bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-Heating Effects In Polysilicon Source Gated Transistors
Authors: Sporea R. A. , Burridge T. , Silva S. R. P. 
Published: September 2015

AbstractSource-gated transistors (SGTs) are thin-film devices which rely on a potential barrier at the source to achieve high gain, tolerance to fabrication variability and low series voltage drop, relevant to a multitude of energy-efficient, large-area, cost effective applications. The current through the reverse-biased source barrier has a potentially high positive temperature coefficient, which may lead to undesirable thermal runaway effects and even device failure through self-heating. Using numerical simulations we show that, even in highly thermally-confined scenarios and at high current levels, self-heating is insufficient to compromise device integrity. Performance is minimally affected through a modest increase in output conductance, which may limit the maximum attainable gain. Measurements on polysilicon devices confirm the simulated results, with even smaller penalties in performance, largely due to improved heat dissipation through metal contacts. We conclude that SGTs can be reliably used for high gain, power efficient analog and digital circuits without significant performance impact due to self-heating. This further demonstrates the robustness of SGTs.
MINCR is a MYC-induced lncRNA able to modulate MYC’s transcriptional network in Burkitt lymphoma cells
Authors: Doose Gero , Haake Andrea , Bernhart Stephan H. , López Cristina , Duggimpudi Sujitha , Wojciech Franziska , Bergmann Anke K. , Borkhardt Arndt , Burkhardt Birgit , Claviez Alexander , Dimitrova Lora , Haas Siegfried , Hoell Jessica I. , Hummel Michael , Karsch Dennis , Klapper Wolfram , Kleo Karsten , Kretzmer Helene , Kreuz Markus , Küppers Ralf , Lawerenz Chris , Lenze Dido , Loeffler Markus , Mantovani-Löffler Luisa , Möller Peter , Ott German , Richter Julia , Rohde Marius , Rosenstiel Philip , Rosenwald Andreas , Schilhabel Markus , Schneider Markus , Scholz Ingrid , Stilgenbauer Stephan , Stunnenberg Hendrik G. , Szczepanowski Monika , Trümper Lorenz , Weniger Marc A. ,   ICGC MMML-Seq Consortium, Hoffmann Steve , Siebert Reiner , Iaccarino Ingram , Richter Gesine , Siebert Reiner , Wagner Susanne , Haake Andrea , Richter Julia , Eils Roland , Lawerenz Chris , Radomski Sylwester , Scholz Ingrid , Borst Christoph , Burkhardt Birgit , Claviez Alexander , Dreyling Martin , Eberth Sonja , Einsele Hermann , Frickhofen Norbert , Haas Siegfried , Hansmann Martin-Leo , Karsch Dennis , Kneba Michael , Lisfeld Jasmin , Mantovani-Löffler Luisa , Rohde Marius , Stadler Christina , Staib Peter , Stilgenbauer Stephan , Ott German , Trümper Lorenz , Zenz Thorsen , Hansmann Martin-Leo , Kube Dieter , Küppers Ralf , Weniger Marc , Haas Siegfried , Hummel Michael , Klapper Wolfram , Kostezka Ulrike , Lenze Dido , Möller Peter , Rosenwald Andreas , Szczepanowski Monika , Ammerpohl Ole , Aukema Sietse , Binder Vera , Borkhardt Arndt , Haake Andrea , Hezaveh Kebria , Hoell Jessica , Leich Ellen , Lichter Peter , Lopez Christina , Nagel Inga , Pischimariov Jordan , Radlwimmer Bernhard , Richter Julia , Rosenstiel Philip , Rosenwald Andreas , Schilhabel Markus , Schreiber Stefan , Vater Inga , Wagner Rabea , Siebert Reiner , Bernhart Stephan H. , Binder Hans , Brors Benedikt , Doose Gero , Eils Jürgen , Eils Roland , Hoffmann Steve , Hopp Lydia , Kretzmer Helene , Kreuz Markus , Korbel Jan , Langenberger David , Loeffler Markus , Radomski Sylwester , Rosolowski Maciej , Schlesner Matthias , Stadler Peter F. , Sungalee Stefanie 
Published: September 2015

Significance
Gains of the MYC gene are the most common imbalances in cancer and are associated with poor prognosis, particularly in B-cell lymphoma. Recent advances in DNA sequencing have revealed the existence of thousands of long noncoding RNAs (lncRNAs) with unknown functional relevance. We have here identified a MYC-regulated lncRNA that we named MYC-induced long noncoding RNA (MINCR) that has a strong correlation with MYC expression in cancer. We show that MINCR is functional and controls cell cycle progression by influencing the expression of MYC-regulated cell cycle genes. MINCR is, therefore, a novel player in MYC’s transcriptional network, with the potential to open new therapeutic windows in the fight against malignant lymphoma and, possibly, all cancers that rely on MYC expression.
Caenorhabditis elegans
ALG-1 antimorphic mutations uncover functions for Argonaute in microRNA guide strand selection and passenger strand disposal
Authors: Zinovyeva Anna Y. , Veksler-Lublinsky Isana , Vashisht Ajay A. , Wohlschlegel James A. , Ambros Victor R. 
Published: September 2015

Significance
Loading of Argonautes with the correct strand of the pre-miRNA duplex and disposal of the other strand are essential steps in microRNA biogenesis. Here we report characterization of the protein and microRNA populations associated with mutant ALG-1 Argonautes that are defective in transitioning from microRNA processing to target repression. We show that mutant Argonaute erroneously associates with the normally discarded microRNA* strands, signifying a role for Argonaute ALG-1 in microRNA strand selection. Accumulation of microRNA* is dependent on the microRNA identity, suggesting that specific microRNA features allow wild-type Argonautes to distinguish among different microRNAs. These findings are relevant to understanding Argonaute roles in microRNA biogenesis and, more broadly, to the functions of microRNAs in development and disease.
TNF-α–stimulated fibroblasts secrete lumican to promote fibrocyte differentiation
Authors: Pilling Darrell , Vakil Varsha , Cox Nehemiah , Gomer Richard H. 
Published: September 2015

SignificanceFibrosis is involved in 30–45% of deaths in the U.S. The disease may involve a runaway positive feedback loop between fibroblasts and monocyte-derived fibrocytes. The signals from fibrocytes to fibroblasts include inflammatory cytokines such as TNF-α, but the signals from TNF-α-stimulated fibroblasts to fibrocytes are unknown. We find that one of these signals is the protein lumican, and show that lumican levels are increased in fibrotic lesions. The identification of lumican as a signal in fibrotic tissues that promotes fibrocyte differentiation represents a major advance in our understanding of the regulation of the innate immune system, supports the positive feedback loop model of fibrosis, and indicates that lumican-inhibiting drugs may be beneficial in regulating fibrosis.
Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens
Authors: Julien Jean-Philippe , Lee Jeong Hyun , Ozorowski Gabriel , Hua Yuanzi , Torrents de la Peña Alba , de Taeye Steven W. , Nieusma Travis , Cupo Albert , Yasmeen Anila , Golabek Michael , Pugach Pavel , Klasse P. J. , Moore John P. , Sanders Rogier W. , Ward Andrew B. , Wilson Ian A. 
Published: September 2015

Significance
A successful HIV-1 vaccine should generate an immune response capable of neutralizing the enormous diversity of globally circulating viruses. Here, we report the discovery and characterization of two clade C recombinant envelope glycoprotein trimers with native-like structural and antigenic properties, including epitopes for all known classes of broadly neutralizing antibodies (bnAbs). Together with previously described trimers from other clades, these two new trimers will aid in immunization strategies designed to induce bnAbs to HIV-1.
Long-term litter decomposition controlled by manganese redox cycling
Authors: Keiluweit Marco , Nico Peter , Harmon Mark E. , Mao Jingdong , Pett-Ridge Jennifer , Kleber Markus 
Published: September 2015

SignificanceThe rate-controlling mechanisms of litter decomposition are of fundamental importance for ecosystem nutrient cycling, productivity, and net carbon (C) balance. Current C cycling models rely primarily on climatic factors and lignin content as the main predictors of litter decomposition rates. Here, we show how the ability of the integrated plant–soil system to promote active redox cycling of manganese (Mn) regulates litter decomposition. Our work suggests that incorporating the coupling of litter decomposition and other elemental cycles, such as the Mn cycle, into conceptual and numerical models may significantly improve our mechanistic understanding and predictions of C cycling in terrestrial ecosystems.
Fibroblast growth factor 9 is a novel modulator of negative affect
Authors: Aurbach Elyse L. , Inui Edny Gula , Turner Cortney A. , Hagenauer Megan H. , Prater Katherine E. , Li Jun Z. , Absher Devin , Shah Najmul , Blandino Peter , Bunney William E. , Myers Richard M. , Barchas Jack D. , Schatzberg Alan F. , Watson Stanley J. , Akil Huda 
Published: September 2015

Significance
Molecular mechanisms mediating negative emotion and contributing to major depression remain elusive: here, we present evidence implicating fibroblast growth factor 9 (FGF9) as a key mediator. We use whole-transcriptome studies of postmortem human tissue to demonstrate that FGF9 is elevated in depression. Reverse translation animal studies demonstrate that both endogenous and exogenous FGF9 promotes anxiety- and depression-like behavior. Conversely, localized blockade of endogenous FGF9 expression decreases anxiety behavior. To our knowledge, this paper is the first description of hippocampal FGF9 function and the first evidence implicating FGF9 in negative affect. Thus, FGF9 represents a novel target for treating affective disorders. Moreover, our findings suggest that FGF2 and FGF9 work in functional opposition; we hypothesize that the balance between FGF factors may prove critical for optimal regulation of mood.
Caspase 3 cleavage of Pax7 inhibits self-renewal of satellite cells
Authors: Dick Sarah A. , Chang Natasha C. , Dumont Nicolas A. , Bell Ryan A. V. , Putinski Charis , Kawabe Yoichi , Litchfield David W. , Rudnicki Michael A. , Megeney Lynn A. 
Published: September 2015

Significance
Satellite cells form the resident stem cell population in adult skeletal muscle, providing the foundation for postnatal growth and repair of this tissue. Satellite cell self-renewal is maintained by the paired-box transcription factor Pax7, suggesting that this protein is a key determinant in managing cell fate decisions for this niche. Here, we show activation of caspase 3 protease limits satellite cell self-renewal, through targeted cleavage and inactivation of Pax7 in a casein kinase (CK2)-dependent manner. Temporal regulation of caspase 3 activity may offer a robust mechanism to control the satellite cell compartment and enhance skeletal muscle regeneration.
A mechanically driven form of Kirigami as a route to 3D mesostructures in micro/nanomembranes
Authors: Zhang Yihui , Yan Zheng , Nan Kewang , Xiao Dongqing , Liu Yuhao , Luan Haiwen , Fu Haoran , Wang Xizhu , Yang Qinglin , Wang Jiechen , Ren Wen , Si Hongzhi , Liu Fei , Yang Lihen , Li Hejun , Wang Juntong , Guo Xuelin , Luo Hongying , Wang Liang , Huang Yonggang , Rogers John A. 
Published: September 2015

Significance
Existing options in three-dimensional (3D) assembly of micro/nanomaterials are constrained by a narrow accessible range of materials and/or 3D geometries. Here we introduce concepts for a form of Kirigami for the precise, mechanically driven assembly of 3D mesostructures from 2D micro/nanomembranes with strategically designed geometries and patterns of cuts. Theoretical and experimental studies in a broad set of examples demonstrate the applicability across length scales from macro to micro and nano, in materials ranging from monocrystalline silicon to metal and plastic, with levels of topographical complexity that significantly exceed those possible with other schemes. The resulting engineering options in functional 3D mesostructures have important implications for construction of advanced micro/nanosystems technologies.
Targeting protein translation, RNA splicing, and degradation by morpholino-based conjugates in
Plasmodium falciparum
Authors: Garg Aprajita , Wesolowski Donna , Alonso Dulce , Deitsch Kirk W. , Ben Mamoun Choukri , Altman Sidney 
Published: September 2015

Significance
Malaria remains a major public health issue worldwide and world health organization estimates ∼198 million cases and ∼584,000 deaths in the year of 2013 alone due to malaria. Lack of an effective vaccine and rapid emergence of drug resistance are two major causes of this persistent problem. Understanding the biology of the parasite and studies of its gene function are essential to identify potential drug targets. Here we report a morpholino oligomer (MO)-based approach to alter gene expression via inhibition of post-transcriptional processes or by targeting mRNAs for degradation. The ease in design of the MO molecules presents a possibility for their use in large-scale genome functional analyses and possibly in malaria therapy.
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel
Authors: Cortés-Ciriano Isidro , van Westen Gerard J. P. , Bouvier Guillaume , Nilges Michael , Overington John P. , Bender Andreas , Malliavin Thérèse E. 
Published: September 2015

Abstract
Motivation: Recent large-scale omics initiatives have catalogued the somatic alterations of cancer cell line panels along with their pharmacological response to hundreds of compounds. In this study, we have explored these data to advance computational approaches that enable more effective and targeted use of current and future anticancer therapeutics.
Results: We modelled the 50% growth inhibition bioassay end-point (GI50) of 17 142 compounds screened against 59 cancer cell lines from the NCI60 panel (941 831 data-points, matrix 93.08% complete) by integrating the chemical and biological (cell line) information. We determine that the protein, gene transcript and miRNA abundance provide the highest predictive signal when modelling the GI50 endpoint, which significantly outperformed the DNA copy-number variation or exome sequencing data (Tukey’s Honestly Significant Difference, P &lt;0.05). We demonstrate that, within the limits of the data, our approach exhibits the ability to both interpolate and extrapolate compound bioactivities to new cell lines and tissues and, although to a lesser extent, to dissimilar compounds. Moreover, our approach outperforms previous models generated on the GDSC dataset. Finally, we determine that in the cases investigated in more detail, the predicted drug-pathway associations and growth inhibition patterns are mostly consistent with the experimental data, which also suggests the possibility of identifying genomic markers of drug sensitivity for novel compounds on novel cell lines.
Contact: terez@pasteur.fr; ab454@ac.cam.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Modeling Continuous Admixture
Authors: Zhou Ying , Qiu Hongxiang , Xu Shuhua 
Published: September 2015

AbstractHuman migration and human isolation serve as the driving forces of modern human civilization. Recent migrations of long isolated populations has resulted in genetically admixed populations. The history of population admixture is generally complex; however, understanding the admixture process is critical to both evolutionary and medical studies. Here, we utilized admixture induced linkage disequilibrium (LD) to infer occurrence of continuous admixture events, which is common for most existing admixed populations. Unlike previous studies, we expanded the typical continuous admixture model to a more general admixture scenario with isolation after a certain duration of continuous gene flow, and we demonstrated that such treatment significantly improved the accuracy of inference under complex admixture scenarios. Based on the extended models, we developed a method based on weighted LD to infer the admixture history considering continuous and complex demographic process of gene flow between populations. We evaluated the performance of the method by computer simulation and applied our method to real data analysis of a few well-known admixed populations.
Integrated Genome Browser: visual analytics platform for genomics
Authors: Freese Nowlan H. , Norris David C. , Loraine Ann E. 
Published: September 2015

AbstractMotivationGenome browsers that support fast navigation through vast data sets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser.ResultsHere we describe multiple updates to IGB, including all-new capability to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of data sets from RNA-Seq, ChIP-Seq, and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related data sets. To facilitate this, we enhanced IGB’s ability to consume data from diverse sources, including Galaxy, Distributed Annotation, and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data.AvailabilityIGB is open source and is freely available fromhttp://bioviz.org/igb.Contactaloraine@uncc.edu
Distinct Regulatory Changes Underlying Differential Expression of TEOSINTE BRANCHED1-CYCLOIDEA-PROLIFERATING CELL FACTOR Genes Associated with Petal Variations in Zygomorphic Flowers of Petrocosmea spp. of the Family Gesneriaceae
Authors: Yang Xia , Zhao Xiao-Ge , Li Chao-Qun , Liu Jing , Qiu Zhi-Jing , Dong Yang , Wang Yin-Zheng 
Published: September 2015

Abstract
CYCLOIDEA (CYC)-like genes, belonging to the plant-specific TCP transcription factor family that is named after TEOSINTE BRANCHED1 (TB1) from maize (Zea mays), CYC from Antirrhinum majus, and the PROLIFERATING CELL FACTORS (PCF) from rice (Oryza sativa), have conserved dorsal identity function in patterning floral zygomorphy mainly through specific expression in dorsal petals of a flower. Their expression changes are usually related to morphological diversity of zygomorphic flowers. However, it is still a challenge to elucidate the molecular mechanism underlying their expression differentiation. It is also unknown whether CINCINNATA (CIN)-like TCP genes, locally controlling cell growth and proliferation, are involved in the evolution of floral zygomorphy. To address these questions, we selected two closely related species, i.e. Petrocosmea glabristoma and Petrocosmea sinensis, with distinct petal morphology to conduct expression, hybridization, mutant, and allele-specific expression analyses. The results show that the size change of the dorsal petals between the two species is mainly mediated by the expression differentiation of CYC1C and CYC1D, while the shape variation of all petals is related to the expression change of CIN1. In reciprocal F1 hybrids, the expression of CYC1C, CYC1D, and CIN1 conforms to an additive inheritance mode, consistent with the petal phenotypes of hybrids. Through allele-specific expression analyses, we find that the expression differentiation of these TCP genes is underlain by distinctly different types of regulatory changes. We suggest that highly redundant paralogs with identical expression patterns and interspecific expression differentiation may be controlled by remarkably different regulatory pathways because natural selection may favor different regulatory modifications rather than coding sequence changes of key developmental genes in generating morphological diversity.
The determinants of tax evasion: a literature review
Authors: khlif Hichem , Achek Imen 
Published: September 2015

Purpose– The purpose of this article is to make a clear-cut distinction between tax evasion and neighbouring notions, present the theoretical justifications for the determinants of tax evasion, discuss some methodological issues related to the measurement of tax evasion and, finally, review the main results related to this topic and provide suggestions for future research. Tax evasion empirical research has been the subject of numerous studies during the past decade in developed and emerging economies.Design/methodology/approach– This paper focuses specifically on cross-country empirical studies.Findings– This paper shows that evidence is still limited, several approaches to measure tax evasion remain unexplored, results are mixed and four categories of variables have been identified in tax evasion literature, including demographic, cultural and behavioural, legal and institutional, and economic variables.Originality/value– This literature review represents a historical record and an introduction for researchers who aim to examine this topic in the future.
Predicting corporate failure: a systematic literature review of methodological issues
Authors: Appiah Kingsley Opoku , Chizema Amon , Arthur Joseph 
Published: September 2015

Purpose– This paper aims to review the existing literature systematically so as to contribute towards a better understanding of methodological problems of the classical statistical techniques, artificially intelligent expert systems and theoretical approaches to solve the corporate failure syndrome.Design/methodology/approach– This paper presented a systematic review of 83 articles reporting 137 prediction failure models published within 1966-2012 in scholarly reviewed journals in four main disciplines, namely, accounting, finance, banking and economics. The authors performed the systematic literature review with five main sources, namely, Science Direct, Google Scholar, Wiley Interscience, Metalib, Web of Science and Business Source Complete of the Social Sciences. The review modified the approaches used by Aziz and Dar (2006), Ravi and Ravi (2007) and Balcaen and Ooghe (2006).Findings– The results indicate significant body of prior literature on prediction of corporate failure, but a theoretically sound, highly accurate, simple and widely used corporate failure prediction model for stakeholders has yet to be developed.Originality/value– This paper contributes towards a systematic understanding of the methodological problems associated with the statistical, artificially intelligent expert systems and theoretical approaches to solve the corporate failure prediction problems faced by firms in 11 countries.
R
&
D expenditures and future innovation: evidence from the chemical industry
Authors: Sun Li 
Published: September 2015

Purpose
– This study aims to investigate whether research and development (R
&
D) expenditures drive future innovation in the chemical industry.

Design/methodology/approach
– This study examines the relation between R
&
D expenditures for the period of 2000-2002 and the innovation effect measured by the Malmquist Productivity Index (MPI) for the period of 2003-2005. Under the MPI, the innovation effect is measured as the “shift” in a firm’s production frontier between two periods (2003-2005).

Findings
– Results indicate that there is a significant and positive relation between R
&
D expenditures and future innovation among chemical firms.

Originality/value
– This study should be of interest to financial accounting policy makers, R
&
D-intensive companies and investors. To policy makers, they may consider the possibility of permitting R
&
D-intensive companies to recognize R
&
D expenditures as assets. In other words, R
&
D-intensive companies can capitalize and amortize their R
&
D expenditures, as R
&
D expenditures can bring them future economic benefits. To R
&
D-intensive companies, the results may encourage them to keep up their R
&
D activities. Moreover, this study can increase individual investors’ confidence in investing companies with high-level R
&
D activities in an R
&
D-intense industry.