bluuebunny/crossref_metadata_2025_split huggingface dataset:
High Civic-Mindedness Reduces Compassion Fatigue in the First 3 Years of Professional Physical Therapist Practice: A Pilot Study
Authors: Palombaro Kerstin M , Erdman Ellen A , McArdle Kelly Duszak , Black Jill D , Stewart Alexander R , Jones Sidney A 
Published: November 2019

Introduction: Clinicians with compassion fatigue (CF) experience behavioral, cognitive, and emotional changes due to repeated exposure to second-hand trauma from the clients with whom they are working. A civic-minded professional possesses the core value of social responsibility. Physical therapy (PT) education programs must balance a focus on developing social responsibility and compassion against the risk of CF. Objective: The objectives of this study were to (1) describe the prevalence of CF in a sample of physical therapists in the early years of practice and (2) to determine whether higher civic-mindedness leads to the development of CF in physical therapists. Method: Three cohorts of recent graduates were administered the Professional Quality of Life (Pro-QOL) survey to measure CF. Thirty-five of 127 surveys sent (27.6% response rate) were completed. Results: A Mann-Whitney U was run to determine differences in the Pro-QOL survey between those scoring high or low in civic-mindedness at graduation. Higher civic-mindedness scores exhibited significantly lower burnout and higher compassion satisfaction. Conclusion: Higher levels of civic-mindedness appear to have a protective effect against developing CF.
Controllable Valley Polarization Using Silicene Double Line Defects Due to Rashba Spin-Orbit Coupling
Authors: Tian Hongyu , Ren ChongDan , Zhou Benhu , Zhang Shaoyin , Lu Weitao , Li Yunfang , Liu Jing 
Published: November 2019

AbstractWe theoretically investigate the valley polarization in silicene with two parallel line defects due to Rashba spin-orbit coupling (RSOC). It is found that as long as RSOC exceeds the intrinsic spin-orbit coupling (SOC), the transmission coefficients of the two valleys oscillate with the same periodicity and intensity, which consists of wide transmission peaks and zero-transmission plateaus. However, in the presence of a perpendicular electric field, the oscillation periodicity of the first valley increases, whereas that of the second valley shortens, generating the corresponding wide peak-zero plateau regions, where perfect valley polarization can be achieved. Moreover, the valley polarizability can be changed from 1 to −1 by controlling the strength of the electric field. Our findings establish a different route for generating valley-polarized current by purely electrical means and open the door for interesting applications of semiconductor valleytronics.
Association between flourishing mental health and occupational stress among workers of Tsukuba Science City, Japan: a cross-sectional study
Authors: Hori Daisuke , Oi Yuichi , Ohtaki Yuh , Andrea Christina-Sylvia , Takahashi Tsukasa , Shiraki Nagisa , Ikeda Tomohiko , Ikeda Yu , Doki Shotaro , Sasahara Shinichiro , Matsuzaki Ichiyo 
Published: November 2019

AbstractBackgroundFlourishing, defined as the coexistence of hedonic and eudaimonic well-being, is the most favorable end of the mental health spectrum. A growing body of evidence has demonstrated the association between flourishing mental health and favorable work-related outcomes. However, epidemiology of flourishing mental health is scarce in Japan. Moreover, the relationship between flourishing mental health and occupational stress has not been elaborated. Therefore, the aim of this study was to elucidate (1) the prevalence of flourishing mental health and (2) the association between flourishing mental health and occupational stress among Japanese workers.MethodsThe present survey was conducted in from February to March 2017 via an anonymous, self-administered, and web-based questionnaire among workers in Tsukuba Science City, Japan. Mental Health Continuum Short Form was used to assess flourishing mental health. We performed binomial logistic regression analyses to calculate the adjusted odds ratios (AOR) and 95% confidence intervals (CI) of occupational stress for flourishing mental health, controlling for sociodemographic factors.ResultsA total of 7012 respondents (4402 men, 2610 women) were analyzed. The overall prevalence of flourishing mental health among the respondents was 12.4%. Full-time (permanent) workers were less likely to be flourishing. Reward from work (AOR = 2.34, 95% CI = 2.04–2.68), support from colleagues and superiors (AOR = 1.67, 95% CI = 1.44–1.94), and workload (AOR = 1.19, 95% CI = 1.05–1.36) were positively associated with flourishing mental health, whereas mental workload (AOR = 0.65, 95% CI = 0.57–0.75) was inversely associated with flourishing mental health.ConclusionsThe findings of the present study shed light on the association between flourishing mental health and occupational stress.
Manhattan++: displaying genome-wide association summary statistics with multiple annotation layers
Authors: Grace Christopher , Farrall Martin , Watkins Hugh , Goel Anuj 
Published: November 2019

Abstract
Background
Over the last 10 years, there have been over 3300 genome-wide association studies (GWAS). Almost every GWAS study provides a Manhattan plot either as a main figure or in the supplement. Several software packages can generate a Manhattan plot, but they are all limited in the extent to which they can annotate gene-names, allele frequencies, and variants having high impact on gene function or provide any other added information or flexibility. Furthermore, in a conventional Manhattan plot, there is no way of distinguishing a locus identified due to a single variant with very significant p-value from a locus with multiple variants which appear to be in a haplotype block having very similar p-values.

Results
Here we present a software tool written in R, which generates a transposed Manhattan plot along with additional features like variant consequence and minor allele frequency to annotate the plot and addresses these limitations. The software also gives flexibility on how and where the user wants to display the annotations. The software can be downloaded from CRAN repository and also from the GitHub project page.

Conclusions
We present a major step up to the existing conventional Manhattan plot generation tools. We hope this form of display along with the added annotations will bring more insight to the reader from this new Manhattan++ plot.
Hierarchical clustering of maximum parsimony reconciliations
Authors: Mawhorter Ross , Libeskind-Hadas Ran 
Published: November 2019

Abstract
Background
Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and species and genes. While efficient algorithms are known for finding maximum parsimony reconciliations, the number of such reconciliations can be exponential in the size of the trees. Since these reconciliations can differ substantially from one another, making inferences from any one reconciliation may lead to conclusions that are not supported, or may even be contradicted, by other maximum parsimony reconciliations. Therefore, there is a need to find small sets of best representative reconciliations when the space of solutions is large and diverse.

Results
We provide a general framework for hierarchical clustering the space of maximum parsimony reconciliations. We demonstrate this framework for two specific linkage criteria, one that seeks to maximize the average support of the events found in the reconciliations in each cluster and the other that seeks to minimize the distance between reconciliations in each cluster. We analyze the asymptotic worst-case running times and provide experimental results that demonstrate the viability and utility of this approach.

Conclusions
The hierarchical clustering algorithm method proposed here provides a new approach to find a set of representative reconciliations in the potentially vast and diverse space of maximum parsimony reconciliations.
Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage
Authors: Nethery Matthew A. , Henriksen Emily DeCrescenzo , Daughtry Katheryne V. , Johanningsmeier Suzanne D. , Barrangou Rodolphe 
Published: November 2019

Abstract

Background
Lactobacillus buchneri is a lactic acid bacterium frequently associated with food bioprocessing and fermentation and has been found to be either beneficial or detrimental to industrial food processes depending on the application. The ability to metabolize lactic acid into acetic acid and 1,2-propandiol makes L. buchneri invaluable to the ensiling process, however, this metabolic activity leads to spoilage in other applications, and is especially damaging to the cucumber fermentation industry. This study aims to augment our genomic understanding of L. buchneri in order to make better use of the species in a wide range of applicable industrial settings.

Results
Whole-genome sequencing (WGS) was performed on seven phenotypically diverse strains isolated from spoiled, fermented cucumber and the ATCC type strain for L. buchneri, ATCC 4005. Here, we present our findings from the comparison of eight newly-sequenced and assembled genomes against two publicly available closed reference genomes, L. buchneri CD034 and NRRL B-30929. Overall, we see ~ 50% of all coding sequences are conserved across these ten strains. When these coding sequences are clustered by functional description, the strains appear to be enriched in mobile genetic elements, namely transposons. All isolates harbor at least one CRISPR-Cas system, and many contain putative prophage regions, some of which are targeted by the host’s own DNA-encoded spacer sequences.

Conclusions
Our findings provide new insights into the genomics of L. buchneri through whole genome sequencing and subsequent characterization of genomic features, building a platform for future studies and identifying elements for potential strain manipulation or engineering.
DNA methylation patterns vary in boar sperm cells with different levels of DNA fragmentation
Authors: Khezri Abdolrahman , Narud Birgitte , Stenseth Else-Berit , Johannisson Anders , Myromslien Frøydis Deinboll , Gaustad Ann Helen , Wilson Robert C. , Lyle Robert , Morrell Jane M. , Kommisrud Elisabeth , Ahmad Rafi 
Published: November 2019

Abstract
Background
Sperm DNA integrity is considered essential for successful transmission of the paternal genome, fertilization and normal embryo development. DNA fragmentation index (DFI, %) has become a key parameter in the swine artificial insemination industry to assess sperm DNA integrity. Recently, in some elite Norwegian Landrace boars (boars with excellent field fertility records), a higher level of sperm DFI has been observed. In order to obtain a better understanding of this, and to study the complexity of sperm DNA integrity, liquid preserved semen samples from elite boars with contrasting DFI levels were examined for protamine deficiency, thiol profile and disulphide bonds. Additionally, the DNA methylation profiles of the samples were determined by reduced representation bisulphite sequencing (RRBS).

Results
In this study, different traits related to sperm DNA integrity were investigated (n = 18 ejaculates). Upon liquid storage, the levels of total thiols and disulphide bonds decreased significantly, while the DFI and protamine deficiency level increased significantly. The RRBS results revealed similar global patterns of low methylation from semen samples with different levels of DFI (low, medium and high). Differential methylation analyses indicated that the number of differentially methylated cytosines (DMCs) increased in the low-high compared to the low-medium and the medium-high DFI groups. Annotating the DMCs with gene and CpG features revealed clear differences between DFI groups. In addition, the number of annotated transcription starting sites (TSS) and associated pathways in the low-high comparison was greater than the other two groups. Pathway analysis showed that genes (based on the closest TSS to DMCs) corresponding to low-high DFI comparison were associated with important processes such as membrane function, metabolic cascade and antioxidant defence system.

Conclusion
To our knowledge, this is the first study evaluating DNA methylation in boar sperm cells with different levels of DFI. The present study shows that sperm cells with varying levels of DNA fragmentation exhibit similar global methylation, but different site-specific DNA methylation signatures. Moreover, with increasing DNA fragmentation in spermatozoa, there is an increase in the number of potentially affected downstream genes and their respective regulatory pathways.
Effect of calcium on the interaction of Acinetobacter baumannii with human respiratory epithelial cells
Authors: Chen Yi , Shao Tingjun , Fang Sanhua , Pan Ping , Jiang Jiahui , Cheng Tongtong , Wan Haitong , Yu Daojun 
Published: November 2019

Abstract
Background
Investigating the factors that influence Acinetobacter baumannii(Ab) adhesion/invasion of host cells is important to understand its pathogenicity. Metal cations have been shown to play an important role in regulating the biofilm formation and increasing the virulence of Ab; however, the effect of calcium on host-bacterial interaction has yet to be clarified. Here, the dynamic process of the interaction between Ab and human respiratory epithelial cells and the effect of calcium on host-bacterial interaction were explored using microscopic imaging, quantitative PCR and real time cellular analysis (RTCA).

Results
The concentration of calcium, multiplicity of infection and co-culture time were all demonstrated to have effects on host-bacterial interaction. A unique “double peak” phenomenon changed to a sharp “single peak” phenomenon during the process of Ab infection under the effect of calcium was observed in the time-dependent cell response profiles. Moreover, calcium can increase Ab adhesion/invasion of epithelial cells by regulating the expression of Ab-related genes (ompA, bfmRS, abaI).

Conclusions
Effective control of calcium concentrations can provide new approaches for the prevention and treatment of multi-drug resistant Ab.
Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates
Authors: López-Malvar A. , Butrón A. , Samayoa L. F. , Figueroa-Garrido D. J. , Malvar R. A. , Santiago R. 
Published: November 2019

AbstractBackgroundThe structural reinforcement of cell walls by hydroxycinnamates has a significant role in defense against pests and pathogens, but it also interferes with forage digestibility and biofuel production. Elucidation of maize genetic variations that contribute to variation for stem hydroxycinnamate content could simplify breeding for cell wall strengthening by using markers linked to the most favorable genetic variants in marker-assisted selection or genomic selection approaches​.ResultsA genome-wide association study was conducted using a subset of 282 inbred lines from a maize diversity panel to identify single nucleotide polymorphisms (SNPs) associated with stem cell wall hydroxycinnamate content. A total of 5, 8, and 2 SNPs were identified as significantly associated top-coumarate, ferulate, and total diferulate concentrations, respectively in the maize pith. Attending to particular diferulate isomers, 3, 6, 1 and 2 SNPs were related to 8–O–4 diferulate, 5–5 diferulate, 8–5 diferulate and 8–5 linear diferulate contents, respectively. This study has the advantage of being done with direct biochemical determinations instead of using estimates based on Near-infrared spectroscopy (NIRS) predictions. In addition, novel genomic regions involved in hydroxycinnamate content were found, such as those in bins 1.06 (for FA), 4.01 (for PCA and FA), 5.04 (for FA), 8.05 (for PCA), and 10.03 and 3.06 (for DFAT and some dimers).ConclusionsThe effect of individual SNPs significantly associated with stem hydroxycinnamate content was low, explaining a low percentage of total phenotypic variability (7 to 10%). Nevertheless, we spotlighted new genomic regions associated with the accumulation of cell-wall-bound hydroxycinnamic acids in the maize stem, and genes involved in cell wall modulation in response to biotic and abiotic stresses have been proposed as candidate genes for those quantitative trait loci (QTL). In addition, we cannot rule out that uncharacterized genes linked to significant SNPs could be implicated in dimer formation and arobinoxylan feruloylation because genes involved in those processes have been poorly characterized. Overall, genomic selection considering markers distributed throughout the whole genome seems to be a more appropriate breeding strategy than marker-assisted selection focused in markers linked to QTL.
Genome-wide characterization of the rose (Rosa chinensis) WRKY family and role of RcWRKY41 in gray mold resistance
Authors: Liu Xintong , Li Dandan , Zhang Shiya , Xu Yaling , Zhang Zhao 
Published: November 2019

Abstract
Background
The WRKYs are a major family of plant transcription factors that play roles in the responses to biotic and abiotic stresses; however, a comprehensive study of the WRKY family in roses (Rosa sp.) has not previously been performed.

Results
In the present study, we performed a genome-wide analysis of the WRKY genes in the rose (Rosa chinensis), including their phylogenetic relationships, gene structure, chromosomal locations, and collinearity. Using a phylogenetic analysis, we divided the 56 RcWRKY genes into three subgroups. The RcWRKYs were unevenly distributed across all seven rose chromosomes, and a study of their collinearity suggested that genome duplication may have played a major role in RcWRKY gene duplication. A Ka/Ks analysis indicated that they mainly underwent purifying selection. Botrytis cinerea infection induced the expression of 19 RcWRKYs, most of which had undergone gene duplication during evolution. These RcWRKYs may regulate rose resistance against B. cinerea. Based on our phylogenetic and expression analyses, RcWRKY41 was identified as a candidate regulatory gene in the response to B. cinerea infection, which was confirmed using virus-induced gene silencing.

Conclusions
This study provides useful information to facilitate the further study of the function of the rose WRKY gene family.
The grapevine homeobox gene VvHB58 influences seed and fruit development through multiple hormonal signaling pathways
Authors: Li Yunduan , Zhang Songlin , Dong Ruzhuang , Wang Li , Yao Jin , van Nocker Steve , Wang Xiping 
Published: November 2019

AbstractBackgroundThe homeobox transcription factor has a diversity of functions during plant growth and development process. Previous transcriptome analyses of seed development in grape hybrids suggested that specific homeodomain transcription factors are involved in seed development in seedless cultivars. However, the molecular mechanism of homeobox gene regulating seed development in grape is rarely reported.ResultsHere, we report that the grapevineVvHB58gene, encoding a homeodomain-leucine zipper (HD-Zip I) transcription factor, participates in regulating fruit size and seed number. TheVvHB58gene was differentially expressed during seed development between seedless and seeded cultivars. Subcellular localization assays revealed that the VvHB58 protein was located in the nucleus. Transgenic expression ofVvHB58in tomato led to loss of apical dominance, a reduction in fruit pericarp expansion, reduced fruit size and seed number, and larger endosperm cells. Analysis of the cytosine methylation levels within theVvHB58promoter indicated that the differential expression during seed development between seedless and seeded grapes may be caused by different transcriptional regulatory mechanisms rather than promoter DNA methylation. Measurements of five classic endogenous hormones and expression analysis of hormone-related genes betweenVvHB58transgenic and nontransgenic control plants showed that expression ofVvHB58resulted in significant changes in auxin, gibberellin and ethylene signaling pathways. Additionally, several DNA methylation-related genes were expressed differentially during seed development stages in seedless and seeded grapes, suggesting changes in methylation levels during seed development may be associated with seed abortion.ConclusionVvHB58 has a potential function in regulating fruit and seed development by impacting multiple hormonal pathways. These results expand understanding of homeodomain transcription factors and potential regulatory mechanism of seed development in grapevine, and provided insights into molecular breeding for grapes.
Towards standardized postprocessing of global longitudinal strain by feature tracking – OptiStrain CMR-FT study
Authors: Heinke Robert , Pathan Faraz , Le Melanie , D’Angelo Tommaso , Winau Lea , Arendt Christophe , Vogl Thomas J. , Zeiher Andreas , Nagel Eike , Puntmann Valentina O. 
Published: November 2019

Abstract
Background
Left ventricular global longitudinal strain (GLS) with cardiovascular magnetic resonance (CMR) is an important prognostic biomarker. Its everyday clinical use is limited due to methodological and postprocessing diversity among the users and vendors. Standardization of postprocessing approaches may reduce the random operator-dependent variability, allowing for comparability of measurements despite the systematic vendor-related differences.

Methods
We investigated the random component of variability in GLS measurements by optimization steps which incrementally improved observer reproducibility and agreement. Cine images in two-, three- and four-chamber-views were serially analysed by two independent observers using two different CMR-FT softwares. The disparity of outcomes after each series was systematically assessed after a number of stepwise adjustments which were shown to significantly reduce the inter-observer and intervendor bias, resulting standardized postprocessing approach. The final analysis was performed in 44 subjects (ischaemic heart disease n = 15, non-ischaemic dilated cardiomyopathy, n = 19, healthy controls, n = 10). All measurements were performed blind to the underlying group allocation and previous measurements. Inter- and intra-observer variability were tested using Bland-Altman analyses, intra-class correlation coefficients (ICCs) and coefficients of variation (CVs).

Results
Compared to controls, mean GLS was significantly lower in patients, as well as between the two subgroups (p < 0.01). These differences were accentuated by standardization procedures, with significant increase in Cohen’s D and AUCs. The benefit of standardization was also evident through improved CV and ICC agreements between observers and the two vendors. Initial intra-observer variability CVs for GLS parameters were 7.6 and 4.6%, inter-observer variability CVs were 11 and 4.7%, for the two vendors, respectively. After standardization, intra- and interobserver variability CVs were 3.1 and 4.3%, and 5.2 and 4.4%, respectively.

Conclusion
Standardization of GLS postprocessing helps to reduce the random component of variability, introduced by inconsistencies of and between observers, and also intervendor variability, but not the systematic inter-vendor bias due to differences in image processing algorithms. Standardization of GLS measurements is an essential step in ensuring the reliable quantification of myocardial deformation, and implementation of CMR-FT in clinical routine.