bluuebunny/crossref_metadata_2025_split huggingface dataset:
Making football global? FIFA, Europe, and the non-European football world, 1912–74
Authors: Dietschy Paul 
Published: June 2013

AbstractThe Fédération Internationale de Football Association (FIFA) played a major role in the transformation of association football into a global game. Between 1912 and 1974, before the era of rapid economic sports globalization, FIFA officials attempted to extend the boundaries of the football empire by creating the World Cup and trying to convert new parts of the world to the people's game. It was not an easy task since they met with resistance, obstruction, and contestation. They had to revise their Eurocentric way of thinking and be willing to negotiate. Far from being a mere imperialist process, the path to world football consisted of a series of exacting exchanges and mutual misunderstandings, especially with the South American associations. It is not clear that FIFA officials always understood the demands of the developing football world but they were often able to negotiate and adapt their discourses towards non-European national associations and continental confederations. By doing so, they helped to create, if not an equal football world, at least an international world space.
Cell cycle-arrested tumor cells exhibit increased sensitivity towards TRAIL-induced apoptosis
Authors: Ehrhardt H , Wachter F , Grunert M , Jeremias I 
Published: June 2013

AbstractResting tumor cells represent a huge challenge during anticancer therapy due to their increased treatment resistance. TNF-related apoptosis-inducing ligand (TRAIL) is a putative future anticancer drug, currently in phases I and II clinical studies. We recently showed that TRAIL is able to target leukemia stem cell surrogates. Here, we tested the ability of TRAIL to target cell cycle-arrested tumor cells. Cell cycle arrest was induced in tumor cell lines and xenografted tumor cells in G0, G1 or G2 using cytotoxic drugs, phase-specific inhibitors or RNA interference against cyclinB and E. Biochemical or molecular arrest at any point of the cell cycle increased TRAIL-induced apoptosis. Accordingly, when cell cycle arrest was disabled by addition of caffeine, the antitumor activity of TRAIL was reduced. Most important for clinical translation, tumor cells from three children with B precursor or T cell acute lymphoblastic leukemia showed increased TRAIL-induced apoptosis upon knockdown of either cyclinB or cyclinE, arresting the cell cycle in G2 or G1, respectively. Taken together and in contrast to most conventional cytotoxic drugs, TRAIL exerts enhanced antitumor activity against cell cycle-arrested tumor cells. Therefore, TRAIL might represent an interesting drug to treat static-tumor disease, for example, during minimal residual disease.
Cotargeting histone deacetylases and oncogenic BRAF synergistically kills human melanoma cells by necrosis independently of RIPK1 and RIPK3
Authors: Lai F , Guo S T , Jin L , Jiang C C , Wang C Y , Croft A , Chi M N , Tseng H-Y , Farrelly M , Atmadibrata B , Norman J , Liu T , Hersey P , Zhang X D 
Published: June 2013

AbstractPast studies have shown that histone deacetylase (HDAC) and mutant BRAF (v-Raf murine sarcoma viral oncogene homolog B1) inhibitors synergistically kill melanoma cells with activating mutations in BRAF. However, the mechanism(s) involved remains less understood. Here, we report that combinations of HDAC and BRAF inhibitors kill BRAFV600E melanoma cells by induction of necrosis. Cotreatment with the HDAC inhibitor suberoylanilide hydroxamic acid (SAHA) or panobinostat (LBH589) and the BRAF inhibitor PLX4720 activated the caspase cascade, but caspases appeared dispensable for killing, in that inhibition of caspases did not invariably block induction of cell death. The majority of dying cells acquired propidium iodide positivity instantly when they became positive for Annexin V, suggesting induction of necrosis. This was supported by caspase-independent release of high-mobility group protein B1, and further consolidated by rupture of the plasma membrane and loss of nuclear and cytoplasmic contents, as manifested by transmission electron microscopic analysis. Of note, neither the necrosis inhibitor necrostatin-1 nor the small interference RNA (siRNA) knockdown of receptor-interacting protein kinase 3 (RIPK3) inhibited cell death, suggesting that RIPK1 and RIPK3 do not contribute to induction of necrosis by combinations of HDAC and BRAF inhibitors in BRAFV600E melanoma cells. Significantly, SAHA and the clinically available BRAF inhibitor vemurafenib cooperatively inhibited BRAFV600E melanoma xenograft growth in a mouse model even when caspase-3 was inhibited. Taken together, these results indicate that cotreatment with HDAC and BRAF inhibitors can bypass canonical cell death pathways to kill melanoma cells, which may be of therapeutic advantage in the treatment of melanoma.
Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust
Authors: Rajeev Lara , da Rocha Ulisses Nunes , Klitgord Niels , Luning Eric G , Fortney Julian , Axen Seth D , Shih Patrick M , Bouskill Nicholas J , Bowen Benjamin P , Kerfeld Cheryl A , Garcia-Pichel Ferran , Brodie Eoin L , Northen Trent R , Mukhopadhyay Aindrila 
Published: June 2013

Abstract
Biological soil crusts (BSCs) cover extensive portions of the earth’s deserts. In order to survive desiccation cycles and utilize short periods of activity during infrequent precipitation, crust microorganisms must rely on the unique capabilities of vegetative cells to enter a dormant state and be poised for rapid resuscitation upon wetting. To elucidate the key events involved in the exit from dormancy, we performed a wetting experiment of a BSC and followed the response of the dominant cyanobacterium, Microcoleus vaginatus, in situ using a whole-genome transcriptional time course that included two diel cycles. Immediate, but transient, induction of DNA repair and regulatory genes signaled the hydration event. Recovery of photosynthesis occurred within 1 h, accompanied by upregulation of anabolic pathways. Onset of desiccation was characterized by the induction of genes for oxidative and photo-oxidative stress responses, osmotic stress response and the synthesis of C and N storage polymers. Early expression of genes for the production of exopolysaccharides, additional storage molecules and genes for membrane unsaturation occurred before drying and hints at preparedness for desiccation. We also observed signatures of preparation for future precipitation, notably the expression of genes for anaplerotic reactions in drying crusts, and the stable maintenance of mRNA through dormancy. These data shed light on possible synchronization between this cyanobacterium and its environment, and provides key mechanistic insights into its metabolism in situ that may be used to predict its response to climate, and or, land-use driven perturbations.
Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits
Authors: Goudenège David , Labreuche Yannick , Krin Evelyne , Ansquer Dominique , Mangenot Sophie , Calteau Alexandra , Médigue Claudine , Mazel Didier , Polz Martin F , Le Roux Frédérique 
Published: June 2013

Abstract
Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed ‘nigritoxin’, is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.
Tailorable stimulated Brillouin scattering in nanoscale silicon waveguides
Authors: Shin Heedeuk , Qiu Wenjun , Jarecki Robert , Cox Jonathan A. , Olsson Roy H. , Starbuck Andrew , Wang Zheng , Rakich Peter T. 
Published: June 2013

AbstractNanoscale modal confinement is known to radically enhance the effect of intrinsic Kerr and Raman nonlinearities within nanophotonic silicon waveguides. By contrast, stimulated Brillouin-scattering nonlinearities, which involve coherent coupling between guided photon and phonon modes, are stifled in conventional nanophotonics, preventing the realization of a host of Brillouin-based signal-processing technologies in silicon. Here we demonstrate stimulated Brillouin scattering in silicon waveguides, for the first time, through a new class of hybrid photonic–phononic waveguides. Tailorable travelling-wave forward-stimulated Brillouin scattering is realized—with over 1,000 times larger nonlinearity than reported in previous systems—yielding strong Brillouin coupling to phonons from 1 to 18 GHz. Experiments show that radiation pressures, produced by subwavelength modal confinement, yield enhancement of Brillouin nonlinearity beyond those of material nonlinearity alone. In addition, such enhanced and wideband coherent phonon emission paves the way towards the hybridization of silicon photonics, microelectromechanical systems and CMOS signal-processing technologies on chip.
Extraordinary levitation height in diamagnetically stabilised levitation system with superconductors
Authors: Küstler G. 
Published: June 2013

The diamagnetically stabilised levitation of an NdFeB cube magnet over superconductors is reported. The achieved levitation height of 44 mm is about three times higher than in a comparable conventional superconducting levitation setup with flux pinning only. The extraordinary levitation height may offer new applications in the field of highly sensitive seismometers or force meters.
Dual‐wideband bandstop filter using transversal signal‐interaction concept
Authors: Xue S.J. , Zhu H.T. , Feng W.J. , Che W.Q. 
Published: June 2013

A dual‐wideband bandstop filter with high selectivity using transversal signal‐interaction concept is proposed. Five transmission poles in the passband between the two stopbands can be achieved due to the superposition of signals for the two transmission paths. A planar dual‐wideband bandstop filter prototype for WLAN bands with 10 dB fractional bandwidths of 76.2% and 26.9% has been designed and fabricated.
Discrete Green's function approach to disjoint domain simulations in 3D FDTD method
Authors: Stefański T.P. 
Published: June 2013

A discrete Green's function (DGF) approach to couple 3D FDTD subdomains is developed. The total‐field/scattered‐field subdomains are simulated using the explicit FDTD method whilst interaction between them is computed as a convolution of the DGF with equivalent current sources measured over Huygens surfaces. In the developed method, the DGF waveforms are truncated using the Hann's window. The error varies in the range − 65 to − 40 dB depending on the DGF length and positions of the subdomains. However, if the DGF length is equal to the number of iterations in a simulation, this approach returns the same results as the direct FDTD method.
Photonic crystal VCSELs with narrow spectral width and high bandwidth operating at low current density
Authors: Tan M. , Fryslie S.T.M. , Guenter J.K. , Tatum J.A. , Johnson R.H. , Choquette K.D. 
Published: June 2013

A photonic crystal vertical‐cavity surface‐emitting laser with a spectral width of 0.16 nm and a 3dB small signal modulation bandwidth of 16.2 GHz is demonstrated. Separation of optical and current apertures enables a narrow spectral width and an extremely low operating current density of ∼ 1 kA/cm2 simultaneously. It can potentially be used as a high‐reliability laser source that enables error‐free transmission over long multimode fibre links at high data rate.
Synthesis of three‐dimensional porous Cu2O microspheres by template‐free solvothermal method
Authors: Zou Jing , Ma Jinai , Jiang Jizhou , Zhang Yuanxiao , Li Lu , Wan Qijin 
Published: June 2013

Three‐dimensional (3D) porous Cu2O microspheres were successfully synthesised by a simple template‐free solvothermal method. Systematic studies showed that solvent, precipitator and temperature reaction parameters played a key role in controlling the morphology and structure of Cu2O. The crystallisation, morphology and composition of the as‐prepared Cu2O was characterised by X‐ray diffraction, a scanning electron microscope and energy‐dispersive spectroscopy, respectively. It revealed that the 3D porous Cu2O microspheres were built from small 2D nanosheets with a thickness of 50–80 nm. Cyclic voltammetry was applied to investigate the electrochemical performance of the products. It was found that the 3D porous Cu2O microspheres possessed high electrocatalytic activity. The growth mechanism of the 3D porous Cu2O microspheres was proposed with a 3D molecule model.
Effects of milling and subsequent heat treatment on preparation of mullite–zirconia nanocomposites
Authors: Ghaffari Somaye , Alizadeh Masoud , Asadian Keivan , Ebadzadeh Touradj , Ghanbari Arezoo 
Published: June 2013

Mullite–zirconia composites were fabricated through reaction sintering of mechanically activated alumina and zircon powder mixtures. X‐ray diffraction results showed that increasing milling time resulted in gradual weakening and broadening of alumina and zircon peaks. For the sample milled for 70 h in which there are no peaks present from zircon, heating at 1200°C resulted in the reappearance of the zircon peaks. Samples sintered at 1500°C achieved complete formation of mullite and zirconia. These samples exhibited the following physical and mechanical properties: density 3.87 g/cm3, open porosity 3.45%, hardness 11.44 ± 0.3 GPa and fracture toughness 4.7 Mpam1/2.
High resolution electron microscopy of Ag-clusters in crystalline and non-crystalline morphologies grown inside superfluid helium nanodroplets
Authors: Volk Alexander , Thaler Philipp , Koch Markus , Fisslthaler Evelin , Grogger Werner , Ernst Wolfgang E. 
Published: June 2013

We present a first investigation of structural properties of Ag clusters with a diameter of up to 5.5 nm grown inside superfluid helium nanodroplets (HeN) and deposited on an amorphous C surface. With high resolution transmission electron microscope images we are able to show that in addition to the crystalline face centered cubic (fcc) structure, noncrystalline icosahedral (Ih), and decahedral (Dh) morphologies are grown. Relative abundances (56% fcc, 31% Dh, and 13% Ih) as well as the size distribution of each morphology (mean diameters \documentclass[12pt]{minimal}\begin{document}$\bar{d}_{\rm fcc}=2.62(5)$\end{document}d¯ fcc =2.62(5) nm, \documentclass[12pt]{minimal}\begin{document}$\bar{d}_{\rm Dh}= 3.34(7)$\end{document}d¯ Dh =3.34(7) nm, and \documentclass[12pt]{minimal}\begin{document}$\bar{d}_{\rm Ih}= 3.93(2)$\end{document}d¯ Ih =3.93(2) nm) do not reflect the situation expected from pure energetic considerations, where small Ihs should be followed by medium sized Dhs and large fccs. Instead, kinetic factors seem to play an important role in the formation of these structures, as it appears to be the case for clusters formed by inert gas aggregation. Considering the low temperatures (0.37 K) and extremely high cooling rates, we discuss basic ideas that might lead to a qualitative picture of the cluster formation process inside HeN.
opm: an R package for analysing OmniLog® phenotype microarray data
Authors: Vaas Lea A. I. , Sikorski Johannes , Hofner Benjamin , Fiebig Anne , Buddruhs Nora , Klenk Hans-Peter , Göker Markus 
Published: June 2013

Abstract
Summary: opm is an R package designed to analyse multidimensional OmniLog® phenotype microarray (PM) data. opm provides management, visualization and statistical analysis of PM data, including curve-parameter estimation and discretization, dedicated and customizable plots, metadata management, automated generation of textual and tabular reports, mapping of substrates to databases, batch conversion of files and export to phylogenetic software in the YAML markup language.
Availability: opm is distributed under the GPL through the Comprehensive R Archive Network (http://cran.r-project.org/package=opm) along with a comprehensive manual and a user-friendly tutorial. Further information may be found at http://www.dsmz.de/research/microorganisms/projects/.
Contact: johannes.sikorski@dsmz.de
Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci
Authors: Buske Fabian A. , Bauer Denis C. , Mattick John S. , Bailey Timothy L. 
Published: June 2013

Abstract
Summary: At the heart of many modern biotechnological and therapeutic applications lies the need to target specific genomic loci with pinpoint accuracy. Although landmark experiments demonstrate technological maturity in manufacturing and delivering genetic material, the genomic sequence analysis to find suitable targets lags behind. We provide a computational aid for the sophisticated design of sequence-specific ligands and selection of appropriate targets, taking gene location and genomic architecture into account.
Availability: Source code and binaries are downloadable from www.bioinformatics.org.au/triplexator/inspector.
Contact: t.bailey@uq.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
An image-based multi-label human protein subcellular localization predictor (iLocator) reveals protein mislocalizations in cancer tissues
Authors: Xu Ying-Ying , Yang Fan , Zhang Yang , Shen Hong-Bin 
Published: June 2013

Abstract
Motivation: Human cells are organized into compartments of different biochemical cellular processes. Having proteins appear at the right time to the correct locations in the cellular compartments is required to conduct their functions in normal cells, whereas mislocalization of proteins can result in pathological diseases, including cancer.
Results: To reveal the cancer-related protein mislocalizations, we developed an image-based multi-label subcellular location predictor, iLocator, which covers seven cellular localizations. The iLocator incorporates both global and local image descriptors and generates predictions by using an ensemble multi-label classifier. The algorithm has the ability to treat both single- and multiple-location proteins. We first trained and tested iLocator on 3240 normal human tissue images that have known subcellular location information from the human protein atlas. The iLocator was then used to generate protein localization predictions for 3696 protein images from seven cancer tissues that have no location annotations in the human protein atlas. By comparing the output data from normal and cancer tissues, we detected eight potential cancer biomarker proteins that have significant localization differences with P-value &lt; 0.01.
Availability: http://www.csbio.sjtu.edu.cn/bioinf/iLocator/
Contact: hbshen@sjtu.edu.cn or zhng@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Insights into polypharmacology from drug-domain associations
Authors: Moya-García Aurelio A. , Ranea Juan A. G. 
Published: June 2013

Abstract
Motivation: Polypharmacology (the ability of a single drug to affect multiple targets) is a key feature that may explain part of the decreasing success of conventional drug discovery strategies driven by the quest for drugs to act selectively on a single target. Most drug targets are proteins that are composed of domains (their structural and functional building blocks).
Results: In this work, we model drug–domain networks to explore the role of protein domains as drug targets and to explain drug polypharmacology in terms of the interactions between drugs and protein domains. We find that drugs are organized around a privileged set of druggable domains.
Conclusions: Protein domains are a good proxy for drug targets, and drug polypharmacology emerges as a consequence of the multi-domain composition of proteins.
Contact: amoyag@uma.es
Supplementary information: Supplementary data are available at Bioinformatics online.
DIGEP-Pred: web service for in silico prediction of drug-induced gene expression profiles based on structural formula
Authors: Lagunin Alexey , Ivanov Sergey , Rudik Anastasia , Filimonov Dmitry , Poroikov Vladimir 
Published: June 2013

Abstract
Summary: Experimentally found gene expression profiles are used to solve different problems in pharmaceutical studies, such as drug repositioning, resistance, toxicity and drug–drug interactions. A special web service, DIGEP-Pred, for prediction of drug-induced changes of gene expression profiles based on structural formulae of chemicals has been developed. Structure–activity relationships for prediction of drug-induced gene expression profiles were determined by Prediction of Activity Spectra for Substances (PASS) software. Comparative Toxicogenomics Database with data on the known drug-induced gene expression profiles of chemicals was used to create mRNA- and protein-based training sets. An average prediction accuracy for the training sets (ROC AUC) calculated by leave-one-out cross-validation on the basis of mRNA data (1385 compounds, 952 genes, 500 up- and 475 down-regulations) and protein data (1451 compounds, 139 genes, 93 up- and 55 down-regulations) exceeded 0.85.
Availability: Freely available on the web at http://www.way2drug.com/GE.
Contact: alexey.lagunin@ibmc.msk.ru
Supplementary information: Supplementary data are available at Bioinformatics online.
A Common Fungal Associate of the Spruce Bark Beetle Metabolizes the Stilbene Defenses of Norway Spruce
Authors: Hammerbacher Almuth , Schmidt Axel , Wadke Namita , Wright Louwrance P. , Schneider Bernd , Bohlmann Joerg , Brand Willi A. , Fenning Trevor M. , Gershenzon Jonathan , Paetz Christian 
Published: June 2013

Abstract
Norway spruce (Picea abies) forests suffer periodic fatal attacks by the bark beetle Ips typographus and its fungal associate, Ceratocystis polonica. Norway spruce protects itself against fungal and bark beetle invasion by the production of terpenoid resins, but it is unclear whether resins or other defenses are effective against the fungus. We investigated stilbenes, a group of phenolic compounds found in Norway spruce bark with a diaryl-ethene skeleton with known antifungal properties. During C. polonica infection, stilbene biosynthesis was up-regulated, as evidenced by elevated transcript levels of stilbene synthase genes. However, stilbene concentrations actually declined during infection, and this was due to fungal metabolism. C. polonica converted stilbenes to ring-opened, deglycosylated, and dimeric products. Chromatographic separation of C. polonica protein extracts confirmed that these metabolites arose from specific fungal enzyme activities. Comparison of C. polonica strains showed that rapid conversion of host phenolics is associated with higher virulence. C. polonica is so well adapted to its host’s chemical defenses that it is even able to use host phenolic compounds as its sole carbon source.