bluuebunny/crossref_metadata_2025_split huggingface dataset:
The linker between the D3 and A1 domains of vWF suppresses A1‐GPIbα catch bonds by site‐specific binding to the A1 domain
Authors: Tischer Alexander , Cruz Miguel A. , Auton Matthew 
Published: June 2013

AbstractPlatelet attachment to von Willebrand factor (vWF) requires the interaction between the platelet GP1bα and exposed vWF‐A1 domains. Structural insights into the mechanism of the A1‐GP1bα interaction have been limited to an N‐terminally truncated A1 domain that lacks residues Q1238 − E1260 that make up the linker between the D3 and A1 domains of vWF. We have demonstrated that removal of these residues destabilizes quaternary interactions in the A1A2A3 tridomain and contributes to platelet activation under high shear (Auton et al., J Biol Chem 2012;287:14579–14585). In this study, we demonstrate that removal of these residues from the single A1 domain enhances platelet pause times on immobilized A1 under rheological shear. A rigorous comparison between the truncated A1‐1261 and full length A1‐1238 domains demonstrates a kinetic stabilization of the A1 domain induced by these N‐terminal residues as evident in the enthalpy of the unfolding transition. This stabilization occurs through site and sequence‐specific binding of the N‐terminal peptide to A1. Binding of free N‐terminal peptide to A1‐1261 has an affinity
and this binding although free to dissociate is sufficient to suppress the platelet pause times to levels comparable to A1‐1238 under shear stress. Our results support a dual‐structure/function role for this linker region involving a conformational equilibria that maintains quaternary A domain associations in the inactive state of vWF at low shear and an intra‐A1‐domain conformation that regulates the strength of platelet GP1bα‐vWF A1 domain associations in the active state of vWF at high shear.
Evaluation of candidate systems for mass trapping against Ceratitis spp. on La Réunion island
Authors: Peñarrubia‐María I Esther , Quilici Serge , Schmitt Chloé , Escudero‐Colomar L Adriana 
Published: June 2013

AbstractBACKGROUNDTwo Ceratitis spp. coexist on the island of La Réunion, Ceratitis rosa (Karsch) and C. capitata (Wiedemann). The effectiveness of candidate systems based on attractants and traps to control both species was evaluated through comparative studies of trap types, attractants, insecticides and commercial complete systems.RESULTSThe Ceratitis spp. most captured in all trials was C. rosa. Captures of C. rosa and C. capitata were not significantly different when Maxitrap® or Tephri‐trap® were used. Captures with the Easy‐trap® were lower for both species. The BioLure® Med Fly lure showed higher catches of C. rosa than Ferag® CC D TM. The proportion of dead C. rosa did not differ significantly when deltamethrin or dichlorvos was used. There were no significant differences in the capture of C. rosa and C. capitata between commercial systems composed of the lure Ferag® CC D TM, the Maxitrap® and dichlorvos and the BioLure® Unipak, the Tephri‐trap® and dichlorvos. The Cera Trap® system performed less effectively.CONCLUSIONThe most effective traps for the capture of C. rosa and C. capitata were Maxitrap® and Tephri‐trap®; the most effective attractants were BioLure® Med Fly for C. rosa and BioLure® Med Fly, BioLure® Unipak and Ferag® CC D TM for C. capitata. However, for both species the most effective commercial combinations of trap and attractant were Maxitrap® with Ferag® CC D TM and Tephri‐trap® with BioLure® Unipak, both using dichlorvos. The insecticide deltamethrin showed good efficacy when used inside traps. © 2013 Society of Chemical Industry
A robust smart card‒based anonymous user authentication protocol for wireless communications
Authors: Wen Fengtong , Susilo Willy , Yang Guomin 
Published: June 2013

ABSTRACTAnonymous user authentication is an important but challenging task for wireless communications. In a recent paper, Das proposed a smart card‒based anonymous user authentication protocol for wireless communications. The scheme can protect user privacy and is believed to be secure against a range of network attacks even if the secret information stored in the smart card is compromised. In this paper, we reanalyze the security of Das' scheme, and show that the scheme is in fact insecure against impersonation attacks. We then propose a new smart card‒based anonymous user authentication protocol for wireless communications. Compared with the existing schemes, our protocol uses a different user authentication mechanism, which does not require different entities to maintain a synchronized clock. We show that the proposed new protocol can provide stronger security and better efficiency and scalability than previous schemes.
Warming effects in the western Antarctic Peninsula ecosystem: the role of population dynamic models for explaining and predicting penguin trends
Authors: Lima Mauricio , Estay Sergio A. 
Published: June 2013

AbstractThe western Antarctica Peninsula and Scotia Sea ecosystems appear to be driven by complex links between climatic variables, primary productivity, krill and Avian predators. There are several studies reporting statistical relationships between climate, krill and Penguin population size. The Adélie (Pygoscelis adeliae), Chinstrap (P. antarctica) and Gentoo (P. papua) penguins appear to be influenced by interannual variability in sea‐ice extent and krill biomass. In this paper we developed simple conceptual models to decipher the role of climate and krill fluctuations on the population dynamics of these three Pygoscelis penguin species inhabiting the Antarctic Peninsula region. Our results suggest that the relevant processes underlying the population dynamics of these penguin species at King George Island (South Shetland Islands) are intra‐specific competition and the combined effects of krill abundance and sea‐ice cover. Our results using population theoretical models appear to support that climate change, specifically regional warming on the western Antarctic Peninsula, represents a major driver. At our study site, penguins showed species‐specific responses to climate change. While Chinstrap penguins were only influenced by krill abundance, the contrasting population trends of Adélie and Gentoo penguins appear to be better explained by the “sea‐ice hypothesis”. We think that proper population dynamic modeling and theory are essential for deciphering and proposing the ecological mechanisms underlying dynamics of these penguin populations.
Time-based comparative transcriptomics in engineered xylose-utilizing Saccharomyces cerevisiae identifies temperature-responsive genes during ethanol production
Authors: Ismail Ku Syahidah Ku , Sakamoto Takatoshi , Hasunuma Tomohisa , Kondo Akihiko 
Published: June 2013

Abstract
Agricultural residues comprising lignocellulosic materials are excellent sources of pentose sugar, which can be converted to ethanol as fuel. Ethanol production via consolidated bioprocessing requires a suitable microorganism to withstand the harsh fermentation environment of high temperature, high ethanol concentration, and exposure to inhibitors. We genetically enhanced an industrial Saccharomyces cerevisiae strain, sun049, enabling it to uptake xylose as the sole carbon source at high fermentation temperature. This strain was able to produce 13.9 g/l ethanol from 50 g/l xylose at 38 °C. To better understand the xylose consumption ability during long-term, high-temperature conditions, we compared by transcriptomics two fermentation conditions: high temperature (38 °C) and control temperature (30 °C) during the first 12 h of fermentation. This is the first long-term, time-based transcriptomics approach, and it allowed us to discover the role of heat-responsive genes when xylose is the sole carbon source. The results suggest that genes related to amino acid, cell wall, and ribosomal protein synthesis are down-regulated under heat stress. To allow cell stability and continuous xylose uptake in order to produce ethanol, hexose transporter HXT5, heat shock proteins, ubiquitin proteins, and proteolysis were all induced at high temperature. We also speculate that the strong relationship between high temperature and increased xylitol accumulation represents the cell’s mechanism to protect itself from heat degradation.
Should the trade of hazardous waste be uniformly regulated? An empirical analysis of export demand for ‘waste and scrap’
Authors: Ichinose Daisuke , Higashida Keisaku , Shinkuma Takayoshi , Kojima Michikazu 
Published: June 2013

AbstractWe examine the substitutability of waste and scrap exported from different countries by estimating the export demand functions of China. In particular, we focus on the export of other ferrous waste and scrap (HS code 720449) and other waste, parings and scrap of plastics (HS code 391590). It is shown that the substitutability of these wastes and scraps is weak among the exporting countries. Our empirical results imply that a uniform ban on trading hazardous waste, represented by the Basel Ban, could be an inefficient environmental policy.
Differential network analysis for the identification of condition-specific pathway activity and regulation
Authors: Gambardella Gennaro , Moretti Maria Nicoletta , de Cegli Rossella , Cardone Luca , Peron Adriano , di Bernardo Diego 
Published: June 2013

AbstractMotivation: Identification of differential expressed genes has led to countless new discoveries. However, differentially expressed genes are only a proxy for finding dysregulated pathways. The problem is to identify how the network of regulatory and physical interactions rewires in different conditions or in disease.Results: We developed a procedure named DINA (DIfferential Network Analysis), which is able to identify set of genes, whose co-regulation is condition-specific, starting from a collection of condition-specific gene expression profiles. DINA is also able to predict which transcription factors (TFs) may be responsible for the pathway condition-specific co-regulation. We derived 30 tissue-specific gene networks in human and identified several metabolic pathways as the most differentially regulated across the tissues. We correctly identified TFs such as Nuclear Receptors as their main regulators and demonstrated that a gene with unknown function (YEATS2) acts as a negative regulator of hepatocyte metabolism. Finally, we showed that DINA can be used to make hypotheses on dysregulated pathways during disease progression. By analyzing gene expression profiles across primary and transformed hepatocytes, DINA identified hepatocarcinoma-specific metabolic and transcriptional pathway dysregulation.Availability: We implemented an on-line web-tool http://dina.tigem.it enabling the user to apply DINA to identify tissue-specific pathways or gene signatures.Contact: dibernardo@tigem.itSupplementary information: Supplementary data are available at Bioinformatics online.
Tasuke: a web-based visualization program for large-scale resequencing data
Authors: Kumagai Masahiko , Kim Jungsok , Itoh Ryutaro , Itoh Takeshi 
Published: June 2013

Abstract
Summary: Because an enormous amount of sequence data is being collected, a method to effectively display sequence variation information is urgently needed. tasuke is a web application that visualizes large-scale resequencing data generated by next-generation sequencing technologies and is suitable for rapid data release to the public on the web. The variation and read depths of multiple genomes, as well as annotations, can be shown simultaneously at various scales. We demonstrate the use of TASUKE by applying it to 50 rice and 100 human genome resequencing datasets.
Availability and implementation: The tasuke program package and user manual are available from http://tasuke.dna.affrc.go.jp/.
Contact: taitoh@affrc.go.jp
Inferring disease association using clinical factors in a combinatorial manner and their use in drug repositioning
Authors: Jung Jinmyung , Lee Doheon 
Published: June 2013

Abstract
Motivation: Complex physiological relationships exist among human diseases. Thus, the identification of disease associations could provide new methods of disease care and diagnosis. To this end, numerous studies have investigated disease associations. However, combinatorial effect of physiological factors, which is the main characteristic of biological systems, has not been considered in most previous studies.
Results: In this study, we inferred disease associations with a novel approach that considered disease-related clinical factors in combinatorial ways by using the National Health and Nutrition Examination Survey data, and the results have been shown as disease networks. Here, the FP-growth algorithm, an association rule mining algorithm, was used to generate a clinical attribute combination profile of each disease. In addition, we characterized the 22 clinical risk attribute combinations frequently discovered from the 26 diseases in this study. Furthermore, we validated that the results of this study have great potential for drug repositioning and outperform other existing disease networks in this regard. Finally, we suggest a few disease pairs as new candidates for drug repositioning and provide the evidence of their associations from the literature.
Contact: dhlee@kaist.ac.kr or jmjung.kr@gmail.com
Supplementary information: Supplementary data are available at the Bioinformatics online.
A simulation framework for evaluating fisheries management decisions using environmental information
Authors: Skagen Dankert W. , Skern-Mauritzen Mette , Dankel Dorothy , Enberg Katja , Kjesbu Olav S. , Nash Richard D. M. 
Published: June 2013

Abstract
Skagen, D. W., Skern-Mauritzen, M., Dankel, D., Enberg, K., Kjesbu, O. S., and Nash, R. D. M. 2013. A simulation framework for evaluating fisheries management decisions using environmental information. – ICES Journal of Marine Science, 70: 743–754. The population dynamics of marine fish stocks are influenced by both physical and biological conditions. Yet, such environmental impacts on stock dynamics, and hence stock production, are rarely included in applied fisheries management. To test the utility of taking ecosystem information into account in management decisions requires efficient tools. We propose a simulation framework for evaluating fisheries management schemes that use environmental information as part of the decision basis. A key feature is to link environmental signals to parameters in functions that define the population dynamics. This allows a direct incorporation of environmental drivers into models of population dynamic processes and emphasizes the need for a quantitative understanding of the influence of environmental drivers on such processes. The utility of the simulation framework is demonstrated through a worked example with different management scenarios, where decisions to increase or decrease the exploitation rely on environmental indicators only, or also on information on stock abundance. In this example, a management that was based on indicators only, without updated measures of the state of the stock itself, failed to respond adequately to changes in stock productivity.
A link between measured neutron star masses and lattice QCD data
Authors: Bombaci Ignazio , Logoteta Domenico 
Published: June 2013

Abstract
We study the hadron–quark phase transition in neutron star matter and the structural properties of hybrid stars using an equation of state (EOS) for the quark phase derived with the field correlator method (FCM). We make use of the measured neutron star masses, and particularly the mass of PSR J1614−2230, to constrain the values of the gluon condensate G2 which is one of the EOS parameter within the FCM. We find that the values of G2 extracted from the mass measurement of PSR J1614−2230 are fully consistent with the values of the same quantity derived, within the FCM, from recent lattice quantum chromodynamics (QCD) calculations of the deconfinement transition temperature at zero baryon chemical potential. The FCM thus provides a powerful tool to link numerical calculations of QCD on a space–time lattice with neutron stars physics.
There's More to the Picture Than Meets the Eye: Nitric Oxide Cross Talk with Ca2+ Signaling
Authors: Jeandroz Sylvain , Lamotte Olivier , Astier Jérémy , Rasul Sumaira , Trapet Pauline , Besson-Bard Angélique , Bourque Stéphane , Nicolas-Francès Valérie , Ma Wei , Berkowitz Gerald A. , Wendehenne David 
Published: June 2013

Abstract
Calcium and nitric oxide (NO) are two important biological messengers. Increasing evidence indicates that Ca2+ and NO work together in mediating responses to pathogenic microorganisms and microbe-associated molecular patterns. Ca2+ fluxes were recognized to account for NO production, whereas evidence gathered from a number of studies highlights that NO is one of the key messengers mediating Ca2+ signaling. Here, we present a concise description of the current understanding of the molecular mechanisms underlying the cross talk between Ca2+ and NO in plant cells exposed to biotic stress. Particular attention will be given to the involvement of cyclic nucleotide-gated ion channels and Ca2+ sensors. Notably, we provide new evidence that calmodulin might be regulated at the posttranslational level by NO through S-nitrosylation. Furthermore, we report original transcriptomic data showing that NO produced in response to oligogalacturonide regulates the expression of genes related to Ca2+ signaling. Deeper insight into the molecules involved in the interplay between Ca2+ and NO not only permits a better characterization of the Ca2+ signaling system but also allows us to further understand how plants respond to pathogen attack.
Hierarchical Nuclear and Cytoplasmic Genetic Architectures for Plant Growth and Defense withinArabidopsis
Authors: Joseph Bindu , Corwin Jason A. , Züst Tobias , Li Baohua , Iravani Majid , Schaepman-Strub Gabriela , Turnbull Lindsay A. , Kliebenstein Daniel J. 
Published: June 2013

AbstractTo understand how genetic architecture translates between phenotypic levels, we mapped the genetic architecture of growth and defense within the Arabidopsis thaliana Kas × Tsu recombinant inbred line population. We measured plant growth using traditional size measurements and size-corrected growth rates. This population contains genetic variation in both the nuclear and cytoplasmic genomes, allowing us to separate their contributions. The cytoplasmic genome regulated a significant variance in growth but not defense, which was due to cytonuclear epistasis. Furthermore, growth adhered to an infinitesimal model of genetic architecture, while defense metabolism was more of a moderate-effect model. We found a lack of concordance between quantitative trait loci (QTL) regulating defense and those regulating growth. Given the published evidence proving the link between glucosinolates and growth, this is likely a false negative result caused by the limited population size. This size limitation creates an inability to test the entire potential genetic landscape possible between these two parents. We uncovered a significant effect of glucosinolates on growth once we accounted for allelic differences in growth QTLs. Therefore, other growth QTLs can mask the effects of defense upon growth. Investigating direct links across phenotypic hierarchies is fraught with difficulty; we identify issues complicating this analysis.
Endothelial caveolar subcellular domain regulation of endothelial nitric oxide synthase
Authors: Ramadoss Jayanth , Pastore Mayra B , Magness Ronald R 
Published: June 2013

SummaryComplex regulatory processes alter the activity of endothelial nitric oxide synthase (eNOS) leading to nitric oxide (NO) production by endothelial cells under various physiological states. These complex processes require specific subcellulareNOSpartitioning between plasma membrane caveolar domains and non‐caveolar compartments.Translocation ofeNOSfrom the plasma membrane to intracellular compartments is important foreNOSactivation and subsequent NO biosynthesis. We present data reviewing and interpreting information regarding: (i) the coupling of endothelial plasma membrane receptor systems in the caveolar structure relative toeNOStrafficking; (ii) howeNOStrafficking relates to specific protein–protein interactions for inactivation and activation ofeNOS; and (iii) how these complex mechanisms confer specific subcellular location relative toeNOSmultisite phosphorylation and signalling.Dysfunction in the regulation ofeNOSactivation may contribute to several disease states, in particular gestational endothelial abnormalities (pre‐eclampsia, gestational diabetes etc.), that have life‐long deleterious health consequences that predispose the offspring to develop hypertensive disease, Type 2 diabetes and adiposity.
Effect of the Addition of Basil Essential Oil on the Degradation of Palm Olein during Repeated Deep Frying of French Fries
Authors: Cardoso‐Ugarte Gabriel Abraham , Morlán‐Palmas C. Christian , Sosa‐Morales María Elena 
Published: June 2013

AbstractThe potential antioxidant power of basil essential oil under frying conditions was explored. Two concentrations (200 or 500 ppm) were added to palm olein (PO) to evaluate their effect on fat oxidation/degradation during repeated frying of French fries at 180 °C. A higher oxidative stability index was detected for PO with basil essential oil at 200 ppm. Both concentrations showed lower p‐anisidine values than PO without basil essential oil after 5 d of frying. Addition at 500 ppm resulted in the lowest total polar compounds and free fatty acids contents. Thus, the addition of basil essential oil improved the performance of PO during repeated frying of French fries.
Inhibitory Activity of Paenibacillus polymyxa on the Biofilm Formation of Cronobacter spp. on Stainless Steel Surfaces
Authors: Yang Soonwook , Kim Seonhwa , Ryu Jee‐Hoon , Kim Hoikyung 
Published: June 2013

AbstractThe objective of this study was to control the survival or biofilm formation of Cronobacter spp. on stainless steel surfaces using Paenibacillus polymyxa. The antibacterial activity of a cell‐free culture supernatant (CFCS) of P. polymyxa against Cronobacter spp. was found to vary with P. polymyxa incubation time. Maximum activity occurred when P. polymyxa was incubated at 25 or 30 °C for 96 h. When the CFCS was introduced to Cronobacter spp. adhered to stainless steel strips at 25 °C for up to 72 h, the CFCS successfully inhibited Cronobacter biofilm formation. Additionally, stainless steel surfaces with a preformed P. polymyxa biofilm were exposed to Cronobacter spp. suspensions in PBS or 0.1% peptone water at 3, 5, or 7 log CFU/mL to facilitate its attachment. The Cronobacter population significantly decreased on this surface, regardless of inoculum level or carrier, when the P. polymyxa biofilm was present. However, the microbial population decreased within 6 h and remained unchanged thereafter when the surface was immersed in an inoculum suspended in 0.1% peptone water at 5 or 7 log CFU/mL. These results indicate that P. polymyxa is able to use a promising candidate competitive‐exclusion microorganism to control Cronobacter spp.
Tropomyosin Contains IgE‐Binding Epitopes Sensitive to Periodate but Not to Enzymatic Deglycosylation
Authors: Ruan Wei‐Wei , Cao Min‐Jie , Chen Feng , Cai Qiu‐Feng , Su Wen‐Jin , Wang You‐Zhao , Liu Guang‐Ming 
Published: June 2013

AbstractGlycosylation has been reported to affect the epitopes of food allergens, however, there are few reports on its role in crab allergen. In the present study, the effect of glycosylation on the IgE‐binding activity of tropomyosin (TM), a major allergen in Scylla paramamosain, was investigated. The results showed that TM was a glycoprotein with a 0.2% carbohydrate moiety and contained O‐glycan. Moreover, enzymatic deglycosylation of TM by glycosidase had no effect on the IgE‐binding activity of TM. In contrast, treatment with periodate resulted in a significant reduction in its IgE‐binding activity.