bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of 40 and 60 milliliters of contrast in assessment of the carotid artery by computed tomography angiography
Authors: Takeyama N. , Ohgiya Y. , Itokawa H. , Takahashi Y. , Obuchi M. , Shinjyo H. , Matsui S. , Hayashi T. , Kato K. , Fujimoto T. , Kinebuchi Y. , Kitahara T. , Gokan T. 
Published: October 2008

Background: Although fast acquisition of multidetector-row computed tomography (MDCT) can make it possible to acquire sufficient early vascular enhancement using small volumes and high concentrations of contrast material (CM), there are still some problems with nephrotoxicity and costs related to CM. Purpose: To compare the qualitative and quantitative performance in cervicocranial CT angiography (CTA) using two different iodine volumes and concentrations of CM. Material and Methods: CTA ranging from the aortic arch (AA) to distal to the circle of Willis (cW) was performed on a 32-MDCT system. Fifty-eight patients were randomly divided into two groups: group A (29 patients) received 60 ml of 300 mg I/ml CM, and group B (the other 29 patients) received 40 ml of 370 mg I/ml CM. Time to peak arterial enhancement at cW (Tc) was calculated. As scan speed was 96.9 mm/s and injection rate was 4.0 ml/s, scanning delay was individually decided according to Tc and scan duration between AA and cW. Arterial attenuation along the z-axis at eight points in the carotid-cerebral artery and venous attenuation of the internal jugular vein (IJV) at carotid bifurcation were measured. Mean attenuation values were then quantitatively analyzed. Postprocessing images were qualitatively assessed. Results: Arterial attenuation profiles revealed maximum attenuation at the distal common carotid artery in both groups. Although there were no significant differences in mean arterial attenuation in group A versus group B (402±70 HU vs. 407±67 HU; P=0.78), venous attenuation of the IJV was lower in group B than in group A (114±57 HU vs. 224±81 HU; P<0.001). Although arterial images demonstrated no difference qualitatively between the two groups, the venous contamination of IVC was less prominent in group B. Conclusion: Although a different amount of CM was administered in both groups, quantitative and qualitative arterial images did not show significant differences between the two groups.
Reproducibility of sonographic measurements of carotid intima-media thickness
Authors: Velázquez F. , Berná J. D. , Abellán J. L. , Serrano L. , Escribano A. , Canteras M. 
Published: October 2008

Background: Carotid intima-media thickness (IMT), measured with B-mode ultrasound, is a marker for atherosclerosis and widely used as an outcome in intervention trials. Purpose: To evaluate the reproducibility of carotid intima-media thickness measurements using tissue harmonic imaging (THI) sonography between two observers with different levels of experience. Material and Methods: IMT measurement was performed in 40 patients: 26 males and 14 females, with a mean age of 62.6 years. The measurements were taken on the posterior wall of the right common carotid artery using a standardized protocol. Observer measurement of the IMT was independent and blind. Statistical analysis was done with parametric tests and Pearson's correlation coefficient. Results: The measurements of the IMT were taken satisfactorily in all cases. IMT measurement time was 5min/study. No significant differences were noted between the means obtained by the two observers. The interobserver correlation of the measurements was very high (97.2%). Conclusion: The results of this study show that carotid IMT measurement using THI sonography and a standardized protocol is accurate and reproducible.
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
Authors: Ondov Brian D. , Varadarajan Anjana , Passalacqua Karla D. , Bergman Nicholas H. 
Published: October 2008

Abstract
Summary: Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of ‘color space’, and it maximizes usable data by allowing a user-specified number of mismatches. Sequence census functions facilitate a variety of functional genomics applications, including transcriptome mapping and profiling, as well as ChIP-Seq.
Availability: Executables, source code, and sample data are available at http://socs.biology.gatech.edu/
Contact: nickbergman@gatech.edu
Supplementary information: Supplementary data are available at Bioinformatics Online.
Systems-level modeling of cellular glycosylation reaction networks: O-linked glycan formation on natural selectin ligands
Authors: Liu Gang , Marathe Dhananjay D. , Matta Khushi L. , Neelamegham Sriram 
Published: October 2008

Abstract
Motivation: The emerging field of Glycomics requires the development of systems-based modeling strategies to relate glycosyltransferase gene expression and enzyme activity with carbohydrate structure and function.
Results: We describe the application of object oriented programming concepts to define glycans, enzymes, reactions, pathways and compartments for modeling cellular glycosylation reaction networks. These class definitions are combined with current biochemical knowledge to define potential reaction networks that participate in the formation of the sialyl Lewis-X (sLeX) epitope on O-glycans linked to a leukocyte cell-surface glycoprotein, P-selectin Glycoprotein Ligand-1 (PSGL-1). Subset modeling, hierarchical clustering, principal component analysis and adjoint sensitivity analysis are applied to refine the reaction network and to quantify individual glycosyltransferase rate constants. Wet-lab experiments validate estimates from computer modeling. Such analysis predicts that sLeX expression varies directly with sialyltransferase α2,3ST3Gal-IV expression and inversely with α2,3ST3Gal-I/II.
Availability: SBML files for all converged models are available at http://www.eng.buffalo.edu/~neel/bio_reaction_network.html
Contact: neel@eng.buffalo.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
CNVDetector: locating copy number variations using array CGH data
Authors: Chen Peng-An , Liu Hsiao-Fei , Chao Kun-Mao 
Published: October 2008

Abstract
Summary: CNVDetector is a program for locating copy number variations (CNVs) in a single genome. CNVDetector has several merits: (i) it can deal with the array comparative genomic hybridization data even if the noise is not normally distributed; (ii) it has a linear time kernel; (iii) its parameters can be easily selected; (iv) it evaluates the statistical significance for each CNV calling.
Availability: CNVDetector (for Windows platform) can be downloaded from http:www.csie.ntu.edu.tw/~kmchao/tools/CNVDetector/. The manual of CNVDetector is also available.
Contact: kmchao@csie.ntu.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
A novel method for comparing topological models of protein structures enhanced with ligand information
Authors: Veeramalai Mallika , Gilbert David 
Published: October 2008

AbstractWe introduce TOPS+ strings, a highly abstract string-based model of protein topology that permits efficient computation of structure comparison, and can optionally represent ligand information. In this model, we consider loops as secondary structure elements (SSEs) as well as helices and strands; in addition we represent ligands as first class objects. Interactions between SSEs and between SSEs and ligands are described by incoming/outgoing arcs and ligand arcs, respectively; and SSEs are annotated with arc interaction direction and type. We are able to abstract away from the ligands themselves, to give a model characterized by a regular grammar rather than the context sensitive grammar of the original TOPS model. Our TOPS+ strings model is sufficiently descriptive to obtain biologically meaningful results and has the advantage of permitting fast string-based structure matching and comparison as well as avoiding issues of Non-deterministic Polynomial time (NP)-completeness associated with graph problems. Our structure comparison method is computationally more efficient in identifying distantly related proteins than BLAST, CLUSTALW, SSAP and TOPS because of the compact and abstract string-based representation of protein structure which records both topological and biochemical information including the functionally important loop regions of the protein structures. The accuracy of our comparison method is comparable with that of TOPS. Also, we have demonstrated that our TOPS+ strings method out-performs the TOPS method for the ligand-dependent protein structures and provides biologically meaningful results.Availability: The TOPS+ strings comparison server is available from http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/topsplus.html.Contact: mallikav@burnham.orgSupplementary information: Supplementary data are available at Bioinformatics online.
A better block partition and ligation strategy for individual haplotyping
Authors: Zhao Yuzhong , Xu Yun , Wang Zhihao , Zhang Hong , Chen Guoliang 
Published: October 2008

Abstract
Motivation: Haplotype played an important role in the association studies of disease gene and drug responsivity over the past years, but the low throughput of expensive biological experiments largely limited its application. Alternatively, some efficient statistical methods were developed to deduce haplotypes from genotypes directly. Because these algorithms usually needed to estimate the frequencies of numerous possible haplotypes, the partition and ligation strategy was widely adopted to reduce the time complexity. The haplotypes were usually partitioned uniformly in the past, but recent studies showed that the haplotypes had their own block structure, which may be not uniform. More reasonable block partition and ligation strategy according to the haplotype structure may further improve the accuracy of individual haplotyping.
Results: In this article, we presented a simple algorithm for block partition and ligation, which provided better accuracy for individual haplotyping. The block partition and ligation could be completed within O(m2 logm+m2n) time complexity, where m represented the length of genotypes and n represented the number of individuals. We tested the performance of our algorithm on both real and simulated dataset. The result showed that our algorithm yielded better accuracy with short running time.
Availability: The software is publicly available at http://mail.ustc.edu.cn/~zyzh.
Contact: xuyun@ustc.edu.cn
The Burkholderia Genome Database: facilitating flexible queries and comparative analyses
Authors: Winsor Geoffrey L. , Khaira Bhavjinder , Van Rossum Thea , Lo Raymond , Whiteside Matthew D. , Brinkman Fiona S. L. 
Published: October 2008

Abstract
Summary: As the genome sequences of multiple strains of a given bacterial species are obtained, more generalized bacterial genome databases may be complemented by databases that are focused on providing more information geared for a distinct bacterial phylogenetic group and its associated research community. The Burkholderia Genome Database represents a model for such a database, providing a powerful, user-friendly search and comparative analysis interface that contains features not found in other genome databases. It contains continually updated, curated and tracked information about Burkholderia cepacia complex genome annotations, plus other Burkholderia species genomes for comparison, providing a high-quality resource for its targeted cystic fibrosis research community.
Availability: http://www.burkholderia.com. Source code: GNU GPL.
Contact: brinkman@sfu.ca.
Faster exact Markovian probability functions for motif occurrences: a DFA-only approach
Authors: Ribeca Paolo , Raineri Emanuele 
Published: October 2008

Abstract
Background: The computation of the statistical properties of motif occurrences has an obviously relevant application: patterns that are significantly over- or under-represented in genomes or proteins are interesting candidates for biological roles. However, the problem is computationally hard; as a result, virtually all the existing motif finders use fast but approximate scoring functions, in spite of the fact that they have been shown to produce systematically incorrect results. A few interesting exact approaches are known, but they are very slow and hence not practical in the case of realistic sequences.
Results: We give an exact solution, solely based on deterministic finite-state automata (DFA), to the problem of finding the whole relevant part of the probability distribution function of a simple-word motif in a homogeneous (biological) sequence. Out of that, the z-value can always be computed, while the P-value can be obtained either when it is not too extreme with respect to the number of floating-point digits available in the implementation, or when the number of pattern occurrences is moderately low. In particular, the time complexity of the algorithms for Markov models of moderate order (0≤m≤2) is far better than that of Nuel, which was the fastest similar exact algorithm known to date; in many cases, even approximate methods are outperformed.
Conclusions: DFA are a standard tool of computer science for the study of patterns; previous works in biology propose algorithms involving automata, but there they are used, respectively, as a first step to write a generating function, or to build a finite Markov-chain imbedding (FMCI). In contrast, we directly rely on DFA to perform the calculations; thus we manage to obtain an algorithm which is both easily interpretable and efficient. This approach can be used for exact statistical studies of very long genomes and protein sequences, as we illustrate with some examples on the scale of the human genome.
Contact: paolo.ribeca@gmail.com
Stochastic dynamics of genetic networks: modelling and parameter identification
Authors: Cinquemani Eugenio , Milias-Argeitis Andreas , Summers Sean , Lygeros John 
Published: October 2008

Abstract
Motivation: Identification of regulatory networks is typically based on deterministic models of gene expression. Increasing experimental evidence suggests that the gene regulation process is intrinsically random. To ensure accurate and thorough processing of the experimental data, stochasticity must be explicitly accounted for both at the modelling stage and in the design of the identification algorithms.
Results: We propose a model of gene expression in prokaryotes where transcription is described as a probabilistic event, whereas protein synthesis and degradation are captured by first-order deterministic kinetics. Based on this model and assuming that the network of interactions is known, a method for estimating unknown parameters, such as synthesis and binding rates, from the outcomes of multiple time-course experiments is introduced. The method accounts naturally for sparse, irregularly sampled and noisy data and is applicable to gene networks of arbitrary size. The performance of the method is evaluated on a model of nutrient stress response in Escherichia coli.
Contact: cinquemani@control.ee.ethz.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
FABSIM: a software for generating F
ST distributions with various ascertainment biases
Authors: Ramírez-Soriano Anna , Calafell Francesc 
Published: October 2008

Abstract
Summary: We have developed a software that applies ascertainment bias on simulated DNA sequences and calculates FST on them, so they can be used to generate neutral distributions that are appropriate to test whether the genetic differentiation of a particular gene between populations is compatible with neutral evolution, or, on the contrary, suggests local adaptation by natural selection.
Availability: FABSIM is available from http://www.snpator.com/public/downloads/aRamirez/FABSIM/.
Contact: francesc.calafell@upf.edu.
Supplementary information: Supplementary data are available at Bioinformatics online. The data from which figures are built can be dowloaded from http://www.snpator.com/public/downloads/aRamirez/.
OSPAR Ecological Quality Objectives: the utility of health indicators for the North Sea
Authors: Heslenfeld Peter , Enserink E. Lisette 
Published: October 2008

Abstract
Heslenfeld, P., and Enserink, E. L. 2008. OSPAR Ecological Quality Objectives: the utility of health indicators for the North Sea. – ICES Journal of Marine Science, 65: 1392–1397. Committed to the ecosystem approach to management, OSPAR has accumulated 15 years of experience in developing a conceptual framework for ecological indicators and objectives, and in applying the framework to the North Sea as a test case. These Ecological Quality Objectives (EcoQOs) have become a model for the implementation of the new European Marine Strategy Framework Directive. We describe the history of EcoQO development, its current status, and future needs. We also present our positive and negative experiences in developing the approach, and conclude that regional sea conventions and marine research institutes in Europe should join forces to accelerate the development of ecosystem indicators and objectives, using existing concepts.
Use of a Phytoplankton Community Index to assess the health of coastal waters
Authors: Tett P. , Carreira C. , Mills D. K. , van Leeuwen S. , Foden J. , Bresnan E. , Gowen R. J. 
Published: October 2008

AbstractTett, P., Carreira, C., Mills, D. K., van Leeuwen, S., Foden, J., Bresnan, E., and Gowen, R. J. 2008. Use of a Phytoplankton Community Index to assess the health of coastal waters. – ICES Journal of Marine Science, 65: 1475–1482. Monitoring of marine-ecosystem status and health requires indicators of community structure and function. As a structural indicator, we propose a Phytoplankton Community Index (PCI) based on the abundance of “life-forms” such as “pelagic diatoms” or “medium-sized autotrophic dinoflagellates”. To calculate the PCI, data showing seasonal variation in these abundances are plotted in “life-form space” of two or more dimensions. Data from a “type-specific reference condition” are then enclosed within a reference envelope. Comparison data are plotted into the same coordinate system, and the PCI is the proportion (between 0 and 1) of these new data that fall within the reference envelope. Results from initial applications of this method are shown for UK coastal waters in the northern North Sea (near Stonehaven), a Scottish fjord (Loch Creran), and the eastern Irish Sea (including Liverpool Bay). The Stonehaven data (1997–2005) were used to compare values obtained from weekly sampling with those from monthly sampling. A spatial comparison between more- and less-nutrient-enriched waters in the eastern Irish Sea (1991–2003) showed little difference in phytoplankton community structure. Loch Creran has experienced a large change in the “balance of organisms”, and hence a reduction in the PCI, between 1979–1981 and 2006/2007, associated with a decrease in chlorophyll but no apparent change in nutrients. These results are discussed in relation to the intended uses of the PCI as an index of biological quality for the Water Framework Directive (WFD) and an index of ecosystem health in the context of eutrophication. Although the method only measures change, it can also be used as an indicator of biological quality if the reference conditions are those defined for a WFD waterbody, and as an indicator of health if appropriately calibrated. Suggestions are made for further development.
Movement patterns of four coral reef fish species in a fragmented habitat in New Caledonia: implications for the design of marine protected area networks
Authors: Chateau Olivier , Wantiez Laurent 
Published: October 2008

AbstractChateau, O., and Wantiez, L. 2009. Movement patterns of four coral reef fish species in a fragmented habitat in New Caledonia: implications for the design of marine protected area networks. – ICES Journal of Marine Science, 66: 50–55. Acoustic telemetry was used to examine the patterns of fish movements between a marine reserve and two unprotected reefs separated by large areas of lagoon soft bottoms (900–2000 m) in the South Lagoon Marine Park of New Caledonia. Four commercial fish species (Epinephelus maculatus, Plectropomus leopardus, Chlorurus microrhinos, and Scarus ghobban) were studied for 17 months (45 fish). Nine fish (20%) were detected on reefs other than the reef onto which they were released. Four patterns of inter-reef movement were identified during the survey, including home range relocations, movements larger than the scale of the study, many inter-reef movements within the study area, and punctual excursions outside the daily home range. The information gathered in this study demonstrates the ability of the fish to carry out medium-scale movements in a fragmented habitat. Consequently, the effectiveness of the reserve to protect the entire population is probably limited for these species. Because all the identified patterns implied at least one movement across the reserve boundaries, our results support the hypothesis that the Larégnère Marine Reserve, part of the South Lagoon Marine Park, could benefit the adjacent fished area through spillover.
Lack of Correlation Between Fecal Elastase‐1 Levels and Fecal Nitrogen Excretion in Preterm Infants
Authors: Corvaglia Luigi , Paoletti Vittoria , Battistini Barbara , Simoni Patrizia , Faldella Giacomo 
Published: October 2008

ABSTRACTWe measured fecal elastase‐1 (FE1) levels in 34 preterm newborns (15 small‐for‐gestational‐age and 19 appropriate‐for‐gestational‐age) during the first 2 months of life and evaluated whether they were correlated with nitrogen loss in stools. FE1 increased over time, and values were similar in both groups of newborns. Fecal nitrogen was significantly higher in small‐for‐gestational‐age infants. There was no correlation between FE1 levels and fecal nitrogen excretion. Pancreatic proteolytic function was efficient at an early stage in enterally fed preterm newborns. Despite the similar FE1 values, fecal nitrogen loss was significantly higher in small‐for‐gestational‐age preterm infants than in appropriate‐for‐gestational‐age preterm infants.