bluuebunny/crossref_metadata_2025_split huggingface dataset:
Embolism resistance in stems of herbaceous Brassicaceae and Asteraceae is linked to differences in woodiness and precipitation
Authors: Dória Larissa Chacon , Meijs Cynthia , Podadera Diego Sotto , Del Arco Marcelino , Smets Erik , Delzon Sylvain , Lens Frederic 
Published: December 2018

AbstractBackground and AimsPlant survival under extreme drought events has been associated with xylem vulnerability to embolism (the disruption of water transport due to air bubbles in conduits). Despite the ecological and economic importance of herbaceous species, studies focusing on hydraulic failure in herbs remain scarce. Here, we assess the vulnerability to embolism and anatomical adaptations in stems of seven herbaceous Brassicaceae species occurring in different vegetation zones of the island of Tenerife, Canary Islands, and merged them with a similar hydraulic–anatomical data set for herbaceous Asteraceae from Tenerife.MethodsMeasurements of vulnerability to xylem embolism using the in situ flow centrifuge technique along with light and transmission electron microscope observations were performed in stems of the herbaceous species. We also assessed the link between embolism resistance vs. mean annual precipitation and anatomical stem characters.Key ResultsThe herbaceous species show a 2-fold variation in stem P50 from –2.1 MPa to –4.9 MPa. Within Hirschfeldia incana and Sisymbrium orientale, there is also a significant stem P50 difference between populations growing in contrasting environments. Variation in stem P50 is mainly explained by mean annual precipitation as well as by the variation in the degree of woodiness (calculated as the proportion of lignified area per total stem area) and to a lesser extent by the thickness of intervessel pit membranes. Moreover, mean annual precipitation explains the total variance in embolism resistance and stem anatomical traits.ConclusionsThe degree of woodiness and thickness of intervessel pit membranes are good predictors of embolism resistance in the herbaceous Brassicaceae and Asteraceae species studied. Differences in mean annual precipitation across the sampling sites affect embolism resistance and stem anatomical characters, both being important characters determining survival and distribution of the herbaceous eudicots.
Condition-dependent foraging strategies in a coastal seabird: evidence for the rich get richer hypothesis
Authors: Geary Brock , Walter Scott T , Leberg Paul L , Karubian Jordan 
Published: December 2018

AbstractThe degree to which foraging individuals are able to appropriately modify their behaviors in response to dynamic environmental conditions and associated resource availability can have important fitness consequences. Despite an increasingly refined understanding of differences in foraging behavior between individuals, we still lack detailed characterizations of within-individual variation over space and time, and what factors may drive this variability. From 2014 to 2017, we used GPS transmitters and accelerometers to document foraging movements by breeding adult Brown Pelicans (Pelecanus occidentalis) in the northern Gulf of Mexico, where the prey landscape is patchy and dynamic at various scales. Assessments of traditional foraging metrics such as trip distance, linearity, or duration did not yield significant relationships between individuals. However, we did observe lower site fidelity and less variation in energy expenditure in birds of higher body condition, despite a population-level trend of increased fidelity as the breeding season progressed. These findings suggest that high-quality individuals are both more variable and more efficient in their foraging behaviors during a period of high energetic demand, consistent with a “rich get richer” scenario in which individuals in better condition are able to invest in more costly behaviors that provide higher returns. This work highlights the importance of considering behavioral variation at multiple scales, with particular reference to within-individual variation, to improve our understanding of foraging ecology in wild populations.
Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing
Authors: Rausch Tobias , Hsi-Yang Fritz Markus , Korbel Jan O , Benes Vladimir 
Published: December 2018

Abstract

Summary
Harmonizing quality control (QC) of large-scale second and third-generation sequencing datasets is key for enabling downstream computational and biological analyses. We present Alfred, an efficient and versatile command-line application that computes multi-sample QC metrics in a read-group aware manner, across a wide variety of sequencing assays and technologies. In addition to standard QC metrics such as GC bias, base composition, insert size and sequencing coverage distributions it supports haplotype-aware and allele-specific feature counting and feature annotation. The versatility of Alfred allows for easy pipeline integration in high-throughput settings, including DNA sequencing facilities and large-scale research initiatives, enabling continuous monitoring of sequence data quality and characteristics across samples. Alfred supports haplo-tagging of BAM/CRAM files to conduct haplotype-resolved analyses in conjunction with a variety of next-generation sequencing based assays. Alfred’s companion web application enables interactive exploration of results and comparison to public datasets.

Availability and implementation
Alfred is open-source and freely available at https://tobiasrausch.com/alfred/.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Randomized, Double-blinded, Placebo-controlled Trial of Sitagliptin for Reducing Inflammation and Immune Activation in Treated and Suppressed Human Immunodeficiency Virus Infection
Authors: Dubé Michael P , Chan Ellen S , Lake Jordan E , Williams Brett , Kinslow Jennifer , Landay Alan , Coombs Robert W , Floris-Moore Michelle , Ribaudo Heather J , Yarasheski Kevin E 
Published: December 2018

Abstract

Background
Dipeptidyl peptidase-4 (DPP-4) inhibitors have pleotropic anti-inflammatory and immune regulatory effects in addition to glucoregulation. We evaluated inflammation and immune markers in suppressed human immunodeficiency virus (HIV) infection during treatment with the DPP-4 inhibitor sitagliptin.

Methods
Virologically suppressed adults with HIV without diabetes on stable antiretroviral therapy (ART) with ≥100/μL CD4 cells were randomized to 16 weeks of sitagliptin 100 mg/day vs placebo in a multicenter trial. The primary endpoint was the change in plasma soluble CD14 (sCD14) from baseline to week 15–16.

Results
Ninety participants were randomized, and 42 from each arm were included in per-protocol analyses. Participants were 45% non-Hispanic white, 38% non-Hispanic black, and 15% Hispanic, with a median age of 51 years; 83% were male; and the median CD4 count was 602 cells/μL. At week 15–16, there was no difference in sCD14 change between the 2 arms (P = .69). Relative to placebo, the sitagliptin arm had 47% greater decline in CXCL10 (95% confidence interval, –57% to –35%) at week 15 (P < .001). There were no significant between-arm differences in other soluble biomarkers, total CD4 and CD8 counts, or markers of lymphocyte or monocyte activation. Sitagliptin was well tolerated.

Conclusions
Sixteen weeks of sitagliptin had no effect on sCD14 levels in virologically suppressed participants with HIV. CXCL10, a chemokine involved in atherogenesis that predicts non-AIDS events during ART, declined markedly with sitagliptin. This suggests that DPP-4 inhibition has the potential to reduce cardiovascular morbidity in treated HIV infection.

Clinical Trials Registration
NCT01426438.
Rate of peri-procedural stroke observed with cerebral embolic protection during transcatheter aortic valve replacement: a patient-level propensity-matched analysis
Authors: Seeger Julia , Kapadia Samir R , Kodali Susheel , Linke Axel , Wöhrle Jochen , Haussig Stephan , Makkar Raj , Mehran Roxana , Rottbauer Wolfgang , Leon Martin 
Published: December 2018

Abstract

Aims
The role of cerebral embolic protection (CEP) in transcatheter aortic valve replacement (TAVR) remains controversial. Randomized trials have not been powered to demonstrate a reduction in stroke rates. The aim of this patient level pooled analysis was to validate the impact of the dual-filter CEP device (Claret Medical Inc., CA, USA) on peri-procedural stroke in a large number of TAVR patients.

Methods and results
Patients from the SENTINEL US IDE trial were combined with the CLEAN-TAVI and SENTINEL-Ulm study in a patient level pooled analysis (N = 1306). Propensity score matching was performed to adjust for possible confounders. The primary endpoint was procedural stroke within 72 h post-TAVR according to Valve Academic Research Consortium-2 criteria. The secondary endpoint was the combination of all-cause mortality or all-stroke within 72 h after TAVR. In the propensity-matched population, 533 patients underwent TAVR without CEP and 533 patients underwent TAVR with CEP. TAVR patients without vs. with CEP were similar with respect to baseline characteristics, procedural approach, or valve type. In patients undergoing TAVR with dual-filter CEP, procedural all-stroke was significantly lower compared with unprotected procedures [1.88% vs. 5.44%, odds ratio 0.35, 95% confidence interval (CI) 0.17–0.72, relative risk reduction 65%, P = 0.0028]. In addition, all-cause mortality and all-stroke were significantly lower (2.06% vs. 6.00%, odds ratio 0.34, 95% CI 0.17–0.68, relative risk reduction 66%, P = 0.0013).

Conclusion
Our findings suggest that TAVR with the dual-filter CEP device is associated with a significant lower rate of peri-procedural stroke compared with unprotected procedures. However, randomized trials are still needed to clarify this issue.
Motivation as a Mediator of the Relation Between Cognitive Reserve and Cognitive Performance
Authors: Vallet Fanny , Mella Nathalie , Ihle Andreas , Beaudoin Marine , Fagot Delphine , Ballhausen Nicola , Baeriswyl Marie , Schlemmer Morgane , Oris Michel , Kliegel Matthias , Desrichard Olivier 
Published: December 2018

AbstractObjectivesInterindividual differences in cognitive aging may be explained by differences in cognitive reserve (CR) that are built up across the life span. A plausible but underresearched mechanism for these differences is that CR helps compensating cognitive decline by enhancing motivation to cope with challenging cognitive situations. Theories of motivation on cognition suggest that perceived capacity and intrinsic motivation may be key mediators in this respect.MethodIn 506 older adults, we assessed CR proxies (education, occupation, leisure activities), motivation (perceived capacity, intrinsic motivation), and a global measure of cognitive functioning.ResultsPerceived capacity, but not intrinsic motivation, significantly mediated the relation between CR and cognitive performance.DiscussionComplementary with neurobiological and cognitive processes, our results suggest a more comprehensive view of the role of motivational aspects built up across the life span in determining differences in cognitive performance in old age.
A mecC allotype, mecC3, in the CoNS Staphylococcus caeli, encoded within a variant SCCmecC
Authors: MacFadyen A C , Harrison E M , Drigo I , Parkhill J , Holmes M A , Paterson G K 
Published: December 2018

AbstractBackgroundMethicillin resistance in staphylococci is conferred by an alternative PBP (PBP2a/2′) with low affinity for most β-lactam antibiotics. PBP2a is encoded by mecA, which is carried on a mobile genetic element known as SCCmec. A variant of mecA, mecC, was described in 2011 and has been found in Staphylococcus aureus from humans and a wide range of animal species as well as a small number of other staphylococcal species from animals.ObjectivesWe characterized a novel mecC allotype, mecC3, encoded by an environmental isolate of Staphylococcus caeli cultured from air sampling of a commercial rabbit holding.MethodsThe S. caeli isolate 82BT was collected in Italy in 2013 and genome sequenced using MiSeq technology. This allowed the assembly and comparative genomic study of the novel SCCmec region encoding mecC3.ResultsThe study isolate encodes a novel mecA allotype, mecC3, with 92% nucleotide identity to mecC. mecC3 is encoded within a novel SCCmec element distinct from those previously associated with mecC, including a ccrAB pairing (ccrA5B3) not previously linked to mecC.ConclusionsThis is the first description of the novel mecC allotype mecC3, the first isolation of a mecC-positive Staphylococcus in Italy and the first report of mecC in S. caeli. Furthermore, the SCCmec element described here is highly dissimilar to the archetypal SCCmec XI encoding mecC in S. aureus and to elements encoding mecC in other staphylococci. Our report highlights the diversity of mecC allotypes and the diverse staphylococcal species, ecological settings and genomic context in which mecC may be found.
Effect of initial immunosuppression on long-term kidney transplant outcome in immunological low-risk patients
Authors: Michielsen Laura A , van Zuilen Arjan D , Verhaar Marianne C , Wisse Bram W , Kamburova Elena G , Joosten Irma , Allebes Wil A , van der Meer Arnold , Baas Marije C , Spierings Eric , Hack Cornelis E , van Reekum Franka E , Bots Michiel L , Drop Adriaan C A D , Plaisier Loes , Seelen Marc A J , Sanders Jan-Stephan F , Hepkema Bouke G , Lambeck Annechien J , Bungener Laura B , Roozendaal Caroline , Tilanus Marcel G J , Voorter Christien E , Wieten Lotte , van Duijnhoven Elizabeth M , Gelens Mariëlle A C J , Christiaans Maarten H L , van Ittersum Frans J , Nurmohamed Shaikh A , Lardy Neubury M , Swelsen Wendy , van der Pant Karlijn A , van der Weerd Neelke C , ten Berge Ineke J M , Bemelman Frederike J , Hoitsma Andries , van der Boog Paul J M , de Fijter Johan W , Betjes Michiel G H , Heidt Sebastiaan , Roelen Dave L , Claas Frans H , Otten Henderikus G , Hilbrands Luuk B 
Published: December 2018

Abstract

Background
Few studies have evaluated the effect of different immunosuppressive strategies on long-term kidney transplant outcomes. Moreover, as they were usually based on historical data, it was not possible to account for the presence of pretransplant donor-specific human-leukocyte antigen antibodies (DSA), a currently recognized risk marker for impaired graft survival. The aim of this study was to evaluate to what extent frequently used initial immunosuppressive therapies increase graft survival in immunological low-risk patients.

Methods
We performed an analysis on the PROCARE cohort, a Dutch multicentre study including all transplantations performed in the Netherlands between 1995 and 2005 with available pretransplant serum (n = 4724). All sera were assessed for the presence of DSA by a luminex single-antigen bead assay. Patients with a previous kidney transplantation, pretransplant DSA or receiving induction therapy were excluded from the analysis.

Results
Three regimes were used in over 200 patients: cyclosporine (CsA)/prednisolone (Pred) (n = 542), CsA/mycophenolate mofetil (MMF)/Pred (n = 857) and tacrolimus (TAC)/MMF/Pred (n = 811). Covariate-adjusted analysis revealed no significant differences in 10-year death-censored graft survival between patients on TAC/MMF/Pred therapy (79%) compared with patients on CsA/MMF/Pred (82%, P = 0.88) or CsA/Pred (79%, P = 0.21). However, 1-year rejection-free survival censored for death and failure unrelated to rejection was significantly higher for TAC/MMF/Pred (81%) when compared with CsA/MMF/Pred (67%, P < 0.0001) and CsA/Pred (64%, P < 0.0001).

Conclusion
These results suggest that in immunological low-risk patients excellent long-term kidney graft survival can be achieved irrespective of the type of initial immunosuppressive therapy (CsA or TAC; with or without MMF), despite differences in 1-year rejection-free survival.
Bronchiectasis and asthma: a dangerous liaison?
Authors: Crimi Claudia , Ferri Sebastian , Crimi Nunzio 
Published: December 2018

Purpose of review
To explore the latest insight of the literature on the asthma/bronchiectasis phenotype providing an updated overview about epidemiological, clinical and biological evidence linking these two conditions.

Recent findings
An increasing body of literature has shown that the association of asthma and bronchiectasis is a frequent phenomenon leading to a more severe disease with frequent exacerbations. The mechanisms by which the two diseases are linked are still not well established but they share several clinical and immunological features and many comorbidities.

Summary
The early identification of bronchiectasis through high-definition computer tomography in patients with severe asthma is crucial in order to provide an adequate treatment for both diseases and therefore to better control symptoms, exacerbations and infections.
Do Mindfulness and Self-Compassion Predict Burnout in Pediatric Residents?
Authors: Kemper Kathi J. , McClafferty Hilary , Wilson Paria M. , Serwint Janet R. , Batra Maneesh , Mahan John D. , Schubert Charles J. , Staples Betty B. , Schwartz Alan ,   on behalf of the Pediatric Resident Burnout-Resilience Study Consortium
Published: December 2018

Purpose
Burnout symptoms are common among health professionals. Gaps remain in understanding both the stability of burnout and compassion over time and relationships among burnout, self-compassion, stress, and mindfulness in pediatric residents.

Method
The authors conducted a prospective cohort study of residents at 31 U.S. residency programs affiliated with the Pediatric Resident Burnout–Resilience Study Consortium. Residents completed online cross-sectional surveys in spring 2016 and 2017. The authors assessed demographic characteristics and standardized measures of mindfulness, self-compassion, stress, burnout, and confidence in providing compassionate care.

Results
Of 1,108 eligible residents, 872 (79%) completed both surveys. Of these, 72% were women. The prevalence of burnout was 58% and the level of mindfulness was 2.8 in both years; levels of stress (16.4 and 16.2) and self-compassion (37.2 and 37.6) were also nearly identical in both years. After controlling for baseline burnout levels in linear mixed-model regression analyses, mindfulness in 2016 was protective for levels of stress and confidence in providing compassionate care in 2017. Self-compassion in 2016 was protective for burnout, stress, and confidence in providing compassionate care in 2017; a one-standard-deviation increase in self-compassion score was associated with a decrease in the probability of burnout from 58% to 48%.

Conclusions
Burnout and stress were prevalent and stable over at least 12 months among pediatric residents. Mindfulness and self-compassion were longitudinally associated with lower stress and greater confidence in providing compassionate care. Future studies are needed to evaluate the effectiveness of training that promotes mindfulness and self-compassion in pediatric residents.
Is the Association Between Pregnancy Weight Gain and Fetal Size Causal?
Authors: Hutcheon Jennifer A. , Stephansson Olof , Cnattingius Sven , Bodnar Lisa M. , Johansson Kari 
Published: December 2018

Background:
Observational cohort studies have consistently shown that maternal weight gain in pregnancy is positively associated with fetal size, but it is unknown whether the association is causal. This study investigated the effect of pregnancy weight gain on fetal growth using a sibling comparison design to control for unmeasured confounding by genetic and shared environmental factors.

Methods:
Our study population included 44,457 infants (21,680 women) with electronic medical records in the Stockholm–Gotland Obstetrical Database, 2008–2014. We standardized pregnancy weight gain into gestational age-specific z-scores. Fetal size was classified as birthweight (gram), and as small- and large-for-gestational-age birth (birthweight <10th or >90th percentiles, respectively). Our sibling comparison analyses used multivariable linear fixed effects models for birthweight and hybrid logistic fixed effects models for small- and large-for-gestational-age birth (SGA and LGA). We repeated analyses using conventional (unmatched) regression models.

Results:
Sibling comparison analyses showed a clinically meaningful association between weight gain and fetal size (e.g., adjusted difference of +89 g birthweight [95% CI = 82, 95 g]; adjusted risk ratios [aRR] for SGA of 0.80 [95% CI = 0.75, 0.86] per 1 z-score increase in weight gain for a woman of body mass index [BMI] = 25). These findings were consistent across the range of BMI. Estimates were only modestly attenuated compared with conventional approach (+97 g [95% CI = 92, 102 g], aRR for SGA of 0.70 [95% CI = 0.67, 0.73] per 1 z-score increase in weight gain).

Conclusion:
The positive association between pregnancy weight gain and fetal size we found using a sibling comparison design suggests that this relation has minimal confounding by familial factors that remain constant between pregnancies.
Upper Extremity Friction Burns in the Pediatric Patient: A 10-year Review
Authors: Marchalik Rachel , Rada Erin M. , Albino Frank P. , Sauerhammer Tina M. , Boyajian Michael J. , Rogers Gary F. , Oh Albert K. 
Published: December 2018

Background:
Upper extremity friction burn due to powered home equipment is a growing problem in the pediatric population. The purpose of this study was to review the etiology, presentation, characteristics, and treatment of this particular type of pediatric mechanism of injury.

Methods:
A retrospective chart review using International Classification of Diseases, version 9, codes for patients treated at a large tertiary care, free-standing children’s hospital was performed to identify all patients presenting with an upper extremity friction burn from 2003 to 2012.

Results:
Sixty-nine patients sustained upper extremity friction burns. The average age at the time of injury was 3.3 years (range, 0.7–10.6) with presentation to our center occurring 16.6 days (range, 0–365 days) following injury. Mean follow-up was 23.3 months (range, 2–104). Mechanism of injury included treadmills (n = 63) and vacuum cleaners (n = 6). Twenty-eight operations were performed on 21 patients (30%). All patients requiring a surgical intervention sustained injury via treadmill mechanism (P = 0.0001). Unlike treadmill burns, vacuum cleaner injuries affected the dorsal hand or a single digit (P = 0.00004). Scar hyperpigmentation was more prevalent in these patients compared with the treadmill group (P = 0.003). All vacuum-induced burn patients had full range of motion and function with conservative treatment alone, whereas only 55.6% of treadmill burn patients had full recovery of range of motion and 50.8% recovery of full hand function.

Conclusions:
Friction burns from vacuum cleaners are less prevalent, have different injury patterns, and can be treated conservatively with excellent functional outcomes. Treadmill friction burns result in more significant injury and risk for dysfunction, requiring surgical intervention.