bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antioxidative and immunomodulatory effects of tributyrin supplementation on experimental colitis
Authors: Leonel Alda J. , Teixeira Lílian G. , Oliveira Rafael P. , Santiago Andrezza F. , Batista Nathália V. , Ferreira Talita R. , Santos Rosana C. , Cardoso Valbert N. , Cara Denise C. , Faria Ana M. C. , Alvarez-Leite Jacqueline 
Published: August 2012

Tributyrin (TBT) is a TAG composed of three butyric acids that has beneficial effects on ulcerative colitis due to its trophic, anti-inflammatory, pro-apoptotic and anti-carcinogenic properties. The goal of the present study was to evaluate the efficacy and mechanisms of action of TBT supplementation in the prevention of mucosal damage in experimental colitis. Mice received either a control diet or a TBT-supplemented diet for 15 d. Colitis was induced by dextran sodium sulphate administration during the last 7 d. Mucosal damage and the activation of immune cells and cytokines were determined by histological score, flow cytometry and ELISA. Leucocyte rolling and adhesion were assessed by intravital microscopy. Oxidative stress was determined by monitoring hydroperoxide concentration and evaluating superoxide dismutase (SOD) and catalase activities. Intestinal permeability was analysed using diethylenetriaminepentaacetate acid (99mTcDTPA). Compared with the colitis group, the animals in the colitis+TBT group had reduced mucosal damage and neutrophil and eosinophil mucosal infiltration, which were associated with a higher percentage of regulatory T cells (Treg) and higher levels of transforming growth factor β and IL-10 in the lamina propria. The level ofin vivoleucocyte adhesion in the colon microvasculature was reduced after TBT supplementation. A lower level of hydroperoxide and higher levels of SOD and catalase activities were associated with TBT supplementation. TBT-supplemented mice showed reduced intestinal permeability to the levels intermediate between the control and colitis groups. In conclusion, the present results show that TBT has positive effects on colonic restructuring in experimental colitis. Additionally, TBT supplementation changes the immune response by controlling inflammation and regulating the expression of anti-inflammatory cytokines and Treg.
Phylogeography ofTrichurispopulations isolated from different Cricetidae rodents
Authors: CALLEJÓN ROCÍO , DE ROJAS MANUEL , FELIÚ CARLOS , BALAO FRANCISCO , MARRUGAL ÁNGELA , HENTTONEN HEIKKI , GUEVARA DIEGO , CUTILLAS CRISTINA 
Published: August 2012

SUMMARYThe phylogeography ofTrichurispopulations (Nematoda) collected from Cricetidae rodents (Muroidea) from different geographical regions was studied. Ribosomal DNA (Internal Transcribed Spacers 1 and 2, and mitochondrial DNA (cytochrome c- oxidasesubunit 1 partial gene) have been used as molecular markers. The nuclear internal transcribed spacers (ITSs) 1 and 2 showed 2 clear-cut geographical and genetic lineages: one of the Nearctic region (Oregon), although the second was widespread throughout the Palaearctic region and appeared as a star-like structure in the minimum spanning network. The mitochondrial results revealed thatT. arvicolaepopulations from the Palaearctic region were separated into 3 clear-cut geographical and genetic lineages: populations from Northern Europe, populations from Southern (Spain) and Eastern Europe (Croatia, Belarus, Kazahstan), and populations from Italy and France (Eastern Pyrénean Mountains). Phylogenetic analysis obtained on the basis of ITS1-5·8S-ITS2 rDNA sequences did not show a differential geographical structure; however, these markers suggest a newTrichurisspecies parasitizingChionomys robertiandCricetulus barabensis. The mitochondrial results revealed thatTrichurispopulations from arvicolinae rodents show signals of a post-glacial northward population expansion starting from the Pyrenees and Italy. Apparently, the Pyrenees and the Alps were not barriers to the dispersal ofTrichurispopulations.
A functional study of nucleocytoplasmic transport signals of the EhNCABP166 protein from Entamoeba histolytica
Authors: URIBE R. , BARRERA MA DE J. ALMARAZ , ROBLES-FLORES M. , HERNÁNDEZ G. MENDOZA , GONZÁLEZ-ROBLES A. , HERNÁNDEZ-RIVAS R. , GUILLEN N. , VARGAS M. 
Published: August 2012

SUMMARYEhNCABP166 is an Entamoeba histolytica actin-binding protein that localizes to the nucleus and cytoplasm. Bioinformatic analysis of the EhNCABP166 amino acid sequence shows the presence of 3 bipartite nuclear localization signals (NLS) and a nuclear export signal (NES). The present study aimed to investigate the functionality of these signals in 3 ways. First, we fused each potential NLS to a cytoplasmic domain of ehFLN to determine whether the localization of this domain could be altered by the presence of the NLSs. Furthermore, the localization of each domain of EhNCABP166 was determined. Similarly, we generated mutations in the first block of bipartite signals from the domains that contained these signals. Additionally, we added an NES to 2 constructs that were then evaluated. We confirmed the intranuclear localization of EhNCABP166 using transmission electron microscopy. Fusion of each NLS resulted in shuttling of the cytoplasmic domain to the nucleus. With the exception of 2 domains, all of the evaluated domains localized within the nucleus. A mutation in the first block of bipartite signals affected the localization of the domains containing an NLS. The addition of an NES shifted the localization of these domains to the cytoplasm. The results presented here establish EhNCABP166 as a protein containing functional nuclear localization signals and a nuclear export signal.
Suppression of predation on the intermediate host by two trophically-transmitted parasites when uninfective
Authors: WEINREICH F. , BENESH D. P. , MILINSKI M. 
Published: August 2012

SUMMARYTrophically-transmitted parasites generally need to undergo a period of development in the intermediate host before reaching infectivity. During this vulnerable period, manipulation of the host to reduce susceptibility to predation would be advantageous for parasites, because it increases the probability of surviving until infectivity and thus the probability of transmission. We tested this ‘predation suppression’ hypothesis in 2 parasite species that use copepods as first hosts: the tapewormSchistocephalus solidusand the nematodeCamallanus lacustris. In a series of prey choice experiments, we found that copepods harbouring uninfective, still-developing worm larvae were less frequently consumed by stickleback predators than uninfected copepods. The levels of predation suppression were similar in the two parasite species, suggestive of convergent evolution. Additionally, copepods harbouring 2 worms of a given species were not more susceptible to predation than those with 1 worm, suggesting that excessive larval parasite growth does not increase host susceptibility to predation. Our results support the idea that parasites can suppress intermediate host susceptibility to predation while uninfective, but we also note that the available studies suggest that this effect is weaker than the frequently observed enhancement of host predation by infective helminth larvae.
On the plurality of gods
Authors: STEINHART ERIC 
Published: August 2012

AbstractOrdinal polytheism is motivated by the cosmological and design arguments. It is also motivated by Leibnizian–Lewisian modal realism. Just as there are many universes, so there are many gods. Gods are necessary concrete grounds of universes. The god-universe relation is one-to-one. Ordinal polytheism argues for a hierarchy of ranks of ever more perfect gods, one rank for every ordinal number. Since there are no maximally perfect gods, ordinal polytheism avoids many of the familiar problems of monotheism. It links theology with counterpart theory, mathematics and computer science. And it entails that the system of universes has an attractive axiological structure.
RWM control studies on RFX-mod with a limited set of active coils*
Authors: Baruzzo M. , Bolzonella T. , Liu Y.Q. , Manduchi G. , Marchiori G. , Soppelsa A. , Takechi M. , Villone F. 
Published: August 2012

Abstract
In this paper, the results of resistive wall mode (RWM) control experiments using several sets of active coils are presented.
The control effectiveness as a function of coil number and covered torus surface is studied in the RFX-mod device, thanks to the powerful and flexible MHD active control system. Active control is tried using similar coil number and size both in the reversed field pinch (RFP) and in the tokamak configurations, giving a good experimental set to exploit the differences between the two cases.
The experimental results are compared with predictions by a new integrated simulator for closed loop RWM growth. The numerical tool couples, in a self-consistent way, a full 3D finite element description of the machine boundaries, a 2D toroidal model of RFP plasma stability and a model of the RFX-mod control system, producing an overall dynamic model cast in the state variable space. In this way a full dynamic flight simulator of RWM control experiments is implemented, where coil coverage and experimental proportional–integral–derivative gains are explored in simulations.
Both in the performed experiments and in simulations wall mode active control is proven to be possible in both the configurations with a very reduced set of active control coils.
PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data
Authors: Sükösd Zsuzsanna , Knudsen Bjarne , Kjems Jørgen , Pedersen Christian N.S. 
Published: August 2012

Abstract
Summary: PPfold is a multi-threaded implementation of the Pfold algorithm for RNA secondary structure prediction. Here we present a new version of PPfold, which extends the evolutionary analysis with a flexible probabilistic model for incorporating auxiliary data, such as data from structure probing experiments. Our tests show that the accuracy of single-sequence secondary structure prediction using experimental data in PPfold 3.0 is comparable to RNAstructure. Furthermore, alignment structure prediction quality is improved even further by the addition of experimental data. PPfold 3.0 therefore has the potential of producing more accurate predictions than it was previously possible.
Availability and implementation: PPfold 3.0 is available as a platform-independent Java application and can be downloaded from http://birc.au.dk/software/ppfold.
Contact: Zsuzsanna Sükösd or zs@birc.au.dk.
BioJava: an open-source framework for bioinformatics in 2012
Authors: Prlić Andreas , Yates Andrew , Bliven Spencer E. , Rose Peter W. , Jacobsen Julius , Troshin Peter V. , Chapman Mark , Gao Jianjiong , Koh Chuan Hock , Foisy Sylvain , Holland Richard , Rimša Gediminas , Heuer Michael L. , Brandstätter–Müller H. , Bourne Philip E. , Willis Scooter 
Published: August 2012

Abstract
Motivation: BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality.
Results: BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model.
Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.6 or higher. All inquiries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists
Contact: andreas.prlic@gmail.com
A novel role of CD1c in regulating CD1d-mediated NKT cell recognition by competitive binding to Ig-like transcript 4
Authors: Li Demin , Hong An , Lu Qiong , Gao George F. , Jin Boquan , Screaton Gavin R. , Xu Xiao-Ning 
Published: August 2012

Abstract
Humans express four MHC-like CD1 molecules CD1a, b, c and d that are capable of presenting a wide variety of self or foreign lipid antigens to T cells. Much progress has been made in elucidating the function of CD1d-restricted NKT cells in both innate and adaptive immune responses. However, knowledge of the other CD1 molecules is less well defined in terms of lipid presentation and immune regulation. We have previously shown that immunoglobulin-like transcript 4 (ILT4) binds to CD1d and inhibits its recognition by NKT cells. In this study, we show that CD1c can also interact specifically with ILT4 with a higher affinity than that of CD1d. Furthermore, changes in CD1c expression seem to modulate CD1d function; up-regulation of CD1c enhances NKT recognition of CD1d and down-regulation reduces CD1d recognition. We propose that CD1c can act as a sink for the inhibitory receptor ILT4: when CD1c is up-regulated, ILT4 is recruited to CD1c, thus reducing the inhibitory effect of ILT4 on CD1d recognition. Consequently, CD1c could be a potential target for modulating NKT activity.Keywords: NKT, CD1d, CD1c, ILT4, antigen presentation
SNF1-Related Protein Kinases Type 2 Are Involved in Plant Responses to Cadmium Stress
Authors: Kulik Anna , Anielska-Mazur Anna , Bucholc Maria , Koen Emmanuel , Szymańska Katarzyna , Żmieńko Agnieszka , Krzywińska Ewa , Wawer Izabela , McLoughlin Fionn , Ruszkowski Dariusz , Figlerowicz Marek , Testerink Christa , Skłodowska Aleksandra , Wendehenne David , Dobrowolska Grażyna 
Published: August 2012

AbstractCadmium ions are notorious environmental pollutants. To adapt to cadmium-induced deleterious effects plants have developed sophisticated defense mechanisms. However, the signaling pathways underlying the plant response to cadmium are still elusive. Our data demonstrate that SnRK2s (for SNF1-related protein kinase2) are transiently activated during cadmium exposure and are involved in the regulation of plant response to this stress. Analysis of tobacco (Nicotiana tabacum) Osmotic Stress-Activated Protein Kinase activity in tobacco Bright Yellow 2 cells indicates that reactive oxygen species (ROS) and nitric oxide, produced mainly via an l-arginine-dependent process, contribute to the kinase activation in response to cadmium. SnRK2.4 is the closest homolog of tobacco Osmotic Stress-Activated Protein Kinase in Arabidopsis (Arabidopsis thaliana). Comparative analysis of seedling growth of snrk2.4 knockout mutants versus wild-type Arabidopsis suggests that SnRK2.4 is involved in the inhibition of root growth triggered by cadmium; the mutants were more tolerant to the stress. Measurements of the level of three major species of phytochelatins (PCs) in roots of plants exposed to Cd2+ showed a similar (PC2, PC4) or lower (PC3) concentration in snrk2.4 mutants in comparison to wild-type plants. These results indicate that the enhanced tolerance of the mutants does not result from a difference in the PCs level. Additionally, we have analyzed ROS accumulation in roots subjected to Cd2+ treatment. Our data show significantly lower Cd2+-induced ROS accumulation in the mutants’ roots. Concluding, the obtained results indicate that SnRK2s play a role in the regulation of plant tolerance to cadmium, most probably by controlling ROS accumulation triggered by cadmium ions.
Composition and Physiological Function of the Wax Layers Coating Arabidopsis Leaves: β-Amyrin Negatively Affects the Intracuticular Water Barrier
Authors: Buschhaus Christopher , Jetter Reinhard 
Published: August 2012

Abstract
Plants prevent dehydration by coating their aerial, primary organs with waxes. Wax compositions frequently differ between species, organs, and developmental stages, probably to balance limiting nonstomatal water loss with various other ecophysiological roles of surface waxes. To establish structure-function relationships, we quantified the composition and transpiration barrier properties of the gl1 mutant leaf waxes of Arabidopsis (Arabidopsis thaliana) to the necessary spatial resolution. The waxes coating the upper and lower leaf surfaces had distinct compositions. Moreover, within the adaxial wax, the epicuticular layer contained more wax and a higher relative quantity of alkanes, whereas the intracuticular wax had a higher percentage of alcohols. The wax formed a barrier against nonstomatal water loss, where the outer layer contributed twice as much resistance as the inner layer. Based on this detailed description of Arabidopsis leaf waxes, structure-function relationships can now be established by manipulating one cuticle component and assessing the effect on cuticle functions. Next, we ectopically expressed the triterpenoid synthase gene AtLUP4 (for lupeol synthase4 or β-amyrin synthase) to compare water loss with and without added cuticular triterpenoids in Arabidopsis leaf waxes. β-Amyrin accumulated solely in the intracuticular wax, constituting up to 4% of this wax layer, without other concomitant changes of wax composition. This triterpenoid accumulation caused a significant reduction in the water barrier effectiveness of the intracuticular wax.
A Nitrogen-Regulated Glutamine Amidotransferase (GAT1_2.1) Represses Shoot Branching in Arabidopsis
Authors: Zhu Huifen , Kranz Robert G. 
Published: August 2012

AbstractShoot branching in plants is regulated by many environmental cues and by specific hormones such as strigolactone (SL). We show that the GAT1_2.1 gene (At1g15040) is repressed over 50-fold by nitrogen stress, and is also involved in branching control. At1g15040 is predicted to encode a class I glutamine amidotransferase (GAT1), a superfamily for which Arabidopsis (Arabidopsis thaliana) has 30 potential members. Most members can be categorized into known biosynthetic pathways, for the amidation of known acceptor molecules (e.g. CTP synthesis). Some members, like GAT1_2.1, are of unknown function, likely involved in amidation of unknown acceptors. A gat1_2.1 mutant exhibits a significant increase in shoot branching, similar to mutants in SL biosynthesis. The results suggest that GAT1_2.1 is not involved in SL biosynthesis since exogenously applied GR24 (a synthetic SL) does not correct the mutant phenotype. The subfamily of GATs (GATase1_2), with At1g15040 as the founding member, appears to be present in all plants (including mosses), but not other organisms. This suggests a plant-specific function such as branching control. We discuss the possibility that the GAT1_2.1 enzyme may activate SLs (e.g. GR24) by amidation, or more likely could embody a new pathway for repression of branching.
The Rice Wall-Associated Receptor-Like Kinase Gene OsDEES1 Plays a Role in Female Gametophyte Development
Authors: Wang Na , Huang Hui-Jia , Ren Su-Ting , Li Jiao-Jiao , Sun Ying , Sun Da-Ye , Zhang Su-Qiao 
Published: August 2012

Abstract
The wall-associated kinase (WAK) gene family is a unique subfamily of receptor-like kinases (RLKs) in plants. WAK-RLKs play roles in cell expansion, pathogen resistance, and metal tolerance in Arabidopsis (Arabidopsis thaliana). Rice (Oryza sativa) has far more WAK-RLK genes than Arabidopsis, but the functions of rice WAK-RLKs are poorly understood. In this study, we found that one rice WAK-RLK gene, DEFECT IN EARLY EMBRYO SAC1 (OsDEES1), is involved in the regulation of early embryo sac development. OsDEES1 silencing by RNA interference caused a high rate of female sterility. Crossing experiments showed that female reproductive organs lacking OsDEES1 carried a functional defect. A detailed investigation of the ovaries from OsDEES1 RNA interference plants indicated that the knockdown of OsDEES1 expression did not affect megasporogenesis but that it disturbed female gametophyte formation, resulting in a degenerated embryo sac and defective seed formation. OsDEES1 exhibited a tissue-specific expression pattern in flowers and seedlings. In the ovary, OsDEES1 was expressed in the megagametophyte region and surrounding nucellus cells in the ovule near the micropylar region. OsDEES1 was found to be a membrane-localized protein with a unique sequence compared with other WAK-RLKs. These data indicate that OsDEES1 plays a role in rice sexual reproduction by regulating female gametophyte development. This study offers new insight into the functions of the WAK-RLK family.
Looking desperately for courage or how to study a polysemic concept
Authors: Harbour Michelle , Kisfalvi Veronika 
Published: August 2012

PurposeThe purpose of this article is to propose an approach using mixed methods appropriate for studying polysemic concepts.Design/methodology/approachAnchored in cognitive approaches, the methods relied on a generally applicable conceptual framework, on cognitive mapping for an intellectualized conception, and on in‐depth interviews for an experiential conception on different participants’ judgments of managerial courage within the same context.FindingsThe mixed methods approach allowed the study first, to uncover two kinds of managerial courage. Second, while the intellectualized conceptions led to the enumeration of a greater number of positive consequences for third parties, the conceptions resulting from recollections of experiences focused more on the consequences for the protagonist. Third, the conceptual framework allowed the authors to distinguish between the results obtained from the two distinct data collection methods: the moral dimension, present in the more intellectualized cognitive maps, was largely absent from the consequences identified by participants in the conception of managerial courage resulting from experience.Originality/valueThis approach has provided two original methodological contributions. The first is the development of a widely applicable conceptual framework useful for studying polysemic concepts and for treating data generated by both approaches. The second is the distinction between conceptions of courage obtained from cognitive maps and those obtained through semi‐structured, in‐depth interviews, highlighting the complementarity of the chosen methods.
A multidimensional model for analyzing employee identification with corporate values
Authors: Agerholm Andersen Mona 
Published: August 2012

PurposeThe purpose of this paper is to explore the use of a multidimensional model from the field of media reception for analyzing how a value statement in a Danish windmill company led to employee identification as well as organizational antecedents that influenced this identification. Further, the paper evaluates whether the proposed model can enhance understanding of the study of employee identification in a specific organizational situation and context.Design/methodology/approachThe identification model extends a multidimensional model for media reception originally proposed by Schrøder in the field of media reception studies. The proposed model includes the following reception dimensions: comprehension, discrimination, implementation, motivation, and position.FindingsThis paper illustrates how employees from a Danish windmill company receive a value statement. A systematic application of the multidimensional model makes it possible to gain detailed insight into the active and complex process of employee identifications with organizational texts and how they may fluctuate in a specific context.Research limitations/implicationsThis analysis only focuses on the reception of a value statement. Future research could include the analysis of employee readings of other types of organizational texts.Originality/valueThe multidimensional identification model is an extension of a media reception model and is new in the field of organizational identification. The model offers a method for analyzing the complexity and multiplicity of employee readings of different types of organizational texts. This may be crucial for both researchers and managers as the model may help to uncover the antecedents that influence how employees receive organizational texts while taking the historical and situational context of the organization into consideration.