bluuebunny/crossref_metadata_2025_split huggingface dataset:
Family Literacy Project
Authors: Louie Belinda , Davis‐Welton Karlyn 
Published: March 2016

AbstractThe purpose of this article is to describe a family literacy project involving a partnership of school‐aged children and their families with in‐service and pre‐service teachers enrolled in a university course on literacy instruction for English language learners. This project consists of family members sharing their stories with their children to be later transformed into bilingual picture books. This project engaged teachers, families, EL learners, and community members to become partners in students’ literacy development. Teachers engaged students from culturally‐ and linguistically‐diverse backgrounds and their families to produce student‐authored and self‐illustrated bilingual picture books in the classroom setting. In this article, we present the instructional process for teachers who are interested in partnering with families to create bilingual books.
Synthesis and Characterization of Novel Aryl Alkyl Sulfonates Based on Nonylphenol
Authors: Niu Ruixia , Wang Chao , Song Hua , Liao Lingzhi , Wang Jingling , Ren Weidong 
Published: March 2016

AbstractA series of nonylphenol‐substituted alkyl sulfonates (Cx NPAS, x = 8, 10, 12, 14, 16) with two hydrocarbon chains and two different hydrophilic groups has been synthesized from α‐olefins and nonylphenol. The respective products have a “pseudo‐gemini” surfactant structure. The structures of the Cx NPAS have been characterized by IR, UV, 1H nuclear magnetic resonance, electrospray ionization mass spectrometry, and elemental analysis. The effects of carbon chain length of the obtained surfactants on properties such as the critical micelle concentrations (CMC) in aqueous solutions, surface tension at the CMC (γCMC), and efficiency of adsorption at the water/air interface (pC20) have been determined. The γCMC of the surfactants first decreased and then increased with increasing length of the carbon chain x, and reached a minimum of 29.25 mN/m at x = 10, which is much lower than that of α‐olefin sulfonate (AOS) (33.52 mN/m). The CMC decreased and pC20 increased with increasing x. The introduction of the hydroxyl group is responsible for multiple molecular conformations at the water/air interface and leads to a greater molecular area Amin and smaller Γmax than those of AOS.
Celastrus Orbiculatus Thunb. Reduces Lipid Accumulation by Promoting Reverse Cholesterol Transport in Hyperlipidemic Mice
Authors: Zhang Ying , Si Yanhong , Zhai Lei , Guo Shoudong , Zhao Jilong , Sang Hui , Pang Xiaofei , Zhang Xue , Chen Anbin , Qin Shucun 
Published: March 2016

AbstractPreviously, we found that Celastrus orbiculatus Thunb. (COT) decreases athero‐susceptibility in lipoproteins and the aorta of guinea pigs fed a high‐fat diet, and increases high‐density lipoprotein (HDL). In the present study, we investigated the effect of COT in reducing lipid accumulation and promoting reverse cholesterol transport (RCT) in vivo and vitro. Healthy male mice were treated with high‐fat diet alone, high‐fat diet with COT (10.0 g/kg/d), or general fodder for 6 weeks. Serum levels of total cholesterol (TC), triglyceride (TG), HDL‐C, non‐HDL‐C, and 3H‐cholesterol in plasma, liver, bile, and feces were determined. Pathological changes and the levels of TC and TG in liver were examined. The expression of hepatic genes and protein associated with RCT were analyzed. COT administration reduced lipid accumulation in the liver, ameliorated the pathological changes, and lessened liver injury, the levels of TG, TC, and non‐HDL‐C in plasma were decreased significantly, and COT led to a significant increase in plasma HDL‐C and apolipoprotein A (apoA1). 3H‐cholesterol in plasma, liver, bile, and feces was also significantly increased in COT‐treated mice compared to controls. Both mRNA and protein expression of SRB1, CYP7A1, LDLR, ATP‐binding cassette transporters ABCA1, ABCG5, and LXRα were improved in COT‐treated mice. An in vitro isotope tracing experiment showed that COT and its bioactive ingredients, such as celastrol, ursolic acid, oleanolic acid, and quercetin, significantly increased the efflux of 3H‐cholesterol. They also increased the expression of SRB1, ABCA1, and ABCG1 significantly in macrophages. Our findings provided a positive role of COT in reducing lipid accumulation by promoting RCT. These effects may be achieved by activating the SRB1 and ABC transporter pathway and promoting cholesterol metabolism via the CYP7A1 pathway in vivo. The effective ingredients in vitro are celastrol, ursolic acid, oleanolic acid, and quercetin.
Preoperative halo-gravity traction with and without thoracoscopic anterior release for skeletal dysplasia patients with severe kyphoscoliosis
Authors: Pourtaheri Sina , Shah Suken A. , Ditro Colleen P. , Holmes Laurens , Mackenzie William G. 
Published: March 2016

Purpose Recent work has shown the safety and efficacy of halo-gravity traction as an operative adjunct. However, there are no reports specifically looking at halo-gravity traction in patients with skeletal dysplasia. Our purpose was to assess the safety and efficacy of traction in children with skeletal dysplasia who present with severe kyphoscoliosis. Methods We retrospectively reviewed eight consecutive children with skeletal dysplasia who were treated with halo-gravity traction preoperatively. Six of the patients had a thoracoscopic anterior release prior to the halo-gravity traction. All patients were ambulatory and presented with severe, rigid kyphoscoliosis. Results The mean duration of traction was 32 days. There were no neurologic complications with traction or after posterior spinal instrumentation. The majority of kyphoscoliosis correction was with the halo-gravity traction alone: major curve (MC) Cobb angle improved 41 %; C7–center sacral vertical line, 75 %; C7–MC apex, 21 %; and T2–T12 kyphosis, 35 %. Trunk height increased 37 % and thoracic height 44 %. An additional amount of correction was obtained with posterior spinal instrumentation (±fusion), decreasing MC Cobb angle an additional 23 %; C7–apex, 16 %; and T2–T12 kyphosis, 10 %. There was no additional correction of thoracic height. Two years after posterior spinal instrumentation (±fusion), a mild-to-moderate amount of correction was lost: MC Cobb angle decreased 23 %; compensatory Cobb angle, 28 %; C7–CSVL, 24 %; C7–S1, 22 %; regional kyphosis, 31 %; thoracic kyphosis, 29 %; and trunk height, 27 %. Conclusions Among children with skeletal dysplasia and severe kyphosis, halo-gravity traction is well tolerated and safe. Most of the corrections in radiographic parameters were achieved with traction alone. Traction improves coronal balance, apical translation, thoracic height, and kyphosis. In this specific population, the potential for neurologic injury during corrective surgery is high. However, preoperative halo-gravity traction provides slow, progressive correction in a safe manner and avoided neurologic injury in these patients. This study did not compare patients without halo-gravity traction to patients with halo-gravity traction, therefore it cannot be concluded that going straight to instrumentation without traction will give a poorer radiographic result. Level of evidence IV.
SORLA regulates calpain‐dependent degradation of synapsin
Authors: Hartl Daniela , Nebrich Grit , Klein Oliver , Stephanowitz Heike , Krause Eberhard , Rohe Michael 
Published: March 2016

AbstractIntroductionSorting‐related receptor with A‐type repeats (SORLA) is an intracellular sorting receptor in neurons and a major risk factor for Alzheimer disease.MethodsHere, we performed global proteome analyses in the brain of SORLA‐deficient mice followed by biochemical and histopathologic studies to identify novel neuronal pathways affected by receptor dysfunction.ResultsWe demonstrate that the lack of SORLA results in accumulation of phosphorylated synapsins in cortex and hippocampus. We propose an underlying molecular mechanism by demonstrating that SORLA interacts with phosphorylated synapsins through 14‐3‐3 adaptor proteins to deliver synapsins to calpain‐mediated proteolytic degradation.DiscussionOur results suggest a novel function for SORLA which is in control of synapsin degradation, potentially impacting on synaptic vesicle endocytosis and/or exocytosis.
Motion-capture-based walking simulation of digital human adapted to laser-scanned 3D as-is environments for accessibility evaluation
Authors: Maruyama Tsubasa , Kanai Satoshi , Date Hiroaki , Tada Mitsunori 
Published: March 2016

AbstractOwing to our rapidly aging society, accessibility evaluation to enhance the ease and safety of access to indoor and outdoor environments for the elderly and disabled is increasing in importance. Accessibility must be assessed not only from the general standard aspect but also in terms of physical and cognitive friendliness for users of different ages, genders, and abilities. Meanwhile, human behavior simulation has been progressing in the areas of crowd behavior analysis and emergency evacuation planning. However, in human behavior simulation, environment models represent only “as-planned” situations. In addition, a pedestrian model cannot generate the detailed articulated movements of various people of different ages and genders in the simulation. Therefore, the final goal of this research was to develop a virtual accessibility evaluation by combining realistic human behavior simulation using a digital human model (DHM) with “as-is” environment models. To achieve this goal, we developed an algorithm for generating human-like DHM walking motions, adapting its strides, turning angles, and footprints to laser-scanned 3D as-is environments including slopes and stairs. The DHM motion was generated based only on a motion-capture (MoCap) data for flat walking. Our implementation constructed as-is 3D environment models from laser-scanned point clouds of real environments and enabled a DHM to walk autonomously in various environment models. The difference in joint angles between the DHM and MoCap data was evaluated. Demonstrations of our environment modeling and walking simulation in indoor and outdoor environments including corridors, slopes, and stairs are illustrated in this study.Highlights An adaptive walking simulation algorithm of the digital human was developed. The environment models are automatically generated from laser-scanned point clouds. A digital human can walk autonomously in various as-built environment models. Simulated walking motion of the digital human is similar to one of real human. Elapsed time of modeling and simulation is short enough for practical application.
La medicina natural y tradicional y su relación con las ciencias básicas
Authors: Vidor Guerra Elizabeth , Padilla Rodríguez Elaine , Guerrero Betancourt Mayren 
Published: March 2016

Estimado editor creo que es importante abordar el tema de la medicina tradicional natural (MTN) ya que esta constituye un sistema de conocimiento armónicamente estructurado, que como toda ciencia contribuye al conocimiento del mundo circundante, en este caso, de forma especial a la salud humana.
Between syntax and discourse
Authors: Laleko Oksana , Polinsky Maria 
Published: March 2016

AbstractThis article examines the knowledge of topic and subject particles in heritage speakers and L2 learners of Japanese and Korean. We assume that topic marking is mediated at the syntax-information structure interface, while subject marking pertains to narrow syntax. In comparing phenomena mediated at different levels of linguistic organization, we provide evidence for the hypothesis that information structure-level phenomena present greater challenges for bilingual speakers than those mediated within syntax. While these results may be interpreted as evidence of generalized interface-related deficits, we show that such a global explanation is not supported. Instead, a more nuanced account is developed, based on the recognition of different types of topic (anaphoric, generic, and contrastive) and different types of subject (descriptive and exhaustive). Under the proposed account, non-native speakers’ deficits follow from three unrelated effects: the status of topic as an interface category, structural complexity, and the memory demands necessary for its interpretation in context.
PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks
Authors: Lu Hui-Chun , Herrera Braga Julián , Fraternali Franca 
Published: March 2016

Abstract
Summary: We present a practical computational pipeline to readily perform data analyses of protein–protein interaction networks by using genetic and functional information mapped onto protein structures. We provide a 3D representation of the available protein structure and its regions (surface, interface, core and disordered) for the selected genetic variants and/or SNPs, and a prediction of the mutants’ impact on the protein as measured by a range of methods. We have mapped in total 2587 genetic disorder-related SNPs from OMIM, 587 873 cancer-related variants from COSMIC, and 1 484 045 SNPs from dbSNP. All result data can be downloaded by the user together with an R-script to compute the enrichment of SNPs/variants in selected structural regions.
Availability and Implementation: PinSnps is available as open-access service at http://fraternalilab.kcl.ac.uk/PinSnps/
Contact: franca.fraternali@kcl.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
FREGAT: an R package for region-based association analysis
Authors: Belonogova Nadezhda M. , Svishcheva Gulnara R. , Axenovich Tatiana I. 
Published: March 2016

AbstractSummary: Several approaches to the region-based association analysis of quantitative traits have recently been developed and successively applied. However, no software package has been developed that implements all of these approaches for either independent or structured samples. Here we introduce FREGAT (Family REGional Association Tests), an R package that can handle family and population samples and implements a wide range of region-based association methods including burden tests, functional linear models, and kernel machine-based regression. FREGAT can be used in genome/exome-wide region-based association studies of quantitative traits and candidate gene analysis. FREGAT offers many useful options to empower its users and increase the effectiveness and applicability of region-based association analysis.Availability and Implementation: https://cran.r-project.org/web/packages/FREGAT/index.htmlSupplementary Information: Supplementary data are available at Bioinformatics Online.Contact: belon@bionet.nsc.ru
HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data
Authors: Gu Zuguang , Eils Roland , Schlesner Matthias 
Published: March 2016

Abstract
Summary: Hilbert curves enable high-resolution visualization of genomic data on a chromosome- or genome-wide scale. Here we present the HilbertCurve package that provides an easy-to-use interface for mapping genomic data to Hilbert curves. The package transforms the curve as a virtual axis, thereby hiding the details of the curve construction from the user. HilbertCurve supports multiple-layer overlay that makes it a powerful tool to correlate the spatial distribution of multiple feature types.
Availability and implementation: The HilbertCurve package and documentation are freely available from the Bioconductor project: http://www.bioconductor.org/packages/devel/bioc/html/HilbertCurve.html
Contact: m.schlesner@dkfz.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Canvas: versatile and scalable detection of copy number variants
Authors: Roller Eric , Ivakhno Sergii , Lee Steve , Royce Thomas , Tanner Stephen 
Published: March 2016

Abstract
Motivation: Versatile and efficient variant calling tools are needed to analyze large scale sequencing datasets. In particular, identification of copy number changes remains a challenging task due to their complexity, susceptibility to sequencing biases, variation in coverage data and dependence on genome-wide sample properties, such as tumor polyploidy or polyclonality in cancer samples.
Results: We have developed a new tool, Canvas, for identification of copy number changes from diverse sequencing experiments including whole-genome matched tumor-normal and single-sample normal re-sequencing, as well as whole-exome matched and unmatched tumor-normal studies. In addition to variant calling, Canvas infers genome-wide parameters such as cancer ploidy, purity and heterogeneity. It provides fast and easy-to-run workflows that can scale to thousands of samples and can be easily incorporated into variant calling pipelines.
Availability and Implementation: Canvas is distributed under an open source license and can be downloaded from https://github.com/Illumina/canvas.
Contact: eroller@illumina.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Quantitative phosphoproteomics-based molecular network description for high-resolution kinase-substrate interactome analysis
Authors: Narushima Yuta , Kozuka-Hata Hiroko , Tsumoto Kouhei , Inoue Jun-Ichiro , Oyama Masaaki 
Published: March 2016

Motivation: Phosphorylation-dependent cellular signaling is known to play a diverse role in regulating multiple cellular processes such as proliferation, differentiation and apoptosis. Recent technological advances in mass spectrometry-based phosphoproteomics have enabled us to measure network-wide signaling dynamics in a comprehensive and quantitative manner. As conventional protein–protein interaction (PPI) information-based network analysis is insufficient to systematically analyze phosphorylation site-dependent complex interaction dynamics, here we develop and evaluate a platform to provide a high-resolution molecular network description for kinase–substrate interactome analysis.
Results: In this study, we developed a Cytoscape-based bioinformatical platform named ‘Post Translational Modification mapper (PTMapper)’ to integrate PPI data with publicly available kinase-substrate relations at the resolution of phosphorylated amino acid residues. The previous phosphoproteome data on EGF-induced cellular signaling in glioblastoma stem cells was applied to evaluate our platform, leading to discovery of phosphorylation-dependent crucial signaling modulation in the p70S6K1-related pathway. Our study revealed that high-resolution cellular network description of phosphorylation-site dependent kinase-substrate signaling regulation should accelerate phosphoproteomics-based exploration of novel drug targets in the context of each disease-related signaling.
Availability and Implementation: PTMapper and the example data for construction of phosphorylation site-oriented networks are available at https://github.com/y-narushima/PTMapper.
Contact: moyama@ims.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Deep models for brain EM image segmentation: novel insights and improved performance
Authors: Fakhry Ahmed , Peng Hanchuan , Ji Shuiwang 
Published: March 2016

Abstract
Motivation: Accurate segmentation of brain electron microscopy (EM) images is a critical step in dense circuit reconstruction. Although deep neural networks (DNNs) have been widely used in a number of applications in computer vision, most of these models that proved to be effective on image classification tasks cannot be applied directly to EM image segmentation, due to the different objectives of these tasks. As a result, it is desirable to develop an optimized architecture that uses the full power of DNNs and tailored specifically for EM image segmentation.
Results: In this work, we proposed a novel design of DNNs for this task. We trained a pixel classifier that operates on raw pixel intensities with no preprocessing to generate probability values for each pixel being a membrane or not. Although the use of neural networks in image segmentation is not completely new, we developed novel insights and model architectures that allow us to achieve superior performance on EM image segmentation tasks. Our submission based on these insights to the 2D EM Image Segmentation Challenge achieved the best performance consistently across all the three evaluation metrics. This challenge is still ongoing and the results in this paper are as of June 5, 2015.
Availability and Implementation: https://github.com/ahmed-fakhry/dive
Contact: sji@eecs.wsu.edu
Salmonella enterica Subspecies diarizonae Maxillary Sinusitis in a Snake Handler: First Report
Authors: Horvath Lukas , Kraft Marcel , Fostiropoulos Karolos , Falkowski Anna , Tarr Philip E. 
Published: March 2016

AbstractIn this study, we report the first case of reptile-associated maxillary sinusitis due to Salmonella enterica subspecies diarizonae in a snake handler and the third case of salmonella-associated sinusitis worldwide. The case highlights the potential of respiratory transmission and atypical salmonellosis presentations.
Pulsed Electromagnetic Fields for Postsurgical Pain Management in Women Undergoing Cesarean Section
Authors: Khooshideh Maryam , Latifi Rostami Seyedeh Sakineh , Sheikh Mahdi , Ghorbani Yekta Batool , Shahriari Ali 
Published: March 2016

Objectives:To evaluate the efficacy of pulsed electromagnetic field (PEMF) in relation to reducing postoperative pain, analgesic use, and wound healing in patients undergoing Cesarean section (C-section).Methods:This randomized, double-blind, placebo-controlled trial evaluated 72 women who underwent elective C-section. Thirty-six patients were assigned to the active-PEMF and 36 to the sham-PEMF groups. The participants were asked to report their pain intensity on a Visual Analog Scale (VAS) at 2, 4, 6, 12, and 24 hours and 2, 4, and 7 days after surgery. The amount of analgesics used was recorded. The surgical site was evaluated to assess the wound-healing process on the seventh postoperative day.Results:Postoperative pain VAS scores were significantly lower in the active-PEMF group in all the measured periods within the early and the late postoperative periods. Fewer women in the active-PEMF group experienced severe postoperative pain within 24 hours postoperatively (36% vs. 72%,P=0.002). Analgesic use during the first 24 hours after C-section was 1.9-times lower in the active-PEMF group (1.6±0.7 vs. 3.1±1.2,P<0.001). The total analgesic use during the seventh postoperative days was 2.1-times lower in the active-PEMF group than in the sham group (1.7±0.7 vs. 3.7±1.1,P<0.001). Seven days postoperatively, patients in the active-PEMF group had better wound healing with no exudate, erythema, or edema (P=0.02).Conclusions:PEMF treatment after C-section decreases postsurgical pain, analgesic use, and surgical wound exudate and edema significantly, and is associated with a high level of patient satisfaction.