bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Healthy Brain Network Serial Scanning Initiative: a resource for evaluating inter-individual differences and their reliabilities across scan conditions and sessions
Authors: O'Connor David , Potler Natan Vega , Kovacs Meagan , Xu Ting , Ai Lei , Pellman John , Vanderwal Tamara , Parra Lucas C. , Cohen Samantha , Ghosh Satrajit , Escalera Jasmine , Grant-Villegas Natalie , Osman Yael , Bui Anastasia , Craddock R. Cameron , Milham Michael P. 
Published: March 2017

Abstract
Background: Although typically measured during the resting state, a growing literature is illustrating the ability to map intrinsic connectivity with functional MRI during task and naturalistic viewing conditions. These paradigms are drawing excitement due to their greater tolerability in clinical and developing populations and because they enable a wider range of analyses (e.g., inter-subject correlations). To be clinically useful, the test-retest reliability of connectivity measured during these paradigms needs to be established. This resource provides data for evaluating test-retest reliability for full-brain connectivity patterns detected during each of four scan conditions that differ with respect to level of engagement (rest, abstract animations, movie clips, flanker task). Data are provided for 13 participants, each scanned in 12 sessions with 10 minutes for each scan of the four conditions. Diffusion kurtosis imaging data was also obtained at each session.
Findings: Technical validation and demonstrative reliability analyses were carried out at the connection-level using the Intraclass Correlation Coefficient and at network-level representations of the data using the Image Intraclass Correlation Coefficient. Variation in intrinsic functional connectivity across sessions was generally found to be greater than that attributable to scan condition. Between-condition reliability was generally high, particularly for the frontoparietal and default networks. Between-session reliabilities obtained separately for the different scan conditions were comparable, though notably lower than between-condition reliabilities.
Conclusions: This resource provides a test-bed for quantifying the reliability of connectivity indices across subjects, conditions and time. The resource can be used to compare and optimize different frameworks for measuring connectivity and data collection parameters such as scan length. Additionally, investigators can explore the unique perspectives of the brain's functional architecture offered by each of the scan conditions.
de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer
Authors: Istace Benjamin , Friedrich Anne , d'Agata Léo , Faye Sébastien , Payen Emilie , Beluche Odette , Caradec Claudia , Davidas Sabrina , Cruaud Corinne , Liti Gianni , Lemainque Arnaud , Engelen Stefan , Wincker Patrick , Schacherer Joseph , Aury Jean-Marc 
Published: March 2017

Abstract
Background: Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from small genomes in a matter of seconds. The Oxford Nanopore technology is truly disruptive; it has the potential to revolutionize genomic applications due to its portability, low cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome. Combined with existing assembler algorithms, near complete genome assemblies can be generated and comprehensive population genomic analyses can be performed. Results: Here, we resequenced the genome of the Saccharomyces cerevisiae S288C strain to evaluate the performance of nanopore-only assemblers. Then we de novo sequenced and assembled the genomes of 21 isolates representative of the S. cerevisiae genetic diversity using the MinION platform. The contiguity of our assemblies was 14 times higher than the Illumina-only assemblies and we obtained one or two long contigs for 65 % of the chromosomes. This high contiguity allowed us to accurately detect large structural variations across the 21 studied genomes. Conclusion: Because of the high completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect structural variants that are generally missed using a short-read sequencing strategy. Our analyses show that the Oxford Nanopore technology is already usable for de novo sequencing and assembly; however, non-random errors in homopolymers require polishing the consensus using an alternate sequencing technology.
drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes
Authors: Lin Hsin-Hung , Liao Yu-Chieh 
Published: March 2017

Abstract
Background: Virus discovery using high-throughput next-generation sequencing has become more commonplace. However, although analysis of deep next-generation sequencing data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data.
Results: This manuscript presents a pipeline, drVM (detect and reconstruct known viral genomes from metagenomes), for rapid viral read identification, genus-level read partition, read normalization, de novo assembly, sequence annotation, and coverage profiling. The first two procedures and sequence annotation rely on known viral genomes as a reference database. drVM was validated via the analysis of over 300 sequencing runs generated by Illumina and Ion Torrent platforms to provide complete viral genome assemblies for a variety of virus types including DNA viruses, RNA viruses, and retroviruses. drVM is available for free download at: https://sourceforge.net/projects/sb2nhri/files/drVM/ and is also assembled as a Docker container, an Amazon machine image, and a virtual machine to facilitate seamless deployment.
Conclusions: drVM was compared with other viral detection tools to demonstrate its merits in terms of viral genome completeness and reduced computation time. This substantiates the platform's potential to produce prompt and accurate viral genome sequences from clinical samples.
Automated identification of implausible values in growth data from pediatric electronic health records
Authors: Daymont Carrie , Ross Michelle E , Russell Localio A , Fiks Alexander G , Wasserman Richard C , Grundmeier Robert W 
Published: March 2017

Abstract

Objective
Large electronic health record (EHR) datasets are increasingly used to facilitate research on growth, but measurement and recording errors can lead to biased results. We developed and tested an automated method for identifying implausible values in pediatric EHR growth data.

Materials and Methods
Using deidentified data from 46 primary care sites, we developed an algorithm to identify weight and height values that should be excluded from analysis, including implausible values and values that were recorded repeatedly without remeasurement. The foundation of the algorithm is a comparison of each measurement, expressed as a standard deviation score, with a weighted moving average of a child’s other measurements. We evaluated the performance of the algorithm by (1) comparing its results with the judgment of physician reviewers for a stratified random selection of 400 measurements and (2) evaluating its accuracy in a dataset with simulated errors.

Results
Of 2 000 595 growth measurements from 280 610 patients 1 to 21 years old, 3.8% of weight and 4.5% of height values were identified as implausible or excluded for other reasons. The proportion excluded varied widely by primary care site. The automated method had a sensitivity of 97% (95% confidence interval [CI], 94–99%) and a specificity of 90% (95% CI, 85–94%) for identifying implausible values compared to physician judgment, and identified 95% (weight) and 98% (height) of simulated errors.

Discussion and Conclusion
This automated, flexible, and validated method for preparing large datasets will facilitate the use of pediatric EHR growth datasets for research.
Surgical Decision Making From Image-Based Biophysical Modeling of Glioblastoma: Not Ready for Primetime
Authors: Amelot Aymeric , Deroulers Christophe , Badoual Mathilde , Polivka Marc , Adle-Biassette Homa , Houdart Emmanuel , Carpentier Antoine F. , Froelich Sebastien , Mandonnet Emmanuel 
Published: March 2017

Abstract

BACKGROUND: Biophysical modeling of glioma is gaining more interest for clinical practice. The most popular model describes aggressivity of tumor cells by two parameters: net proliferation rate (ρ) and propensity to migrate (D). The ratio ρ/D, which can be estimated from a single preoperative magnetic resonance imaging (MRI), characterizes tumor invasiveness profile (high ρ/D: nodular; low ρ/D: diffuse). A recent study reported, from a large series of glioblastoma multiforme (GBM) patients, that gross total resection (GTR) would improve survival only in patients with nodular tumors.

OBJECTIVE: To replicate these results, that is to verify that benefit of GTR would be only observed for nodular tumors.

METHODS: Between 2005 and 2012, we considered 234 GBM patients with pre- and postoperative MRI. Stereotactic biopsy (BST) was performed in 109 patients. Extent of resection was assessed on postoperative MRI and classified as GTR or partial resection (PR). Invasiveness ρ/D was estimated from the preoperative tumor volumes on T1-Gadolinium-enhanced and fluid-attenuated inversion recovery sequences.

RESULTS: We demonstrate that patients with diffuse GBM (low ρ/D), as well as more nodular (mid and high ρ/D) GBM, presented significant survival benefit from GTR over PR/BST (P < .001).

CONCLUSION: Whatever the degree of tumor invasiveness, as estimated from MRI-driven biophysical modeling, GTR improves survival of GBM patients, compared to PR or BST. This conflicting result should motivate further studies.
Anatomic Features of Paraclinoid Aneurysms: Computed Tomography Angiography Study of 144 Aneurysms in 136 Consecutive Patients
Authors: Rafiei Ahmadreza , Hafez Ahmad , Jahromi Behnam Rezai , Kivisaari Riku , Canato Bruno , Choque Joham , Colasanti Roberto , Fransua Sharafeddin , Lehto Hanna , Andrade-Barazarte Hugo , Hernesniemi Juha 
Published: March 2017

Abstract

BACKGROUND
Paraclinoid aneurysms are among the most challenging aneurysms to treat. Computed tomography (CT) angiography helps in evaluating the radiological characteristics of these aneurysms next to bony structures.

OBJECTIVE
To present the CT angiography characteristics of paraclinoid aneurysms in order to better understand such pathology.

METHODS
The study examined CT angiography-based anatomical characteristics obtained retrospectively from 136 patients with 144 paraclinoid aneurysms selected from single-defined catchment populations in Finland. We examined the diameters of the parent artery (internal carotid artery), the location of the aneurysm, its dimensions (width, height, neck), and aneurysm wall irregularity.

RESULTS
We analyzed 144 paraclinoid aneurysms in 136 patients admitted to the hospital during 2000-2014. Multivariable analysis reveals that rupture aneurysms have the following radiological features: aneurysm larger than 5 mm in diameter (P = .006), irregular wall (P = .046), superior location, larger aspect ratio (P = .039), and neck wider than parent artery (P < .001).

CONCLUSION
Smaller diameter of the internal carotid artery and superior location, as well as a large and irregular aneurysm wall, are radiological characteristics of ruptured paraclinoid aneurysms, which CT angiography can measure easily.
Effect of Body Mass Index on Venous Sinus Pressures in Idiopathic Intracranial Hypertension Patients Before and After Endovascular Stenting
Authors: Raper Daniel M S , Ding Dale , Buell Thomas J , Crowley R Webster , Starke Robert M , Liu Kenneth C 
Published: March 2017

Abstract

BACKGROUND
Elevated body mass index (BMI) has been correlated with worse outcomes after treatment for idiopathic intracranial hypertension (IIH). Venous sinus stenting (VSS) has emerged as a safe and effective treatment for a subset of patients with IIH and evidence of venous sinus stenosis. However, the association between BMI and the efficacy of VSS remains poorly characterized.

OBJECTIVE
To determine, in a retrospective cohort study, the effect of BMI on preoperative mean intracranial venous pressure (MVP) and post-VSS outcomes.

METHODS
We performed a retrospective evaluation of a prospectively collected database of patients with IIH and intracranial venous sinus stenosis who underwent VSS. Patient demographics and treatment factors, including pre- and postprocedural trans-stenosis pressure gradients, were analyzed to identify the relationship between BMI and outcomes after VSS.

RESULTS
Increasing BMI was significantly correlated with higher maximum MVP (P = .013) and higher trans-stenosis pressure gradient (P = .043) prior to treatment. The degrees of improvement in maximum MVP and pressure gradient after VSS were greatest for obese and morbidly obese patients (BMI > 30 kg/m2). Maximum poststent MVP, clinical outcomes, and stent-adjacent stenosis requiring retreatment after VSS were not significantly associated with BMI.

CONCLUSION
We provide direct evidence for a positive correlation between BMI and intracranial venous pressure in patients with IIH. VSS affords a significantly greater amelioration of intracranial venous hypertension and stenosis for IIH patients with higher BMIs. As such, obesity should not be a deterrent for the use of VSS in the management of IIH.
A Rapid Epidemiological Tool to Measure the Burden of Norovirus Infection and Disease in Resource-Limited Settings
Authors: Olson Daniel , Lamb Molly M. , Lopez Maria Renee , Paniagua-Avila M. Alejandra , Zacarias Alma , Samayoa-Reyes Gabriela , Cordon-Rosales Celia , Asturias Edwin J. 
Published: March 2017

Abstract

Background
Rapid, cost-effective tools are needed to estimate the disease burden of acute gastroenteritis (AGE) and norovirus (NoV) in resource-limited settings.

Methods
Households with children (6 weeks–17 years) in rural Guatemala were randomly enrolled into 2 parallel AGE surveillance systems: (1) a prospective cohort, which included an enrollment visit followed by 1 year of prospective observation using a smartphone-based weekly symptom diary; and (2) 2 sequential cross-sectional rapid active sampling (RAS) surveys. Norovirus testing was performed during enrollment (all subjects) and for prospective AGE episodes (prospective cohort only).

Results
The prospective cohort enrolled 207 households (469 children) from April to September 2015 followed by 471 person-years of observation; RAS survey 1 enrolled 210 households (402 children) during October to November 2015, and RAS survey 2 enrolled 210 separate households (368 children) during January to February 2016. The prospective cohort detected a NoV+ AGE prevalence of 11% and a population-attributable fraction (PAF) of −1.6% at enrollment, followed by an incidence of 1.4 episodes/100 person-years. Rapid active sampling surveys 1 and 2 identified a NoV+ AGE prevalence of 14%–21% and a PAF of 3.2%–12.4%.

Conclusions
Rapid active sampling surveys were practical and identified more cases of NoV infection and disease compared with a parallel prospective cohort in rural Guatemala.
Evaluating the Discriminant Validity of the Pediatric Evaluation of Disability Inventory: Computer Adaptive Test in Children With Cerebral Palsy
Authors: Shore Benjamin J. , Allar Benjamin G. , Miller Patricia E. , Matheney Travis H. , Snyder Brian D. , Fragala-Pinkham Maria A. 
Published: March 2017

AbstractBackground. The Pediatric Evaluation of Disability Inventory-Computer Adaptive Test (PEDI-CAT) is a new clinical assessment for children and youth from birth through 20 years of age.Objective. To determine the discriminant validity of the PEDI-CAT according to the Gross Motor Function Classification System (GMFCS) and Manual Ability Classification System (MACS) in children with cerebral palsy (CP).Design. A prospective convenience cross-sectional sample of 101 school-age children with CP was stratified by GMFCS level.Methods. Participants were excluded if they underwent recent surgery (&lt;6 months). Receiver operating characteristics curve analysis was used to quantify the discriminant validity of the PEDI-CAT domains to distinguish the level of independence in fine and gross motor function. General linear modeling was used to assess discriminant ability across all GMFCS and MACS levels.Results. Mean age was 11 years, 11 months (SD 3.7). Mobility and Daily Activities domains exhibited excellent discriminant validity distinguishing between ambulatory and nonambulatory participants [area under the curve (AUC) = 0.98 and 0.97, respectively] and the Daily Activities domain exhibited excellent discriminant validity distinguishing between independent and dependent hand function (AUC = 0.93). All PEDI-CAT domains were able to discriminate between ambulatory (GMFCS levels I–III) or nonambulatory (GMFCS levels IV–V) as well as manually independent (MACS levels I–II) or manually dependent functional levels (MACS levels III–V) (P &lt; .001).Limitations. Our convenience cross-sectional sample included school-age children with primarily Caucasian, middle-income parents and may not be representative of other cultural, socioeconomic backgrounds. Not all participants had a MACS level assigned, however, no differences were found in PEDI-CAT scores between those with and without MACS scores.Conclusions. These results demonstrate that the PEDI-CAT is a valid outcome instrument for measuring functional abilities in children with CP, able to differentiate across fine and gross motor functional levels.
Proinflammatory Cytokines IL-1β and TNF-α Influence Human Annulus Cell Signaling Cues for Neurite Growth
Authors: Gruber Helen E. , Jones Brittany , Marrero Emilio , Hanley Edward N. 
Published: March 2017

Study Design.
Institutional review board–approved research using human annulus cells cocultured with F11 nerve cells.

Objective.
To perform functional, kinetic assays of neurite dynamics and media neurotrophin measurements to test whether proinflammatory cytokines influence annulus cells’ signaling cues for neurite growth/repulsion.

Summary of Background Data.
Nerves grow in response to signaling molecules called neurotrophins, which disc cells produce (e.g., brain-derived neurotrophic factor [BDNF], glial cell line–derived neurotrophic factor [GDNF], and neurotrophin 3 [NT3]) and which influence neuron survival, differentiation, and migration. How proinflammatory cytokines influence disc signaling cues for neurite growth/repulsion is poorly understood.

Methods.
Studies used our previous model of 4-day human annulus cell-F11 nerve cell coculture to assess effects of added proinflammatory cytokines interleukin 1 beta (IL-1β; 102 pmol/L) or tumor necrosis factor alpha (TNF-α) (103 pmol/L). Annulus cells were cultured from 6 Thompson grade I, 9 grade II, 8 grade III, 11 grade IV, and 7 grade V discs. Neurite lengths were measured following control conditions or with added IL-1β or TNF-α, and conditioned media assayed with RayBiotech Growth Factor Arrays. Standard statistical methods used analysis of variance and Spearman correlation coefficient testing associations of neurite length with neurotrophin levels.

Results.
IL-1-β or TNF-α significantly increased neurite lengths (P < 0.001) and BDNF, NT3, and GDNF media levels (P ≤ 0.01) versus controls. Significant positive correlations were present between media neurotrophin levels for BDNF, NT3, and GDNF and neurite lengths under control conditions, following addition of IL-1β, and following addition of TNF-α. Novel data showed production of the neurotrophin amphiregulin.

Conclusion.

In vitro data supported the hypothesis that nerve-disc cell interactions may be influenced by the heightened proinflammatory milieu present in degenerating discs, leading to increased nerve migration. Data may have direct clinical relevance/implications for nerve ingrowth and pain in the outer annulus (where disc cell numbers are high), and in regions where nerves penetrate into the disc via annular tears.

Level of Evidence: N/A
Damage Identification on Vertebral Bodies During Compressive Loading Using Digital Image Correlation
Authors: Gustafson Hannah M. , Melnyk Angela D. , Siegmund Gunter P. , Cripton Peter A. 
Published: March 2017

Study Design.

Ex vivo compression experiments on isolated cadaveric vertebrae.

Objective.
To qualitatively compare the fracture locations identified in video analysis with the locations of high compressive strain measured with digital image correlation (DIC) on vertebral bodies and to evaluate the timing of local damage to the cortical shell relative to the global yield force.

Summary of Background Data.
In previous ex vivo experiments, cortical bone fracture has been identified using various methods including acoustic emission sensors, strain gages, video analysis, or force signals. These methods are, however, limited in their ability to detect the location and timing of fracture. We propose use of DIC, a noncontact optical technique that measures surface displacement, to quantify variables related to damage.

Methods.
Isolated thoracolumbar human cadaveric vertebral bodies (n = 6) were tested in compression to failure at a quasi-static rate, and the force applied was measured using a load cell. The surface displacement and strain were measured using DIC. Video analysis was performed to identify fractures.

Results.
The location of fractures identified in the video corresponded well with the locations of high compressive strain on the bone. Before reaching the global yield force, more than 10% of the DIC measurements reached a minimum principal strain of 1.0%, a previously reported threshold for cortical bone damage.

Conclusion.
DIC measurements provide an objective measure that can be used to identify the location and timing of fractures during ex vivo vertebral experiments. This is important for understanding fracture mechanics and for validating vertebral computational models that incorporate failure.

Level of Evidence: N /A