bluuebunny/crossref_metadata_2025_split huggingface dataset:
High Rate of Return to Running for Athletes After Hip Arthroscopy for the Treatment of Femoroacetabular Impingement and Capsular Plication
Authors: Levy David M. , Kuhns Benjamin D. , Frank Rachel M. , Grzybowski Jeffrey S. , Campbell Kirk A. , Brown Sara , Nho Shane J. 
Published: September 2016

Background: Femoroacetabular impingement (FAI) is most commonly diagnosed in athletes who sustain repetitive flexion loading to their hips. No studies to date have focused solely on patients’ return-to-running ability after hip arthroscopy. Purpose: To evaluate patients’ ability to return to running after hip arthroscopy for FAI and capsular plication. Study Design: Case series; Level of evidence, 4. Methods: Clinical data were retrospectively retrieved for 51 consecutive patients with FAI (22 men, 29 women) who had undergone hip arthroscopy for the treatment of FAI and identified themselves as recreational or competitive runners on intake forms. Two-year outcome measures included the modified Harris Hip Score (mHHS) and the Hip Outcome Score Activities of Daily Living (HOS-ADL) and Sport-Specific (HOS-SS) subscales. A postoperative return-to-running survey was used to obtain running-specific information. Results: Patient age and body mass index (BMI) were a mean (±SD) of 26.3 ± 7.8 years and 23.7 ± 3.3 kg/m2, respectively. Before surgery, patients had refrained from running because of pain for a mean of 8.1 ± 5.7 months. After surgery, 48 patients (94%) returned to running at a mean of 8.5 ± 4.2 months. Patients who had discontinued running for more than 8 months before surgery had a longer return-to-running time than did those who had stopped for less than 8 months (10.6 ± 4.2 vs 7.6 ± 4.1 months; P = .01). After 2 years, mean preoperative distance had decreased significantly ( P < .01) from 9.5 ± 6.5 miles per week when healthy to 6.4 ± 5.8 miles postoperatively. Despite decreased mileage, all 2-year outcomes scores improved significantly ( P < .001). Conclusion: Recreational and competitive runners with FAI returned to running 94% of the time at a mean of 8.5 months after hip arthroscopy. However, runners should be counseled before their surgery that they may run fewer miles than when they were pain free. Additionally, patients with a higher BMI and/or longer preoperative lull may have a longer recovery time.
Nursing’s professional respect as experienced by hospital and community nurses
Authors: Stievano Alessandro , Bellass Sue , Rocco Gennaro , Olsen Douglas , Sabatino Laura , Johnson Martin 
Published: September 2016

Background: There is growing awareness that patient care suffers when nurses are not respected. Therefore, to improve outcomes for patients, it is crucial that nurses operate in a moral work environment that involves both recognition respect, a form of respect that ought to be accorded to every single person, and appraisal respect, a recognition of the relative and contingent value of respect modulated by the relationships of the healthcare professionals in a determined context. Research question/aim: The purpose of this study was to develop better understandings of perceptions of nursing’s professional respect in community and hospital settings in England. Research design: The research design was qualitative. Focus groups were chosen as the most appropriate method for eliciting discussion about nursing’s professional respect. Participants and research context: A total of 62 nurses who had been qualified for at least a year and were working in two localities in England participated in this study. Methods: Data were collected using 11 focus group sessions. The data were analysed by means of an inductive content analysis, extracting meaning units from the information retrieved and classifying the arising phenomena into conceptually meaningful categories and themes. Ethical considerations: To conduct the research, permission was obtained from the selected universities. Results: Recognition respect of human beings was perceived as ingrained in the innermost part of nurses. Regarding appraisal respect, a great importance was placed on: the interactions among healthcare professionals, the time to build trust in these relationships, the influences of the workplace characteristics and nurses’ professional autonomy and decision-making. Conclusion: Recognition respect of persons was embedded in the inmost part of nurses as individuals. Concerning appraisal respect, it was thought to be deeply enshrined in the inter- and intra-healthcare professional interactions. The forging of trusting relationships over time was deemed to be strongly associated with good quality interactions with other healthcare professionals.
Relationship of Radiographic and Clinical Parameters With Hallux Valgus and Second Ray Pathology
Authors: Gribbin Caitlin K. , Ellis Scott J. , Nguyen Joseph , Williamson Emilie , Cody Elizabeth A. 
Published: September 2016

Background: Hallux valgus is frequently associated with additional forefoot pathologies, including hammertoes and midfoot osteoarthritis (OA). However, the pathogenesis of these concurrent pathologies remains to be elucidated. We sought to determine whether there is a relationship between demographic and radiographic parameters and the incidence of secondary pathologies in the setting of a bunion, with an emphasis on second tarsometatarsal (TMT) OA and hammertoes. Methods: A total of 153 patients (172 feet) who underwent reconstruction for hallux valgus were divided into 3 groups: (1) bunion only (61 patients), (2) bunion with hammertoe without second TMT joint OA (78 patients), and (3) bunion with second TMT joint OA (14 patients). Preoperative age, sex, and body mass index (BMI) as well as hallux valgus angle (HVA), intermetatarsal angle (IMA), metatarsus adductus angle (MAA), ratio of second to first metatarsal length, and Meary’s angle were recorded. One-way analysis of variance (normality demonstrated) and Kruskal-Wallis (normality not demonstrated) tests were used to assess differences in continuous variables. Post hoc tests were conducted with the Bonferroni technique. Associations between discrete variables and the study groups were analyzed using χ2 tests. Following the univariate analysis, multinomial logistic regression models were built to determine potential risk factors for hammertoe or TMT OA group placement. Results: Patients in the hammertoe and TMT OA groups were significantly older than patients in the bunion only group ( P < .001 for both pairwise comparisons) and had significantly higher BMIs ( P = .024 and P < .001, respectively). Patients in the TMT OA group had a significantly higher mean HVA than patients in the bunion-only group ( P = .004) and a significantly higher mean MAA relative to both other study groups ( P ≤ .001 for both comparisons). IMA, Meary’s angle, and the ratio of second to first metatarsal length did not differ significantly between groups. In the multivariate analysis, hammertoe group assignment was predicted only by age and HVA, while midfoot OA group assignment was predicted by age, HVA, BMI, and MAA. Conclusion: Our data show that older age and increased HVA were predictors of both second ray pathologies studied. Higher BMI and MAA were predictive only of TMT joint OA. These data may help identify patients with hallux valgus who are at greater risk for developing secondary pathologies. Level of Evidence: Level III, retrospective comparative series.
IL1RAP antibodies block IL-1–induced expansion of candidate CML stem cells and mediate cell killing in xenograft models
Authors: Ågerstam Helena , Hansen Nils , von Palffy Sofia , Sandén Carl , Reckzeh Kristian , Karlsson Christine , Lilljebjörn Henrik , Landberg Niklas , Askmyr Maria , Högberg Carl , Rissler Marianne , Porkka Kimmo , Wadenvik Hans , Mustjoki Satu , Richter Johan , Järås Marcus , Fioretos Thoas 
Published: September 2016

Key PointsIL-1 activates signaling and promotes proliferation of primitive CML cells. IL1RAP antibodies block IL-1–induced effects and mediate cell killing in chronic and blast phase CML in vivo models.
NBLDA: negative binomial linear discriminant analysis for RNA-Seq data
Authors: Dong Kai , Zhao Hongyu , Tong Tiejun , Wan Xiang 
Published: September 2016

Abstract
Background
RNA-sequencing (RNA-Seq) has become a powerful technology to characterize gene expression profiles because it is more accurate and comprehensive than microarrays. Although statistical methods that have been developed for microarray data can be applied to RNA-Seq data, they are not ideal due to the discrete nature of RNA-Seq data. The Poisson distribution and negative binomial distribution are commonly used to model count data. Recently, Witten (Annals Appl Stat 5:2493–2518, 2011) proposed a Poisson linear discriminant analysis for RNA-Seq data. The Poisson assumption may not be as appropriate as the negative binomial distribution when biological replicates are available and in the presence of overdispersion (i.e., when the variance is larger than or equal to the mean). However, it is more complicated to model negative binomial variables because they involve a dispersion parameter that needs to be estimated.

Results
In this paper, we propose a negative binomial linear discriminant analysis for RNA-Seq data. By Bayes’ rule, we construct the classifier by fitting a negative binomial model, and propose some plug-in rules to estimate the unknown parameters in the classifier. The relationship between the negative binomial classifier and the Poisson classifier is explored, with a numerical investigation of the impact of dispersion on the discriminant score. Simulation results show the superiority of our proposed method. We also analyze two real RNA-Seq data sets to demonstrate the advantages of our method in real-world applications.

Conclusions
We have developed a new classifier using the negative binomial model for RNA-seq data classification. Our simulation results show that our proposed classifier has a better performance than existing works. The proposed classifier can serve as an effective tool for classifying RNA-seq data. Based on the comparison results, we have provided some guidelines for scientists to decide which method should be used in the discriminant analysis of RNA-Seq data. R code is available at http://www.comp.hkbu.edu.hk/~xwan/NBLDA.Ror https://github.com/yangchadam/NBLDA
Tissue enrichment analysis for C. elegans genomics
Authors: Angeles-Albores David , N. Lee Raymond Y. , Chan Juancarlos , Sternberg Paul W. 
Published: September 2016

AbstractBackgroundOver the last ten years, there has been explosive development in methods for measuring gene expression. These methods can identify thousands of genes altered between conditions, but understanding these datasets and forming hypotheses based on them remains challenging. One way to analyze these datasets is to associate ontologies (hierarchical, descriptive vocabularies with controlled relations between terms) with genes and to look for enrichment of specific terms. Although Gene Ontology (GO) is available forCaenorhabditis elegans, it does not include anatomical information.ResultsWe have developed a tool for identifying enrichment ofC. eleganstissues among gene sets and generated a website GUI where users can access this tool. Since a common drawback to ontology enrichment analyses is its verbosity, we developed a very simple filtering algorithm to reduce the ontology size by an order of magnitude. We adjusted these filters and validated our tool using a set of 30 gold standards from Expression Cluster data in WormBase. We show our tool can even discriminate between embryonic and larval tissues and can even identify tissues down to the single-cell level. We used our tool to identify multiple neuronal tissues that are down-regulated due to pathogen infection inC. elegans.ConclusionsOur Tissue Enrichment Analysis (TEA) can be found within WormBase, and can be downloaded using Python’s standard pip installer. It tests a slimmed-downC. eleganstissue ontology for enrichment of specific terms and provides users with a text and graphic representation of the results.
A haplotype-based normalization technique for the analysis and detection of allele specific expression
Authors: Hodgkinson Alan , Grenier Jean-Christophe , Gbeha Elias , Awadalla Philip 
Published: September 2016

Abstract
Background
Allele specific expression (ASE) has become an important phenotype, being utilized for the detection of cis-regulatory variation, nonsense mediated decay and imprinting in the personal genome, and has been used to both identify disease loci and consider the penetrance of damaging alleles. The detection of ASE using high throughput technologies relies on aligning short-read sequencing data, a process that has inherent biases, and there is still a need to develop fast and accurate methods to detect ASE given the unprecedented growth of sequencing information in big data projects.

Results
Here, we present a new approach to normalize RNA sequencing data in order to call ASE events with high precision in a short time-frame. Using simulated datasets we find that our approach dramatically improves reference allele quantification at heterozygous sites versus default mapping methods and also performs well compared to existing techniques for ASE detection, such as filtering methods and mapping to parental genomes, without the need for complex and time consuming manipulation. Finally, by sequencing the exomes and transcriptomes of 96 well-phenotyped individuals of the CARTaGENE cohort, we characterise the levels of ASE across individuals and find a significant association between the proportion of sites undergoing ASE within the genome and smoking.

Conclusions
The correct treatment and analysis of RNA sequencing data is vital to control for mapping biases and detect genuine ASE signals. By normalising RNA sequencing information after mapping, we show that this approach can be used to identify biologically relevant signals in personal genomes.
Riemann solvers and Alfven waves in black hole magnetospheres
Authors: Punsly Brian , Balsara Dinshaw , Kim Jinho , Garain Sudip 
Published: September 2016

AbstractIn the magnetosphere of a rotating black hole, an inner Alfven critical surface (IACS) must be crossed by inflowing plasma. Inside the IACS, Alfven waves are inward directed toward the black hole. The majority of the proper volume of the active region of spacetime (the ergosphere) is inside of the IACS. The charge and the totally transverse momentum flux (the momentum flux transverse to both the wave normal and the unperturbed magnetic field) are both determined exclusively by the Alfven polarization. Thus, it is important for numerical simulations of black hole magnetospheres to minimize the dissipation of Alfven waves. Elements of the dissipated wave emerge in adjacent cells regardless of the IACS, there is no mechanism to prevent Alfvenic information from crossing outward. Thus, numerical dissipation can affect how simulated magnetospheres attain the substantial Goldreich-Julian charge density associated with the rotating magnetic field. In order to help minimize dissipation of Alfven waves in relativistic numerical simulations we have formulated a one-dimensional Riemann solver, called HLLI, which incorporates the Alfven discontinuity and the contact discontinuity. We have also formulated a multidimensional Riemann solver, called MuSIC, that enables low dissipation propagation of Alfven waves in multiple dimensions. The importance of higher order schemes in lowering the numerical dissipation of Alfven waves is also catalogued.
Neoadjuvant Therapy Followed by Resection Versus Upfront Resection for Resectable Pancreatic Cancer: A Propensity Score Matched Analysis
Authors: Mokdad Ali A. , Minter Rebecca M. , Zhu Hong , Augustine Mathew M. , Porembka Matthew R. , Wang Sam C. , Yopp Adam C. , Mansour John C. , Choti Michael A. , Polanco Patricio M. 
Published: September 2016

Purpose To compare overall survival between patients who received neoadjuvant therapy (NAT) followed by resection and those who received upfront resection (UR)—as well as a subgroup of UR patients who also received adjuvant therapy—for early-stage resectable pancreatic adenocarcinoma. Patients and Methods Adult patients with resected, clinical stage I or II adenocarcinoma of the head of the pancreas were identified in the National Cancer Database from 2006 to 2012. Patients who underwent NAT followed by curative-intent resection were matched by propensity score with patients whose tumors were resected upfront. Overall survival was compared by using a Cox proportional hazards regression model. Early postoperative and oncologic outcomes were evaluated. Results We identified 15,237 patients with clinical stage I or II resected pancreatic head adenocarcinoma. From the NAT group, 2,005 patients (95%) were matched with 6,015 patients who underwent UR. The NAT group was associated with improved survival compared with UR (median survival, 26 months v 21 months, respectively; stratified log-rank P < .01; hazard ratio, 0.72; 95% CI, 0.68 to 0.78). Patients in the UR group had higher pathologic T stage (pT3 and T4: 86% v 73%; P < .01), higher positive lymph nodes (73% v 48%; P < .01), and higher positive resection margin (24% v 17%; P < .01). Compared with a subset of UR patients who received adjuvant therapy, NAT patients had a better survival (adjusted hazard ratio, 0.83; 95% CI, 0.73 to 0.89). Conclusion NAT followed by resection has a significant survival benefit compared with UR in early-stage, resected pancreatic head adenocarcinoma. These findings support the use of NAT, particularly as a patient selection tool, in the management of resectable pancreatic adenocarcinoma.
Systematic Quality Assessment of Published Antishivering Protocols
Authors: Choi Ko-Eun , Park Bomi , Moheet Asma M. , Rosen Amanda , Lahiri Shouri , Rosengart Axel 
Published: September 2016

Shivering is a common side effect of targeted temperature modulation and general anesthesia. Antishivering strategies often employ a stepwise approach involving both pharmacological and physical interventions. However, approaches to treat shivering are often empiric and vary widely across care environments. We evaluated the quality of published antishivering protocols and guidelines with respect to methodological rigor, reliability, and consistency of recommendations.
Using 4 medical databases, we identified 4027 publications that addressed shivering therapy, and excluded 3354 due to lack of relevance. After applying predefined eligibility criteria with respect to minimal protocol standards, 18 protocols/guidelines remained. Each was assessed using a modified Appraisal of Guidelines for Research and Evaluation II (mAGREE II) instrument containing 23 quality items within 6 domains (maximal score 23). Among 18 protocols/guidelines, only 3 incorporated systematically reviewed recommendations, whereas 15 merely targeted practice standardization. Fifteen of 18 protocols/guidelines addressed shivering during therapeutic cooling in which skin counterwarming and meperidine were most commonly cited. However, their mAGREE II scores were within the lowest tertile (1 to 7 points) and the median for all 18 protocols was 5. The quality domains most commonly absent were stakeholder involvement, rigor of development, and editorial independence. Three of 18 protocols/guidelines addressed postanesthetic antishivering. Of these, the American Society of Anesthesiologists guidelines recommending forced-air warming and meperidine received the highest mAGREE II score (14 points), whereas the remaining 2 recommendations had low scores (<5 points).
Current published antishivering protocols/guidelines lack methodological rigor, reliability, and strength, and even the highest scoring of the 18 protocols/guidelines fulfilled only 60% of quality items. To be consistent with evidence-based protocol/guideline development processes, future antishivering treatment algorithms should increase methodological rigor and transparency.
The centrosomal deubiquitylase USP21 regulates Gli1 transcriptional activity and stability
Authors: Heride Claire , Rigden Daniel J. , Bertsoulaki Erithelgi , Cucchi Danilo , De Smaele Enrico , Clague Michael J. , Urbé Sylvie 
Published: September 2016

ABSTRACT
USP21 is a centrosome-associated deubiquitylase (DUB) that has been implicated in the formation of primary cilia – crucial organelles for the regulation of the Hedgehog (Hh) signaling pathway in vertebrates. Here, we identify KCTD6 – a cullin-3 E3-ligase substrate adapter that has been previously linked to Hh signaling – as well as Gli1, the key transcription factor responsible for Hh signal amplification, as new interacting partners of USP21. We identify a cryptic structured protein interaction domain in KCTD6, which is predicted to have a similar fold to Smr domains. Importantly, we show that both depletion and overexpression of catalytically active USP21 suppress Gli1-dependent transcription. Gli proteins are negatively regulated through protein kinase A (PKA)-dependent phosphorylation. We provide evidence that USP21 recruits and stabilises Gli1 at the centrosome where it promotes its phosphorylation by PKA. By revealing an intriguing functional pairing between a spatially restricted deubiquitylase and a kinase, our study highlights the centrosome as an important hub for signal coordination.
1,4-Diaryl-1-oxy-1,3-butadiene Conjugated System Incorporated in a Dibenzobarrelene Skeleton: Synthesis, Photophysical Properties, and Comparison with the Heavier Group 16 Congeners
Authors: Ishii Akihiko , Shibata Mari , Nakata Norio 
Published: September 2016

AbstractWe have synthesized the 1,4-diaryl-1-thio-, seleno- and telluro-1,3-butadiene derivatives incorporated in a dibenzobarrelene skeleton and found that the thio and seleno derivatives are highly fluorescent in solution at room temperature. We report here the synthesis of the oxygen congener. The compounds were synthesized by the reaction of anthranolate with 1,4-diaryl-1,3-butadiyne followed by an intramolecular cycloaddition. Their structures were analyzed by X-ray crystallography to reveal high planarity of the 1,4-diaryl-1-oxy-1,3-butadiene moieties compared with the heavier chalcogen congeners. The oxy compounds are fluorescent similarly to the thio and seleno congeners; the diphenyl and bis(4-trifluorophenyl) derivatives exhibited somewhat red-shifted fluorescence spectra with vibrational structure. Fluorescence of the D-π-A type derivatives reached to the red and near infrared regions. The bonding characters in the 1-chalcogeno-1,3-butadiene moieties are discussed on the basis of DFT calculations.
Analysis of the EAT-26 in a non-clinical sample
Authors: Rogoza Radosław , Brytek-Matera Anna , Garner David 
Published: September 2016

Aim of the studyThe Eating Attitudes Test (EAT) is one of the most commonly used measures of abnormal eating habits; however, it has been criticized for its unstable factorial structure. Different studies proposed different solutions; however, up to date there is no consensus whether three-, five-, or seven-factor solution is appropriate.Subject or material and methodsIn the current study, we examined the cues provided by studies that investigated the structure of the EAT-26, and analyzed our expectations in a nonclinical group of 617 women.ResultsBased upon bi-factor confirmatory factor analyses, we demonstrated that the EAT measures general eating pathology, but it also measures more specific factors, such as social pressure, food awareness, food preoccupation and purging behaviours.DiscussionAmong distinguished specific factors, social pressure seems to be promising scale to be used for screening purposes. The food awareness factor could be interpreted in terms of orthorexia nervosa; however, further evidence is required to support this conclusion. We also provided evidence that bulimia and food preoccupation factors should be maintained within the EAT-26 as an important behavioural aspects of eating pathology.ConclusionsThese results shed new light on this measure and provide the bases for a discussion of its psychometric issues.