bluuebunny/crossref_metadata_2025_split huggingface dataset:
How Predictable Are the Arctic and North Atlantic Oscillations? Exploring the Variability and Predictability of the Northern Hemisphere
Authors: Domeisen Daniela I. V. , Badin Gualtiero , Koszalka Inga M. 
Published: November 2017

ABSTRACT
The North Atlantic Oscillation (NAO) and the Arctic Oscillation (AO) describe the dominant part of the variability in the Northern Hemisphere extratropical troposphere. Because of the strong connection of these patterns with surface climate, recent years have shown an increased interest and an increasing skill in forecasting them. However, it is unclear what the intrinsic limits of short-term predictability for the NAO and AO patterns are. This study compares the variability and predictability of both patterns, using a range of data and index computation methods for the daily NAO and AO indices. Small deviations from Gaussianity are found along with characteristic decorrelation time scales of around one week. In the analysis of the Lyapunov spectrum it is found that predictability is not significantly different between the AO and NAO or between reanalysis products. Differences exist, however, between the indices based on EOF analysis, which exhibit predictability time scales around 12–16 days, and the station-based indices, exhibiting a longer predictability of 18–20 days. Both of these time scales indicate predictability beyond that currently obtained in ensemble prediction models for short-term predictability. Additional longer-term predictability for these patterns may be gained through local feedbacks and remote forcing mechanisms for particular atmospheric conditions.
Daily to Decadal Modulation of Jet Variability
Authors: Woollings Tim , Barnes Elizabeth , Hoskins Brian , Kwon Young-Oh , Lee Robert W. , Li Camille , Madonna Erica , McGraw Marie , Parker Tess , Rodrigues Regina , Spensberger Clemens , Williams Keith 
Published: November 2017

AbstractThe variance of a jet’s position in latitude is found to be related to its average speed: when a jet becomes stronger, its variability in latitude decreases. This relationship is shown to hold for observed midlatitude jets around the world and also across a hierarchy of numerical models. North Atlantic jet variability is shown to be modulated on decadal time scales, with decades of a strong, steady jet being interspersed with decades of a weak, variable jet. These modulations are also related to variations in the basinwide occurrence of high-impact blocking events. A picture emerges of complex multidecadal jet variability in which recent decades do not appear unusual. An underlying barotropic mechanism is proposed to explain this behavior, related to the change in refractive properties of a jet as it strengthens, and the subsequent effect on the distribution of Rossby wave breaking.
‘Knowledge’ in English primary schools’ decision-making about sex and relationships education
Authors: Wilder Rachel 
Published: November 2017

Objective: To assess what kinds of knowledge policymakers in a sample of English primary schools utilised to make decisions about their school’s sex and relationships education policy. Method: Semi-structured interviews were conducted with policymakers at three primary schools in the southwest of England, and documentary analysis of the schools’ sex and relationships education policies was done. Policymakers included head teachers, subject leads and other teachers. A social constructivist approach informed the research design and data analysis. Results: In all three schools, the principal sources of knowledge in the policy-making processes for sex and relationships education were a commercially available curriculum package and staff knowledge (including staff opinions). All three schools drew on policies from other schools, but at times this process appeared procedural rather than critical. Local authority expertise was a source of knowledge for two schools. Conclusion: Findings emphasise the importance of having trained and experienced educators for sex and relationships education in schools and the need for schools to have ongoing support to share learning and identify new knowledge on the topic.
Effects of positive end-expiratory pressure on intraoperative core temperature in patients undergoing posterior spine surgery: prospective randomised trial
Authors: Seo Hyungseok , Do Son Je , Lee Hyung-Chul , Oh Hyung-Min , Jung Chul-Woo , Park Hee-Pyoung 
Published: November 2017

Objective Positive end-expiratory pressure (PEEP) causes carotid baroreceptor unloading, which leads to thermoregulatory peripheral vasoconstriction. However, the effects of PEEP on intraoperative thermoregulation in the prone position remain unknown. Methods Thirty-seven patients undergoing spine surgery in the prone position were assigned at random to receive either 10 cmH2O PEEP (Group P) or no PEEP (Group Z). The primary endpoint was core temperature 180 minutes after intubation. Secondary endpoints were delta core temperature (difference in core temperature between 180 minutes and immediately after tracheal intubation), incidence of intraoperative hypothermia (core temperature of <36°C), and peripheral vasoconstriction-related data. Results The median [interquartile range] core temperature 180 minutes after intubation was 36.1°C [35.9°C–36.2°C] and 36.0°C [35.9°C–36.4°C] in Groups Z and P, respectively. The delta core temperature and incidences of intraoperative hypothermia and peripheral vasoconstriction were not significantly different between the two groups. The peripheral vasoconstriction threshold (36.2°C±0.5°C vs. 36.7°C±0.6°C) was lower and the onset of peripheral vasoconstriction (66 [60–129] vs. 38 [28–70] minutes) was slower in Group Z than in Group P. Conclusions Intraoperative PEEP did not reduce the core temperature decrease in the prone position, although it resulted in an earlier onset and higher threshold of peripheral vasoconstriction.
Understanding Parkinson’s through visual narratives: “I’m not Mrs. Parkinson’s”
Authors: Lutz Sara G , Holmes Jeffrey D , Rudman Debbie Laliberte , Johnson Andrew M , LaDonna Kori A , Jenkins Mary E 
Published: November 2017

Introduction Although it is accepted that individuals with Parkinson’s disease must navigate challenges such as receiving their diagnosis and changing daily occupations, little is known about how they navigate. The purpose of this study is to deepen the current understanding of the experience of living with Parkinson’s disease and its implications for occupation through a narrative visual methodology (photo-elicitation). Method Six individuals with Parkinson’s disease were asked to take photographs and share verbal narrative accounts to illustrate their experience of living with Parkinson’s disease. Findings Results highlight the interrelationship between occupation and identity, as many of the participants’ stories were interpreted as foregrounding the negotiation of occupation, and how such negotiation shaped their sense of identity. Overall, three major themes were identified: (1) Framing the meaning of Parkinson’s disease (accepting the disease as part of who they were); (2) Negotiating engagement in occupation (ongoing deliberation over whether to continue engaging in certain aspects of life as Parkinson’s disease progressed); and (3) Being ready to accept changes that impact personal or social identity (readiness to accept help and to identify as someone with Parkinson’s disease). Conclusion Attending to insights regarding the lived experience of Parkinson’s disease will enhance quality of care through informing an enriched client-centered, occupation-based approach.
The effect of nurses’ ethical leadership and ethical climate perceptions on job satisfaction
Authors: Özden Dilek , Arslan Gülşah Gürol , Ertuğrul Büşra , Karakaya Salih 
Published: November 2017

Background: The development of ethical leadership approaches plays an important role in achieving better patient care. Although studies that analyze the impact of ethical leadership on ethical climate and job satisfaction have gained importance in recent years, there is no study on ethical leadership and its relation to ethical climate and job satisfaction in our country. Objectives: This descriptive and cross-sectional study aimed to determine the effect of nurses’ ethical leadership and ethical climate perceptions on their job satisfaction. Methods: The study sample is composed of 285 nurses who agreed to participate in this research and who work at the internal, surgical, and intensive care units of a university hospital and a training and research hospital in İzmir, Turkey. Data were collected using Ethical Leadership Scale, Hospital Ethical Climate Scale, and Minnesota Satisfaction Scale. While the independent sample t-test, analysis of variance, Mann–Whitney U test, and Kruskal–Wallis test were used to analyze the data, the correlation analysis was used to determine the relationship between the scales. Ethical considerations: The study proposal was approved by the ethics committee of the Faculty of Medicine, Dokuz Eylül University. Findings: The nurses’ mean scores were 59.05 ± 14.78 for the ethical leadership, 92.62 ± 17 for the ethical climate, and 62.15 ± 13.46 for the job satisfaction. The correlation between the nurses’ ethical leadership and ethical climate mean scores was moderately positive and statistically significant (r = +0.625, p = 0.000), was weak but statistically significant between their ethical leadership and job satisfaction mean scores (r = +0.461, p = 0.000), and was moderately positive and statistically significant between their ethical climate and job satisfaction mean scores (r = +0.603, p = 0.000). Conclusion: The nurses’ ethical leadership, ethical climate, and job satisfaction levels are moderate, and there is a positive relationship between them. The nurses’ perceptions of ethical leadership are influenced by their educational status, workplace, and length of service.
Gaussian Quadrature Formulae for Arbitrary Positive Measures
Authors: Fernandes Andrew D. , Atchley William R. 
Published: November 2017

We present computational methods and subroutines to compute Gaussian quadrature integration formulas for arbitrary positive measures. For expensive integrands that can be factored into well-known forms, Gaussian quadrature schemes allow for efficient evaluation of high-accuracy and -precision numerical integrals, especially compared to general ad hoc schemes. In addition, for certain well-known density measures (the normal, gamma, log-normal, Student's t, inverse-gamma, beta, and Fisher's F) we present exact formulae for computing the respective quadrature scheme. Availability: Source code is freely available online as a C-linkable ISO C++ library under a BSD-style license from http://www.fernandes.org/gaussqr . The library may be built using single, double, or extended precision arithmetic.
Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction
Authors: Höhl Michael , Rigoutsos Isidore , Ragan Mark A. 
Published: November 2017

We have developed an alignment-free method that calculates phylogenetic distances using a maximum-likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic accuracy of our method, and to conduct a comprehensive comparison of existing alignment-free methods (freely available as Python package decaf+py at http://www.bioinformatics.org.au ), we have created a data set of reference trees covering a wide range of phylogenetic distances. Amino acid sequences were evolved along the trees and input to the tested methods; from their calculated distances we infered trees whose topologies we compared to the reference trees. We find our pattern-based method statistically superior to all other tested alignment-free methods. We also demonstrate the general advantage of alignment-free methods over an approach based on automated alignments when sequences violate the assumption of collinearity. Similarly, we compare methods on empirical data from an existing alignment benchmark set that we used to derive reference distances and trees. Our pattern-based approach yields distances that show a linear relationship to reference distances over a substantially longer range than other alignment-free methods. The pattern-based approach outperforms alignment-free methods and its phylogenetic accuracy is statistically indistinguishable from alignment-based distances.
Assessing the Applicability of the GTR Nucleotide Substitution Model through Simulations
Authors: Gatto Laurent , Catanzaro Daniele , Milinkovitch Michel C. 
Published: November 2017

The General Time Reversible (GTR) model of nucleotide substitution is at the core of many distance-based and character-based phylogeny inference methods. The procedure described by Waddell and Steel (1997), for estimating distances and instantaneous substitution rate matrices, R, under the GTR model, is known to be inapplicable under some conditions, ie, it leads to the inapplicability of the GTR model. Here, we simulate the evolution of DNA sequences along 12 trees characterized by different combinations of tree length, (non-)homogeneity of the substitution rate matrix R, and sequence length. We then evaluate both the frequency of the GTR model inapplicability for estimating distances and the accuracy of inferred alignments. Our results indicate that, inapplicability of the Waddel and Steel's procedure can be considered a real practical issue, and illustrate that the probability of this inapplicability is a function of substitution rates and sequence length. We also discuss the implications of our results on the current implementations of maximum likelihood and Bayesian methods.
A Fast and Specific Alignment Method for Minisatellite Maps
Authors: Bérard Sèverine , Nicolas François , Buard Jérôme , Gascuel Olivier , Rivals Eric 
Published: November 2017

Background Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or gene regulation regions, like for the cystatin B gene, and be associated or implicated in diseases: the Creutzfeld-Jakob disease and the myoclonus epilepsy type 1, for our examples. When it affects neutrally evolving regions, the polymorphism in length ( i.e., in number of copies) of minisatellites proved useful in population genetics. Motivation In these tandem repeat sequences, different mutational mechanisms let the number of copies, as well as the copies themselves, vary. Especially, the interspersion of events of tandem duplication/contraction and of punctual mutation makes the succession of variant repeats much more informative than the sole allele length. To exploit this information requires the ability to align minisatellite alleles by accounting for both punctual mutations and tandem duplications. Results We propose a minisatellite maps alignment program that improves on previous solutions. Our new program is faster, simpler, considers an extended evolutionary model, and is available to the community. We test it on the data set of 609 alleles of the MSY1 (DYF155S1) human minisatellite and confirm its ability to recover known evolutionary signals. Our experiments highlight that the informativeness of minisatellites resides in their length and composition polymorphisms. Exploiting both simultaneously is critical to unravel the implications of variable minisatellites in the control of gene expression and diseases. Availability Software is available at http://atgc.lirmm.fr/ms_align/
A Simple Derivation of the Distribution of Pairwise Local Protein Sequence Alignment Scores
Authors: Bastien Olivier 
Published: November 2017

Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. In the asymptotic limit of long sequences, the Karlin-Altschul model computes a P-value assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Using a simple approach combined with recent results in reliability theory, we demonstrate here that the Karlin-Altshul model can be derived with no reference to the extreme events theory. Sequences were considered as systems in which components are amino acids and having a high redundancy of Information reflected by their alignment scores. Evolution of the information shared between aligned components determined the Shared Amount of Information (SA.I.) between sequences, i.e. the score. The Gumbel distribution parameters of aligned sequences scores find here some theoretical rationale. The first is the Hazard Rate of the distribution of scores between residues and the second is the probability that two aligned residues do not lose bits of information (i.e. conserve an initial pairing score) when a mutation occurs.
Association of Vascular Endothelial Growth Factor Polymorphisms with Asthma in Tunisian Children
Authors: Lachheb Jihene , Chelbi Hanene , Dhifallah Imen Ben , Ammar Jamel , Hamzaoui Kamel , Hamzaoui Agnès 
Published: November 2017

Background Previous studies demonstrated that the vascular endothelial growth factor (VEGF) was being implicated in the airways inflammation and remodeling process in patients with asthma. Aims We explored the relationship of three polymorphisms in the VEGF gene with asthma in both case control and family studies. Methods We Genotyped a total of 210 children with asthma, 224 unrelated controls and 160 parents for the +936 C > T (rs3025039), –634 G > C (rs2010963) and –2549 –2567 del 18 of the VEGF promoter region. The Mutations were identified with polymerase chain reaction followed by restriction fragment length polymorphism (RFLP) analysis for the +936 C > T, and –634 G > C polymorphisms. Results Of the three polymorphisms studied, a borderline association with asthma was found for the G allele in the –634 G > C polymorphism (p = 0.059). No Statistically significant differences were observed for both +936 C > T, and –2549 –2567 del 18 polymorphisms between asthmatic patients and controls, considering either allelic or genotypic frequencies. The distribution of genotypes according to the severity status revealed a significant differences for the +936 C > T, and –2549 –2567 del 18 polymorphisms. In addition, association was found with the haplotypes inferred by the three polymorphisms and asthma susceptibility. Conclusion We suggest that VEGF Gene polymorphisms can be implicated in asthma.
Mechanical diagnosis and therapy enhances attitude toward self-management in people with musculoskeletal disorders: A preliminary evidence with a before–after design
Authors: Takasaki Hiroshi 
Published: November 2017

Objectives: Mechanical diagnosis and therapy is one of the most common approaches for the management of low back pain. In mechanical diagnosis and therapy, a great emphasis is placed on patient education so that patients can manage their problems by themselves. However, there has been no evidence that mechanical diagnosis and therapy actually enhances patient’s self-management skills. This study aimed to preliminarily investigate whether self-reported skills of self-management for musculoskeletal problems are enhanced through the course of mechanical diagnosis and therapy. Method: Outpatients with musculoskeletal disorders in a local orthopedic clinic were included. The primary outcome measures were the “Self-monitoring and Insight” and “Skill and Technique Acquisition” scores of the Health Education Impact Questionnaire, where higher scores indicate greater self-management skills. Mechanical diagnosis and therapy was undertaken up to a maximum of twice per week for 1 month. The Self-monitoring and Insight and Skill and Technique Acquisition scores before and 1 month after the mechanical diagnosis and therapy interventions were compared. Proportions of patients who exceed the threshold for “reliable change” in the Health Education Impact Questionnaire scores (% >positive “reliable change”) and proportions of patients with the net positive “reliable change” (% net positive “reliable change”) were investigated. Results: Forty-five patients participated and 97.8% completed the 1-month follow-up. The Self-monitoring and Insight and Skill and Technique Acquisition scores significantly increased at the follow-up (Self-monitoring and Insight, p = 0.002; Skill and Technique Acquisition, p < 0.001. The % >positive “reliable change” (Self-monitoring and Insight = 22.2%, Skill and Technique Acquisition = 48.9%) and % net positive “reliable change” (Self-monitoring and Insight = 13.3%, Skill and Technique Acquisition = 46.7%) in this study were comparative to or greater than self-management programs in previous studies (%> positive “reliable change’: Self-monitoring and Insight = 20.5%, Skill and Technique Acquisition = 30.7%; % net positive “reliable change”: Self-monitoring and Insight = 14.1%, Skill and Technique Acquisition = 23.0%). Conclusion: This study provides a preliminary evidence that mechanical diagnosis and therapy enhances patient’s self-management skills, particularly in the self-monitoring skills for symptoms/functions and the self-management skill for symptoms/problems.
Novel LRPPRC Mutation in a Boy With Mild Leigh Syndrome, French–Canadian Type Outside of Québec
Authors: Han Velda Xinying , Tan Teresa S. , Wang Furene S. , Tay Stacey Kiat-Hong 
Published: November 2017

Background: Leigh syndrome, French–Canadian type is unique to patients from a genetic isolate in the Saguenay–Lac-Saint-Jean region of Québec. It has also been recently described in 10 patients with LRPPRC mutation outside of Québec. It is an autosomal recessive genetic disorder with fatal metabolic crisis and severe neurological morbidity in infancy caused by LRPPRC mutation. Methods and Results: The authors report a boy with a novel LRPPRC compound heterozygous missense mutations c.3130C>T, c.3430C>T, and c.4078G>A found on whole-exome sequencing which correlated with isolated cytochrome c-oxidase deficiency found in skeletal muscle. Conclusion: LRPPRC mutation is a rare cause of cytochrome c-oxidase–deficient form of Leigh syndrome outside of Québec. Our patient broadens the spectrum of phenotypes of Leigh syndrome, French–Canadian type. LRPPRC mutation should be considered in children with early childhood neurodegenerative disorder, even in the absence of metabolic crisis. Early evaluation with whole-exome sequencing is useful for early diagnosis and for genetic counseling.
CRISPR-mediated TCR replacement generates superior anticancer transgenic T cells
Authors: Legut Mateusz , Dolton Garry , Mian Afsar Ali , Ottmann Oliver G. , Sewell Andrew K. 
Published: November 2017

Key Points
Endogenous TCR knockout increases the expression and functional activity of simultaneously transduced TCR (TCR replacement). TCR replacement results in superior targeting of hematological malignancies by T cells transduced with a non–HLA-restricted γδ TCR.