bluuebunny/crossref_metadata_2025_split huggingface dataset:
Health Literacy in Hospital Outpatient Waiting Areas: An Observational Study of What Is Available to and Accessed by Consumers
Authors: McDonald Cassie E. , Remedios Louisa J. , Said Catherine M. , Granger Catherine L. 
Published: September 2020

Aim: To investigate: (1) the types of health information, resources, and supports available to consumers in hospital outpatient waiting areas and (2) whether these are accessed by consumers. Background: Outpatient waiting areas commonly offer health information, resources, and supports to improve the health literacy of waiting consumers. It is not known what is available to or accessed by consumers in hospital outpatient rehabilitation waiting areas. Methods: A multicenter, prospective, observational, cross-sectional study was conducted in the waiting areas of two hospital outpatient rehabilitation services. Direct observations (in person and video recordings) of the waiting areas were used to describe what health information, resources, and supports were available and, if present, what was being accessed and for how long by consumers. Results: Fifteen hours of in-person and video-recorded observations were documented on purpose-designed instruments across the two sites during 18 observation sessions over 8 days. A total of 68 different health information and resources were identified. Approximately half were specifically for consumers (Site 1: 57%; Site 2: 53%). Only seven (10%) were accessed by consumers across both sites. Each resource ( n = 7) was only accessed once. Health resources were used by consumers for 0.8% (3/360 min) of the observation time at each site. Health and social supports and use of other non health resources were also observed. Conclusions: Available health information, resources, and supports were infrequently and briefly accessed by consumers. Further research is required to explore what consumers want and need to improve the health literacy responsiveness of hospital outpatient waiting areas.
Demographics and Epidemiology of Discoid Menisci of the Knee: Analysis of a Large Regional Insurance Database
Authors: Grimm Nathan L. , Pace James Lee , Levy Benjamin J. , Arthur D’Ann , Portman Mark , Solomito Matthew J. , Weiss Jennifer M. 
Published: September 2020

Background: A discoid meniscus is a morphological variant of normal knee joint meniscus shape and ultrastructure that can lead to traumatic tearing of this tissue and early joint osteoarthritis. Purpose/Hypothesis: The purpose of this study was to determine the prevalence of discoid menisci in a large, ethnically diverse regional cohort and to evaluate possible risk factors. The hypothesis was that there would be no difference in the epidemiological distribution of discoid menisci based on ethnicity or sex. Study Design: Descriptive epidemiology study. Methods: The study population was from a regional, integrated health care system cohort from Kaiser Permanente of Southern California that, as of 2016, included more than 4.5 million patients. Patient demographics included age, sex, and ethnicity within this cohort. Potential risk factors analyzed included age, sex, ethnicity, and body mass index (BMI). Unique characteristics of a discoid meniscus were analyzed, including a symptomatic versus asymptomatic meniscus, location of meniscal tear and type of meniscus, and frequency of meniscal surgical treatment. Results: A total of 223 patients with a confirmed discoid meniscus were identified, yielding an overall prevalence rate of 4.88 per 100,000 patients. Those identifying as Black had the lowest prevalence (2.68/100,000), while Hispanic ethnicity had the highest (6.01/100,000). However, there was no significant difference with regard to ethnicity ( P = .283), nor any significant difference between sexes. BMI did not significantly influence the rate of discoid menisci ( P = .504). A majority (77.5%) of patients were symptomatic, while 22.5% of patients with discoid menisci were asymptomatic and discovered incidentally. Symptomatic discoid menisci were more likely to be operated on compared with asymptomatic discoid menisci (71% vs 14%, respectively; P = .001; odds ratio, 14.8 [95% CI, 5.8-37.2]). Horizontal and bucket-handle tears were the more common tear types. Of the discoid menisci in this cohort, 55.6% underwent surgery, with 95.2% undergoing reported saucerization. Conclusion: In this very diverse population-based cohort of patients, there did not seem to be a significant predilection of discoid menisci with regard to ethnicity. Neither sex nor BMI significantly influenced the rate of discoid menisci. More than three-quarters of those with a diagnosed discoid meniscus were symptomatic. Of the tears that occurred with discoid menisci, horizontal and bucket-handle tears made up the largest proportion.
The traffic signal control problem for intersections: a review
Authors: Eom Myungeun , Kim Byung-In 
Published: September 2020

Abstract
Background
The intersection traffic signal control problem (ITSCP) has become even more important as traffic congestion has been more intractable. The ITSCP seeks an efficient schedule for traffic signal settings at intersections with the goal of maximizing traffic flow while considering various factors such as real-time strategies, signal timing constraints, rapid developments in traffic systems, and practical implementation. Since the factors constituting the ITSCP exhibit stochastically complicated interactions, it is essential to identify these factors to propose solution methods that can address this complexity and still be practically implemented.

Objective
The objective of this review is to provide a survey of problems, methods, and practices in the evaluation of the ITSCP. In this paper, a unified terminology for the ITSCP and a citation network of the current body of relevant research are accordingly presented, and various assumptions, constraints, and solution approaches are summarized. A review across the entire body of knowledge throughout the history of the ITSCP is therefore provided. This review also highlights open issues and challenges that remain to be addressed by future research.
NEDD: a network embedding based method for predicting drug-disease associations
Authors: Zhou Renyi , Lu Zhangli , Luo Huimin , Xiang Ju , Zeng Min , Li Min 
Published: September 2020

Abstract
Background
Drug discovery is known for the large amount of money and time it consumes and the high risk it takes. Drug repositioning has, therefore, become a popular approach to save time and cost by finding novel indications for approved drugs. In order to distinguish these novel indications accurately in a great many of latent associations between drugs and diseases, it is necessary to exploit abundant heterogeneous information about drugs and diseases.

Results
In this article, we propose a meta-path-based computational method called NEDD to predict novel associations between drugs and diseases using heterogeneous information. First, we construct a heterogeneous network as an undirected graph by integrating drug-drug similarity, disease-disease similarity, and known drug-disease associations. NEDD uses meta paths of different lengths to explicitly capture the indirect relationships, or high order proximity, within drugs and diseases, by which the low dimensional representation vectors of drugs and diseases are obtained. NEDD then uses a random forest classifier to predict novel associations between drugs and diseases.

Conclusions
The experiments on a gold standard dataset which contains 1933 validated drug–disease associations show that NEDD produces superior prediction results compared with the state-of-the-art approaches.
GPU acceleration of Darwin read overlapper for de novo assembly of long DNA reads
Authors: Ahmed Nauman , Qiu Tong Dong , Bertels Koen , Al-Ars Zaid 
Published: September 2020

Abstract
Background
In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo assembly methods at a large scale in the field. Darwin is a fast and accurate read overlapper that can be used for de novo assembly of state-of-the-art third generation long DNA reads. Darwin is designed to be hardware-friendly and can be accelerated on specialized computer system hardware to achieve higher performance.

Results
This work accelerates Darwin on GPUs. Using real Pacbio data, our GPU implementation on Tesla K40 has shown a speedup of 109x vs 8 CPU threads of an Intel Xeon machine and 24x vs 64 threads of IBM Power8 machine. The GPU implementation supports both linear and affine gap, scoring model. The results show that the GPU implementation can achieve the same high speedup for different scoring schemes.

Conclusions
The GPU implementation proposed in this work shows significant improvement in performance compared to the CPU version, thereby making it accessible for utilization as a practical read overlapper in a DNA assembly pipeline. Furthermore, our GPU acceleration can also be used for performing fast Smith-Waterman alignment between long DNA reads. GPU hardware has become commonly available in the field today, making the proposed acceleration accessible to a larger public. The implementation is available at https://github.com/Tongdongq/darwin-gpu.
Optimal reference genes for gene expression analysis in polyploid of Cyprinus carpio and Carassius auratus
Authors: Liu Wenbin , Yuan Xiudan , Yuan Shuli , Dai Liuye , Dong Shenghua , Liu Jinhui , Peng Liangyue , Wang Minmeng , Tang Yi , Xiao Yamei 
Published: September 2020

Abstract
Background
Reference genes are usually stably expressed in various cells and tissues. However, it was reported that the expression of some reference genes may be distinct in different species. In this study, we intend to answer whether the expression of reported traditional reference genes changes or not in the polyploid fish

Results
By retrieving the mRNA sequencing data of three different ploidy fish from the NCBI SRA database, we selected 12 candidate reference genes, and examined their expression levels in the 10 tissues and in the four cell lines of three different ploidy fish by real-time PCR. Then, the expression profiles of these 12 candidate reference genes were systematically evaluated by using the software platforms: BestKeeper, NormFinder and geNorm.

Conclusion
The 28S ribosomal protein S5 gene (RPS5) and the ribosomal protein S18 gene (RPS18) are the most suitable reference genes for the polyploid of Cyprinus carpio and Carassius auratus, demonstrated by both of the tissues and the cultured cells.
EttA is likely non-essential in Staphylococcus aureus persistence, fitness or resistance to antibiotics
Authors: Meir Michal , Rozenblit Anna , Fliger Simona , Geffen Yuval , Barkan Daniel 
Published: September 2020

Abstract
Background
Tolerance to antibiotics and persistence are associated with antibiotic treatment failures, chronic-relapsing infections, and emerging antibiotic resistance in various bacteria, including Staphylococcus aureus. Mechanisms of persistence are largely unknown, yet have been linked to physiology under low-ATP conditions and the metabolic-inactive state. EttA is an ATP-binding cassette protein, linked in Eschrechia coli to ribosomal hibernation and fitness in stationary growth phase, yet its role in S. aureus physiology is unknown.

Results
Using whole genome sequencing (WGS) of serial clinical isolates, we identified an EttA-negative S. aureus mutant (ettAstop), and its isogenic wild-type counterpart. We used these two isogenic clones to investigate the role of ettA in S. aureus physiology in starvation and antibiotic stress, and test its role in persistence and antibiotic tolerance. ettAstop and its WT counterpart were similar in their antibiotic resistance profiles to multiple antibiotics. Population dynamics of ettAstop and the WT were similar in low-nutrient setting, with similar recovery from stationary growth phase or starvation. Supra-bacteriocidal concentration of cefazolin had the same killing effect on ettAstop and WT populations, with no difference in persister formation.

Conclusions
Lack of ettA does not affect S. aureus antibiotic resistance, beta-lactam tolerance, resilience to starvation or fitness following starvation. We conclude the role of ettA in S. aureus physiology is limited or redundant with another, unidentified gene. WGS of serial clinical isolates may enable investigation of other single genes involved in S. aureus virulence, and specifically persister cell formation.
NGF receptors and PI3K/AKT pathway involved in glucose fluctuation-induced damage to neurons and α-lipoic acid treatment
Authors: Yan Ting , Zhang Zhihui , Li Danqing 
Published: September 2020

AbstractBackgroundGlucose fluctuation promotes neuronal apoptosis, which plays a central role in diabetic encephalopathy (DE). Nerve growth factor (NGF), and its interaction with high-affinity (TrkA) and low-affinity (p75NTR) receptors, are involved in neuronal survival. NGF/TrkA contributes to the activation of the PI3K/AKT pathway, which is beneficial for neuronal survival, and α-Lipoic acid (ALA) exerts clinically favorable neuroprotective effects in the periphery. Whether NGF receptors and the PI3K/AKT pathway are involved in glucose fluctuation-induced neuronal damage, as well as the potential molecular mechanism of ALA in protecting glucose fluctuation-induced neuronal damage, remain unclear.ResultsThe results indicated that constant high glucose (CHG) and intermittent high glucose (IHG) significantly increased the expression of Bax and caspase-3, and decreased the expression of TrkA/p75NTR and p-AKT/AKT, while ALA stimulation reversed the above proteins in PC12 cells. IHG stimulates apoptosis more effectively than CHG in PC12 cells, which is related to the PI3K/AKT pathway but not to the TrkA/p75NTR. Furthermore, neuronal apoptosis induced by IHG was aggravated by the TrkA inhibitor K252a or the PI3K/AKT inhibitor LY294002, but this effect was alleviated by the p75NTR inhibitor TAT-pep5.ConclusionGlucose fluctuation induced cell apoptosis by regulating the TrkA/p75NTR and PI3K/AKT pathway, meanwhile ALA exhibited neuroprotective effects in response to IHG and CHG. These observations indicated that the PI3K/AKT pathway and the balance of TrkA/p75NTR are likely to serve as potential therapeutic targets for DE. In addition, ALA could be a possible therapeutic drug for DE.
Predictive scoring models for persistent gram-negative bacteremia that reduce the need for follow-up blood cultures: a retrospective observational cohort study
Authors: Jung Jongtak , Song Kyoung-Ho , Jun Kang Il. , Kang Chang Kyoung , Kim Nak-Hyun , Choe Pyoeng Gyun , Park Wan Beom , Bang Ji Hwan , Kim Eu Suk , Park Sang-Won , Kim Nam Joong , Oh Myoung-don , Kim Hong Bin 
Published: September 2020

Abstract
Background
Although the risk factors for positive follow-up blood cultures (FUBCs) in gram-negative bacteremia (GNB) have not been investigated extensively, FUBC has been routinely carried out in many acute care hospitals. We attempted to identify the risk factors and develop a predictive scoring model for positive FUBC in GNB cases.

Methods
All adults with GNB in a tertiary care hospital were retrospectively identified during a 2-year period, and GNB cases were assigned to eradicable and non-eradicable groups based on whether removal of the source of infection was possible. We performed multivariate logistic analyses to identify risk factors for positive FUBC and built predictive scoring models accordingly.

Results
Out of 1473 GNB cases, FUBCs were carried out in 1268 cases, and the results were positive in 122 cases. In case of eradicable source of infection, we assigned points according to the coefficients from the multivariate logistic regression analysis: Extended spectrum beta-lactamase-producing microorganism (+ 1 point), catheter-related bloodstream infection (+ 1), unfavorable treatment response (+ 1), quick sequential organ failure assessment score of 2 points or more (+ 1), administration of effective antibiotics (− 1), and adequate source control (− 2). In case of non-eradicable source of infection, the assigned points were end-stage renal disease on hemodialysis (+ 1), unfavorable treatment response (+ 1), and the administration of effective antibiotics (− 2). The areas under the curves were 0.861 (95% confidence interval [95CI] 0.806–0.916) and 0.792 (95CI, 0.724–0.861), respectively. When we applied a cut-off of 0, the specificities and negative predictive values (NPVs) in the eradicable and non-eradicable sources of infection groups were 95.6/92.6% and 95.5/95.0%, respectively.

Conclusions
FUBC is commonly carried out in GNB cases, but the rate of positive results is less than 10%. In our simple predictive scoring model, zero scores—which were easily achieved following the administration of effective antibiotics and/or adequate source control in both groups—had high NPVs. We expect that the model reported herein will reduce the necessity for FUBCs in GNB cases.
A de novo synonymous variant in EFTUD2 disrupts normal splicing and causes mandibulofacial dysostosis with microcephaly: case report
Authors: Jacob Arthur , Pasquier Jennifer , Carapito Raphael , Auradé Frédéric , Molitor Anne , Froguel Philippe , Fakhro Khalid , Halabi Najeeb , Viot Géraldine , Bahram Seiamak , Rafii Arash 
Published: September 2020

AbstractBackgroundMandibulofacial dysostosis with microcephaly (MFDM) is a rare autosomal dominant genetic disease characterized by intellectual and growth retardations, as well as major microcephaly, induced by missense and splice site variants or microdeletions in theEFTUD2gene.Case presentationHere, we investigate the case of a young girl with symptoms of MFDM and a normal karyotype. Whole-exome sequencing of the family was performed to identify genetic alterations responsible for this phenotype. We identified a de novo synonymous variant in theEFTUD2gene. We demonstrated that this synonymous variant disrupts the donor splice-site in intron 9 resulting in the skipping of exon 9 and a frameshift that leads to a premature stop codon.ConclusionsWe present the first case of MFDM caused by a synonymous variant disrupting the donor splice site, leading to exon skipping.
Whole-exome sequencing reveals ANO8 as a genetic risk factor for intrahepatic cholestasis of pregnancy
Authors: Liu Xianxian , Lai Hua , Zeng Xiaoming , Xin Siming , Nie Liju , Liang Zhenyi , Wu Meiling , Chen Yu , Zheng Jiusheng , Zou Yang 
Published: September 2020

Abstract
Background
Intrahepatic cholestasis of pregnancy (ICP) is characterized by pruritus and cholestasis in late pregnancy and results in adverse pregnancy outcomes, including preterm delivery and birth weight, which are affected by the genetic and environmental background. However, until now, the genetic architecture of ICP has remained largely unclear.

Methods
Twenty-six clinical data points were recorded for 151 Chinese ICP patients. The data generated from whole-exome sequencing (WES) using the BGISEQ-500 platform were further analyzed by Burrows-Wheeler Aligner (BWA) software, Genome Analysis Toolkit (GATK), ANNOVAR tool, etc. R packages were used to conduct t-test, Fisher’s test and receiver operating characteristic (ROC) curve analyses.

Results
We identified eighteen possible pathogenic loci associated with ICP disease in known genes, covering ABCB4, ABCB11, ATP8B1 and TJP2. The loci Lys386Gln, Gly527Gln and Trp708Ter in ABCB4, Leu589Met, Gln605Pro and Gln1194Ter in ABCB11, and Arg189Ser in TJP2 were novel discoveries. In addition, WES analysis indicated that the gene ANO8 involved in the transport of bile salts is newly identified as associated with ICP. The functional network of the ANO8 gene confirmed this finding. ANO8 contained 8 rare missense mutations that were found in eight patients among the 151 cases and were absent from 1029 controls. Out of the eight SNPs, 3 were known, and the remaining five are newly identified. These variants have a low frequency, ranging from 0.000008 to 0.00001 in the ExAC, gnomAD – Genomes and TOPMED databases. Bioinformatics analysis showed that the sites and their corresponding amino acids were both highly conserved among vertebrates. Moreover, the influences of all the mutations on protein function were predicted to be damaging by the SIFT tool. Combining clinical data, it was found that the mutation group (93.36 µmol/L) had significantly (P = 0.038) higher total bile acid (TBA) levels than the wild-type group (40.81 µmol/L).

Conclusions
To the best of our knowledge, this is the first study to employ WES technology to detect genetic loci for ICP. Our results provide new insights into the genetic basis of ICP and will benefit the final identification of the underlying mutations.
Exploring health literacy in Wuhan, China: a cross-sectional analysis
Authors: Mei Xin , Zhong Qing , Chen Gong , Huang Yuanxia , Li Junlin 
Published: September 2020

Abstract
Background
In recent years, research on health literacy has become increasingly focused on the health care system and public health. This cross-sectional study aimed to investigate health literacy and analyse the risk factors that affect health literacy in Wuhan, China.

Methods
Multistage stratified random sampling was used to select 5304 urban and rural residents aged 15 to 69 years from 204 monitoring points in 15 districts of Wuhan. Using the Chinese Citizen Health Literacy Questionnaire (HLQ) (2018 edition), a face-to-face survey was conducted from November to December 2018. Risk factors that may affect health literacy were assessed using the Chi-square test and multivariate logistic regression models.

Results
The knowledge rate of health literacy was relatively low (19.3%). The knowledge rate of health-related behaviour and lifestyle (BAL, 17.3%) was the lowest of the three aspects of health literacy, and the knowledge rate of chronic diseases (CD, 19.0%) was the lowest of the six dimensions of health literacy. Respondents who lived in urban areas, had higher education levels, worked as medical staff, had a higher household income and did not suffer from chronic diseases were likely to have higher health literacy.

Conclusions
The health literacy levels of citizens in Wuhan are insufficient and need to improve.