bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of an HIV Postexposure Prophylaxis (PEP) Protocol for Trainees Engaging in Academic Global Health Experiences
Authors: Arora Gitanjli , Hoffman Risa M. 
Published: April 2017

Problem
Global health (GH) education programs have become increasingly common in U.S. medical schools and graduate medical education programs, with growing numbers of medical students, residents, and fellows participating in clinical experiences in settings with high HIV prevalence and limited resources. However, there are no guidelines for provision of HIV postexposure prophylaxis (PEP) to trainees engaging in these academic GH experiences.

Approach
Faculty of the Global Health Education Programs (GHEP) at the David Geffen School of Medicine at UCLA and GH partner institutions recognized the need for PEP access for trainees engaged in GH experiences. In 2013–2014, key UCLA faculty collaborated in the development of the UCLA GHEP PEP Protocol, which includes provision of PEP medications to trainees prior to departure, an on-call infectious disease/HIV specialist to advise trainees who have exposures, and a system for following up with exposed trainees while on the GH rotation and after their return.

Outcomes
Between February 2014 and September 2016, 112 medical students and 110 residents received education on the PEP protocol during their predeparture orientation. The protocol was used for 28 exposures (27 occupational, 1 nonoccupational), with PEP recommended in 3 occupational cases (all needlesticks) and the single nonoccupational case. There were no reported HIV seroconversions.

Next Steps
The authors plan to formally evaluate the PEP protocol, conduct a qualitative assessment with trainees and both UCLA and GH partner faculty, and discuss best practices with institutions across the United States and with GH partners.
A Study of Pediatricians’ Debt Repayment a Decade After Completing Residency
Authors: Cull William L. , Katakam Shesha K. , Starmer Amy Jost , Gottschlich Elizabeth A. , Miller Ashley A. , Frintner Mary Pat 
Published: April 2017

Purpose
Pediatricians’ education debt has been increasing. Less is known about the pace of their debt repayment. The authors examined patterns of debt repayment for pediatricians who completed residency from 2002–2004.

Method
The authors analyzed weighted 2013 survey data from the American Academy of Pediatrics Pediatrician Life and Career Experience Study. They categorized participants based on education debt level at residency completion ($0; $1–$49,999; $50,000–$99,999; $100,000–$149,999; ≥ $150,000) and explored debt repayment and well-being by starting debt group using multivariable logistic regression.

Results
Of 830 pediatricians surveyed, 266 (32%) had no starting debt and 166 (20%) had ≥ $150,000 in starting debt. A decade after residency, the percentage of participants who completely repaid their debt varied from 76% (68/89) of those with $1–$49,999 of starting debt to 15% (25/164) of those with ≥ $150,000 of starting debt. The percentage of participants concerned about their debt increased with starting debt level, with over half of those in the highest group concerned. Starting debt was associated with all examined measures of debt repayment and with recent financial difficulties among those in the two highest debt groups ($100,000–$149,999: adjusted odds ratio = 3.82, confidence interval = 1.17–12.43; ≥ $150,000: adjusted odds ratio = 4.55, confidence interval = 1.47–14.14).

Conclusions
A decade after completing residency, pediatricians had made progress repaying their debt, yet many still expressed concern, especially those with the greatest amount of starting debt. As debt levels continue to increase, these issues could worsen.
Hydrogen Sulfide Confers Lung Protection During Mechanical Ventilation via Cyclooxygenase 2, 15-deoxy Δ12,14-Prostaglandin J2, and Peroxisome Proliferator-Activated Receptor Gamma
Authors: Spassov Sashko G. , Faller Simone , Hummel Matthias , Helo Khaled , Ihle Andreas , Ryter Stefan W. , Strosing Karl M. , Hoetzel Alexander 
Published: April 2017

Objectives:
Hydrogen sulfide reduces ventilator-induced lung injury in mice. Here, we have examined the underlying mechanisms of hydrogen sulfide-mediated lung protection and determined the involvement of cyclooxygenase 2, 15-deoxy Δ12,14-prostaglandin J2, and peroxisome proliferator-activated receptor gamma in this response.

Design:
Randomized, experimental study.

Setting:
University medical center research laboratory.

Subjects:
C57BL/6 mice and in vitro cell catheters.

Interventions:
The effects of hydrogen sulfide were analyzed in a mouse ventilator-induced lung injury model in vivo as well as in a cell stretch model in vitro in the absence or presence of hydrogen sulfide. The physiologic relevance of our findings was confirmed using pharmacologic inhibitors of cyclooxygenase 2 and peroxisome proliferator-activated receptor gamma.

Measurements and Main Results:
Mechanical ventilation caused significant lung inflammation and injury that was prevented in the presence of hydrogen sulfide. Hydrogen sulfide-mediated protection was associated with induction of cyclooxygenase 2 and increases of its product 15-deoxy Δ12,14-prostaglandin J2 as well as cyclooxygenase 2/15-deoxy Δ12,14-prostaglandin J2-dependent activation of peroxisome proliferator-activated receptor gamma. Hydrogen sulfide-dependent effects were mainly observed in macrophages. Applied mechanical stretch to RAW 264.7 macrophages resulted in increased expression of interleukin receptor 1 messenger RNA and release of macrophage inflammatory protein-2. In contrast, incubation of stretched macrophages with sodium hydrosulfide prevented the inflammatory response dependent on peroxisome proliferator-activated receptor gamma activity. Finally, application of a specific peroxisome proliferator-activated receptor gamma inhibitor abolished hydrogen sulfide-mediated protection in ventilated animals.

Conclusions:
One hydrogen sulfide-triggered mechanism in the protection against ventilator-induced lung injury involves cyclooxygenase 2/15-deoxy Δ12,14-prostaglandin J2-dependent activation of peroxisome proliferator-activated receptor gamma and macrophage activity.
An Innovative Risk-Reducing Approach to Postmastectomy Radiation Delivery after Autologous Breast Reconstruction
Authors: Piper Merisa L. , Evangelista Maristella , Amara Dominic , Daar David , Foster Robert D. , Fowble Barbara , Sbitany Hani 
Published: April 2017

Introduction:
Postmastectomy radiation therapy (PMRT) has known deleterious side effects in immediate autologous breast reconstruction. However, plastic surgeons are rarely involved in PMRT planning. Our institution has adopted a custom bolus approach for all patients receiving PMRT. This offers uniform distribution of standard radiation doses, thereby minimizing radiation-induced changes while maintaining oncologic safety. We present our 8-year experience with the custom bolus approach for PMRT delivery in immediate autologous breast reconstruction.

Methods:
All immediate autologous breast reconstruction patients requiring PMRT after 2006 were treated with the custom bolus approach. Retrospective chart review was performed to compare the postirradiation complications, reconstruction outcomes, and oncologic outcomes of these patients with those of previous patients at our institution who underwent standard bolus, and to historical controls from peer-reviewed literature.

Results:
Over the past 10 years, of the 29 patients who received PMRT, 10 were treated with custom bolus. Custom bolus resulted in fewer radiation-induced skin changes and less skin tethering/fibrosis than standard bolus (0% vs 10% and 20% vs 35%, respectively), and less volume loss and contour deformities compared with historical controls (10% vs 22.8% and 10% vs 30.7%, respectively).

Conclusions:
Custom bolus PMRT minimizes radiation delivery to the internal mammary vessels, anastomoses, and skin; uniformly doses the surgical incision; and provides the necessary radiation dose to prevent recurrence. Because custom bolus PMRT may reduce the deleterious effects of radiation on reconstructive outcomes while maintaining safe oncologic results, we encourage all plastic surgeons to collaborate with radiation oncologists to consider this technique.
Difference in Success Treating Proximal Interphalangeal and Metacarpophalangeal Joints with Collagenase: Results of 208 Treatments
Authors: Hansen Karina Liv , Werlinrud Jens Christian , Larsen Søren , Ipsen Tune , Lauritsen Jens 
Published: April 2017

Background:
Dupuytren disease (DD) is a fibroproliferative disorder of the palmar fasciae causing extension deficit and impaired hand function. Treatment with injection of collagenase clostridium histolyticum (CCH) is a nonsurgical treatment method. The aim of this study was to evaluate the difference in efficiency and recurrence at 12-month follow-up when treating metacarpophalangeal (MP) and proximal interphalangeal (PIP) joints with CCH. None of the patients had received previous treatments of their condition.

Methods:
This study is a prospective study of a consecutive series of patients with DD presenting with an extension deficit greater than 20° affecting the MP or PIP joint.

Results:
We found a mean reduction in extension deficit of 47° (91%) for MP joints and 47° (76%) for PIP joints. Full correction (max 5° deficit) was achieved in 76% of MP and 28% of PIP joints. Skin rupture was seen in 34% of treatments. The 1-year relapse rate was 15% for MP and 67% for PIP joints. The reduction in quickDASH score was only statistically significant for MP joints at 1 year. Eighty-one percent of all patients reported being satisfied or very satisfied. No major adverse events were recorded.

Conclusion:
Excellent results can be achieved in the treatment of MP-joint contractures, whereas the success rate is significantly lower and recurrence rate is greater for PIP joints.
Rapid Intraocular Tube Trimming for Glaucoma Drainage Implant Devices
Authors: Baciu Paul , Moster Stephen J. , Lee Richard K. 
Published: April 2017

Purpose:
To describe a new approach for shortening silicone tubes of glaucoma drainage devices (GDDs).

Materials and Methods:
A retrospective intervention case series describing 3 patients undergoing the same treatment at a single institutional center

Results:
Three patients underwent successful ab interno trimming of GDD silicone tubes without complication

Conclusions:
This technique allows for rapid and successful shortening of GDD tubes via an ab interno approach avoiding risks of traditional glaucoma tube trimming approaches.
Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
Authors: Ryu Ann H. , Eckalbar Walter L. , Kreimer Anat , Yosef Nir , Ahituv Nadav 
Published: April 2017

AbstractStandard cell culture guidelines often use media supplemented with antibiotics to prevent cell contamination. However, relatively little is known about the effect of antibiotic use in cell culture on gene expression and the extent to which this treatment could confound results. To comprehensively characterize the effect of antibiotic treatment on gene expression, we performed RNA-seq and ChIP-seq for H3K27ac on HepG2 cells, a human liver cell line commonly used for pharmacokinetic, metabolism and genomic studies, cultured in media supplemented with penicillin-streptomycin (PenStrep) or vehicle control. We identified 205 PenStrep-responsive genes, including transcription factors such as ATF3 that are likely to alter the regulation of other genes. Pathway analyses found a significant enrichment for “xenobiotic metabolism signaling” and “PXR/RXR activation” pathways. Our H3K27ac ChIP-seq identified 9,514 peaks that are PenStrep responsive. These peaks were enriched near genes that function in cell differentiation, tRNA modification, nuclease activity and protein dephosphorylation. Our results suggest that PenStrep treatment can significantly alter gene expression and regulation in a common liver cell type such as HepG2, advocating that antibiotic treatment should be taken into account when carrying out genetic, genomic or other biological assays in cultured cells.
Neural Correlates of human cognitive abilities during sleep
Authors: Fang Zhuo , Ray Laura B. , Owen Adrian M. , Fogel Stuart M. 
Published: April 2017

ABSTRACTInter-individual differences in sleep spindles are highly correlated with “Reasoning” abilities (problem solving skills; i.e., the ability to employ logic, identify complex patterns), but not Short Term Memory or Verbal abilities. Simultaneous electroencephalography and functional magnetic resonance imaging (EEG-fMRI) have revealed brain activations time-locked to spindles (e.g., thalamic, paralimbic, and motor cortical areas)–yet the functional significance of inter-individual differences in spindle-related brain activation remains to be investigated. Using EEG-fMRI during sleep, we identified, for the first time, the neural activation patterns time-locked to spindles that are correlated with cognitive abilities. Similar to previous studies, activations time-locked to spindles were observed in thalamocortical circuitry and basal ganglia regions. Importantly, spindle-related activation in a subset of these regions were specifically related to inter-individual differences in Reasoning, but not STM or Verbal abilities. These results may help elucidate the physiological mechanisms which support the function of sleep for the capacity for reasoning.
Lacer: accurate base quality score recalibration for improving variant calling from next-generation sequencing data in any organism
Authors: Chung Jade C.S. , Chen Swaine L. 
Published: April 2017

AbstractNext-generation sequencing data is accompanied by quality scores that quantify sequencing error. Inaccuracies in these quality scores propagate through all subsequent analyses; thus base quality score recalibration is a standard step in many next-generation sequencing workflows, resulting in improved variant calls. Current base quality score recalibration algorithms rely on the assumption that sequencing errors are already known; for human resequencing data, relatively complete variant databases facilitate this. However, because existing databases are still incomplete, recalibration is still inaccurate; and most organisms do not have variant databases, exacerbating inaccuracy for non-human data. To overcome these logical and practical problems, we introduce Lacer, which recalibrates base quality scores without assuming knowledge of correct and incorrect bases and without requiring knowledge of common variants. Lacer is the first logically sound, fully general, and truly accurate base recalibrator. Lacer enhances variant identification accuracy for resequencing data of human as well as other organisms (which are not accessible to current recalibrators), simultaneously improving and extending the benefits of base quality score recalibration to nearly all ongoing sequencing projects. Lacer is available at:https://github.com/swainechen/lacer.
Widespread dysregulation of the circadian clock in human cancer
Authors: Shilts Jarrod , Chen Guanhua , Hughey Jacob J. 
Published: April 2017

AbstractThe mammalian circadian clock is a critical regulator of metabolism and cell division. Although multiple lines of evidence indicate that systemic disruption of the circadian clock can promote cancer, whether the clock is disrupted in primary human tumors is unknown. Here we used transcriptome data from mice to define a signature of the mammalian circadian clock based on the co-expression of 12 genes that form the core clock or are directly controlled by the clock. Our approach can be applied to samples that are not labeled with time of day and were not acquired over the entire circadian (24-h) cycle. We validated the clock signature in transcriptome data from healthy human tissues, then developed a metric we call the delta clock correlation distance (ΔCCD) to describe the extent to which the signature is perturbed in samples from one condition relative to another. We calculated the ΔCCD comparing human tumor and non-tumor samples from The Cancer Genome Atlas and eight independent datasets, discovering widespread dysregulation of clock gene co-expression in tumor samples. Subsequent analysis of data from clock gene knockouts in mice suggested that clock dysregulation in human cancer is not caused solely by loss of activity of clock genes. Furthermore, by analyzing a large set of genes previously inferred to be rhythmic in healthy human lung, we found that dysregulation of the clock in human lung cancer is accompanied by dysregulation of broader patterns of circadian co-expression. Our findings suggest that clock dysregulation is a common means by which human cancers achieve unrestrained growth and division, and that restoring clock function could be a viable therapeutic strategy in multiple cancer types. In addition, our approach opens the door to using publicly available transcriptome data to quantify clock disruption in a multitude of human phenotypes. Our method is available as a web application athttps://hugheylab.shinyapps.io/deltaccd.
Mass univariate testing biases the detection of interaction effects in whole-brain analysis of variance
Authors: Chavez Robert S. , Wagner Dylan D. 
Published: April 2017

AbstractWhole-brain analysis of variance (ANOVA) is a common analytic approach in cognitive neuroscience. Researchers are often interested in exploring whether brain activity reflects to the interaction of two factors. Disordinal interactions — where there is a reversal of the effect of one independent variable at a level of a second independent variable — are common in the literature. It is well established in power-analyses of factorial ANOVAs that certain patterns of interactions, such as disordinal (e.g., cross-over interactions) require less power than others to detect. This fact, combined with the perils of mass univariate testing suggests that testing for interactions in whole-brain ANOVAs, may be biased towards the detection of disordinal interactions. Here, we report on a series of simulated analysis --including whole-brain fMRI data using realistic multi-source noise parameters-- that demonstrate a bias towards the detection of disordinal interactions in mass-univariate contexts. Moreover, results of these simulations indicated that spurious disordinal interactions are found at common thresholds and cluster sizes at the group level. Moreover, simulations based on implanting true ordinal interaction effects can nevertheless appear like crossover effects at realistic levels of signal-to-noise ratio (SNR) when performing mass univariate testing at the whole-brain level, potentially leading to erroneous conclusions when interpreted as is. Simulations of varying sample sizes and SNR levels show that this bias is driven primarily by SNR and larger sample sizes do little to ameliorate this issue. Together, the results of these simulations argue for caution when searching for ordinal interactions in whole-brain ANOVA.
Investigating the friction coefficient in functionally graded rapid prototyping of Al–Al2O3 composite prepared by fused deposition modelling
Authors: Singh Rupinder , Singh Sunpreet 
Published: April 2017

Purpose
The present research work aims to study the friction coefficient in functionally graded rapid prototyping of Al–Al2O3 composite prepared via fused deposition modelling (FDM)-assisted investment casting (IC) process. The optimized settings of the process parameters (namely, filament proportion, volume of FDM pattern, density of FDM pattern, barrel finishing (BF) time, BF media weight and number of IC slurry layers) suggested in the present research work will help fabricate parts possessing higher frictional coefficient.

Design/methodology/approach
Initially, melt flow index (MFI) of two different proportions of Nylon6-Al–Al2O3 (to be used as an alternative FDM filament material) was tested on the melt flow indexer and matched with MFI of commercially used acrylonitrile–butadiene–styrene filament. After this, the selected proportions of Nylon6-Al–Al2O3 were prepared in the form of the FDM filament by using a single screw extruder. Further, this FDM filament has been used for developing sacrificial IC patterns in the existing FDM system which was barely finished to improve their surface finish. Castings developed were tested for their wear resistance properties on a pin-on-disc-type tribo-tester under dry conditions at sliding conditions to check their suitability as a frictional device for industrial applications. In the methodology part, Taguchi L18 orthogonal array was used to study the effect of selected process variables on the coefficient of friction (μ).

Findings
It has been found that filament proportion, volume of FDM pattern and density of FDM pattern have significantly affected the μ-values. Further, density of the FDM pattern was found to have 91.62 per cent contribution in obtaining μ-values. Scanning electron micrographs highlighted uniform distribution of Al2O3 particles in the Al-matrix at suggested optimized settings.

Practical implications
The present methodology shows the development of a functional graded material that consisted of surface reinforcement with Al2O3 particles, which could have applications for manufacturing friction surfaces such as clutch plates, brake drum, etc.

Originality/value
This paper describes the effect of process parameters on wear properties of the Al–Al2O3 composite developed as a functionally graded material by the FDM-based pattern in the IC process.
Force control for a rigid dual peg-in-hole assembly
Authors: Zhang Kuangen , Shi MinHui , Xu Jing , Liu Feng , Chen Ken 
Published: April 2017

Purpose
This paper aims to realize the automatic assembly process for multiple rigid peg-in-hole components.

Design/methodology/approach
This paper develops fuzzy force control strategies for the rigid dual peg-in-hole assembly. Firstly the fuzzy force control strategies are presented. Secondly the contact states and contact forces are analyzed to prove the availability of the force control strategies.

Findings
The rigid dual peg-in-hole assembly experimental results show the effectiveness of the control strategies.

Originality/value
This paper proposes fuzzy force control strategies for a rigid dual peg-in-hole assembly task.