bluuebunny/crossref_metadata_2025_split huggingface dataset:
ModLink+: improving fold recognition by using protein–protein interactions
Authors: Fornes Oriol , Aragues Ramon , Espadaler Jordi , Marti-Renom Marc A. , Sali Andrej , Oliva Baldo 
Published: April 2009

Abstract
Motivation:Several strategies have been developed to predict the fold of a target protein sequence, most of which are based on aligning the target sequence to other sequences of known structure. Previously, we demonstrated that the consideration of protein–protein interactions significantly increases the accuracy of fold assignment compared with PSI-BLAST sequence comparisons. A drawback of our method was the low number of proteins to which a fold could be assigned. Here, we present an improved version of the method that addresses this limitation. We also compare our method to other state-of-the-art fold assignment methodologies.
Results: Our approach (ModLink+) has been tested on 3716 proteins with domain folds classified in the Structural Classification Of Proteins (SCOP) as well as known interacting partners in the Database of Interacting Proteins (DIP). For this test set, the ratio of success [positive predictive value (PPV)] on fold assignment increases from 75% for PSI-BLAST, 83% for HHSearch and 81% for PRC to &gt;90% for ModLink+at the e-value cutoff of 10−3. Under this e-value, ModLink+can assign a fold to 30–45% of the proteins in the test set, while our previous method could cover &lt;25%. When applied to 6384 proteins with unknown fold in the yeast proteome, ModLink+combined with PSI-BLAST assigns a fold for domains in 3738 proteins, while PSI-BLAST alone covers only 2122 proteins, HHSearch 2969 and PRC 2826 proteins, using a threshold e-value that would represent a PPV &gt;82% for each method in the test set.
Availability: The ModLink+server is freely accessible in the World Wide Web at http://sbi.imim.es/modlink/.
Contact: boliva@imim.es.
Supplementary information: Supplementary data are available at Bioinformatics online.
WebGBrowse—a web server for GBrowse
Authors: Podicheti Ram , Gollapudi Rajesh , Dong Qunfeng 
Published: April 2009

Abstract
Summary: The Generic Genome Browser (GBrowse) is one of the most widely used tools for visualizing genomic features along a reference sequence. However, the installation and configuration of GBrowse is not trivial for biologists. We have developed a web server, WebGBrowse that allows users to upload genome annotation in the GFF3 format, configure the display of each genomic feature by simply using a web browser and visualize the configured genomic features with the integrated GBrowse software.
Availability: WebGBrowse is accessible via http://webgbrowse.cgb.indiana.edu/ and the system is also freely available for local installations.
Contact: dongq@indiana.edu
Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy
Authors: Tuncbag Nurcan , Gursoy Attila , Keskin Ozlem 
Published: April 2009

Abstract
Motivation:Hot spots are residues comprising only a small fraction of interfaces yet accounting for the majority of the binding energy. These residues are critical in understanding the principles of protein interactions. Experimental studies like alanine scanning mutagenesis require significant effort; therefore, there is a need for computational methods to predict hot spots in protein interfaces.
Results:We present a new intuitive efficient method to determine computational hot spots based on conservation (C), solvent accessibility [accessible surface area (ASA)] and statistical pairwise residue potentials (PP) of the interface residues. Combination of these features is examined in a comprehensive way to study their effect in hot spot detection. The predicted hot spots are observed to match with the experimental hot spots with an accuracy of 70% and a precision of 64% in Alanine Scanning Energetics Database (ASEdb), and accuracy of 70% and a precision of 73% in Binding Interface Database (BID). Several machine learning methods are also applied to predict hot spots. Performance of our empirical approach exceeds learning-based methods and other existing hot spot prediction methods. Residue occlusion from solvent in the complexes and pairwise potentials are found to be the main discriminative features in hot spot prediction.
Conclusion:Our empirical method is a simple approach in hot spot prediction yet with its high accuracy and computational effectiveness. We believe that this method provides insights for the researchers working on characterization of protein binding sites and design of specific therapeutic agents for protein interactions.
Availability:The list of training and test sets are available as Supplementary Data at http://prism.ccbb.ku.edu.tr/hotpoint/supplement.doc
Contact: agursoy@ku.edu.tr; okeskin@ku.edu.tr
Supplementary information: Supplementary data are available at Bioinformatics online.
Measurements of acoustic backscatter and density of captive Atlantic cod with synchronized 300-kHz multibeam and 120-kHz split-beam echosounders
Authors: Gurshin Christopher W. D. , Jech J. Michael , Howell W. Huntting , Weber Thomas C. , Mayer Larry A. 
Published: April 2009

Abstract
Gurshin, C. W. D., Jech, J. M., Howell, W. H., Weber, T. C., and Mayer, L. A. 2009. Measurements of acoustic backscatter and density of captive Atlantic cod with synchronized 300-kHz multibeam and 120-kHz split-beam echosounders. – ICES Journal of Marine Science, 66: 1303–1309. Effective management strategies for Atlantic cod (Gadus morhua) in the Gulf of Maine require stock assessments based on accurate estimates of its abundance and distribution. If multibeam echosounders are to provide data for such estimates, the relationship between acoustic backscatter and fish biology must be better understood. Working towards this goal, a series of acoustic measurements was made using a 120 kHz, split-beam echosounder (Simrad EK60) and a 300 kHz, multibeam echosounder (Kongsberg EM3002). The transducers from both systems were fixed to a platform over a submerged 98 m3 cage made of 5 cm stretched-nylon mesh. After standard-sphere calibrations, the cage was stocked with live, mature Atlantic cod, with a mean total length of 80.7 cm (range: 51.5–105.0 cm). The echosounders synchronously collected acoustic data, while the cod were monitored with two underwater video cameras. Cod were incrementally removed from the cage to provide a time-series of acoustic backscatter at four densities (n = 128, 116, 66, and 23). Backscatter measurements of cod are compared between echosounders and over time, and the factors affecting the acoustically derived density estimates are discussed. The benefits and limitations of the EM3002 are highlighted.
Modelling demersal fishing effort based on landings and days absence from port, to generate indicators of “activity”
Authors: Greenstreet S. P. R. , Holland G. J. , Fraser T. W. K. , Allen V. J. 
Published: April 2009

Abstract
Greenstreet, S. P. R., Holland, G. J., Fraser, T. W. K., and Allen, V. J. 2009. Modelling demersal fishing effort based on landings and days absence from port, to generate indicators of “activity”. – ICES Journal of Marine Science, 66: 886–901. For many components of marine ecosystems, the derivation of biologically significant, operational “pressure” indicators will rely on modelling fishing mortality from indicators of anthropogenic “activity”. This essentially expands the well established Pressure–State–Response framework to one of Activity–Pressure–State–Response. Within the Common Fisheries Policy, the reporting of fishing effort data, the basic indicator of activity, is not mandatory. A modelling approach is therefore developed that utilizes the data that fishers are obliged to report (days absence from port, landings from each rectangle fished, and the gear used) to provide modelled estimates of fishing effort. The model is parameterized for the Scottish demersal fishing fleet using data collected through the Scottish discards observer scheme, and fishing effort over the period 1997–2004 is modelled. Reported effort data for the period 1960–1998 allowed validation of the model through direct comparison of modelled with reported data in 1997 and 1998. Combining the modelled and reported datasets revealed that Scottish fishing activity levels, remarkably constant over four decades, had declined markedly since 2000. Temporal trends in UK quotas for the main targeted demersal species are considered to assess the effectiveness of catch limitation management as a means of regulating fishing activity. Spatial patterns in effort by the four main gear types used by the Scottish demersal fleet are described, and in general terms, these have changed little over the period 1960–2004. However, distinct spatial patterns emerged in the temporal trends in each ICES rectangle, associated with the recent overall decline in Scottish demersal fishing activity. These patterns were not intuitive, and the implications of this for an ecosystem approach to management are discussed.
The sensitivity of the Seychelles–Chagos thermocline ridge to large-scale wind anomalies
Authors: Hermes Juliet C. , Reason Chris J. C. 
Published: April 2009

Abstract
Hermes, J. C., and Reason, C. J. C. 2009. The sensitivity of the Seychelles–Chagos thermocline ridge to large-scale wind anomalies. – ICES Journal of Marine Science, 66: 1455–1466. The Seychelles–Chagos thermocline ridge (SCTR) in the southwest tropical Indian Ocean is important for regional climate, the Madden–Julian Oscillation, as well as upper-ocean nutrients and related phytoplankton and zooplankton densities. Subsurface variability in this region has been proved to influence the overlying sea surface temperatures, which in turn can influence eastern African rainfall. There is evidence that austral summers with a deeper (shallower) SCTR tend to have more (less) tropical cyclone (TC) days in the Southwest Indian Ocean. The importance of this relationship was underlined during the 2006/2007 austral summer, when areas of Madagascar and central Mozambique experienced devastating floods, because of ten named tropical storms, including several intense TCs, effecting on these areas. At the same time, the SCTR during this season was anomalously deep, partly because of a downwelling Rossby wave that propagated across the South Indian Ocean during the previous austral winter/spring. In this paper, a regional ocean model is used to investigate the effect of remote forcing on this region and to study the sensitivity of the SCTR to changes in the large-scale winds over the South Indian Ocean, with a particular focus on the events of the 2006/2007 austral summer.
A bottom-up approach to technological development and its management implications in a commercial fishery
Authors: Eigaard Ole Ritzau 
Published: April 2009

Abstract
Eigaard, O. R. 2009. A bottom-up approach to technological development and its management implications in a commercial fishery. – ICES Journal of Marine Science, 66: 916–927. Analyses of electronic equipment on board Danish trawlers and gillnetters show that newer, larger vessels have a significantly higher “technological level” than older, smaller vessels. A hypothesis of linkage between fish-finding and navigation technology on board and standard vessel characteristics was tested based on the definition of a technological index. Using a proportional odds model, vessel length accounted for most of the variation in technological level on board, with odds of 1.17 (95% confidence interval: 1.16–1.18) of a higher index value for each increase in vessel length of 1 m. Vessel age was also significantly correlated with index values. In considering the technological index as an indicator of fishing power, the results have important implications for capacity-reduction schemes intended to reduce harvest pressure on fish stocks. In the course of such structural management plans, older, smaller vessels of a fleet are often replaced with newer, larger vessels within a fixed or reduced nominal capacity limit (e.g. total fleet tonnage), but according to the findings presented, nominal capacity reduction in fleet level may be undermined by increases in individual vessel fishing power.
Measurements of acoustic-scattering spectra from the whole and parts of Atlantic mackerel
Authors: Nesse Tonje Lexau , Hobæk Halvor , Korneliussen Rolf J. 
Published: April 2009

Abstract
Nesse, T. L., Hobæk, H., and Korneliussen, R. J. 2009. Measurements of acoustic-scattering spectra from the whole and parts of Atlantic mackerel. – ICES Journal of Marine Science, 66: 1169–1175. Atlantic mackerel (Scomber scombrus) are weak sound scatterers compared with fish that have swimbladders. Accurate acoustic estimates of mackerel abundance require estimates of target strength. Different parts of mackerel may dominate the backscattering spectra. Mackerel schools are acoustically recognized mainly by backscatter four times stronger at 200 kHz than at 38 kHz. Simulations have established that backscatter from only the flesh and the backbone could explain this frequency response, although there are uncertainties in the model parameters and simplifications. In this paper, experiments conducted in a laboratory tank to investigate the complexity of mackerel backscatter are discussed. Acoustic backscatter was measured over the frequency range 65–470 kHz from individual dead mackerel, and their backbones, heads, and skulls. Backscatter from the backbones was measured at several angles of incidence. Grating lobes (Bragg scattering) appeared at different angles, depending on the acoustic frequency and the spacing of the vertebrae. These lobes were evident in backbone backscatter after propagating through the flesh and can be used, in principle, to determine mackerel size acoustically. The frequency response of individual, ex situ Atlantic mackerel estimated from these measurements did not match that from the measurements of in situ mackerel schools. Further investigation is warranted.
Dynamic Localization of the DNA Replication Proteins MCM5 and MCM7 in Plants
Authors: Shultz Randall W. , Lee Tae-Jin , Allen George C. , Thompson William F. , Hanley-Bowdoin Linda 
Published: April 2009

AbstractGenome integrity in eukaryotes depends on licensing mechanisms that prevent loading of the minichromosome maintenance complex (MCM2-7) onto replicated DNA during S phase. Although the principle of licensing appears to be conserved across all eukaryotes, the mechanisms that control it vary, and it is not clear how licensing is regulated in plants. In this work, we demonstrate that subunits of the MCM2-7 complex are coordinately expressed during Arabidopsis (Arabidopsis thaliana) development and are abundant in proliferating and endocycling tissues, indicative of a role in DNA replication. We show that endogenous MCM5 and MCM7 proteins are localized in the nucleus during G1, S, and G2 phases of the cell cycle and are released into the cytoplasmic compartment during mitosis. We also show that MCM5 and MCM7 are topologically constrained on DNA and that the MCM complex is stable under high-salt conditions. Our results are consistent with a conserved replicative helicase function for the MCM complex in plants but not with the idea that plants resemble budding yeast by actively exporting the MCM complex from the nucleus to prevent unauthorized origin licensing and rereplication during S phase. Instead, our data show that, like other higher eukaryotes, the MCM complex in plants remains in the nucleus throughout most of the cell cycle and is only dispersed in mitotic cells.
Interaction Transcriptome Analysis Identifies Magnaporthe oryzae BAS1-4 as Biotrophy-Associated Secreted Proteins in Rice Blast Disease
Authors: Mosquera Gloria , Giraldo Martha C. , Khang Chang Hyun , Coughlan Sean , Valent Barbara 
Published: April 2009

Abstract
Biotrophic invasive hyphae (IH) of the blast fungus Magnaporthe oryzae secrete effectors to alter host defenses and cellular processes as they successively invade living rice (Oryza sativa) cells. However, few blast effectors have been identified. Indeed, understanding fungal and rice genes contributing to biotrophic invasion has been difficult because so few plant cells have encountered IH at the earliest infection stages. We developed a robust procedure for isolating infected-rice sheath RNAs in which ∼20% of the RNA originated from IH in first-invaded cells. We analyzed these IH RNAs relative to control mycelial RNAs using M. oryzae oligoarrays. With a 10-fold differential expression threshold, we identified known effector PWL2 and 58 candidate effectors. Four of these candidates were confirmed to be fungal biotrophy-associated secreted (BAS) proteins. Fluorescently labeled BAS proteins were secreted into rice cells in distinct patterns in compatible, but not in incompatible, interactions. BAS1 and BAS2 proteins preferentially accumulated in biotrophic interfacial complexes along with known avirulence effectors, BAS3 showed additional localization near cell wall crossing points, and BAS4 uniformly outlined growing IH. Analysis of the same infected-tissue RNAs with rice oligoarrays identified putative effector-induced rice susceptibility genes, which are highly enriched for sensor-transduction components rather than typically identified defense response genes.
Suppression of Repeat-Mediated Gross Mitochondrial Genome Rearrangements by RecA in the Moss Physcomitrella patens
Authors: Odahara Masaki , Kuroiwa Haruko , Kuroiwa Tsuneyoshi , Sekine Yasuhiko 
Published: April 2009

Abstract
RecA and its ubiquitous homologs are crucial components in homologous recombination. Besides their eukaryotic nuclear counterparts, plants characteristically possess several bacterial-type RecA proteins localized to chloroplasts and/or mitochondria, but their roles are poorly understood. Here, we analyzed the role of the only mitochondrial RecA in the moss Physcomitrella patens. Disruption of the P. patens mitochondrial recA gene RECA1 caused serious defects in plant growth and development and abnormal mitochondrial morphology. Analyses of mitochondrial DNA in disruptants revealed that frequent DNA rearrangements occurred at multiple loci. Structural analysis suggests that the rearrangements, which in some cases were associated with partial deletions and amplifications of mitochondrial DNA, were due to aberrant recombination between short (&lt;100 bp) direct and inverted repeats in which the sequences were not always identical. Such repeats are abundant in the mitochondrial genome, and interestingly many are located in group II introns. These results suggest that RECA1 does not promote but rather suppresses recombination among short repeats scattered throughout the mitochondrial genome, thereby maintaining mitochondrial genome stability. We propose that RecA-mediated homologous recombination plays a crucial role in suppression of short repeat-mediated genome rearrangements in plant mitochondria.
Extended treatment of older cigarette smokers
Authors: Hall Sharon M. , Humfleet Gary L. , Muñoz Ricardo F. , Reus Victor I. , Robbins Julie A. , Prochaska Judith J. 
Published: April 2009

ABSTRACTAims  Tobacco dependence treatments achieve abstinence rates of 25–30% at 1 year. Low rates may reflect failure to conceptualize tobacco dependence as a chronic disorder. The aims of the present study were to determine the efficacy of extended cognitive behavioral and pharmacological interventions in smokers ≥ 50 years of age, and to determine if gender differences in efficacy existed.Design  Open randomized clinical trial.Setting  A free‐standing, smoking treatment research clinic.Participants  A total of 402 smokers of ≥ 10 cigarettes per day, all 50 years of age or older.Intervention  Participants completed a 12‐week treatment that included group counseling, nicotine replacement therapy (NRT) and bupropion. Participants, independent of smoking status, were then assigned randomly to follow‐up conditions: (i) standard treatment (ST; no further treatment); (ii) extended NRT (E‐NRT; 40 weeks of nicotine gum availability); (iii) extended cognitive behavioral therapy (E‐CBT; 11 cognitive behavioral sessions over a 40‐week period); or (iv) E‐CBT plus E‐NRT (E‐combined; 11 cognitive behavioral sessions plus 40 weeks nicotine gum availability).Measurements  Primary outcome variable was 7‐day point prevalence cigarette abstinence verified biochemically at weeks 24, 52, 64 and 104.Findings  The most clinically important findings were significant main effects for treatment condition, time and the treatment × time interaction. The E‐CBT condition produced high cigarette abstinence rates that were maintained throughout the 2‐year study period [(week 24 (58%), 52 (55%), 64 (55%) and 104 (55%)], and was significantly more effective than E‐NRT and ST across that period. No other treatment condition was significantly different to ST. No effects for gender were found.Conclusions  Extended cognitive behavioral treatments can produce high and stable cigarette abstinence rates for both men and women. NRT does not add to the efficacy of extended CBT, and may hamper its efficacy. Research is needed to determine if these results can be replicated in a sample with a greater range of ages, and improved upon with the addition of medications other than NRT.
Quantitative trait loci underlying milk production traits in sheep
Authors: Gutiérrez‐Gil B. , El‐Zarei M. F. , Alvarez L. , Bayón Y. , De La Fuente L. F. , San Primitivo F. , Arranz J.‐J. 
Published: April 2009

SummaryImprovement of milk production traits in dairy sheep is required to increase the competitiveness of the industry and to maintain the production of high quality cheese in regions of Mediterranean countries with less favourable conditions. Additional improvement over classical selection could be reached if genes with significant effects on the relevant traits were specifically targeted by selection. However, so far, few studies have been undertaken to detect quantitative trait loci (QTL) in dairy sheep. In this study, we present a complete genome scan performed in a commercial population of Spanish Churra sheep to identify chromosomal regions associated with phenotypic variation observed in milk production traits. Eleven half‐sib families, including a total of 1213 ewes, were analysed following a daughter design. Genome‐wise multi‐marker regression analysis revealed a genome‐wise significant QTL for milk protein percentage on chromosome 3. Eight other regions, localized on chromosomes 1, 2, 20, 23 and 25, showed suggestive significant linkage associations with some of the analysed traits. To our knowledge, this study represents the first complete genome scan for milk production traits reported in dairy sheep. The experiment described here shows that analysis of commercial dairy sheep populations has the potential to increase our understanding of the genetic determinants of complex production‐related traits.