bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance in a GO/NOGO perceptual task reflects a balance between impulsive and instrumental components of behaviour
Authors: Berditchevskaia A. , Cazé R. D. , Schultz S. R. 
Published: June 2016

AbstractIn recent years, simple GO/NOGO behavioural tasks have become popular due to the relative ease with which they can be combined with technologies such as in vivo multiphoton imaging. To date, it has been assumed that behavioural performance can be captured by the average performance across a session, however this neglects the effect of motivation on behaviour within individual sessions. We investigated the effect of motivation on mice performing a GO/NOGO visual discrimination task. Performance within a session tended to follow a stereotypical trajectory on a Receiver Operating Characteristic (ROC) chart, beginning with an over-motivated state with many false positives, and transitioning through a more or less optimal regime to end with a low hit rate after satiation. Our observations are reproduced by a new model, the Motivated Actor-Critic, introduced here. Our results suggest that standard measures of discriminability, obtained by averaging across a session, may significantly underestimate behavioural performance.
Hepatocellular carcinoma cell lines retain the genomic and transcriptomic landscapes of primary human cancers
Authors: Qiu Zhixin , Zou Keke , Zhuang Liping , Qin Jianjie , Li Hong , Li Chao , Zhang Zhengtao , Chen Xiaotao , Cen Jin , Meng Zhiqiang , Zhang Haibin , Li Yixue , Hui Lijian 
Published: June 2016

AbstractHepatocellular carcinoma (HCC) cell lines are useful in vitro models for the study of primary HCCs. Because cell lines acquire additional mutations in culture, it is important to understand to what extent HCC cell lines retain the genetic landscapes of primary HCCs. Most HCC cell lines were established during the last century, precluding comparison between cell lines and primary cancers. In this study, 9 Chinese HCC cell lines with matched patient-derived cells at low passages (PDCs) were established in the defined culture condition. Whole genome analyses of 4 HCC cell lines showed that genomic mutation landscapes, including mutations, copy number alterations (CNAs) and HBV integrations, were highly stable during cell line establishment. Importantly, genetic alterations in cancer drivers and druggable genes were reserved in cell lines. HCC cell lines also retained gene expression patterns of primary HCCs during in vitro culture. Finally, sequential analysis of HCC cell lines and PDCs at different passages revealed their comparable and stable genomic and transcriptomic levels if maintained within proper passages. These results show that HCC cell lines largely retain the genomic and transcriptomic landscapes of primary HCCs, thus laying the rationale for testing HCC cell lines as preclinical models in precision medicine.
A-site compositional effects in Ga-doped hollandite materials of the form BaxCsyGa2x+yTi8−2x−yO16: implications for Cs immobilization in crystalline ceramic waste forms
Authors: Xu Yun , Wen Yi , Grote Rob , Amoroso Jake , Shuller Nickles Lindsay , Brinkman Kyle S. 
Published: June 2016

AbstractThe hollandite structure is a promising crystalline host for Cs immobilization. A series of Ga-doped hollandite BaxCsyGa2x+yTi8−2x−yO16 (x = 0, 0.667, 1.04, 1.33; y = 1.33, 0.667, 0.24, 0) was synthesized through a solid oxide reaction method resulting in a tetragonal hollandite structure (space group I4/m). The lattice parameter associated with the tunnel dimension was found to increases as Cs substitution in the tunnel increased. A direct investigation of cation mobility in tunnels using electrochemical impedance spectroscopy was conducted to evaluate the ability of the hollandite structure to immobilize cations over a wide compositional range. Hollandite with the largest tunnel size and highest aspect ratio grain morphology resulting in rod-like microstructural features exhibited the highest ionic conductivity. The results indicate that grain size and optimized Cs stoichiometry control cation motion and by extension, the propensity for Cs release from hollandite.
Intra-cage dynamics of molecular hydrogen confined in cages of two different dimensions of clathrate hydrates
Authors: Russina Margarita , Kemner Ewout , Mezei Ferenc 
Published: June 2016

AbstractIn porous materials the molecular confinement is often realized by means of weak Van der Waals interactions between the molecule and the pore surface. The understanding of the mechanism of such interactions is important for a number of applications. In order to establish the role of the confinement size we have studied the microscopic dynamics of molecular hydrogen stored in the nanocages of clathrate hydrates of two different dimensions. We have found that by varying the size of the pore the diffusive mobility of confined hydrogen can be modified in both directions, i.e. reduced or enhanced compared to that in the bulk solid at the same temperatures. In the small cages with a mean crystallographic radius of 3.95 Å the confinement reduces diffusive mobility by orders of magnitude. In contrast, in large cages with a mean radius of 4.75 Å hydrogen molecules displays diffusive jump motion between different equilibrium sites inside the cages, visible at temperatures where bulk H2 is solid. The localization of H2 molecules observed in small cages can promote improved functional properties valuable for hydrogen storage applications.
A 2-Cys peroxiredoxin in response to oxidative stress in the pine wood nematode, Bursaphelenchus xylophilus
Authors: Li Zhen , Zhang Qingwen , Zhou Xuguo 
Published: June 2016

AbstractThe pine wood nematode,Bursaphelenchus xylophilus, is the causal agent of pine wilt disease that has devastated pine forests in Asia. Parasitic nematodes are known to have evolved antioxidant stress responses that defend against host plant defenses. In this study, the infestation of whitebark pine,Pinus bungean, withB. xylophilusled to a significant increase in plant hydrogen peroxide (H2O2) and salicylic acid levels. Correspondingly, the expression of an antioxidative enzyme, 2-Cysteine peroxiredoxin (BxPrx), was elevated inB. xylophilusfollowing the H2O2treatments. Recombinant BxPrx, a thermal stabile and pH tolerant enzyme, exhibited high level of antioxidant activity against H2O2, suggesting that it is capable of protecting cells from free radical attacks. Immunohistochemical localization study showed that BxPrx was broadly expressed across different tissues and could be secreted outside the nematode. Finally, the number of BxPrx homologs in both dauer-like and fungi-feedingB. xylophiluswere comparable based on bioinformatics analysis of existing EST libraries, indicating a potential role of BxPrx in both propagative and dispersal nematodes. These combined results suggest that BxPrx is a key genetic factor facilitating the infestation and distribution ofB. xylophiluswithin pine hosts and consequently the spread of pine wilt disease.
Tumour Suppressor Adenomatous Polyposis Coli (APC) localisation is regulated by both Kinesin-1 and Kinesin-2
Authors: Ruane Peter T. , Gumy Laura F. , Bola Becky , Anderson Beverley , Wozniak Marcin J. , Hoogenraad Casper C. , Allan Victoria J. 
Published: June 2016

AbstractMicrotubules and their associated proteins (MAPs) underpin the polarity of specialised cells. Adenomatous polyposis coli (APC) is one such MAP with a multifunctional agenda that requires precise intracellular localisations. Although APC has been found to associate with kinesin-2 subfamily members, the exact mechanism for the peripheral localization of APC remains unclear. Here we show that the heavy chain of kinesin-1 directly interacts with the APC C-terminus, contributing to the peripheral localisation of APC in fibroblasts. In rat hippocampal neurons the kinesin-1 binding domain of APC is required for its axon tip enrichment. Moreover, we demonstrate that APC requires interactions with both kinesin-2 and kinesin-1 for this localisation. Underlining the importance of the kinesin-1 association, neurons expressing APC lacking kinesin-1-binding domain have shorter axons. The identification of this novel kinesin-1-APC interaction highlights the complexity and significance of APC localisation in neurons.
Significant decrease in peripheral regulatory B cells is an immunopathogenic feature of dermatomyositis
Authors: Li Wenli , Tian Xiaolan , Lu Xin , Peng Qinglin , Shu Xiaoming , Yang Hanbo , Li Yuanli , Wang Yan , Zhang Xuezhi , Liu Qingyan , Wang Guochun 
Published: June 2016

AbstractRegulatory B cells (Bregs) are critical in maintaining self-tolerance. Their role in dermatomyositis (DM), an autoimmune disease characterized by inappropriate regulation of hyperactivated B and T cells, has not been clearly defined. In the current study, we performed flow cytometry analysis of studied CD19+ CD24highCD38high Breg subpopulations in blood samples from 30 patients with DM, 37 diseased controls and 23 healthy controls. A significant decrease was observed in the frequency of Bregs in DM patients compared to that in diseased controls (p < 0.0001) and in healthy controls (p < 0.0001). And the prevalence of Bregs deficiency (defined as Bregs/B cells < 0.50% in this study) in DM patients went as high as 73.3%. Furthermore, DM patients with positive myositis specific autoantibody often had lower Bregs levels than negative patients (p = 0.036) and lower level of Bregs was also found in DM patients with interstitial lung disease than in DM patients without (p = 0.041). In a follow-up study, seven DM patients were considered to be in remission stage and their Breg levels were found to have significantly increased after treatment (p = 0.022). Our research revealed that Breg deficiency is an immunopathogenic feature of DM and provided insights into the design of new immunotherapy target for DM clinical interventions.
Novel TetR family transcriptional factor regulates expression of multiple transport-related genes and affects rifampicin resistance in Mycobacterium smegmatis
Authors: Liu Huicong , Yang Min , He Zheng-Guo 
Published: June 2016

AbstractTransport-related genes significantly affect bacterial antibiotic resistance. However, the effects of these genes and their regulation of bacterial drug resistance in several mycobacterial species, including the fast-growing Mycobacterium smegmatis, the pathogen M. tuberculosis and M. avium have not been clearly characterized. We identified Ms4022 (MSMEG_4022) as a novel TetR family regulator that activates the expression of seven transport-related genes and affects drug resistance in M. smegmatis. Overexpression of Ms4022 inhibited M. smegmatis growth and enhanced mycobacterial resistance to the anti-tuberculosis drug rifampicin (RIF). By contrast, the Ms4022-deleted mycobacterial strain has shown sensitive to RIF. Ms4022 recognized three 19 bp non-palindromic motifs containing a 9 bp conserved region at their 5′ end and it directly regulated seven transport-related genes, which affects mycobacterial resistance to RIF. Overexpression of three of seven transport-related genes (Ms1448, Ms1613 and Ms5278) inhibited the growth of M. smegmatis. This study improves our understanding of the function of mycobacterial transport-related genes and their regulation of bacterial drug resistance.
An Atomic Force Microscope with Dual Actuation Capability for Biomolecular Experiments
Authors: Sevim Semih , Shamsudhin Naveen , Ozer Sevil , Feng Luying , Fakhraee Arielle , Ergeneman Olgaç , Pané Salvador , Nelson Bradley J. , Torun Hamdi 
Published: June 2016

AbstractWe report a modular atomic force microscope (AFM) design for biomolecular experiments. The AFM head uses readily available components and incorporates deflection-based optics and a piezotube-based cantilever actuator. Jetted-polymers have been used in the mechanical assembly, which allows rapid manufacturing. In addition, a FeCo-tipped electromagnet provides high-force cantilever actuation with vertical magnetic fields up to 0.55 T. Magnetic field calibration has been performed with a micro-hall sensor, which corresponds well with results from finite element magnetostatics simulations. An integrated force resolution of 1.82 and 2.98 pN, in air and in DI water, respectively was achieved in 1 kHz bandwidth with commercially available cantilevers made of Silicon Nitride. The controller and user interface are implemented on modular hardware to ensure scalability. The AFM can be operated in different modes, such as molecular pulling or force-clamp, by actuating the cantilever with the available actuators. The electromagnetic and piezoelectric actuation capabilities have been demonstrated in unbinding experiments of the biotin-streptavidin complex.
CACNA1C hypermethylation is associated with bipolar disorder
Authors: Starnawska A , Demontis D , Pen A , Hedemand A , Nielsen A L , Staunstrup N H , Grove J , Als T D , Jarram A , O'Brien N L , Mors O , McQuillin A , Børglum A D , Nyegaard M 
Published: June 2016

AbstractThe CACNA1C gene, encoding a subunit of the L-type voltage-gated calcium channel is one of the best-supported susceptibility genes for bipolar disorder (BD). Genome-wide association studies have identified a cluster of non-coding single-nucleotide polymorphisms (SNPs) in intron 3 to be highly associated with BD and schizophrenia. The mechanism by which these SNPs confer risk of BD appears to be through an altered regulation of CACNA1C expression. The role of CACNA1C DNA methylation in BD has not yet been addressed. The aim of this study was to investigate if CACNA1C DNA methylation is altered in BD. First, the methylation status of five CpG islands (CGIs) across CACNA1C in blood from BD subjects (n=40) and healthy controls (n=38) was determined. Four islands were almost completely methylated or completely unmethylated, while one island (CGI 3) in intron 3 displayed intermediate methylation levels. In the main analysis, the methylation status of CGI 3 was analyzed in a larger sample of BD subjects (n=582) and control individuals (n=319). Out of six CpG sites that were investigated, five sites showed significant hypermethylation in cases (lowest P=1.16 × 10−7 for CpG35). Nearby SNPs were found to influence the methylation level, and we identified rs2238056 in intron 3 as the strongest methylation quantitative trait locus (P=2.6 × 10−7) for CpG35. In addition, we found an increased methylation in females, and no difference between bipolar I and II. In conclusion, we find that CACNA1C methylation is associated with BD and suggest that the regulatory effect of the non-coding risk variants involves a shift in DNA methylation.
Tunable triangular pulse‐generator for ISM band radar
Authors: Won Y.‐S. , Kim C.‐H. , Lee H.‐I. , Lee S.‐G. 
Published: June 2016

A simple tunable triangular pulse‐generator for 24 GHz ISM band pulse radar is reported, which consists of V–I converters and charge pumps where the control signals are produced by a resistive ladder, digital logic, and switches. In the proposed pulse‐generator, by applying tunable input signals to the V–I converters, the amount of currents flowing through the charge pumps can be controlled without requiring the current source switching, and thus the switching noise can be avoided. Implemented in a 0.13 μm CMOS technology, measured tuning ranges of pulse‐width and ‐amplitude are 12.7–28.5 ns and 15.0–216.1 mVpp, respectively, while dissipating 4.5 mW from a 1.5 V supply.
Calculation of the inductance and AC resistance of planar rectangular coils
Authors: Kim D.‐H. , Park Y.‐J. 
Published: June 2016

An effective calculation method for AC resistance and the inductance of planar rectangular spiral coils is proposed. For the calculation, a volume filament model and its equivalent circuit are provided. By using the method, AC resistance and inductance are calculated accurately in megahertz frequency range by including both skin and proximity effects. The method is verified with experiments and used to optimise rectangular spiral coils for the maximum quality factor (Q‐factor) at 6.78 MHz. A small planar rectangular coil is shown to have the maximum Q‐factor when the width of the innermost coil loop is about a half of that of the outermost coil loop.
Revealing a paradox in scientific advice to governments: the struggle between modernist and reflexive logics within the PBL Netherlands Environmental Assessment Agency
Authors: Kunseler Eva-Maria 
Published: June 2016

AbstractWhile governmental scientific advisers attempt to innovate their practices to become more reflexive and interactive, they cannot escape the modernist fundaments that constitute these practices. How do governmental scientific advisers make sense of this paradoxical situation? Using the transition process in the PBL Netherlands Environmental Assessment Agency as a paradigmatic case, this article explores how four actor groups—the PBL management team, clients, PBL practitioners and external peers—involved in PBL’s transition process disclose their views on institutional redesign and, while doing that, express their beliefs on what they think scientific advice “is” and “should do”. Frame analysis identifies three coexisting frames of PBL’s (future) role and identity—PBL as integrated assessment specialist, PBL as think tank and PBL as trustworthy expert. Implicated in these frames are reflexive beliefs in a “professional culture of humility” that seem to replace the modernist “science speaking truth to power” mode of advising in the PBL organization. At the same time modernist beliefs in the science/politics demarcation, objectivity and scientific privilege persist, in part by revisiting them in view of the newly found reflexive principles of humility, transparency and deliberation. In conclusion, this empirical work illustrates how questioning and deliberating about the role and identity of one’s own organization is the first step to advance institutional redesign in scientific advice to governments. The challenge for governmental science advisers is to “translate” processes of institutional redesign into concrete social and cultural changes, bringing about a transformation in conceptions of what scientific advice is and should do all along. This article is published as part of a thematic collection on scientific advice to governments.
Musashi-2 (MSI2) supports TGF-β signaling and inhibits claudins to promote non-small cell lung cancer (NSCLC) metastasis
Authors: Kudinov Alexander E. , Deneka Alexander , Nikonova Anna S. , Beck Tim N. , Ahn Young-Ho , Liu Xin , Martinez Cathleen F. , Schultz Fred A. , Reynolds Samuel , Yang Dong-Hua , Cai Kathy Q. , Yaghmour Khaled M. , Baker Karmel A. , Egleston Brian L. , Nicolas Emmanuelle , Chikwem Adaeze , Andrianov Gregory , Singh Shelly , Borghaei Hossein , Serebriiskii Ilya G. , Gibbons Don L. , Kurie Jonathan M. , Golemis Erica A. , Boumber Yanis 
Published: June 2016

Significance
The evolutionarily conserved RNA-binding protein Musashi-2 (MSI2) regulates mRNA translation and influences multiple biological processes, including maintenance of stem cell identity. This work for the first time, to our knowledge, identifies that more aggressive patient tumors have higher MSI2 levels. We define a critical role for MSI2 in supporting non-small cell lung cancer (NSCLC) invasiveness and further define claudins 3, 5, and 7 (CLDN3, CLDN5, and CLDN7), TGF-β receptor 1 (TGFβR1), and the small mothers against decapentaplegic homolog 3 (SMAD3) as targets through which MSI2 regulates this process. The observation that MSI2 expression is progressively elevated from an early stage in human NSCLC tumors suggests that this protein may play an essential role in the reprogramming of TGF-β signaling from growth-inhibiting to invasion-promoting during oncogenesis.
Overexpression of a pH-sensitive nitrate transporter in rice increases crop yields
Authors: Fan Xiaorong , Tang Zhong , Tan Yawen , Zhang Yong , Luo Bingbing , Yang Meng , Lian Xingming , Shen Qirong , Miller Anthony John , Xu Guohua 
Published: June 2016

SignificanceSignificant progress has been made in our understanding of plant adaptive responses to maintain cellular pH under varied N supply forms. Rice is a plant adapted to grow in waterlogged or dryland environments, in contrast to other crops, such as wheat, soybean, and maize. The nitrate transporter OsNRT2.3b provides a molecular mechanism explaining plant adaptation to the ammonium-nitrate supply shift between the waterlogged and drained soil environments. The sensing of cytosolic pH by OsNRT2.3b can function to improve rice nitrogen use efficiency and pH balance, providing an explanation for plant adaptation to changes in the form of N supply.
IGF-1 degradation by mouse mast cell protease 4 promotes cell death and adverse cardiac remodeling days after a myocardial infarction
Authors: Tejada Thor , Tan Lin , Torres Rebecca A. , Calvert John W. , Lambert Jonathan P. , Zaidi Madiha , Husain Murtaza , Berce Maria D. , Naib Hussain , Pejler Gunnar , Abrink Magnus , Graham Robert M. , Lefer David J. , Naqvi Nawazish , Husain Ahsan 
Published: June 2016

SignificanceCoronary heart disease is a leading cause of death worldwide. After acute myocardial infarction, early reperfusion limits infarct progression and improves clinical outcomes. However, despite reperfusion, the incidence of heart failure and cardiovascular deaths remains unacceptably high. Here, we report that a few days after ischemia, the reperfused heart transiently elaborates the cardioprotective polypeptide, insulin-like growth factor-1 (IGF-1). However, tissue IGF-1 levels increase only transiently because it is rapidly degraded by the chymase, mouse mast cell protease 4. Mouse mast cell protease 4 deletion promotes cardiac cell survival by reducing IGF-1 degradation, which ameliorates cardiac dysfunction caused by ischemic injury. Our findings suggest that chymase inhibition may be a viable therapeutic approach to enhance late cardioprotection in postischemic heart disease.
Coherent two-dimensional terahertz-terahertz-Raman spectroscopy
Authors: Finneran Ian A. , Welsch Ralph , Allodi Marco A. , Miller Thomas F. , Blake Geoffrey A. 
Published: June 2016

Significance
The thermally populated motions of liquids, including hydrogen bonds, low-energy bending vibrations, conformational torsions, and hindered rotations, are resonant in the terahertz region of the spectrum. These motions regulate solvation, macromolecular structure, and vibrational energy flow in liquid-phase chemistry. By exciting terahertz motions nonlinearly with multiple pulses of terahertz light, we can measure their anharmonic coupling and distribution of chemical environments. We can also begin to control their quantum coherence and population, a critical step forward in the control of liquid-phase chemistry with light.
Group III-nitride nanowires
Authors: Bao A. 
Published: June 2016

Group III-nitride nanowires have attracted a lot of research interest in the past decade. They contain both the intrinsic properties of III-nitride materials and some unique properties induced by the nanowire structures. This article reviews the growth methods to obtain III-nitride nanowires, and discusses the pros and cons of both top-down and bottom-up approaches, with detailed discussions on different epitaxy methods. The most widely used catalyst-induced epitaxy and extrinsic particle free epitaxy to grow III-nitride nanowires are compared. The properties of those nanowires make them promising candidates for a broad range of applications, including optoelectronic, electronic and electromechanical devices, which are also presented, with a focus on the current challenges and recent progresses. This review was submitted as part of the 2016 Materials Literature Review Prize of the Institute of Materials, Minerals and Mining run by the Editorial Board of MST. Sponsorship of the prize by TWI Ltd is gratefully acknowledged.