bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analytical modelling of multi‐mass flexible rocking structures
Authors: Acikgoz Sinan , DeJong Matthew J. 
Published: April 2016

SummaryThis paper presents a new analytical model for describing the large rocking response of an elastic multi‐mass structure resting on ideally rigid ground. Using the experimental results from a rocking steel column, the ability of the proposed analytical model to estimate the rocking and translational acceleration response under free vibration, pulse and earthquake excitations is evaluated. It is observed that the classical treatment of impact may result in an unrealistically large transfer of energy to vibrations. Therefore a new Dirac‐delta type impact model that spreads the effects of impact over time and space is proposed. The use of a Dirac‐delta model and accurate restitution factors play a pivotal role in prediction of rocking and acceleration responses. In order to characterize the nonlinear response better, a modal analysis of the linearized system is proposed. With this approach, the vibration mode frequencies and shapes during rocking action were determined. A comparison of analytical and experimental modal estimations suggests good agreement. The results emphasize that the vibration characteristics of several vibration modes are affected by rocking action, and these modes may be excited at impact. Copyright © 2016 John Wiley & Sons, Ltd.
Trend analysis of temperature and precipitation extremes in major grain producing area of China
Authors: Tian Jiyang , Liu Jia , Wang Jianhua , Li Chuanzhe , Nie Hanjiang , Yu Fuliang 
Published: April 2016

ABSTRACTTo identify whether the spatial and temporal distribution of temperature extremes and precipitation extremes has changed in central and eastern China including Henan, Shandong, Anhui and Jiangsu provinces, the spatial and temporal distributions of extreme temperature and precipitation indices trends during 1961–2011 were investigated and analysed. To guarantee the accuracy of trend analysis, daily maximum and minimum surface temperature and daily precipitation from 299 meteorological stations were used. Eight extreme temperature indices and seven extreme precipitation indices were chosen. Mann–Kendall method was used to check the statistical significance of trends, while Sen's nonparametric method was used to calculate the trend magnitudes. The analyses of extreme temperature indices detected significant and stable trends in the majority of the stations, especially for the most part of southern Anhui and southern Jiangsu provinces. The strongly stable downward trends in cold extremes and the strongly stable upward trends in hot extremes were recorded in most of the regions. In contrast, significant and stable positive trends were insignificantly recorded for precipitation extremes in the study area, which predominantly occurred in the southern part of the region. Furthermore, the positive trends were more frequent than the negative trends in most extreme precipitation indices. The results may provide a reference for a more particular knowledge of the climate change in this region and provide guidance for agriculture development.
Quality‐control of an hourly rainfall dataset and climatology of extremes for the UK
Authors: Blenkinsop Stephen , Lewis Elizabeth , Chan Steven C. , Fowler Hayley J. 
Published: April 2016

ABSTRACTSub‐daily rainfall extremes may be associated with flash flooding, particularly in urban areas but, compared with extremes on daily timescales, have been relatively little studied in many regions. This paper describes a new, hourly rainfall dataset for the UK based on ∼1600 rain gauges from three different data sources. This includes tipping bucket rain gauge data from the UK Environment Agency (EA), which has been collected for operational purposes, principally flood forecasting. Significant problems in the use of such data for the analysis of extreme events include the recording of accumulated totals, high frequency bucket tips, rain gauge recording errors and the non‐operation of gauges. Given the prospect of an intensification of short‐duration rainfall in a warming climate, the identification of such errors is essential if sub‐daily datasets are to be used to better understand extreme events. We therefore first describe a series of procedures developed to quality control this new dataset. We then analyse ∼380 gauges with near‐complete hourly records for 1992–2011 and map the seasonal climatology of intense rainfall based on UK hourly extremes using annual maxima, n‐largest events and fixed threshold approaches. We find that the highest frequencies and intensities of hourly extreme rainfall occur during summer when the usual orographically defined pattern of extreme rainfall is replaced by a weaker, north–south pattern. A strong diurnal cycle in hourly extremes, peaking in late afternoon to early evening, is also identified in summer and, for some areas, in spring. This likely reflects the different mechanisms that generate sub‐daily rainfall, with convection dominating during summer. The resulting quality‐controlled hourly rainfall dataset will provide considerable value in several contexts, including the development of standard, globally applicable quality‐control procedures for sub‐daily data, the validation of the new generation of very high‐resolution climate models and improved understanding of the drivers of extreme rainfall.
The Importance of Relative Reaction Rates in the Optimization of Detailed Kinetic Models
Authors: Manion Jeffrey A. , McGivern W. Sean 
Published: April 2016

ABSTRACTNumerous mathematical tools intended to adjust rate constants employed in complex detailed kinetic models to make them consistent with multiple sets of experimental data have been reported in the literature. Application of such model optimization methods typically begins with the assignment of uncertainties in the absolute rate constants in a starting model, followed by variation of the rate constants within these uncertainty bounds to tune rate parameters to match model outputs to experimental observations. The present work examines the impact of including information on relative reaction rates in the optimization strategy, which is not typically done in current implementations. It is shown that where such rate constant data are available, the available parameter space changes dramatically due to the correlations inherent in such measurements. Relative rate constants are typically measured with greater relative accuracy than corresponding absolute rate constant measurements. This greater accuracy further reduces the available parameter space, which significantly affects the uncertainty in the model outcomes as a result of kinetic parameter uncertainties. We demonstrate this effect by considering a simple example case emulating an ignition event and show that use of relative rate measurements leads to a significantly smaller uncertainty in the output ignition delay time in comparison with results based on absolute measurements. This is true even though the same range of absolute rate constants is sampled in each case. Implications of the results with respect to the maintenance of physically realistic kinetics in optimized models are discussed, and suggestions are made for the path forward in the refinement of detailed kinetic models.
Posterior cricoarytenoid muscle electrophysiologic changes are predictive of vocal cord paralysis with recurrent laryngeal nerve compressive injury in a canine model
Authors: Puram Sidharth V. , Chow Harold , Wu Che‐Wei , Heaton James T. , Kamani Dipti , Gorti Gautham , Chiang Feng Yu , Dionigi Gianlorenzo , Barczynski Marcin , Schneider Rick , Dralle Henning , Lorenz Kerstin , Randolph Gregory W. 
Published: April 2016

Objectives/HypothesisInjury to the recurrent laryngeal nerve (RLN) is a dreaded complication of endocrine surgery. Intraoperative neural monitoring (IONM) has been increasingly utilized to assess the functional status of the RLN. Although the posterior cricoarytenoid muscle (PCA) is innervated by the RLN as the abductor of the larynx, PCA electromyography (EMG) is infrequently recorded during IONM and PCA activity after RLN compressive injury remains poorly characterized.Study DesignSingle‐subject prospective animal study.MethodsWe employed a canine model to identify postcricoid EMG correlates of postoperative vocal cord paralysis (VCP). Postcricoid electrode recordings were obtained before and after compressive RLN injury associated with VCP.ResultsNormative postcricoid recordings revealed mean amplitude of 1288 microvolt (μV) and latency of 8.2 millisecond (ms) with maximum (1 milliamp [mA]) vagal stimulation, and mean amplitude of 1807 μV and latency of 3.5 ms with maximum (1 mA) RLN stimulation. Following injury that was associated with VCP, there was 62.1% decrement in postcricoid EMG amplitude with maximum vagal stimulation and 80% decrement with maximum RLN stimulation. Threshold stimulation of the vagus increased by 23%, and there was a corresponding 42% decrease in amplitude. For RLN stimulation, latency increased by 17.3% following injury, whereas threshold stimulation increased by 61% with 35.5% decrement in EMG amplitude. Thus, if RLN amplitude decreases by ≥ 80%, with absolute amplitude of ≤ 300 μV or less and latency increase of ≥ 10%, RLN injury is likely associated with VCP.ConclusionOur results predict postoperative VCP based on postcricoid electromyographic IONM and may guide surgical decision making.Level of EvidenceNA Laryngoscope, 126:2744–2751, 2016
Polymeric Nanohybrids as a New Class of Therapeutic Biotransporters
Authors: Whitlow Jonathan , Pacelli Settimio , Paul Arghya 
Published: April 2016

A possible solution to enhance existing drug and gene therapies is to develop hybrid nanocarriers capable of delivering therapeutic agents in a controlled and targeted manner. This goal can be achieved by designing nanohybrid systems, which combine organic or inorganic nanomaterials with biomacromolecules into a single composite. The unique combination of properties along with their facile fabrication enables the design of smart carriers for both drug and gene delivery. These hybrids can be further modified with cell targeting motifs to enhance their biological interactivity. In this Talents and Trends article, an overview of emerging nanohybrid‐based technologies will be provided to highlight their potential use as innovative platforms for improved cancer therapies and new strategies in regenerative medicine. The clinical relevance of these systems will be reviewed to define the current challenges which still need to be addressed to allow these therapies to move from bench to bedside.
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Study of the composition and morphology of new modifications of titanium‐magnesium catalysts with improved properties in ethylene polymerization
Authors: Mikenas Tatiana B. , Koshevoy Evgeny I. , Cherepanova Svetlana V. , Zakharov Vladimir A. 
Published: April 2016

ABSTRACTData on new modifications of supported titanium‐magnesium catalysts (TMCs) with improved performance in ethylene polymerization are reported. These catalysts possess a high and stable activity, an enhanced ability to regulate molecular weight of the polymer by hydrogen, a controllable particle size at a narrow particle size distribution, and the ability to produce the polymer with an increased bulk density. Various physicochemical methods were used to obtain data on the chemical composition of novel supports and catalysts, their phase composition and crystal structure as well as the pore structure. The results obtained were used to discuss possible correlations between composition and structure of TMCs and their catalytic properties. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 2545–2558
LIMK Regulates Tumor-Cell Invasion and Matrix Degradation Through Tyrosine Phosphorylation of MT1-MMP
Authors: Lagoutte Emilie , Villeneuve Clémentine , Lafanechère Laurence , Wells Claire M. , Jones Gareth E. , Chavrier Philippe , Rossé Carine 
Published: April 2016

AbstractDuring their metastatic spread, cancer cells need to remodel the extracellular matrix in order to migrate through stromal compartments adjacent to the primary tumor. Dissemination of breast carcinoma cells is mediated by membrane type 1-matrix metalloproteinase (MT1-MMP/MMP14), the main invadopodial matrix degradative component. Here, we identify MT1-MMP as a novel interacting partner of dual-specificity LIM Kinase-1 and -2 (LIMK1/2) and provide several evidence for phosphorylation of tyrosine Y573 in the cytoplasmic domain of MT1-MMP by LIMK. Phosphorylation of Y573 influences association of F-actin binding protein cortactin to MT1-MMP-positive endosomes and invadopodia formation and matrix degradation. Moreover, we show that LIMK1 regulates cortactin association to MT1-MMP-positive endosomes, while LIMK2 controls invadopodia-associated cortactin. In turn, LIMK1 and LIMK2 are required for MT1-MMP-dependent matrix degradation and cell invasion in a three-dimensional type I collagen environment. This novel link between LIMK1/2 and MT1-MMP may have important consequences for therapeutic control of breast cancer cell invasion.
Logical operations with single x-ray photons via dynamically-controlled nuclear resonances
Authors: Gunst Jonas , Keitel Christoph H. , Pálffy Adriana 
Published: April 2016

AbstractPhotonic qubits lie at the heart of quantum information technology, often encoding information in their polarization state. So far, only low-frequency optical and infrared photons have been employed as flying qubits, as the resources that are at present easiest to control. With their essentially different way of interacting with matter, x-ray qubits would bear however relevant advantages: they are extremely robust, penetrate deep through materials and can be focused down to few-nm waveguides, allowing unprecedented miniaturization. Also, x-rays are resonant to nuclear transitions, which are very well isolated from the environment and present long coherence times. Here, we show theoretically that x-ray polarization qubits can be dynamically controlled by nuclear Mössbauer resonances. The control knob is played by nuclear hyperfine magnetic fields, that allow via fast rotations precise processing of single x-ray quanta polarization. With such rotations, single-qubit and binary logical operations such as a destructive C-NOT gate can be implemented.
Macrophage TCF-4 co-activates p65 to potentiate chronic inflammation and insulin resistance in mice
Authors: Kang Xia , Hou Along , Wang Rui , Liu Da , Xiang Wei , Xie Qingyun , Zhang Bo , Gan Lixia , Zheng Wei , Miao Hongming 
Published: April 2016

Transcription factor 4 (TCF-4) was recently identified as a candidate gene for the cause of type 2 diabetes, although the mechanisms have not been fully elucidated. In the present study, we demonstrated that the TCF-4 transgene in macrophages aggravated high-fat diet (HFD)-induced insulin resistance and chronic inflammation, characterized by the elevation of proinflammatory cytokines in the blood, liver and white adipose tissue, as well as a proinflammatory profile of immune cells in visceral fats in mice. Mechanistically, TCF-4 functioned as a co-activator of p65 to amplify the saturated free fatty acid (FFA)-stimulated promoter activity, mRNA transcription and secretion of proinflammatory cytokines in primary macrophages. Blockage of p65 with a specific interfering RNA or inhibitor could prevent TCF-4-enhanced expression of proinflammatory cytokines in FFA/lipopolysaccharide-treated primary macrophages. The p65 inhibitor could abolish macrophage TCF-4 transgene-aggravated systemic inflammation, glucose intolerance and insulin resistance in HFD-treated mice. In addition, we demonstrated that the mRNA expression of TCF-4 in the peripheral blood monocytes from humans was positively correlated to the levels of interleukin (IL)-1β, tumour necrosis factor α, IL-6 and fasting plasma glucose. In summary, we identified TCF-4 as a co-activator of p65 in the potentiation of proinflammatory cytokine production in macrophages and aggravation of HFD-induced chronic inflammation and insulin resistance in mice.
Canonical and noncanonical intraflagellar transport regulates craniofacial skeletal development
Authors: Noda Kazuo , Kitami Megumi , Kitami Kohei , Kaku Masaru , Komatsu Yoshihiro 
Published: April 2016

Significance
Intraflagellar transport (IFT) plays a critical role in assembling primary cilia that mediate growth factor signaling. The disruption or dysfunction of IFT components can generate multiple diseases, including skeletal dysplasia. However, the mechanism by which IFT regulates skeletogenesis remains elusive. In the present study, we show that neural crest-specific deletion of the gene that encodes intraflagellar transport 20 (IFT20) in mice compromises ciliogenesis and the intracellular transport of collagen, leading to osteopenia in the face. Our findings highlight a unique function of IFT beyond its role in cilium assembly during craniofacial development, suggesting that IFT20 is indispensable for the regulation of not only ciliogenesis but also the intracellular trafficking of collagen in the unique multipotent stem cell population of cranial neural crests.
Human DDX3 protein is a valuable target to develop broad spectrum antiviral agents
Authors: Brai Annalaura , Fazi Roberta , Tintori Cristina , Zamperini Claudio , Bugli Francesca , Sanguinetti Maurizio , Stigliano Egidio , Esté José , Badia Roger , Franco Sandra , Martinez Miguel A. , Martinez Javier P. , Meyerhans Andreas , Saladini Francesco , Zazzi Maurizio , Garbelli Anna , Maga Giovanni , Botta Maurizio 
Published: April 2016

Significance
Human DEAD-box polypeptide 3 (DDX3) is an ATPase/RNA helicase involved in the replication of many viral pathogens. We reported herein the first inhibitor, to our knowledge, of the helicase binding site of DDX3 endowed with a broad spectrum antiviral activity [HIV-1 WT, HIV drug-resistant strains, Hepatitis C virus (HCV), Dengue virus (DENV), and West Nile virus (WNV)]. The good toxicity profile suggests that the DDX3 activity, although essential for viruses, could be dispensable to the cells, validating DDX3 as a pharmaceutical target. Our results clearly showed that DDX3 inhibitors could be exploited to treat HIV/HCV coinfections, emerging infectious diseases (such as DENV and WNV), and HIV-1 patients carrying drug-resistant strains. Each of these three medical conditions currently represents a major challenge for clinical treatment.
Single-enzyme biomineralization of cadmium sulfide nanocrystals with controlled optical properties
Authors: Dunleavy Robert , Lu Li , Kiely Christopher J. , McIntosh Steven , Berger Bryan W. 
Published: April 2016

SignificanceBiomineralization is a promising, yet complex, route toward the scalable and green biomanufacturing of functional nanomaterials, involving multiple biomolecules acting in unison to control mineralization and crystal structure. Unraveling the interdependent complexity of biomineralization is a barrier to completely realize this approach. We distill this complexity to a single enzyme that both catalyzes the formation of the reactive precursors required for mineralization and templates nanocrystal growth in solution. This is the first report of a single enzyme capable of providing all of the required functionality for active biomineralization from otherwise unreactive solution. This work provides insight into the mechanism of metal sulfide biomineralization and is an example of the elegance in green functional material synthesis achievable through engineered biomineralization.
TnT: a set of libraries for visualizing trees and track-based annotations for the web
Authors: Pignatelli Miguel 
Published: April 2016

Abstract
Summary: There is an increasing need for rich and dynamic biological data visualizations in bioinformatic web applications. New standards in web technologies, like SVG or Canvas, are now supported by most modern web browsers allowing the blossoming of powerful visualizations in biological data analysis. The exploration of different ways to visualize genomic data is still challenging due to the lack of flexible tools to develop them. Here, I present a set of libraries aimed at creating powerful tree- and track-based visualizations for the web. Its modularity and rich API facilitate the development of many different visualizations ranging from simple species trees to complex visualizations comprising per-node data annotations or even simple genome browsers.
Availability and Implementation: The TnT libraries have been written in Javascript, licensed under the APACHE 2.0 license and hosted at https://github.com/tntvis.
Contact: mp@ebi.ac.uk
Estimating IBD tracts from low coverage NGS data
Authors: Vieira Filipe G. , Albrechtsen Anders , Nielsen Rasmus 
Published: April 2016

Abstract
Motivation: The amount of IBD in an individual depends on the relatedness of the individual’s parents. However, it can also provide information regarding mating system, past history and effective size of the population from which the individual has been sampled.
Results: Here, we present a new method for estimating inbreeding IBD tracts from low coverage NGS data. Contrary to other methods that use genotype data, the one presented here uses genotype likelihoods to take the uncertainty of the data into account. We benchmark it under a wide range of biologically relevant conditions and show that the new method provides a marked increase in accuracy even at low coverage.
Availability and implementation: The methods presented in this work were implemented in C/C ++ and are freely available for non-commercial use from https://github.com/fgvieira/ngsF-HMM.
Contact: fgvieira@snm.ku.dk
Supplementary information: Supplementary data are available at Bioinformatics online.
DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases
Authors: Queralt-Rosinach Núria , Piñero Janet , Bravo Àlex , Sanz Ferran , Furlong Laura I. 
Published: April 2016

Abstract
Motivation: DisGeNET-RDF makes available knowledge on the genetic basis of human diseases in the Semantic Web. Gene-disease associations (GDAs) and their provenance metadata are published as human-readable and machine-processable web resources. The information on GDAs included in DisGeNET-RDF is interlinked to other biomedical databases to support the development of bioinformatics approaches for translational research through evidence-based exploitation of a rich and fully interconnected linked open data.
Availability and implementation: http://rdf.disgenet.org/
Contact: support@disgenet.org
CaFE: a tool for binding affinity prediction using end-point free energy methods
Authors: Liu Hui , Hou Tingjun 
Published: April 2016

Abstract
Summary: Accurate prediction of binding free energy is of particular importance to computational biology and structure-based drug design. Among those methods for binding affinity predictions, the end-point approaches, such as MM/PBSA and LIE, have been widely used because they can achieve a good balance between prediction accuracy and computational cost. Here we present an easy-to-use pipeline tool named Calculation of Free Energy (CaFE) to conduct MM/PBSA and LIE calculations. Powered by the VMD and NAMD programs, CaFE is able to handle numerous static coordinate and molecular dynamics trajectory file formats generated by different molecular simulation packages and supports various force field parameters.
Availability and implementation: CaFE source code and documentation are freely available under the GNU General Public License via GitHub at https://github.com/huiliucode/cafe_plugin. It is a VMD plugin written in Tcl and the usage is platform-independent.
Contact: tingjunhou@zju.edu.cn