bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks
Authors: Hanson Jack , Yang Yuedong , Paliwal Kuldip , Zhou Yaoqi 
Published: October 2016

Abstract

Motivation
Capturing long-range interactions between structural but not sequence neighbors of proteins is a long-standing challenging problem in bioinformatics. Recently, long short-term memory (LSTM) networks have significantly improved the accuracy of speech and image classification problems by remembering useful past information in long sequential events. Here, we have implemented deep bidirectional LSTM recurrent neural networks in the problem of protein intrinsic disorder prediction.

Results
The new method, named SPOT-Disorder, has steadily improved over a similar method using a traditional, window-based neural network (SPINE-D) in all datasets tested without separate training on short and long disordered regions. Independent tests on four other datasets including the datasets from critical assessment of structure prediction (CASP) techniques and &gt;10 000 annotated proteins from MobiDB, confirmed SPOT-Disorder as one of the best methods in disorder prediction. Moreover, initial studies indicate that the method is more accurate in predicting functional sites in disordered regions. These results highlight the usefulness combining LSTM with deep bidirectional recurrent neural networks in capturing non-local, long-range interactions for bioinformatics applications.

Availability and Implementation
SPOT-disorder is available as a web server and as a standalone program at: http://sparks-lab.org/server/SPOT-disorder/index.php.

Supplementary information
Supplementary data is available at Bioinformatics online.
HYSYS: have you swapped your samples?
Authors: Schröder Jan , Corbin Vincent , Papenfuss Anthony T 
Published: October 2016

Abstract

Motivation
The application of a genomics assay to samples from a cohort is a frequently applied experimental design in cancer genomics studies. The collection and analysis of cancer sequencing data in the clinical setting is an elaborate process that may involve consenting patients, obtaining possibly-multiple DNA samples, sequencing and analysis. Many of these steps are manual. At any stage mistakes can occur that cause a DNA sample to be labelled incorrectly. However, there is a paucity of methods in the literature to identify such swaps specifically in cancer studies.

Results
Here, we introduce a simple method, HYSYS, to estimate the relatedness of samples and test for sample swaps and contamination. The test uses the concordance of homozygous SNPs between samples. The method is motivated by the observation that homozygous germline population variants rarely change in the disease and are not affected by loss of heterozygosity. Our tools include visualization and a testing framework to flag possible sample swaps. We demonstrate the utility of this approach on a small cohort.

Availability and Implementation
http://github.com/PapenfussLab/HaveYouSwappedYourSamples

Supplementary information
Supplementary data are available at Bioinformatics online.
ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data
Authors: Baskin Elizabeth , Farouni Rick , Mathé Ewy A 
Published: October 2016

Abstract

Summary
Regulatory elements regulate gene transcription, and their location and accessibility is cell-type specific, particularly for enhancers. Mapping and comparing chromatin accessibility between different cell types may identify mechanisms involved in cellular development and disease progression. To streamline and simplify differential analysis of regulatory elements genome-wide using chromatin accessibility data, such as DNase-seq, ATAC-seq, we developed ALTRE (ALTered Regulatory Elements), an R package and associated R Shiny web app. ALTRE makes such analysis accessible to a wide range of users—from novice to practiced computational biologists.

Availability and Implementation
https://github.com/Mathelab/ALTRE

Supplementary information
Supplementary data are available at Bioinformatics online.
Differential Weighting for Subcomponent Measures of Integrated Clinical Encounter Scores Based on the USMLE Step 2 CS Examination: Effects on Composite Score Reliability and Pass–Fail Decisions
Authors: Park Yoon Soo , Lineberry Matthew , Hyderi Abbas , Bordage Georges , Xing Kuan , Yudkowsky Rachel 
Published: October 2016

Purpose
Medical schools administer locally developed graduation competency examinations (GCEs) following the structure of the United States Medical Licensing Examination Step 2 Clinical Skills that combine standardized patient (SP)-based physical examination and the patient note (PN) to create integrated clinical encounter (ICE) scores. This study examines how different subcomponent scoring weights in a locally developed GCE affect composite score reliability and pass–fail decisions for ICE scores, contributing to internal structure and consequential validity evidence.

Method
Data from two M4 cohorts (2014: n = 177; 2015: n = 182) were used. The reliability of SP encounter (history taking and physical examination), PN, and communication and interpersonal skills scores were estimated with generalizability studies. Composite score reliability was estimated for varying weight combinations. Faculty were surveyed for preferred weights on the SP encounter and PN scores. Composite scores based on Kane’s method were compared with weighted mean scores.

Results
Faculty suggested weighting PNs higher (60%–70%) than the SP encounter scores (30%–40%). Statistically, composite score reliability was maximized when PN scores were weighted at 40% to 50%. Composite score reliability of ICE scores increased by up to 0.20 points when SP–history taking (SP-Hx) scores were included; excluding SP-Hx only increased composite score reliability by 0.09 points. Classification accuracy for pass–fail decisions between composite and weighted mean scores was 0.77; misclassification was < 5%.

Conclusions
Medical schools and certification agencies should consider implications of assigning weights with respect to composite score reliability and consequences on pass–fail decisions.
The Impact of Emotion on Learners’ Application of Basic Science Principles to Novel Problems
Authors: McConnell Meghan M. , Monteiro Sandra , Pottruff Molly M. , Neville Alan , Norman Geoff R. , Eva Kevin W. , Kulasegaram Kulamakan 
Published: October 2016

Purpose
Training to become a physician is an emotionally laden experience. Research in cognitive psychology indicates that emotions can influence learning and performance, but the materials used in such research (e.g., word lists) rarely reflect the complexity of material presented in medical school. The present study examined whether emotions influence learning of basic science principles.

Method
Fifty-five undergraduate psychology students were randomly assigned to write about positive, negative, or neutral life events for nine minutes. Participants were then taught three physiological concepts, each in the context of a single organ system. Testing consisted of 13 clinical cases, 7 presented with the same concept/organ system pairing used during training (“near transfer”) and 6 with novel pairings (“far transfer”). Testing was repeated after one week with 13 additional cases.

Results
Forty-nine students provided complete data. Higher test scores were found when the concept/organ system pairing was held constant (near transfer = 51% correct vs. far = 33%; P < .001). Emotion condition influenced participants’ overall performance, with individuals in the neutral condition (50.1%) performing better than those in the positive (38.2%, P < .05) and negative (37.7%, P < .001) emotion conditions.

Conclusions
These data suggest that regardless of whether the emotion is positive or negative, mild affective states can impair learning of basic science concepts by novices. Demands on working memory and subsequent cognitive load provide a potential explanation. Future work will examine the extent to which these findings generalize to medical trainees.
The Perils and Rewards of Critical Consciousness Raising in Medical Education
Authors: Bleakley Alan 
Published: October 2016

Inequalities in society are reflected in patterns of disease and access to health care, where the disadvantaged suffer most. Traditionally, doctors have kept politics out of their work, even though politics often shape medicine. What political responsibilities, then, should doctors have as they facilitate the learning of medical students? The article in this issue by Kumagai, Jackson, and Razack goes straight to the heart of this question. These authors ask whether educators should be wary of “cutting close to the bone” in discussing issues that may restimulate trauma in some medical students.
Kumagai and colleagues suggest that it is actually the ethical responsibility of educators to introduce students to discomfort as a means of raising students’ critical consciousness or their ability to sensitively gauge the positions of others and to engage in dialogue to address issues such as inequality and inequity so that previously silent and silenced voices can be heard. The author of this Commentary expands on this argument, further supporting the need to democratize medical culture and politicize doctors. Educators, as expert facilitators of this new critical consciousness raising, must create safe spaces for students to work through issues to avoid educational iatrogenesis. Such an approach to medical education is an extension of the traditional art of medicine, at the core of which are patient care and tolerance. Ethics, aesthetics, and politics can come together in such a reflexive medicine curriculum.
Interprofessional Team Training at the Prelicensure Level: A Review of the Literature
Authors: Nelson Sioban , White Catriona F. , Hodges Brian D. , Tassone Maria 
Published: October 2016

Purpose
The authors undertook a descriptive analysis review to gain a better understanding of the various approaches to and outcomes of team training initiatives in prelicensure curricula since 2000.

Method
In July and August 2014, the authors searched the MEDLINE, PsycINFO, Embase, Business Source Premier, and CINAHL databases to identify evaluative studies of team training programs’ effects on the team knowledge, communication, and skills of prelicensure students published from 2000 to August 2014. The authors identified 2,568 articles, with 17 studies meeting the selection criteria for full text review.

Results
The most common study designs were single-group, pre/posttest studies (n = 7), followed by randomized controlled or comparison trials (n = 6). The Situation, Background, Assessment, Recommendation communication tool (n = 5); crisis resource management principles (n = 6); and high-fidelity simulation (n = 4) were the most common curriculum bases used. Over half of the studies (n = 9) performed training with students from more than one health professions program. All but three used team performance assessments, with most (n = 8) using observed behavior checklists created for that specific study. The majority of studies (n = 16) found improvements in team knowledge, communication, and skills.

Conclusions
Team training appears effective in improving team knowledge, communication, and skills in prelicensure learners. Continued exploration of the best method of team training is necessary to determine the most effective way to move forward in prelicensure interprofessional team education.
Factors That Predict Risk of Cervical Instability in Rheumatoid Arthritis Patients
Authors: Han Myung-Hoon , Ryu Je Il , Kim Choong Hyun , Kim Jae Min , Cheong Jin Hwan , Bak Koang Hum , Chun Hyoung Joon , Yi Hyeong-Joong , Jun Jae Bum , Chung Jae Woo 
Published: October 2016

Study Design.
Retrospective data analysis.

Objective.
To identify factors affecting the atlantodental interval, the Ranawat value, and subaxial translation after rheumatoid arthritis (RA) diagnosis. In addition, factors predictive for cervical spine instability (CSI) development after RA diagnosis were examined.

Summary of Background Data.
Development of CSI affects the prognosis and mortality of RA patients. Previous studies described that obesity is associated with reduced radiographic joint damage in RA patients. We hypothesized that body mass index (BMI) is also associated with radiographic cervical damage in RA patients.

Methods.
Cervical radiographs were taken at full flexion, neutral position, and full extension to measure the geometric length of the anterior atlantodental interval, the Ranawat value, and subaxial translation. These values were entered into multivariable linear regression analysis based on potential associated factors. Hazard ratios were calculated to identify independent factors predictive of CSI.

Results.
Of the patients diagnosed with RA between January 2005 and August 2015, 1611 who underwent at least one cervical radiograph were included. After adjusting for sex, age, BMI category, CSI, rheumatoid factor, and RA medication, multivariate analysis revealed that the risk of atlantoaxial subluxation in the underweight and normal BMI groups was about 1.6-fold (hazard ratio, 1.63; 95% CI, 1.10–2.43; P = 0.015) and 1.7-fold higher, respectively, than that in the obese group, and that the risk of vertical subluxation was about 2.5-fold (hazard ratio, 2.52; 95% CI, 1.32–4.83; P = 0.005) higher in the underweight group than in the obese group. We also found that the rheumatoid factor positivity was a predictive risk factor for CSI development.

Conclusion.
We identified risk factors predictive for CSI occurrence after RA diagnosis through cervical radiograph assessment. We found that BMI was an independent predictor for development of CSI. Further large-scale prospective studies are required to confirm these findings.

Level of Evidence: 3
Stand-alone Lateral Recess Decompression Without Discectomy in Patients Presenting With Claudicant Radicular Pain and MRI Evidence of Lumbar Disc Herniation
Authors: Kulkarni Arvind G. , Patel Ravish , Dutta Shumayou , Patil Vishwanath 
Published: October 2016

Study Design.
A prospective study.

Objective.
The aim of this study was to analyze the outcomes of stand-alone lateral recess decompression without discectomy in patients with claudicant radicular pain and magnetic resonance imaging (MRI) showing LRS (lateral recess stenosis) with lumbar disc herniation.

Summary of Background Data.
Discectomy is the gold standard treatment for symptomatic lumbar disc herniations refractory to conservative care. Typically, patients with positive SLR (Straight leg raising test) and flexion dominant leg pain are the ideal candidates who can be benefited from discectomy. There is a subset of patients with morphological features of lumbar disc herniation with LRS on MRI and presenting with diametrically opposite symptoms such as claudicant leg pain, extension dominant leg pain, relief on flexion, and a negative SLR. Until now, no focused prospective study in the literature highlights stand-alone lateral recess decompression in this group of patients.

Methods.
From January 2007 to June 2013, 55 patients having unilateral claudicant radicular pain were selected to undergo stand-alone lateral recess decompression with tubular retractors. Intraoperatively, disc consistency and presence of sequestrated fragments were analyzed. Visual Analogue Scale (VASleg), Oswestry Disability Index (ODI) score, and Macnab criteria were used to measure outcomes.

Results.
Out of 55 patients, stand-alone lateral recess decompression was successfully executed in 51 patients and remaining four patients had sequestrated discs that required removal. Mean age at presentation was 54.5 years (41–67 years), male:female ratio was 1.12:1, and mean follow-up was 3.8 years (3–5.8 years). Significant improvement (P < 0.0001) was noticed between preoperative and postoperative VASleg score (8.39 ± 0.84 vs. 2.5 ± 0.48) and ODI score (46.79 ± 1.85 vs. 18.71 ± 2.41). As per Macnab criteria, 94% patients were satisfied with surgery.

Conclusion.
Stand-alone lateral recess decompression without discectomy is clinically effective for a large majority of patients with claudicant radicular pain and MRI evidence of LRS with associated lumbar disc herniation. The ability to perform it with minimal invasive techniques makes it focused and targeted with minimal morbidity.

Level of Evidence: 4
Haemorrhage at caesarean section: a framework for prevention and research
Authors: Jardine Jennifer E. , Law Penny , Hogg Matthew , Murphy Deirdre , Khan Khalid S. 
Published: October 2016

Purpose of review
Caesarean section rates are increasing across the world. Postpartum haemorrhage is a major cause of morbidity and mortality; major haemorrhage is more common after caesarean delivery. There is a wide range of practice in the prevention and treatment of postpartum haemorrhage at caesarean section. The aim of this review is to summarize current opinion in the management of postpartum haemorrhage at caesarean section.

Recent findings
Recent large randomized controlled trials have shown a possible effect from the routine use of tranexamic acid and ergometrine. Small randomized controlled trials have shown a possible benefit from using carbetocin.

Summary
The impact of postpartum haemorrhage can be reduced by antenatal correction of anaemia. Intraoperative medical management consists of oxytocinon, additional oxytocics +/− tranexamic acid, with at present limited evidence as to the order in which these should be considered. Trials of routine use of cell salvage and tranexamic acid are currently underway.
Utility of Indocyanine Green Angiography in Arterial Selection during Free Flap Harvest in Patients with Severe Peripheral Vascular Disease
Authors: Maxwell Anne K. , Deleyiannis Frederic W.-B. 
Published: October 2016

Summary:
Indocyanine green angiography (SPY) was used to guide arterial selection for an anterolateral thigh free flap in the setting of severe peripheral vascular disease. SPY technology serves as a novel and sensitive intraoperative tool to predict decreased tissue perfusion from vessel sacrifice for flap harvest. Change in SPY time parameters measuring superficial blood flow distal to the donor site while temporarily intraoperatively clamping different possible arterial pedicles can optimize free flap design to avoid iatrogenic critical limb ischemia.
Hospital cultural competency as a systematic organizational intervention
Authors: Weech-Maldonado Robert , Dreachslin Janice L. , Epané Josué Patien , Gail Judith , Gupta Shivani , Wainio Joyce Anne 
Published: October 2016

Background:
Cultural competency or the ongoing capacity of health care systems to provide for high-quality care to diverse patient populations (National Quality Forum, 2008) has been proposed as an organizational strategy to address disparities in quality of care, patient experience, and workforce representation. But far too many health care organizations still do not treat cultural competency as a business imperative and driver of strategy.

Purposes:
The aim of the study was to examine the impact of a systematic, multifaceted, and organizational level cultural competency initiative on hospital performance metrics at the organizational and individual levels.

Methodology/Approach:
This demonstration project employs a pre–post control group design. Two hospital systems participated in the study. Within each system, two hospitals were selected to serve as the intervention and control hospitals. Executive leadership (C-suite) and all staff at one general medical/surgical nursing unit at the intervention hospitals experienced a systematic, planned cultural competency intervention. Assessments and interventions focused on three organizational level competencies of cultural competency (diversity leadership, strategic human resource management, and patient cultural competency) and three individual level competencies (diversity attitudes, implicit bias, and racial/ethnic identity status). In addition, we evaluated the impact of the intervention on diversity climate and workforce diversity.

Findings:
Overall performance improvement was greater in each of the two intervention hospitals than in the control hospital within the same health care system. Both intervention hospitals experienced improvements in the organizational level competencies of diversity leadership and strategic human resource management. Similarly, improvements were observed in the individual level competencies for diversity attitudes and implicit bias for Blacks among the intervention hospitals. Furthermore, intervention hospitals outperformed their respective control hospitals with respect to diversity climate.

Practice Implications:
A focused and systematic approach to organizational change when coupled with interventions that encourage individual growth and development may be an effective approach to building culturally competent health care organizations.
Professional networks and the alignment of individual perceptions about medical innovation
Authors: Iacopino Valentina , Mascia Daniele , Cicchetti Americo 
Published: October 2016

Background:
In recent decades, the role of technology in health care organizations has become increasingly relevant because it enhances health care outcomes and the achievement of clinical goals. Extant research demonstrates that the effectiveness of a medical innovation depends largely on health care professionals’ perceptions of its usefulness and impact on their activities and practices. We also know that interaction among social actors contributes to the shaping of their judgments and opinions regarding innovation.

Purpose:
This study investigated the role of professionals’ social networks and social capital in the formation of similar individual perceptions about a highly innovative robotic surgical system.

Methodology:
We collected data from a sample of 50 professionals, including both physicians and nurses, working in three hospital wards belonging to an Italian hospital organization. Using a survey, we gathered data on professionals’ demographic characteristics, the adoption and impact of the new technology, and social networks. We tested our hypotheses using a dyadic perspective and logistic regression quadratic assignment procedures.

Findings:
Our findings document that professionals’ perceptions regarding technological change were more likely to be similar when they were connected and exhibited similarity in some social capital characteristics and adoption behavior.

Practice Implications:
These results have important implications for health care executives and administrators, as well as for health professionals characterized by high degrees of autonomy and for which organizational change can be affected by professional or organizational resistance.