bluuebunny/crossref_metadata_2025_split huggingface dataset:
National trends in the diagnosis and repair of SLAP lesions in the United States
Authors: Dougherty Mark C , Kulenkamp J Erik , Boyajian Haroutioun , Koh Jason L , Lee Michael J , Shi Lewis L 
Published: December 2019

Background: Since superior labrum anterior-to-posterior (SLAP) tear was introduced as an International Classification of Diseases-Ninth Revision, Clinical Modification diagnosis in 1994, awareness, diagnosis, and surgical treatment of this disorder has increased. Here, we aim to clarify trends in the frequency of SLAP tear diagnosis and arthroscopic SLAP repair surgery in the United States. Methods: Using private insurance claims from 2003 to 2013 in MarketScan (approximately 55 million Americans), we identified patients with SLAP tear diagnosis or arthroscopic SLAP repair surgery. Population-based rates of SLAP diagnosis and related shoulder procedures were calculated. Results: A total of 329,643 patients in the MarketScan database received a SLAP tear diagnosis. In all, 62.8% underwent some form of shoulder surgery after diagnosis. SLAP diagnosis increased from 28.0 per 100,000 in 2003 to 142.4 per 100,000 in 2013 ( p < 0.0001); the rate of shoulder surgery in these patients increased from 20.1 per 100,000 in 2003 to 74.1 per 100,000 in 2013 ( p < 0.0001). However, the percentage of patients with SLAP tears who got shoulder surgery decreased ( p < 0.0001). In 2003, almost no patient got biceps tenodesis for SLAP tears; by 2013, 18.1% of surgeries for SLAP tear were biceps tenodesis. Isolated arthroscopic SLAP repairs peaked in 2009 at 28.4 per 100,000 and stabilized thereafter. Conclusion: We confirmed prior reports that SLAP diagnosis increased from 2003 to 2013, although the percentage of these patients who underwent surgery decreased over this period. Arthroscopic SLAP repair doubled but then plateaued after 2009. Biceps tenodesis now accounts for a substantial portion of surgeries for SLAP tear. This may reflect an improved understanding of superior labrum anatomy and biomechanics.
Analysis of Non-Game Injuries in Major League Baseball
Authors: Esquivel Amanda , Freehill Michael T. , Curriero Frank C. , Rand Kevin L. , Conte Stan , Tedeschi Thomas , Lemos Stephen E. 
Published: December 2019

Background: Numerous studies have investigated injuries and treatments in the baseball athlete. The majority of these studies have focused on the throwing shoulder and elbow. However, more recent literature is reporting injuries to other regions in this cohort, including the knee, head, hip, and hamstring. Purpose/Hypothesis: The purpose of the current study was to determine the number and type of injuries in Major League Baseball (MLB) and Minor League Baseball (MiLB) players that do not occur during the actual game but are related to baseball participation. Our hypothesis was that there would be a substantial number of injuries that occurred in professional baseball players during non-game situations. Study Design: Descriptive epidemiological study. Methods: Deidentified, anonymous data were collected from the 2011 through 2016 seasons from the MLB Health and Injury Tracking System (HITS) medical record database. All injuries that were identified as a primary diagnosis and resulted in at least 1 day out of play from both MLB and MiLB were examined. Injuries were categorized as occurring during the game (“game” injuries) or not during the game. A “non-game” injury was defined as occurring at any time other than during the scheduled game from the first to last pitch. Results: There were 51,548 total injuries in MLB and MiLB players from 2011 to 2016, almost 40% of which were attributed to non–game-related injuries (n = 19,201; 37.2%). The remainder occurred during a game (n = 32,347; 62.8%). A significantly greater percentage of non-game injuries were season ending (10.8%) compared with the percentage of game-related season-ending injuries (8.4%) ( P < .0001). Pitchers had significantly more non–game-related injuries than game-related injuries ( P < .0001). Conclusion: A large number of injuries occur in professional baseball outside of actual games. MiLB players, specifically pitchers, are particularly at risk for these types of injuries. It is feasible that the overall injury rate in professional baseball players could be reduced by analyzing these injuries in more detail to develop prevention strategies.
Design of Split Hexagonal Patch Array Shaped Nano-metaabsorber with Ultra-wideband Absorption for Visible and UV Spectrum Application
Authors: Hoque Ahasanul , Islam Mohammad Tariqul , Almutairi Ali F. , Faruque Mohammad Rashed Iqbal 
Published: December 2019

AbstractSolar energy is one of the ambient sources where energy can be scavenged easily without pollution. Intent scavenging by the solar cell to recollect energy requires a state-of-the-art technique to expedite energy absorption to electron flow for producing more electricity. Structures of the solar cell have been researched to improve absorption efficiency, though most of them can only efficiently absorb with narrow-angle tolerance and polarization sensitivity. So, there is a strong demand for broadband absorption with minimal polarization sensitivity absorber, which is required for effective solar energy harvesting. In this paper, we proposed a new Split Hexagonal Patch Array (SHPA) shape metamaterial absorber with Double-negative (DNG) characteristics, which will provide a wide absorption band with low polarization sensitivity for solar spectrum energy harvesting. The proposed new SHPA shape consists of six nano-arms with a single vertical split which with arrowhead symmetry. This arm will steer electromagnetic (EM) resonance to acquire absolute negative permittivity and permeability, ensuring DNG property. This DNG metamaterial features analyzed based on the photoconversion quantum method for maximum photon absorption. The symmetric characteristics of the proposed structure enable the absorber to show polarization insensitivity and wide incident angle absorption capabilities. Simulated SHPA shows a visible and ultraviolet (UV) spectrum electromagnetic wave absorption capacity of more than 95%. The quantum method gives an advantage in the conversion efficiency of the absorber, and the numerical analysis of the proposed SHPA structure provides absorbance quality for THz regime energy harvesting through solar cell or photonic application.
Efficient computation of stochastic cell-size transient dynamics
Authors: Nieto-Acuna Cesar Augusto , Vargas-Garcia Cesar Augusto , Singh Abhyudai , Pedraza Juan Manuel 
Published: December 2019

Abstract
Background
How small, fast-growing bacteria ensure tight cell-size distributions remains elusive. High-throughput measurement techniques have propelled efforts to build modeling tools that help to shed light on the relationships between cell size, growth and cycle progression. Most proposed models describe cell division as a discrete map between size at birth and size at division with stochastic fluctuations assumed. However, such models underestimate the role of cell size transient dynamics by excluding them.

Results
We propose an efficient approach for estimation of cell size transient dynamics. Our technique approximates the transient size distribution and statistical moment dynamics of exponential growing cells following an adder strategy with arbitrary precision.

Conclusions
We approximate, up to arbitrary precision, the distribution of division times and size across time for the adder strategy in rod-shaped bacteria cells. Our approach is able to compute statistical moments like mean size and its variance from such distributions efficiently, showing close match with numerical simulations. Additionally, we observed that these distributions have periodic properties. Our approach further might shed light on the mechanisms behind gene product homeostasis.
Old drug repositioning and new drug discovery through similarity learning from drug-target joint feature spaces
Authors: Zheng Yi , Peng Hui , Zhang Xiaocai , Zhao Zhixun , Gao Xiaoying , Li Jinyan 
Published: December 2019

AbstractBackgroundDetection of new drug-target interactions by computational algorithms is of crucial value to both old drug repositioning and new drug discovery. Existing machine-learning methods rely only on experimentally validated drug-target interactions (i.e., positive samples) for the predictions. Their performance is severely impeded by the lack of reliable negative samples.ResultsWe propose a method to construct highly-reliable negative samples for drug target prediction by a pairwise drug-target similarity measurement and OCSVM with a high-recall constraint. On one hand, we measure the pairwise similarity between every two drug-target interactions by combining the chemical similarity between their drugs and the Gene Ontology-based similarity between their targets. Then we calculate the accumulative similarity with all known drug-target interactions for each unobserved drug-target interaction. On the other hand, we obtain the signed distance from OCSVM learned from the known interactions with high recall (≥0.95) for each unobserved drug-target interaction. After normalizing all accumulative similarities and signed distances to the range [0,1], we compute the score for each unobserved drug-target interaction via averaging its accumulative similarity and signed distance. Unobserved interactions with lower scores are preferentially served as reliable negative samples for the classification algorithms. The performance of the proposed method is evaluated on the interaction data between 1094 drugs and 1556 target proteins. Extensive comparison experiments using four classical classifiers and one domain predictive method demonstrate the superior performance of the proposed method. A better decision boundary has been learned from the constructed reliable negative samples.ConclusionsProper construction of highly-reliable negative samples can help the classification models learn a clear decision boundary which contributes to the performance improvement.
iProDNA-CapsNet: identifying protein-DNA binding residues using capsule neural networks
Authors: Nguyen Binh P. , Nguyen Quang H. , Doan-Ngoc Giang-Nam , Nguyen-Vo Thanh-Hoang , Rahardja Susanto 
Published: December 2019

Abstract
Background
Since protein-DNA interactions are highly essential to diverse biological events, accurately positioning the location of the DNA-binding residues is necessary. This biological issue, however, is currently a challenging task in the age of post-genomic where data on protein sequences have expanded very fast. In this study, we propose iProDNA-CapsNet – a new prediction model identifying protein-DNA binding residues using an ensemble of capsule neural networks (CapsNets) on position specific scoring matrix (PSMM) profiles. The use of CapsNets promises an innovative approach to determine the location of DNA-binding residues. In this study, the benchmark datasets introduced by Hu et al. (2017), i.e., PDNA-543 and PDNA-TEST, were used to train and evaluate the model, respectively. To fairly assess the model performance, comparative analysis between iProDNA-CapsNet and existing state-of-the-art methods was done.

Results
Under the decision threshold corresponding to false positive rate (FPR) ≈ 5%, the accuracy, sensitivity, precision, and Matthews’s correlation coefficient (MCC) of our model is increased by about 2.0%, 2.0%, 14.0%, and 5.0% with respect to TargetDNA (Hu et al., 2017) and 1.0%, 75.0%, 45.0%, and 77.0% with respect to BindN+ (Wang et al., 2010), respectively. With regards to other methods not reporting their threshold settings, iProDNA-CapsNet also shows a significant improvement in performance based on most of the evaluation metrics. Even with different patterns of change among the models, iProDNA-CapsNets remains to be the best model having top performance in most of the metrics, especially MCC which is boosted from about 8.0% to 220.0%.

Conclusions
According to all evaluation metrics under various decision thresholds, iProDNA-CapsNet shows better performance compared to the two current best models (BindN and TargetDNA). Our proposed approach also shows that CapsNet can potentially be used and adopted in other biological applications.
Deep mixed model for marginal epistasis detection and population stratification correction in genome-wide association studies
Authors: Wang Haohan , Yue Tianwei , Yang Jingkang , Wu Wei , Xing Eric P. 
Published: December 2019

Abstract
Background
Genome-wide Association Studies (GWAS) have contributed to unraveling associations between genetic variants in the human genome and complex traits for more than a decade. While many works have been invented as follow-ups to detect interactions between SNPs, epistasis are still yet to be modeled and discovered more thoroughly.

Results
In this paper, following the previous study of detecting marginal epistasis signals, and motivated by the universal approximation power of deep learning, we propose a neural network method that can potentially model arbitrary interactions between SNPs in genetic association studies as an extension to the mixed models in correcting confounding factors. Our method, namely Deep Mixed Model, consists of two components: 1) a confounding factor correction component, which is a large-kernel convolution neural network that focuses on calibrating the residual phenotypes by removing factors such as population stratification, and 2) a fixed-effect estimation component, which mainly consists of an Long-short Term Memory (LSTM) model that estimates the association effect size of SNPs with the residual phenotype.

Conclusions
After validating the performance of our method using simulation experiments, we further apply it to Alzheimer’s disease data sets. Our results help gain some explorative understandings of the genetic architecture of Alzheimer’s disease.
Modelling the evolution of cognitive styles
Authors: Liedtke Jannis , Fromhage Lutz 
Published: December 2019

Abstract
Background
Individuals consistently differ in behaviour, exhibiting so-called personalities. In many species, individuals differ also in their cognitive abilities. When personalities and cognitive abilities occur in distinct combinations, they can be described as ‘cognitive styles’. Both empirical and theoretical investigations produced contradicting or mixed results regarding the complex interplay between cognitive styles and environmental conditions.

Results
Here we use individual-based simulations to show that, under just slightly different environmental conditions, different cognitive styles exist and under a variety of conditions, can also co-exist. Co-existences are based on individual specialization on different resources, or, more generally speaking, on individuals adopting different niches or microhabitats.

Conclusions
The results presented here suggest that in many species, individuals of the same population may adopt different cognitive styles. Thereby the present study may help to explain the variety of styles described in previous studies and why different, sometimes contradicting, results have been found under similar conditions.
Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle
Authors: Lee Isaiah Paolo A. , Andam Cheryl P. 
Published: December 2019

Abstract
Background
Cronobacter sakazakii is an emerging opportunistic bacterial pathogen known to cause neonatal and pediatric infections, including meningitis, necrotizing enterocolitis, and bacteremia. Multiple disease outbreaks of C. sakazakii have been documented in the past few decades, yet little is known of its genomic diversity, adaptation, and evolution. Here, we analyzed the pan-genome characteristics and phylogenetic relationships of 237 genomes of C. sakazakii and 48 genomes of related Cronobacter species isolated from diverse sources.

Results
The C. sakazakii pan-genome contains 17,158 orthologous gene clusters, and approximately 19.5% of these constitute the core genome. Phylogenetic analyses reveal the presence of at least ten deep branching monophyletic lineages indicative of ancestral diversification. We detected enrichment of functions involved in proton transport and rotational mechanism in accessory genes exclusively found in human-derived strains. In environment-exclusive accessory genes, we detected enrichment for those involved in tryptophan biosynthesis and indole metabolism. However, we did not find significantly enriched gene functions for those genes exclusively found in food strains. The most frequently detected virulence genes are those that encode proteins associated with chemotaxis, enterobactin synthesis, ferrienterobactin transporter, type VI secretion system, galactose metabolism, and mannose metabolism. The genes fos which encodes resistance against fosfomycin, a broad-spectrum cell wall synthesis inhibitor, and mdf(A) which encodes a multidrug efflux transporter were found in nearly all genomes. We found that a total of 2991 genes in the pan-genome have had a history of recombination. Many of the most frequently recombined genes are associated with nutrient acquisition, metabolism and toxin production.

Conclusions
Overall, our results indicate that the presence of a large accessory gene pool, ability to switch between ecological niches, a diverse suite of antibiotic resistance, virulence and niche-specific genes, and frequent recombination partly explain the remarkable adaptability of C. sakazakii within and outside the human host. These findings provide critical insights that can help define the development of effective disease surveillance and control strategies for Cronobacter-related diseases.
Evaluation of peripheral perfusion index and heart rate variability as early predictors for intradialytic hypotension in critically ill patients
Authors: Mostafa Hanan , Shaban Mohamed , Hasanin Ahmed , Mohamed Hassan , Fathy Shymaa , Abdelreheem Hossam M. , Lotfy Ahmed , Abougabal Ayman , Mukhtar Ahmed , El-adawy Akram 
Published: December 2019

AbstractBackgroundIntradialytic hypotension is a serious complication during renal replacement therapy in critically ill patients. Early prediction of intradialytic hypotension could allow adequate prophylactic measures. In this study we evaluated the ability of peripheral perfusion index (PPI) and heart rate variability (HRV) to predict intradialytic hypotension.MethodsA prospective observational study included 36 critically ill patients with acute kidney injury during their first session of intermittent hemodialysis. In addition to basic vital signs, PPI was measured using Radical-7 (Masimo) device. Electrical cardiometry (ICON) device was used for measuring cardiac output, systemic vascular resistance, and HRV. All hemodynamic values were recorded at the following time points: 30 min before the hemodialysis session, 15 min before the start of hemodialysis session, every 5 min during the session, and 15 min after the conclusion of the session. The ability of all variables to predict intradialytic hypotension was assessed through area under receiver operating characteristic (AUROC) curve calculation.ResultsTwenty-three patients (64%) had intradialytic hypotension. Patients with pulmonary oedema showed higher risk for development of intradialytic hypotension {Odds ratio (95% CI): 13.75(1.4–136)}. Each of baseline HRV, and baseline PPI showed good predictive properties for intradialytic hypotension {AUROC (95% CI): 0.761(0.59–0.88)}, and 0.721(0.547–0.857)} respectively.ConclusionsEach of low PPI, low HRV, and the presence of pulmonary oedema are good predictors of intradialytic hypotension.
The prevalence and clinical correlates of adverse childhood experiences in a cross-sectional study of primary care patients with cardiometabolic disease or risk factors
Authors: Maunder Robert G. , Tannenbaum David W. , Permaul Joanne A. , Nutik Melissa , Haber Cleo , Mitri Mira , Costantini Daniela , Hunter Jonathan J. 
Published: December 2019

Abstract
Background
Adverse childhood experiences (ACEs) are associated with risk of poor adult health, including cardiometabolic diseases. Little is known about the correlates of ACEs for adults who have already developed cardiometabolic diseases, or who are at elevated risk.

Methods
Adult primary care patients with cardiometabolic disease (hypertension, diabetes, stroke, angina, myocardial infarction, coronary artery bypass graft, angioplasty) or with a risk factor (obesity, smoking, high cholesterol, family history) were surveyed regarding ACEs, psychological distress, attachment insecurity, quality of life, behavior change goals, stages of change, and attitudes toward potential prevention strategies.

Results
Of 387 eligible patients, 74% completed the ACEs survey. Exposure to ACEs was reported by 174 participants (61%). Controlling for age, gender, relationship status and income, number of ACEs was associated with psychological distress (F = 3.7, p = .01), quality of life (F = 8.9, p = .001), attachment anxiety (F = 3.4, p = .02), drinking alcohol most days (F = 4.0, p = .008) and smoking (F = 2.7, p = .04). Greater ACE exposure was associated with less likelihood of selecting diet or physical activity as a behavior change goal (linear-by-linear association p = .009). Stage of change was not associated with ACEs. ACEs exposure was not related to preferred resources for behavior change.

Conclusions
ACEs are common among patients at cardiometabolic risk and are related to quality of life, psychological factors that influence cardiometabolic outcomes and behavior change goals. ACEs should be taken into account when managing cardiometabolic risk in family medicine.
Improvement of Asia-Pacific colorectal screening score and evaluation of its use combined with fecal immunochemical test
Authors: He Xu-xia , Yuan Si-yi , Li Wen-bin , Yang Hong , Ji Wen , Wang Zhi-qiang , Hao Jian-yu , Chen Chuan , Chen Wei-qing , Gao Ying-xin , Li Ling-bo , Cheng Kai-liang , Qian Jia-ming , Wang Li , Li Jing-nan 
Published: December 2019

Abstract
Background
The Asia-Pacific Colorectal Screening (APCS) score is effective to screen high-risk groups of advanced colorectal neoplasia (ACN) patients but needs revising and can be combined with the fecal immunochemical test (FIT). This paper aimed to improve the APCS score and evaluate its use with the FIT in stratifying the risk of ACN.

Methods
This prospective and multicenter study enrolled 955 and 1201 asymptomatic Chinese participants to form the derivation and validation set, respectively. Participants received the risk factor questionnaire, colonoscopy and FIT. Multiple logistic regression was applied, and C-statistic, sensitivity and negative predictive values (NPVs) were used to compare the screening efficiency.

Results
A modified model was developed incorporating age, body mass index (BMI), family history, diabetes, smoking and drinking as risk factors, stratifying subjects into average risk (AR) or high risk (HR). In the validation set, the HR tier group had a 3.4-fold (95% CI 1.8–6.4) increased risk for ACN. The C-statistic for the modified score was 0.69 ± 0.04, and 0.67 ± 0.04 for the original score. The sensitivity of the modified APCS score combined with FIT for screening ACN high-risk cohorts was 76.7% compared with 36.7% of FIT alone and 70.0% of the modified APCS score alone. The NPVs of the modified score combined with FIT for ACN were 98.0% compared with 97.0% of FIT alone and 97.9% of the modified APCS score alone.

Conclusions
The modified score and its use with the FIT are efficient in selecting the HR group from a Chinese asymptomatic population.