bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advancing Nursing Practice
Authors: O’Brien Joanne , Keaveny Joseph , Pollard Valerie , Nugent Linda Elizabeth 
Published: April 2017

Purpose/Aims:The purpose of this study was to examine the management of patient’s neuropathic pain with capsaicin 8% in a nurse-led clinic when administered by 1 registered advanced nurse practitioner without physician supervision.Design:A longitudinal, single-group, descriptive research design was used to assess pain scores and quality of life 3 times over 3 months after treatment.Methods:Patients with a diagnosis of neuropathic pain were assessed and treated with capsaicin 8% by 1 advanced nurse practitioner with prescriptive authority in a nurse-led clinic. Pain scores were collected at baseline, and self-assessed pain, activity level, and quality of life were assessed at 1 week, 4 weeks, and 3 months after treatment. Twenty-four patients were recruited, and data were analyzed using Friedman’s test. In post hoc analysis, Wilcoxon signed-rank test was used with Bonferroni correction.Results:Pain scores differed from pretreatment to posttreatment at each of the 3 time points, at rest (χ23= 20.54,P= .001) and on movement (χ23= 23.644,P= .001), and remained significant after Bonferroni correction. Overall, 62.5% (n = 15) of patients achieved at least a 30% reduction in self-reported pain at rest from pretreatment to 3 months, and 54% (n = 13) achieved the same reduction in pain on movement. Most improvements in patient’s quality of life occurred between 1 and 4 weeks. Patient satisfaction was high, with 83% stating that they would be happy to have the treatment repeated.Conclusion:Single-dose capsaicin 8% decreased neuropathic pain after being administered in an outpatient setting by an experienced registered advanced nurse practitioner. Further multicenter research led by advanced nurse practitioners is needed to support high-quality, safe treatment of neuropathic pain with high-concentration capsaicin in nurse-led chronic pain clinics.
Availability of Foodborne Illness Reporting Mechanisms for the Public on Local Health Department Web Sites
Authors: Harris Jenine K. , Wong Roger , Matthew Megan G. , Mansour Raed 
Published: April 2017

Context:
Foodborne illness is a serious and preventable public health problem, with high health and economic tolls in the United States. Local governments play an important role in food safety, with local health departments (LHDs) responsible for licensing and inspecting restaurants. Foodborne illness complaints from the public result in identification of more serious and critical food safety violations than regularly scheduled inspections; however, few people report foodborne illness. Availability of existing methods for the public to report foodborne illness to LHDs across the United States was examined.

Objective:
In 2016, data were collected and analyzed from a nationally representative stratified sample of 816 LHDs. Each LHD Web site was examined to determine whether the Web site included a way for constituents to report a suspected foodborne illness.

Results:
Just 27.6% of LHD Web sites included a way for constituents to report a suspected foodborne illness. LHDs with reporting mechanisms were serving significantly larger populations and had significantly more staff members, higher revenues, and higher expenditures. Health departments with reporting mechanisms were also significantly more likely to conduct environmental health surveillance activities, to regulate, inspect, and/or license food service establishments, and to be involved in food safety policy.

Conclusions:
Consumer reports of suspected foodborne illness help identify serious and critical food safety violations in food establishments; however, foodborne illness is vastly underreported by the US public. While more evidence is needed on how current systems are working, increasing the visibility and availability of Web-based reporting mechanisms through the following strategies is recommended: (1) test and modify search functions on LHD Web sites to ensure consumers find reporting mechanisms; (2) add a downloadable form as an option for reporting; (3) coordinate with state health departments to ensure clear instructions are available for reporting at both state and local levels; and (4) consider linking directly to state health department reporting mechanisms.
Lifelong Prophylaxis With Trimethoprim-Sulfamethoxazole for Prevention of Outbreak of Pneumocystis jirovecii Pneumonia in Kidney Transplant Recipients
Authors: Goto Norihiko , Takahashi-Nakazato Ai , Futamura Kenta , Okada Manabu , Yamamoto Takayuki , Tsujita Makoto , Hiramitsu Takahisa , Narumi Shunji , Tsuchiya Kiyoto , Gatanaga Hiroyuki , Watarai Yoshihiko , Oka Shinichi 
Published: April 2017

Background
Outbreaks of Pneumocystis jirovecii pneumonia (PCP) in kidney transplant recipients are frequently reported worldwide. However, the general guidelines propose only short-term prophylaxis with trimethoprim-sulfamethoxazole after kidney transplantation. We experienced 3 PCP outbreaks in the last 10 years despite providing the recommended prophylaxis. The purpose of this study was to find a prophylaxis regimen that could successfully prevent future PCP outbreaks in immunosuppressed kidney transplant recipients.

Methods
Occurrence of PCP at our hospital since 2004 was reviewed. A total of 48 cases were diagnosed from July 2004 through December 2014. Genotypes of P. jirovecii were determined in these cases.

Results
Three PCP outbreaks by 3 different genotypes of P. jirovecii in each outbreak occurred with 2-year intervals in last 10 years. Molecular analysis showed that each intraoutbreak was caused by identical P. jirovecii, whereas interoutbreaks were caused by different genotypes. Although short-term prophylaxis was provided to all kidney recipients after each outbreak after identification of a single PCP case, additional outbreaks were not prevented because the universal prophylaxis had already been completed when new case of PCP emerged.

Conclusions
The contagious nature of P. jirovecii allows easy development of outbreaks of PCP in immunosuppressed kidney transplant recipients. Although the universal short-term prophylaxis is effective in controlling ongoing outbreak, lifelong prophylaxis of kidney transplant recipients should be considered to prevent new outbreaks.
DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP
Authors: Mitra Sneha , Biswas Anushua , Narlikar Leelavati 
Published: April 2017

AbstractA high-throughput chromatin immunoprecipitation (ChIP) experiment is like a black-box: it reports all regions that are associated with the profiled protein based on the initial cross-linking step. These regions can be a highly diverse set of DNA sequences, with some making direct contact with the protein, some binding through intermediaries, and some being a result of long-range interactions involving the protein. We presentdiversity, a method that identifies the distinct components of such a mixture, leaving no data behind, while at the same time, using no prior motif knowledge. Using the example of the REST protein, we show that these different components give insights into the various complexes that may be forming along the chromatin and their regulatory functions.http://diversity.ncl.res.in/(webserver)https://github.com/NarlikarLab/DIVERSITY(standalone for Mac OSX/Linux)
A novel ultra high-throughput 16S rRNA amplicon sequencing library preparation method on the Illumina HiSeq platform
Authors: de Muinck Eric J. , Trosvik Pål , Gilfillan Gregor D. , Sundaram Arvind Y. M. 
Published: April 2017

AbstractBackgroundAdvances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost, and benchmarking the techniques so that potential sources of bias can be better characterized.ResultsWe present a triple-index amplicon sequencing strategy that uses a two-stage PCR protocol. The strategy was extensively benchmarked through analysis of a mock community in order to assess biases introduced by sample indexing, number of PCR cycles, and template concentration. We further evaluated the method through re-sequencing of a standardized environmental sample. Finally, we evaluated our protocol on a set of fecal samples from a small cohort of healthy adults, demonstrating good performance in a realistic experimental setting. Between-sample variation was mainly related to batch effects, such as DNA extraction, while sample indexing was also a significant source of bias. PCR cycle number strongly influenced chimera formation and affected relative abundance estimates of species with high GC content. Libraries were sequenced using the Illumina HiSeq and MiSeq platforms to demonstrate that this protocol is highly scalable to sequence thousands of samples at a very low cost.ConclusionsHere, we provide the most comprehensive study of performance and bias inherent to a 16S rRNA gene amplicon sequencing method to date. Triple-indexing greatly reduces the number of long custom DNA oligos required for library preparation, while the inclusion of variable length heterogeneity spacers minimizes the need for PhiX spike-in. This design results in a significant cost reduction of highly multiplexed amplicon sequencing. The biases we characterize highlight the need for highly standardized protocols. Reassuringly, we find that the biological signal is a far stronger structuring factor than the various sources of bias.
Properties of genomic relationships for estimating current genetic variances within and genetic correlations between populations
Authors: Wientjes Yvonne C.J. , Bijma Piter , Vandenplas Jérémie , Calus Mario P.L. 
Published: April 2017

ABSTRACTDifferent methods are available to calculate multi-population genomic relationship matrices. Since those matrices differ in base population, it is anticipated that the method used to calculate the genomic relationship matrix affect the estimate of genetic variances, covariances and correlations. The aim of this paper is to define a multi-population genomic relationship matrix to estimate current genetic variances within and genetic correlations between populations. The genomic relationship matrix containing two populations consists of four blocks, one block for population 1, one block for population 2, and two blocks for relationships between the populations. It is known, based on literature, that current genetic variances are estimated when the current population is used as base population of the relationship matrix. In this paper, we theoretically derived the properties of the genomic relationship matrix to estimate genetic correlations and validated it using simulations. When the scaling factors of the genomic relationship matrix fulfill the property, the genetic correlation is estimated even though estimated variance components are not necessarily related to the current population. When this property is not met, the correlation based on estimated variance components should be multiplied byto rescale the genetic correlation. In this study we present a genomic relationship matrix which directly results in current genetic variances as well as genetic correlations between populations.
Evaluation of the 3D fractal dimension as a marker of structural brain complexity in multiple-acquisition MRI
Authors: Krohn Stephan , Froeling Martijn , Leemans Alexander , Ostwald Dirk , Villoslada Pablo , Finke Carsten , Esteban Francisco J. 
Published: April 2017

AbstractFractal analysis represents a promising new approach to structural neuroimaging data, yet systematic evaluation of the fractal dimension (FD) as a marker of structural brain complexity is scarce. Here we present in-depth methodological assessment of FD estimation in structural brain MRI. On the computational side, we show that spatial scale optimization can significantly improve FD estimation accuracy, as suggested by simulation studies with known FD values. For empirical evaluation, we analyzed two recent open-access neuroimaging data sets (MASSIVE and Midnight Scan Club), stratified by fundamental image characteristics including registration, sequence weighting, spatial resolution, segmentation procedures, tissue type, and image complexity. Deviation analyses showed high repeated-acquisition stability of the FD estimates across both data sets, with differential deviation susceptibility according to image characteristics. While less frequently studied in the literature, FD estimation in T2-weighted images yielded robust outcomes. Importantly, we observed a significant impact of image registration on absolute FD estimates. Applying different registration schemes, we found that unbalanced registration induced i) repeated-measurement deviation clusters around the registration target, ii) strong bidirectional correlations among image analysis groups, and iii) spurious associations between the FD and an index of structural similarity, and these effects were strongly attenuated by reregistration in both data sets. Indeed, differences in FD between scans did not simply track differences in structure per se, suggesting that structural complexity and structural similarity represent distinct aspects of structural brain MRI. In conclusion, scale optimization can improve FD estimation accuracy, and empirical FD estimates are reliable yet sensitive to image characteristics.
HadoopCNV: A dynamic programming imputation algorithm to detect copy number variants from sequencing data
Authors: Yang Hui , Chen Gary , Lima Leandro , Fang Han , Jimenez Laura , Li Mingyao , Lyon Gholson J , He Max , Wang Kai 
Published: April 2017

ABSTRACTBACKGROUNDWhole-genome sequencing (WGS) data may be used to identify copy number variations (CNVs). Existing CNV detection methods mostly rely on read depth or alignment characteristics (paired-end distance and split reads) to infer gains/losses, while neglecting allelic intensity ratios and cannot quantify copy numbers. Additionally, most CNV callers are not scalable to handle a large number of WGS samples.METHODSTo facilitate large-scale and rapid CNV detection from WGS data, we developed a Dynamic Programming Imputation (DPI) based algorithm called HadoopCNV, which infers copy number changes through both allelic frequency and read depth information. Our implementation is built on the Hadoop framework, enabling multiple compute nodes to work in parallel.RESULTSCompared to two widely used tools – CNVnator and LUMPY, HadoopCNV has similar or better performance on both simulated data sets and real data on the NA12878 individual. Additionally, analysis on a 10-member pedigree showed that HadoopCNV has a Mendelian precision that is similar or better than other tools. Furthermore, HadoopCNV can accurately infer loss of heterozygosity (LOH), while other tools cannot. HadoopCNV requires only 1.6 hours for a human genome with 30X coverage, on a 32-node cluster, with a linear relationship between speed improvement and the number of nodes. We further developed a method to combine HadoopCNV and LUMPY result, and demonstrated that the combination resulted in better performance than any individual tools.CONCLUSIONSThe combination of high-resolution, allele-specific read depth from WGS data and Hadoop framework can result in efficient and accurate detection of CNVs.
Salt-inducible kinase 3 regulates the mammalian circadian clock by destabilizing PER2 protein
Authors: Hayasaka Naoto , Hirano Arisa , Miyoshi Yuka , Tokuda Isao T. , Yoshitane Hikari , Matsuda Junichiro , Fukada Yoshitaka 
Published: April 2017

AbstractSalt-inducible kinase 3 (SIK3) plays a crucial role in various aspects of metabolism. In the course of investigating metabolic defects inSik3-deficient mice (Sik3-/-), we observed that circadian rhythmicity of the metabolisms was phase-delayed.Sik3-/-mice also exhibited other circadian abnormalities, including lengthening of the period, impaired entrainment to the light-dark cycle, phase variation in locomotor activities, and aberrant physiological rhythms.Ex vivosuprachiasmatic nucleus slices fromSik3-/-mice exhibited destabilized and desynchronized molecular rhythms among individual neurons. In cultured cells,Sik3-knockdown resulted in abnormal bioluminescence rhythms. Expression levels of PER2, a clock protein, were elevated inSik3-knockdown cells but down-regulated inSik3-overexpressing cells, which could be attributed to a phosphorylation-dependent decrease in PER2 protein stability. This was further confirmed by PER2 accumulation in theSik3-/-fibroblasts and liver. Collectively, SIK3 plays key roles in circadian rhythms by facilitating phosphorylation-dependent PER2 destabilization, either directly or indirectly.
The fundamental principles of antibody repertoire architecture revealed by large-scale network analysis
Authors: Miho Enkelejda , Greifft Victor , Roškar Rok , Reddy Sai T. 
Published: April 2017

ABSTRACTThe antibody repertoire is a vast and diverse collection of B-cell receptors and antibodies that confer protection against a plethora of pathogens. The architecture of the antibody repertoire, defined by the network similarity landscape of its sequences, is unknown. Here, we established a novel high-performance computing platform to construct large-scale networks from high-throughput sequencing data (>100’000 unique antibodies), in order to uncover the architecture of antibody repertoires. We identified three fundamental principles of antibody repertoire architecture across B-cell development: reproducibility, robustness and redundancy. Reproducibility of network structure explains clonal expansion and selection. Robustness ensures a functional immune response even under extensive loss of clones (50%). Redundancy in mutational pathways suggests that there is a pre-programmed evolvability in antibody repertoires. Our analysis provides guidelines for a quantitative network analysis of antibody repertoires, which can be applied to other facets of adaptive immunity (e.g., T cell receptors), and may direct the construction of synthetic repertoires for biomedical applications.
Beyond the labeled line: variation in visual reference frames from intraparietal cortex to frontal eye fields and the superior colliculus
Authors: Caruso V. C. , Pages D. S. , Sommer M. A. , Groh J. M. 
Published: April 2017

ABSTRACTWe accurately perceive the visual scene despite moving our eyes ~3 times per second, an ability that requires incorporation of eye position and retinal information. We assessed how this neural computation unfolds across three interconnected structures: frontal eye fields (FEF), intraparietal cortex (LIP/MIP), and the superior colliculus (SC). Single unit activity was assessed in head-restrained monkeys performing visually-guided saccades from different initial fixations. As previously shown, the receptive fields of most LIP/MIP neurons shifted to novel positions on the retina for each eye position, and these locations were not clearly related to each other in either eye- or head-centered coordinates (hybrid coordinates). In contrast, the receptive fields of most SC neurons were stable in eye-centered coordinates. In FEF, visual signals were intermediate between those patterns: around 60% were eye-centered, whereas the remainder showed changes in receptive field location, boundaries, or responsiveness that rendered the response patterns hybrid or occasionally head-centered. These results suggest that FEF may act as a transitional step in an evolution of coordinates between LIP/MIP and SC. The persistence across cortical areas of hybrid representations that do not provide unequivocal location labels in a consistent reference frame has implications for how these representations must be read-out.New & NoteworthyHow we perceive the world as stable using mobile retinas is poorly understood. We compared the stability of visual receptive fields across different fixation positions in three visuomotor regions. Irregular changes in receptive field position were ubiquitous in intraparietal cortex, evident but less common in the frontal eye fields, and negligible in the superior colliculus (SC), where receptive fields shifted reliably across fixations. Only the SC provides a stable labelled-line code for stimuli across saccades.
The ethics conundrum in Recall by Genotype (RbG) research: Perspectives from birth cohort participants
Authors: Minion Joel T , Butcher Frances , Timpson Nicholas , Murtagh Madeleine J 
Published: April 2017

AbstractRecall by genotype (RbG) research involves recruiting participants on the basis of genetic variation. The recent use of this approach in the Avon Longitudinal Study of Parents and Children (ALSPAC) has presented an important challenge for ethical conduct: for example, to inform participants of their genetic information and to deviate from existing policies of non-disclosure of results and risk unanticipated harms, or mask the full structure of the study design and miss an opportunity to open a process of disclosure within genotype directed research. Here we report analysis of 53 semi-structured interviews conducted with young adult ALSPAC participants. We found that the deep trust and faith participants developed over their long-term relationship with the study, alongside a naturally limited knowledge of genetics and modest interest in reported research outcomes, meant most reported few immediate concerns about being recruited by genotype. Participants considered themselves part of the ALSPAC team and in this vein identified constructive concerns about being informed of RbG research in recruitment documents as well as what general results would be most valuable and informative. Our findings highlight the importance of solidarity, reciprocity and co-production in biobank/participant relations, especially in long-term birth cohort studies where relationships develop over a lifetime. We argue that strong trusting relationships between study and participant confer great responsibility on researchers regarding duty of care. We make recommendations for conducting RbG research in longitudinal studies beyond those already available in the literature for other study-types.Conflict of InterestThe authors declare no conflict of interest.
The effect of sales promotions on consumers’ organic food response
Authors: Liang Austin Rong-Da , Yang Wan , Chen Dun-Ji , Chung Yu-Fang 
Published: April 2017

PurposeOwing to the wave of consumers concern about food quality, the organic food market has grown rapidly. However, how organic food promotions outweigh the negative impacts of high prices has become a pressing issue scholars need to discuss. Hence, with the value perspective as the basis, the purpose of this paper is to attempt to understand whether or not organic food consumers have preferences for specific promotional programs as opposed to other promotional programs.Design/methodology/approachThe two-stage study design was adopted to explore these issues. In the first stage, 225 copies of promotional program documents were collected, and middle-ranking and high-ranking supervisors from seven organic food distributors were interviewed. According to the value perspective, the promotional programs were divided into four types: discount category, member category, free giveaway category, and limited time offer category, which were used to develop the questionnaire questions. In the second stage, 1,017 copies of valid questionnaires were recovered.FindingsThe logistic regression analysis was adopted to discuss the impact of the various promotional program actions on consumers’ choices. The empirical results indicate that the consumers preferred the programs in the discount category and the free giveaway category, while the programs in the member category and limited time offer category reduced the purchase intention.Originality/valueThe stringent qualitative and quantitative design in this study shall serve as a reference for follow-up research. The important implications of the operators’ promotion practices are covered in the discussion.