of continuous metal pollution in soil on variation and differentiation in the plants, Rumex crispus L. populations exposed to different levels of long-term persistent toxic metal pollution were studied, and corresponding R. crispus populations that had not been exposed to pollution were used as controls. Results: Six phenotypic traits of R. crispus—root diameter, leaf area, leaf length, leaf width, leaf perimeter, and leaf length-to-width ratio—differed significantly among and within populations. Traits ranked in descending order of coefficient of variation were leaf area, leaf perimeter, root diameter, leaf length, leaf width, leaf length-to-width ratio. The average coefficient of variation was 46%. Phenotypic variation in R. crispus was much greater among populations (92.69%) than within populations (6.55%). The mean phenotypic differentiation coefficient (Vst) of 93.37% indicates that the interpopulation variability was the main source of phenotypic variation in R. crispus. Finally, root diameter was significantly positively correlated with metal factors, but leaf area, leaf length, and leaf aspect ratio were significantly negatively correlated with Pb, Zn, Mn, and Fe contents. Overall, underground growth is superior to aboveground growth in populations that have experienced long-term exposure to toxic metal pollution, and there were phenotypic differences between uncontaminated and contaminated populations. Conclusions: These results indicate that R. crispus adapts to the heterogeneous environment caused by toxic metal pollution through rich phenotypic variation, and ecological differentiation has occurred among different populations.
Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in arid environments
Authors: Al-Ashhab Ashraf , Meshner Shiri , Alexander-Shani Rivka , Dimerets Hana , Brandwein Michael , Bar-Lavan Yael , Winters Gidon 
Published: February 2020

Abstract
Background: The evolutionary relationships between plants and their microbiome are of high importance to the survival of plants in extreme conditions. Changes in microbiome of plants can affect plant development, growth and health. Along the arid Arava, southern Israel, acacia trees ( Acacia raddiana and Acacia tortilis ) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate (different areas within the tree canopies) and seasonality on the endophytic and epiphytic microbiome associated with these two tree species. 186 leaf samples were collected along different seasons throughout the year and their microbial communities were studied using the diversity of the 16S rDNA gene sequenced on the 150-PE Illumina sequencing platform. Results: our results showed amplifying V4 region of the 16S rDNA better presented the bacterial communities of both end and epiphytes of Acacia trees than V2, V3 and V5 regions of the 16S r DNA. When comparing the bacterial diversity of endo and epiphytes of the two acacia trees (shannon, choa1, PD and observed number of OTU’s), the epiphytes diversity indices showed about twice higher diversity compared to endophytes. The bacterial community compositions comparing both end and epiphytes were also significantly different. Interestingly, Acacia tortilis (umbral canopy shape) had a higher epiphytes bacterial diversity compared to Acacia raddiana, but were not statistically different. However the endophyte bacterial communities were significantly different compared to the two Acacia species (Firmicutes dominated Acacia raddiana and Proteobacteria dominated the Acacia tortilis ) . Alongside the biotic factor, Abiotic factors such as air temperature and precipitation also showed to significantly effect endo and epiphytes bacterial communities, while air humidity only affected the epiphytes bacterial communities.Conclusions: These results shed light on the unique desert phyllosphere microbiome in mitigating stress conditions highlighting the importance of epiphytic and endophytic microbial communities which are driven by different genotypic and abiotic factors. This paper also shows only a few bacteria species (OTUS’s) to dominate both epi and endophytes highlighting the importance of climate change (precipitation, Air temperature) in affecting arid land ecosystems where acacia trees are considered keystone species in many arid regions.
Self-reported Precipitating Factors for the Development of Eating Disorders in Young Adulthood: A Preliminary Study
Authors: Lenza Cassandra 
Published: February 2020

Abstract
Objective: This study aimed to identify the perceived precipitating factors for seeking eating disorder treatment in the Millennial population. The purpose of this study was to understand the Millennial population, and determine if self-reported causes of eating concerns are different for this age demographic than that of the general population. Method: An exploratory analysis of the charts of one hundred individuals, mainly women, who sought eating disorder treatment at an outpatient eating disorder treatment center, for the period of 2014-2018, was completed. Respondents met the age criteria and were 18-36 years old. Results: The majority of individuals reported beginning dieting behaviors or restricting their food intake as the main cause of their eating disorder (44%). Discussion: Millennial individuals are comparative to the general public when self-reporting precipitating events that lead to the development of an eating disorder. Risk factors inherent to eating disorders, such as early dieting, body dissatisfaction, anxiety, and depression remain the same for this population.
A predict model to evaluate the HbeAg-positive of Chronic Hepatitis B in clinic: a cross-sectional study
Authors: Zheng Jinli , Zhu Yunfeng , Jiang Li 
Published: February 2020

Abstract
Background: The previous studies showed the correlation between HBsAg and serum HBV DNA levels were weak or missing. Objective：The study aims to investigate the correlation between HBeAg and HBV DNA levels, and to find an alternative tool to evaluate the HBV DNA level for clinicians. Methods: We enrolled 1020 patients in this cross-sectional study. We divided the patients into four groups as: HBeAg positivity and negativity groups, high and low HBV DNA levels groups. Further, as to the levels of HBV DNA, we performed subgroups’ in HBeAg-positive and HBeAg-negative groups. Results: Results showed that the ALT, ALB and HBeAg are independent factors to estimate the serum HBV DNA in CHB patients. When the level of HBeAg is higher than 16.15 S/CO, predicting the patient with high levels of HBV DNA and 4 folds to have the high levels of HBV DNA than the HBeAg-negativ. The levels of ALT and TB are the independent risk factors in HBeAg-negative group. Conclusion: HBeAg is an independent factor that reflects the levels of serum HBV DNA with a strong correlation, and we draw a predict model to evaluate the HBV DNA levels as: Y1 (high HBV DNA levels) = 1.412 × (1 for HBeAg-positive >16.15 S/CO or 0 for others) + 0.004 × (1 for ALT > 42.5 U/L or 0 for others) −0.029 × (1 for ALB > 25.5 g/L or 0 for others) + 0.779. For the patients with HBeAg(-), we should evaluate by the levels of ALT and TB, and the predict model is:Y2 (low levels of HBV DNA) = 0.385 − 0.005 × (1 for ALT > 36.5 IU/L or 0 for others) − 0.006 × (1 for TB > 11.15 umol/L or 0 for others).
Inequalities in participation and time spent in moderate-to-vigorous physical activity: analysis using the Health Surveys for England 2008, 2012, and 2016
Authors: Scholes Shaun , Mindell Jennifer S 
Published: March 2020

Abstract
Background
Evidence is unclear on whether inequalities in average levels of moderate-to-vigorous physical activity (MVPA) reflect differences in participation, differences in the amount of time spent active, or both. Using self-reported data from 24,882 adults (Health Survey for England 2008, 2012, 2016), we examined gender-specific inequalities in these separate aspects for total and domain-specific MVPA.
Methods
Hurdle models accommodate continuous data with excess zeros and positive skewness. Such models were used to assess differences between income groups in three aspects: (1) the probability of doing any MVPA, (2) the average hours/week spent in MVPA, and (3) the average hours/week spent in MVPA conditional on participation (MVPA-active). Absolute inequalities were summarised using average marginal effects (AMEs) after confounder adjustment.
Results
Inequalities were robust to adjustment in each aspect for total MVPA and for sports/exercise. Differences between adults in high-income versus low-income households in sports/exercise MVPA were 2.2 hours/week among men (95% confidence interval (CI): 1.6, 2.8) and 1.7 hours/week among women (95% CI: 1.3, 2.1); differences in sports/exercise MVPA-active were 1.3 hours/week (95% CI: 0.4, 2.1) and 1.0 hours/week (95% CI: 0.5, 1.6) for men and women, respectively. Heterogeneity in associations was evident for the other domains. For example, adults in high-income versus low-income households were more likely to do any walking (men: 13.0% (95% CI: 10.3, 15.8%); women: 10.2% (95% CI: 7.6, 12.8%)). Among all adults (including those who did no walking), the average hours/week spent walking showed no difference by income. Among those who did any walking, adults in high-income versus low-income households walked on average 1 hour/week less (men: -0.9 hours/week (95% CI: -1.7, -0.2); women: -1.0 hours/week (95% CI: -1.7, -0.2)).
Conclusions
Participation and the amount of time spent in MVPA typically favours those in high-income households. Monitoring inequalities requires assessing different aspects of the distribution within each domain. Reducing inequalities in sports/exercise requires policy actions and interventions to move adults in low-income households from inactivity to activity, and to enable those already active to do more. Measures to promote walking should focus efforts on reducing the sizeable income gap in the propensity to do any walking.