bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Semantic Feature Analysis to Improve Contextual Discourse in Adults With Aphasia
Authors: Rider Jill Davis , Wright Heather Harris , Marshall Robert C. , Page Judith L. 
Published: April 2008

Purpose
Semantic feature analysis (SFA) was used to determine whether training contextually related words would improve the discourse of individuals with nonfluent aphasia in preselected contexts.

Method
A modified multiple-probes-across-behaviors design was used to train target words using SFA in 3 adults with nonfluent aphasia. Pretreatment, posttreatment, and follow-up sessions obtained language samples for the preselected contexts. Contexts included 4 story retellings and 4 procedure explanations.

Results
All participants improved naming ability for treated words. No generalization to untrained items was found. Within discourse samples, participants increased number of target words produced from pretreatment to posttreatment sessions but did not increase lexical diversity across samples. Participants maintained performance on standardized measures from the beginning to the end of the study.

Conclusions
Results support and extend previous research by indicating that SFA improves confrontational naming ability and may benefit word retrieval in discourse production of closed-set contexts.
gpDB: a database of GPCRs, G-proteins, effectors and their interactions
Authors: Theodoropoulou Margarita C. , Bagos Pantelis G. , Spyropoulos Ioannis C. , Hamodrakas Stavros J. 
Published: April 2008

Abstract
Summary: gpDB is a publicly accessible, relational database, containing information about G-proteins, G-protein coupled receptors (GPCRs) and effectors, as well as information concerning known interactions between these molecules. The sequences are classified according to a hierarchy of different classes, families and subfamilies based on literature search. The main innovation besides the classification of G-proteins, GPCRs and effectors is the relational model of the database, describing the known coupling specificity of GPCRs to their respective alpha subunits of G-proteins, and also the specific interaction between G-proteins and their effectors, a unique feature not available in any other database.
Availability: http://bioinformatics.biol.uoa.gr/gpDB
Contact: shamodr@biol.uoa.gr
Supplementary information: Supplementary data are available at Bioinformatics online.
Depth-dependent target strength of anchovy (Engraulis japonicus) measured in situ
Authors: Zhao Xianyong , Wang Yong , Dai Fangqun 
Published: April 2008

Abstract
Zhao, X., Wang, Y., and Dai, F. 2008. Depth-dependent target strength of anchovy (Engraulis japonicus) measured in situ. – ICES Journal of Marine Science, 65: 882–888. Three sets of target strength (TS) data were collected in the southern part of the Yellow Sea using a calibrated, 38 kHz, Simrad EK500 split-beam echosounder. Midwater trawl sampling showed that >97% of the catch by number was anchovy (Engraulis japonicus), with total lengths ranging from 6 to 15 cm, and that the arithmetic-mean length and root-mean-square length were 10.6 and 10.8 cm, respectively. The mean TS of anchovy in the 10–45-m layer was estimated to be –50.9 dB, with a 95% confidence interval of (–51.0, –50.8) dB. The TS data showed, however, a clear depth-dependence that was very close to and not significantly different from what might be expected according to Boyle’s law. The TS model was estimated to be TS = 20 log L − 71.6 for the conventional relationship between TS and length, but TS = 20 log L− (20/3) log (1+z/10) − 67.6 when the depth (z, m) effect was included according to Boyle’s law. These results may have a significant influence on abundance estimates of anchovy derived from acoustic surveys, both in the Yellow Sea and in other parts of the world.
Variations in echosounder–transducer performance with water temperature
Authors: Demer David A. , Renfree Josiah S. 
Published: April 2008

Abstract
Demer, D. A., and Renfree, J. S. 2008. Variations in echosounder–transducer performance with water temperature. – ICES Journal of Marine Science, 65: 1021–1035. Electro-acoustic transducers are central components of multifrequency echosounders used in remote-target identification and acoustic surveys for fish and zooplankton. Appreciable changes in echosounder system gains can result from shifts in transducer frequency responses with water temperature. Because it is standard practice to calibrate echosounder systems for fisheries surveys in one environment and apply the resulting gains to interpret data collected over the range of sea temperatures encountered during a survey, the results may be biased. Such biases may be different for estimates derived from each echosounder frequency. In moving to quantify and mitigate these effects, the performances have been measured for ten commonly used survey transducers in water temperatures ranging from ∼1°C to 18°C, using three techniques. Results show that the transducer impedances all change with temperature, potentially changing the signal-to-noise ratio from 5 to >20 dB. The resonance frequencies and quality factors also change with temperature, ranging from ∼0.2% to 2.8% and 2.5% to >130%, respectively. Corresponding directly to changes in the echosounder gains, the transmitting-current and receiver-voltage responses changed 1 dB or less with temperature, except for the Simrad ES120-7, which showed a 2 dB increase. Generally, the magnitudes of frequency-dependent biases in echosounder-system gains depend primarily on the temperature-dependent performances of the survey transducers, the range of temperatures encountered, and whether the operational frequencies are less or greater than the resonance frequency.
Sense of Coherence and Physical Health. A “Copenhagen Interpretation” of Antonovsky's SOC Concept
Authors: Endler P. Christian , Haug Thomas M. , Spranger Heinz 
Published: April 2008

According to Antonovsky's (Aaron Antonovsky, 1923–1994) sense of coherence (SOC) model, persons with a high SOC have the ability to benefit from their general defense mechanisms in order to overcome stressful situations. In a health-disease continuum, this leads to the development towards health. However, Antonovsky's global hypothesis that the strength of the SOC may influence the physical health status of a person could not be proven.Flensborg-Madsen et al. from Copenhagen were able to provide a new access regarding SOC and health. They investigated the mixture of emotional aspects and mental constructions as a possible cause for fairly low correlation between SOC and physical health. Thus, in an empirical way, they described “emotional coherence” in relation to physical health, while “mental coherence” was linked topsychologicalhealth. These authors introduced the idea of applying a shortened version of the original 29-item SOC questionnaire, but have not yet developed or tested the shortened questionnaire. Backed by their important findings, it appears to be promising to consider the use of the SOC questionnaire as standardized by Antonovsky, but cleared of the items regarding “predictability”, i.e., Flensborg-Madsen et al. suggested that the items on “predictability” be excluded from the SOC scale when a correlation to physical health is to be investigated. Further investigations in this area of research will be of high impact, not only for health sciences, but also for medical practice.
Evidence for Abscisic Acid Biosynthesis in Cuscuta reflexa, a Parasitic Plant Lacking Neoxanthin
Authors: Qin Xiaoqiong , Yang Seung Hwan , Kepsel Andrea C. , Schwartz Steven H. , Zeevaart Jan A.D. 
Published: April 2008

Abstract
Abscisic acid (ABA) is a plant hormone found in all higher plants; it plays an important role in seed dormancy, embryo development, and adaptation to environmental stresses, most notably drought. The regulatory step in ABA synthesis is the cleavage reaction of a 9-cis-epoxy-carotenoid catalyzed by the 9-cis-epoxy-carotenoid dioxygenases (NCEDs). The parasitic angiosperm Cuscuta reflexa lacks neoxanthin, one of the common precursors of ABA in all higher plants. Thus, is C. reflexa capable of synthesizing ABA, or does it acquire ABA from its host plants? Stem tips of C. reflexa were cultured in vitro and found to accumulate ABA in the absence of host plants. This demonstrates that this parasitic plant is capable of synthesizing ABA. Dehydration of detached stem tips caused a big rise in ABA content. During dehydration, 18O was incorporated into ABA from 18O2, indicating that ABA was synthesized de novo in C. reflexa. Two NCED genes, CrNCED1 and CrNCED2, were cloned from C. reflexa. Expression of CrNCEDs was up-regulated significantly by dehydration. In vitro enzyme assays with recombinant CrNCED1 protein showed that the protein is able to cleave both 9-cis-violaxanthin and 9′-cis-neoxanthin to give xanthoxin. Thus, despite the absence of neoxanthin in C. reflexa, the biochemical activity of CrNCED1 is similar to that of NCEDs from other higher plants. These results provide evidence for conservation of the ABA biosynthesis pathway among members of the plant kingdom.
Functional Identification of Arabidopsis Stress Regulatory Genes Using the Controlled cDNA Overexpression System
Authors: Papdi Csaba , Ábrahám Edit , Joseph Mary Prathiba , Popescu Cristina , Koncz Csaba , Szabados László 
Published: April 2008

Abstract
Responses to environmental stresses in higher plants are controlled by a complex web of abscisic acid (ABA)-dependent and independent signaling pathways. To perform genetic screens for identification of novel Arabidopsis (Arabidopsis thaliana) loci involved in the control of abiotic stress responses, a complementary DNA (cDNA) expression library was created in a Gateway version of estradiol-inducible XVE binary vector (controlled cDNA overexpression system [COS]). The COS system was tested in three genetic screens by selecting for ABA insensitivity, salt tolerance, and activation of a stress-responsive ADH1-LUC (alcohol dehydrogenase-luciferase) reporter gene. Twenty-seven cDNAs conferring dominant, estradiol-dependent stress tolerance phenotype, were identified by polymerase chain reaction amplification and sequence analysis. Several cDNAs were recloned into the XVE vector and transformed recurrently into Arabidopsis, to confirm that the observed conditional phenotypes were due to their estradiol-dependent expression. Characterization of a cDNA conferring insensitivity to ABA in germination assays has identified the coding region of heat shock protein HSP17.6A suggesting its implication in ABA signal transduction. Screening for enhanced salt tolerance in germination and seedling growth assays revealed that estradiol-controlled overexpression of a 2-alkenal reductase cDNA confers considerable level of salt insensitivity. Screening for transcriptional activation of stress- and ABA-inducible ADH1-LUC reporter gene has identified the ERF/AP2-type transcription factor RAP2.12, which sustained high-level ADH1-LUC bioluminescence, enhanced ADH1 transcription rate, and increased ADH enzyme activity in the presence of estradiol. These data illustrate that application of the COS cDNA expression library provides an efficient strategy for genetic identification and characterization of novel regulators of abiotic stress responses.
Knocking Out Cytosolic Cysteine Synthesis Compromises the Antioxidant Capacity of the Cytosol to Maintain Discrete Concentrations of Hydrogen Peroxide in Arabidopsis
Authors: López-Martín M. Carmen , Becana Manuel , Romero Luis C. , Gotor Cecilia 
Published: April 2008

AbstractPlant cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes involved in cysteine (Cys) biosynthesis and located in different subcellular compartments. These enzymes are made up of a complex variety of isoforms resulting in different subcellular Cys pools. To unravel the contribution of cytosolic Cys to plant metabolism, we characterized the knockout oas-a1.1 and osa-a1.2 mutants, deficient in the most abundant cytosolic OASTL isoform in Arabidopsis (Arabidopsis thaliana). Total intracellular Cys and glutathione concentrations were reduced, and the glutathione redox state was shifted in favor of its oxidized form. Interestingly, the capability of the mutants to chelate heavy metals did not differ from that of the wild type, but the mutants have an enhanced sensitivity to cadmium. With the aim of establishing the metabolic network most influenced by the cytosolic Cys pool, we used the ATH1 GeneChip for evaluation of differentially expressed genes in the oas-a1.1 mutant grown under nonstress conditions. The transcriptomic footprints of mutant plants had predicted functions associated with various physiological responses that are dependent on reactive oxygen species and suggested that the mutant was oxidatively stressed. Evidences that the mutation caused a perturbation in H2O2 homeostasis are that, in the knockout, H2O2 production was localized in shoots and roots; spontaneous cell death lesions occurred in the leaves; and lignification and guaiacol peroxidase activity were significantly increased. All these findings indicate that a deficiency of OAS-A1 in the cytosol promotes a perturbation in H2O2 homeostasis and that Cys is an important determinant of the antioxidative capacity of the cytosol in Arabidopsis.
Artificial trans-Acting siRNAs Confer Consistent and Effective Gene Silencing
Authors: de la Luz Gutiérrez-Nava Maria , Aukerman Milo J. , Sakai Hajime , Tingey Scott V. , Williams Robert W. 
Published: April 2008

Abstract
Manipulating gene expression is critical to exploring gene function and a useful tool for altering commercial traits. Techniques such as hairpin-based RNA interference, virus-induced gene silencing, and artificial microRNAs take advantage of endogenous posttranscriptional gene silencing pathways to block translation of designated transcripts. Here we present a novel gene silencing method utilizing artificial trans-acting small interfering RNAs in Arabidopsis (Arabidopsis thaliana). Replacing the endogenous small interfering RNAs encoded in the TAS1c gene with sequences from the FAD2 gene silenced FAD2 activity to levels comparable to the fad2-1 null allele in nearly all transgenic events. Interestingly, exchanging the endogenous miR173 target sequence in TAS1c with an miR167 target sequence led to variable, inefficient silencing of FAD2, suggesting a specific requirement for the miR173 trigger for production of small interfering RNAs from the TAS1c locus.
REBELOTE,SQUINT, andULTRAPETALA1Function Redundantly in the Temporal Regulation of Floral Meristem Termination inArabidopsis thaliana
Authors: Prunet Nathanaël , Morel Patrice , Thierry Anne-Marie , Eshed Yuval , Bowman John L. , Negrutiu Ioan , Trehin Christophe 
Published: April 2008

AbstractIn Arabidopsis thaliana, flowers are determinate, showing a fixed number of whorls. Here, we report on three independent genes, a novel gene REBELOTE (RBL; protein of unknown function), SQUINT (SQN; a cyclophilin), and ULTRAPETALA1 (ULT1; a putative transcription factor) that redundantly influence floral meristem (FM) termination. Their mutations, combined with each other or with crabs claw, the genetic background in which they were isolated, trigger a strong FM indeterminacy with reiterations of extra floral whorls in the center of the flower. The range of phenotypes suggests that, in Arabidopsis, FM termination is initiated from stages 3 to 4 onwards and needs to be maintained through stage 6 and beyond, and that RBL, SQN, and ULT1 are required for this continuous regulation. We show that mutant phenotypes result from a decrease of AGAMOUS (AG) expression in an inner 4th whorl subdomain. However, the defect of AG activity alone does not explain all reported phenotypes, and our genetic data suggest that RBL, SQN, and, to a lesser extent, ULT1 also influence SUPERMAN activity. Finally, from all the molecular and genetic data presented, we argue that these genes contribute to the more stable and uniform development of flowers, termed floral developmental homeostasis.
Functional and Physiological Characterization of Arabidopsis INOSITOL TRANSPORTER1, a Novel Tonoplast-Localized Transporter for myo-Inositol
Authors: Schneider Sabine , Beyhl Diana , Hedrich Rainer , Sauer Norbert 
Published: April 2008

Abstract
Arabidopsis thaliana INOSITOL TRANSPORTER1 (INT1) is a member of a small gene family with only three more genes (INT2 to INT4). INT2 and INT4 were shown to encode plasma membrane–localized transporters for different inositol epimers, and INT3 was characterized as a pseudogene. Here, we present the functional and physiological characterization of the INT1 protein, analyses of the tissue-specific expression of the INT1 gene, and analyses of phenotypic differences observed between wild-type plants and mutant lines carrying the int1.1 and int1.2 alleles. INT1 is a ubiquitously expressed gene, and Arabidopsis lines with T-DNA insertions in INT1 showed increased intracellular myo-inositol concentrations and reduced root growth. In Arabidopsis, tobacco (Nicotiana tabacum), and Saccharomyces cerevisiae, fusions of the green fluorescent protein to the C terminus of INT1 were targeted to the tonoplast membranes. Finally, patch-clamp analyses were performed on vacuoles from wild-type plants and from both int1 mutant lines to study the transport properties of INT1 at the tonoplast. In summary, the presented molecular, physiological, and functional studies demonstrate that INT1 is a tonoplast-localized H+/inositol symporter that mediates the efflux of inositol that is generated during the degradation of inositol-containing compounds in the vacuolar lumen.
Crystal structural analysis of protein–protein interactions drastically destabilized by a single mutation
Authors: Urakubo Yoshiaki , Ikura Teikichi , Ito Nobutoshi 
Published: April 2008

AbstractThe complex of barnase (bn) and barstar (bs), which has been widely studied as a model for quantitative analysis of protein–protein interactions, is significantly destabilized by a single mutation, namely, bs Asp39 → Ala, which corresponds to a change of 7.7 kcal·mol−1 in the free energy of binding. However, there has been no structural information available to explain such a drastic destabilization. In the present study, we determined the structure of the mutant complex at 1.58 Å resolution by X‐ray crystallography. The complex was similar to the wild‐type complex in terms of overall and interface structures; however, the hydrogen bond network mediated by water molecules at the interface was significantly different. Several water molecules filled the cavity created by the mutation and consequently caused rearrangement of the hydrated water molecules at the interface. The water molecules were redistributed into a channel‐like structure that penetrated into the complex. Furthermore, molecular dynamics simulations showed that the mutation increased the mobility of water molecules at the interface. Since such a drastic change in hydration was not observed in other mutant complexes of bn and bs, the significant destabilization of the interaction may be due to this channel‐like structure of hydrated water molecules.
Using multiple templates to improve quality of homology models in automated homology modeling
Authors: Larsson Per , Wallner Björn , Lindahl Erik , Elofsson Arne 
Published: April 2008

AbstractWhen researchers build high‐quality models of protein structure from sequence homology, it is today common to use several alternative target‐template alignments. Several methods can, at least in theory, utilize information from multiple templates, and many examples of improved model quality have been reported. However, to our knowledge, thus far no study has shown that automatic inclusion of multiple alignments is guaranteed to improve models without artifacts. Here, we have carried out a systematic investigation of the potential of multiple templates to improving homology model quality. We have used test sets consisting of targets from both recent CASP experiments and a larger reference set. In addition to Modeller and Nest, a new method (Pfrag) for multiple template‐based modeling is used, based on the segment‐matching algorithm from Levitt's SegMod program. Our results show that all programs can produce multi‐template models better than any of the single‐template models, but a large part of the improvement is simply due to extension of the models. Most of the remaining improved cases were produced by Modeller. The most important factor is the existence of high‐quality single‐sequence input alignments. Because of the existence of models that are worse than any of the top single‐template models, the average model quality does not improve significantly. However, by ranking models with a model quality assessment program such as ProQ, the average quality is improved by ∼5% in the CASP7 test set.
Sequence dependence of kinetics and morphology of collagen model peptide self‐assembly into higher order structures
Authors: Kar Karunakar , Wang Yuh‐Hwa , Brodsky Barbara 
Published: April 2008

AbstractThe process of self‐assembly of the triple‐helical peptide (Pro‐Hyp‐Gly)10 into higher order structure resembles the nucleation‐growth mechanism of collagen fibril formation in many features, but the irregular morphology of the self‐assembled peptide contrasts with the ordered fibers and networks formed by collagen in vivo. The amino acid sequence in the central region of the (Pro‐Hyp‐Gly)10 peptide was varied and found to affect the kinetics of self‐assembly and nature of the higher order structure formed. Single amino acid changes in the central triplet produced irregular higher order structures similar to (Pro‐Hyp‐Gly)10, but the rate of self‐association was markedly delayed by a single change in one Pro to Ala or Leu. The introduction of a Hyp‐rich hydrophobic sequence from type IV collagen resulted in a more regular suprastructure of extended fibers that sometimes showed supercoiling and branching features similar to those seen for type IV collagen in the basement membrane network. Several peptides, where central Pro‐Hyp sequences were replaced by charged residues or a nine‐residue hydrophobic region from type III collagen, lost the ability to self‐associate under standard conditions. The inability to self‐assemble likely results from loss of imino acids, and lack of an appropriate distribution of hydrophobic/electrostatic residues. The effect of replacement of a single Gly residue was also examined, as a model for collagen diseases such as osteogenesis imperfecta and Alport syndrome. Unexpectedly, the Gly to Ala replacement interfered with self‐assembly of (Pro‐Hyp‐Gly)10, while the peptide with a Gly to Ser substitution self‐associated to form a fibrillar structure.
Insect herbivore stoichiometry: the relative importance of host plants and ant mutualists
Authors: ABBOT PATRICK , GRINATH JOSH , BROWN JULIA , PEEDEN EMILY , ERICKSON DAN , BILLICK IAN 
Published: April 2008

Abstract 1. Mutualistic associations can vary over spatial and ecological gradients. For herbivorous insects that engage in mutualisms with ants, plant quality can be a particularly important source of variation, because of the upward transfer of nutrients from plants to herbivores to ants.2. A previous study demonstrated that mutualistic ants, Formica obscuripes, exert a top‐down effect on the carbon and nitrogen concentrations (stoichiometry) in an herbivorous membracid, Publilia modesta. We characterised the consequences of mutualism for carbon and nitrogen stoichiometry between the same species pair, yet on an alternative, geographically‐distinct host plant.3. We found no top‐down effect of ants on the carbon or nitrogen in the herbivore, but a strong, bottom‐up effect of individual plants on membracid nitrogen concentration.4. These results suggests that spatial heterogeneity in host plant traits, and ultimately the diet breadth of herbivore mutualists, may be important factors mediating stoichiometric patterns in mutualistic associations.