bluuebunny/crossref_metadata_2025_split huggingface dataset:
LINC01225 promotes occurrence and metastasis of hepatocellular carcinoma in an epidermal growth factor receptor-dependent pathway
Authors: Wang X , Zhang W , Tang J , Huang R , Li J , Xu D , Xie Y , Jiang R , Deng L , Zhang X , Chai Y , Qin X , Sun B 
Published: March 2016

AbstractThe long noncoding RNAs (lncRNAs) have long been clarified to participate in hepatocellular carcinoma (HCC) as a biomarker. We carried out the present study in order to identify HCC-related lncRNAs and elucidate the functional roles in the development and progression of HCC. Our previous study has provided that LINC01225 may be an HCC-related gene. Here, we verified that LINC01225 was upregulated in HCC. Knockdown of LINC01225 resulted in inhibited cell proliferation and invasion with activated apoptosis and cell cycle arrest in vitro. Overexpression of LINC01225 in LINC01225 knockdown cells presented that attenuated cell proliferation and invasion were restored and enhanced. Subcutaneous and tail vein/intraperitoneal injection xenotransplantation model in vivo validated reduced tumor progression and metastasis. Investigation of mechanism found that LINC01225 could bind to epidermal growth factor receptor (EGFR) and increase the protein level of EGFR, and subsequently fine tune the EGFR/Ras/Raf-1/MEK/MAPK signaling pathway. Analysis with clinicopathological information suggested a high expression of LINC01225 is positively associated with poor prognosis. We also proved that LINC01225 was stably expressed in serum and can act as a novel biomarker in predicting the diagnosis of HCC. As a conclusion, LINC01225 plays a crucial role in HCC and can act as a biomarker for the diagnosis and prognosis of HCC.
Itk is required for Th9 differentiation via TCR-mediated induction of IL-2 and IRF4
Authors: Gomez-Rodriguez Julio , Meylan Françoise , Handon Robin , Hayes Erika T. , Anderson Stacie M. , Kirby Martha R. , Siegel Richard M. , Schwartzberg Pamela L. 
Published: March 2016

AbstractTh9 cells produce interleukin (IL)-9, a cytokine implicated in allergic asthma and autoimmunity. Here we show that Itk, a mediator of T cell receptor signalling required for Th2 immune responses and the development of asthma, is a positive regulator of Th9 differentiation. In a model of allergic lung disease, Itk-deficient mice show reduced pulmonary inflammation and IL-9 production by T cells and innate lymphoid type 2 cells (ILC2), despite normal early induction of ILC2s. In vitro, Itk−/− CD4+ T cells do not produce IL-9 and have reduced levels of IRF4 (Interferon Regulator Factor 4), a critical transcription factor for effector T cell function. Both IL-9 and IRF4 expression are rescued by either IL-2 or constitutively active STAT5, but not NFATc1. STAT5 binds the Irf4 promoter, demonstrating one mechanism by which IL-2 rescues weakly activated T cells. Itk inhibition also reduces IL-9 expression by human T cells, implicating ITK as a key regulator of Th9 induction.
Single-cell differences in matrix gene expression do not predict matrix deposition
Authors: Cote Allison J. , McLeod Claire M. , Farrell Megan J. , McClanahan Patrick D. , Dunagin Margaret C. , Raj Arjun , Mauck Robert L. 
Published: March 2016

AbstractMesenchymal stem cells (MSCs) display substantial cell-to-cell heterogeneity, complicating their use in regenerative medicine. However, conventional bulk assays mask this variability. Here we show that both chondrocytes and chondrogenically induced MSCs exhibit substantial mRNA expression heterogeneity. Single-molecule RNA FISH to measure mRNA expression of differentiation markers in single cells reveals that sister cell pairs have high levels of mRNA variability, suggesting that marker expression is not heritable. Surprisingly, this variability does not correlate with cell-to-cell differences in cartilage-like matrix production. Transcriptome-wide analysis suggests that no combination of markers can predict functional potential. De-differentiating chondrocytes also show a disconnect between mRNA expression of the cartilage marker aggrecan and cartilage-like matrix accumulation. Altogether, these quantitative analyses suggest that sorting subpopulations based on these markers would only marginally enrich the progenitor population for ‘superior’ MSCs. Our results suggest that instantaneous mRNA abundance of canonical markers is tenuously linked to the chondrogenic phenotype at the single-cell level.
Temperature mapping of operating nanoscale devices by scanning probe thermometry
Authors: Menges Fabian , Mensch Philipp , Schmid Heinz , Riel Heike , Stemmer Andreas , Gotsmann Bernd 
Published: March 2016

AbstractImaging temperature fields at the nanoscale is a central challenge in various areas of science and technology. Nanoscopic hotspots, such as those observed in integrated circuits or plasmonic nanostructures, can be used to modify the local properties of matter, govern physical processes, activate chemical reactions and trigger biological mechanisms in living organisms. The development of high-resolution thermometry techniques is essential for understanding local thermal non-equilibrium processes during the operation of numerous nanoscale devices. Here we present a technique to map temperature fields using a scanning thermal microscope. Our method permits the elimination of tip–sample contact-related artefacts, a major hurdle that so far has limited the use of scanning probe microscopy for nanoscale thermometry. We map local Peltier effects at the metal–semiconductor contacts to an indium arsenide nanowire and self-heating of a metal interconnect with 7 mK and sub-10 nm spatial temperature resolution.
Chronic cough and a normal chest X-ray - a simple systematic approach to exclude common causes before referral to secondary care: a retrospective cohort study
Authors: Turner Richard D , Bothamley Graham H 
Published: March 2016

AbstractChronic cough is common in the community and can cause significant morbidity. It is not clear how closely treatment guidelines are used in general practice, or how often specialist referral is indicated. We aimed to assess the management of chronic cough in primary care before referral to a cough clinic, and to assess the outcome of managing chronic cough with an approach of simple investigation and empirical treatment trials. Data were extracted from the records of all patients attending a district general hospital respiratory clinic over a two-year period with isolated chronic cough lasting ⩾8 weeks. The clinic assessed symptoms with a cough-severity visual analogue scale and the Leicester Cough Questionnaire. Among 266 patients, the most frequent diagnoses were asthma (29%), gastro-oesophageal reflux (22%) and angiotensin-converting enzyme inhibitor use (14%). In all, 12% had unexplained chronic cough. Common diagnoses had often not been excluded in primary care: only 21% had undergone spirometry, 86% had undergone chest radiography and attempts to exclude asthma with corticosteroids had been made only in 39%. In the clinic few investigations were conducted that were not available in primary care. Substantial improvements in symptoms occurred with a median (interquartile range) total of 2 (2–3) clinic visits. We estimated that 87% of patients could have been managed solely in primary care; we did not identify distinguishing characteristics among this group. Most cases of chronic cough referred to secondary care could be managed with a simple and systematic approach, which is potentially transferrable to a community setting.
Pathways on demand: automated reconstruction of human signaling networks
Authors: Ritz Anna , Poirel Christopher L , Tegge Allison N , Sharp Nicholas , Simmons Kelsey , Powell Allison , Kale Shiv D , Murali TM 
Published: March 2016

AbstractSignaling pathways are a cornerstone of systems biology. Several databases store high-quality representations of these pathways that are amenable for automated analyses. Despite painstaking and manual curation, these databases remain incomplete. We present PATHLINKER, a new computational method to reconstruct the interactions in a signaling pathway of interest. PATHLINKER efficiently computes multiple short paths from the receptors to transcriptional regulators (TRs) in a pathway within a background protein interaction network. We use PATHLINKER to accurately reconstruct a comprehensive set of signaling pathways from the NetPath and KEGG databases. We show that PATHLINKER has higher precision and recall than several state-of-the-art algorithms, while also ensuring that the resulting network connects receptor proteins to TRs. PATHLINKER’s reconstruction of the Wnt pathway identified CFTR, an ABC class chloride ion channel transporter, as a novel intermediary that facilitates the signaling of Ryk to Dab2, which are known components of Wnt/β-catenin signaling. In HEK293 cells, we show that the Ryk–CFTR–Dab2 path is a novel amplifier of β-catenin signaling specifically in response to Wnt 1, 2, 3, and 3a of the 11 Wnts tested. PATHLINKER captures the structure of signaling pathways as represented in pathway databases better than existing methods. PATHLINKER’s success in reconstructing pathways from NetPath and KEGG databases point to its applicability for complementing manual curation of these databases. PATHLINKER may serve as a promising approach for prioritizing proteins and interactions for experimental study, as illustrated by its discovery of a novel pathway in Wnt/β-catenin signaling. Our supplementary website at http://bioinformatics.cs.vt.edu/~murali/supplements/2016-sys-bio-applications-pathlinker/ provides links to the PATHLINKER software, input datasets, PATHLINKER reconstructions of NetPath pathways, and links to interactive visualizations of these reconstructions on GraphSpace.
Effects of local structure of Ce3+ ions on luminescent properties of Y3Al5O12:Ce nanoparticles
Authors: He Xiaowu , Liu Xiaofang , Li Rongfeng , Yang Bai , Yu Kaili , Zeng Min , Yu Ronghai 
Published: March 2016

AbstractCe3+-doped yttrium aluminum garnet (YAG:Ce) nanocrystals were successfully synthesized via a facile sol-gel method. Multiple characterization techniques were employed to study the structure, morphology, composition and photoluminescence properties of YAG:Ce nanophosphors. The YAG:Ce0.0055 sintered at 1030 °C exhibited a typical 5d1-4f1 emission band with the maximum peak located at 525 nm, and owned a short fluorescence lifetime τ1 (~28 ns) and a long fluorescence lifetime τ2 (~94 ns). Calcination temperature and Ce3+ doping concentration have significant effects on the photoluminescence properties of the YAG:Ce nanophosphors. The emission intensity was enhanced as the calcination temperature increased from 830 to 1030 °C, but decreased dramatically with the increase of Ce3+ doping concentration from 0.55 to 5.50 at.% due to the concentration quenching. By optimizing the synthesized condition, the strongest photoluminescence emission intensity was achieved at 1030 °C with Ce3+ concentration of 0.55 at.%.
Intranasal Delivery of Recombinant AAV Containing BDNF Fused with HA2TAT: a Potential Promising Therapy Strategy for Major Depressive Disorder
Authors: Ma Xian-cang , Liu Peng , Zhang Xiao-ling , Jiang Wen-hui , Jia Min , Wang Cai-xia , Dong Ying-ying , Dang Yong-hui , Gao Cheng-ge 
Published: March 2016

AbstractDepression is a disturbing psychiatric disease with unsatisfied therapy. Not all patients are sensitive to anti-depressants currently in use, side-effects are unavoidable during therapy and the cases with effectiveness are always accompanied with delayed onset of clinical efficacy. Delivering brain-derived neurotrophic factor (BDNF) to brain seems to be a promising therapy. However, a better approach to delivery is still rudimentary. The purpose of our present work is to look for a rapid-onset and long-lasting therapeutic strategy for major depressive disorder (MDD) by effectively delivering BDNF to brain. BDNF, fused with cell-penetrating peptides (TAT and HA2), was packaged in adenovirus associated virus (AAV) to construct the BDNF-HA2TAT/AAV for intranasally delivering BDNF to central nervous system (CNS) via nose-brain pathway. Intranasal administration of BDNF-HA2TAT/AAV to normal mice displayed anti-depression effect in forced swimming test when the delivery lasted relatively longer. The AAV applied to mice subjected to chronic mild stress (CMS) through intranasal administration for 10 days also alleviated depression-like behaviors. Western-blotting analysis revealed that BDNF-HA2TAT/AAV nasal administration enhanced hippocampal BDNF content. These results indicate intranasal administration of constructed BDNF-HA2TAT/AAV exerts anti-depression effect in CMS mice by increasing hippocampal BDNF, suggesting that this strategy holds a promising therapeutic potential for MDD.
RNA sequencing reveals region-specific molecular mechanisms associated with epileptogenesis in a model of classical hippocampal sclerosis
Authors: Vieira A. S. , de Matos A. H. , do Canto A. M. , Rocha C. S. , Carvalho B. S. , Pascoal V. D. B. , Norwood B. , Bauer S. , Rosenow F. , Gilioli R. , Cendes F. , Lopes-Cendes I. 
Published: March 2016

AbstractWe report here the first complete transcriptome analysis of the dorsal (dDG) and ventral dentate gyrus (vDG) of a rat epilepsy model presenting a hippocampal lesion with a strict resemblance to classical hippocampal sclerosis (HS). We collected the dDG and vDG by laser microdissection 15 days after electrical stimulation and performed high-throughput RNA-sequencing. There were many differentially regulated genes, some of which were specific to either of the two sub-regions in stimulated animals. Gene ontology analysis indicated an enrichment of inflammation-related processes in both sub-regions and of axonal guidance and calcium signaling processes exclusively in the vDG. There was also a differential regulation of genes encoding molecules involved in synaptic function, neural electrical activity and neuropeptides in stimulated rats. The data presented here suggests, in the time point analyzed, a remarkable interaction among several molecular components which takes place in the damaged hippocampi. Furthermore, even though similar mechanisms may function in different regions of the DG, the molecular components involved seem to be region specific.
The Lipid Bilayer Provides a Site for Cortisone Crystallization at High Cortisone Concentrations
Authors: Alsop Richard J. , Khondker Adree , Hub Jochen S. , Rheinstädter Maikel C. 
Published: March 2016

AbstractCortisone is an injected anti-inflammatory drug that can cause painful side effects known as “steroid flares” which are caused by cortisone crystallizing at the injection site. We used molecular dynamics simulations and X-ray diffraction to study the interaction of cortisone with model lipid membranes made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) at drug concentrations from 0 mol% to 50 mol%. Cortisone was found to partition in the lipid bilayer and locate in the hydrophilic to hydrophobic interface of the membranes. Cortisone strongly affects the integrity of the membrane, as quantified by a decreased membrane thickness, increased area per lipid and decreased lipid tail order parameters. At cortisone concentrations of more than 20 mol%, signals from crystallized cortisone were observed. These crystallites are embedded in the bilayers and orient with the membranes. While the cortisone molecules align parallel to the bilayers at low concentrations, they start to penetrate the hydrophobic core at higher concentrations. Trans-membrane crystallites start to nucleate when the membrane thickness has decreased such that cortisone molecules in the different leaflets can find partners from the opposite leaflet resulting in a non-zero density of cortisone molecules in the bilayer center. We suggest that the lipid bilayer provides a site for cortisone crystallization.
Small Molecule Inhibition of Ligand-Stimulated RAGE-DIAPH1 Signal Transduction
Authors: Manigrasso Michaele B. , Pan Jinhong , Rai Vivek , Zhang Jinghua , Reverdatto Sergey , Quadri Nosirudeen , DeVita Robert J. , Ramasamy Ravichandran , Shekhtman Alexander , Schmidt Ann Marie 
Published: March 2016

AbstractThe receptor for advanced glycation endproducts (RAGE) binds diverse ligands linked to chronic inflammation and disease. NMR spectroscopy and x-ray crystallization studies of the extracellular domains of RAGE indicate that RAGE ligands bind by distinct charge- and hydrophobicity-dependent mechanisms. The cytoplasmic tail (ct) of RAGE is essential for RAGE ligand-mediated signal transduction and consequent modulation of gene expression and cellular properties. RAGE signaling requires interaction of ctRAGE with the intracellular effector, mammalian diaphanous 1 or DIAPH1. We screened a library of 58,000 small molecules and identified 13 small molecule competitive inhibitors of ctRAGE interaction with DIAPH1. These compounds, which exhibit in vitro and in vivo inhibition of RAGE-dependent molecular processes, present attractive molecular scaffolds for the development of therapeutics against RAGE-mediated diseases, such as those linked to diabetic complications, Alzheimer’s disease, and chronic inflammation, and provide support for the feasibility of inhibition of protein-protein interaction (PPI).
Functioning free gracilis transfer to reconstruct elbow flexion and quality of life in global brachial plexus injured patients
Authors: Yang Yi , Yang Jian-Tao , Fu Guo , Li Xiang-Ming , Qin Ben-Gang , Hou Yi , Qi Jian , Li Ping , Liu Xiao-Lin , Gu Li-Qiang 
Published: March 2016

AbstractIn the study, the functional recovery and relative comprehensive quality of life of cases of global brachial plexus treated with free functioning muscle transfers were investigated. Patients who received functioning gracilis muscle transfer between August 1999 and October 2014 to reconstruct elbow flexion, wrist and fingers extension were recruited. The mean age of the patients was 26.36 (range, 16–42) years. The mean period of time from gracilis transfer to the last follow-up was 54.5 months (range, 12–185 months). Muscle power, active range of motion of the elbow flexion, wrist extension and total active fingers extension were recorded. SDS, SAS and DASH questionnaires were given to estimate patients’ quality of life. 35.71% reported good elbow flexion and 50.00% reported excellent elbow flexion. The average ROM of the elbow flexion was 106.5° (range, 0–142°) and was 17.00° (range, 0–72°) for wrist extension. The average DASH score was 51.14 (range, 17.5–90.8). The prevalence of anxiety and depression were 42.86% and 45.24%. Thrombosis and bowstringing were the most common short and long-term complications. Based on these findings, free gracilis transfer using accessory nerve as donor nerve is a satisfactory treatment to reconstruct the elbow flexion and wrist extension in global-brachial-plexus-injured patients.
On the Dynamical Regimes of Pattern-Accelerated Electroconvection
Authors: Davidson Scott M. , Wessling Matthias , Mani Ali 
Published: March 2016

AbstractRecent research has established that electroconvection can enhance ion transport at polarized surfaces such as membranes and electrodes where it would otherwise be limited by diffusion. The onset of such overlimiting transport can be influenced by the surface topology of the ion selective membranes as well as inhomogeneities in their electrochemical properties. However, there is little knowledge regarding the mechanisms through which these surface variations promote transport. We use high-resolution direct numerical simulations to develop a comprehensive analysis of electroconvective flows generated by geometric patterns of impermeable stripes and investigate their potential to regularize electrokinetic instabilities. Counterintuitively, we find that reducing the permeable area of an ion exchange membrane, with appropriate patterning, increases the overall ion transport rate by up to 80%. In addition, we present analysis of nonpatterned membranes and find a novel regime of electroconvection where a multivalued current is possible due to the coexistence of multiple convective states.
Directly Predicting Water Quality Criteria from Physicochemical Properties of Transition Metals
Authors: Wang Ying , Wu Fengchang , Mu Yunsong , Zeng Eddy Y. , Meng Wei , Zhao Xiaoli , Giesy John P. , Feng Chenglian , Wang Peifang , Liao Haiqing , Chen Cheng 
Published: March 2016

AbstractTransition metals are a group of elements widespread in aquatic environments that can be hazardous when concentrations exceeding threshold values. Due to insufficient data, criteria maximum concentrations (CMCs) of only seven transition metals for protecting aquatic life have been recommended by the USEPA. Hence, it is deemed necessary to develop empirical models for predicting the threshold values of water quality criteria (WQC) for other transition metals for which insufficient information on toxic potency is available. The present study established quantitative relationships between recommended CMCs and physicochemical parameters of seven transition metals, then used the developed relationships to predict CMCs for other transition metals. Seven of 26 physicochemical parameters examined were significantly correlated with the recommended CMCs. Based on this, five of the seven parameters were selected to construct a linear free energy model for predicting CMCs. The most relevant parameters were identified through principle component analysis and the one with the best correlation with the recommended CMCs was a combination of covalent radius, ionic radius and electron density. Predicted values were largely consistent with their toxic potency values. The present study provides an alternative approach to develop screening threshold level for metals which have insufficient information to use traditional methods.
Effects of whole-body vibration training on physical function, bone and muscle mass in adolescents and young adults with cerebral palsy
Authors: Gusso Silmara , Munns Craig F , Colle Patrícia , Derraik José G B , Biggs Janene B , Cutfield Wayne S , Hofman Paul L 
Published: March 2016

AbstractWe performed a clinical trial on the effects of whole-body vibration training (WBVT) on muscle function and bone health of adolescents and young adults with cerebral palsy. Forty participants (11.3–20.8 years) with mild to moderate cerebral palsy (GMFCS II–III) underwent 20-week WBVT on a vibration plate for 9 minutes/day 4 times/week at 20 Hz (without controls). Assessments included 6-minute walk test, whole-body DXA, lower leg pQCT scans, and muscle function (force plate). Twenty weeks of WBVT were associated with increased lean mass in the total body (+770 g; p = 0.0003), trunk (+410 g; p = 0.004), and lower limbs (+240 g; p = 0.012). Bone mineral content increased in total body (+48 g; p = 0.0001), lumbar spine (+2.7 g; p = 0.0003), and lower limbs (+13 g; p < 0.0001). Similarly, bone mineral density increased in total body (+0.008 g/cm2; p = 0.013), lumbar spine (+0.014 g/cm2; p = 0.003), and lower limbs (+0.023 g/cm2; p < 0.0001). Participants reduced the time taken to perform the chair test, and improved the distance walked in the 6-minute walk test by 11% and 35% for those with GMFCS II and III, respectively. WBVT was associated with increases in muscle mass and bone mass and density, and improved mobility of adolescents and young adults with cerebral palsy.