bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do subjective assessments of running patterns reflect objective parameters?
Authors: Lussiana Thibault , Gindre Cyrille , Mourot Laurent , Hébert‐Losier Kim 
Published: May 2017

AbstractRunning patterns are often categorized into subgroups according to common features before data analysis and interpretation. The Volodalen® method is a simple field‐based tool used to classify runners into aerial or terrestrial using a 5‐item subjective rating scale. We aimed to validate the Volodalen® method by quantifying the relationship between its subjective scores and 3D biomechanical measures. Fifty‐four runners ran 30 s on a treadmill at 10, 12, 14, 16, and 18 km h−1 while their kinematics were assessed subjectively using the Volodalen® method and objectively using 3D motion capture. For each runner and speed, two researchers scored the five Volodalen® items on a 1‐to‐5 scale, which addressed vertical oscillation, upper‐body motion, pelvis and foot position at ground contact, and footstrike pattern. Seven 3D biomechanical parameters reflecting the subjective items were also collected and correlated to the subjective scores. Twenty‐eight runners were classified as aerial and 26 as terrestrial. Runner classification did not change with speed, but the relative contribution of the biomechanical parameters to the subjective classification was speed dependent. The magnitude of correlations between subjective and objective measures ranged from trivial to very large. Five of the seven objective parameters significantly differed between aerial and terrestrial runners, and these parameters demonstrated the strongest correlations to the subjective scores. Our results support the validity of the Volodalen® method, whereby the visual appreciation of running gait reflected quantifiable objective parameters. Two minor modifications to the method are proposed to simplify its use and improve agreement between subjective and objective measures.
IGESS: a statistical approach to integrating individual-level genotype data and summary statistics in genome-wide association studies
Authors: Dai Mingwei , Ming Jingsi , Cai Mingxuan , Liu Jin , Yang Can , Wan Xiang , Xu Zongben 
Published: May 2017

AbstractMotivationResults from genome-wide association studies (GWAS) suggest that a complex phenotype is often affected by many variants with small effects, known as ‘polygenicity’. Tens of thousands of samples are often required to ensure statistical power of identifying these variants with small effects. However, it is often the case that a research group can only get approval for the access to individual-level genotype data with a limited sample size (e.g. a few hundreds or thousands). Meanwhile, summary statistics generated using single-variant-based analysis are becoming publicly available. The sample sizes associated with the summary statistics datasets are usually quite large. How to make the most efficient use of existing abundant data resources largely remains an open question.ResultsIn this study, we propose a statistical approach, IGESS, to increasing statistical power of identifying risk variants and improving accuracy of risk prediction by integrating individual level genotype data and summary statistics. An efficient algorithm based on variational inference is developed to handle the genome-wide analysis. Through comprehensive simulation studies, we demonstrated the advantages of IGESS over the methods which take either individual-level data or summary statistics data as input. We applied IGESS to perform integrative analysis of Crohns Disease from WTCCC and summary statistics from other studies. IGESS was able to significantly increase the statistical power of identifying risk variants and improve the risk prediction accuracy from 63.2% (±0.4%) to 69.4% (±0.1%) using about 240 000 variants.Availability and implementationThe IGESS software is available at https://github.com/daviddaigithub/IGESS.Supplementary informationSupplementary data are available at Bioinformatics online.
The neXtProt peptide uniqueness checker: a tool for the proteomics community
Authors: Schaeffer Mathieu , Gateau Alain , Teixeira Daniel , Michel Pierre-André , Zahn-Zabal Monique , Lane Lydie 
Published: May 2017

Abstract

Summary
The neXtProt peptide uniqueness checker allows scientists to define which peptides can be used to validate the existence of human proteins, i.e. map uniquely versus multiply to human protein sequences taking into account isobaric substitutions, alternative splicing and single amino acid variants.

Availability and implementation
The pepx program is available at https://github.com/calipho-sib/pepx and can be launched from the command line or through a cgi web interface. Indexing requires a sequence file in FASTA format. The peptide uniqueness checker tool is freely available on the web at https://www.nextprot.org/tools/peptide-uniqueness-checker and from the neXtProt API at https://api.nextprot.org/.
MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization
Authors: McCoy Katherine Maia , Antonio Margaret L , van Opijnen Tim 
Published: May 2017

Abstract

Motivation
Transposon insertion sequencing (Tn-Seq) is a microbial systems-level tool, that can determine on a genome-wide scale and in high-throughput, whether a gene, or a specific genomic region, is important for fitness under a specific experimental condition.

Results
Here, we present MAGenTA, a suite of analysis tools which accurately calculate the growth rate for each disrupted gene in the genome to enable the discovery of: (i) new leads for gene function, (ii) non-coding RNAs; (iii) genes, pathways and ncRNAs that are involved in tolerating drugs or induce disease; (iv) higher order genome organization; and (v) host-factors that affect bacterial host susceptibility. MAGenTA is a complete Tn-Seq analysis pipeline making sensitive genome-wide fitness (i.e. growth rate) analysis available for most transposons and Tn-Seq associated approaches (e.g. TraDis, HiTS, IN-Seq) and includes fitness (growth rate) calculations, sliding window analysis, bottleneck calculations and corrections, statistics to compare experiments and strains and genome-wide fitness visualization.

Availability and implementation
MAGenTA is available at the Galaxy public ToolShed repository and all source code can be found and are freely available at https://vanopijnenlab.github.io/MAGenTA/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Are star formation rates of galaxies bimodal?
Authors: Feldmann Robert 
Published: May 2017

Abstract
Star formation rate (SFR) distributions of galaxies are often assumed to be bimodal with modes corresponding to star-forming and quiescent galaxies, respectively. Both classes of galaxies are typically studied separately, and SFR distributions of star-forming galaxies are commonly modelled as lognormals. Using both observational data and results from numerical simulations, I argue that this division into star-forming and quiescent galaxies is unnecessary from a theoretical point of view and that the SFR distributions of the whole population can be well fitted by zero-inflated negative binomial distributions. This family of distributions has three parameters that determine the average SFR of the galaxies in the sample, the scatter relative to the star-forming sequence and the fraction of galaxies with zero SFRs, respectively. The proposed distributions naturally account for (i) the discrete nature of star formation, (ii) the presence of ‘dead’ galaxies with zero SFRs and (iii) asymmetric scatter. Excluding ‘dead’ galaxies, the distribution of log SFR is unimodal with a peak at the star-forming sequence and an extended tail towards low SFRs. However, uncertainties and biases in the SFR measurements can create the appearance of a bimodal distribution.
Core Competencies or a Competent Core? A Scoping Review and Realist Synthesis of Invasive Bedside Procedural Skills Training in Internal Medicine
Authors: Brydges Ryan , Stroud Lynfa , Wong Brian M. , Holmboe Eric S. , Imrie Kevin , Hatala Rose 
Published: May 2017

Purpose
Invasive bedside procedures are core competencies for internal medicine, yet no formal training guidelines exist. The authors conducted a scoping review and realist synthesis to characterize current training for lumbar puncture, arthrocentesis, paracentesis, thoracentesis, and central venous catheterization. They aimed to collate how educators justify using specific interventions, establish which interventions have the best evidence, and offer directions for future research and training.

Method
The authors systematically searched Medline, Embase, the Cochrane Library, and ERIC through April 2015. Studies were screened in three phases; all reviews were performed independently and in duplicate. The authors extracted information on learner and patient demographics, study design and methodological quality, and details of training interventions and measured outcomes. A three-step realist synthesis was performed to synthesize findings on each study’s context, mechanism, and outcome, and to identify a foundational training model.

Results
From an initial 6,671 studies, 149 studies were further reduced to 67 (45%) reporting sufficient information for realist synthesis. Analysis yielded four types of procedural skills training interventions. There was relative consistency across contexts and significant differences in mechanisms and outcomes across the four intervention types. The medical procedural service was identified as an adaptable foundational training model.

Conclusions
The observed heterogeneity in procedural skills training implies that programs are not consistently developing residents who are competent in core procedures. The findings suggest that researchers in education and quality improvement will need to collaborate to design training that develops a “competent core” of proceduralists using simulation and clinical rotations.
Radial Head Ingrowth Anatomic Implant Versus Smooth Stem Monoblock Implant in Acute Terrible Triad Injury: A Prospective Comparative Study
Authors: Rodriguez-Quintana David , Comulada David Beaton , Rodriguez-Quintana Natalie , Lopez-Gonzalez Francisco 
Published: May 2017

Objective:
This study aimed to compare clinical outcomes and radiographic findings between patients who received 2 different implants (smooth-stemmed modular implant or an anatomic press-fit implant) on patients with acute terrible triad injuries.

Design:
Prospective cohort.

Setting:
Level II Trauma center, University hospital.

Patients/Participants:
Thirty-four patients with an isolated terrible triad injury were divided into 2 study groups (n = 17 each) with different sets of radial head implants and followed for 2 years. A total of 14 patients in each group (n = 28) completed the study.

Intervention:
Group 1 received a smooth-stemmed round modular monopolar implant. Group 2 received an in-growth modular monopolar press-fit anatomic implant.

Main Outcome Measurements:
Clinical outcomes were evaluated using the Visual Analog Scale, Mayo Index, and Disabilities of the Arm, Shoulder, and Hand (DASH) survey. Radiographs were evaluated for ectopic bone formation and loosening.

Results:
No difference in clinical outcome when comparing range of motion and functionally scores between groups. Ectopic bone formation occurred equally with implants. Bone formation at the proximal radius under the implant occurred more in group 1 (85.7%), (P = 0.046). Five press-fit stems had radiolucent lines at 2-year follow-up. Two were removed because of symptomatic loosening.

Conclusions:
Short-term outcomes for both implants showed to be equally effective treatment options. The in vitro biomechanical advantages of anatomic implants do not translate into short-term improved outcomes. Symptomatic aseptic loosening in anatomic implants is common. Bone formation at the proximal radial neck was observed more with smooth-stemmed implants; further studies should assess this findings and clinical implication.

Level of Evidence:
Therapeutic Level II. See Instructions for Authors for a complete description of levels of evidence.
A Novel Computerized Test for Detecting and Monitoring Visual Attentional Deficits and Delirium in the ICU
Authors: Green Cameron , Hendry Kirsty , Wilson Elizabeth S. , Walsh Timothy , Allerhand Mike , MacLullich Alasdair M. J. , Tieges Zoë 
Published: May 2017

Objectives:
Delirium in the ICU is associated with poor outcomes but is under-detected. Here we evaluated performance of a novel, graded test for objectively detecting inattention in delirium, implemented on a custom-built computerized device (Edinburgh Delirium Test Box–ICU).

Design:
A pilot study was conducted, followed by a prospective case-control study.

Setting:
Royal Infirmary of Edinburgh General ICU.

Patients:
A pilot study was conducted in an opportunistic sample of 20 patients. This was followed by a validation study in 30 selected patients with and without delirium (median age, 63 yr; range, 23–84) who were assessed with the Edinburgh Delirium Test Box–ICU on up to 5 separate days. Presence of delirium was assessed using the Confusion Assessment Method for the ICU.

Measurements and Main Results:
The Edinburgh Delirium Test Box–ICU involves a behavioral assessment and a computerized test of attention, requiring patients to count slowly presented lights. Thirty patients were assessed a total of 79 times (n = 31, 23, 15, 8, and 2 for subsequent assessments; 38% delirious). Edinburgh Delirium Test Box–ICU scores (range, 0–11) were lower for patients with delirium than those without at the first (median, 0 vs 9.5), second (median, 3.5 vs 9), and third (median, 0 vs 10.5) assessments (all p < 0.001). An Edinburgh Delirium Test Box–ICU score less than or equal to 5 was 100% sensitive and 92% specific to delirium across assessments. Longitudinally, participants’ Edinburgh Delirium Test Box–ICU performance was associated with delirium status.

Conclusions:
These findings suggest that the Edinburgh Delirium Test Box–ICU has diagnostic utility in detecting ICU delirium in patients with Richmond Agitation and Sedation Scale Score greater than –3. The Edinburgh Delirium Test Box–ICU has potential additional value in longitudinally tracking attentional deficits because it provides a range of scores and is sensitive to change.
PREDICTORS OF REFRACTORY MACULAR EDEMA AFTER BRANCH RETINAL VEIN OCCLUSION FOLLOWING INTRAVITREAL BEVACIZUMAB
Authors: Moon Byung Gil , Cho Ah Ran , Kim You Na , Kim June-Gone 
Published: May 2017

Purpose:
To evaluate the predictors of refractory macular edema (ME) that develops despite multiple bevacizumab injections in patients with branch retinal vein occlusion (BRVO).

Methods:
A total of 107 patients who followed at least 2 years were assigned to 2 groups: a refractory group (n = 56) and a responsive group (n = 51). Baseline characteristics, treatment response at 3 months, and fluorescein angiographic findings at 6 months were compared. Then we tried to identify factors associated with refractory ME development.

Results:
Compared to the responsive group, the refractory group had older age, longer pre-treatment duration, and shorter occlusion distance from disk. At 3 months, the refractory group exhibited lower visual acuity, thicker central retinal thickness (CRT), and larger proportion of external limiting membrane (ELM) and outer plexiform layer disruption. After 6 months, proportion of unresolved vein occlusion, macular ischemia, number of microaneurysms, and non-perfusion areas were higher in the refractory group. Refractory ME was associated with pre-treatment duration ≥3 months, short occlusion distance from disk, thick CRT and ELM disruption at 3 months, and unresolved vein occlusion at 6 months.

Conclusion:
If BRVO-ME patients exhibit the above-mentioned characteristics, they may have refractory ME, which should inform treatment decisions.
DYSFUNCTIONAL AUTONOMIC REGULATION OF THE CHOROID IN CENTRAL SEROUS CHORIORETINOPATHY
Authors: Nathaniel Roybal C. , Sledz Elisabeth , Elshatory Yasser , Zhang Li , Almeida David R. P. , Chin Eric K. , Critser Brice , Abramoff Michael D. , Russell Stephen R. 
Published: May 2017

Purpose:
To study the effect of changing perfusion pressures on retinal and choroidal structure in central serous chorioretinopathy (CSC).

Methods:
This prospective observational case series included seven healthy volunteers (14 eyes) and seven patients (14 eyes) with CSC. Each patient underwent spectral domain optical coherence tomography with enhanced depth imaging in the upright (sitting) and supine positions. Image segmentation focused on central macular thickness, subretinal fluid, total macular volume, choroidal thickness, and choriocapillaris thickness. Blood pressure and heart rate were measured in the upright and supine positions.

Results:
Choriocapillaris thickness was thicker in CSC participants (34.23 μm; range, 30.9–36.5 μm) compared with healthy controls (13.96 μm; range, 7.15–23.87 μm) (P ≤ 0.001). The choroid was similarly thicker in CSC participants (371.4 μm; range, 200.2–459.4 μm) compared with healthy controls (231.4 μm; range 161.8–287.5 μm) (P ≤ 0.001). Choroidal thickness increased in patients with CSC when transitioning from upright (371.4 μm) to supine (377.8 μm) (P ≤ 0.01). By contrast, there was an 11.97% decrease in choroid thickness in normal controls when transitioning from upright (231.4 μm) to supine (203.9 μm). There were no significant hemodynamic changes.

Conclusion:
We demonstrated that choroidal thickness increased in response to increased perfusion pressures in patients with CSC and not in normal controls. These findings likely represent an autonomic dysregulation of choroidal blood flow in patients with CSC.
CLASSIFICATION OF HALLER VESSEL ARRANGEMENTS IN ACUTE AND CHRONIC CENTRAL SEROUS CHORIORETINOPATHY IMAGED WITH EN FACE OPTICAL COHERENCE TOMOGRAPHY
Authors: Savastano Maria C. , Dansingani Kunal K. , Rispoli Marco , Virgili Gianni , Savastano Alfonso , Freund K. Bailey , Lumbroso Bruno 
Published: May 2017

Purpose:
To compare the prevailing patterns of Haller vessel arrangements at the posterior pole between healthy eyes and those with central serous chorioretinopathy (CSC) using en face optical coherence tomography.

Methods:
Eyes of normal subjects and patients with acute or chronic CSC underwent optical coherence tomography imaging (RTVue 100; Optovue Inc, Fremont, CA). En face sections at the level of the Haller layer were classified by two masked graders into five mutually exclusive morphologic categories (temporal herringbone, branched from below, laterally diagonal, double arcuate, and reticular). The relative prevalence of each Haller vessel arrangement pattern was determined for each phenotype.

Results:
Numbers of eyes examined were as follows: 154 eyes of 77 normal subjects; 41 eyes of 31 patients with acute CSC; and 39 eyes of 33 patients with chronic CSC. The mean age of participants was 44.4 ± 14.6 years for healthy subjects (M:F = 37:40), 48.5 ± 8.2 years (M:F = 24:7) for acute CSC, and 65.3 ± 13.1 years (M:F = 28:5) for chronic CSC. The relative prevalence of each Haller vessel arrangement pattern differed by phenotype. The temporal herringbone pattern was most prevalent in healthy eyes (49.2%), whereas a reticular pattern was most prevalent in eyes with acute and/or chronic CSC (combined, 48.8%).

Conclusion:
A significant difference was observed in the prevalence of respective Haller vessel arrangement patterns between eyes of normal subjects and those of patients with either acute or chronic CSC. Although further study is needed to determine the mechanistic factors underlying these differences, and the hemodynamic implications, our data suggest that en face optical coherence tomography may find a formal role in choroidal disease classification.
Femtosecond Laser Assisted Pterygium Surgery
Authors: Fuest Matthias , Liu Yu-Chi , Coroneo Minas T. , Mehta Jodhbir S. 
Published: May 2017

Purpose:
Pterygium is a prevalent ocular surface disorder. Conjunctival autografting (CAG) after pterygium resection is the gold standard treatment. Thinner CAGs without Tenon tissue provide better results but are technically difficult to achieve. We report on the first femtosecond laser (FSL)-assisted pterygium surgery (FLAPS) in humans.

Methods:
In a clinical trial, we treated 6 eyes of 5 patients with FLAPS. After manual removal of the pterygium, CAGs were dissected with the Ziemer Z8 at 60-μm depth and glued into the resection defect. CAG thickness and diameter were measured.

Results:
The CAG area measured 17.9% smaller than the laser settings (P = 0.03). Central (75.6 ± 13.7 μm) and peripheral (77.7 ± 13.2 μm) CAG thickness did not differ significantly (P = 0.3). No buttonholes or CAG tags occurred. The mean dissection time was 19.5 ± 1.2 seconds, and the time to remove the FSL-prepared CAG and to unfold it onto the cornea was 10.3 ± 3.8 seconds. During 35.8 ± 38.0 days of follow-up, no postoperative complication or recurrences occurred. The conjunctival epithelium had healed at the CAG resection site within 1 week with no evidence of scarring.

Conclusions:
FLAPS is a new technique, in which the preparation of an ultrathin CAG is done by the FSL. After optimization in porcine eyes, the clinical trial in the first 6 eyes was performed without any complications and the FSL might assist in further standardizing the surgical procedure. Longer follow-up and larger cohorts are needed to assess recurrence rates.
Bilateral Herpetic Keratitis After Bilateral Intravitreal Bevacizumab for Exudative Macular Degeneration
Authors: Derham Angeline M. , Chen Eric , Bunya Vatinee Y. , O'Malley Ronan E. 
Published: May 2017

Purpose:
To report a case of bilateral herpetic epithelial keratitis after bilateral intravitreal bevacizumab injections for the treatment of exudative age-related macular degeneration.

Methods:
A 66-year-old man with diabetes and an extensive history of bilateral anti-vascular endothelial growth factor treatments for exudative age-related macular degeneration received an intravitreal bevacizumab injection in the right eye and triple therapy (bevacizumab, photodynamic therapy, and triamcinolone acetonide) in the left eye. After 4 days, he presented with pain, photophobia, tearing, and decreased vision in both eyes. Slit-lamp examination revealed bilateral dendritic epithelial lesions with terminal bulbs, and he was diagnosed with bilateral herpes simplex epithelial keratitis.

Results:
The patient was treated with ganciclovir ophthalmic ointment and oral acyclovir with resolution of signs and symptoms.

Conclusions:
To our knowledge, this is the first documented account of bilateral herpetic epithelial keratitis after bilateral intravitreal bevacizumab injections.