bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sacral Agenesis: A Neglected Deformity That Increases the Incidence of Postoperative Coronal Imbalance in Congenital Lumbosacral Deformities
Authors: Zhang Tianyuan , Shu Shibin , Jing Wenting , Gu Qi , Liu Zhen , Sun Xu , Wang Bin , Qiu Yong , Zhu Zezhang , Bao Hongda 
Published: November 2020

Study Design: A retrospective study. Objectives: To identify if there is a link between sacral agenesis (SA) and post-operative coronal imbalance in patients with congenital lumbosacral deformities. Methods: This study reviewed a consecutive series of patients with congenital lumbosacral deformities. They had a minimum follow-up of 2 years. According to different diagnosis, they were divided into SA and non-SA group. Comparison analysis was performed between patients with and without post-operative coronal imbalance and risk factors were identified. Results: A total of 45 patients (18 in SA group and 27 in non-SA group) were recruited into this study, among whom 33 patients maintained coronal balance while 12 demonstrated postoperative coronal imbalance at last follow-up (14.32 ± 7.67 mm vs 35.53 ± 3.91 mm, P < 0.001). Univariate analysis showed that preoperative lumbar Cobb angle, immediate postoperative coronal balance distance and diagnosis of SA were significantly different between patients with and without post-operative coronal imbalance (P < 0.05). Binary logistic regression analysis showed that SA was an independent risk factor for postoperative coronal imbalance. Conclusions: As an independent risk factor for postoperative coronal imbalance, high level of suspicion of SA should be aware in children with congenital lumbosacral deformities. Sufficient bone grafts at sacroiliac joint are recommended for SA patients to prevent postoperative coronal imbalance.
A Rare Case of Brugada Phenocopy in A Patient With Takotsubo Cardiomyopathy Masquerading as an Acute Coronary Syndrome
Authors: Mahadevappa Manjappa , Kulkarni Prashanth , KS Poornima 
Published: November 2020

Brugada phenocopies (BrP) are clinical entities that are etiologically distinct from true congenital Brugada syndrome. BrP are characterized by type 1 or 2 Brugada electrocardiogram (ECG) patterns in precordial leads V1-V3. However, BrP is elicited by various underlying clinical conditions such as myocardial ischemia, pulmonary embolism, electrolyte abnormalities, or poor ECG filters. Upon resolution of the inciting underlying pathological condition, the BrP ECG subsequently normalizes. Takotsubo (octopus fishing pot) cardiomyopathy (TCM) also known as stress cardiomyopathy is an acute cardiac condition characterized by transient systolic dysfunction of the left ventricular apex and mid-ventricle with depressed LV function mimicking acute coronary syndrome (ACS) and recovers within a few weeks. TCM is most commonly seen in postmenopausal women with intense physical and or emotional stress. We are reporting a rare case of BrP in a patient with TCM masquerading as ACS posing a diagnostic and therapeutic challenge.
Management of ureteric avulsion during ureteroscopy: a systematic review and our experience
Authors: Shekar P. Ashwin , Kochhar Gaurav , Reddy Dinesh , Dumra Anuj 
Published: November 2020

Abstract
Background
Ureteric avulsion is a disastrous intraoperative complication that can happen to any urologist during a common endoscopic procedure like ureteroscopy. The aim of this study is to evaluate the various management options of ureteric avulsion during ureteroscopy and also report our relevant experience in this topic.

Results
The Preferred Reporting Items for Systematic Reviews and Meta-Analyses of existing literature in English language was used in the period 1967–2019 with a literature search in PubMed, Cochrane Library and Google Scholar. Forty-three patients in twenty-three articles who had undergone management of ureteric avulsion during ureteroscopy were identified for review. There were 15 proximal, 19 two-point (“scabbard”) and 9 distal avulsions. All distal avulsions were managed successfully with ureteroneocystostomies or Boari flaps. Boari flaps and ureteropyelostomy with ureterovesicostomy were the common procedures used for proximal avulsions. Proximal avulsions had more varied outcomes with salvage rates of 86.9%. Procedures which incorporated the avulsed distal ureter for reconstruction had poor results.

Conclusion
Management of ureteric avulsion during ureteroscopy is a surgical challenge. While management of distal avulsions is straightforward in the form of ureteroneocystostomies and has uniformly good results in most hands, proximal avulsions need expertise in management and choosing ideal reconstruction, with variable results following reconstruction. Extended Boari flaps, ileal ureter and autotransplantation are good options for proximal avulsions. Reconstruction using the distal avascular ureter should be avoided for better long-term results.
GODoc: high-throughput protein function prediction using novel k-nearest-neighbor and voting algorithms
Authors: Liu Yi-Wei , Hsu Tz-Wei , Chang Che-Yu , Liao Wen-Hung , Chang Jia-Ming 
Published: November 2020

Abstract
Background
Biological data has grown explosively with the advance of next-generation sequencing. However, annotating protein function with wet lab experiments is time-consuming. Fortunately, computational function prediction can help wet labs formulate biological hypotheses and prioritize experiments. Gene Ontology (GO) is a framework for unifying the representation of protein function in a hierarchical tree composed of GO terms.

Results
We propose GODoc, a general protein GO prediction framework based on sequence information which combines feature engineering, feature reduction, and a novel ​k​-nearest-neighbor algorithm to resolve the multiple GO prediction problem. Comprehensive evaluation on CAFA2 shows that GODoc performs better than two baseline models. In the CAFA3 competition (68 teams), GODoc ranks 10th in Cellular Component Ontology. Regarding the species-specific task, the proposed method ranks 10th and 8th in the eukaryotic Cellular Component Ontology and the prokaryotic Molecular Function Ontology, respectively. In the term-centric task, GODoc performs third and is tied for first for the biofilm formation of Pseudomonas aeruginosa and the long-term memory of Drosophila melanogaster, respectively.

Conclusions
We have developed a novel and effective strategy to incorporate a training procedure into the k-nearest neighbor algorithm (instance-based learning) which is capable of solving the Gene Ontology multiple-label prediction problem, which is especially notable given the thousands of Gene Ontology terms.
MADA: a web service for analysing DNA methylation array data
Authors: Hu Xinyu , Tang Li , Wang Linconghua , Wu Fang-Xiang , Li Min 
Published: November 2020

Abstract
Background
DNA methylation in the human genome is acknowledged to be widely associated with biological processes and complex diseases. The Illumina Infinium methylation arrays have been approved as one of the most efficient and universal technologies to investigate the whole genome changes of methylation patterns. As methylation arrays may still be the dominant method for detecting methylation in the anticipated future, it is crucial to develop a reliable workflow to analysis methylation array data.

Results
In this study, we develop a web service MADA for the whole process of methylation arrays data analysis, which includes the steps of a comprehensive differential methylation analysis pipeline: pre-processing (data loading, quality control, data filtering, and normalization), batch effect correction, differential methylation analysis, and downstream analysis. In addition, we provide the visualization of pre-processing, differentially methylated probes or regions, gene ontology, pathway and cluster analysis results. Moreover, a customization function for users to define their own workflow is also provided in MADA.

Conclusions
With the analysis of two case studies, we have shown that MADA can complete the whole procedure of methylation array data analysis. MADA provides a graphical user interface and enables users with no computational skills and limited bioinformatics background to carry on complicated methylation array data analysis. The web server is available at: http://120.24.94.89:8080/MADA
TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification
Authors: Tang Yunxia , Wang Yu , Wang Jiaqian , Li Miao , Peng Linmin , Wei Guochao , Zhang Yixing , Li Jin , Gao Zhibo 
Published: November 2020

Abstract
Background
Neoantigen-based personal vaccines and adoptive T cell immunotherapy have shown high efficacy as a cancer treatment in clinical trials. Algorithms for the accurate prediction of neoantigens have played a pivotal role in such studies. Some existing bioinformatics methods, such as MHCflurry and NetMHCpan, identify neoantigens mainly through the prediction of peptide-MHC binding affinity. However, the predictive accuracy of immunogenicity of these methods has been shown to be low. Thus, a ranking algorithm to select highly immunogenic neoantigens of patients is needed urgently in research and clinical practice.

Results
We develop TruNeo, an integrated computational pipeline to identify and select highly immunogenic neoantigens based on multiple biological processes. The performance of TruNeo and other algorithms were compared based on data from published literature as well as raw data from a lung cancer patient. Recall rate of immunogenic ones among the top 10-ranked neoantigens were compared based on the published combined data set. Recall rate of TruNeo was 52.63%, which was 2.5 times higher than that predicted by MHCflurry (21.05%), and 2 times higher than NetMHCpan 4 (26.32%). Furthermore, the positive rate of top 10-ranked neoantigens for the lung cancer patient were compared, showing a 50% positive rate identified by TruNeo, which was 2.5 times higher than that predicted by MHCflurry (20%).

Conclusions
TruNeo, which considers multiple biological processes rather than peptide-MHC binding affinity prediction only, provides prioritization of candidate neoantigens with high immunogenicity for neoantigen-targeting personalized immunotherapies.
Social engagement within the facility increased life expectancy in nursing home residents: a follow-up study
Authors: Pastor-Barriuso Roberto , Padrón-Monedero Alicia , Parra-Ramírez Lina M. , García López Fernando J. , Damián Javier 
Published: November 2020

Abstract
Background
Social engagement (SE) has been consistently shown to improve survival among community-dwelling older people, but the evidence in nursing home residents is inconclusive and prone to short-term reverse causation and confounding by major health determinants. Our main objective was to study the potential causal effect of within-the-facility social engagement (SE) on long-term all-cause mortality in care home residents.

Methods
A representative cohort of 382 nursing home residents in Madrid without severe physical and cognitive impairments at baseline was followed up for 10-year all-cause mortality. Standardized mortality curves for residents with low/null, moderate, and high levels of SE at baseline were estimated using Kaplan-Meier methods and spline-based survival models with inverse probability of exposure weights conditional on baseline sociodemographic characteristics, facility features, comorbidity, and disability. Standardized 5-year mortality risks and median survival times were compared across levels of SE.

Results
The baseline prevalences of low/null, moderate, and high SE were 36, 44, and 20%, respectively. Compared with residents with low/null SE at baseline, the standardized differences (95% confidence intervals) in 5-year mortality risk were − 2.3% (− 14.6 to 10.0%) for moderately engaged residents and − 18.4% (− 33.8 to − 2.9%) for highly engaged residents. The median survival time increased by 0.4 (− 1.4 to 2.2) and 3.0 (0.8 to 5.2) years, respectively.

Conclusion
Residents with high SE within the nursing home had an 18% lower 5-year mortality risk and a 3-year increase in their median survival, as compared with residents with similar health determinants but low/null SE. The development of adequate tailored intervention programs, addressed to increase SE in nursing home residents, could improve their long-term survival, in addition to expected gains in quality of life.
Association between length of residence and prevalence of MRSA colonization among residents in geriatric long-term care facilities
Authors: Sasahara Teppei , Ae Ryusuke , Yoshimura Akio , Kosami Koki , Sasaki Kazumasa , Kimura Yumiko , Akine Dai , Ogawa Masanori , Hamabata Kenji , Hatakeyama Shuji , Cui Longzhu 
Published: November 2020

Abstract
Background
A high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) colonization has been reported among residents in geriatric long-term care facilities (LTCFs). Some studies indicate that MRSA might be imported from hospitals into LTCFs via resident transfer; however, other studies report that high MRSA prevalence might be caused by cross-transmission inside LTCFs. We aimed to assess which factors have a large impact on the high MRSA prevalence among residents of geriatric LTCFs.

Methods
We conducted a cohort study among 260 residents of four geriatric LTCFs in Japan. Dividing participants into two cohorts, we separately analyzed (1) the association between prevalence of MRSA carriage and length of LTCF residence (Cohort 1: n = 204), and (2) proportion of residents identified as MRSA negative who were initially tested at admission but subsequently identified as positive in secondary testing performed at ≥2 months after their initial test (Cohort 2: n = 79).

Results
Among 204 residents in Cohort 1, 20 (9.8%) were identified as positive for MRSA. Compared with residents identified as MRSA negative, a larger proportion of MRSA-positive residents had shorter periods of residence from the initial admission (median length of residence: 5.5 vs. 2.8 months), although this difference was not statistically significant (p = 0.084). Among 79 residents in Cohort 2, 60 (75.9%) were identified as MRSA negative at the initial testing. Of these 60 residents, only one (1.7%) had subsequent positive conversion in secondary MRSA testing. In contrast, among 19 residents identified as MRSA positive in the initial testing, 10 (52.6%) were negative in secondary testing.

Conclusions
The prevalence of MRSA was lower among residents with longer periods of LTCF residence than among those with shorter periods. Furthermore, few residents were found to become MRSA carrier after their initial admission. These findings highlight that MRSA in LTCFs might be associated with resident transfer rather than spread via cross-transmission inside LTCFs.
Proposal of COVID-19 Clinical Risk Score for the management of suspected COVID-19 cases: a case control study
Authors: Nakakubo Sho , Suzuki Masaru , Kamada Keisuke , Yamashita Yu , Nakamura Junichi , Horii Hiroshi , Sato Kazuki , Matsumoto Munehiro , Abe Yuki , Tsuji Kosuke , Ishiguro Nobuhisa , Nasuhara Yasuyuki , Konno Satoshi 
Published: November 2020

AbstractBackgroundNo clinical scoring system has yet been established to estimate the likelihood of coronavirus disease (COVID-19) and determine the suitability of diagnostic testing in suspected COVID-19 patients.MethodsThis was a single-center, retrospective, observational study of patients with suspected COVID-19 and confirmed COVID-19. Patient background, clinical course, laboratory and computed tomography (CT) findings, and the presence of alternative diagnoses were evaluated. Clinical risk scores were developed based on clinical differences between patients with and without COVID-19.ResultsAmong 110 patients suspected of having COVID-19, 60.9% underwent polymerase chain reaction (PCR) testing based on the judgment of physicians. Two patients were found to have COVID-19. The clinical characteristics of 108 non-COVID-19 patients were compared with those of 23 confirmed COVID-19 patients. Patients with COVID-19 were more likely to have a history of high-risk exposures and an abnormal sense of taste and smell. The COVID-19 group had significantly higher rates of subnormal white blood cell counts, lower eosinophil counts, and lower procalcitonin levels than the non-COVID-19 group. When blood test results, CT findings, and the presence of alternative diagnoses were scored on an 11-point scale (i.e., “COVID-19 Clinical Risk Score”), the COVID-19 group scored significantly higher than the non-COVID-19 group, more than four points in the COVID-19 group. All non-COVID patients who did not undergo PCR had a score of 4 or less.ConclusionsThe COVID-19 Clinical Risk Score may enable the risk classification of patients suspected of having COVID-19 and can help in decision-making in clinical practice, including appropriateness of diagnostic testing. Further studies and prospective validation with an increased sample size are required.
A comprehensive multivariate model of biopsychosocial factors associated with opioid misuse and use disorder in a 2017–2018 United States national survey
Authors: Montiel Ishino Francisco A. , McNab Philip R. , Gilreath Tamika , Salmeron Bonita , Williams Faustine 
Published: November 2020

AbstractBackgroundFew studies have comprehensively and contextually examined the relationship of variables associated with opioid use. Our purpose was to fill a critical gap in comprehensive risk models of opioid misuse and use disorder in the United States by identifying the most salient predictors.MethodsA multivariate logistic regression was used on the 2017 and 2018 National Survey on Drug Use and Health, which included all 50 states and the District of Columbia of the United States. The sample included all noninstitutionalized civilian adults aged 18 and older (N = 85,580; weightedN = 248,008,986). The outcome of opioid misuse and/or use disorder was based on reported prescription pain reliever and/or heroin use dependence, abuse, or misuse. Biopsychosocial predictors of opioid misuse and use disorder in addition to sociodemographic characteristics and other substance dependence or abuse were examined in our comprehensive model. Biopsychosocial characteristics included socioecological and health indicators. Criminality was the socioecological indicator. Health indicators included self-reported health, private health insurance, psychological distress, and suicidality. Sociodemographic variables included age, sex/gender, race/ethnicity, sexual identity, education, residence, income, and employment status. Substance dependence or abuse included both licit and illicit substances (i.e., nicotine, alcohol, marijuana, cocaine, inhalants, methamphetamine, tranquilizers, stimulants, sedatives).ResultsThe comprehensive model found that criminality (adjusted odds ratio [AOR] = 2.58, 95% confidence interval [CI] = 1.98–3.37,p < 0.001), self-reported health (i.e., excellent compared to fair/poor [AOR = 3.71, 95% CI = 2.19–6.29,p < 0.001], good [AOR = 3.43, 95% CI = 2.20–5.34, p < 0.001], and very good [AOR = 2.75, 95% CI = 1.90–3.98,p < 0.001]), no private health insurance (AOR = 2.12, 95% CI = 1.55–2.89,p < 0.001), serious psychological distress (AOR = 2.12, 95% CI = 1.55–2.89,p < 0.001), suicidality (AOR = 1.58, 95% CI = 1.17–2.14,p = 0.004), and other substance dependence or abuse were significant predictors of opioid misuse and/or use disorder. Substances associated were nicotine (AOR = 3.01, 95% CI = 2.30–3.93,p < 0.001), alcohol (AOR = 1.40, 95% CI = 1.02–1.92,p = 0.038), marijuana (AOR = 2.24, 95% CI = 1.40–3.58,p = 0.001), cocaine (AOR = 3.92, 95% CI = 2.14–7.17,p < 0.001), methamphetamine (AOR = 3.32, 95% CI = 1.96–5.64,p < 0.001), tranquilizers (AOR = 16.72, 95% CI = 9.75–28.65,p < 0.001), and stimulants (AOR = 2.45, 95% CI = 1.03–5.87,p = 0.044).ConclusionsBiopsychosocial characteristics such as socioecological and health indicators, as well as other substance dependence or abuse were stronger predictors of opioid misuse and use disorder than sociodemographic characteristics.
Joint association of physical work demands and leg pain intensity for work limitations due to pain in senior workers: cross-sectional study
Authors: Skovlund Sebastian Venge , Bláfoss Rúni , Sundstrup Emil , Thomassen Kristina , Andersen Lars L. 
Published: November 2020

AbstractBackgroundLeg pain, especially of the knees and hips, is common among senior workers and may limit the ability to perform physically demanding work. In light of the aging workforce, this study determined the joint association of physical work demands and leg pain intensity for work-limiting pain in senior workers.MethodsCurrently employed senior workers (≥50 years) participated in the SeniorWorkingLife study in 2018 (n = 12,879). Associations between the combination of physical work demands and leg pain intensity (interaction) with work-limiting pain (outcome) were modeled using binary logistic regression analyses while controlling for potential covariates.ResultsWe found a significant interaction (P < 0.001) between physical work demands and leg pain intensity for work-limiting pain. The combination of higher physical work demands and higher leg pain intensity had the worst outcome in terms of the odds of experiencing work-limiting pain. For example, 70% of those with the combination of high physical work demands and leg pain intensity ≥7 (scale 0–10) experienced that the pain limited them to at least some degree in their work.ConclusionsThe combination of high physical work demands and high leg pain intensity are associated with limited ability to perform work among senior workers. These findings highlight the importance of prioritizing the physical work environment in physically demanding occupations, particularly among senior workers, for prolonging working life. Thus, adjusting the work demands, e.g. through use of assistive devices, and lowering the pain, e.g. through physical rehabilitation, may be necessary to sustain work ability to a high age in this group of workers.Trial registrationThis was registered as a cohort study in ClinicalTrials.gov (Identifier:NCT03634410) on the 18th of August 2018 (Retrospectively registered).