bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduction in the Cesarean Delivery Rate After Obstetric Care Consensus Guideline Implementation
Authors: Wilson-Leedy Jonas G. , DiSilvestro Alexis J. , Repke John T. , Pauli Jaimey M. 
Published: June 2016

OBJECTIVE:To evaluate the rate of primary cesarean delivery after adopting labor management guidelines.METHODS:This is a before–after retrospective cohort study at a single academic center. This center adopted guidelines from the Consensus for the Prevention of the Primary Cesarean Delivery. Nulliparous women attempting vaginal delivery with viable, singleton, vertex fetuses were included. For the primary outcome of cesarean delivery rate among induced or augmented patients, 200 consecutive women managed before guideline adoption were compared with 200 similar patients afterward. Secondary outcomes of overall cesarean delivery rate, maternal morbidity, neonatal outcomes, and labor management practices were analyzed with inclusion of intervening spontaneously laboring women.RESULTS:Between September 13, 2013, and September 28, 2014, 275 women preguideline and 292 postguideline were identified to include 200 deliveries after induction or augmentation each. Among women delivering after induction or augmentation, the cesarean delivery rate decreased from 35.5% to 24.5% (odds ratio [OR] 0.59, 95% confidence interval [CI] 0.38–0.91). The overall cesarean delivery rate decreased from 26.9% to 18.8% (adjusted OR 0.59, CI 0.38–0.92). Composite maternal morbidity was reduced (adjusted OR 0.66, CI 0.46–0.94). The frequency of cesarean delivery documenting arrest of dilation at less than 6 cm decreased from 7.1% to 1.1% postguideline (n=182 and 176 preguideline and postguideline, respectively,P=.006) with no change in other indications.CONCLUSION:Postguideline, the cesarean delivery rate among nulliparous women attempting vaginal delivery was substantially reduced in association with decreased frequency in the diagnosis of arrest of dilation at less than 6 cm.
Venous Thromboembolism in Minimally Invasive Compared With Open Hysterectomy for Endometrial Cancer
Authors: Barber Emma L. , Gehrig Paola A. , Clarke-Pearson Daniel L. 
Published: June 2016

OBJECTIVE:
To evaluate whether minimally invasive surgery for endometrial cancer is independently associated with a decreased odds of venous thromboembolism compared with open surgery.

METHODS:
We performed a secondary analysis cohort study of prospectively collected quality improvement data and examined patients undergoing hysterectomy for endometrial cancer from 2008 to 2013 recorded in the National Surgical Quality Improvement Program database. Patients undergoing minimally invasive (laparoscopic or robotic) surgery were compared with those undergoing open surgery with respect to 30-day postoperative venous thromboembolism. Demographic and procedure variables were examined as potential confounders. Data regarding receipt of perioperative venous thromboembolism prophylaxis were not available. Bivariable tests and logistic regression were used for analysis.

RESULTS:
Of 9,948 patients who underwent hysterectomy for the treatment of endometrial cancer, 61.9% underwent minimally invasive surgery and 38.1% underwent open surgery. Patients undergoing minimally invasive surgery had a lower venous thromboembolism incidence (0.7%, n=47) than patients undergoing open surgery (2.2%, n=80) (P<.001). In a multivariate model adjusting for age, body mass index, race, operative time, Charlson comorbidity score, and surgical complexity, minimally invasive surgery remained associated with decreased odds of venous thromboembolism (adjusted odds ratio 0.36, 95% confidence interval 0.24–0.53) compared with open surgery.

CONCLUSION:
Minimally invasive surgery for the treatment of endometrial cancer is independently associated with decreased odds of venous thromboembolism compared with open surgery.
Rasch Analysis of the Standard Patient Evaluation of Eye Dryness Questionnaire
Authors: Asiedu Kofi 
Published: June 2016

Background:
This study sought to investigate, if the Standard Patient Evaluation of Eye Dryness (SPEED) questionnaire acts as a measure of dry eye severity and whether it is unidimensional using Rasch analysis.

Methods:
This is a hospital-based cross-sectional study. The study included 127 patients with glaucoma with either a clinical diagnosis of dry eye or an Ocular Surface Disease Index score of ≥13. Participants completed questionnaires (SPEED) delivered directly to them.

Results:
A total of 127 participants met the inclusion criteria and were included in the analysis. Category response analysis revealed that the average logit measures for the response category increased with higher response category from −4.93 to +5.41 logit. Item infit mean square statistics of the individual items ranged from 0.57 to 1.33, with a mean of 0.99±0.2. The individual item outfit mean square ranged from 0.58 to 1.36, with a mean of 1.02±0.0. The person separation index (PSI) and separation reliability of the SPEED were 2.23 and 0.83, respectively. Principal component analysis (PCA) of the standardized model residuals revealed evidence of multidimensionality, with first contrast eigenvalue of 2.5 and the second contrast eigenvalue of 1.7. Because fit statistics of all items were within 0.5 to 1.7 and considered adequate for clinical observations, no item was removed. However, the six items of the SPEED that asked about the commonest dry eye symptoms as reported by patients with dry eye were analyzed separately to determine how they behaved. The item fit statistics of these six items were within the range of 0.6 to 1.4. The outfit statistics range from 0.62 to 1.26, with a mean of 1.00±0.1. The infit statistics range from 0.61 to 1.24, with a mean of 0.99±0.2. The PSI and reliability were 2.2 and 0.83, respectively. Finally, PCA of the standardized model residuals revealed no evidence of multidimensionality, with first contrast eigenvalue of 2.0.

Conclusion:
In summary, this study showed that the SPEED had an ordered response category and was a measure of dry eye severity. However, PCA of the standardized model residuals revealed evidence of multidimensionality. A proposed six-item SPEED was unidimensional and was also a measure of disease severity. Hence, the SPEED questionnaire score may be used as a measure of dry eye severity in clinical practice and epidemiological studies.
Co-Recovery of Mycobacterium avium Complex and Mycobacterium tuberculosis in Patients With Pulmonary Tuberculosis
Authors: Dogbey-Smith M. Christina , Schlossberg David 
Published: June 2016

Background
Patients eventually shown to have pulmonary tuberculosis often grow both Mycobacterium avium complex (MAC) and Mycobacterium tuberculosis (MTB) from sputum. If the MAC grows first, patients may erroneously be assumed to have MAC disease, with discontinuation of isolation, contact investigation and alterations in chemotherapy. In patient with compatible disease, it would be helpful to know the likelihood of recovering both MAC and MTB as well as the predictive value of a positive sputum smear.

Methods
During 2012 and 2013 the Tuberculosis Control Program of the Philadelphia Department of Public health evaluated the relative incidence of MAC versus MTB in patients with suspected pulmonary tuberculosis, the time to culture growth from the initial smear for MTB and MAC, and determined the positive predictive value of a positive acid fast smear.

Results
In this setting, 22% of patients that were culture positive for MTB also grew MAC, with 78% of them growing MAC before MTB. The positive predictive value of a positive acid fast smear was 89% for MTB versus MAC.

Conclusions
There is a relatively high frequency of recovering MAC in TB patients Therefore, the recovery of MAC in a patient with a positive acid fast smear and compatible disease should not rule out MTB until cultures are final.
Nonceliac gluten sensitivity: an approach to diagnosis and management
Authors: Collyer Elizabeth M. , Kaplan Barbara S. 
Published: June 2016

Purpose of review
Symptoms attributed to gluten consumption are frequently reported evoking the need for differentiating nonceliac gluten sensitivity (NCGS) from other gluten-related disorders such as celiac disease and wheat allergy. This review discusses diagnostic criteria and research to date on the pathogenesis and diagnosis of NCGS.

Recent findings
There is recent evidence to support NCGS as a distinct clinical entity. The symptoms attributed to NCGS are nonspecific, overlapping with those reported in patients with celiac disease and irritable bowel syndrome. In contrast to celiac disease and wheat allergy, the diagnosis of NCGS is more challenging because there are no specific clinical biomarkers and because the pathogenesis of NCGS is largely not well understood. The pathogenesis of NCGS may reflect alterations in innate immunity to gluten or other components of wheat, may be linked with autoimmunity, or is a result of a reaction to gluten as a fermentable carbohydrate.

Summary
NCGS is a newly characterized and evolving clinical entity that requires ruling out other causes of wheat-related or gluten-related gastrointestinal symptoms, including celiac disease and wheat allergy, coupled with double-blind placebo-controlled crossover challenge with gluten.
Effectiveness of Stretch Interventions for Children With Neuromuscular Disabilities: Evidence-Based Recommendations
Authors: Craig Jason , Hilderman Courtney , Wilson Geoffrey , Misovic Robyn 
Published: June 2016

Purpose:
To determine whether casting, orthoses, stretching, or supported standing programs are effective in improving or maintaining body functions and structures, activity, or participation in children with neuromuscular disabilities.

Methods:
A systematic review was conducted using 6 electronic databases to identify Level 1 and 2 studies investigating stretch interventions for children aged 0 to 19 years with neuromuscular disabilities. Interventions were coded using the International Classification of Function and rated with Grading of Recommendation Assessment, Development and Evaluation, the Oxford Levels of Evidence, and the Evidence Alert Traffic Light System.

Results:
Sixteen studies evaluated the effectiveness of stretch interventions. Low-grade evidence supports casting temporarily increasing ankle range of motion, orthoses improving gait parameters while they are worn, and supported standing programs improving bone mineral density.

Conclusion:
There is limited evidence suggesting stretch interventions benefit body functions and structures. There is inconclusive evidence to support or refute stretching interventions for preventing contractures or impacting a child's activity or participation.

Trial Registration:
Prospero CRD42014013807.
Immediate Effect of Positioning Devices on Infant Leg Movement Characteristics
Authors: Jiang Crystal , de Armendi Joyce T. , Smith Beth A. 
Published: June 2016

Purpose:
To determine the immediate effects of constraining or encouraging positioning devices on leg movement of infants with typical development (TD) and at-risk for developmental delay (AR).

Methods:
Twenty-six infants (13 TD, 13 AR) were placed in the supine position, a jungle gym, or a car seat. Movement sensors on infants' ankles measured acceleration and angular velocity. We calculated the number of leg movements, peak acceleration, and peak rotational rate of each leg movement. A 2 (group) × 3 (condition) analysis of variance with repeated measures on condition tested for a group effect, a condition effect, and a group by condition interaction for leg movement quantity, average peak acceleration, and average peak rotation.

Results:
Leg movement quantity and average peak acceleration were significantly lower for the car seat condition compared with the supine position or the gym.

Conclusions:
Positioning device use has an immediate effect on infant leg movement characteristics. Long-term effects remain unknown.
Withholding versus withdrawing treatment: artificial nutrition and hydration as a model
Authors: Somers Emma , Grey Carl , Satkoske Valerie 
Published: June 2016

Purpose of review
This article explores various cultural perspectives of withholding and withdrawing of life-sustaining treatment utilizing a case involving artificial nutrition and hydration (ANH) to guide ethical discussion.

Recent findings
In the United States, there is a general consensus in the medical, ethical, and legal communities that the withholding and withdrawing of life-sustaining treatment are morally equivalent at the end of life. Despite this consensus, the withdrawal of treatment is still emotionally difficult, particularly with ANH. Recent literature challenges the evidence base that feeding tubes for people with advanced dementia lead to significant harm. In light of these new findings, we will reconsider end-of-life decision making that concerns ANH to determine whether these new findings undermine previous ethical arguments and to consider how to best educate and support patients and families during the decision-making process.

Summary
Despite many believing that there is no ethical, medical, or moral difference between withholding and withdrawing of life-sustaining treatment, there is no denying it is emotionally taxing, particularly withdrawal of ANH. Upholding the patient's values during high-quality shared decision making, facilitating rapport, and utilizing time limited trials will help, even when treatment is considered medically ineffective.
Reassessment of T Lymphocytes Crossmatches Results Prediction With Luminex Class I Single Antigen Flow Beads Assay
Authors: Visentin Jonathan , Bachelet Thomas , Borg Cécile , Franchini Nicolas , Nong Thoa , Lee Jar-How , Couzi Lionel , Merville Pierre , Guidicelli Gwendaline , Taupin Jean-Luc 
Published: June 2016

Background
In virtual crossmatch (XM) strategies, a correct anticipation of XM results is required for appropriately allocating organs. We reassessed the ability to predict T lymphocyte flow cytometry and complement dependent cytotoxicity XM results with the mean fluorescence intensity (MFI) in Luminex class I single antigen flow beads (SAFB) assay, after correction of complement interference and exclusion of antidenatured HLA antibodies.

Methods
Among 432 XM with T lymphocytes (T-XM), 407 were analyzed after exclusion of antidenatured HLA antibodies. Only ethylenediaminetetraacetic acid-treated serum MFI was considered. Only 1 cellular target HLA antigen for the serum was expressed in 238 cases, 209 and 29 being heterozygous and homozygous for this antigen, respectively. For the remaining 169 cases, at least 2 antigens were recognized. Single antigen flow bead MFI thresholds allowing XM positivity to be predicted were calculated with receiver operating characteristic curves.

Results
T-XM results were tightly associated with SAFB MFI values. Anti-HLA-A and anti-HLA-B antibodies behaved similarly. Prediction and sensitivity SAFB MFI thresholds were determined, respectively, assessing the highest sensitivity/specificity ratio and at least 95% sensitivity for predicting T-XM positivity. Both were slightly lower for HLA-B than for HLA-A, whereas anti-HLA-Cw antibodies induced random XM results. Both thresholds were only slightly diminished for homozygous and for multiple HLA targets, considering the immunodominant, but not the sum, of antibodies MFI.

Conclusions
Antibodies against HLA-A, -B, or -Cw behave differently. A homozygous HLA target does not trigger a twice higher XM positivity. Multiple antibodies are better evaluated through the immunodominant DSA MFI than through the sum of DSA MFI.
The Effects of Computerized Cognitive Testing of Older Patients on Primary Care Physicians’ Approaches to Care
Authors: Tierney Mary C. , Charles Jocelyn , Naglie Gary , Jaakkimainen Liisa , Moineddin Rahim 
Published: June 2016

Background:
We evaluated effects of providing primary care physicians (PCPs) with reports of their patients’ results on the Computer Assessment of Mild Cognitive Impairment (CAMCI) by examining their documented care approaches after receipt of the report.

Methods:
Patients were 65 years and above, without a diagnosis or previous workup for dementia, seen consecutively over 2 months by one of 13 PCPs. PCPs indicated whether they, patients, or families had concerns about patients’ cognition. A total of 259 patients individually completed the CAMCI and results were provided to the PCP. Two raters blind to CAMCI results recorded care approaches documented by PCPs at the first visit within 3 months of report (n=181).

Results:
In total, 28 different care approaches were grouped as related to Cognition or Safety/Self-Care. Negative binomial regression revealed that the number of care approaches was significantly associated with performance on the CAMCI for both Cognition and Safety/Self-care domains. These findings remained significant when covariates included PCPs’ cognitive concern before CAMCI results, and patients’ age, sex, number of comorbidities, and living arrangements.

Conclusions:
Our findings indicate that PCPs documented more care approaches in patients with greater cognitive impairment based on the CAMCI results and this was independent of their, the patients’, or families’ prior concerns about their patients’ cognition.
Congenital Tonic Pupils Associated With Congenital Central Hypoventilation Syndrome and Hirschsprung Disease
Authors: Mehta Viraj J. , Ling Joseph J. , Martinez Elizabeth G. , Reddy Anvesh C. , Donahue Sean P. 
Published: June 2016

Abstract:
Autonomic dysfunction can be associated with pupillary abnormalities. We describe a rare association of tonic pupils, congenital central hypoventilation syndrome, and Hirschsprung disease in a newborn with a mutation in the PHOX2B gene, a key regulator of neural crest cells. Hirschsprung disease is characterized by the congenital absence of neural crest–derived intrinsic ganglion cells. Tonic pupils may result from an abnormality of the ciliary ganglion, another structure of neural crest origin. The close association of these conditions in this child suggests a common abnormality in neural crest migration and differentiation.
DNA methylation adjusts the specificity of memories depending on the learning context and promotes relearning
Authors: Biergans Stephanie D , Claudianos Charles , Reinhard Judith , Galizia C Giovanni 
Published: June 2016

AbstractThe activity of the epigenetic writers DNA methyltransferases (Dnmts) after olfactory reward conditioning is important for both stimulus-specific long-term memory (LTM) formation and extinction. It, however, remains unknown which components of memory formation Dnmts regulate (e.g. associative vs. non-associative) and in what context (e.g. varying training conditions). Here we address these aspects in order to clarify the role of Dnmt-mediated DNA methylation in memory formation. We used a pharmacological Dnmt inhibitor and classical appetitive conditioning in the honeybeeApis mellifera, a well characterized model for classical conditioning. We quantified the effect of DNA methylation on naïve odour and sugar responses, and on responses following olfactory reward conditioning. We show that (1) Dnmts do not influence naïve odour or sugar responses, (2) Dnmts do not affect the learning of new stimuli, but (3) Dnmts influence odour-coding, i.e. 'correct' (stimulus-specific) LTM formation. Particularly, Dnmts reduce memory specificity when experience is low (one-trial training), and increase memory specificity when experience is high (multiple-trial training), generating an ecologically more useful response to learning. (4) In reversal learning conditions, Dnmts are involved in regulating both excitatory (re-acquisition) and inhibitory (forgetting) processes.
Using reference-free compressed data structures to analyse sequencing reads from thousands of human genomes
Authors: Dolle Dirk D. , Liu Zhicheng , Cotten Matthew , Simpson Jared T. , Iqbal Zamin , Durbin Richard , McCarthy Shane A. , Keane Thomas M. 
Published: June 2016

AbstractWe are rapidly approaching the point where we have sequenced millions of human genomes. There is a pressing need for new data structures to store raw sequencing data and efficient algorithms for population scale analysis. Current reference based data formats do not fully exploit the redundancy in population sequencing nor take advantage of shared genetic variation. In recent years, the Burrows-Wheeler transform (BWT) and FM-index have been widely employed as a full text searchable index for read alignment and de novo assembly. We introduce the concept of a population BWT and use it to store and index the sequencing reads of 2,705 samples from the 1000 Genomes Project. A key feature is that as more genomes are added, identical read sequences are increasingly observed and compression becomes more efficient. We assess the support in the 1000 Genomes read data for every base position of two human reference assembly versions, identifying that 3.2 Mbp with population support was lost in the transition from GRCh37 with 13.7 Mbp added to GRCh38. We show that the vast majority of variant alleles can be uniquely described by overlapping 31-mers and show how rapid and accurate SNP and indel genotyping can be carried out across the genomes in the population BWT. We use the population BWT to carry out non-reference queries to search for the presence of all known viral genomes, and discover human T-lymphotropic virus 1 integrations in six samples in a recognised epidemiological distribution.
aRNApipe: A balanced, efficient and distributed pipeline for processing RNA-seq data in high performance computing environments
Authors: Alonso Arnald , Lasseigne Brittany N. , Williams Kelly , Nielsen Josh , Ramaker Ryne C. , Hardigan Andrew A. , Johnston Bobbi , Roberts Brian S. , Cooper Sara J. , Marsal Sara , Myers Richard M. 
Published: June 2016

AbstractSummaryThe wide range of RNA-seq applications and their high computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing, and sequence variant calling. aRNApipe is project-oriented and dynamic so users can easily update analyses to include or exclude samples or enable additional processing modules. Workflow parameters are easily set using a single configuration file that provides centralized tracking of all analytical processes. Finally, aRNApipe incorporates interactive web reports for sample tracking and a tool for managing the genome assemblies available to perform an analysis.Availability and documentationhttps://github.com/HudsonAlpha/aRNAPipe; DOI:10.5281/zenodo.202950Contactrmyers@hudsonalpha.orgSupplementary informationSupplementary data are available at Bioinformatics online.