bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a novel UHPLC-MS/MS-based platform to quantify amines, amino acids and methylarginines for applications in human disease phenotyping
Authors: Ahmetaj-Shala Blerina , Olanipekun Michael , Tesfai Abel , MacCallum Niall , Kirkby Nicholas S. , Quinlan Gregory J. , Shih Chih-Chin , Kawai Ryota , Mumby Sharon , Paul-Clark Mark , Want Elizabeth J. , Mitchell Jane A. 
Published: September 2018

AbstractAmine quantification is an important strategy in patient stratification and personalised medicine. This is because amines, including amino acids and methylarginines impact on many homeostatic processes. One important pathway regulated by amine levels is nitric oxide synthase (NOS). NOS is regulated by levels of (i) the substrate, arginine, (ii) amino acids which cycle with arginine and (iii) methylarginine inhibitors of NOS. However, biomarker research in this area is hindered by the lack of a unified analytical platform. Thus, the development of a common metabolomics platform, where a wide range of amino acids and methylarginines can be measured constitutes an important unmet need. Here we report a novel high-throughput ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) platform where ≈40 amine analytes, including arginine and methylarginines can be detected and quantified on a molar basis, in a single sample of human plasma. To validate the platform and to generate biomarkers, human plasma from a well-defined cohort of patients before and after coronary artery bypass surgery, who developed systemic inflammatory response syndrome (SIRS), were analysed. Bypass surgery with SIRS significantly altered 26 amine analytes, including arginine and ADMA. Consequently, pathway analysis revealed significant changes in a range of pathways including those associated with NOS.
3D multiscale imaging of human vocal folds using synchrotron X-ray microtomography in phase retrieval mode
Authors: Bailly Lucie , Cochereau Thibaud , Orgéas Laurent , Henrich Bernardoni Nathalie , Rolland du Roscoat Sabine , McLeer-Florin Anne , Robert Yohann , Laval Xavier , Laurencin Tanguy , Chaffanjon Philippe , Fayard Barbara , Boller Elodie 
Published: September 2018

AbstractHuman vocal folds possess outstanding abilities to endure large, reversible deformations and to vibrate up to more than thousand cycles per second. This unique performance mainly results from their complex specific 3D and multiscale structure, which is very difficult to investigate experimentally and still presents challenges using either confocal microscopy, MRI or X-ray microtomography in absorption mode. To circumvent these difficulties, we used high-resolution synchrotron X-ray microtomography with phase retrieval and report the first ex vivo 3D images of human vocal-fold tissues at multiple scales. Various relevant descriptors of structure were extracted from the images: geometry of vocal folds at rest or in a stretched phonatory-like position, shape and size of their layered fibrous architectures, orientation, shape and size of the muscle fibres as well as the set of collagen and elastin fibre bundles constituting these layers. The developed methodology opens a promising insight into voice biomechanics, which will allow further assessment of the micromechanics of the vocal folds and their vibratory properties. This will then provide valuable guidelines for the design of new mimetic biomaterials for the next generation of artificial larynges.
Proteome analysis reveals a role of rainbow trout lymphoid organs during Yersinia ruckeri infection process
Authors: Kumar Gokhlesh , Hummel Karin , Noebauer Katharina , Welch Timothy J. , Razzazi-Fazeli Ebrahim , El-Matbouli Mansour 
Published: September 2018

AbstractYersinia ruckeriis the causative agent of enteric redmouth disease in salmonids. Head kidney and spleen are major lymphoid organs of the teleost fish where antigen presentation and immune defense against microbes take place. We investigated proteome alteration in head kidney and spleen of the rainbow trout followingY.ruckeristrains infection. Organs were analyzed after 3, 9 and 28 days post exposure with a shotgun proteomic approach. GO annotation and protein-protein interaction were predicted using bioinformatic tools. Thirty four proteins from head kidney and 85 proteins from spleen were found to be differentially expressed in rainbow trout during theY.ruckeriinfection process. These included lysosomal, antioxidant, metalloproteinase, cytoskeleton, tetraspanin, cathepsin B and c-type lectin receptor proteins. The findings of this study regarding the immune response at the protein level offer new insight into the systemic response toY.ruckeriinfection in rainbow trout. This proteomic data facilitate a better understanding of host-pathogen interactions and response of fish againstY.ruckeribiotype 1 and 2 strains. Protein-protein interaction analysis predicts carbon metabolism, ribosome and phagosome pathways in spleen of infected fish, which might be useful in understanding biological processes and further studies in the direction of pathways.
Isolated hallucination is less predictive than thought disorder in psychosis: Insight from a longitudinal study in a clinical population at high risk for psychosis
Authors: Zhang TianHong , Xu LiHua , Tang YingYing , Cui HuiRu , Wei YanYan , Tang XiaoChen , Hu Qiang , Wang Yan , Zhu YiKang , Jiang LiJuan , Hui Li , Liu XiaoHua , Li ChunBo , Wang JiJun 
Published: September 2018

AbstractPerceptual abnormalities (PAs) such as auditory hallucinations are one of the most common symptoms of psychotic patients. However, it remains unclear whether symptoms of sub-clinical PAs also play a key role in predicting psychosis. In an ongoing prospective follow-up study of individuals at a clinical high risk (CHR) of psychosis, we evaluated the potential of first-time experience of PAs and/or thought content disorders (TCDs) to predict psychosis. Conversion to psychosis was the major focus of this follow-up study. A total of 511 CHRs were recruited, of whom 443 (86.7%) completed the clinical follow-up of at least 6 months and up to 2 years. CHRs were divided into four groups according to the presence of PAs and/or TCDs. At the follow-up endpoint, 39 (19.9%) CHRs in the “TCDs-only” group, 2 (8.3%) in the “PAs-only” group, 45 (17.0%) in the “TCDs-and-PAs” group, and 1 (3.8%) in the “None” group converted to psychosis. Survival analysis revealed a higher conversion rate in CHRs with TCDs compared with those with PAs only. CHRs with isolated PAs had shown a higher level of dysphoric mood at baseline compared with those with TCDs. About 89% TCDs contents were related with their experienced PAs. Compared with TCDs, the isolated PAs are not strongly associated with increased susceptibility to psychosis.
Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China
Authors: Zhang Mengxiang , Ma Wei , Zhang Juan , He Yi , Wang Juan 
Published: September 2018

AbstractAutism spectrum disorder (ASD) is a set of complex neurodevelopmental disorders. Recent studies reported that children with ASD have altered gut microbiota profiles compared with typical development (TD) children. However, few studies on gut bacteria of children with ASD have been conducted in China. Here, in order to elucidate changes of fecal microbiota in children with ASD, 16S rRNA sequencing was conducted and the 16S rRNA (V3-V4) gene tags were amplified. We investigated differences in fecal microbiota between 35 children with ASD and 6 TD children. At the phylum level, the fecal microbiota of ASD group indicated a significant increase of the Bacteroidetes/Firmicutes ratio. At the genus level, we found that the relative abundance of Sutterella, Odoribacter and Butyricimonas was much more abundant in the ASD group whereas the abundance of Veillonella and Streptococcus was decreased significantly compared to the control group. Functional analysis demonstrated that butyrate and lactate producers were less abundant in the ASD group. In addition, we downloaded the association data set of microbe–disease from human microbe–disease association database and constructed a human disease network including ASD using our gut microbiome results. In this microbe–disease network based on microbe similarity of diseases, we found that ASD is positively correlated with periodontal, negatively related to type 1 diabetes. Therefore, these results suggest that microbe-based disease analysis is able to predict novel connection between ASD and other diseases and may play a role in revealing the pathogenesis of ASD.
Cultivated and wild Pleurotus ferulae ethanol extracts inhibit hepatocellular carcinoma cell growth via inducing endoplasmic reticulum stress- and mitochondria-dependent apoptosis
Authors: Yang Yi , Yuan Pengfei , Wei Xianxian , Fu Changshuang , Li Jinyu , Wang Weilan , Wang Xinhui , Li Yijie , Li Jinyao 
Published: September 2018

AbstractPleurotus ferulae is a kind of editable mushroom and has various biological functions such as antitumor, antioxidation and immunoregulation. Wild P. ferulae was successfully domesticated but the antitumor function and mechanisms of cultivated and wild P. ferulae need to be compared and explored. Here, we prepared cultivated and wild P. ferulae ethanol extracts (PFEE-C and PFEE-W) and compared their antitumor effect on hepatocellular carcinoma. Our data showed that PFEE-C and PFEE-W significantly inhibited the growth of H22 and HepG2 cells through induction of apoptosis. PFEE-W exhibited higher antitumor activity than PFEE-C. Both PFEE-C and PFEE-W induced endoplasmic reticulum (ER) stress characterized by the up-regulated levels of phosphorylated JNK, cleaved caspase-12 and HSP70, and mitochondrial dysfunction characterized by the reduction of mitochondrial membrane potential and the release of cytochrome c, which promoted the cleavage of caspase-3, -7, -9 and PARP. Moreover, PFEE-C and PFEE-W significantly increased ROS generation in H22 cells and suppressed H22 cell migration through reducing the levels of matrix metalloproteinase -2 and -9. Further, PFEE-C inhibited H22 tumor growth in mouse model and improved the survival of tumor mice. These results indicated that PFEE-C and PFEE-W could inhibit hepatocellular carcinoma cell growth through ER stress- and mitochondria-dependent apoptotic pathways.
Direct observation of dynamic interaction between a functional group in a single SBR chain and an inorganic matter surface
Authors: Shinohara Ken-ichi , Makida Yuu 
Published: September 2018

AbstractAs a composite of hybrid organic-inorganic materials, blending hydrophilic silica microparticles with oil-extended rubber can improve vehicle tire performance but the nanometer scale effects of microparticle inclusion have not been thoroughly studied. Here, we used atomic force microscopy (AFM) video imaging to closely investigate the behavior of functionalized and unmodified styrene-butadiene rubber (SBR), as models for tire rubber, on mica surfaces. The hydrophilic silica microparticle surface could be simulated by a mica substrate because both have silanol groups on their surface. Using AFM video imaging, we tracked the behavior of individual SBR polymer chains on mica surfaces to reveal how polymer modification affects the interaction of SBR with mica surfaces. We measured the diffusion coefficients and spring constants of single SBR polymer chains for the first time, demonstrating that it is possible to parameterize the relationship between the molecular dynamic structure of a polymer and rubber properties of the vulcanized compound.
The effect of the heart rate lowering drug Ivabradine on hemodynamics in atherosclerotic mice
Authors: Xing R. , Moerman A. M. , Ridwan R. Y. , Gaalen K. van , Meester E. J. , van der Steen A. F. W. , Evans P. C. , Gijsen F. J. H. , Van der Heiden K. 
Published: September 2018

AbstractThe heart rate lowering drug Ivabradine was shown to improve cardiac outcome in patients with previous heart failure. However, in patients without heart failure, no beneficial effect of Ivabradine was observed. Animal studies suggested a preventive effect of Ivabradine on atherosclerosis which was due to an increase in wall shear stress (WSS), the blood flow-induced frictional force exerted on the endothelium, triggering anti-inflammatory responses. However, data on the effect of Ivabradine on WSS is sparse. We aim to study the effect of Ivabradine on (i) the 3D WSS distribution over a growing plaque and (ii) plaque composition. We induced atherosclerosis in ApoE−/− mice by placing a tapered cast around the right common carotid artery (RCCA). Five weeks after cast placement, Ivabradine was administered via drinking water (15 mg/kg/day) for 2 weeks, after which the RCCA was excised for histology analyses. Before and after Ivabradine treatment, animals were imaged with Doppler Ultrasound to measure blood velocity. Vessel geometry was obtained using contrast-enhanced micro-CT. Time-averaged WSS during systole, diastole and peak WSS was subsequently computed. Ivabradine significantly decreased heart rate (459 ± 28 bpm vs. 567 ± 32 bpm, p < 0.001). Normalized peak flow significantly increased in the Ivabradine group (124.2% ± 40.5% vs. 87.3% ± 25.4%, p < 0.05), reflected by an increased normalized WSS level during systole (110.7% ± 18.4% vs. 75.4% ± 24.6%, p < 0.05). However, plaque size or composition including plaque area, relative necrotic core area and macrophage content were not altered in mice treated with Ivabradine compared to controls. We conclude that increased WSS in response to Ivabradine treatment did not affect plaque progression in a murine model.
Variability in Interpreting “Educational Performance” for Children With Speech Sound Disorders
Authors: Farquharson Kelly , Boldini Lisa 
Published: September 2018

Purpose
Speech sound disorders (SSDs) can have a negative impact on literacy development, social–emotional well-being, and participation across the life span. Despite this, many public schools do not provide appropriate or timely services to this population of children. In large part, this is a result of variation in how state and local agencies interpret “educational performance” as outlined within the Individuals With Disabilities Education Act. The purpose of this study was to explore which educational performance factors speech-language pathologists (SLPs) consider when determining eligibility for children with SSDs.

Method
This study surveyed public school SLPs to investigate how educational performance is interpreted for children with SSDs. Data from 575 SLPs across the United States are included.

Results
Results supported variability in interpretation of educational performance within a nationwide sample of SLPs. Specifically, SLPs appear to consider educational performance as multidimensional. We also found within-state and between-states variability, indicating ambiguity in interpreting federal mandates. Finally, caseload size and number of years of experience were significantly related to which educational performance factors SLPs chose.

Conclusion
There is significant variability across the United States with respect to factors considered part of educational performance for children with SSD. This variability reflects the general quality and specificity of guidelines and/or special education code published by individual states. Clinical and legislative recommendations are included.
Fast immunofluorescence lateral flow test strip approach for detection of homocysteine
Authors: Chen Wei , Ang Chaoman , Lou Doudou , Ji Yongxin , Huang Ling , Zhu Yefei , Guo Zhirui , Gu Ning , Zhang Yu 
Published: September 2018

The study developed a novel quantitative detection method of homocysteine (Hcy), an independent risk factor for cardiovascular disease, based on an immunofluorescent test strip. The fluorescent nanospheres (F‐NSs) were prepared by embedding fluorophores (Cy5) into poly(styrene‐acrylate) copolymer nanospheres, then conjugated with streptavidin (SA) to obtain SA/F‐NSs as a signal amplification label stored in sample diluents. Biotin–antibody was fixed on the conjugate pad to specifically capture S ‐adenosyl Hcy (SAH) in the sample, where SAH was transformed from S ‐adenosyl methionine (SAM) by Hcy S ‐methyltransferase catalysis using Hcy as a substrate, the formed SAH could be trapped by SA/F‐NSs and biotin–antibody conjugates in a competitive way with SAH–bovine serum albumin fixed on the test line, a detection limit of 0.27 μM Hcy was achieved. The fluorescence intensity of F‐NSs remained stable during 273 days of storage, the bioactivity of the test strip was stable during 12 months of storage, and the strip possessed good reproducibility (intra‐assay variability of 5.8%). Furthermore, other structural analogues SAM and cysteine showed negative results, validating the excellent specificity of the strips.
Chemoselective and Metal-Free Synthesis of Aryl Esters from the Corresponding Benzylic Alcohols in Aqueous Medium Using TBHP/TBAI as an Efficient Catalytic System
Authors: Bhar Sanjay , Nandy Sneha , Ghatak Avishek , Das Asit 
Published: September 2018

A novel and transition-metal-free strategy has been developed for the synthesis of aryl esters starting from corresponding benzylic primary alcohols as the exclusive substrates using tert-butyl hydroperoxide (TBHP) as a terminal oxidant in the presence of catalytic amount of tetrabutylammonium iodide (TBAI) and imidazole, where the aliphatic alcohols remained unaffected. These reactions are highly chemoselective and associated with high yield and wide applicability accommodating a wide range of substituents. Excellent chemoselectivity has also been demonstrated through intramolecular competition experiments. This protocol can be considered as an important analogue of Tishchenko reaction using benzylic alcohols as the substrates instead of benzaldehydes.
A Heuristic Evaluation to Assess Use of After Visit Summaries for Supporting Continuity of Care
Authors: Tremoulet Patrice , Krishnan Ramya , Karavite Dean , Muthu Naveen , Regli Susan , Will Amy , Michel Jeremy 
Published: September 2018

Background Outpatient providers often do not receive discharge summaries from acute care providers prior to follow-up visits. These outpatient providers may use the after-visit summaries (AVS) that are given to patients to obtain clinical information. It is unclear how effectively AVS support care coordination between clinicians.
Objectives Goals for this effort include: (1) developing usability heuristics that may be applied both for assessment and to guide generation of medical documents in general, (2) conducting a heuristic evaluation to assess the use of AVS for communication between clinicians, and (3) providing recommendations for generating AVS that effectively support both patient/caregiver use and care coordination.
Methods We created a 17-item heuristic evaluation instrument for assessing usability of medical documents. Eight experts used the instrument to assess each of four simulated AVS. The simulations were created using examples from two hospitals and two pediatric patient cases developed by the National Institute of Standards and Technology.
Results Experts identified 224 unique usability problems ranging in severity from mild to catastrophic. Content issues (e.g., missing medical history, marital status of a 2-year-old) were rated as most severe, but widespread formatting and structural problems (e.g., inconsistent indentation, fonts, and headings; confusing ordering of information) were so distracting that they significantly reduced readers' ability to efficiently use the documents. Overall, issues in the AVS from Hospital 2 were more severe than those in the AVS from Hospital 1.
Conclusion The new instrument allowed for quick, inexpensive evaluations of AVS. Usability issues such as unnecessary information, poor organization, missing information, and inconsistent formatting make it hard for patients, caregivers, and clinicians to use the AVS. The heuristics in the new instrument may be used as guidance to adapt electronic health record systems so that they generate more useful and usable medical documents.
Do Walmart Supercenters Improve Food Security?
Authors: Courtemanche Charles , Carden Art , Zhou Xilin , Ndirangu Murugi 
Published: September 2018

AbstractThis paper examines the effect that Walmart Supercenters, which lower food prices and expand food availability, have on food insecurity. Data come from the 2001–2012 Current Population Survey Food Security Supplements matched to Walmart Supercenter entry dates and locations. Using instrumental variables models that leverage Walmart’s predictable expansion pattern outward from corporate headquarters, we find that closer proximity to a Walmart Supercenter improves household and child food security, as measured by affirmative responses to a food insecurity questionnaire and an indicator for food insecurity. The effects are largest among low‐income households and children but are also sizeable for middle‐income children.
Explaining the 2016 Vote for President Trump across U.S. Counties
Authors: Goetz Stephan J. , Davlasheridze Meri , Han Yicheol , Fleming-Muñoz David A. 
Published: September 2018

AbstractWe examine how county characteristics affected voting outcomes in the 2016 presidential election, including the populist component represented by the President Trump to Mitt Romney vote difference. Different voter groups could be harmed or helped by policies proposed during the campaign, such as withdrawal from trade agreements, environmental deregulation, and spending cuts. We investigate whether average county‐level voting patterns reflected such proposals. Race and educational attainment had large statistical impacts, but economic factors and religious adherence also mattered. The Trump vote share and Trump‐Romney vote margin were larger in counties with more farming and coal employment.
Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)
Authors: Zhao Hansheng , Gao Zhimin , Wang Le , Wang Jiongliang , Wang Songbo , Fei Benhua , Chen Chunhai , Shi Chengcheng , Liu Xiaochuan , Zhang Hailin , Lou Yongfeng , Chen LianFu , Sun Huayu , Zhou Xianqiang , Wang Sining , Zhang Chi , Xu Hao , Li Lichao , Yang Yihong , Wei Yanli , Yang Wei , Gao Qiang , Yang Huanming , Zhao Shancen , Jiang Zehui 
Published: September 2018

Abstract

Background
Bamboo is one of the most important nontimber forestry products worldwide. However, a chromosome-level reference genome is lacking, and an evolutionary view of alternative splicing (AS) in bamboo remains unclear despite emerging omics data and improved technologies.

Results
Here, we provide a chromosome-level de novo genome assembly of moso bamboo (Phyllostachys edulis) using additional abundance sequencing data and a Hi-C scaffolding strategy. The significantly improved genome is a scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version. A total of 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,711 unique AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and Pacific Biosciences sequencing platforms. Through comparisons with orthologous genes in related plant species, we observed that the AS genes are concentrated among more conserved genes that tend to accumulate higher transcript levels and share less tissue specificity. Furthermore, gene family expansion, abundant AS, and positive selection were identified in crucial genes involved in the lignin biosynthetic pathway of moso bamboo.

Conclusions
These fundamental studies provide useful information for future in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo.