bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic polymorphisms in glycolytic pathway are associated with the prognosis of patients with early stage non-small cell lung cancer
Authors: Lee Shin Yup , Jin Cheng Cheng , Choi Jin Eun , Hong Mi Jeong , Jung Deuk Kju , Do Sook Kyung , Baek Sun Ah , Kang Hyo Jung , Kang Hyo-Gyoung , Choi Sun Ha , Lee Won Kee , Seok Yangki , Lee Eung Bae , Jeong Ji Yun , Shin Kyung Min , Cho Sukki , Yoo Seung Soo , Lee Jaehee , Cha Seung Ick , Kim Chang Ho , Lee You Mie , Lee In-Kyu , Jheon Sanghoon , Park Jae Yong 
Published: October 2016

AbstractThis study was conducted to investigate whether polymorphisms of genes involved in glycolysis are associated with the prognosis of patients with non-small cell lung cancer (NSCLC) after surgical resection. Forty-four single nucleotide polymorphisms (SNPs) of 17 genes in glycolytic pathway were investigated in a total of 782 patients with NSCLC who underwent curative surgical resection. The association of the SNPs with overall survival (OS) and disease free survival (DFS) were analyzed. Among the 44 SNPs investigated, four SNPs (ENO1 rs2274971A > G, PFKM rs11168417C > T, PFKP rs1132173C > T, PDK2 rs3785921G > A) were significantly associated with survival outcomes in multivariate analyses. When stratified by tumor histology, three SNPs (ENO1 rs2274971A > G, PFKM rs11168417C > T, and PDK2 rs3785921G > A) were significantly associated with OS and/or DFS only in squamous cell carcinoma, whereas PFKP rs1132173C > T exhibited a significant association with survival outcomes only in adenocarcinoma. When the four SNPs were combined, OS and DFS decreased as the number of bad genotypes increased (Ptrend = 8 × 10−4 and 3 × 10−5, respectively). Promoter assays showed that ENO1 rs2274971G allele had significantly higher promoter activity compared to the rs2274971A allele. The four SNPs, especially ENO1 rs2274971A > G, may be useful for the prediction of prognosis in patients with surgically resected NSCLC.
Relaxation dynamics of glasses along a wide stability and temperature range
Authors: Rodríguez-Tinoco C. , Ràfols-Ribé J. , González-Silveira M. , Rodríguez-Viejo J. 
Published: October 2016

AbstractWhile lots of measurements describe the relaxation dynamics of the liquid state, experimental data of the glass dynamics at high temperatures are much scarcer. We use ultrafast scanning calorimetry to expand the timescales of the glass to much shorter values than previously achieved. Our data show that the relaxation time of glasses follows a super-Arrhenius behaviour in the high-temperature regime above the conventional devitrification temperature heating at 10 K/min. The liquid and glass states can be described by a common VFT-like expression that solely depends on temperature and limiting fictive temperature. We apply this common description to nearly-isotropic glasses of indomethacin, toluene and to recent data on metallic glasses. We also show that the dynamics of indomethacin glasses obey density scaling laws originally derived for the liquid. This work provides a strong connection between the dynamics of the equilibrium supercooled liquid and non-equilibrium glassy states.
d-PET-controlled “off-on” Polarity-sensitive Probes for Reporting Local Hydrophilicity within Lysosomes
Authors: Zhu Hao , Fan Jiangli , Mu Huiying , Zhu Tao , Zhang Zhen , Du Jianjun , Peng Xiaojun 
Published: October 2016

AbstractPolarity-sensitive fluorescent probes are powerful chemical tools for studying biomolecular structures and activities both in vitro and in vivo. However, the lack of “off-on” polarity-sensing probes has limited the accurate monitoring of biological processes that involve an increase in local hydrophilicity. Here, we design and synthesize a series of “off-on” polarity-sensitive fluorescent probes BP series consisting of the difluoroboron dippyomethene (BODIPY) fluorophore connected to a quaternary ammonium moiety via different carbon linkers. All these probes showed low fluorescence quantum yields in nonpolar solution but became highly fluorescent in polar media. BP-2, which contains a two-carbon linker and a trimethyl quaternary ammonium, displayed a fluorescence intensity and quantum yield that were both linearly correlated with solvent polarity. In addition, BP-2 exhibited high sensitivity and selectivity for polarity over other environmental factors and a variety of biologically relevant species. BP-2 can be synthesized readily via an unusual Mannich reaction followed by methylation. Using electrochemistry combined with theoretical calculations, we demonstrated that the “off-on” sensing behavior of BP-2 is primarily due to the polarity-dependent donor-excited photoinduced electron transfer (d-PET) effect. Live-cell imaging established that BP-2 enables the detection of local hydrophilicity within lysosomes under conditions of lysosomal dysfunction.
Silencing microRNA-143 protects the integrity of the blood-brain barrier: implications for methamphetamine abuse
Authors: Bai Ying , Zhang Yuan , Hua Jun , Yang Xiangyu , Zhang Xiaotian , Duan Ming , Zhu Xinjian , Huang Wenhui , Chao Jie , Zhou Rongbin , Hu Gang , Yao Honghong 
Published: October 2016

AbstractMicroRNA-143 (miR-143) plays a critical role in various cellular processes; however, the role of miR-143 in the maintenance of blood-brain barrier (BBB) integrity remains poorly defined. Silencing miR-143 in a genetic animal model or via an anti-miR-143 lentivirus prevented the BBB damage induced by methamphetamine. miR-143, which targets p53 unregulated modulator of apoptosis (PUMA), increased the permeability of human brain endothelial cells and concomitantly decreased the expression of tight junction proteins (TJPs). Silencing miR-143 increased the expression of TJPs and protected the BBB integrity against the effects of methamphetamine treatment. PUMA overexpression increased the TJP expression through a mechanism that involved the NF-κB and p53 transcription factor pathways. Mechanistically, methamphetamine mediated up-regulation of miR-143 via sigma-1 receptor with sequential activation of the mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3′ kinase (PI3K)/Akt and STAT3 pathways. These results indicated that silencing miR-143 could provide a novel therapeutic strategy for BBB damage-related vascular dysfunction.
Oxytocin modulates GABAAR subunits to confer neuroprotection in stroke in vitro
Authors: Kaneko Yuji , Pappas Colleen , Tajiri Naoki , Borlongan Cesar V. 
Published: October 2016

AbstractOxytocin protects against ischemia-induced inflammation and oxidative stress, and is associated with GABA (γ-aminobutyric acid, an inhibitory neurotransmitter) signaling transduction in neurons. However, the molecular mechanism by which oxytocin affords neuroprotection, especially the interaction between oxytocin receptor and GABAA receptor (GABAAR), remains to be elucidated. Primary rat neural cells were exposed to oxytocin before induction of experimental acute stroke model via oxygen-glucose deprivation-reperfusion (OGD/R) injury. Pretreatment with oxytocin increased cell viability, decreased the cell damage against oxidative stress, and prevented the release of high mobility group box1 during OGD/R. However, introduction of oxytocin during OGD/R did not induce neuroprotection. Although oxytocin did not affect the glutathione-related cellular metabolism before OGD, oxytocin modulated the expression levels of GABAAR subunits, which function to remove excessive neuronal excitability via chloride ion influx. Oxytocin-pretreated cells significantly increased the chloride ion influx in response to GABA and THIP (δ-GABAAR specific agonist). This study provides evidence that oxytocin regulated GABAAR subunits in affording neuroprotection against OGD/R injury.
Molecular dynamics simulation of nanoindentation on Cu/Ni nanotwinned multilayer films using a spherical indenter
Authors: Fu Tao , Peng Xianghe , Chen Xiang , Weng Shayuan , Hu Ning , Li Qibin , Wang Zhongchang 
Published: October 2016

AbstractWe performed molecular dynamics simulation of nanoindentation on Cu/Ni nanotwinned multilayer films using a spherical indenter, aimed to investigate the effects of hetero-twin interface and twin thickness on hardness. We found that both twinning partial slip (TPS) and partial slip parallel with twin boundary (PSPTB) can reduce hardness and therefore should not be ignored when evaluating mechanical properties at nanoscale. There is a critical range of twin thickness λ (~25 Å < λ < ~31 Å), in which hardness of the multilayer films is maximized. At a smaller λ, TPSs appear due to the reaction between partial dislocations and twin boundary accounts for the softening-dominated mechanism. We also found that the combination of the lowered strengthening due to confined layer slips and the softening due to TPSs and PSPTBs results in lower hardness at a larger λ.
Nondestructive Detection and Quantification of Blueberry Bruising using Near-infrared (NIR) Hyperspectral Reflectance Imaging
Authors: Jiang Yu , Li Changying , Takeda Fumiomi 
Published: October 2016

AbstractCurrently, blueberry bruising is evaluated by either human visual/tactile inspection or firmness measurement instruments. These methods are destructive, time-consuming, and subjective. The goal of this paper was to develop a non-destructive approach for blueberry bruising detection and quantification. Experiments were conducted on 300 samples of southern highbush blueberry (Camellia, Rebel, and Star) and on 1500 samples of northern highbush blueberry (Bluecrop, Jersey, and Liberty) for hyperspectral imaging analysis, firmness measurement, and human evaluation. An algorithm was developed to automatically calculate a bruise ratio index (ratio of bruised to whole fruit area) for bruise quantification. The spectra of bruised and healthy tissues were statistically separated and the separation was independent of cultivars. Support vector machine (SVM) classification of the spectra from the regions of interest (ROIs) achieved over 94%, 92%, and 96% accuracy on the training set, independent testing set, and combined set, respectively. The statistical results showed that the bruise ratio index was equivalent to the measured firmness but better than the predicted firmness in regard to effectiveness of bruise quantification, and the bruise ratio index had a strong correlation with human assessment (R2 = 0.78 − 0.83). Therefore, the proposed approach and the bruise ratio index are effective to non-destructively detect and quantify blueberry bruising.
miR-200 family controls late steps of postnatal forebrain neurogenesis via Zeb2 inhibition
Authors: Beclin Christophe , Follert Philipp , Stappers Elke , Barral Serena , Coré Nathalie , de Chevigny Antoine , Magnone Virginie , Lebrigand Kévin , Bissels Ute , Huylebroeck Danny , Bosio Andreas , Barbry Pascal , Seuntjens Eve , Cremer Harold 
Published: October 2016

AbstractDuring neurogenesis, generation, migration and integration of the correct numbers of each neuron sub-type depends on complex molecular interactions in space and time. MicroRNAs represent a key control level allowing the flexibility and stability needed for this process. Insight into the role of this regulatory pathway in the brain is still limited. We performed a sequential experimental approach using postnatal olfactory bulb neurogenesis in mice, starting from global expression analyses to the investigation of functional interactions between defined microRNAs and their targets. Deep sequencing of small RNAs extracted from defined compartments of the postnatal neurogenic system demonstrated that the miR-200 family is specifically induced during late neuronal differentiation stages. Using in vivo strategies we interfered with the entire miR-200 family in loss- and gain-of-function settings, showing a role of miR-200 in neuronal maturation. This function is mediated by targeting the transcription factor Zeb2. Interestingly, so far functional interaction between miR-200 and Zeb2 has been exclusively reported in cancer or cultured stem cells. Our data demonstrate that this regulatory interaction is also active during normal neurogenesis.
In-situ growth of superconducting SmO1−xFxFeAs thin films by pulsed laser deposition
Authors: Haindl Silvia , Hanzawa Kota , Sato Hikaru , Hiramatsu Hidenori , Hosono Hideo 
Published: October 2016

AbstractOxypnictide thin film growth by pulsed laser deposition (PLD) is one of many insufficiently resolved issues in the research of iron-based superconductors. Here we report on the successful realization of superconducting SmO1−xFxFeAs oxypnictide thin film growth by in-situ PLD on CaF2 (fluorite) substrates. CaF2 acts as fluorine supplier by diffusion and thus enables superconducting oxypnictide thin film growth by PLD. Films are grown heteroepitaxially and characteristically have a broad resistive normal-to-superconducting transition. Best films have onset transition temperatures around 40 K. The proposed in-situ PLD film growth offers an alternative and cheap route for the fabrication of iron oxypnictides. PLD becomes now an additional option for iron oxypnictide synthesis.
The first complete mitochondrial genome for the subfamily Limacodidae and implications for the higher phylogeny of Lepidoptera
Authors: Liu Qiu-Ning , Xin Zhao-Zhe , Bian Dan-Dan , Chai Xin-Yue , Zhou Chun-Lin , Tang Bo-Ping 
Published: October 2016

AbstractThe mitochondrial genome (mitogenome) provides important information for understanding molecular evolution and phylogeny. To determine the systematic status of the family Limacodidae within Lepidoptera, we infer a phylogenetic hypothesis based on the complete mitogenome ofMonema flavescens(Lepidoptera: Limacodidae). The mitogenome ofM. flavescensis 15,396 base pairs (bp), and includes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The AT skew of this mitogenome is slightly negative and the nucleotide composition is also biased towards A + T nucleotides (80.5%). All PCGs are initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which is initiated by CGA. All tRNAs display the typical clover-leaf structure characteristic of mitochondrial tRNAs, with the exception oftrnS1(AGN). The mitogenome CR is 401 bp and consists of several features common to Lepidoptera. Phylogenetic analysis using Bayesian Inference (BI) and Maximum Likelihood (ML) based on nucleotide and amino acid sequences of 13 mitochondrial PCGs indicates thatM. flavescensbelongs to Zygaenoidea. We obtain a well-supported phylogenetic tree consisting of Yponomeutoidea + (Tortricoidea + Zygaenoidea + (Papilionoidea + (Pyraloidea + (Noctuoidea + (Geometroidea + Bombycoidea))))).
A multimodality imaging model to track viable breast cancer cells from single arrest to metastasis in the mouse brain
Authors: Parkins Katie M. , Hamilton Amanda M. , Makela Ashley V. , Chen Yuanxin , Foster Paula J. , Ronald John A. 
Published: October 2016

AbstractCellular MRI involves sensitive visualization of iron-labeled cells in vivo but cannot differentiate between dead and viable cells. Bioluminescence imaging (BLI) measures cellular viability, and thus we explored combining these tools to provide a more holistic view of metastatic cancer cell fate in mice. Human breast carcinoma cells stably expressing Firefly luciferase were loaded with iron particles, injected into the left ventricle, and BLI and MRI were performed on days 0, 8, 21 and 28. The number of brain MR signal voids (i.e., iron-loaded cells) on day 0 significantly correlated with BLI signal. Both BLI and MRI signals decreased from day 0 to day 8, indicating a loss of viable cells rather than a loss of iron label. Total brain MR tumour volume on day 28 also correlated with BLI signal. Overall, BLI complemented our sensitive cellular MRI technologies well, allowing us for the first time to screen animals for successful injections, and, in addition to MR measures of cell arrest and tumor burden, provided longitudinal measures of cancer cell viability in individual animals. We predict this novel multimodality molecular imaging framework will be useful for evaluating the efficacy of emerging anti-cancer drugs at different stages of the metastatic cascade.
High‐speed error‐free wireless data transmission using a terahertz resonant tunnelling diode transmitter and receiver
Authors: Diebold S. , Nishio K. , Nishida Y. , Kim J.‐Y. , Tsuruda K. , Mukai T. , Fujita M. , Nagatsuma T. 
Published: October 2016

An error‐free wireless transmission of a 9 Gbit/s on–off keying modulated signal as well as a 4 k video signal is demonstrated using resonant tunnelling diodes as active elements in both the transmitter and the receiver. The employed system and the modulation scheme enabling the high data rate are discussed.
PDE1C deficiency antagonizes pathological cardiac remodeling and dysfunction
Authors: Knight Walter E. , Chen Si , Zhang Yishuai , Oikawa Masayoshi , Wu Meiping , Zhou Qian , Miller Clint L. , Cai Yujun , Mickelsen Deanne M. , Moravec Christine , Small Eric M. , Abe Junichi , Yan Chen 
Published: October 2016

Significance
Heart failure is the leading global cause of death; therefore developing a greater understanding of disease etiology and identifying novel therapeutic targets is critical. Here, we describe the role of the cyclic nucleotide-degrading protein phosphodiesterase 1C (PDE1C) in the context of pathological cardiac remodeling. In cardiac myocytes, we found that PDE1C regulates both cyclic AMP- and cyclic GMP-mediated signaling pathways under different conditions. In both isolated cells and mice we found that inhibition of PDE1C could potentiate protective signaling and prevent the development of many aspects of heart failure, potentially by signaling through multiple cell types. PDE1 inhibition therefore may represent a viable therapeutic strategy for treatment of heart failure.
Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning
Authors: Hocking Toby Dylan , Goerner-Potvin Patricia , Morin Andreanne , Shao Xiaojian , Pastinen Tomi , Bourque Guillaume 
Published: October 2016

Abstract

Motivation
Many peak detection algorithms have been proposed for ChIP-seq data analysis, but it is not obvious which algorithm and what parameters are optimal for any given dataset. In contrast, regions with and without obvious peaks can be easily labeled by visual inspection of aligned read counts in a genome browser. We propose a supervised machine learning approach for ChIP-seq data analysis, using labels that encode qualitative judgments about which genomic regions contain or do not contain peaks. The main idea is to manually label a small subset of the genome, and then learn a model that makes consistent peak predictions on the rest of the genome.

Results
We created 7 new histone mark datasets with 12 826 visually determined labels, and analyzed 3 existing transcription factor datasets. We observed that default peak detection parameters yield high false positive rates, which can be reduced by learning parameters using a relatively small training set of labeled data from the same experiment type. We also observed that labels from different people are highly consistent. Overall, these data indicate that our supervised labeling method is useful for quantitatively training and testing peak detection algorithms.

Availability and Implementation
Labeled histone mark data http://cbio.ensmp.fr/~thocking/chip-seq-chunk-db/, R package to compute the label error of predicted peaks https://github.com/tdhock/PeakError

Supplementary information
Supplementary data are available at Bioinformatics online.
Judicial Intervention and Industrial Relations: Exploring Industrial Disputes Cases in West Bengal
Authors: Banerjee Supurna , Mahmood Zaad 
Published: October 2016

Abstract
This paper examines a relatively neglected dimension of industrial relation in India, namely judicial intervention in industrial disputes. Through an interrogation of judicial intervention in capital-labour disputes in the state of West Bengal, the paper makes an original contribution to the literature. Through quantitative as well as qualitative examination of court cases, the paper addresses some important questions concerning the nature of judicial intervention. Does the declining force of trade union movements signify a corresponding shift to judicial recourse or an increasing pro-labour judiciary? How are the disputes read by the judiciary: do they adhere to a strict legalistic understanding or does their intervention involve going beyond the letter of the law? Is there uniformity in the nature of verdicts along the spectrum of the judiciary, ie, from the labour tribunals to the higher judiciary (High Court/Supreme Court)? Through an extensive case study of court judgments from labour tribunal to High Court to Supreme Court (where applicable), the paper situates the answers to these questions in the unique context of the sub-state of West Bengal with its specific political framework. Investigating the disjuncture between the legal prescriptions and their invisible implications, or between the jurisprudence at different levels, the paper provides clues to understanding not only the way judicial intervention plays out but also the way in which industrial relations are managed and understood in the context of West Bengal.
Suzaku observations of spectral variations of the ultra-luminous X-ray source Holmberg IX X-1
Authors: Kobayashi Shogo B. , Nakazawa Kazuhiro , Makishima Kazuo 
Published: October 2016

Abstract
Observations of the ultra-luminous X-ray source (ULX) Holmberg IX X-1 were carried out with Suzaku twice, once on 2012 April 13 and then on 2012 October 24, with exposures of 180 ks and 217 ks, respectively. The source showed a hard power-law shaped spectrum with a mild cutoff at ∼8 keV, which is typical of ULXs when they are relatively dim. On both occasions, the 0.6–11 keV spectrum was explained successfully in terms of a cool (∼0.2 keV) multi-color disk blackbody emission model and thermal Comptonization emission produced by an electron cloud with a relatively low temperature and high optical depth, assuming that a large fraction of the disk-blackbody photons are Comptonized whereas the rest are observed directly. The 0.5–10 keV luminosity was 1.2 × 1040 erg s−1 in April, and ∼14% higher in October. This brightening was accompanied by spectral softening in ≥2 keV, with little change in the ≤2 keV spectral shape. This behavior can be understood if the accretion disk remains unchanged while the electron cloud covers a variable fraction of the disk. The absorbing column density was consistent with the galactic line-of sight value, and did not vary by more than 1.6 × 1021 cm−2. Together with the featureless spectra, these properties may not be reconciled easily with the super-critical accretion scenario of this source.