bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors Related to Increased Ulnar Collateral Ligament Thickness on Stress Sonography of the Elbow in Asymptomatic Youth and Adolescent Baseball Pitchers
Authors: Atanda Alfred , Averill Lauren W. , Wallace Maegen , Niiler Tim A. , Nazarian Levon N. , Ciccotti Michael G. 
Published: September 2016

Background: Stress ultrasound (SUS) of the elbow has demonstrated changes in the anterior band of the ulnar collateral ligament (UCL) in professional and high school–aged pitchers. However, there have been no large reports correlating pitching history data with SUS changes in youth and adolescent baseball pitchers. Hypothesis: Changes of the UCL on SUS will correlate with pitching volume in youth and adolescent baseball pitchers. Study Design: Cross-sectional study; Level of evidence, 3. Methods: SUS of the elbow was performed in both elbows of 102 youth and adolescent baseball pitchers. UCL thickness and the width of the ulnohumeral joint, at rest and with 150 N of valgus stress, were measured using a standardized, instrumented device. Demographic data, arm measurements, and a pitching history questionnaire were recorded as well. The pitchers were separated into 2 groups based on age: group 1 (12-14 years) and group 2 (15-18 years). SUS findings of the dominant elbows were compared between the 2 groups. Correlation analysis and linear regression were used to identify relationships between SUS findings and pitching history data. Results: In all pitchers, the mean UCL thickness was 4.40 mm in the dominant elbow and 4.11 mm in the nondominant elbow ( P =.03). There was no significant difference between elbows in any joint space characteristics. A comparison of group 1 versus group 2 demonstrated significant differences in UCL thickness (4.13 vs 4.96 mm; P < .001), resting joint space width (6.56 vs 4.04 mm; P < .001), and stressed joint space width (7.68 vs 4.07 mm; P < .001). There was no difference in the change in joint space width between the 2 groups (1.11 vs 0.76 mm; P = .05). The UCL was significantly thicker in pitchers who threw more than 67 pitches per appearance (4.69 vs 4.14 mm), who pitched more than 5 innings per appearance (4.76 vs 4.11 mm), and who had more than 5.5 years of pitching experience (4.71 vs 4.07 mm; P < .001). Linear regression demonstrated that age, weight, and pitches per appearance ( R2 = 0.114, 0.370, and 0.326, respectively) significantly correlated with UCL thickness. Conclusion: These findings suggest that UCL thickness increases as pitchers get older and heavier and as they increase their pitch volumes.
The lupus impact tracker is responsive to changes in clinical activity measured by the systemic lupus erythematosus responder index
Authors: Devilliers H , Bonithon-Kopp C , Jolly M 
Published: September 2016

Objective The lupus impact tracker (LIT) is a 10-item patient reported outcome tool to measure the impact of systemic lupus erythematosus or its treatment on patients’ daily lives. Herein, we describe the responsiveness of the LIT and LupusQoL to changes in disease activity, using the systemic lupus erythematosus responder index (SRI). Methods A total of 325 adult systemic lupus erythematosus patients were enrolled in an observational, longitudinal, multicentre study, conducted across the USA and Canada. Data (demographics, LIT, LupusQoL, BILAG, SELENA–SLEDAI) were obtained three months apart. Modified SRI was defined as: a decrease in SELENA–SLEDAI (4 points); no new BILAG A, and no greater than one new BILAG B; and no increase in the physician global assessment. Standardised response mean and effect size for LIT and LupusQoL domains were calculated among SRI responders and non-responders. Wilcoxon’s test was used to compare the LIT and LupusQoL variation by SRI responder status. Results Of the participants 90% were women, 53% were white, 33% were of African descendant and 17% were Hispanic. Mean (SD) age and SELENA–SLEDAI at baseline were 42.3 (16.2) years and 4.3 (3.8), respectively. Mean (SD) LIT score at baseline was 39.4 (22.9). LIT standardised response mean (effect size) among SRI responders and non-responders were −0.69 (−0.36) and −0.20 (−0.12), respectively ( P = 0.02). For LupusQoL, two domains were responsive to SRI: standardised response mean (effect size) for physical health and pain domains were 0.42 (0.23) and 0.65 (0.44), respectively. Conclusions LIT is moderately responsive to SRI in patients with systemic lupus erythematosus. Inclusion of this tool in clinical care and clinical trials may provide further insights into its responsiveness. This is the first systemic lupus erythematosus patient reported outcome tool to be evaluated against composite responder index (SRI) used in clinical trials.
Bone Marrow Edema Syndrome in the Foot and Ankle
Authors: Mirghasemi Seyed Alireza , Trepman Elly , Sadeghi Mohammad Saleh , Rahimi Narges , Rashidinia Shervin 
Published: September 2016

Bone marrow edema syndrome (BMES) is an uncommon and self-limited syndrome characterized by extremity pain of unknown etiology. Symptoms may include sudden or gradual onset of swelling and pain at rest or during activity, usually at night. This syndrome mostly affects middle-aged men and younger women who have pain in the lower extremities. The most common sites involved with BMES, in decreasing order of frequency, are the bones about the hip, knee, ankle, and foot. The diagnosis of BMES is confirmed with magnetic resonance imaging to exclude other causes of bone marrow edema. The correct diagnosis in the foot and ankle often is delayed because of the low prevalence and nonspecific signs. This delay may intensify bone pain and impair patient function and quality of life. The goal of BMES treatment is to relieve pain and shorten disease duration. Treatment options are limited and may include symptomatic treatment, pharmacologic treatment, and surgery. Level of Evidence: Level V, expert opinion.
The Nellix™ EndoVascular sealing system in patients with abdominal aortic aneurysms in conjunction with iliac artery occlusive disease
Authors: van Sterkenburg Steven MM , van den Ham Leo H , Smeets Luuk , Lardenoije Jan-Willem , Reijnen Michel MPJ 
Published: September 2016

Introduction Concomitant abdominal aortic aneurysm formation and aortoiliac occlusive disease is a challenging combination, often requiring open reconstructive surgery. In this study, we have assessed a single center experience of the Nellix EndoVascular Aneurysm Sealing System in the treatment of an abdominal aortic aneurysm in conjunction with iliac artery occlusive disease. Methods Retrospectively case files of patients treated with Nellix EndoVascular Aneurysm Sealing System in a single center were reviewed. The primary endpoints of the study were the technical success of Nellix EndoVascular Aneurysm Sealing System in patients with coincidental iliac artery occlusive disease and the successful exclusion of the aneurysm during follow-up. Results Of the 96 patients that were treated with Nellix EndoVascular Aneurysm Sealing System, five were identified that had an abdominal aortic aneurysm in conjunction with iliac artery occlusive disease. Treated patients had either unilateral (n = 4) or bilateral (n = 1) common iliac artery occlusive disease varying from 70% stenosis to complete occlusions. The lesion length varied from 5 to 50 mm and in two cases it involved an occluded bare metal stent. The indication for surgery was the abdominal aortic aneurysm in all patients, including three also suffering from claudication. In all patients the iliac artery occlusive disease was pretreated with balloon-expandable covered stents. Technical success was achieved in all five patients. After a median follow-up of nine months all stents were patent with no signs of endoleak and stable aneurysm diameters. All patients were free of intermittent claudication or ischemic wounds. Conclusion Nellix EndoVascular Aneurysm Sealing System seems feasible and safe in patients with a combination of abdominal aortic aneurysm and iliac artery occlusive disease.
Upper airway and systemic inflammation in obstructive sleep apnoea
Authors: Vicente Eugenio , Marin Jose M. , Carrizo Santiago J. , Osuna Carlos S. , González Ricardo , Marin-Oto Marta , Forner Marta , Vicente Paul , Cubero Pablo , Gil Ana V. , Soler Xavier 
Published: September 2016

Obstructive sleep apnoea (OSA) is associated with pharyngeal inflammation, but the coexistence of systemic inflammation is controversial. This study investigated whether local and systemic inflammatory biomarkers are related in patients with OSA. An uncontrolled extension to the study assessed the response to effective treatment.We recruited 89 patients with OSA (apnoea/hypopnoea index (AHI) ≥5 events·h−1), 28 snorers and 26 healthy controls. Pharyngeal lavage (PHAL) and plasma samples were collected at baseline and after a 1-year follow-up. Inflammatory cells were evaluated by flow cytometry; interleukin (IL)-6, IL-8 and tumour necrosis factor-α were evaluated by immunoassay.In PHAL, CD4+T-cells, IL-6 and IL-8 were higher in OSA patients than in snorers or healthy controls (p<0.05). The AHI correlated with CD4+, IL-6 and IL-8 in PHAL (all p-values <0.05). There were no differences in the inflammatory biomarkers in plasma between the study groups and no relationship between plasma and PHAL biomarkers. Biomarkers decreased significantly in PHAL but not in plasma after 1 year of therapy with continuous positive airway pressure or surgery.In patients with OSA, increased levels of inflammatory biomarkers were found in PHAL, which were reduced with effective treatment. No simultaneous increase in plasma inflammatory biomarkers was found.
Control theory prediction of resolved Cheyne−Stokes respiration in heart failure
Authors: Sands Scott A. , Edwards Bradley A. , Kee Kirk , Stuart-Andrews Christopher , Skuza Elizabeth M. , Roebuck Teanau , Turton Anthony , Hamilton Garun S. , Naughton Matthew T. , Berger Philip J. 
Published: September 2016

Cheyne–Stokes respiration (CSR) foretells deleterious outcomes in patients with heart failure. Currently, the size of therapeutic intervention is not guided by the patient's underlying pathophysiology. In theory, the intervention needed to resolve CSR, as a control system instability (loop gain >1), can be predicted knowing the baseline loop gain and how much it falls with therapy.In 12 patients with heart failure, we administered an inspiratory carbon dioxide fraction of 1–3% during CSR (n=95 interventions) as a means to reduce loop gain. We estimated the loop gain on therapy (LGtherapy), using the baseline loop gain (using hyperpnoea length/cycle length) and its expected reduction (18% per 1% inspired carbon dioxide), and tested the specific hypothesis that LGtherapypredicts CSR persistence (LGtherapy>1)versusresolution (LGtherapy<1).As predicted, when LGtherapy>1.0, CSR continued during therapy in 23 out of 25 (92%) trials. A borderline loop gain zone (0.8<LGtherapy<1) yielded an unpredictable outcome, while LGtherapy<0.8 consistently yielded CSR resolution (37 out of 37 trials). A threshold of LGtherapy=0.9 determined outcome in 76 out of 95 (80%) trials.We establish proof-of-concept that control theory provides predictive insight into CSR resolution in heart failure. Thus, we now have a means to calculate the size of interventions needed to ameliorate CSR on a patient-by-patient basis.
The parameter sensitivity of random forests
Authors: Huang Barbara F.F. , Boutros Paul C. 
Published: September 2016

AbstractBackgroundThe Random Forest (RF) algorithm for supervised machine learning is an ensemble learning method widely used in science and many other fields. Its popularity has been increasing, but relatively few studies address the parameter selection process: a critical step in model fitting. Due to numerous assertions regarding the performance reliability of the default parameters, many RF models are fit using these values. However there has not yet been a thorough examination of the parameter-sensitivity of RFs in computational genomic studies. We address this gap here.ResultsWe examined the effects of parameter selection on classification performance using the RF machine learning algorithm on two biological datasets with distinctp/nratios: sequencing summary statistics (lowp/n) and microarray-derived data (highp/n). Here,p,refers to the number of variables and,n, the number of samples. Our findings demonstrate that parameterization is highly correlated with prediction accuracy and variable importance measures (VIMs). Further, we demonstrate that different parameters are critical in tuning different datasets, and that parameter-optimization significantly enhances upon the default parameters.ConclusionsParameter performance demonstrated wide variability on both low and highp/ndata. Therefore, there is significant benefit to be gained by model tuning RFs away from their default parameter settings.
MMinte: an application for predicting metabolic interactions among the microbial species in a community
Authors: Mendes-Soares Helena , Mundy Michael , Soares Luis Mendes , Chia Nicholas 
Published: September 2016

Abstract
Background
The explosive growth of microbiome research has yielded great quantities of data. These data provide us with many answers, but raise just as many questions. 16S rDNA—the backbone of microbiome analyses—allows us to assess α-diversity, β-diversity, and microbe-microbe associations, which characterize the overall properties of an ecosystem. However, we are still unable to use 16S rDNA data to directly assess the microbe-microbe and microbe-environment interactions that determine the broader ecology of that system. Thus, properties such as competition, cooperation, and nutrient conditions remain insufficiently analyzed. Here, we apply predictive community metabolic models of microbes identified with 16S rDNA data to probe the ecology of microbial communities.

Results
We developed a methodology for the large-scale assessment of microbial metabolic interactions (MMinte) from 16S rDNA data. MMinte assesses the relative growth rates of interacting pairs of organisms within a community metabolic network and whether that interaction has a positive or negative effect. Moreover, MMinte’s simulations take into account the nutritional environment, which plays a strong role in determining the metabolism of individual microbes. We present two case studies that demonstrate the utility of this software. In the first, we show how diet influences the nature of the microbe-microbe interactions. In the second, we use MMinte’s modular feature set to better understand how the growth of Desulfovibrio piger is affected by, and affects the growth of, other members in a simplified gut community under metabolic conditions suggested to be determinant for their dynamics.

Conclusion
By applying metabolic models to commonly available sequence data, MMinte grants the user insight into the metabolic relationships between microbes, highlighting important features that may relate to ecological stability, susceptibility, and cross-feeding. These relationships are at the foundation of a wide range of ecological questions that impact our ability to understand problems such as microbially-derived toxicity in colon cancer.
JNK inhibition reduces lung remodeling and pulmonary fibrotic systemic markers
Authors: van der Velden Jos L. J. , Ye Ying , Nolin James D. , Hoffman Sidra M. , Chapman David G. , Lahue Karolyn G. , Abdalla Sarah , Chen Peng , Liu Yong , Bennett Brydon , Khalil Nasreen , Sutherland Donna , Smith William , Horan Gerald , Assaf Mahmoud , Horowitz Zebulun , Chopra Rajesh , Stevens Randall M. , Palmisano Maria , Janssen‐Heininger Yvonne M. W. , Schafer Peter H. 
Published: September 2016

AbstractBackgroundLung remodeling and pulmonary fibrosis are serious, life‐threatening conditions resulting from diseases such as chronic severe asthma and idiopathic pulmonary fibrosis (IPF). Preclinical evidence suggests that JNK enzyme function is required for key steps in the pulmonary fibrotic process. However, a selective JNK inhibitor has not been investigated in translational models of lung fibrosis with clinically relevant biomarkers, or in IPF patients.MethodsThe JNK inhibitor CC‐930 was evaluated in the house dust mite‐induced fibrotic airway mouse model, in a phase I healthy volunteer pharmacodynamic study, and subsequently in a phase II multicenter study of mild/moderate IPF (n = 28), with a 4‐week, placebo‐controlled, double‐blind, sequential ascending‐dose period (50 mg QD, 100 mg QD, 100 mg BID) and a 52‐week open‐label treatment‐extension period.ResultsIn the preclinical model, CC‐930 attenuated collagen 1A1 gene expression, peribronchiolar collagen deposition, airway mucin MUC5B expression in club cells, and MMP‐7 expression in lung, bronchoalveolar lavage fluid, and serum. In the phase I study, CC‐930 reduced c‐Jun phosphorylation induced by UV radiation in skin. In the phase II IPF study, there was a CC‐930 dose‐dependent trend in reduction of MMP‐7 and SP‐D plasma protein levels. The most commonly reported adverse events were increased ALT, increased AST, and upper respiratory tract infection (six subjects each, 21.4 %). A total of 13 subjects (46.4 %) experienced adverse events that led to discontinuation of study drug. Nine out of 28 subjects experienced progressive disease in this study. The mean FVC (% predicted) declined after 26–32 weeks at doses of 100 mg QD and 100 mg BID. Changes in MMP‐7, SP‐D, and tenascin‐C significantly correlated with change in FVC (% predicted).ConclusionsThese results illustrate JNK enzymatic activity involvement during pulmonary fibrosis, and support systemic biomarker use for tracking disease progression and the potential clinical benefit of this novel intervention in IPF.Trial registration ClinicalTrials.gov NCT01203943
Multi-analytical investigation into painting materials and techniques: the wall paintings of Abuna Yemata Guh church
Authors: Gebremariam Kidane Fanta , Kvittingen Lise , Nicholson David Graham 
Published: September 2016

Abstract
Abuna Yemata Guh is one of the nine Saints who are traditionally claimed to have come to Northern Ethiopia in the beginning of the sixth century and established monasteries in the Tigray region. The church, named after him, is hewn out of the side of one of the highest sandstone spires in the Gheralta area. Though the local tradition claims earlier dates, the paintings in the church are suggested to belong to the second half of the fifteenth century on the basis of their theme, style and iconography. We report here the investigation into the materials and techniques of the paintings using diverse complementary analytical techniques: Polarized light microscopy (PLM), portable X-ray fluorescence spectrometer (pXRF), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM–EDS), synchrotron-based X-ray diffraction (SR-XRD), pyrolysis gas chromatography-mass spectrometry (Py-GC/MS), micro-Raman spectroscopy (MRS) and micro-Fourier transform infrared spectroscopy (micro-FTIR). Earth materials based on hematite, goethite and terra verte were the main findings, but cinnabar, orpiment, lead white and carbon black were also identified. The stratigraphic analyses of samples from different locations coupled with SR-XRD analysis indicated the presence of anhydrite, gypsum, calcite and lime in the preparation layer. The pigments identified together with close visual examination showed repainting and retouching within the area in which the Marian figure is depicted, as well as in a nearby figure. The ground preparatory layer consisted of red mud reinforced by straw applied to the chiseled sandstone support. The egg-based binding medium suggests that tempera technique was used. Technical studies of Ethiopian wall paintings are scant, but highly needed as this world heritage is threatened due to limited conservation. Our documentation of the materials and techniques is therefore aimed to stem this loss, as well as to provide information for art historical studies.
Genomic sequence analysis of a plant-associated Photobacterium halotolerans MELD1: from marine to terrestrial environment?
Authors: Mathew Dony Chacko , Lo Shou-Chen , Mathew Gincy Marina , Chang Kung-Hao , Huang Chieh-Chen 
Published: September 2016

AbstractMercury impacts the function and development of the central nervous system in both humans and wildlife by being a potent neurotoxin. Microbial bioremediation is an important means of remediation of mercury-contaminated soil. The rhizospheric Photobacterium halotolerans strain MELD1 was isolated from mercury and dioxin contaminated site from Tainan, Taiwan. It has been shown to reduce Hg2+ to Hg0. The 4,758,027 bp genome of P. halotolerans MELD1 has a G + C content of 50.88 % and contains 4198 protein-coding and 106 RNA genes. Genomic analysis revealed the presence of a number of interesting gene cluster that maybe involved in heavy metal resistance, rhizosphere competence and colonization of the host plant.
Draft genome sequence of Acinetobacter baumannii strain NCTC 13423, a multidrug-resistant clinical isolate
Authors: Michiels Joran E. , Van den Bergh Bram , Fauvart Maarten , Michiels Jan 
Published: September 2016

AbstractAcinetobacter baumannii is a pathogen that is becoming increasingly important and causes serious hospital-acquired infections. We sequenced the genome of A. baumannii NCTC 13423, a multidrug-resistant strain belonging to the international clone II group, isolated from a human infection in the United Kingdom in 2003. The 3,937,944 bp draft genome has a GC-content of 39.0 % and a total of 3672 predicted protein-coding sequences. The availability of genome sequences of multidrug-resistant A. baumannii isolates will fuel comparative genomic studies to help understand the worrying spread of multidrug resistance in this pathogen.
Gli2 gene-environment interactions contribute to the etiological complexity of holoprosencephaly: evidence from a mouse model
Authors: Heyne Galen W. , Everson Joshua L. , Ansen-Wilson Lydia J. , Melberg Cal G. , Fink Dustin M. , Parins Kia F. , Doroodchi Padydeh , Ulschmid Caden M. , Lipinski Robert J. 
Published: September 2016

ABSTRACT
Holoprosencephaly (HPE) is a common and severe human developmental abnormality marked by malformations of the forebrain and face. Although several genetic mutations have been linked to HPE, phenotypic outcomes range dramatically, and most cases cannot be attributed to a specific cause. Gene-environment interaction has been invoked as a premise to explain the etiological complexity of HPE, but identification of interacting factors has been extremely limited. Here, we demonstrate that mutations in Gli2, which encodes a Hedgehog pathway transcription factor, can cause or predispose to HPE depending upon gene dosage. On the C57BL/6J background, homozygous GLI2 loss of function results in the characteristic brain and facial features seen in severe human HPE, including midfacial hypoplasia, hypotelorism and medial forebrain deficiency with loss of ventral neurospecification. Although normally indistinguishable from wild-type littermates, we demonstrate that mice with single-allele Gli2 mutations exhibit increased penetrance and severity of HPE in response to low-dose teratogen exposure. This genetic predisposition is associated with a Gli2 dosage-dependent attenuation of Hedgehog ligand responsiveness at the cellular level. In addition to revealing a causative role for GLI2 in HPE genesis, these studies demonstrate a mechanism by which normally silent genetic and environmental factors can interact to produce severe outcomes. Taken together, these findings provide a framework for the understanding of the extreme phenotypic variability observed in humans carrying GLI2 mutations and a paradigm for reducing the incidence of this morbid birth defect.