bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are sex and history of pruritic skin conditions factors which affect the phenomenon of visually evoked itch? An exploratory study
Authors: Lloyd Donna M. , Dodd Rebecca , Higgins Caroline , Burke Melanie R. , McGlone Francis 
Published: November 2017

Introduction:
We have previously shown that sensations of itch and the scratch response can be evoked using itch-related images. However, we did not determine whether individual differences in a person’s experience of itch could moderate this effect. This exploratory study aimed to determine whether sex or a history of pruritic skin conditions (PSCs) could influence the effects of visually evoked itch and scratch.

Methods:
Forty-one participants (19 males; 16 with a history of PSCs) viewed static images that could either be itch or nonitch related. These were further separated by picture type: “skin contact” (ants crawling on the hand vs. a butterfly on the finger); “skin response” (scratching an insect bite vs. washing the hands); “skin condition” (psoriasis vs. freckles) or “context only” (insects vs. birds). Images were rated using a 10-point scale by answering: “How itchy do you feel?” (Self-rating) and “How itchy do you think the person in the picture feels?” (Other-rating). Frequency and location of scratching was also recorded.

Results:
The highest itch scores were to itch-related skin contact pictures. Females gave higher itch ratings than males, and people with a history of PSCs gave higher itch ratings when viewing images of people scratching. There was no correlation between itch ratings and scratch response, and no relationship between body site viewed and location of scratching.

Discussion:
There is a heightened response to itch-related cues in females and those with PSCs, indicating a more centrally mediated pathway bringing subconscious itch sensations into conscious awareness in these populations. These findings could influence personalized treatment interventions aimed at reducing awareness of itch sensations in susceptible individuals.
Neural Breathing Pattern and Patient-Ventilator Interaction During Neurally Adjusted Ventilatory Assist and Conventional Ventilation in Newborns
Authors: Mally Pradeep V. , Beck Jennifer , Sinderby Christer , Caprio Martha , Bailey Sean M. 
Published: November 2017

Objective:
To compare neurally adjusted ventilatory assist and conventional ventilation on patient-ventilator interaction and neural breathing patterns, with a focus on central apnea in preterm infants.

Design:
Prospective, observational cross-over study of intubated and ventilated newborns. Data were collected while infants were successively ventilated with three different ventilator conditions (30 min each period): 1) synchronized intermittent mandatory ventilation (SIMV) combined with pressure support at the clinically prescribed, SIMV with baseline settings (SIMVBL), 2) neurally adjusted ventilatory assist, 3) same as SIMVBL, but with an adjustment of the inspiratory time of the mandatory breaths (SIMV with adjusted settings [SIMVADJ]) using feedback from the electrical activity of the diaphragm).

Setting:
Regional perinatal center neonatal ICU.

Patients:
Neonates admitted in the neonatal ICU requiring invasive mechanical ventilation.

Measurements and Main Results:
Twenty-three infants were studied, with median (range) gestational age at birth 27 weeks (24–41 wk), birth weight 780 g (490–3,610 g), and 7 days old (1–87 d old). Patient ventilator asynchrony, as quantified by the NeuroSync index, was lower during neurally adjusted ventilatory assist (18.3% ± 6.3%) compared with SIMVBL (46.5% ±11.7%; p < 0.05) and SIMVADJ (45.8% ± 9.4%; p < 0.05). There were no significant differences in neural breathing parameters, or vital signs, except for the end-expiratory electrical activity of the diaphragm, which was lower during neurally adjusted ventilatory assist. Central apnea, defined as a flat electrical activity of the diaphragm more than 5 seconds, was significantly reduced during neurally adjusted ventilatory assist compared with both SIMV periods. These results were comparable for term and preterm infants.

Conclusions:
Patient-ventilator interaction appears to be improved with neurally adjusted ventilatory assist. Analysis of the neural breathing pattern revealed a reduction in central apnea during neurally adjusted ventilatory assist use.
Procedural Training and Assessment for Pediatric Emergency Medicine Physicians Within the United States and Canada
Authors: Burns Rebekah A. , Uspal Neil G. 
Published: November 2017

Objectives
The aims of this study were to determine current practices in procedural training and skill assessment for attending physicians working in pediatric emergency departments within the United States and Canada and identify barriers to providing training and assessment.

Methods
This was a cross-sectional survey study. Members of the pediatric emergency medicine fellowship program directors and associate program directors Listserv were invited to participate in an anonymous survey about attending physician training and assessment practices for 9 specific procedures and barriers to training and assessment.

Results
Eighty-two (56.2%) of 146 recipients responded, with 79 surveys fully completed; 58.5% of responders report that their division offers procedural training, whereas 14.6% report assessment of procedural skills. The most common procedure for which participants report training and assessment is orotracheal intubation (53.1% and 7.5%, respectively), with training rates for other procedures ranging from 2.5% to 43.0%. Most sites that report training use simulation in some form for education. For assessment, simulation is used almost exclusively. Cost (50.6%), lack of faculty interest (36.7%), and lack of standardized guidelines (36.7%) are the most common barriers to training. Lack of standardized guidelines (51.9%), cost (43.0%), and lack of faculty interest (38.0%) are the most common barriers for assessment.

Conclusions
Although pediatric emergency medicine physicians may be required to perform emergent procedures, opportunities to receive training and assessment in these procedures are limited. Simulation and other educational modalities are being used to provide skill training and assessment, but cost and lack of resources, standardized protocols, and faculty interest are barriers to the implementation of training and assessment programs.
Innovative Methods for Designing Actionable Program Evaluation
Authors: Nesbit Brandon , Hertz Marci , Thigpen Sally , Castellanos Ted , Brown Michelle , Porter Jamila , Williams Amber 
Published: November 2017

Context:
For most programs, whether funded through governmental agencies or nongovernmental organizations, demonstrating the impact of implemented activities is vital to ensuring continued funding and support.

Objective:
Program evaluation is a critical tool that serves the dual purpose of describing impact and identifying areas for program improvement. From a funder's perspective, describing the individual and collective impact of state-based programs can be challenging due to variations in strategies being implemented and types of data being collected.

Design:
A case study was used to describe the actionable, mixed-methods evaluation of the Core Violence and Injury Prevention Program (Core VIPP), including how the evaluation design and approach shifted to address evolving challenges faced by award recipients over time. Particular emphasis is given to innovative methods for collecting, analyzing, and disseminating data for key state and federal stakeholders.

Results:
The results of the Core VIPP evaluation showed how this funding played a vital role in building injury and violence prevention capacity in state health departments, leading to a decrease in both intermediate and long-term outcomes.

Conclusions:
The lessons learned through the mixed-method evaluation of the Core VIPP informed the structure of the subsequent funding cycle (Core SVIPP) to include more prescriptive requirements for evidence-based implementation and a state support team structure for delivery of training and technical assistance.
Rehabilitation Outcomes in Spinal Abscess Patients With and Without a History of Intravenous Substance Abuse
Authors: Raut Namrata , Nagar Vittal R. , Springer Joe E. , Sawaki Lumy , Salles Sara S. 
Published: November 2017

Objective
The aim of the study was to compare functional outcomes of acute inpatient rehabilitation for spinal epidural abscess patients with and without history of intravenous substance abuse.

Design
This is a retrospective case series study in freestanding rehabilitation hospital.

Methods
Charts of 28 spinal epidural abscess patients admitted from January 2012 to September 2015: 13 with intravenous substance abuse and 15 without intravenous substance abuse were reviewed. Both groups received standard-of-care rehabilitation. Statistical analyses of Functional Independence Measure scores were conducted using individual 2 (substance use) × 2 (rehabilitation status) repeated measures analysis of variance. Functional outcomes were defined by total Functional Independence Measure scores as well as motor and cognitive subsets. Length of stay and morphine equivalents were also compared.

Results
There were no significant differences between the two groups. There was a significant main effect of treatment on total Functional Independence Measure scores (P < 0.001), Functional Independence Measure motor scores (P < 0.001), and Functional Independence Measure cognitive scores (P < 0.01) from admission to discharge. Subsequent Student's t tests revealed that the scores of both groups significantly improved on all Functional Independence Measure components. There were no group differences on length of stay and morphine equivalents at discharge.

Conclusions
Acute inpatient rehabilitation can effectively improve functional outcomes in spinal epidural abscess patients with or without intravenous substance abuse, even though these two patient groups can vary in clinical factors.
Preoperative Exposure of Sigmoid Sinus Trajectory in Posterolateral Cranial Base Approaches Using a New Landmark Through a Neurosurgical Perspective
Authors: Doğan Ihsan , Özgüral Onur , Eroğlu Ümit , Al-Beyati Eyyub S. M. , Kilinç Cemil M. , Cömert Ayhan , Uğur Hasan Çağlar 
Published: November 2017

Abstract
The location of burr holes in posterolateral cranial base approaches should be appropriate to provide an adequate operative field, and surgical freedom is crucial for bone window opening. The aim of this study was to search for more convenient and easily detectable landmarks in comparison with current landmarks in posterolateral cranial base surgery. Twenty 3-dimensional reconstructed head and neck computed tomography angiography images (group 1) and 20 cadaver heads (group 2) were evaluated. An imaginary line connecting the angle of the mandible and the mastoid tip was extended upward. A second line passing through the lateral edge of the zygomatic arch was also extended posteriorly. The authors examined if the first line met with the sigmoid sinus throughout its course and determined the location of the intersection point of these 2 lines relative to the sigmoid-transverse sinus junction. The intersection point did not correspond to the sinus region in 3 images from group 1 and 4 specimens from group 2. The matching of the mandibula-mastoid line trajectory with the sigmoid sinus course was unacceptable in 4 images and 5 cadavers. For venous anatomy preservation and anatomic skull base fossa orientation during posterolateral cranial base approaches, upward extension of the mandibula-mastoid line can be a proper landmark for surgical planning in this region. The authors’ proposed superficial anatomical line and intersection point over the skull could be used as a reliable indicator for the external projection of the sigmoid sinus and an appropriate initial burr-hole location.
BURRITO: An interactive multi-omic tool for visualizing taxa-function relationships in microbiome data
Authors: McNally Colin P , Eng Alexander , Noecker Cecilia , Gagne-Maynard William C , Borenstein Elhanan 
Published: November 2017

AbstractThe abundance of both taxonomic groups and gene categories in microbiome samples can now be easily assayed via various sequencing technologies, and visualized using a variety of software tools. However, the assemblage of taxa in the microbiome and its gene content are clearly linked, and tools for visualizing the relationship between these two facets of microbiome composition and for facilitating exploratory analysis of their co-variation are lacking. Here we introduce BURRITO, a web tool for interactive visualization of microbiome multi-omic data with paired taxonomic and functional information. BURRITO simultaneously visualizes the taxonomic and functional compositions of multiple samples and dynamically highlights relationships between taxa and functions to capture the underlying structure of these data. Users can browse for taxa and functions of interest and interactively explore the share of each function attributed to each taxon across samples. BURRITO supports multiple input formats for taxonomic and metagenomic data, allows adjustment of data granularity, and can export generated visualizations as static publication-ready formatted figures. In this paper, we describe the functionality of BURRITO, and provide illustrative examples of its utility for visualizing various trends in the relationship between the composition of taxa and functions in complex microbiomes.
Novel bacterial lineages associated with boreal moss species
Authors: Holland-Moritz Hannah , Stuart Julia , Lewis Lily R. , Miller Samantha , Mack Michelle C. , McDaniel Stuart F. , Fierer Noah 
Published: November 2017

AbstractMosses are critical components of boreal ecosystems where they typically account for a large proportion of net primary productivity and harbor diverse bacterial communities that can be the major source of biologically-fixed nitrogen in these ecosystems. Despite their ecological importance, we have limited understanding of how microbial communities vary across boreal moss species and the extent to which local environmental conditions may influence the composition of these bacterial communities. We used marker gene sequencing to analyze bacterial communities associated with eight boreal moss species collected near Fairbanks, AK USA. We found that host identity was more important than site in determining bacterial community composition and that mosses harbor diverse lineages of potential N2- fixers as well as an abundance of novel taxa assigned to understudied bacterial phyla (including candidate phylum WPS-2). We performed shotgun metagenomic sequencing to assemble genomes from the WPS-2 candidate phylum and found that these moss-associated bacteria are likely anoxygenic phototrophs capable of carbon fixation via RuBisCo with an ability to utilize byproducts of photorespiration from hosts via a glyoxylate shunt. These results give new insights into the metabolic capabilities of understudied bacterial lineages that associate with mosses and the importance of plant hosts in shaping their microbiomes.
No changes in parieto-occipital alpha during neural phase locking to visual quasi-periodic theta-, alpha-, and beta-band stimulation
Authors: Keitel Christian , Benwell Christopher SY , Thut Gregor , Gross Joachim 
Published: November 2017

ABSTRACTRecent studies have probed the role of the parieto-occipital alpha rhythm (8 – 12 Hz) in human visual perception through attempts to drive its neural generators. To that end, paradigms have used high-intensity strictly-periodic visual stimulation that created strong predictions about future stimulus occurrences and repeatedly demonstrated perceptual consequences in line with an entrainment of parieto-occipital alpha. Our study, in turn, examined the case of alpha entrainment by non-predictive low-intensity quasi-periodic visual stimulation within theta-(4 – 7 Hz), alpha-(8 – 13 Hz) and beta (14 – 20 Hz) frequency bands, i.e. a class of stimuli that resemble the temporal characteristics of naturally occurring visual input more closely. We have previously reported substantial neural phase-locking in EEG recording during all three stimulation conditions. Here, we studied to what extent this phase-locking reflected an entrainment of intrinsic alpha rhythms in the same dataset. Specifically, we tested whether quasi-periodic visual stimulation affected several properties of parieto-occipital alpha generators. Speaking against an entrainment of intrinsic alpha rhythms by non-predictive low-intensity quasi-periodic visual stimulation, we found none of these properties to show differences between stimulation frequency bands. In particular, alpha band generators did not show increased sensitivity to alpha band stimulation and Bayesian inference corroborated evidence against an influence of stimulation frequency. Our results set boundary conditions for when and how to expect effects of entrainment of alpha generators and suggest that the parieto-occipital alpha rhythm may be more inert to external influences than previously thought.
ChIPdig: a comprehensive user-friendly tool for mining multi-sample ChIP-seq data
Authors: Esse Ruben , Grishok Alla 
Published: November 2017

AbstractBackgroundIn recent years, epigenetic research has enjoyed explosive growth as high-throughput sequencing technologies become more accessible and affordable. However, this advancement has not been matched with similar progress in data analysis capabilities from the perspective of experimental biologists not versed in bioinformatic languages. For instance, chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is at present widely used to identify genomic loci of transcription factor binding and histone modifications. Basic ChIP-seq data analysis, including read mapping and peak calling, can be accomplished through several well-established tools, but more sophisticated analyzes aimed at comparing data derived from different conditions or experimental designs constitute a significant bottleneck. We reason that the implementation of a single comprehensive ChIP-seq analysis pipeline could be beneficial for many experimental (wet lab) researchers who would like to generate genomic data.ResultsHere we present ChIPdig, a stand-alone application with adjustable parameters designed to allow researchers to perform several analyzes, namely read mapping to a reference genome, peak calling, annotation of regions based on reference coordinates (e.g. transcription start and termination sites, exons, introns, 5′ UTRs and 3′ UTRs), and generation of heatmaps and metaplots for visualizing
coverage. Importantly, ChIPdig accepts multiple ChIP-seq datasets as input, allowing genome-wide differential enrichment analysis in regions of interest to be performed. ChIPdig is written in R and enables access to several existing and highly utilized packages through a simple user interface powered by the Shiny package. Here, we illustrate the utility and user-friendly features of ChIPdig by analyzing H3K36me3 and H3K4me3 ChIP-seq profiles generated by the modENCODE project as an example.ConclusionsChIPdig offers a comprehensive and user-friendly pipeline for analysis of multiple sets of ChIP-seq data by both experimental and computational researchers. It is open source and available at https://github.com/rmesse/ChIPdig.
Behavioral and neural representations of spatial directions across words, schemas, and images
Authors: Weisberg Steven M. , Marchette Steven A. , Chatterjee Anjan 
Published: November 2017

AbstractModern spatial navigation requires fluency with multiple representational formats, including visual scenes, signs, and words. These formats convey different information. Visual scenes are rich and specific, but contain extraneous details. Arrows, as an example of signs, are schematic representations in which the extraneous details are eliminated, but analog spatial properties are preserved. Words eliminate all spatial information and convey spatial directions in a purely abstract form. How does the human brain compute spatial directions within and across these formats? To investigate this question, we conducted two experiments on men and women: a behavioral study that was preregistered, and a neuroimaging study using multivoxel pattern analysis of fMRI data to uncover similarities and differences among representational formats. Participants in the behavioral study viewed spatial directions presented as images, schemas, or words (e.g., “left”), and responded to each trial, indicating whether the spatial direction was the same or different as the one viewed previously. They responded more quickly to schemas and words than images, despite the visual complexity of stimuli being matched. Participants in the fMRI study performed the same task, but responded only to occasional catch trials. Spatial directions in images were decodable in the intraparietal sulcus (IPS) bilaterally, but were not in schemas and words. Spatial directions were also decodable between all three formats. These results suggest that IPS plays a role in calculating spatial directions in visual scenes, but this neural circuitry may be bypassed when the spatial directions are presented as schemas or words.Significance StatementHuman navigators encounter spatial directions in various formats: words (“turn left”), schematic signs (an arrow showing a left turn), and visual scenes (a road turning left). The brain must transform these spatial directions into a plan for action. Here, we investigate similarities and differences between neural representations of these formats. We found that bilateral intraparietal sulci represents spatial directions in visual scenes and across the three formats. We also found that participants respond quickest to schemas, then words, then images, suggesting that spatial directions in abstract formats are easier to interpret than concrete formats. These results support a model of spatial direction interpretation in which spatial directions are either computed for real world action, or computed for efficient visual comparison.
Exploring Applications of Crowdsourcing to Cryo-EM
Authors: Bruggemann Jacob , Lander Gabriel C. , Su Andrew I. 
Published: November 2017

AbstractExtraction of particles from cryo-electron microscopy (cryo-EM) micrographs is a crucial step in processing single-particle datasets. Although algorithms have been developed for automatic particle picking, these algorithms generally rely on two-dimensional templates for particle identification, which may exhibit biases that can propagate artifacts through the reconstruction pipeline. Manual picking is viewed as a gold-standard solution for particle selection, but it is too time-consuming to perform on data sets of thousands of images. In recent years, crowdsourcing has proven effective at leveraging the open web to manually curate datasets. In particular, citizen science projects such as Galaxy Zoo have shown the power of appealing to users' scientific interests to process enormous amounts of data. To this end, we explored the possible applications of crowdsourcing in cryo-EM particle picking, presenting a variety of novel experiments including the production of a fully annotated particle set from untrained citizen scientists. We show the possibilities and limitations of crowdsourcing particle selection tasks, and explore further options for crowdsourcing cryo-EM data processing.