bluuebunny/crossref_metadata_2025_split huggingface dataset:
Instrument constituencies and epistemic community theory
Authors: Zito Anthony R 
Published: December 2017

AbstractThis contribution fleshes out the insights that the epistemic community (EC) approach can make to studying the public policy process and to how policy instruments are formulated and implemented. This contribution places the EC concept in the context of how policy instruments evolve and are supported by a separate network type, the instrument constituency (IC). It studies the conceptual differences between the EC and IC, analyses the conceptual progress and research output of the EC literature, and then reviews the EC literature to develop new analytical propositions about how epistemic communities, in relation to instrument constituencies, shape instrument change. This contribution then explores the value of these network concepts and propositions by examining four United States federal environmental policy instruments. It concludes that there is strong evidence for the role of ICs, and to a lesser extent, ECs, and that such public policy analysis would benefit from a greater network conceptualization.
DiffGraph: an R package for identifying gene network rewiring using differential graphical models
Authors: Zhang Xiao-Fei , Ou-Yang Le , Yang Shuo , Hu Xiaohua , Yan Hong 
Published: December 2017

Abstract

Summary
We develop DiffGraph, an R package that integrates four influential differential graphical models for identifying gene network rewiring under two different conditions from gene expression data. The input and output of different models are packaged in the same format, making it convenient for users to compare different models using a wide range of datasets and carry out follow-up analysis. Furthermore, the inferred differential networks can be visualized both non-interactively and interactively. The package is useful for identifying gene network rewiring from input datasets, comparing the predictions of different methods and visualizing the results.

Availability and implementation
The package is available at https://github.com/Zhangxf-ccnu/DiffGraph.

Supplementary information
Supplementary data are available at Bioinformatics online.
Tailor-made exopolysaccharides—CRISPR-Cas9 mediated genome editing in Paenibacillus polymyxa
Authors: Rütering Marius , Cress Brady F , Schilling Martin , Rühmann Broder , Koffas Mattheos A G , Sieber Volker , Schmid Jochen 
Published: December 2017

Abstract
Application of state-of-the-art genome editing tools like CRISPR-Cas9 drastically increase the number of undomesticated micro-organisms amenable to highly efficient and rapid genetic engineering. Adaptation of these tools to new bacterial families can open up entirely new possibilities for these organisms to accelerate as biotechnologically relevant microbial factories, also making new products economically competitive. Here, we report the implementation of a CRISPR-Cas9 based vector system in Paenibacillus polymyxa, enabling fast and reliable genome editing in this host. Homology directed repair allows for highly efficient deletions of single genes and large regions as well as insertions. We used the system to investigate the yet undescribed biosynthesis machinery for exopolysaccharide (EPS) production in P. polymyxa DSM 365, enabling assignment of putative roles to several genes involved in EPS biosynthesis. Using this simple gene deletion strategy, we generated EPS variants that differ from the wild-type polymer not only in terms of monomer composition, but also in terms of their rheological behavior. The developed CRISPR-Cas9 mediated engineering approach will significantly contribute to the understanding and utilization of socially and economically relevant Paenibacillus species and extend the polymer portfolio.
Choroidal Microvasculature Dropout is Not Associated With Myopia, But is Associated With Glaucoma
Authors: Shin Joong Won , Kwon Junki , Lee Jiyun , Kook Michael S. 
Published: December 2017

Purpose:
To investigate the frequency of choroidal microvasculature dropout (CMvD) in healthy myopic eyes in comparison with that of myopic open-angle glaucoma (OAG) eyes and determine whether myopia is independently associated with CMvD.

Patients and Methods:
Choroidal layer microvasculature images were obtained using optical coherence tomography angiography in 89 myopic OAG patients and 89 age-matched and refractive error-matched healthy myopic eyes. CMvD was defined as a complete loss of the microvasculature network on the choroidal layer vessel density (VD) map. The frequency of CMvD was compared between myopic OAG and healthy myopic eyes. Hemispheric comparisons of various parameters were performed between CMvD-affected and CMvD-unaffected hemiretina. The association of myopia with the presence and angular circumference of CMvD was evaluated using logistic and linear regression analyses.

Results:
CMvD was identified in 40 eyes (47.6%) with myopic OAG, whereas no CMvD was found in healthy myopic eyes. Mean hemispheric visual field sensitivity (294.9±321.1 vs. 610.5±387.5, P=0.006), retinal nerve fiber layer thickness (68.9±11.5 vs. 82.5±20.6 μm, P=0.001), and circumpapillary VD (50.5%±7.3% vs. 53.9%±8.8%, P=0.048) were significantly worse in the CMvD-affected hemiretina than in the CMvD-unaffected hemiretina. The presence and angular circumference of CMvD was significantly associated with parameters (visual field mean deviation, retinal nerve fiber layer thickness, and circumpapillary VD; P<0.05) representing glaucoma severity rather than parameters (refractive error and axial length; P>0.05) representing myopic change.

Conclusions:
CMvD was observed only in glaucomatous eyes and associated with severity of glaucomatous damage in myopic OAG subjects. The angular circumference of CMvD was significantly related to glaucoma severity.
Online Depressive Symptom Self-Management: Comparing Program Outcomes for Adults With Multiple Sclerosis Versus Those With Other Chronic Diseases
Authors: Tietjen Kiira , Wilson Marian , Amiri Solmaz , Dietz Jeremy 
Published: December 2017

ABSTRACT

Aims: The goals of the study were to evaluate participant engagement and effects of an Internet-based, self-directed program for depressive symptoms. We compared outcomes of adults with multiple sclerosis (MS) with those of adults with other chronic diseases. Methods: This was a secondary analysis of a randomized controlled pilot study. Data were explored for differences between people diagnosed with MS and those with other chronic disease diagnoses. Data were obtained from 47 participants who participated in the original parent study (11 had MS). Participants with at least a moderate preexisting depressive symptom burden on the Patient Health Questionnaire (PHQ) were randomly divided into either a control group or the 8-week “Think Clearly About Depression” online depression self-management program. Study tools were administered at baseline, week 4, and week 8 to evaluate whether the online program improved depressive symptom self-management. Analysis examined differences between participants with and without an MS diagnosis in the treatment and control groups. Results: Average baseline depressive symptom burdens were severe for those with MS and those without MS as measured by the PHQ. Number needed to treat analysis indicated that 1 in every 2 treatment group participants with MS found clinically significant reductions in depressive symptoms by week 8. All participants with MS completed all online program modules. When compared with those with other chronic diseases, participants with MS showed a trend toward greater improvements in the PHQ and health distress scores in addition to self-efficacy in exercising regularly, social/recreational activities, and controlling/managing depression at the end of 8 weeks. Conclusions: An online depressive symptom self-management program is acceptable to people with MS and may be helpful to address undertreated depressive symptoms. The number of participants limits available statistics and ability to generalize results.
The Relationship Between Pain Interference and Psychosocial Well-Being Among Veterans With Spinal Cord Injuries/Disorders
Authors: Etingen Bella , Miskevics Scott , LaVela Sherri L. 
Published: December 2017

ABSTRACT

Objectives: The study objectives were to compare psychosocial well-being in individuals with spinal cord injuries/disorders (SCI/D) and above-mean (“high”) versus below-mean (“low”) pain interference, and to determine whether psychosocial well-being was negatively associated with pain interference. Methods: Data were collected via a cross-sectional survey mailed in late 2014 to early 2015 to a national sample of veterans with SCI/D who received prior-year Veterans Affairs healthcare and assessed demographics, injury-related factors, select health conditions, pain interference, and psychosocial well-being. Bivariate comparisons and multivariate linear regressions identified factors related to higher pain interference. Results: Approximately 79% of the sample (n = 813) reported high pain interference. Veterans with high (vs. low) pain interference reported worse perceptions of all included psychosocial well-being measures. Regression results indicated that higher pain interference was associated with higher grief/loss (β = 0.38, P < .0001) and negative psychosocial illness impact (β = 0.39, P < .0001), and lower positive affect (β = −0.39, P < .0001), resilience (β = −0.31, P < .0001), and life satisfaction (β = −0.39, P < .0001). Conclusions: The pain experience is independently associated with poor psychosocial well-being among individuals with SCI/D. Efforts to decrease perceptions of pain interference and improve factors associated with psychosocial well-being may symbiotically improve outcomes in SCI/D cohorts. Such efforts may focus on effective pain management programs aligned with patients’ treatment preferences.
Return to Sport After Short-Stem Total Hip Arthroplasty
Authors: Ortmaier Reinhold , Pichler Hannes , Hitzl Wolfgang , Emmanuel Katja , Mattiassich Georg , Plachel Fabian , Hochreiter Josef 
Published: December 2017

Objectives:
Information about sport activity after short-stem total hip arthroplasty (THA) is scarce in the literature. We therefore aimed to evaluate the rate of return to sport after short-stem THA.

Methods:
We evaluated the sport pattern, rate of return to sport, activity level, extent of sport activity, and subjective rating and sense of well-being in 137 patients (137 hips) after short-stem THA. The minimum follow-up time was 18 months. All results were analyzed according to gender (male and female) and age (≤60, >60-≤70, and >70 years).

Results:
Ninety-two percent of all patients practiced sport before surgery, and 91% of the patients returned to sport. Most patients returned to sport within the first 6 months after surgery. There was a decline in the number of sport disciplines from preoperatively to postoperatively, which was from 2.9 to 2.6 (P = 0.025). High-impact activities decreased postoperatively, but most low-impact activities did not change significantly. Eighty percent of all patients were involved in recreational sports.

Conclusion:
In this study, we observed an excellent rate of return to sport after short-stem THA. Most patients returned to the same level of sport activity that they had before the onset of restricting symptoms, with the majority of patients having a great sense of well-being during and after sports, and almost no pain in the affected hip.
On the decidability of population size histories from finite allele frequency spectra
Authors: Baharian Soheil , Gravel Simon 
Published: December 2017

AbstractUnderstanding the historical events that shaped current genomic diversity has applications in historical, biological, and medical research. However, the amount of historical information that can be inferred from genetic data is finite, which leads to an identifiability problem. For example, different historical processes can lead to identical distribution of allele frequencies. This identifiability issue casts a shadow of uncertainty over the results of any study which uses the frequency spectrum to infer past demography. It has been argued that imposing mild ‘reasonableness’ constraints on demographic histories can enable unique reconstruction, at least in an idealized setting where the length of the genome is nearly infinite. Here, we discuss this problem for finite sample size and genome length. Using the diffusion approximation, we obtain bounds on likelihood differences between similar demographic histories, and use them to construct pairs of very different reasonable histories that produce almost-identical frequency distributions. The finite-genome problem therefore remains poorly determined even among reasonable histories. Where fits to few-parameter models produce narrow parameter confidence intervals, large uncertainties lurk hidden by model assumption.
Phylofactorization: a graph-partitioning algorithm to identify phylogenetic scales of ecological data
Authors: Washburne Alex D. , Silverman Justin D. , Morton James T. , Becker Daniel J. , Crowley Daniel , Mukherjee Sayan , David Lawrence A. , Plowright Raina K. 
Published: December 2017

AbstractThe problem of pattern and scale is a central challenge in ecology. The problem of scale is central to community ecology, where functional ecological groups are aggregated and treated as a unit underlying an ecological pattern, such as aggregation of “nitrogen fixing trees” into a total abundance of a trait underlying ecosystem physiology. With the emergence of massive community ecological datasets, from microbiomes to breeding bird surveys, there is a need to objectively identify the scales of organization pertaining to well-defined patterns in community ecological data.The phylogeny is a scaffold for identifying key phylogenetic scales associated with macroscopic patterns. Phylofactorization was developed to objectively identify phylogenetic scales underlying patterns in relative abundance data. However, many ecological data, such as presence-absences and counts, are not relative abundances, yet it is still desireable and informative to identify phylogenetic scales underlying a pattern of interest. Here, we generalize phylofactorization beyond relative abundances to a graph-partitioning algorithm for any community ecological data.Generalizing phylofactorization connects many tools from data analysis to phylogenetically-informe analysis of community ecological data. Two-sample tests identify three phylogenetic factors of mammalian body mass which arose during the K-Pg extinction event, consistent with other analyses of mammalian body mass evolution. Projection of data onto coordinates defined by the phylogeny yield a phylogenetic principal components analysis which refines our understanding of the major sources of variation in the human gut microbiome. These same coordinates allow generalized additive modeling of microbes in Central Park soils and confirm that a large clade of Acidobacteria thrive in neutral soils. Generalized linear and additive modeling of exponential family random variables can be performed by phylogenetically-constrained reduced-rank regression or stepwise factor contrasts. We finish with a discussion of how phylofac-torization produces an ecological species concept with a phylogenetic constraint. All of these tools can be implemented with a new R package available online.
Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies
Authors: Ziegler Samantha J. , Liu Chang , Landau Mark , Buzovetsky Olga , Desimmie Belete A. , Zhao Qi , Sasaki Tomoaki , Burdick Ryan C. , Pathak Vinay K. , Anderson Karen S. , Xiong Yong 
Published: December 2017

AbstractHuman apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 (A3) proteins are a family of cytidine deaminases that catalyze the conversion of cytidine to uridine in single-stranded DNA (ssDNA). A3 proteins act in the innate immune response to viral infection by mutating the viral ssDNA. One of the most well-studied human A3 family members is A3G, which is a potent inhibitor of HIV-1. Each A3 protein prefers a specific substrate sequence for catalysis - for example, A3G deaminates the third cytidine in the CCCA sequence motif. However, the interaction between A3G and ssDNA is difficult to characterize due to poor solution behavior of the full-length protein and loss of DNA affinity of the truncated protein. Here, we present a novel DNA-anchoring fusion strategy, which we have used to capture an A3G-ssDNA interaction. We characterized an A3G-DNA binding pocket that is important for the enzyme to scan the DNA for its hotspot. The results provide insights into the mechanism by which A3G selects and deaminates its preferred substrates and help define how A3 proteins are tailored to recognize specific DNA sequences. This knowledge contributes to a better understanding of the mechanism of DNA substrate selection by A3G, as well as A3G antiviral activity against HIV-1.
Identification of methylation and hydroxymethylation haplotype blocks as distal regulatory elements aids in deconvolution of heterogeneous brain tissues
Authors: Ma Qin , Xu Zhengzheng , Lu Huan , Xu Ziying , Zhou Yuanyuan , Yuan Bifeng , Ci Weimin 
Published: December 2017

Abstract5-Hydroxymethylcytosine (5hmC) is an oxidation product of 5-methylcytosine (5mC), and adjacent CpG sites in the mammalian genome can be co-methylated and co-hydroxymethylated due to the processivity of DNMT and TET enzymes. We applied TAB-seq and oxBS-seq to selectively detect 5hmC and 5mC, respectively, at base resolution in the mouse cortex, olfactory bulb and cerebellum tissues. We found that majority of the called 5hmC CpG sites frequently had 5mC modification simultaneously and enriched in gene body regions of neuron development related genes in brain tissues. These results supported a prominent role of oxidizing 5mC to 5hmC as new epigenetic mark. Strikingly, by a systematic search of regions that show highly coordinated methylation and hydroxymethylation (MHBs and hMHBs), we found that MHBs significantly overlapped with hMHBs in gene body regions which further supported that oxidized 5mC to 5hmC co-ordinately in a subset of cells within heterogeneous brain tissues. Consistently, using a metric called methylation haplotype load, we defined a subset of 1,361 tissue-specific MHBs and 3,818 shared MHBs which were predominantly regulatory elements, and aids in deconvolution of heterogeneous brain tissues. Our results provide new insights into the role of co-ordinately oxidized 5mC to 5hmC as distal regulatory elements may involve in regulating tissue identity.
Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
Authors: Guiblet Wilfried M. , Cremona Marzia A. , Cechova Monika , Harris Robert S. , Kejnovska Iva , Kejnovsky Eduard , Eckert Kristin , Chiaromonte Francesca , Makova Kateryna D. 
Published: December 2017

ABSTRACTDNA conformation may deviate from the classical B-form in ~13% of the human genome. Non-B DNA regulates many cellular processes; however, its effects on DNA polymerization speed and accuracy have not been investigated genome-wide. Such an inquiry is critical for understanding neurological diseases and cancer genome instability. Here we present the first simultaneous examination of DNA polymerization kinetics and errors in the human genome sequenced with Single-Molecule-Real-Time technology. We show that polymerization speed differs between non-B and B-DNA: it decelerates at G-quadruplexes and fluctuates periodically at disease-causing tandem repeats. Analyzing polymerization kinetics profiles, we predict and validate experimentally non-B DNA formation for a novel motif. We demonstrate that several non-B motifs affect sequencing errors (e.g., G-quadruplexes increase error rates) and that sequencing errors are positively associated with polymerase slowdown. Finally, we show that highly divergent G4 motifs have pronounced polymerization slowdown and high sequencing error rates, suggesting similar mechanisms for sequencing errors and germline mutations.
Diversification, sympatry, and the emergence of mega-diverse tropical assemblages
Authors: Socolar Jacob B. , Lees Alexander C. 
Published: December 2017

ABSTRACTGeographic gradients in species richness, including latitudinal gradients, can arise from geographic variation in any of three mechanisms: the geologic age of habitats, net rates of evolutionary diversification, or rates of sympatry among diversifying lineages. Here we show that variation in rates of sympatry is a dominant force structuring geographic richness gradients in birds. Species-rich sites contain disproportionately high numbers of recently diverged sympatric species but contain lineages with slower-than-average diversification rates. The positive sympatry-diversity relationship consistently overwhelms the negative diversification-diversity relationship, particularly among high-diversity sites (>250 species). These patterns repeat across biomes and continents with striking regularity, and remain consistent across multiple timescales, including the recent evolutionary past. Biogeographic and evolutionary patterns in birds are consistent with a role for ecological conditions in promoting species coexistence, which allows sister species to co-occur and potentially lowers extinction rates.
Variations in disability and quality of life with age and sex between eight lower income and middle-income countries: data from the INDEPTH WHO-SAGE collaboration
Authors: Gomez-Olive Francesc Xavier , Schröders Julia , Aboderin Isabella , Byass Peter , Chatterji Somnath , Davies Justine I , Debpuur Cornelius , Hirve Siddhivinayak , Hodgson Abraham , Juvekar Sanjay , Kahn Kathleen , Kowal Paul , Nathan Rose , Ng Nawi , Razzaque Abdur , Sankoh Osman , Streatfield Peter K , Tollman Stephen M , Wilopo Siswanto A , Witham Miles D 
Published: December 2017

BackgroundDisability and quality of life are key outcomes for older people. Little is known about how these measures vary with age and gender across lower income and middle-income countries; such information is necessary to tailor health and social care policy to promote healthy ageing and minimise disability.MethodsWe analysed data from participants aged 50 years and over from health and demographic surveillance system sites of the International Network for the Demographic Evaluation of Populations and their Health Network in Ghana, Kenya, Tanzania, South Africa, Vietnam, India, Indonesia and Bangladesh, using an abbreviated version of the WHO Study on global AGEing survey instrument. We used the eight-item WHO Quality of Life (WHOQoL) tool to measure quality of life and theWHO Disability Assessment Schedule, version 2 (WHODAS-II) tool to measure disability. We collected selected health status measures via the survey instrument and collected demographic and socioeconomic data from linked surveillance site information. We performed regression analyses to quantify differences between countries in the relationship between age, gender and both quality of life and disability, and we used anchoring vignettes to account for differences in interpretation of disability severity.ResultsWe included 43 935 individuals in the analysis. Mean age was 63.7 years (SD 9.7) and 24 434 (55.6%) were women. In unadjusted analyses across all countries, WHOQoL scores worsened by 0.13 points (95% CI 0.12 to 0.14) per year increase in age and WHODAS scores worsened by 0.60 points (95% CI 0.57 to 0.64). WHODAS-II and WHOQoL scores varied markedly between countries, as did the gradient of scores with increasing age. In regression analyses, differences were not fully explained by age, socioeconomic status, marital status, education or health factors. Differences in disability scores between countries were not explained by differences in anchoring vignette responses.ConclusionsThe relationship between age, sex and both disability and quality of life varies between countries. The findings may guide tailoring of interventions to individual country needs, although these associations require further study.