bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of volleyball match‐induced fatigue on knee joint position sense
Authors: Ribeiro Fernando , Santos Fernando , Gonçalves Pedro , Oliveira José 
Published: November 2008

AbstractIt has been suggested that a greater number of injuries during the last third of practice sessions or matches could be related to alteration of lower limb neuromuscular control due to neuromuscular fatigue. This fatigue‐related effect can be mediated by changes in joint proprioception. In athletes, the use of functional fatigue protocols could have the advantage of mimicking the demands of sporting activity, thus reflecting more specifically the changes in neuromuscular control and proprioception observed in sport settings. The purpose of the present study was to assess the effect of fatigue induced by a volleyball match on knee joint position sense in elite volleyball players. Seventeen female volleyball players aged 18.9±4.2 years from the Portuguese national team volunteered for the study. Knee joint position sense was evaluated by an open kinetic chain technique and active knee positioning, and was reported using absolute, relative, and variable angular errors. Joint position sense measures were obtained before and immediately after a simulated volleyball match of five sets. To ensure that the match was sufficiently intense to induce fatigue, the perceived exertion or exercise intensity was assessed at the end of the match using Borg’ s rating of perceived exertion (RPE) scale. All participants completed the volleyball match (90min duration), reaching or exceeding 15 on the RPE scale (15.59±0.71; range 15–17), equivalent to “hard/heavy work”. After the volleyball match, a significant increase in absolute (2.11°) and relative (1.71°) angular errors was detected. Match‐induced fatigue significantly exacerbated the overestimation of the test position. Moreover, the reliability and accuracy in estimating knee angles decreased from rest to the fatigued state, as shown by the increase (264%) in variable error. Our results show that fatigue induced by a volleyball match has a marked effect on knee joint position sense in elite female volleyball players. Knee joint position sense was less accurate and less consistent after the volleyball match. Fatigue induced by a simulated competitive volleyball match resulted in proprioceptive deficits, decreasing sensorimotor system acuity in female volleyball players.
Readability statistics of patient information leaflets in a Speech and Language Therapy Department
Authors: Pothier Louise , Day Rachael , Harris Catherine , Pothier David D. 
Published: November 2008

Background: Information leaflets are commonly used in Speech and Language Therapy Departments. Despite widespread use, they can be of variable quality.Aims: To revise current departmental leaflets using the National Health Service (NHS) Toolkit for Producing Patient Information and to test the effect that this has on the readability scores of the text.Methods & Procedures: Twenty existing leaflets were revised with the help of the NHS Toolkit for Producing Patient Information. Readability statistics were calculated for each leaflet before and after revision.Outcomes & Results: The mean Flesch Reading Ease (FRE) score and the Flesch–Kincaid Reading Grade Level (FKRGL) were significantly better in the revised leaflets (p<0.01 and <0.01, respectively). The variability of readability outcome measures was lower in the revised group. Only 25% of the original leaflets met recommended levels of readability, while 75% of the revised leaflets met these standards.Conclusions: Readability is a vital component to consider in the production of information leaflets. Following simple guidelines on the production of leaflets for patients considerably improves their quality.
CRONOS: the cross-reference navigation server
Authors: Waegele Brigitte , Dunger-Kaltenbach Irmtraud , Fobo Gisela , Montrone Corinna , Mewes H.-Werner , Ruepp Andreas 
Published: November 2008

Abstract
Summary: Cross-mapping of gene and protein identifiers between different databases is a tedious and time-consuming task. To overcome this, we developed CRONOS, a cross-reference server that contains entries from five mammalian organisms presented by major gene and protein information resources. Sequence similarity analysis of the mapped entries shows that the cross-references are highly accurate. In total, up to 18 different identifier types can be used for identification of cross-references. The quality of the mapping could be improved substantially by exclusion of ambiguous gene and protein names which were manually validated. Organism-specific lists of ambiguous terms, which are valuable for a variety of bioinformatics applications like text mining are available for download.
Availability: CRONOS is freely available to non-commercial users at http://mips.gsf.de/genre/proj/cronos/index.html, web services are available at http://mips.gsf.de/CronosWSService/CronosWS?wsdl.
Contact: brigitte.waegele@helmholtz-muenchen.de
Supplementary information: Supplementary data are available at Bioinformatics online. The online Supplementary Material contains all figures and tables referenced by this article.
Align human interactome with phenome to identify causative genes and networks underlying disease families
Authors: Wu Xuebing , Liu Qifang , Jiang Rui 
Published: November 2008

Abstract
Motivation: Understanding the complexity in gene–phenotype relationship is vital for revealing the genetic basis of common diseases. Recent studies on the basis of human interactome and phenome not only uncovers prevalent phenotypic overlap and genetic overlap between diseases, but also reveals a modular organization of the genetic landscape of human diseases, providing new opportunities to reduce the complexity in dissecting the gene–phenotype association.
Results: We provide systematic and quantitative evidence that phenotypic overlap implies genetic overlap. With these results, we perform the first heterogeneous alignment of human interactome and phenome via a network alignment technique and identify 39 disease families with corresponding causative gene networks. Finally, we propose AlignPI, an alignment-based framework to predict disease genes, and identify plausible candidates for 70 diseases. Our method scales well to the whole genome, as demonstrated by prioritizing 6154 genes across 37 chromosome regions for Crohn's disease (CD). Results are consistent with a recent meta-analysis of genome-wide association studies for CD.
Availability: Bi-modules and disease gene predictions are freely available at the URL http://bioinfo.au.tsinghua.edu.cn/alignpi/
Contact: ruijiang@tsinghua.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors
Authors: Bateman Alex , Finn Robert D. , Sims Peter J. , Wiedmer Therese , Biegert Andreas , Söding Johannes 
Published: November 2008

Abstract
Motivation: Phospholipid scramblases (PLSCRs) constitute a family of cytoplasmic membrane-associated proteins that were identified based upon their capacity to mediate a Ca2+-dependent bidirectional movement of phospholipids across membrane bilayers, thereby collapsing the normally asymmetric distribution of such lipids in cell membranes. The exact function and mechanism(s) of these proteins nevertheless remains obscure: data from several laboratories now suggest that in addition to their putative role in mediating transbilayer flip/flop of membrane lipids, the PLSCRs may also function to regulate diverse processes including signaling, apoptosis, cell proliferation and transcription. A major impediment to deducing the molecular details underlying the seemingly disparate biology of these proteins is the current absence of any representative molecular structures to provide guidance to the experimental investigation of their function.
Results: Here, we show that the enigmatic PLSCR family of proteins is directly related to another family of cellular proteins with a known structure. The Arabidopsis protein At5g01750 from the DUF567 family was solved by X-ray crystallography and provides the first structural model for this family. This model identifies that the presumed C-terminal transmembrane helix is buried within the core of the PLSCR structure, suggesting that palmitoylation may represent the principal membrane anchorage for these proteins. The fold of the PLSCR family is also shared by Tubby-like proteins. A search of the PDB with the HHpred server suggests a common evolutionary ancestry. Common functional features also suggest that tubby and PLSCR share a functional origin as membrane tethered transcription factors with capacity to modulate phosphoinositide-based signaling.
Contact: agb@sanger.ac.uk
Combining multiple positive training sets to generate confidence scores for protein–protein interactions
Authors: Yu Jingkai , Finley Russell L. 
Published: November 2008

Abstract
Motivation: High-throughput experimental and computational methods are generating a wealth of protein–protein interaction data for a variety of organisms. However, data produced by current state-of-the-art methods include many false positives, which can hinder the analyses needed to derive biological insights. One way to address this problem is to assign confidence scores that reflect the reliability and biological significance of each interaction. Most previously described scoring methods use a set of likely true positives to train a model to score all interactions in a dataset. A single positive training set, however, may be biased and not representative of true interaction space.
Results: We demonstrate a method to score protein interactions by utilizing multiple independent sets of training positives to reduce the potential bias inherent in using a single training set. We used a set of benchmark yeast protein interactions to show that our approach outperforms other scoring methods. Our approach can also score interactions across data types, which makes it more widely applicable than many previously proposed methods. We applied the method to protein interaction data from both Drosophila melanogaster and Homo sapiens. Independent evaluations show that the resulting confidence scores accurately reflect the biological significance of the interactions.
Contact: rfinley@wayne.edu
Supplementary information: Supplementary data are available at Bioinformatics Online.
Combined Proteomic and Cytological Analysis of Ca2+-Calmodulin Regulation inPicea meyeriPollen Tube Growth
Authors: Chen Tong , Wu Xiaoqin , Chen Yanmei , Li Xiaojuan , Huang Mei , Zheng Maozhong , Baluška František , Šamaj Jozef , Lin Jinxing 
Published: November 2008

AbstractCa2+-calmodulin (Ca2+-CaM) is a critical molecule that mediates cellular functions by interacting with various metabolic and signaling pathways. However, the protein expression patterns and accompanying serial cytological responses in Ca2+-CaM signaling deficiency remain enigmatic. Here, we provide a global analysis of the cytological responses and significant alterations in protein expression profiles after trifluoperazine treatment in Picea meyeri, which abrogates Ca2+-CaM signaling. Ninety-three differentially displayed proteins were identified by comparative proteomics at different development stages and were assigned to different functional categories closely related to tip growth machinery. The inhibition of Ca2+-CaM signaling rapidly induced an increase in extracellular Ca2+ influx, resulting in dramatically increased cytosolic Ca2+ concentrations and ultrastructural abnormalities in organelles as the primary responses. Secondary and tertiary alterations included actin filament depolymerization, disrupted patterns of endocytosis and exocytosis, and cell wall remodeling, ultimately resulting in perturbed pollen tube extension. In parallel with these cytological events, time-course experiments revealed that most differentially expressed proteins showed time-dependent quantitative changes (i.e. some signaling proteins and proteins involved in organelle functions and energy production changed first, followed by alterations in proteins related to cytoskeletal organization, secretory pathways, and polysaccharide synthesis). Taken together, Ca2+-CaM dysfunction induced serial cytological responses and temporal changes in protein expression profiles, indicating the pivotal role of Ca2+-CaM in the regulation of tip growth machinery.
OsFRDL1 Is a Citrate Transporter Required for Efficient Translocation of Iron in Rice
Authors: Yokosho Kengo , Yamaji Naoki , Ueno Daisei , Mitani Namiki , Ma Jian Feng 
Published: November 2008

Abstract
Multidrug and toxic compound extrusion (MATE) transporters represent a large family in plants, but their functions are poorly understood. Here, we report the function of a rice (Oryza sativa) MATE gene (Os03g0216700, OsFRDL1), the closest homolog of barley (Hordeum vulgare) HvAACT1 (aluminum [Al]-activated citrate transporter 1), in terms of metal stress (iron [Fe] deficiency and Al toxicity). This gene was mainly expressed in the roots and the expression level was not affected by either Fe deficiency or Al toxicity. Knockout of this gene resulted in leaf chlorosis, lower leaf Fe concentration, higher accumulation of zinc and manganese concentration in the leaves, and precipitation of Fe in the root's stele. The concentration of citrate and ferric iron in the xylem sap was lower in the knockout line compared to the wild-type rice. Heterologous expression of OsFRDL1 in Xenopus oocytes showed transport activity for citrate. Immunostaining showed that OsFRDL1 was localized at the pericycle cells of the roots. On the other hand, there was no difference in the Al-induced secretion of citrate from the roots between the knockout line and the wild-type rice. Taken together, our results indicate that OsFRDL1 is a citrate transporter localized at the pericycle cells, which is necessary for efficient translocation of Fe to the shoot as a Fe-citrate complex.
A Germin-Like Protein Gene Family Functions as a Complex Quantitative Trait Locus Conferring Broad-Spectrum Disease Resistance in Rice
Authors: Manosalva Patricia M. , Davidson Rebecca M. , Liu Bin , Zhu Xiaoyuan , Hulbert Scot H. , Leung Hei , Leach Jan E. 
Published: November 2008

Abstract
Plant disease resistance governed by quantitative trait loci (QTL) is predicted to be effective against a broad spectrum of pathogens and long lasting. Use of these QTL to improve crop species, however, is hindered because the genes contributing to the trait are not known. Five disease resistance QTL that colocalized with defense response genes were accumulated by marker-aided selection to develop blast-resistant varieties. One advanced backcross line carrying the major-effect QTL on chromosome (chr) 8, which included a cluster of 12 germin-like protein (OsGLP) gene members, exhibited resistance to rice (Oryza sativa) blast disease over 14 cropping seasons. To determine if OsGLP members contribute to resistance and if the resistance was broad spectrum, a highly conserved portion of the OsGLP coding region was used as an RNA interference trigger to silence a few to all expressed chr 8 OsGLP family members. Challenge with two different fungal pathogens (causal agents of rice blast and sheath blight diseases) revealed that as more chr 8 OsGLP genes were suppressed, disease susceptibility of the plants increased. Of the 12 chr 8 OsGLPs, one clustered subfamily (OsGER4) contributed most to resistance. The similarities of sequence, gene organization, and roles in disease resistance of GLP family members in rice and other cereals, including barley (Hordeum vulgare) and wheat (Triticum aestivum), suggest that resistance contributed by the chr 8 OsGLP is a broad-spectrum, basal mechanism conserved among the Gramineae. Natural selection may have preserved a whole gene family to provide a stepwise, flexible defense response to pathogen invasion.
Analysis of Intraspecies Diversity in Wheat and Barley Genomes Identifies Breakpoints of Ancient Haplotypes and Provides Insight into the Structure of Diploid and Hexaploid Triticeae Gene Pools
Authors: Wicker Thomas , Krattinger Simon G. , Lagudah Evans S. , Komatsuda Takao , Pourkheirandish Mohammad , Matsumoto Takashi , Cloutier Sylvie , Reiser Laurenz , Kanamori Hiroyuki , Sato Kazuhiro , Perovic Dragan , Stein Nils , Keller Beat 
Published: November 2008

AbstractA large number of wheat (Triticum aestivum) and barley (Hordeum vulgare) varieties have evolved in agricultural ecosystems since domestication. Because of the large, repetitive genomes of these Triticeae crops, sequence information is limited and molecular differences between modern varieties are poorly understood. To study intraspecies genomic diversity, we compared large genomic sequences at the Lr34 locus of the wheat varieties Chinese Spring, Renan, and Glenlea, and diploid wheat Aegilops tauschii. Additionally, we compared the barley loci Vrs1 and Rym4 of the varieties Morex, Cebada Capa, and Haruna Nijo. Molecular dating showed that the wheat D genome haplotypes diverged only a few thousand years ago, while some barley and Ae. tauschii haplotypes diverged more than 500,000 years ago. This suggests gene flow from wild barley relatives after domestication, whereas this was rare or absent in the D genome of hexaploid wheat. In some segments, the compared haplotypes were very similar to each other, but for two varieties each at the Rym4 and Lr34 loci, sequence conservation showed a breakpoint that separates a highly conserved from a less conserved segment. We interpret this as recombination breakpoints of two ancient haplotypes, indicating that the Triticeae genomes are a heterogeneous and variable mosaic of haplotype fragments. Analysis of insertions and deletions showed that large events caused by transposable element insertions, illegitimate recombination, or unequal crossing over were relatively rare. Most insertions and deletions were small and caused by template slippage in short homopolymers of only a few base pairs in size. Such frequent polymorphisms could be exploited for future molecular marker development.
The Zeaxanthin-Independent and Zeaxanthin-Dependent qE Components of Nonphotochemical Quenching Involve Common Conformational Changes within the Photosystem II Antenna in Arabidopsis
Authors: Johnson Matthew P. , Pérez-Bueno María L. , Zia Ahmad , Horton Peter , Ruban Alexander V. 
Published: November 2008

Abstract
The light-harvesting antenna of higher plant photosystem II (LHCII) has the intrinsic capacity to dissipate excess light energy as heat in a process termed nonphotochemical quenching (NPQ). Recent studies suggest that zeaxanthin and lutein both contribute to the rapidly relaxing component of NPQ, qE, possibly acting in the minor monomeric antenna complexes and the major trimeric LHCII, respectively. To distinguish whether zeaxanthin and lutein act independently as quenchers at separate sites, or alternatively whether zeaxanthin fulfills an allosteric role regulating lutein-mediated quenching, the kinetics of qE and the qE-related conformational changes (ΔA 535) were compared in Arabidopsis (Arabidopsis thaliana) mutant/antisense plants with altered contents of minor antenna (kolhcb6, aslhcb4), trimeric LHCII (aslhcb2), lutein (lut2, lut2npq1, lut2npq2), and zeaxanthin (npq1, npq2). The kinetics of the two components of NPQ induction arising from zeaxanthin-independent and zeaxanthin-dependent qE were both sensitive to changes in the protein composition of the photosystem II antenna. The replacement of lutein by zeaxanthin or violaxanthin in the internal Lhcb protein-binding sites affected the kinetics and relative amplitude of each component as well as the absolute chlorophyll fluorescence lifetime. Both components of qE were characterized by a conformational change leading to nearly identical absorption changes in the Soret region that indicated the involvement of the LHCII lutein 1 domain. Based on these observations, we suggest that both components of qE arise from a common quenching mechanism based upon a conformational change within the photosystem II antenna, optimized by Lhcb subunit-subunit interactions and tuned by the synergistic effects of external and internally bound xanthophylls.
Role of the Rice HexokinasesOsHXK5andOsHXK6as Glucose Sensors
Authors: Cho Jung-Il , Ryoo Nayeon , Eom Joon-Seob , Lee Dae-Woo , Kim Hyun-Bi , Jeong Seok-Won , Lee Youn-Hyung , Kwon Yong-Kook , Cho Man-Ho , Bhoo Seong Hee , Hahn Tae-Ryong , Park Youn-Il , Hwang Ildoo , Sheen Jen , Jeon Jong-Seong 
Published: November 2008

AbstractThe Arabidopsis (Arabidopsis thaliana) hexokinase 1 (AtHXK1) is recognized as an important glucose (Glc) sensor. However, the function of hexokinases as Glc sensors has not been clearly demonstrated in other plant species, including rice (Oryza sativa). To investigate the functions of rice hexokinase isoforms, we characterized OsHXK5 and OsHXK6, which are evolutionarily related to AtHXK1. Transient expression analyses using GFP fusion constructs revealed that OsHXK5 and OsHXK6 are associated with mitochondria. Interestingly, the OsHXK5ΔmTP-GFP and OsHXK6ΔmTP-GFP fusion proteins, which lack N-terminal mitochondrial targeting peptides, were present mainly in the nucleus with a small amount of the proteins seen in the cytosol. In addition, the OsHXK5NLS-GFP and OsHXK6NLS-GFP fusion proteins harboring nuclear localization signals were targeted predominantly in the nucleus, suggesting that these OsHXKs retain a dual-targeting ability to mitochondria and nuclei. In transient expression assays using promoter∷luciferase fusion constructs, these two OsHXKs and their catalytically inactive alleles dramatically enhanced the Glc-dependent repression of the maize (Zea mays) Rubisco small subunit (RbcS) and rice α-amylase genes in mesophyll protoplasts of maize and rice. Notably, the expression of OsHXK5, OsHXK6, or their mutant alleles complemented the Arabidopsis glucose insensitive2-1 mutant, thereby resulting in wild-type characteristics in seedling development, Glc-dependent gene expression, and plant growth. Furthermore, transgenic rice plants overexpressing OsHXK5 or OsHXK6 exhibited hypersensitive plant growth retardation and enhanced repression of the photosynthetic gene RbcS in response to Glc treatment. These results provide evidence that rice OsHXK5 and OsHXK6 can function as Glc sensors.