bluuebunny/crossref_metadata_2025_split huggingface dataset:
LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis
Authors: Zheng Jie , Erzurumluoglu A Mesut , Elsworth Benjamin L , Kemp John P , Howe Laurence , Haycock Philip C , Hemani Gibran , Tansey Katherine , Laurin Charles ,   Early Genetics and Lifecourse Epidemiology (EAGLE) Eczema Consortium, Pourcain Beate St , Warrington Nicole M , Finucane Hilary K , Price Alkes L , Bulik-Sullivan Brendan K , Anttila Verneri , Paternoster Lavinia , Gaunt Tom R , Evans David M , Neale Benjamin M 
Published: September 2016

Abstract

Motivation
LD score regression is a reliable and efficient method of using genome-wide association study (GWAS) summary-level results data to estimate the SNP heritability of complex traits and diseases, partition this heritability into functional categories, and estimate the genetic correlation between different phenotypes. Because the method relies on summary level results data, LD score regression is computationally tractable even for very large sample sizes. However, publicly available GWAS summary-level data are typically stored in different databases and have different formats, making it difficult to apply LD score regression to estimate genetic correlations across many different traits simultaneously.

Results
In this manuscript, we describe LD Hub - a centralized database of summary-level GWAS results for 173 diseases/traits from different publicly available resources/consortia and a web interface that automates the LD score regression analysis pipeline. To demonstrate functionality and validate our software, we replicated previously reported LD score regression analyses of 49 traits/diseases using LD Hub; and estimated SNP heritability and the genetic correlation across the different phenotypes. We also present new results obtained by uploading a recent atopic dermatitis GWAS meta-analysis to examine the genetic correlation between the condition and other potentially related traits. In response to the growing availability of publicly accessible GWAS summary-level results data, our database and the accompanying web interface will ensure maximal uptake of the LD score regression methodology, provide a useful database for the public dissemination of GWAS results, and provide a method for easily screening hundreds of traits for overlapping genetic aetiologies.

Availability and Implementation
The web interface and instructions for using LD Hub are available at http://ldsc.broadinstitute.org/

Supplementary information
Supplementary data are available at Bioinformatics online.
Improved methods for multi-trait fine mapping of pleiotropic risk loci
Authors: Kichaev Gleb , Roytman Megan , Johnson Ruth , Eskin Eleazar , Lindström Sara , Kraft Peter , Pasaniuc Bogdan 
Published: September 2016

Abstract

Motivation
Genome-wide association studies (GWAS) have identified thousands of regions in the genome that contain genetic variants that increase risk for complex traits and diseases. However, the variants uncovered in GWAS are typically not biologically causal, but rather, correlated to the true causal variant through linkage disequilibrium (LD). To discern the true causal variant(s), a variety of statistical fine-mapping methods have been proposed to prioritize variants for functional validation.

Results
In this work we introduce a new approach, fastPAINTOR, that leverages evidence across correlated traits, as well as functional annotation data, to improve fine-mapping accuracy at pleiotropic risk loci. To improve computational efficiency, we describe an new importance sampling scheme to perform model inference. First, we demonstrate in simulations that by leveraging functional annotation data, fastPAINTOR increases fine-mapping resolution relative to existing methods. Next, we show that jointly modeling pleiotropic risk regions improves fine-mapping resolution compared to standard single trait and pleiotropic fine mapping strategies. We report a reduction in the number of SNPs required for follow-up in order to capture 90% of the causal variants from 23 SNPs per locus using a single trait to 12 SNPs when fine-mapping two traits simultaneously. Finally, we analyze summary association data from a large-scale GWAS of lipids and show that these improvements are largely sustained in real data.

Availability and Implementation
The fastPAINTOR framework is implemented in the PAINTOR v3.0 package which is publicly available to the research community http://bogdan.bioinformatics.ucla.edu/software/paintor

Supplementary information
Supplementary data are available at Bioinformatics online.
What is a large-scale dynamo?
Authors: Nigro G. , Pongkitiwanichakul P. , Cattaneo F. , Tobias S. M. 
Published: September 2016

Abstract
We consider kinematic dynamo action in a sheared helical flow at moderate to high values of the magnetic Reynolds number (Rm). We find exponentially growing solutions which, for large enough shear, take the form of a coherent part embedded in incoherent fluctuations. We argue that at large Rm large-scale dynamo action should be identified by the presence of structures coherent in time, rather than those at large spatial scales. We further argue that although the growth rate is determined by small-scale processes, the period of the coherent structures is set by mean-field considerations.
CO Multi-line Imaging of Nearby Galaxies (COMING). I. Physical properties of molecular gas in the barred spiral galaxy NGC 2903
Authors: Muraoka Kazuyuki , Sorai Kazuo , Kuno Nario , Nakai Naomasa , Nakanishi Hiroyuki , Takeda Miho , Yanagitani Kazuki , Kaneko Hiroyuki , Miyamoto Yusuke , Kishida Nozomi , Hatakeyama Takuya , Umei Michiko , Tanaka Takahiro , Tomiyasu Yuto , Saita Chey , Ueno Saeko , Matsumoto Naoko , Salak Dragan , Morokuma-Matsui Kana 
Published: September 2016

Abstract
We present simultaneous mappings of J = 1–0 emission of 12CO, 13CO, and C18O molecules toward the whole disk (8′ × 5′ or 20.8 kpc × 13.0 kpc) of the nearby barred spiral galaxy NGC 2903 with the Nobeyama Radio Observatory 45 m telescope at an effective angular resolution of 20″ (or 870 pc). We detected 12CO(J = 1–0) emission over the disk of NGC 2903. In addition, significant 13CO(J = 1–0) emission was found at the center and bar-ends, whereas we could not detect any significant C18O(J = 1–0) emission. In order to improve the signal-to-noise ratio of CO emission and to obtain accurate line ratios of 12CO(J = 2–1)/12CO(J = 1–0) (R2−1/1−0) and 13CO(J = 1–0)/12CO(J = 1–0) (R13/12), we performed the stacking analysis for our 12CO(J = 1–0), 13CO(J = 1–0), and archival 12CO(J = 2–1) spectra with velocity axis alignment in nine representative regions of NGC 2903. We successfully obtained the stacked spectra of the three CO lines, and could measure averaged R2−1/1−0 and R13/12 with high significance for all the regions. We found that both R2−1/1−0 and R13/12 differ according to the regions, which reflects the difference in the physical properties of molecular gas, i.e., density ($n_{\rm H_2}$) and kinetic temperature (TK). We determined $n_{\rm H_2}$ and TK using R2−1/1−0 and R13/12 based on the large velocity gradient approximation. The derived $n_{\rm H_2}$ ranges from ∼1000 cm−3 (in the bar, bar-ends, and spiral arms) to 3700 cm−3 (at the center) and the derived TK ranges from 10 K (in the bar and spiral arms) to 30 K (at the center). We examined the dependence of star formation efficiencies (SFEs) on $n_{\rm H_2}$ and TK, and found a positive correlation between SFE and $n_{\rm H_2}$ with correlation coefficient for the least-squares power-law fit R2 of 0.50. This suggests that molecular gas density governs the spatial variations in SFEs.
Utility of a Cesarean Delivery Surgical Skills Simulation Session for Family Medicine Residents Pursuing Surgical Obstetrics Training
Authors: Kremer Timothy 
Published: September 2016

BACKGROUND:
Family medicine residents pursuing surgical obstetrics training face the challenge of limited opportunities for intraoperative experience during their formal training. The utility of both low and high fidelity surgical simulation models have been demonstrated to increase technical skill development. Obstetrical emergencies have been taught to family medicine utilizing simulation, but have not included cesarean delivery.

METHODS:
Family medicine residents enrolled in the surgical obstetrics tract underwent a cesarean delivery surgical simulation session. Surgical performance evaluations were obtained from live surgeries performed immediately before and after the simulation session utilizing a previously validated global rating score. De-identified surgical evaluations were used for statistical analysis. Unpaired T test was performed to assess for statistical difference in pre-session and post session scores.

RESULTS:
Seven residents participated in the simulation session. Fourteen surgical evaluations were completed before the session; 9 evaluations were completed after the session. Global rating scores increased from 21.5 (±0.66) to 28.2 (±0.84), reaching statistical significance (P=.008). All subcomponent scores increased, with tissue respect, time and motion, instrument handling, flow, assistance usage, and procedural knowledge reaching statistical significance.

DISCUSSION:
A single simulation session utilizing a low fidelity model did show statistical improvement in global surgical skill ratings and its subcomponents.
Simulation to Improve Trainee Knowledge and Comfort About Twin Vaginal Birth
Authors: Easter Sarah Rae , Gardner Roxane , Barrett Jon , Robinson Julian N. , Carusi Daniela 
Published: September 2016

OBJECTIVE:
To describe a simulation-based curriculum on twin vaginal delivery and evaluate its effects on trainee knowledge and comfort about twin vaginal birth.

METHODS:
Trainees participated in a three-part simulation consisting of a patient counseling session, a twin delivery scenario, and a breech extraction skills station. Consenting trainees completed a 21-item presimulation survey and a 22-item postsimulation survey assessing knowledge, experience, attitudes, and comfort surrounding twin vaginal birth. Presimulation and postsimulation results were compared using univariate analysis. Our primary outcomes were change in knowledge and comfort before and after the simulation.

RESULTS:
Twenty-four obstetrics and gynecology residents consented to participation with 18 postsimulation surveys available for comparison (75%). Trainees estimated their participation in 445 twin deliveries (median 19, range 0–52) with only 20.4% of these as vaginal births. Participants reported a need for more didactic or simulated training on this topic (64% and 88%, respectively). Knowledge about twin delivery improved after the simulation (33.3% compared with 58.3% questions correct, P<.01). Before training, 33.3% of participants reported they would strongly counsel a patient to attempt vaginal birth instead of elective cesarean delivery for twins compared with 50% after training (P=.52). Personal comfort with performing a breech extraction of a nonvertex second twin improved from 5.5% to 66.7% after the simulation (P<.01).

CONCLUSION:
Resident exposure to twin vaginal birth is infrequent and variable with a demonstrable need for more training. Our contemporary obstetric climate is prioritizing vaginal birth despite less frequent operative obstetric interventions. We describe a reproducible twin delivery simulation associated with a favorable effect on resident knowledge and comfort levels.
Narrative Medicine Workshops for Obstetrics and Gynecology Residents and Association With Burnout Measures
Authors: Winkel Abigail Ford , Feldman Nathalie , Moss Haley , Jakalow Holli , Simon Julia , Blank Stephanie 
Published: September 2016

OBJECTIVE:
To determine whether a workshop Narrative Medicine curriculum can improve burnout among obstetrics and gynecology residents.

METHODS:
A Narrative Medicine curriculum was conducted at three obstetrics and gynecology training programs. An explanatory research design examined correlation between Narrative Medicine attendance and changes in survey responses. Residents completed a pretest and 1-year posttest survey that included validated measures of burnout and empathy. A within-participants design used baseline pretest scores as an internal control and measured changes in individual scores. The primary outcome of the study was change in burnout rates. Mann–Whitney U and Kruskal–Wallis tests were used to analyze the data.

RESULTS:
A total of 66 residents at three institutions participated in the Narrative Medicine curriculum. Of those, 54 (81%) enrolled in the study by completing any part of the surveys, and 43 (80%) of those enrolled had complete data for analysis. Burnout was high on all Maslach Burnout Inventory subscales and increased over 1 year. Participants with high Narrative Medicine attendance had decreased burnout on the Emotional Exhaustion subscale (−4.1 [±8.1]) points compared with an increase of 0.5 (±6.0) for low-attendance participants (U=134, P=.02, d=0.65). Lower self-care ratings were associated with improved Personal Accomplishment (+0.5 [±5.0]) compared with +2.0 (±2.7), U=84, P=.01]. Other characteristics did not significantly correlate with burnout or empathy.

CONCLUSION:
Burnout was high and worsened over time among obstetrics and gynecology residents in these three programs. Higher attendance at Narrative Medicine workshops was associated with improved Emotional Exhaustion.
Comfort With Skills and Knowledge After Immediate Postpartum Intrauterine Device Training
Authors: Goldthwaite Lisa M. , Sheeder Jeanelle , Teal Stephanie B. , Tocce Kristina M. 
Published: September 2016

OBJECTIVE:
To estimate whether a standardized immediate postpartum intrauterine device (IUD) simulation results in sustained improvement in perceived comfort with procedural skills.

METHODS:
From November 2013 to April 2015, obstetric health care providers at two teaching hospitals participated in a 30-minute immediate postpartum IUD simulation workshop and program evaluation. We assessed knowledge of indications, insertion technique, safety, and comfort with knowledge and skills preintervention immediately after and 6 months posttraining.

RESULTS:
Training participants (N=84) included 39 residents and 45 attendings (25 certified nurse–midwives and 20 obstetrician–gynecologists). Fifty-seven participants (68%) completed the 6-month assessments. Many participants had placed immediate postpartum IUDs before the training (54% of residents compared with 64% of attendings, P=.32); 60% were comfortable with their knowledge and 52% with their insertion skills defined by self-assessment of 7 or greater on a 10-point scale. On the pretest, 77% answered 80% or greater of the knowledge-based questions correctly; this proportion rose to 95% and 97% on the immediate and 6-month assessments, respectively, and were similar between residents and attendings. Immediately posttraining, 94% of participants rated their comfort with knowledge at 7 or greater out of 10; this fell to 86% by 6 months. Likewise, 87% and 74% scored their comfort with skills at 7 or greater out of 10 immediately and at 6 months, respectively. By 6 months, 81% reported placing one or more immediate postpartum IUDs(92% of residents and 71% of attendings, P=.05).

CONCLUSION:
Residents and attendings demonstrate sustained improvement in knowledge and comfort with immediate postpartum IUDs 6 months after a standardized simulation workshop.
What Is New in Trauma-Related Amputations
Authors: Tintle Scott M. , LeBrun Christopher , Ficke James R. , Potter Benjamin K. 
Published: September 2016

Summary:
Traumatic and trauma-related amputations represent unfortunate sequelae of severe injury, but should not be viewed as a treatment failure and may represent the best reconstructive option for some patients. Lessons from recent military conflicts have guided the evolution of modern surgical techniques and rehabilitation management of this challenging patient population, and treatment at a specialty center may improve patient outcomes. Despite appropriate management, however, surgical complications remain common and revision surgery is often necessary. Bridge synostosis procedures remain controversial, and clinical equipoise remains regarding their functional benefits. Based on European experience over the last 3 decades, osseointegration has evolved into a viable clinical alternative for patients unable to achieve acceptable function using conventional sockets, and several devices are being developed or tested in the United States. Targeted muscle reinnervation and advanced pattern recognition may dramatically improve the functional potential of many upper extremity amputees, and the procedure may also relieve neuroma-related pain. Furthermore, exciting new research may eventually facilitate haptic feedback and restore useful sensation for amputees. Natural disasters and global terrorism events, in addition to conventional trauma resulting in limb loss, make a working knowledge of current amputation surgical techniques essential to the practicing orthopaedic trauma surgeon.
Prognostication in Developmental Dysplasia of the Hip Using the Ossific Nucleus Center Edge Angle
Authors: Firth Gregory B. , Robertson Anthony J.F. , Ramguthy Yammesh , Ramachandran Manoj , Schepers Anton 
Published: September 2016

Background:
The aim of this paper was to determine the prognostic potential of the ossific nucleus center edge angle (ONCEA) in patients below 5 years of age treated for developmental dysplasia of the hip (DDH) to predict final outcome and the need for a secondary procedure.

Methods:
The interobserver and intraobserver reliability was calculated using the intraclass correlation coefficient for measurement of the ONCEA. The ONCEA was divided a priori into 3 groups: group A≥10 degrees, group B −9 to 9 degrees, and group C ≤−10 degrees. Final outcome was measured using the McKay score and Severin classification. The presence of osteonecrosis was recorded at final follow-up.

Results:
One hundred one patients with 133 dislocated hips underwent closed or open reduction for DDH. Mean age at presentation was 19 months with a mean age at final follow-up of 12.4 years. A significant difference was shown in a comparison of the 3 ONCEA groups using the McKay score, Severin classification, and need for a secondary procedure. Eighty seven of the 101 patients underwent ONCEA reliability measurements. The ONCEA was shown to have a mean intrarater reliability of 0.89, and a mean interrater reliability of 0.77.

Conclusions:
The ONCEA is a reliable measurement in predicting medium-term outcome of the hip post reduction in children under the age of 5 years with DDH and might be useful as a predictor for a secondary procedure before the age of 5 years.

Level of Evidence:
Level III—prognostic case control study.

Clinical Relevance:
This case control study shows the importance of measuring the ONCEA within 6 months of removing the final cast after reduction of a dislocated hip and its implications for further management and outcome.
Comparison of Three Reconstructive Techniques in the Surgical Management of Patients With Four-Level Cervical Spondylotic Myelopathy
Authors: Li Zhonghai , Wang Huadong , Tang Jiaguang , Ren Dongfeng , Li Li , Hou Shuxun , Zhang Hailong , Hou Tiesheng 
Published: September 2016

Study Design.
Retrospective clinical series.

Objective.
To compare perioperative parameters, clinical outcomes, radiographic parameters, and complication rates of three reconstructive techniques after the anterior decompression of four-level cervical spondylotic myelopathy (CSM).

Summary of Background Data.
At present, the decision to treat multilevel CSM, especially four-level CSM, remains controversial. No one compares multilevel anterior cervical discectomy and fusion (mACDF), segmental anterior cervical corpectomy and fusion (sACCF) to multilevel anterior cervical discectomy and fusion with cage alone (mACDF-CA) in four-level constructs.

Methods.
Between July 2006 and February 2014, 97 consecutive patients with four-level CSM were enrolled in this study and divided into sACCF (n = 39) group, mACDF (n = 31) group, and mACDF-CA (n = 27) group. The study compared perioperative parameters, complication rates, clinical and radiologic parameters of three reconstructive techniques after the anterior decompression of four-level CSM.

Results.
The mACDF-CA group had the least bleeding and cost of index surgery compared with the sACCF group having the most bleeding and cost. Although significant pain relief and functional activity improvement have been achieved in the three groups at the final follow-up, there was no significant difference in the Japanese Orthopedic Association, SF-36 and NDI scores among the three groups (P >0.05). The mACDF group maintained the best cervical lordosis at the final follow-up, compared with the sACCF group maintained the worst cervical lordosis. Solid fusion was achieved in 87.1% of subjects in sACCF group, 90.3% in mACDF, and in 88.9% in mACDF-CA. The mACDF-CA group had a higher rate of subsidence and lower rate of dysphagia than other two groups.

Conclusion.
mACDF-CA can be considered an effective and safe alternative procedure in the treatment of the four-level CSM.

Level of Evidence: 4
Development and Validation of a Photonumeric Scale for Evaluation of Facial Fine Lines
Authors: Carruthers Jean , Donofrio Lisa , Hardas Bhushan , Murphy Diane K. , Jones Derek , Carruthers Alastair , Sykes Jonathan M. , Creutz Lela , Marx Ann , Dill Sara 
Published: September 2016

BACKGROUND
A validated scale is needed for objective and reproducible comparisons of facial fine lines before and after treatment in practice and clinical studies.

OBJECTIVE
To describe the development and validation of the 5-point photonumeric Allergan Fine Lines Scale.

METHODS
The Allergan Fine Lines Scale was developed to include an assessment guide, verbal descriptors, morphed images, and real subject images for each scale grade. The clinical significance of a 1-point score difference was evaluated in a review of multiple image pairs representing varying differences in severity. Interrater and intrarater reliability was evaluated in a live subject validation study (N = 289) completed during 2 sessions occurring 3 weeks apart.

RESULTS
A score difference of ≥1 point was shown to reflect a clinically significant difference (mean [95% CI] absolute score difference, 1.06 [0.92–1.21] for clinically different image pairs and 0.50 [0.38–0.61] for not clinically different pairs). Intrarater agreement between the 2 live subject validation sessions was almost perfect (weighted kappa = 0.85). Interrater agreement was substantial during the second rating session (0.76, primary end point).

CONCLUSION
The Allergan Fine Lines Scale is a validated and reliable scale for physician rating of severity of superficial fine lines.