bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of vitamin D supplementation on cardiovascular disease risk factors and exercise performance in healthy participants: a randomized placebo-controlled preliminary study
Authors: Al-Dujaili Emad A. S. , Munir Nimrah , Iniesta Raquel Revuelta 
Published: June 2016

Background and objectives: Evidence suggests associations between vitamin D deficiency and cardiovascular disease (CVD) risk factors, including hypertension and excessive cortisol levels. Also, vitamin D levels may impact exercise performance. Thus, we aimed to investigate the effects of vitamin D intake on cardiovascular risk factors, free urinary cortisol and exercise performance. Methods: A randomized placebo-controlled single-blinded parallel trial was conducted in healthy participants ( n = 15). They received 2000 IU (50 µg) vitamin D3 per day ( n = 9) or placebo (lactose) ( n = 6) for 14 days. Body composition, systolic blood pressure (SBP), diastolic blood pressure (DBP) and arterial elasticity (as measured by pulse wave velocity, PWV) were recorded at baseline, day 7 and day 14 of intervention. A total of two 24-hour urine samples were collected to estimate free cortisol and cortisone levels. Exercise performance was assessed at the baseline and day 14 of the intervention using a bike ergometer in which BP and PWV were measured before and after exercise. The distance cycled in 20 minutes and the Borg Scale rate of perceived exertion (RPE) were recorded. Results: In the intervention arm, at day 14, vitamin D supplementation significantly reduced SBP and DBP from 115.8 ± 17.1 and 75.4 ± 10.3 at baseline to 106.3 ± 10.9 ( p = 0.022) and 68.5 ± 10.1 mmHg ( p = 0.012) respectively. Also arterial stiffness was markedly reduced in the vitamin D group (from 7.45 ± 1.55 to 6.11 ± 1.89, p = 0.049). Urinary free cortisol levels and cortisol/cortisone ratio were significantly reduced from 162.65 ± 58.9 nmol/day and 2.22 ± 0.7 to 96.4 ± 37.2 ( p = 0.029) and 1.04 ± 0.4 ( p = 0.017) respectively. Exercise-induced SBP and DBP were significantly reduced post vitamin D intake from 130.7 ± 12.2 to 116.1 ± 8.1 ( p = 0.012) and from 76.2 ± 8.4 to 70.5 ± 7.7 mmHg ( p = 0.042) respectively. The distance cycled in 20 minutes significantly increased from 4.98 ± 2.65 to 6.51 ± 2.28km ( p = 0.020), while the Borg Scale RPE reduced from 5.13 ± 1.36 to 4.25 ± 0.71 RPE ( p = 0.021). In the placebo arm, no significant effects on CVD risk factors and exercise performance were observed. Conclusion: These results suggest that daily vitamin D supplementation may ameliorate CVD risk factors including a decrease in 11β-HSD1 activity, as evidenced by the decrease in the cortisol/cortisone ratio, and improve exercise performance in healthy individuals. However, large scale studies are required to verify our findings.
Feasibility and acceptability of Facebook for health promotion among people with serious mental illness
Authors: Naslund John A , Aschbrenner Kelly A , Marsch Lisa A , Bartels Stephen J 
Published: June 2016

Objective Elevated obesity rates are a major contributor to the significantly reduced life expectancy impacting people with serious mental illness. With over 1.5 billion Facebook users worldwide, this platform may afford opportunities for reaching individuals with serious mental illness outside professional settings and fostering social support for adopting healthier behaviors. In this mixed methods pilot study, we explored the feasibility and acceptability of using Facebook to support a group lifestyle intervention for weight loss among obese adults with serious mental illness. Methods Nine of eleven participants enrolled in a six-month lifestyle intervention delivered through a community mental health center agreed to join a private Facebook group to support their healthy eating and exercise goals. We measured participants’ use of the Facebook group and collected post-intervention feasibility and acceptability questionnaires followed by in-depth qualitative interviews to elicit participants’ perspectives and recommendations for improving the use of Facebook. Results Of 188 posts to the Facebook group, the majority (79%) were from participants compared to study staff (21%). Participants also posted 186 comments, 299 likes, and recorded 1316 page views. Participants were positive about opportunities to interact and support each other outside group sessions, found content posted by other participants to be helpful, and indicated that the Facebook group was safe to use. Participants provided constructive feedback, including recommendations for more detailed instructions for accessing the group and posting content, finding ways to encourage more interaction within the group, and tips for responding to notifications or alerts directly from the Facebook website. Conclusions These findings suggest that Facebook may be feasible for supporting health promotion efforts targeting people with serious mental illness. Participants provided valuable feedback that can inform the use of Facebook for future health promotion efforts targeting this high-risk group.
Inertial and frictional influences of instrumented wheelchair wheels
Authors: Sprigle Stephen , Huang Morris , Lin Jui-Te 
Published: June 2016

Background Instrumented wheelchair wheels can be used to study the kinematics and kinetics of manual wheelchair propulsion. The objective of this study was to evaluate the impact of instrumented wheels on the inertial and frictional parameters of a wheelchair system. Methods This study compared mechanical parameters of an ultralightweight rigid frame wheelchair configured with pairs of SMARTwheels and spoke pneumatic wheels and loaded with an ISO 75 kg wheelchair dummy. Rectilinear and turning inertia of the occupied wheelchair and the rotational inertia of drive wheels were measured. A coast-down test measured frictional energy loss during straight and turning trajectories. Findings The addition of instrumented wheels increased occupied system mass by about 6% and turning inertia by about 16%. Frictional energy loss increased by over 40% in a straight trajectory and over 30% during turning. Interpretation Addition of instrumented increased the inertia and frictional energy loss of the wheelchair system. These relative effects will impact the wheelchair operator and increase the instantaneous propulsion torque during wheelchair maneuvers. The impacts will be less under conditions involving little or no change in velocity. Researchers should be encouraged to report changes in mass and weight distribution induced by addition of instrumented wheelchair wheels.
EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics
Authors: Andersen John J. , Nelson Bradley J. , Brown Jeremy M. 
Published: June 2016

Abstract
Background
Branch-length parameters are a central component of phylogenetic models and of intrinsic biological interest. Default branch-length priors in some Bayesian phylogenetic software can be unintentionally informative and lead to branch- and tree-length estimates that are unreasonable. Alternatively, priors may be uninformative, but lead to diffuse posterior estimates. Despite the widespread availability of relevant datasets from other groups, biologists rarely leverage outside information to specify branch-length priors that are specific to the analysis they are conducting.

Results
We developed the software package EmpPrior to facilitate the collection and incorporation of relevant, outside information when setting branch-length priors for phylogenetics. EmpPrior efficiently queries TreeBASE to find data that are similar to focal data, in terms of taxonomic and genetic sampling, and uses them to inform branch-length priors for the focal analysis. EmpPrior consists of two components: EmpPrior-search, written in Java to query TreeBASE, and EmpPrior-fit, written in R to parameterize branch-length distributions. In an example analysis, we show how the use of relevant, outside data is made possible by EmpPrior and improves tree-length estimates from a focal dataset.

Conclusion
EmpPrior is easy to use, fast, and improves both the accuracy and precision of branch-length estimates in many circumstances. While EmpPrior’s focus is on branch lengths, the strategy it employs could easily be extended to address other prior parameterization problems in phylogenetics.
Non-Markovian effects on protein sequence evolution due to site dependent substitution rates
Authors: Rizzato Francesca , Rodriguez Alex , Laio Alessandro 
Published: June 2016

Abstract
Background
Many models of protein sequence evolution, in particular those based on Point Accepted Mutation (PAM) matrices, assume that its dynamics is Markovian. Nevertheless, it has been observed that evolution seems to proceed differently at different time scales, questioning this assumption. In 2011 Kosiol and Goldman proved that, if evolution is Markovian at the codon level, it can not be Markovian at the amino acid level. However, it remains unclear up to which point the Markov assumption is verified at the codon level.

Results
Here we show how also the among-site variability of substitution rates makes the process of full protein sequence evolution effectively not Markovian even at the codon level. This may be the theoretical explanation behind the well known systematic underestimation of evolutionary distances observed when omitting rate variability. If the substitution rate variability is neglected the average amino acid and codon replacement probabilities are affected by systematic errors and those with the largest mismatches are the substitutions involving more than one nucleotide at a time. On the other hand, the instantaneous substitution matrices estimated from alignments with the Markov assumption tend to overestimate double and triple substitutions, even when learned from alignments at high sequence identity.

Conclusions
These results discourage the use of simple Markov models to describe full protein sequence evolution and encourage to employ, whenever possible, models that account for rate variability by construction (such as hidden Markov models or mixture models) or substitution models of the type of Le and Gascuel (2008) that account for it explicitly.
Local injection of bone marrow progenitor cells for the treatment of anal sphincter injury: in-vitro expanded versus minimally-manipulated cells
Authors: Mazzanti Benedetta , Lorenzi Bruno , Borghini Annalisa , Boieri Margherita , Ballerini Lara , Saccardi Riccardo , Weber Elisabetta , Pessina Federica 
Published: June 2016

Abstract
Background
Anal incontinence is a disabling condition that adversely affects the quality of life of a large number of patients, mainly with anal sphincter lesions. In a previous experimental work, in-vitro expanded bone marrow (BM)-derived mesenchymal stem cells (MSC) were demonstrated to enhance sphincter healing after injury and primary repair in a rat preclinical model. In the present article we investigated whether unexpanded BM mononuclear cells (MNC) may also be effective.

Methods
Thirty-two rats, divided into groups, underwent sphincterotomy and repair (SR) with primary suture of anal sphincters plus intrasphincteric injection of saline (CTR), or of in-vitro expanded MSC, or of minimally manipulated MNC; moreover, the fourth group underwent sham operation. At day 30, histologic, morphometric, in-vitro contractility, and functional analysis were performed.

Results
Treatment with both MSC and MNC improved muscle regeneration and increased contractile function of anal sphincters after SR compared with CTR (p < 0.05). No significant difference was observed between the two BM stem cell types used. GFP-positive cells (MSC and MNC) remained in the proximity of the lesion site up to 30 days post injection.

Conclusions
In the present study we demonstrated in a preclinical model that minimally manipulated BM-MNC were as effective as in-vitro expanded MSC for the recovery of anal sphincter injury followed by primary sphincter repair. These results may serve as a basis for improving clinical applications of stem cell therapy in human anal incontinence treatment.
Updated Outcomes and Impact of Age With Lenalidomide and Low-Dose Dexamethasone or Melphalan, Prednisone, and Thalidomide in the Randomized, Phase III FIRST Trial
Authors: Hulin Cyrille , Belch Andrew , Shustik Chaim , Petrucci Maria Teresa , Dührsen Ulrich , Lu Jin , Song Kevin , Rodon Philippe , Pégourié Brigitte , Garderet Laurent , Hunter Hannah , Azais Isabelle , Eek Richard , Gisslinger Heinz , Macro Margaret , Dakhil Shaker , Goncalves Cristina , LeBlanc Richard , Romeril Ken , Royer Bruno , Doyen Chantal , Leleu Xavier , Offner Fritz , Leupin Nicolas , Houck Vanessa , Chen Guang , Ervin-Haynes Annette , Dimopoulos Meletios A. , Facon Thierry 
Published: June 2016

Purpose This analysis of the FIRST trial in patients with newly diagnosed multiple myeloma (MM) ineligible for stem-cell transplantation examined updated outcomes and impact of patient age. Patients and Methods Patients with untreated symptomatic MM were randomly assigned at a one-to-one-to-one ratio to lenalidomide plus low-dose dexamethasone until disease progression (Rd continuous), Rd for 72 weeks (18 cycles; Rd18), or melphalan, prednisone, and thalidomide (MPT; 72 weeks), stratified by age (≤ 75 v > 75 years), disease stage (International Staging System stage I/II v III), and country. The primary end point was progression-free survival. Rd continuous and MPT were primary comparators. Results Between August 21, 2008, and March 7, 2011, 1,623 patients were enrolled (Rd continuous, n = 535; Rd18, n = 541; MPT, n = 547), including 567 (35%) age older than 75 years. Higher rates of advanced-stage disease and renal impairment were observed in patients older than 75 versus 75 years of age or younger. Rd continuous reduced the risk of progression or death compared with MPT by 31% (hazard ratio [HR], 0.69; 95% CI, 0.59 to 0.80; P < .001) overall, 36% (HR, 0.64; 95% CI, 0.53 to 0.77; P < .001) in patients age 75 years or younger, and 20% (HR, 0.80; 95% CI, 0.62 to 1.03; P = .084) in those age older than 75 years. Median overall survival was longer with Rd continuous than with MPT, including a 14-month difference in patients age older than 75 years. Progression-free survival with Rd18 was similar to that with MPT, and overall survival with Rd18 was marginally inferior to that with Rd continuous. Rates of grade 3 to 4 treatment-emergent adverse events were similar for Rd continuous–treated patients age 75 years or older and those age older than 75 years; however, older patients had more frequent lenalidomide dose reductions. Conclusion Results support Rd continuous treatment as a new standard of care for stem-cell transplantation–ineligible patients with newly diagnosed MM of all ages.
Ανισότητες του κεϕαλαίου. Επίκαιρες θεωρήσεις της δυναμικής των ανισοτήτων στην πολιτική οικονομία του σύγχρονου καπιταλισμού
Authors: Σκομβούλης Μιχάλης 
Published: June 2016

<p class="p1"><span class="s1">Σ</span>κοπός του άρθρου είναι να καταδείξει τη σημασία και τα όρια των πρόσϕατων θεματοποιήσεων της σύνδεσης των ανισοτήτων με τη δυναμική του κεϕαλαίου εντός της συγκυρίας της τρέχουσας οικονομικής κρίσης των αναπτυγμένων καπιταλιστικών οικονομιών. Το κείμενο λαμβάνει επομένως ως βάση του τη διάσπαρτη στη σύγχρονη βιβλιογραϕία των κοινωνικών επιστημών διαπίστωση ότι η επίταση των κοινωνικών ανισοτήτων συμβαδίζει και τροϕοδοτείται από τους πρόσϕατους ασθενείς ρυθμούς μεγέθυνσης του προϊόντος. Εντός αυτού του πλαισίου θα αναϕερθούμε και θα αναλύσουμε την επιχειρηματολογία τριών πρόσϕατων σημαντικών προσπαθειών στις κοινωνικές επιστήμες για τη θεματοποίηση του ρόλου των ανισοτήτων στον σύγχρονο καπιταλισμό. πρόκειται για τα <span class="s2">βιβλία των </span>J. Stiglitz<span class="s2">, </span>The Price of Inequality <span class="s2">(</span><span class="s3">2012</span><span class="s2">), </span>W. Streeck<span class="s2">, </span>Gekaufte Zeit: Die Vertage Krise des demokratischen Kapitalismus <span class="s2">(</span><span class="s3">2013</span><span class="s2">) και </span>T. Piketty<span class="s2">, </span>Le Capital au <span class="s4">xxI</span><span class="s5">e </span>Siècle <span class="s2">(</span><span class="s3">2013</span><span class="s2">). Σκοπός </span>μας όμως δεν είναι απλώς να υιοθετήσουμε την ισχυρή κριτική που τα παραπάνω επιχειρήματα προβάλλουν ενάντια στην επίταση των κοινωνικών ανισοτήτων, αλλά να καταδείξουμε τα βασικά θεωρητικά τους όρια ως προς την αντίληψή τους για την έννοια του κεϕαλαίου.</p>
Bioconductor workflow for microbiome data analysis: from raw reads to community analyses
Authors: Callahan Ben J. , Sankaran Kris , Fukuyama Julia A. , McMurdie Paul J. , Holmes Susan P. 
Published: June 2016

High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using theR packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package.
Evaluation of a paramedic student patient hand-off curriculum using simulation
Authors: Stevens Andrew , Turner Joseph S. , Meyer Colin A. , Soultz Megan D. , Bell Leon H. , Cooper Dylan D. 
Published: June 2016

Introduction: Even though patient handoffs are at high risk for errors and adverse events, there is not a standardised approach to how these should be taught to paramedic students. The goal of this study was to evaluate the feasibility and effectiveness of implementing a lecture-based training involving the IMIST-AMBO mnemonic in paramedic education. Methods: Paramedic students were randomised into a control group of standard national paramedicine curriculum and an intervention group who received an additional EMS patient handover lecture including IMIST-AMBO protocol. Outcomes were measured through simulation exercises, with learners randomised to either a low-fidelity tabletop or high-fidelity mannequin-based session. Results: There were three paramedic student teams in each arm of the study. There were no statistical differences in the reporting of any of the IMIST-AMBO components or the total number reported between the control and the intervention group. The intervention group took significantly longer to give their patient handoff: 78.2 s versus 49.2 s. Discussions: The formal education on patient handoffs was successfully implemented. There was a trend toward more data being reported in the intervention group but this came at the cost of a significantly longer report. Conclusions: We were able to successfully implement formal education on patient handoffs but the small size of the study limited the ability to evaluate its effectiveness. Patient handoffs are a high-risk area in medicine and more studies are needed to determine the most effective way to teach this to paramedic students.
Impact of pedicle-lengthening osteotomy on spinal canal volume and neural foramen size in three types of lumbar spinal stenosis
Authors: Li P. , Qian L. , Wu W. D. , Wu C. F. , Ouyang J. 
Published: June 2016

Objectives Pedicle-lengthening osteotomy is a novel surgery for lumbar spinal stenosis (LSS), which achieves substantial enlargement of the spinal canal by expansion of the bilateral pedicle osteotomy sites. Few studies have evaluated the impact of this new surgery on spinal canal volume (SCV) and neural foramen dimension (NFD) in three different types of LSS patients. Methods CT scans were performed on 36 LSS patients (12 central canal stenosis (CCS), 12 lateral recess stenosis (LRS), and 12 foraminal stenosis (FS)) at L4-L5, and on 12 normal (control) subjects. Mimics 14.01 workstation was used to reconstruct 3D models of the L4-L5 vertebrae and discs. SCV and NFD were measured after 1 mm, 2 mm, 3 mm, 4 mm, or 5 mm pedicle-lengthening osteotomies at L4 and/or L5. One-way analysis of variance was used to examine between-group differences. Results In the intact state, SVC and NFD were significantly larger in the control group compared with the LSS groups (P<0.05). After lengthening at L4, the percentage increase in SCV (per millimetre) was LRS>CCS>FS>Control. After lengthening at L5 and L4-L5, the percentage increase in SCV (per millimetre) was LRS>FS>CCS>Control. After lengthening at L4 and L4-L5, the percentage increase in NFD (per millimetre) was FS>CCS>LRS>Control. After lengthening at L5, the percentage increase in NFD (per millimetre) was CCS>LRS>control>FS. Conclusions LRS patients are the most suitable candidates for treatment with pedicle-lengthening osteotomy. Lengthening L4 pedicles produced larger percentage increases in NFD than lengthening L5 pedicles (p < 0.05). Lengthening L4 pedicles may be the most effective option for relieving foraminal compression in LSS patients. Cite this article: P. Li, L. Qian, W. D. Wu, C. F. Wu, J. Ouyang. Impact of pedicle-lengthening osteotomy on spinal canal volume and neural foramen size in three types of lumbar spinal stenosis. Bone Joint Res 2016;5:239–246. DOI: 10.1302/2046-3758.56.2000469.
Thirteen Years of an International External Quality Assessment Scheme for Genotyping: Results and Recommendations
Authors: Haselmann Verena , Geilenkeuser Wolf J , Helfert Simona , Eichner Romy , Hetjens Svetlana , Neumaier Michael , Ahmad-Nejad Parviz 
Published: June 2016

Abstract

BACKGROUND
Suboptimal laboratory procedures resulting in genotyping errors, misdiagnosis, or incorrect reporting bear greatly on a patient's health management, therapeutic decisions made on their behalf, and ultimate outcome. Participation in external quality assessment (EQA) is a key element of quality assurance in molecular genetic diagnostics. Therefore, the Reference Institute for Bioanalytics has tried for 13 years to improve the quality of genetic testing by offering an EQA for different clinically relevant sequence variations.

METHODS
Within each of the biannual EQA schemes offered, up to 18 samples of lyophilized human genomic DNA were provided for up to 50 different molecular genetic tests. Laboratories were asked to use their routine procedures for genotyping. At least 2 expert peer assessors reviewed the final returns. Data from 2002 to 2014 were evaluated.

RESULTS
In total, 82 462 reported results from 812 characterized samples were evaluated. Globally, the number of participants increased each year along with the number of sequence variations offered. The error rate decreased significantly over the years with an overall error rate of 1.44%. Additionally, a decreased error rate for samples repeated over time was noted. Interestingly, the error rate showed a high difference depending on the locus analyzed and the method used.

CONCLUSIONS
Based on the evaluation of this long-term EQA scheme, various recommendations can be given to improve the quality of molecular genetic testing, such as the use of 2 different methods for genotyping. Furthermore, some methods are inappropriate for analysis of certain sequence variations.