bluuebunny/crossref_metadata_2025_split huggingface dataset:
From Closed to Open: Chinese Foundations’ ‘Ways’ of Distributing Funds
Authors: Yushan () Xu 
Published: November 2010

AbstractThis article focuses on how Chinese foundations distribute funds, i.e. the ways in which they spend their money and how these ways are changing. By reviewing the practices of numerous domestic foundations, this paper identifies two methods of distribution. These methods, referred to as the “closed way” and the “open way,” are differentiated by the fields in which funding recipient institutions work and by the ways in which foundations select funding recipients. The “closed way” tends to be monopolized, mandated top-down, bureaucratic, low-cost, and tends to involve small disbursements. While its simplicity and speed help reduce administrative costs, thereby better leveraging resources, the “closed way” may also corrode foundations’ independence and blur the boundary between governments and foundations. The “open way” tends to be open, transparent, competitive, and selective. This method of distribution facilitates the entry of donations into the civil society sector, and puts resources to work in society. A party to civil organizations’ broad progress over the last 30 years, foundations in China are shifting their methods of distribution from “closed” to “open,” a change we see expressed both in the growth of foundations’ operating partners and in the increasing use of competitive mechanisms. Taking the “open way” will increase foundations’ role in supporting the third sector and help foundations become engines of civil society in China.
Paradoxical embolism following thromboaspiration of an arteriovenous fistula thrombosis: a case report
Authors: Bentaarit Bouteina , Duval Anne Marie , Maraval Anne , Dahmane Djamal , Dahan Karine , Amara Brahim , Lang Philippe , Sahali Djillali 
Published: November 2010

Abstract

Introduction
Paradoxical embolism is an increasingly reported cause of arterial embolism. Several embolic sources have been described, but thrombosis of an arteriovenous fistula as a paradoxical emboligenic source has not, to the best of our knowledge, been reported.

Case presentation
A 50-year-old Caucasian woman received a renal graft for primary hyperoxaluria. After transplantation, she was maintained on daily hemodialysis. Thrombosis of her arteriovenous fistula occurred two weeks post-transplantation and was treated by thromboaspiration, which was partially successful. During a hemodialysis session immediately following thromboaspiration, she developed a coma with tetraplegia requiring intensive cardiorespiratory resuscitation. Brain magnetic resonance imaging revealed various hyperdense areas in the vertebrobasilar territory resulting from bilateral occlusion of posterior cerebral arteries. Transesophageal echocardiographic examination showed a patent foramen ovale, while pulse echography of the arteriovenous fistula revealed the persistence of extensive clots that were probably the embolic source. A paradoxical embolus through a patent foramen ovale was suggested because of the proximity of the neurological event to the thrombectomy procedure.

Conclusions
The risk of paradoxical embolism in a hemodialyzed patient with a patent foramen ovale deserves consideration and requires careful evaluation in situations of arteriovenous fistula thrombosis.
Single-molecule fluorescence resonance energy transfer techniques on rotary ATP synthases
Authors: Börsch Michael 
Published: November 2010

Abstract
Conformational changes of proteins can be monitored in real time by fluorescence resonance energy transfer (FRET). Two different fluorophores have to be attached to those protein domains which move during function. Distance fluctuations between the fluorophores are measured by relative fluorescence intensity changes or fluorescence lifetime changes. The rotary mechanics of the two motors of FoF1-ATP synthase have been studied in vitro by single-molecule FRET. The results are summarized and perspectives for other transport ATPases are discussed.
Actin-Bundling Protein L-Plastin Regulates T Cell Activation
Authors: Wang Chen , Morley Sharon Celeste , Donermeyer David , Peng Ivan , Lee Wyne P. , Devoss Jason , Danilenko Dimitry M. , Lin Zhonghua , Zhang Juan , Zhou Jie , Allen Paul M. , Brown Eric J. 
Published: November 2010

AbstractEngagement of TCRs induces actin rearrangements, which are critical for T cell activation. T cell responses require new actin polymerization, but the significance of higher-order actin structures, such as microfilament bundles, is unknown. To determine the role of the actin-bundling protein leukocyte-plastin (L-plastin; LPL) in this process, T cells from LPL−/− mice were studied. LPL−/− T cells were markedly defective in TCR-mediated cytokine production and proliferation. LPL−/− T cells also spread inefficiently on surfaces with immobilized TCR ligands and formed smaller immunological synapses with APCs, likely due to defective formation of lamellipodia. LPL−/− mice showed delayed rejection of skin allografts after release from immunosuppression. Moreover, LPL−/− mice developed much less severe neurologic symptoms in experimental autoimmune encephalomyelitis, which correlated with impaired T cell responses to Ag, manifested by reduced proliferation and production of IFN-γ and IL-17. Thus, LPL-dependent actin bundling facilitates the formation of lamellipodia and normal immunological synapses and thereby enables T cell activation.
A Conserved Enhancer Element Differentially Regulates Developmental Expression of CD5 in B and T Cells
Authors: Berland Robert , Fiering Steven , Wortis Henry H. 
Published: November 2010

AbstractWe previously identified an enhancer element upstream of the mouse cd5 gene that was required in reporter assays for the induction of cd5 promoter activity by BCR cross-linking. This element is highly conserved in placental mammals. To determine its physiological role, we have now generated mice with a targeted deletion of the enhancer. The result is the loss of CD5 expression in peritoneal and splenic B-1a cells of adult mice and an inability to induce CD5 by cross-linking of the BCR on splenic B-2 cells. Surprisingly, CD5 expression on B-1a cells of neonatal mice was only minimally compromised. Cd5 enhancer deletion also had only a modest effect on CD5 expression in the T lineage. Thus, this enhancer provides age- and tissue-specific regulation of CD5 expression and is an example of the utilization of different modes of regulation of expression in T and B cells.
The Inflammatory Response after an Epidermal Burn Depends on the Activities of Mouse Mast Cell Proteases 4 and 5
Authors: Younan George , Suber Freeman , Xing Wei , Shi Tong , Kunori Yuichi , Åbrink Magnus , Pejler Gunnar , Schlenner Susan M. , Rodewald Hans-Reimer , Moore Francis D. , Stevens Richard L. , Adachi Roberto , Austen K. Frank , Gurish Michael F. 
Published: November 2010

AbstractA second-degree epidermal scald burn in mice elicits an inflammatory response mediated by natural IgM directed to nonmuscle myosin with complement activation that results in ulceration and scarring. We find that such burn injury is associated with early mast cell (MC) degranulation and is absent in WBB6F1-KitW/KitWv mice, which lack MCs in a context of other defects due to a mutation of the Kit receptor. To address further an MC role, we used transgenic strains with normal lineage development and a deficiency in a specific secretory granule component. Mouse strains lacking the MC-restricted chymase, mouse MC protease (mMCP)-4, or elastase, mMCP-5, show decreased injury after a second-degree scald burn, whereas mice lacking the MC-restricted tryptases, mMCP-6 and mMCP-7, or MC-specific carboxypeptidase A3 activity are not protected. Histologic sections showed some disruption of the epidermis at the scald site in the protected strains suggesting the possibility of topical reconstitution of full injury. Topical application of recombinant mMCP-5 or human neutrophil elastase to the scalded area increases epidermal injury with subsequent ulceration and scarring, both clinically and morphologically, in mMCP-5–deficient mice. Restoration of injury requires that topical administration of recombinant mMCP-5 occurs within the first hour postburn. Importantly, topical application of human MC chymase restores burn injury to scalded mMCP-4–deficient mice but not to mMCP-5–deficient mice revealing nonredundant actions for these two MC proteases in a model of innate inflammatory injury with remodeling.
Synthesis of studies of palsa formation underlining the importance of local environmental and physical characteristics
Authors: Seppälä Matti 
Published: November 2010

AbstractThis review presents a synthesis of four decades of palsa studies based on field experiments and observations mainly in Fennoscandia, as well as laboratory measurements. Palsas are peat-covered mounds with a permanently frozen core; in Finnish Lapland, they range from 0.5 to 7 m in height and from 2 to 150 m in diameter. These small landforms are characteristic of the southern margin of the discontinuous permafrost zone. Palsa formation requires certain environmental conditions: long-lasting air temperature below 0°C, thin snow cover, and low summer precipitation. The development and persistence of their frozen core is sensitive to the physical properties of peat. The thermal conductivity of wet and frozen peat is high, and it decreases significantly as the peat dries and thaws. This affects the development of the active layer and makes its response to climate change complex. The insulating properties of dry peat during hot and dry summers moderate the thawing of the active layer on palsas. In contrast, humid and wet weather during the summer causes deep thawing and may destroy the frozen core of palsas. Ice layers in palsas have previously been interpreted as ice segregation features but because peat is not frost-susceptible, the ice layers are now reinterpreted as resulting from ice growth at the base of a frozen core that is effectively floating in a mire.
Late Quaternary dietary shifts of the Cape grysbok (Raphicerus melanotis) in southern Africa
Authors: Faith J. Tyler 
Published: November 2010

AbstractThe Cape grysbok is endemic to southern Africa's Cape Floral Region where it selectively browses various species of dicotyledonous vegetation. Fossil evidence indicates that the grysbok persisted under glacial and interglacial conditions throughout the late Quaternary and inhabited a range of environments. This study employs mesowear analysis to reconstruct grysbok diets over time and in response to changing environments at Nelson Bay Cave, Die Kelders Cave 1, Klasies River Mouth, and Swartklip 1. Results indicate that the amount of grasses (monocots) versus leafy vegetation (dicots) included in the diet fluctuated over time and largely in agreement with changes in faunal community structure. The case for dietary flexibility is particularly clear at Nelson Bay Cave, where there is a significant trend from mixed feeding towards increased browsing from the late Pleistocene (~ 18,500 14C yr BP) through the Holocene. Dietary shifts at Nelson Bay Cave are consistent with the hypothesis that declining grassland productivity is responsible for the terminal Pleistocene extinction of several large ungulates in southern Africa. Furthermore, the short-term dietary shifts demonstrated here (100s to 1000s of years) provide an important caution against relying on taxonomic uniformitarianism when reconstructing the dietary preferences of fossil ungulates, both extant and extinct.
QuACN: an R package for analyzing complex biological networks quantitatively
Authors: Mueller Laurin A. J. , Kugler Karl G. , Dander Andreas , Graber Armin , Dehmer Matthias 
Published: November 2010

Abstract
Motivation: Network-based representations of biological data have become an important way to analyze high-throughput data. To interpret the large amount of data that is produced by different high-throughput technologies, networks offer multifaceted aspects to analyze the data. As networks represent biological relationships within their structure, it turned out to be fruitful to analyze their topology. Therefore, we developed a freely available, open source R-package called Quantitative Analysis of Complex Networks (QuACN) to meet this challenge. QuACN contains different, information-theoretic and non-information-theoretic, topological network descriptors to analyze, classify and compare biological networks.
Availability: QuACN is freely available under LGPL via CRAN (http://cran.r-project.org/web/packages/QuACN/).
Contact: laurin.mueller@umit.at
Protein Peeling 3D: new tools for analyzing protein structures
Authors: Gelly Jean-Christophe , de Brevern Alexandre G. 
Published: November 2010

Abstract
Summary: We present an improved version of our Protein Peeling web server dedicated to the analysis of protein structure architecture through the identification of protein units produced by an iterative splitting algorithm. New features include identification of structural domains, detection of unstructured terminal elements and evaluation of the stability of protein unit structures.
Availability: The website is free and open to all users with no login requirements at http://www.dsimb.inserm.fr/dsimb-tools/peeling3.
Contact: jean-christophe.gelly@univ-paris-diderot.fr
Analyzing marginal cases in differential shotgun proteomics
Authors: Carvalho Paulo C. , Fischer Juliana S. G. , Perales Jonas , Yates John R. , Barbosa Valmir C. , Bareinboim Elias 
Published: November 2010

Abstract
Summary: We present an approach to statistically pinpoint differentially expressed proteins that have quantitation values near the quantitation threshold and are not identified in all replicates (marginal cases). Our method uses a Bayesian strategy to combine parametric statistics with an empirical distribution built from the reproducibility quality of the technical replicates.
Availability:The software is freely available for academic use at http://pcarvalho.com/patternlab.
Contact: paulo@pcarvalho.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Evolutionary design principles and functional characteristics based on kingdom-specific network motifs
Authors: Kim Tae-Hwan , Kim Junil , Heslop-Harrison Pat , Cho Kwang-Hyun 
Published: November 2010

Abstract
Background: Network motifs within biological networks show non-random abundances in systems at different scales. Large directed protein networks at the cellular level are now well defined in several diverse species. We aimed to compare the nature of significantly observed two- and three-node network motifs across three different kingdoms (Arabidopsis thaliana for multicellular plants, Saccharomyces cerevisiae for unicellular fungi and Homo sapiens for animals).
Results: ‘Two-node feedback’ is the most significant motif in all three species. By considering the sign of each two-node feedback interaction, we examined the enrichment of the three types of two-node feedbacks [positive–positive (PP), negative–negative (NN) and positive–negative (PN)]. We found that PN is enriched in the network of A.thaliana, NN in the network of S.cerevisiae and PP and NN in the network of H.sapiens. Each feedback type has characteristic features of robustness, multistability and homeostasis.
Conclusions: We suggest that amplification of particular network motifs emerges from contrasting dynamical and topological properties of the motifs, reflects the evolutionary design principles selected by the characteristic behavior of each species and provides a signature pointing to their behavior and function.
Contact: ckh@kaist.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
TE Displayer for post-genomic analysis of transposable elements
Authors: Rooke Rebecca , Yang Guojun 
Published: November 2010

AbstractSummary: TE Displayer can be used to retrieve genetic polymorphisms caused by transposable elements (TEs) in large-genomic datasets and present the results on virtual gel images. This enables researchers to compare TE profiles in silico and provides reference profiles for experimental analyses.Availability and implementation: Freely available on the web at http://labs.csb.utoronto.ca/yang/TE_Displayer.Contact: gage.yang@utoronto.caSupplementary Information: Supplementary data are available at Bioinformatics online.
Zooming the macroscope: medium-resolution remote sensing as a framework for the assessment of a small-scale fishery
Authors: Amoroso Ricardo O. , Parma Ana M. , Orensanz J. M. (Lobo) , Gagliardini Domingo A. 
Published: November 2010

Abstract
Amoroso, R. O., Parma, A. M., Orensanz, J. M., and Gagliardini, D. A. 2011. Zooming the macroscope: medium-resolution remote sensing as a framework for the assessment of a small-scale fishery. – ICES Journal of Marine Science, 68: 696–706. Management of small-scale fisheries targeting sedentary stocks requires integration of information about processes operating and observable at different spatial and temporal scales. An integrated approach was developed with a scallop (Aequipecten tehuelchus) fishery in a small, semi-enclosed Patagonian basin as a demonstration case. Medium-resolution (30 m2) satellite (Landsat) data, used to identify circulation patterns, were combined with information from fishery surveys and recruitment experiments to link oceanographic processes with population dynamics. A frontal system splits San José Gulf (northern Argentine Patagonia) into two oceanographic domains (East and West) with distinct hydrographic regimes. In the West Domain, where circulation is highly advective and governed by turbulent vorticial fluxes, larval settlement on artificial collectors was insignificant over five reproductive seasons and no important scallop grounds were ever found. In the East Domain, where the main fishing grounds are, spat abundance varied between sites and years, but was always significant. Growth rates displayed strong clinal variation within the East Domain, decreasing clockwise away from the entrance to the Gulf and reflecting inferred circulation and gradual nutrient extinction. A physical mechanism capable of dispersing larvae over long distances towards the north, into the adjacent San Matias Gulf, was identified from Landsat images. The large-scale patterns of variation in growth, distribution, and recruitment of the Tehuelche scallop stock could not have been interpreted without an integrative approach to data assemblage and analysis, including satellite remote sensing.
Cyanide, a Coproduct of Plant Hormone Ethylene Biosynthesis, Contributes to the Resistance of Rice to Blast Fungus
Authors: Seo Shigemi , Mitsuhara Ichiro , Feng Jiao , Iwai Takayoshi , Hasegawa Morifumi , Ohashi Yuko 
Published: November 2010

Abstract
Rice (Oryza sativa) plants carrying the Pi-i resistance gene to blast fungus Magnaporthe oryzae restrict invaded fungus in infected tissue via hypersensitive reaction or response (HR), which is accompanied by rapid ethylene production and formation of small HR lesions. Ethylene biosynthesis has been implicated to be important for blast resistance; however, the individual roles of ethylene and cyanide, which are produced from the precursor 1-aminocyclopropane-1-carboxylic acid, remain unevaluated. In this study, we found that Pi-i-mediated resistance was compromised in transgenic rice lines, in which ethylene biosynthetic enzyme genes were silenced and then ethylene production was inhibited. The compromised resistance in transgenic lines was recovered by exogenously applying cyanide but not ethephon, an ethylene-releasing chemical in plant tissue. In a susceptible rice cultivar, treatment with cyanide or 1-aminocyclopropane-1-carboxylic acid induced the resistance to blast fungus in a dose-dependent manner, while ethephon did not have the effect. Cyanide inhibited the growth of blast fungus in vitro and in planta, and application of flavonoids, secondary metabolites that exist ubiquitously in the plant kingdom, enhanced the cyanide-induced inhibition of fungal growth. These results suggested that cyanide, whose production is triggered by HR in infected tissue, contributes to the resistance in rice plants via restriction of fungal growth.
Mechanical Properties of Plant Cell Walls Probed by Relaxation Spectra
Authors: Hansen Steen Laugesen , Ray Peter Martin , Karlsson Anders Ola , Jørgensen Bodil , Borkhardt Bernhard , Petersen Bent Larsen , Ulvskov Peter 
Published: November 2010

Abstract
Transformants and mutants with altered cell wall composition are expected to display a biomechanical phenotype due to the structural role of the cell wall. It is often quite difficult, however, to distinguish the mechanical behavior of a mutant's or transformant's cell walls from that of the wild type. This may be due to the plant’s ability to compensate for the wall modification or because the biophysical method that is often employed, determination of simple elastic modulus and breakstrength, lacks the resolving power necessary for detecting subtle mechanical phenotypes. Here, we apply a method, determination of relaxation spectra, which probes, and can separate, the viscoelastic properties of different cell wall components (i.e. those properties that depend on the elastic behavior of load-bearing wall polymers combined with viscous interactions between them). A computer program, BayesRelax, that deduces relaxation spectra from appropriate rheological measurements is presented and made accessible through a Web interface. BayesRelax models the cell wall as a continuum of relaxing elements, and the ability of the method to resolve small differences in cell wall mechanical properties is demonstrated using tuber tissue from wild-type and transgenic potatoes (Solanum tuberosum) that differ in rhamnogalacturonan I side chain structure.