bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survival and cause‐specific mortality rates of female sika deer in eastern Hokkaido, Japan
Authors: Uno Hiroyuki , Kaji Koichi 
Published: September 2005

AbstractSurvival and cause‐specific mortality rates of female sika deer (Cervus nippon) were studied using radio telemetry in eastern Hokkaido, Japan. We captured and radio‐collared 18 female deer, and monitored their survival from April 1993 to May 1996. Estimated annual survival rate for adult females was 0.779 (95% confidence interval was 0.609–0.997). The harvest mortality rate of adult females was higher than the natural mortality rate. Experimental female hunting during 1994–1996 contributed to an increase in the mortality rate for females and was useful in the control of the sika deer population.
The effect of physical training in chronic heart failure
Authors: Jónsdóttir Sólrún , Andersen Karl K. , Sigurðsson Axel F. , Sigurðsson Stefán B. 
Published: September 2005

AbstractBackground:Supervised cardiac rehabilitation programs have been offered to patients following myocardial infarct (MI), coronary artery bypass graft surgery (CABG) and percutaneous coronary intervention (PCI) for many years. However, limited information is available on the usefulness of rehabilitation programs in chronic heart failure (CHF). The aim of our study was to evaluate the outcome of supervised physical training on CHF patients by measuring both central and peripheral factors.Methods:This was a prospective randomized study, including 43 patients with CHF, New York Heart Association (NYHA) class II or III, mean age 68 years. After initial measurements of VO2peak, 6 min walk distance, muscle strength, plasma levels of atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP), echocardiogram, measurements of pulmonary function and quality of life questionnaire, patients were randomized to either a training group (n=21) or a control group (n=22). The training group had supervised aerobic and resistance training program twice a week for five months. After the training program was completed, all measurements were repeated in both groups.Results:No training related adverse events were reported. Significant improvement was found between groups in the six minute walk test (+37.1 m vs. +5.3 m, p=0.01), work load on the bicycle exercise test (+6.1 W vs. +2.1 W, p=0.03), time on the bicycle exercise test (+41 s vs. +0 s, p=0.02) and quadriceps muscle strength test (+2.8 kg. vs. +0.2 kg., p=0.003). Quality of life factors that reflect exercise tolerance and general health, improved significantly in the training group compared to the control group. No other significant changes were found between the two groups.Conclusion:Supervised physical training as used in this study appears safe for CHF patients in NYHA class II or III. The improvement in functional capacity observed in the training group seems to be related to peripheral factors rather than in central cardiovascular performance.
Changes in recruitment, growth, and stock size of northern shrimp (Pandalus borealis) at West Greenland: temperature and density-dependent effects at released predation pressure
Authors: Wieland Kai 
Published: October 2005

Abstract
Stock size of northern shrimp (Pandalus borealis) in West Greenland waters has been fairly stable from the late 1980s to the mid-1990s. Thereafter, survey estimates of biomass increased substantially, and the exploitation rate declined slightly in the most recent years. The present analysis was carried out on a spatially disaggregated basis in order to account for the latitudinal differences in bottom temperature and shrimp density. Changes in recruitment and, with a lag of 2 years, in stock biomass were most pronounced in the northern part of its distributional range, while bottom temperature increased in all survey regions since the mid-1990s. Length-at-age was positively correlated with temperature in general, but a trend towards slower growth was observed in areas with the highest stock densities in the most recent years. It is concluded that the moderate increase in temperature above a lower threshold of the optimal range in the northern regions has extended the distributional area that is most favourable for northern shrimp. This, together with a decreasing rate of exploitation and a continuous low predation pressure, resulted in an increase of the stock to a level at which density-dependent effects have become prominent in parts of study area.
Determinants of stock option use by Japanese companies
Authors: Uchida Konari 
Published: September 2005

AbstractJapanese data show a negative relation between leverage and the probability of firms' use of stock options. Such a relation is more marked for firms affiliated with specific keiretsu or main banks. This evidence reflects the fact that Japanese companies are more reliant on debt financing and that the agency cost of debt is a central issue in corporate governance. Results show that the frequency of the firms' use of stock options is positively associated with firm size. Finally, independent firms, which reveal more concern about shareholder wealth, are more likely to use stock options.
Augmented cell-graphs for automated cancer diagnosis
Authors: Demir Cigdem , Gultekin S. Humayun , Yener Bülent 
Published: October 2005

Abstract
Summary: This work reports a novel computational method based on augmented cell-graphs (ACG), which are constructed from low-magnification tissue images for the mathematical diagnosis of brain cancer (malignant glioma). An ACG is a simple, undirected, weighted and complete graph in which a node represents a cell cluster and an edge between a pair of nodes defines a binary relationship between them. Both the nodes and the edges of an ACG are assigned weights to capture more information about the topology of the tissue. In this work, the experiments are conducted on a dataset that is comprised of 646 human brain biopsy samples from 60 different patients. It is shown that the ACG approach yields sensitivity of 97.53% and specificities of 93.33 and 98.15% (for the inflamed and healthy, respectively) at the tissue level in glioma diagnosis.
Contact: demir@cs.rpi.edu
A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors
Authors: de Juan David , Mellado Mario , Rodríguez-Frade José Miguel , Hernanz-Falcón Patricia , Serrano Antonio , del Sol Antonio , Valencia Alfonso , Martínez-A Carlos , Rojas Ana María 
Published: October 2005

Abstract
Summary: Solving relevant biological problems requires answering complex questions. Addressing such questions traditionally implied the design of time-consuming experimental procedures which most of the time are not accessible to average-sized laboratories. The current trend is to move towards a multidisciplinary approach integrating both theoretical knowledge and experimental work. This combination creates a powerful tool for shedding light on biological problems. To illustrate this concept, we present here a descriptive example of where computational methods were shown to be a key aspect in detecting crucial players in an important biological problem: the dimerization of chemokine receptors. Using evolutionary based sequence analysis in combination with structural predictions two CCR5 residues were selected as important for dimerization and further validated experimentally. The experimental validation of computational procedures demonstrated here provides a wealth of valuable information not obtainable by any of the individual approaches alone.
Contact: arojas@cnb.uam.es
Supplementary information: Supplementary data are available at Bioinformatics online.
A query language for biological networks
Authors: Leser Ulf 
Published: October 2005

Abstract
Motivation: Many areas of modern biology are concerned with the management, storage, visualization, comparison and analysis of networks, but no appropriate query language for such complex data structures yet exists.
Results: We have designed and implemented the pathway query language (PQL) for querying large protein interaction or pathway databases. PQL is based on a simple graph data model with extensions reflecting properties of biological objects. Queries match subgraphs in the database based on node properties and paths between nodes. The syntax is easy to learn for anybody familiar with SQL. As an important feature, a query may require a certain structure in the database to exist but return a different subgraph. We have tested PQL queries on networks of up to 16 000 nodes and found it to scale very well.
Availability: The code is available on request from the author.
Contact: leser@informatik.hu-berlin.de
Adding Some SPICE to DAS
Authors: Prlić Andreas , Down Thomas A. , Hubbard Tim J. P. 
Published: October 2005

Abstract
Summary: The distributed annotation system (DAS) defines a communication protocol used to exchange biological annotations. It is motivated by the idea that annotations should not be provided by single centralized databases but instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is carried out by DAS clients. The original DAS protocol was designed to serve annotation of genomic sequences. We have extended the protocol to be applicable to macromolecular structures. Here we present SPICE, a new DAS client that can be used to visualize protein sequence and structure annotations.
Availability: http://www.efamily.org.uk/software/dasclients/spice/
Contact: ap3@sanger.ac.uk
Predicting protein stability changes from sequences using support vector machines
Authors: Capriotti Emidio , Fariselli Piero , Calabrese Remo , Casadio Rita 
Published: October 2005

Abstract
Motivation: The prediction of protein stability change upon mutations is key to understanding protein folding and misfolding. At present, methods are available to predict stability changes only when the atomic structure of the protein is available. Methods addressing the same task starting from the protein sequence are, however, necessary in order to complete genome annotation, especially in relation to single nucleotide polymorphisms (SNPs) and related diseases.
Results: We develop a method based on support vector machines that, starting from the protein sequence, predicts the sign and the value of free energy stability change upon single point mutation. We show that the accuracy of our predictor is as high as 77% in the specific task of predicting the ΔΔG sign related to the corresponding protein stability. When predicting the ΔΔG values, a satisfactory correlation agreement with the experimental data is also found. As a final blind benchmark, the predictor is applied to proteins with a set of disease-related SNPs, for which thermodynamic data are also known. We found that our predictions corroborate the view that disease-related mutations correspond to a decrease in protein stability.
Availability: http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi
Contact: casadio@alma.unibo.it
Less is more: towards an optimal universal description of protein folds
Authors: Szustakowski Joseph D. , Kasif Simon , Weng Zhiping 
Published: October 2005

Abstract
Motivation: Identification and characterization of protein structure regularities can reveal the mechanisms governing protein structure, function and evolution. Here we focus on an intermediate level of regularity. We have developed automated methods to systematically construct a dictionary of supersecondary structures that can be used as ‘protein parts’ to describe fold-sized structures.
Results: The dictionary was constructed by aligning representative structures of all known folds, clustering similar substructures and selecting the most descriptive substructures in a minimum description length fashion. We show that the dictionary is compact and descriptive, capable of describing a substantial fraction of all known protein folds. We performed simulations using independent sets of training and testing folds. Dictionaries generated using the training set had high coverage over the folds in the testing set, suggesting that dictionary entries reflect general features of protein structures and should be capable of describing novel protein folds.
Contact: zhiping@bu.edu
Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering
Authors: Leyfer Dmitriy , Weng Zhiping 
Published: October 2005

Abstract
Motivation: A holistic approach to the study of cellular processes is identifying both gene-expression changes and regulatory elements promoting such changes. Cellular regulatory processes can be viewed as transcriptional modules (TMs), groups of coexpressed genes regulated by groups of transcription factors (TFs). We set out to devise a method that would identify TMs while avoiding arbitrary thresholds on TM sizes and number.
Method: Assuming that gene expression is determined by TFs that bind to the gene's promoter, clustering of genes based on TF binding sites (cis-elements) should create gene groups similar to those obtained by gene expression clustering. Intersections between the expression and cis-element-based gene clusters reveal TMs. Statistical significance assigned to each TM allows identification of regulatory units of any size.
Results: Our method correctly identifies the number and sizes of TMs on simulated datasets. We demonstrate that yeast experimental TMs are biologically relevant by comparing them with MIPS and GO categories. Our modules are in statistically significant agreement with TMs from other research groups. This work suggests that there is no preferential division of biological processes into regulatory units; each degree of partitioning exhibits a slice of biological network revealing hierarchical modular organization of transcriptionalregulation.
Contact: dleyfer@gnsbiotech.com
Decomposing protein networks into domain–domain interactions
Authors: Albrecht Mario , Huthmacher Carola , Tosatto Silvio C. E. , Lengauer Thomas 
Published: October 2005

Abstract
Summary: The application of novel experimental techniques has generated large networks of protein–protein interactions. Frequently, important information on the structure and cellular function of protein–protein interactions can be gained from the domains of interacting proteins. We have designed a Cytoscape plugin that decomposes interacting proteins into their respective domains and computes a putative network of corresponding domain–domain interactions. To this end, the network graph of proteins has been extended by additional node and edge types for domain interactions, including different node and edge shapes and coloring schemes used for visualization. An additional plugin provides supplementary web links to Internet resources on domain function and structure.
Availability: Both Cytoscape plugins can be downloaded from http://www.cytoscape.org
Contact: mario.albrecht@mpi-inf.mpg.de
Horizontal gene transfer depends on gene content of the host
Authors: Pál Csaba , Papp Balázs , Lercher Martin J. 
Published: October 2005

Abstract
Horizontal gene transfer is a major contributor to the evolution of bacterial genomes. We examine this process through a combination of comparative genomics and in silico analysis of the Escherichia coli metabolic network. We validate our horizontal transfer estimates by confirming the predicted gradual amelioration of GC content over time. We find that the chance of acquiring a gene by horizontal transfer is up to six times higher if an enzyme that catalyses a coupled metabolite flux is already encoded in the host genome.
Contact: Lercher@embl.de
Functional stoichiometric analysis of metabolic networks
Authors: Urbanczik R. , Wagner C. 
Published: September 2005

AbstractMotivation: An important tool in Systems Biology is the stoichiometric modeling of metabolic networks, where the stationary states of the network are described by a high-dimensional polyhedral cone, the so-called flux cone. Exhaustive descriptions of the metabolism can be obtained by computing the elementary vectors of this cone but, owing to a combinatorial explosion of the number of elementary vectors, this approach becomes computationally intractable for genome scale networks.Result: Hence, we propose to instead focus on the conversion cone, a projection of the flux cone, which describes the interaction of the metabolism with its external chemical environment. We present a direct method for calculating the elementary vectors of this cone and, by studying the metabolism of Saccharomyces cerevisiae, we demonstrate that such an analysis is computationally feasible even for genome scale networks.Contact: robert.urbanczik@pki.unibe.ch
Bioinformatics analyses of circular dichroism protein reference databases
Authors: Janes Robert W. 
Published: September 2005

Abstract
Motivation: Circular dichroism (CD) spectroscopy has become established as a key method for determining the secondary structure contents of proteins which has had a significant impact on molecular biology. Many excellent mathematical protocols have been developed for this purpose and their quality is above question. However, reference database sets of proteins, with CD spectra matched to secondary structure components derived from X-ray structures, provide the key resource for this task. These databases were created many years ago, before most CD spectrophotometers became standardized and before it was commonplace to validate X-ray structures prior to publication. The analyses presented here were undertaken to investigate the overall quality of these reference databases in light of their extensive usage in determining protein secondary structure content from CD spectra.
Results: The analyses show that there are a number of significant problems associated with the CD reference database sets in current use. There are disparities between CD spectra for the same protein collected by different groups. These include differences in magnitudes, peak positions or both. However, many current reference sets are now amalgamations of spectra from these groups, introducing inconsistencies that can lead to inaccuracies in the determination of secondary structure components from the CD spectra. A number of the X-ray structures used fall short on the validation criteria now employed as standard for structure determination. Many have substantial percentages of residues in the disallowed regions of the Ramachandran plot. Hence their calculated secondary structure components, used as a foundation for the reference databases, are likely to be in error. Additionally, the coverage of secondary structure space in the reference datasets is poorly correlated to the secondary structure components found in the Protein Data Bank. A conclusion is that a new reference CD database with cross-correlated, machine-independent CD spectra and validated X-ray structures that cover more secondary structure components, including diverse protein folds, is now needed. However, that reasonably accurate values for the secondary structure content of proteins can be determined from spectra is a testament to CD spectroscopy being a very powerful technique.
Contact: r.w.janes@qmul.ac.uk
MACiE: a database of enzyme reaction mechanisms
Authors: Holliday Gemma L. , Bartlett Gail J. , Almonacid Daniel E. , O'Boyle Noel M. , Murray-Rust Peter , Thornton Janet M. , Mitchell John B. O. 
Published: September 2005

Abstract
Summary: MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction.
Availability:
Contact: jbom1@cam.ac.uk
Mapping PDB chains to UniProtKB entries
Authors: Martin Andrew C. R. 
Published: September 2005

Abstract
Motivation: UniProtKB/SwissProt is the main resource for detailed annotations of protein sequences. This database provides a jumping-off point to many other resources through the links it provides. Among others, these include other primary databases, secondary databases, the Gene Ontology and OMIM. While a large number of links are provided to Protein Data Bank (PDB) files, obtaining a regularly updated mapping between UniProtKB entries and PDB entries at the chain or residue level is not straightforward. In particular, there is no regularly updated resource which allows a UniProtKB/SwissProt entry to be identified for a given residue of a PDB file.
Results: We have created a completely automatically maintained database which maps PDB residues to residues in UniProtKB/SwissProt and UniProtKB/trEMBL entries. The protocol uses links from PDB to UniProtKB, from UniProtKB to PDB and a brute-force sequence scan to resolve PDB chains for which no annotated link is available. Finally the sequences from PDB and UniProtKB are aligned to obtain a residue-level mapping.
Availability: The resource may be queried interactively or downloaded from
Contact: andrew@bioinf.org.uk
Medusa: a simple tool for interaction graph analysis
Authors: Hooper Sean D. , Bork Peer 
Published: September 2005

Abstract
Summary: Medusa is a Java application for visualizing and manipulating graphs of interaction, such as data from the STRING database. It features an intuitive user interface developed with the help of biologists. Medusa is optimized for accessing protein interaction data from STRING, but can be used for any type of graph from any scientific field.
Availability: Medusa, along with sample datasets and instructions, can be downloaded from
Contact: hooper@embl.de
Poor Intraoperative Blood Glucose Control Is Associated with a Worsened Hospital Outcome after Cardiac Surgery in Diabetic Patients
Authors: Ouattara Alexandre , Lecomte Patrick , Le Manach Yannick , Landi Marc , Jacqueminet Sophie , Platonov Igor , Bonnet Nicolas , Riou Bruno , Coriat Pierre 
Published: September 2005

Background
Tight perioperative control of blood glucose improves the outcome of diabetic patients undergoing cardiac surgery. Because stress response and cardiopulmonary bypass can induce profound hyperglycemia, intraoperative glycemic control may become difficult. The authors undertook a prospective cohort study to determine whether poor intraoperative glycemic control is associated with increased intrahospital morbidity.

Methods
Two hundred consecutive diabetic patients undergoing on-pump heart surgery were enrolled. A standard insulin protocol based on subcutaneous intermediary insulin was given the morning of the surgery. Intravenous insulin therapy was initiated intraoperatively from blood glucose concentrations of 180 mg/dl or greater and titrated according to a predefined protocol. Poor intraoperative glycemic control was defined as four consecutive blood glucose concentrations greater than 200 mg/dl without any decrease in despite insulin therapy. Postoperative blood glucose concentrations were maintained below 140 mg/dl by using aggressive insulin therapy. The main endpoints were severe cardiovascular, respiratory, infectious, neurologic, and renal in-hospital morbidity.

Results
Insulin therapy was required intraoperatively in 36% of patients, and poor intraoperative glycemic control was observed in 18% of patients. Poor intraoperative glycemic control was significantly more frequent in patients with severe postoperative morbidity (37% vs. 10%; P < 0.001). The adjusted odds ratio for severe postoperative morbidity among patients with a poor intraoperative glycemic control as compared with patients without was 7.2 (95% confidence interval, 2.7-19.0).

Conclusion
Poor intraoperative control of blood glucose concentrations in diabetic patients undergoing cardiac surgery is associated with a worsened hospital outcome after surgery.