bluuebunny/crossref_metadata_2025_split huggingface dataset:
The shapes of bird beaks are highly controlled by nondietary factors
Authors: Bright Jen A. , Marugán-Lobón Jesús , Cobb Samuel N. , Rayfield Emily J. 
Published: April 2016

Significance
We show that beak and skull shapes in birds of prey (“raptors”) are strongly coupled and largely controlled by size. This relationship means that, rather than being able to respond independently to natural selection, beak shapes are highly constrained to evolve in a particular way. The main aspects of shape variation seem to correspond with specific genes active during development. Because raptors are not each other’s closest relatives, similar shape constraints may therefore have been present in the ancestors of all modern songbirds, including Darwin’s finches, the classic example of explosive evolution in birds. If this hypothesis is true, then such classic examples may be unusual, needing first to break a genetic lock before their beaks could evolve new shapes.
δ-COP modulates Aβ peptide formation via retrograde trafficking of APP
Authors: Bettayeb Karima , Chang Jerry C. , Luo Wenjie , Aryal Suvekshya , Varotsis Dante , Randolph Lisa , Netzer William J. , Greengard Paul , Flajolet Marc 
Published: April 2016

Significance
Alzheimer’s disease (AD) is characterized by the presence of amyloid plaques resulting from the aggregation of amyloid-β (Aβ) peptides produced via sequential cleavage of amyloid precursor protein (APP). Cleavages happen concomitantly with APP trafficking from the plasma membrane to late endosomes. However, the role of an early trafficking pathway, the coat protein complex I (COPI)-dependent trafficking, has been overlooked. The present study demonstrates that, using a complex set of imaging technologies coupled to biochemical experiments, COPI subunit δ (δ-COP) affects the biology of APP, including its subcellular localization, cell surface expression, and trafficking, as well as its metabolism. Altogether, these findings demonstrate the physiological relevance of δ-COP in AD pathogenesis.
Seriously, Get to Know Your Audience
Authors: Nguyen Vivian 
Published: April 2016

Abstract
A version of this article was originally published on the Canadian Science Publishing blog as part of the series “Making Waves: The Future of #Scicomm in Fisheries Sciences.” The series was spawned from the science communication session held at last year's Annual Meeting in Portland. An introduction to the blog series is available at cdnsciencepub.com/blog.
Seasonal and developmental differences in blubber stores of beluga whales in Bristol Bay, Alaska using high-resolution ultrasound
Authors: Cornick Leslie A. , Quakenbush Lori T. , Norman Stephanie A. , Pasi Coral , Maslyk Pamela , Burek Kathy A. , Goertz Caroline E. C. , Hobbs Roderick C. 
Published: April 2016

AbstractDiving mammals use blubber for a variety of structural and physiological functions, including buoyancy, streamlining, thermoregulation, and energy storage. Estimating blubber stores provides proxies for body condition, nutritional status, and health. Blubber stores may vary topographically within individuals, across seasons, and with age, sex, and reproductive status; therefore, a single full-depth blubber biopsy does not provide an accurate measure of blubber depth, and additional biopsies are limited because they result in open wounds. We examined high-resolution ultrasound as a noninvasive method for assessing blubber stores by sampling blubber depth at 11 locations on beluga whales in Alaska. Blubber mass was estimated as a proportion of body mass (40% from the literature) and compared to a function of volume calculated using ultrasound blubber depth measurements in a truncated cone. Blubber volume was converted to total and mass-specific blubber mass estimates based on the density of beluga blubber. There was no significant difference in mean total blubber mass between the 2 estimates (R2 = 0.88); however, body mass alone predicted only 68% of the variation in mass-specific blubber stores in juveniles, 7% for adults in the fall, and 33% for adults in the spring. Mass-specific blubber stores calculated from ultrasound measurements were highly variable. Adults had significantly greater blubber stores in the fall (0.48±0.02kg/kgMB) than in the spring (0.33±0.02kg/kgMB). There was no seasonal effect in juveniles. High-resolution ultrasound is a more powerful, noninvasive method for assessing blubber stores in wild belugas, allowing for precise measurements at multiple locations.
Trabeculectomy With Moorfields Conjunctival Closure Technique Offers Safety Without Astigmatism Induction
Authors: Willekens Koen , Pinto Luìs A. , Delbeke Heleen , Vandewalle Evelien , Stalmans Ingeborg 
Published: April 2016

Purpose:
To evaluate the safety profile and possible change in corneal astigmatism following trabeculectomy with a fornix-based conjunctival flap which is closed with 4 corneal groove-embedded sutures.

Materials and Methods:
Patients scheduled for a primary trabeculectomy were included in this single center, prospective trial between February and April 2013. Refractive status was assessed with an automated refractokeratometer preoperatively and at months 1, 3, 6, and 18 postoperatively, together with clinical assessment of intraocular pressure, visual acuity, postoperative complications, and medication use. Preoperative and postoperative variables were compared using paired samples t tests and vector analysis for corneal astigmatism change was performed.

Results:
Forty-four eyes of 44 patients were included. Vector analysis showed a transient significant with-the-rule shift in astigmatism without influence on spherical equivalent. Visual acuity was transiently reduced in the first month but recovered to preoperative values with no need to change optical correction. Two patients developed postoperative wound leakage, which was successfully treated with a bandage corneoscleral contact lens.

Conclusions:
Trabeculectomy with a fornix-based conjunctival flap closed by 4 corneal groove-embedded sutures results in a low complication rate. This safe suturing technique induces a transient shift of with-the-rule astigmatism, reverting to the preoperative values within 3 months of surgery. Adjustments to refractive correction are recommended to be postponed until after this period.
Development of a BPPV Algorithm for Earlier Physical Therapy Consultation in the Acute Care Setting
Authors: McArdle Kelly Duszak , Hyon Alicia , Thielman Gregory 
Published: April 2016

Purpose:
Diagnosing and managing individuals with dizziness, imbalance, and vertigo are a challenge in health care. Benign paroxysmal positional vertigo is a common source of these symptoms. Individuals are often misdiagnosed or undiagnosed, causing overuse of medical testing or hospitalizations, suboptimal care, and increased costs. Physical therapists (PTs) are often overlooked in the consultation process until medical testing is completed. Practice pattern differences among the medical and rehabilitation communities and a lack of established interdisciplinary guidelines exist. This case report highlights the potential for resolution of these problems.

Methods:
An individual with symptoms of dizziness, vertigo, shoulder and neck pain, and imbalance was admitted to an acute care hospital for a 5-day length of stay. PT was not consulted until admission day 3 after medical workup and when left posterior canalithiasis was suspected. This led to the development of a benign paroxysmal positional vertigo consultant algorithm the medical and PT staff could use as a screen in determining if PT consultation was necessary. The medical and PT staff were given an in-service.

Results:
Symptoms were successfully alleviated with PT intervention, including a canalith repositioning maneuver and education.

Conclusion:
Barriers, including clinical competency and delayed consultation, resulted in an increased length of stay and costs. Internal education and algorithm development for PT referral were generated. Earlier PT consultation in collaboration with medical workup may decrease health care costs and improve quality of care.
Validity of the Agency for Health Care Research and Quality Patient Safety Indicators and the Centers for Medicare and Medicaid Hospital-acquired Conditions
Authors: Winters Bradford D. , Bharmal Aamir , Wilson Renee F. , Zhang Allen , Engineer Lilly , Defoe Deidre , Bass Eric B. , Dy Sydney , Pronovost Peter J. 
Published: April 2016

Background:
The Agency for Health Care Research and Quality Patient Safety Indicators (PSIs) and Centers for Medicare and Medicaid Services Hospital-acquired Conditions (HACs) are increasingly being used for pay-for-performance and public reporting despite concerns over their validity. Given the potential for these measures to misinform patients, misclassify hospitals, and misapply financial and reputational harm to hospitals, these need to be rigorously evaluated. We performed a systematic review and meta-analysis to assess PSI and HAC measure validity.

Methods:
We searched MEDLINE and the gray literature from January 1, 1990 through January 14, 2015 for studies that addressed the validity of the HAC measures and PSIs. Secondary outcomes included the effects of present on admission (POA) modifiers, and the most common reasons for discrepancies. We developed pooled results for measures evaluated by ≥3 studies. We propose a threshold of 80% for positive predictive value or sensitivity for pay-for-performance and public reporting suitability.

Results:
Only 5 measures, Iatrogenic Pneumothorax (PSI 6/HAC 17), Central Line–associated Bloodstream Infections (PSI 7), Postoperative hemorrhage/hematoma (PSI 9), Postoperative deep vein thrombosis/pulmonary embolus (PSI 12), and Accidental Puncture/Laceration (PSI 15), had sufficient data for pooled meta-analysis. Only PSI 15 (Accidental Puncture and Laceration) met our proposed threshold for validity (positive predictive value only) but this result was weakened by considerable heterogeneity. Coding errors were the most common reasons for discrepancies between medical record review and administrative databases. POA modifiers may improve the validity of some measures.

Conclusion:
This systematic review finds that there is limited validity for the PSI and HAC measures when measured against the reference standard of a medical chart review. Their use, as they currently exist, for public reporting and pay-for-performance, should be publicly reevaluated in light of these findings.
Meningiomatosis in an AIDS Patient Receiving Highly Active Antiretroviral Therapy (HAART)
Authors: Romero César F. , Soto-Hernández José L. , Bonnet Cecilia , Cárdenas Graciela 
Published: April 2016

Introduction:
Currently, AIDS is the worldwide leading cause of death among 15- to 59-year-old individuals. This trend has had particularly harsh social and economic consequences in sub-Saharan Africa, where more than half of global AIDS deaths take place. In the United States, an estimated 1.2 million people are infected with HIV. In 2012, a worldwide estimate of 1.7 million deaths due to AIDS-related causes was reported.
About 10% to 12% of all AIDS patients will develop intracranial tumors. Differential diagnosis should rule out brain tumors such as central nervous system lymphoma and gliomas, as well as infectious processes such as toxoplasmosis, tuberculosis, and cryptococcosis.

Case Report:
A 27-year-old homosexual man was referred to our care center after 2 months of disabling left frontal headache. Upon AIDS diagnosis, the patient was given abacavir (ABC), lamivudine (3TC), and efavirenz (EFV), but he discontinued the treatment after 9 months and failed to attend follow-up appointments. Three years later, the patient returned to the hospital and received ABC, 3TC, and lopinavir/ritonavir (LPV/r). On admission, computed tomographic scan reported multiple contrast-enhancing lesions compatible with meningiomas. The patient underwent uncomplicated surgical resection of the frontal basal lesion originating in the left olfactory bulb. No new neurological deficits were reported during the postoperative stay.

Conclusions:
According to a literature revision, it is likely that associated meningiomas are more aggressive in AIDS patients. Severe immunosuppression and the HIV-Tat protein may be involved in the pathogenesis of tumoral growth.
Cerebral Venous Sinus Thrombosis From a Tertiary Care Teaching Hospital in India
Authors: Kalita Jayantee , Chandra Satish , Kumar Bishwanath , Bansal Vikas , Misra Usha K. 
Published: April 2016

Objective:
The prognosis of cerebral venous sinus thrombosis (CVST) may be dependent on underlying causes and magnetic resonance imaging findings. We report the clinical, laboratory, and radiologic spectrum, and outcome of consecutive patients with CVST.

Methods:
Consecutive patients with CVST over the last 15 years were subjected to detailed history, clinical examination, and laboratory tests as per fixed protocol. The diagnosis of CVST was based on MR venography. The magnetic resonance imaging findings and the sinuses involved were noted. The patients were treated with low–molecular-weight heparin or unfractionated heparin for 14 days, followed by oral anticoagulation. Hospital mortality and 3-month outcome (good or poor) were recorded and correlated with various clinical and laboratory parameters.

Results:
There were 86 patients whose median age was 30 (6 to 76) years; 47 of them were females. Headache was present in 91.9%, vomiting in 68.6%, focal weakness in 53.5%, seizure in 51.2%, and altered sensorium in 53.5%. Female-specific etiology was present in 34%, prothrombotic condition in 62.8%, infections in 19.8%, and malignancy in 2.8%; no cause could be established in 25.6% of patients. Hyperhomocystinemia was present in 45.9% of patients. Five patients died in the unfractionated heparin group. At 3 months, 77 patients were followed up, of whom 68 had complete, 3 had partial, and 6 had poor recovery. The 3-month outcome was related to Glasgow Coma Scale score and type of heparin used.

Conclusions:
In our study multiple prothrombotic conditions were common, and low–molecular-weight heparin reduces mortality and results in good outcome.
Limiting Cumulative HIV Viremia Copy-Years by Early Treatment Reduces Risk of AIDS and Death
Authors: Olson Ashley D. , Walker A. Sarah , Suthar Amitabh B. , Sabin Caroline , Bucher Heiner C. , Jarrin Inma , Moreno Santiago , Perez-Hoyos Santiago , Porter Kholoud , Ford Deborah ,   on behalf of CASCADE Collaboration in EuroCoord
Published: April 2016

Background:
Viremia copy-years (VCY), a time-updated measure of cumulative HIV exposure, predicts AIDS/death; although its utility in deciding when to start combination antiretroviral therapy (cART) remains unclear. We aimed to assess the impact of initiating versus deferring cART on risk of AIDS/death by levels of VCY both independent of and within CD4 cell count strata ≥500 cells per cubic millimeter.

Methods:
Using Concerted Action on Seroconversion to AIDS and Death in Europe (CASCADE) data, we created a series of nested “trials” corresponding to consecutive months for individuals ≥16 years at seroconversion after 1995 who were cART-naive and AIDS-free. Pooling across all trials, time to AIDS/death by CD4, and VCY strata was compared in those initiating vs. deferring cART using Cox models adjusted for: country, sex, risk group, seroconversion year, age, time since last HIV-RNA, and current CD4, VCY, HIV-RNA, and mean number of previous CD4/HIV-RNA measurements/year.

Results:
Of 9353 individuals, 5312 (57%) initiated cART and 486 (5%) acquired AIDS/died. Pooling CD4 strata, risk of AIDS/death associated with initiating vs. deferring cART reduced as VCY increased. In patients with high CD4 cell counts, ≥500 cells per cubic millimeter, there was a trend for a greater reduction for those initiating vs. deferring with increasing VCY (P = 0.09), with the largest benefit in the VCY ≥100,000 copy-years/mL group [hazard ratio (95% CI) = 0.41 (0.19 to 0.87)].

Conclusions:
For individuals with CD4 ≥500 cells per cubic millimeter, limiting the cumulative HIV burden to <100,000 copy-years/mL through cART may reduce the risk of AIDS/death.
Higher Time-Updated Body Mass Index: Association With Improved CD4+ Cell Recovery on HIV Treatment
Authors: Koethe John R. , Jenkins Cathy A. , Lau Bryan , Shepherd Bryan E. , Wester William , Rebeiro Peter F. , Silverberg Michael J. , Thorne Jennifer E. , Gill John , Mayor Angel M. , Willig Amanda , Bosch Ronald , Horberg Michael A. , Justice Amy C. , Sterling Timothy R. , Moore Richard D. ,   for the North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD)
Published: April 2016

Background:
Prior studies found overweight or obese HIV-infected individuals had greater early CD4+ cell recovery on antiretroviral therapy (ART), but the results have been inconsistent. We assessed the longitudinal relationship between body mass index (BMI) and CD4+ cell recovery on ART in a large, multisite cohort to identify potential physiologic links between adiposity and CD4+ cell expansion.

Methods:
We modeled the relationship of time-updated BMI with CD4+ count in patients starting ART from 17 North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) cohorts. The primary analysis used a linear mixed effects model incorporating up to 13 years of data per patient and adjusted for age, sex, race, ART regimen, baseline CD4+ count and other covariates. Sensitivity analyses limited the cohort to patients with sustained viral suppression or censored at virologic failure.

Results:
Fourteen thousand eighty-four HIV-infected individuals initiating ART contributed data between 1998 and 2010. Time-updated BMI was significantly associated with CD4+ cell recovery over time (P < 0.001). After 5 years of ART, the mean CD4+ count at a BMI of 30 kg/m2 was 22% higher than at a BMI of 22 kg/m2 (606 vs. 498 cells per microliter) and 34% higher at a BMI of 40 kg/m2 (665 vs. 498 cells per microliter). Results were similar in the sensitivity analyses.

Discussion:
Higher BMI is associated with long-term advantages in immune recovery on ART. Although it is unclear if this impacts health outcomes, including balancing the negative health effects of obesity, elucidating the underlying mechanism could identify therapies for patients with suboptimal immune reconstitution.
Whole genome sequencing identifies independent outbreaks of Shigellosis in 2010 and 2011 in La Pampa Province, Argentina
Authors: Chinen Isabel , Galas Marcelo , Tuduri Ezequiel , Viñas Maria Rosa , Carbonari Carolina , Della Gaspera Anabella , Nápoli Daniela , Aanensen David M , Argimón Silvia , Thomson Nicholas R , Hughes Darren , Baker Stephen , Guzmán-Verri Caterina , Holden Matthew TG , Abdala Alejandra M , Alvarez Lucia P , Alvez Beatriz , Barros Rosana , Budall Shirley , Campano Constanza , Chamosa Luciana S , Cheddie Paul , Cisterna Daniel , De Belder Denise , Dropa Milena , Durand David , Elena Alan , Fontecha Gustavo , Huber Claudia , Lemos Ana Paula , Melli Luciano , Paul Roxana Elizabeth , Suarez Lesly , Torres Flores Julian , Campos Josefina 
Published: April 2016

AbstractShigella sonneiis an emergent cause of diarrheal disease in middle-income countries. The organism causes endemic disease and is also associated with sporadic outbreaks in susceptible populations. In 2010 and 2011 there were two suspected outbreaks of diarrheal disease caused byS. sonneiin La Pampa province in central Argentina. Aiming to confirm these as outbreaks and provide insight into the relationship of the strains causing these infections we combined antimicrobial susceptibility testing and pulsed field gel electrophoresis (PFGE) with whole genome sequencing (WGS). Antimicrobial susceptibility testing suggested the two events were unrelated; organisms isolated in 2010 exhibited resistance to trimethoprim sulphate whereas the 2011S. sonneiwere non-susceptible against ampicillin, trimethoprim sulphate and cefpodoxime. PFGE profiling confirmed the likelihood of two independent outbreaks, separating the isolates into two main XbaI restriction profiles. We additionally performed WGS on 17 isolates associated with these outbreaks. The resulting phylogeny confirmed the PFGE structure and separated the organisms into two comparatively distantly related clones. Antimicrobial resistant genes were common, and the presence of an OXA-1 was likely associated with resistance to cefpodoxime in the second outbreak. We additionally identified novel horizontally transferred genetic material that may impinge on the pathogenic phenotype of the infecting strains. Our study shows that even with a lack of supporting routine data WGS is an indispensible method for the tracking and surveillance of bacterial pathogens during outbreaks and is becoming a vital tool for the monitoring of antimicrobial resistant strains ofS. sonnei.
Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-CF bronchiectasis patients
Authors: Cox Michael J , Turek Elena M , Hennessy Catherine , Mirza Ghazala K , James Phillip L , Coleman Meg , Jones Andrew , Wilson Robert , Bilton Diana , Cookson William O. C. , Moffatt Miriam F. , Loebinger Michael 
Published: April 2016

AbstractBackgroundBronchiectasis is accompanied by chronic bronchial infection that may drive disease progression. However, the evidence base for antibiotic therapy is limited. DNA based methods offer better identification and quantification of microbial constituents of sputum than standard clinical culture and may help inform patient management strategies. Our study objective was to determine the longitudinal variability of the non-CF bronchiectasis microbiome in sputum with respect to clinical variables.Eighty-five patients with non-cystic fibrosis (CF) bronchiectasis and daily sputum production were recruited from outpatient clinics and followed for six months. Monthly sputum samples and clinical measurements were taken, together with additional samples during exacerbations. 16S rRNA gene sequencing of the sputum microbiota was successful for 381 samples from 76 patients and analysed in conjunction with clinical data.ResultsMicrobial communities were highly individual in composition and stability, usually with limited diversity and often containing multiple pathogens. When compared to DNA sequencing, microbial culture had restricted sensitivity in identifying common pathogens. With some exceptions, community characteristics showed poor correlations with clinical features including underlying disease, antibiotic use and exacerbations, with the subject showing the strongest association with community structure. When present, certain pathogens may also shape the structure of the rest of the microbial community.ConclusionsThe use of microbial community analysis of sputum added to information from microbial culture. A simple model of exacerbations driven by bacterial overgrowth was not supported, suggesting a need for revision of principles for antibiotic therapy. In individual patients, the management of chronic bronchial infection may be improved by therapy specific to their microbiome, taking into account pathogen load, community stability, and acute and chronic community responses to antibiotics.