bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in Insulin Resistance After Initiation of Raltegravir or Protease Inhibitors With Tenofovir-Emtricitabine: AIDS Clinical Trials Group A5260s
Authors: Dirajlal-Fargo Sahera , Moser Carlee , Brown Todd T. , Kelesidis Theodoros , Dube Michael P. , Stein James H. , Currier Judith , McComsey Grace A. 
Published: August 2016

Abstract
Background.  Antiretroviral therapy (ART) can alter glucose metabolism, but little data exist on the association of raltegravir (RAL) with insulin resistance.
Methods.  A5260s was a substudy of A5257, a prospective open-label randomized trial in which human immunodeficiency virus (HIV)-infected treatment-naive participants were randomized to tenofovir-emtricitabine (TDF/FTC) plus atazanavir-ritonavir (ATV/r), darunavir-ritonavir (DRV/r), or RAL over 96 weeks. Baseline and changes in insulin resistance as estimated by the homeostatic model assessment of insulin resistance (HOMA-IR) were assessed. Wilcoxon rank-sum tests were used to assess shifts in the distribution of fold increase from baseline between treatment arms, and Spearman correlation was used to assess associations between HOMA-IR and measures of inflammation and body composition.
Results.  Three hundred twenty-eight participants were randomized; 90% were male, baseline median age was 36, HIV ribonucleic acid copies were 4.55 log10 copies/mL, and CD4 cell count was 349/mm3. Overall, HOMA-IR increased significantly after 4 weeks (1.9-fold change; 95% confidence interval, 1.73–2.05) then plateaued over the remainder of the study. Changes in HOMA-IR were not different between the arms (P ≥ .23). Changes in HOMA-IR were associated with changes in body mass index at weeks 48 and 96 (r = 0.12–0.22; P ≤ .04). There was a trend with increases in HOMA-IR and increases in visceral abdominal fat at week 96 (r = 0.12; P = .06). At 48 and 96 weeks, HOMA-IR correlated with interleukin-6, high-sensitivity C-reactive protein, and soluble CD163 (r = 0.16–0.27; P ≤ .003).
Conclusions.  Insulin resistance increased rapidly and then plateaued in treatment-naive participants initiating ART with TDF/FTC, and no differences were found with RAL when compared with ATV/r or DRV/r.
Characteristics of Biostatistics, Epidemiology, and Research Design Programs in Institutions With Clinical and Translational Science Awards
Authors: Rahbar Mohammad H. , Dickerson Aisha S. , Ahn Chul , Carter Rickey E. , Hessabi Manouchehr , Lindsell Christopher J. , Nietert Paul J. , Oster Robert A. , Pollock Brad H. , Welty Leah J. 
Published: August 2016

Purpose
To learn the size, composition, and scholarly output of biostatistics, epidemiology, and research design (BERD) units in U.S. academic health centers (AHCs).

Method
Each year for four years, the authors surveyed all BERD units in U.S. AHCs that were members of the Clinical and Translational Science Award (CTSA) Consortium. In 2010, 46 BERD units were surveyed; in 2011, 55; in 2012, 60; and in 2013, 61.

Results
Response rates to the 2010, 2011, 2012, and 2013 surveys were 93.5%, 98.2%, 98.3%, and 86.9%, respectively. Overall, the size of BERD units ranged from 3 to 86 individuals. The median FTE in BERD units remained similar and ranged from 3.0 to 3.5 FTEs over the years. BERD units reported more availability of doctoral-level biostatisticians than doctoral-level epidemiologists. In 2011, 2012, and 2013, more than a third of BERD units provided consulting support on 101 to 200 projects. A majority of BERD units reported that between 25% and 75% (in 2011) and 31% to 70% (in 2012) of their consulting was to junior investigators. More than two-thirds of BERD units reported their contributions to the submission of 20 or more non-BERD grant or contract applications annually. Nearly half of BERD units reported 1 to 10 manuscripts submitted annually with a BERD practitioner as the first or corresponding author.

Conclusions
The findings regarding BERD units provide a benchmark against which to compare BERD resources and may be particularly useful for institutions planning to develop new units to support programs such as the CTSA.
Preclinical Pain Research
Authors: Clark J. David 
Published: August 2016

Abstract
Regrettably, the list of unique analgesic tools has expanded very slowly during the past few decades. Many very promising drugs have failed once tested in clinical populations, and the associated costs of these translational failures have been extremely high. Part of this problem can be traced to the ways we select and use preclinical tools and perhaps to the way we report our findings. We are beginning to reevaluate our selection of animal models and the methods we use to measure pain-related responses in these animals. In addition, many journals now require a clear statement of the experimental hypothesis, the details of the experimental methods, a description of the statistical approach to analyzing the data, and the disclosure of conflicts of interest. These new practices pose challenges to laboratory-based research groups. However, a more rigorous approach to preclinical investigations may be necessary for the successful development of new analgesics.
Rebound of Frontal Plane Malalignment After Tension Band Plating
Authors: Farr Sebastian , Alrabai Hamza M. , Meizer Elisabeth , Ganger Rudolf , Radler Christof 
Published: August 2016

Background:
Despite the popularity of tension band plating (TBP) current literature lacks clinical data concerning recurrence (“rebound”) of frontal plane malalignment. This study investigated the rebound phenomenon after TBP in idiopathic genu varum/valgum deformities. We analyzed factors that may contribute to the development of rebound after removal of TBP.

Methods:
Patients who had correction of idiopathic valgus or varus deformities by TBP at the distal femoral and/or proximal tibial growth plate were selected from a prospective consecutive database. Only patients who had plates removed for at least 1 year and had a long standing radiograph of the lower limbs before plate removal were included. Patients who had presumably not yet reached skeletal maturity (age under 14 y for girls and under 16 y for boys) were excluded. The change of the mechanical axis from plate removal to follow-up after skeletal maturity was evaluated and a statistical analysis was performed.

Results:
Twenty-nine patients (64 extremities) were eligible. The mean follow-up was 39.1 months (range, 12.3 to 67.3 mo). The mean mechanical axis deviation (MAD) was +0.8 mm (range, −26 to +22 mm) after plate removal and −2.4 mm (range, −29 to +27 mm) at follow-up, accounting for a significant change of MAD (P=0.046). We observed a mean, relative recurrence of frontal plate malalignment into valgus direction of −3.2 mm (range, −48 to +23 mm). Twenty extremities (31%) showed <3 mm of MAD change; 27 extremities (42%) showed >3 mm of MAD change into valgus, and 17 extremities (27%) >3 mm of MAD change into varus direction. Patients with <3 mm MAD change had only 0.8 years, and those >3 mm a mean of 2.0 years of remaining growth until skeletal maturity. Each additional m2/kg of body mass index increased the risk of valgus recurrence by 12.1%. The 3 genua vara patients revealed to have an even higher rate of malalignment recurrence (4 of 6 limbs) at final follow-up.

Conclusions:
Given our strict criteria, there is a high rate of radiologic recurrence of frontal plane malalignment after TBP. Children who are more than 1 year before skeletal maturity at TBP removal, and those with increased body mass index are at higher risk for rebound growth.

Level of Evidence:
Level IV—consecutive therapeutic case series.
MULTIMODAL IMAGING OF POSTERIOR POLAR ANNULAR CHOROIDAL DYSTROPHY
Authors: Forte Raimondo , Aptel Florent , Feldmann Audrey , Chiquet Christophe 
Published: August 2016

Background:
Posterior polar annular choroidal dystrophy (PPACD) is a rare disease. Patients with PPACD show loss of retinal pigment epithelium and choriocapillaries surrounding the vascular arcades and optic nerve.

Methods:
Two patients with PPACD were evaluated with multimodal imaging, including fundus autofluorescence (FAF) and adaptive optics (AO).

Report of Cases:
One patient (32 year old, one eye) with PPACD was followed up for 3 years. Best-corrected visual acuity (BCVA) was stable at 20/40, whereas a slight enlargement of paravascular atrophy of pigment epithelium was observed at fundus autofluorescence (FAF). Adaptive optics obtained at last examination showed reduced density of foveal cone photoreceptors. The second patient (30 year old, two eyes) with PPACD showed bilateral normal BCVA, associated with reduction in the density of foveal cone photoreceptors.

Conclusion:
At FAF, longitudinal follow-up of PPACD showed progression of the paravascular atrophy of the pigment epithelium. Foveal cone photoreceptors can be reduced even in the presence of preserved visual acuity.
Development and Real World Use of a Vibratory Haptic Feedback System for Upper-Limb Prosthetic Users
Authors: Rosenbaum-Chou Teri , Daly Wayne , Austin Ray , Chaubey Pravin , Boone David A. 
Published: August 2016

ABSTRACT

Introduction
Sensory feedback is largely unavailable for persons with upper-limb amputation with conventional prostheses. The current study created a portable vibratory haptic feedback system integrated into the prosthesis to test its usefulness in gripping objects during daily life.

Materials and Methods
Development involved optimizing a mapping algorithm between the force sensor and the feedback tactor vibration, developing a custom process for mounting a wireless force sensor onto the prosthetic thumb with reliable output, and developing an instrumented object for testing grip force accuracy. Clinical testing involved optimizing tactor placement, measuring grip force accuracy, measuring the ability to perform daily gripping tasks, and surveying prosthetic users' opinion of the system after using the vibratory haptic device at home. A total of six individuals with unilateral transradial amputation participated in this study.

Results
The results demonstrated optimal tactor placement more proximal versus distal on the forearm. Accuracy with haptic versus no haptic feedback demonstrated that haptic feedback improved the grip force accuracy by 129% (adjusted P = 0.041) for light grip force target (2 lb or 0.9 kg) in the nonportable system and 21% (adjusted P = 0.051) for medium grip force target (10 lb or 4.5 kg) in the portable system. Haptic feedback did not statistically improve grip accuracy at strong grip forces (20 lb or 9.1 kg). Haptic feedback improved the gripping technique during the Assessment of Capacity for Myoelectric Control (ACMC) by 1.22 points, although this was not statistically significant (P = 0.27, n = 4). The participants provided specific positive examples of how the vibratory haptic system was useful at home. The overall usability score was 3.6 where 4 indicated excellent and 0 indicated poor.

Conclusions
This kind of system has potential to improve the lives of upper-limb prosthetic users.
Combining the Absence of Electromagnetic Fields and Mirror Therapy to Improve Outcomes for Persons with Lower-Limb Vascular Amputation
Authors: Houston Helen , Dickerson Anne E. , Wu Qiang 
Published: August 2016

ABSTRACT

Objective
The objective of this pilot study was to explore whether or not the combination of using a residual limb cover to eliminate electromagnetic fields and a mirror therapy exercise program facilitates healing and decreases pain for individuals with lower-limb vascular amputation.

Materials and Methods
A cross-sectional repeated measures design compared two groups based on the time of amputation. Participants in the acute group (n = 11) began treatment within 48 hrs of their amputation, and those who had surgery at least 6 weeks before starting the study comprised the chronic group (n = 5). Effectiveness was measured by physical factors (e.g., edema, temperature) and perception of phantom limb pain (e.g., intensity, frequency, bothersomeness) at three times: pretreatment, posttreatment at 4 weeks, and maintenance after 8 weeks (interval of 4 weeks of no treatment).

Results
For acute participants, edema, temperature, frequency, and bothersomeness demonstrated significant differences, whereas for the chronic group, temperature, pain intensity, frequency, and bothersomeness were significantly different. Unanticipated results were that the residual limb incisions of the individuals with acute amputations were sufficiently healed to begin prosthetic fitting a month earlier than the typical protocol—a decrease from 12 weeks to 8 weeks—and that wearing tolerance increased from 0 to 2 hrs to 8 to 12 hrs for the individuals with chronic amputations after completion of this treatment intervention.

Conclusions
Results suggest that this combined treatment may improve outcomes for individuals with vascular lower-limb amputations and should be investigated further.
Effect of a Knee-Ankle-Foot Orthosis on Knee Kinematics and Kinetics in an Individual with Varus Knee Alignment
Authors: Alfatafta Huda H. , Hutchins Stephen , Liu Anmin , Jones Richard 
Published: August 2016

ABSTRACT

Background
Knee valgus braces are used to reduce knee load and varus deformities in individuals with medial compartment osteoarthritis (OA). The purpose of this study was to determine whether the kinematics and kinetics of the knee are improved when wearing a knee-ankle-foot orthosis (KAFO) compared with knee valgus braces while walking and stair climbing.

Materials and Methods
One male individual (with 10° of knee varus) was assessed with a control shoe, custom, and off-the-shelf (OTS) Unloader knee valgus braces, and a custom-made KAFO in situ during walking and stair climbing.

Results
The KAFO significantly reduced the knee varus angle compared with the shoe and both knee valgus braces during walking and stair climbing, as well as the first peak of the external knee adduction moment (EKAM) during walking and the knee adduction angular impulse (KAAI) during ascending compared with the shoe. No significant differences were noted between the custom and OTS knee valgus braces in any measures.

Conclusions
Knee-ankle-foot orthoses may be recommended for individuals with high knee varus angles.
Obesity and government
Authors: Kahan Scott , Zvenyach Tracy 
Published: August 2016

Purpose of review
Despite much effort, obesity prevalence and disease severity continues to worsen. The purpose of this review is to describe the leading government supported food and nutrition interventions and policies to prevent and address obesity in the USA. The review also summarizes obesity interventions and policies that the government plays a role in, but further development is warranted.

Recent findings
The government's role in obesity has largely focused on interventions and policies such as national surveillance, obesity education and awareness, grant-based food subsidy programs, zoning for food access, school-based nutrition programs, dietary guidelines, nutrition labeling, and food marketing and pricing policies. The government has played a lesser role in obesity interventions and policies that provide access to evidence-based obesity care to people affected by the disease.

Summary
Given the magnitude of the obesity epidemic, the government should explore multiple evidence-based interventions and policies across prevention and clinical care.
Serum amyloid A and atherosclerosis
Authors: Getz Godfrey S. , Krishack Paulette A. , Reardon Catherine A. 
Published: August 2016

Purpose of review
Atherosclerosis is a chronic inflammation associated with increased expression of the acute phase isoforms of serum amyloid A (SAA) and in humans is a plasma biomarker for future cardiovascular events. However, whether SAA is only a biomarker or participates in the development of cardiovascular disease is not well characterized. The purpose of this review is to summarize putative functions of SAA relevant to atherogenesis and in-vivo murine studies that directly examine the effect of SAA on atherosclerosis.

Recent findings
Modulation of the expression of SAA1 and/or SAA2 in murine models of atherosclerosis suggests that SAA promotes early atherogenesis. SAA secreted from bone-marrow-derived cells contributes to this antiatherogenic phenotype. SAA also promotes angiotensin-induced abdominal aneurysm in atherogenic mouse models. The reduction in atherosclerosis may be due, at least in part, to remodeling of the acute phase HDL to reduce its capacity to promote cholesterol efflux and reduce its anti-inflammatory ability.

Summary
SAA is more than a marker of cardiovascular disease and is a participant in the early atherogenic process.
Balance, Body Motion, and Muscle Activity After High-Volume Short-Term Dance-Based Rehabilitation in Persons With Parkinson Disease: A Pilot Study
Authors: McKay J. Lucas , Ting Lena H. , Hackney Madeleine E. 
Published: August 2016

Background and Purpose:
The objectives of this pilot study were to (1) evaluate the feasibility and investigate the efficacy of a 3-week, high-volume (450 minutes per week) Adapted Tango intervention for community-dwelling individuals with mild-moderate Parkinson disease (PD) and (2) investigate the potential efficacy of Adapted Tango in modifying electromyographic (EMG) activity and center of body mass (CoM) displacement during automatic postural responses to support surface perturbations.

Methods:
Individuals with PD (n = 26) were recruited for high-volume Adapted Tango (15 lessons, 1.5 hour each over 3 weeks). Twenty participants were assessed with clinical balance and gait measures before and after the intervention. Nine participants were also assessed with support-surface translation perturbations.

Results:
Overall adherence to the intervention was 77%. At posttest, peak forward CoM displacement was reduced (4.0 ± 0.9 cm, pretest, vs 3.7 ± 1.1 cm, posttest; P = 0.03; Cohen's d = 0.30) and correlated to improvements on Berg Balance Scale (ρ = −0.68; P = 0.04) and Dynamic Gait Index (ρ = −0.75; P = 0.03). Overall antagonist onset time was delayed (27 ms; P = 0.02; d = 0.90) and duration was reduced (56 ms, ≈39%, P = 0.02; d = 0.45). Reductions in EMG magnitude were also observed (P < 0.05).

Discussion and Conclusions:
Following participation in Adapted Tango, changes in kinematic and some EMG measures of perturbation responses were observed in addition to improvements in clinical measures. We conclude that 3-week, high-volume Adapted Tango is feasible and represents a viable alternative to longer duration adapted dance programs.

Video Abstract available for more insights from the authors (see Supplemental Digital Content 1, http://links.lww.com/JNPT/A143).
The Reading Frame Surveillance Hypothesis
Authors: Gray John T. 
Published: August 2016

AbbreviationsRFSReading Frame SurveillanceRdRPRNA-dependent RNA PolymerasefrRNAsFraming RNAsLSULarge SubunitSSUSmall SubunittRFTransfer RNA derived FragmentntnucleotideAbstractAn alternative model for protein translation is presented wherein ribosomes utilize a complementary RNA copy of protein coding sequences to monitor the progress of messenger RNAs during their translation to reduce the frequency of frameshifting errors. The synthesis of this ‘framing RNA’ is postulated to be catalyzed by the small subunit of the ribosome, in the decoding center, by excising and concatemerizing tRNA anticodons bound to each codon of the mRNA template. Various components of the model are supported by previous observations of tRNA mutants that impact ribosomal frameshifting, unique globin-coding RNAs in developing erythroblasts, and the epigenetic, intergenerational transfer of phenotypic traits via mammalian sperm RNA. Confirmation of the proposed translation mechanism is experimentally tractable and might significantly enhance our understanding of several fundamental biological processes.
Trends in dissolved organic matter cycling, sediment microbiomes, and methylmercury production across vegetation heterogeneity in a Great Lakes wetland
Authors: Graham Emily B. , Knelman Joseph E. , Gabor Rachel S. , Schooler Shon , McKnight Diane M. , Nemergut Diana R. 
Published: August 2016

AbstractRecent advances have allowed for greater investigation into microbial regulation of mercury toxicity in the environment. In wetlands in particular, dissolved organic matter (DOM) may influence methylmercury (MeHg) production both through chemical interactions and through substrate effects on microbiomes. We conducted microcosm experiments in two disparate wetland environments (oligotrophic unvegetated and high-C vegetated sediments) to examine the impacts of plant leachate and inorganic mercury loadings (20 mg/L HgCl2) on microbiomes, DOM cycling, and MeHg production in the St. Louis River Estuary. Our research reveals the greater relative capacity for mercury methylation in vegetated over unvegetated sediments. Further, our work shows how mercury cycling in oligotrophic unvegetated sediments may be susceptible to DOM inputs in the St. Louis River Estuary: microcosms receiving leachate produced substantially more MeHg than unamended microcosms. We also demonstrate (1) changes in microbiome structure towardsClostridia, (2) metagenomic shifts toward fermentation, and (3) degradation of complex DOM; all of which coincide with elevated net MeHg production in unvegetated microcosms receiving leachate. Finally, we examine microbial operational taxonomic units (OTUs) classified as known potential methylators and identify important organisms for future research in the Great Lakes region. Together, our work shows the influence of wetland vegetation in controlling MeHg production in the Great Lakes region and provides evidence that this may be due to both enhanced microbial activity as well as differences in microbiome composition.
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
Authors: Schneider Valerie A. , Graves-Lindsay Tina , Howe Kerstin , Bouk Nathan , Chen Hsiu-Chuan , Kitts Paul A. , Murphy Terence D. , Pruitt Kim D. , Thibaud-Nissen Françoise , Albracht Derek , Fulton Robert S. , Kremitzki Milinn , Magrini Vince , Markovic Chris , McGrath Sean , Steinberg Karyn Meltz , Auger Kate , Chow Will , Collins Joanna , Harden Glenn , Hubbard Tim , Pelan Sarah , Simpson Jared T. , Threadgold Glen , Torrance James , Wood Jonathan , Clarke Laura , Koren Sergey , Boitano Matthew , Li Heng , Chin Chen-Shan , Phillippy Adam M. , Durbin Richard , Wilson Richard K. , Flicek Paul , Church Deanna M. 
Published: August 2016

AbstractThe human reference genome assembly plays a central role in nearly all aspects of today’s basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009 and reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that while the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.