bluuebunny/crossref_metadata_2025_split huggingface dataset:
Starting With Lucy: Focusing on Human Similarities Rather Than Differences to Address Health Care Disparities
Authors: Clementz Laura , McNamara Megan , Burt Nicole M. , Sparks Matthew , Singh Mamta K. 
Published: March 2017

Problem
Multicultural or cultural competence education to address health care disparities using the traditional categorical approach can lead to inadvertent adverse consequences. Nontraditional approaches that address these drawbacks while promoting humanistic care are needed.

Approach
In September 2014, the Cleveland VA Medical Center’s Center of Excellence in Primary Care Education Transforming Outpatient Care (CoEPCE-TOPC) collaborated with the Cleveland Museum of Natural History (CMNH) to develop the Original Identity program, which uses a biocultural anthropologic framework to help learners recognize and address unconscious bias and starts with a discussion of humans’ shared origins. The program comprises a two-hour initial learning session at the CMNH (consisting of an educational tour in a museum exhibit, a didactic and discussion section, and patient case studies) and a one-hour wrap-up session at the Louis Stokes Cleveland VA Medical Center.

Outcomes
The authors delivered the complete Original Identity program four times between March and November 2015, with 30 CoEPCE-TOPC learners participating. Learners’ mean ratings (n = 29; response rate: 97%) for the three initial learning session questions were consistently high (4.2–4.6) using a five-point scale. Comments to an open-ended question and during the audio-recorded wrap-up sessions also addressed the program objectives and key elements (e.g., bias, assumptions, stereotyping).

Next Steps
The authors are completing additional qualitative analysis on the wrap-up session transcriptions to clarify factors that make the program successful, details of learners’ experience, and any interprofessional differences in interpreting content. The authors believe this innovative addition to health care education warrants further research.
Effectiveness and Safety of Surgical Excision in the Treatment of Digital Mucoid Cysts
Authors: Balakirski Galina , Loeser Christoph , Baron Jens M. , Dippel Edgar , Schmitt Laurenz 
Published: March 2017

BACKGROUND
Digital mucoid cysts have a tendency for recurrence after operative intervention. Several procedures are in use.

OBJECTIVE
Retrospective evaluation for effectiveness, safety and patient satisfaction by using a questionnaire after treatment for digital mucoid cysts with targeted surgical excision and closure by flap-design.

MATERIALS AND METHODS
All patients treated with surgical excision for digital mucoid cysts at the Dermatology Department of the Ludwigshafen City Hospital between 2007 and 2011 were evaluated using a specially designed questionnaire.

RESULTS
We evaluated 31 patients. The patient group consisted of 65% women, the median age was 61 years. Seventy-eight percent of patients with nail involvement had a marked improvement or complete resolution of this complaint after surgery. A few complications (e.g., redness, pain or hematoma) were observed after treatment, but no patients required oral antibiotics. Patient evaluation of cosmetic outcome revealed high satisfaction with the procedure, nevertheless recurrence of the digital mucoid cysts was observed in 22.5% of all cases.

CONCLUSION
Surgical excision in treatment of digital mucoid cysts was shown to be effective and safe. However, possible advantages and disadvantages of this treatment option should be discussed with the patients before a decision on the kind of therapy is reached.
Biomarkers of Environmental Enteric Dysfunction Among Children in Rural Bangladesh
Authors: Campbell Rebecca K. , Schulze Kerry J. , Shaikh Saijuddin , Mehra Sucheta , Ali Hasmot , Wu Lee , Raqib Rubhana , Baker Sarah , Labrique Alain , West Keith P. , Christian Parul 
Published: March 2017

ABSTRACTObjectives:Environmental enteric dysfunction (EED) may inhibit growth and development in low‐ and middle‐income countries, but available assessment methodologies limit its study. In rural Bangladesh, we measured EED using the widely used lactulose mannitol ratio (L:M) test and a panel of intestinal and systemic health biomarkers to evaluate convergence among biomarkers and describe risk factors for EED.Methods:In 539 18‐month‐old children finishing participation in a randomized food supplementation trial, serum, stool, and urine collected after lactulose and mannitol dosing were analyzed for biomarkers of intestinal absorption, inflammation, permeability and repair, and systemic inflammation. EED scores for each participant were developed using principal component analysis and partial least squares regression. Associations between scores and L:M and with child sociodemographic and health characteristics were evaluated using regression analysis.Results:EED prevalence (L:M > 0.07) was 39.0%; 60% had elevated acute phase proteins (C‐reactive protein >5 mg/L or α‐1 acid glycoprotein >100 mg/dL). Correlations between intestinal biomarkers were low, with the highest between myeloperoxidase and α‐1 antitrypsin (r = 0.33, P < 0.01), and biomarker values did not differ by supplementation history. A 1‐factor partial least squares model with L:M as the dependent variable explained only 8.6% of L:M variability. In adjusted models, L:M was associated with child sex and socioeconomic status index, whereas systemic inflammation was predicted mainly by recent illness, not EED.Conclusions:Impaired intestinal health is widespread in this setting of prevalent stunting, but a panel of serum and stool biomarkers demonstrated poor agreement with L:M. Etiologies of intestinal and systemic inflammation are likely numerous and complex in resource‐poor settings, underscoring the need for a better case definition with corresponding diagnostic methods to further the study of EED.
Use of High-Fidelity Simulation to Enhance Interdisciplinary Collaboration and Reduce Patient Falls
Authors: Bursiek April A. , Hopkins Matthew R. , Breitkopf Daniel M. , Grubbs Pamela L. , Joswiak Mary Ellen , Klipfel Janee M. , Johnson Kristine M. 
Published: March 2017

Objectives
This pilot study aimed to determine the effect of nurse/physician interdisciplinary team training on patient falls. Specifically, we evaluated team training in a simulation center as a method for targeting and minimizing breakdowns in perceptions of respect, collaboration, communication, and role misunderstanding behaviors between care disciplines.

Methods
Registered nurses (RNs) were randomly assigned to participate. Residents were divided into groups and assigned based on their availability and clinical responsibility. All participants completed a demographic form, the Professional Practice Environment Assessment Scale (PPEAS), and the Mayo High Performance Teamwork Scale (MHPTS) after consenting and before participation in simulation training. The PPEAS and the MHPTS were readministered at 2 and 6 months after the simulation experience. Differences in MHPTS and PPEAS scores between the baseline and 2- and 6-month assessments were analyzed; fall rates over time were evaluated using Cochran-Armitage trend tests.

Results
After the team training exercises, teamwork as measured by the MHPTS improved significantly at both 2 and 6 months (P = 0.01; P < 0.001) compared with baseline measurement. Practice environment subscores, with the exception of positive organizational characteristics, also increased when measured 6 months after training. The primary outcome, reduction in anticipated patient falls, improved significantly (P = 0.02) over the course of the study.

Conclusions
Results of this pilot study show that team training exercises result in improvement in both patient safety (anticipated patient falls) and team member perception of their work environment. If validated by other studies, improvement in this patient safety metric would represent an important benefit of simulation and team training.
Barriers and Facilitators of Adverse Event Reporting by Adolescent Patients and Their Families
Authors: Sawhney Payal Naresh , Davis Linda Sue , Daraiseh Nancy M. , Belle Lisa , Walsh Kathleen E. 
Published: March 2017

Objectives
The objectives were (1) to describe barriers and facilitators of adverse event reporting by adolescent patients and parents in a pediatric hospital and (2) to identify characteristics the participants wished to have in a formal reporting system of adverse events.

Methods
We used a qualitative design in which 6 focus groups, 3 with parents and 3 with adolescents, were conducted. The transcripts of audio recordings, notes of team debriefings, and written field notes of group behaviors were analyzed using NVivo software for qualitative data analysis.

Results
Participants reported that the quality of the experience with the health care system, type of communication with health care providers, and degree of personal self-confidence in communication within the health care system were 3 interacting factors influencing willingness to report adverse events. Preferred reporting mechanisms were different for different participants and included face-to-face meetings with hospital representatives, Web sites, smart phone capability, phone calls from a human, and paper mail. Reporting systems should be easy to use, ensure confidentiality, and provide user feedback.

Conclusions
Experience, communication, and confidence are 3 factors that can engage an adolescent patient and parents in their health care. Confident adolescent patients and parents in turn have a possibility of reporting an adverse safety event given an opportunity.
Real-World Efficacy of Daclatasvir and Sofosbuvir, With and Without Ribavirin, in HIV/HCV Coinfected Patients With Advanced Liver Disease in a French Early Access Cohort
Authors: Lacombe Karine , Fontaine Hélène , Dhiver Catherine , Metivier Sophie , Rosenthal Eric , Antonini Teresa , Valantin Marc Antoine , Miailhes Patrick , Harent Stanislas , Batisse Dominique , Pageaux Georges-Philippe , Chas Julie , Aumaitre Hugues , Dominguez Stephanie , Allegre Thierry , Lafeuillade Alain , Billaud Eric , De Truchis Pierre , Perre Philippe , Leroy Vincent , De Ledinghen Victor , Sogni Philippe , Dabis François , Zhao Yue , Filipovics Anne , Fedchuk Larysa , Akremi Raoudha , Bennai Yacia , Salmon Ceron Dominique 
Published: March 2017

Background:
Efficacious, well-tolerated, direct antiviral agents have drastically changed the prognosis of hepatitis C virus (HCV) disease, but real-world data for oral treatments are limited in key populations such as HIV/HCV coinfection with advanced liver disease. Daclatasvir (DCV) efficacy and safety was assessed in the French “Autorisation Temporaire d'Utilisation” (ATU) program, providing DCV ahead of market authorization to patients with advanced HCV disease without other treatment options.

Methods:
This was a subanalysis of HIV/HCV coinfected ATU patients treated with DCV plus sofosbuvir (SOF). Recommended duration was 24 weeks; addition of ribavirin (RBV) and/or shorter treatment was at the physician's discretion. The primary efficacy analysis was sustained virologic response at posttreatment week 12 (SVR12; modified intention-to-treat). Safety was assessed by spontaneous adverse event reporting.

Results:
The efficacy population (N = 407) was mostly cirrhotic (72%, of whom 18% were decompensated), HCV treatment–experienced (82%), and infected with genotypes 1 (69%), 3 (12%), or 4 (19%). Median CD4 was 555 cells/mm3; 95% had HIV RNA <50 copies/mL. Most (74%) were treated for 24 weeks; 14% received RBV. SVR12 was 92% overall (95% confidence interval: 88.6% to 94.0%); 90% (86.4% to 93.2%) in patients with cirrhosis; 95% (88.9% to 97.5%) in patients without cirrhosis. SVR12 was consistent across HCV genotypes and antiretroviral regimens. Among 617 patients with safety data, 7 discontinued for an adverse event and 10 died.

Conclusions:
DCV+SOF±RBV achieved high SVR12 and was well tolerated in this large real-world cohort of HIV/HCV coinfected patients with advanced liver disease.
Electroconvulsive Therapy at a Veterans Health Administration Medical Center
Authors: Wilkinson Samuel T. , Rosenheck Robert A. 
Published: March 2017

Objectives
Little epidemiologic research has examined the practice of electroconvulsive therapy (ECT). We investigated sociodemographic and clinical characteristics, service use, and psychotropic medication prescription patterns associated with ECT use at a Veterans Health Administration Medical Center.

Methods
Among veterans receiving specialty mental health services, we compared those who received ECT with those who did not using bivariate χ

2
and t tests and multivariate logistic regression.

Results
In fiscal year 2012, 11,117 veterans received specialty mental health services, of whom 50 received ECT (0.45%) in FY2012 or FY2013. Those who received ECT were more likely to be diagnosed with major depressive or bipolar disorders and had substantially higher levels of mental health service usage (Cohen d > 0.75) and psychotropic prescription fills, including antidepressants (Cohen d = 2.66), antipsychotics (Cohen d = 2.15), lithium (Cohen d = 1.34), mood stabilizers (Cohen d = 1.30), and anxiolytic/sedative/hypnotics (Cohen d = 1.34).

Conclusions
Our findings suggest that ECT is used as a treatment of last resort, although available evidence and guidelines recommend wider use.
Effective purifying selection in ancient asexual oribatid mites
Authors: Brandt Alexander , Schaefer Ina , Glanz Julien , Schwander Tanja , Maraun Mark , Scheu Stefan , Bast Jens 
Published: March 2017

AbstractSex is beneficial in the long-term, because it can prevent mutational meltdown through increased effectiveness of selection. This idea is supported by empirical evidence of deleterious mutation accumulation in species with a recent transition to asexuality. Here, we studied the effectiveness of purifying selection in oribatid mites, which have lost sex millions of years ago and diversified into different families and species while reproducing asexually. We compared the accumulation of deleterious coding and non-coding mutations between three asexual and three sexual lineages using transcriptome data. Contrasting studies of young asexual lineages, we find evidence for strong purifying selection that is more effective in asexual compared to sexual oribatid mite lineages. Our results suggest that large populations likely sustain effective purifying selection and facilitate the escape of mutational meltdown in the absence of sex. Thus, sexper seis not a prerequisite for the long-term persistence of animal lineages.
Odor concentration change detectors in the Olfactory Bulb
Authors: Parabucki Ana , Bizer Alexander , Morris Genela , Smear Matthew C. , Shusterman Roman 
Published: March 2017

AbstractDynamical changes in the environment strongly impact our perception1,2. Consistent with this, sensory systems preferentially represent stimulus changes, enhancing temporal contrast3,4. In olfaction, odor concentration changes across consecutive inhalations (ΔCt) can guide odor source localization. Yet the neural representation of ΔCthas not been studied in vertebrates. We have found that a subset of mitral/tufted (M/T) cells in the olfactory bulb explicitly represent ΔCt. These concentration change detectors are direction selective: some respond to positive ΔCt, while others represent negative ΔCt. This change detection enhances the contrast between different concentrations and the magnitude of contrast enhancement scales with the size of the concentration step. Further, ΔCtcan be read out from the total spike count per sniff, unlike odor identity and intensity, which are represented by fast temporal spike patterns. Our results demonstrate that a subset of M/T cells explicitly represents ΔCt, providing a signal that may instruct navigational decisions in downstream olfactory circuits.
Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing
Authors: Hong Jungeui , Gresham David 
Published: March 2017

Quantitative analysis of next-generation sequencing data requires discriminating duplicate reads generated by PCR from identical molecules that are of unique origin. Typically, PCR duplicates are defined as sequence reads that align to the same genomic coordinates using reference-based alignment. However, identical molecules can be independently generated during library preparation. The false positive rate of coordinate-based deduplication has not been well characterized and may introduce unforeseen biases during analyses. We developed a cost-effective sequencing adapter design by modifying Illumina TruSeq adapters to incorporate a unique molecular identifier (UMI) while maintaining the capacity to undertake multiplexed sequencing. Incorporation of UMIs enables identification of bona fide PCR duplicates as identically mapped reads with identical UMIs. Using TruSeq adapters containing UMIs (TrUMIseq adapters), we find that accurate removal of PCR duplicates results in enhanced data quality for quantitative analysis of allele frequencies in heterogeneous populations and gene expression.Method SummaryTrUMIseq adapters incorporate unique molecular identifiers in TruSeq adapters while maintaining the capacity to multiplex sequencing libraries using existing workflows. The use of UMIs increases the accuracy of quantitative sequencing assays, including RNAseq and allele frequency estimation, by enabling accurate detection of PCR duplicates.
Early biomarker discovery in urine of Walker 256 subcutaneous rat model
Authors: Wu Jianqiang , Guo Zhengguang , Gao Youhe 
Published: March 2017

AbstractDespite advances in cancer treatments, early detection of cancer is still the most promising way to improve outcomes. Without homeostatic control, urine reflects early changes in the body and can potentially be used for early cancer diagnosis. In this study, a Walker 256 tumor rat model was established by subcutaneous injection of Walker 256 tumor cells. To identify urinary proteome changes during cancer development, urine samples from Walker 256 tumor-bearing rats were collected at five time points corresponding to before cancer cell implantation, before tumor mass palpability, at tumor mass appearance, during rapid tumor growth, and at cachexia. The urinary protein patterns changed significantly as the tumors progressed, as measured using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The urinary proteome of tumor-bearing rats was identified using Fusion Lumos mass spectrometry with label-free quantification. Then, 30 dynamically changed urinary proteins during cancer progression were selected as more reliable cancer biomarkers, and they were validated by targeted proteomics. Combined with the results of label-free and targeted proteome quantification, a total of 10 urinary proteins (HPT, APOA4, CO4, B2MG, A1AG, CATC, VCAM1, CALB1, CSPG4, and VTDB) changed significantly even before a tumor mass was palpable, and these early changes in urine could also be identified with differential abundance at late stages of cancer. Our study indicated that urine is a sensitive biomarker source for early detection of cancer.
A novel method for large-scale identification of polymorphic microsatellites through comparative transcriptome analysis
Authors: Luo Wei , Qu Hongyue , Wang Xin , Zhan Qin , Lin Qiang 
Published: March 2017

ABSTRACTMicrosatellite (SSR) is one of the most popular markers for applied genetic research, but generally the current methods to develop SSRs are relatively time-consuming and expensive. Although high-throughput sequencing (HTS) approach has become a practical and relatively inexpensive option so far, only a small percentage of SSR markers turn out to be polymorphic. Here, we designed a new method to enrich polymorphic SSRs through the comparative transcriptome analysis. This program contains five main steps: 1) transcriptome data downloading or RNA-seq; 2) sequence assembly; 3) SSR mining and enrichment of sequences containing SSRs; 4) sequence alignment; 5) enrichment of sequences containing polymorphic SSRs. A validation experiment was performed and the results showed almost all markers (> 90%) that were indicated as putatively polymorphic by this method were indeed polymorphic. The frequency of polymorphic SSRs was significantly higher (P< 0.05) but the cost and running time were much lower than those of traditional and HTS approaches. The method has a practical value for polymorphic SSRs development and might be widely used for genetic analyses in any species.
BRANE Clust: Cluster-Assisted Gene Regulatory Network Inference Refinement
Authors: Pirayre Aurélie , Couprie Camille , Duval Laurent , Pesquet Jean-Christophe 
Published: March 2017

AbstractDiscovering meaningful gene interactions is crucial for the identification of novel regulatory processes in cells. Building accurately the related graphs remains challenging due to the large number of possible solutions from available data. Nonetheless, enforcing apriorion the graph structure, such as modularity, may reduce network indeterminacy issues. BRANE Clust (Biologically-Related A priori Network Enhancement with Clustering) refines gene regulatory network (GRN) inference thanks to cluster information. It works as a post-processing tool for inference methods (i.e. CLR, GENIE3). In BRANE Clust, the clustering is based on the inversion of a system of linear equations involving a graph-Laplacian matrix promoting a modular structure. Our approach is validated on DREAM4 and DREAM5 datasets with objective measures, showing significant comparative improvements. We provide additional insights on the discovery of novel regulatory or co-expressed links in the inferredEscherichia colinetwork evaluated using the STRING database. The comparative pertinence of clustering is discussed computationally (SIMoNe, WGCNA, X-means) and biologically (RegulonDB). BRANE Clust software is available at:http://www-syscom.univ-mlv.fr/∼pirayre/Codes-GRN-BRANE-clust.html
Genome-Wide Analysis of Facial Regionalization in Zebrafish
Authors: Askary Amjad , Xu Pengfei , Barske Lindsey , Bay Maxwell , Bump Paul , Balczerski Bartosz , Bonaguidi Michael A. , Gage Crump J. 
Published: March 2017

AbstractPatterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite the significance for craniofacial development, how genetic programs drive this regionalization remains incompletely understood. Here we use combinatorial labeling of zebrafish cranial neural crest-derived cells (CNCCs) to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region-specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 (Edn1) signaling in the intermediate joint-forming region yet a surprisingly minor role in ventral-most regions. Analysis of co-variance across multiple sequencing experiments further reveals clusters of coregulated genes, with in situ hybridization confirming the domain-specific expression of novel genes. We then performed mutational analysis of a number of these genes, which uncovered antagonistic functions of two new Edn1 targets,follistatin a(fsta) andemx2, in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in zebrafish arch CNCCs reveals complex regulation by Ednl and points to novel candidates for craniofacial disorders.Summary StatementUsing zebrafish to purify distinct groups of embryonic cells, Askary et al. have created a detailed map of how thousands of genes are deployed to shape the developing face.