bluuebunny/crossref_metadata_2025_split huggingface dataset:
An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks
Authors: Ching Wai-Ki , Zhang Shuqin , Ng Michael K. , Akutsu Tatsuya 
Published: April 2007

AbstractMotivation: Probabilistic Boolean networks (PBNs) have been proposed to model genetic regulatory interactions. The steady-state probability distribution of a PBN gives important information about the captured genetic network. The computation of the steady-state probability distribution usually includes construction of the transition probability matrix and computation of the steady-state probability distribution. The size of the transition probability matrix is 2n-by-2n where n is the number of genes in the genetic network. Therefore, the computational costs of these two steps are very expensive and it is essential to develop a fast approximation method.Results: In this article, we propose an approximation method for computing the steady-state probability distribution of a PBN based on neglecting some Boolean networks (BNs) with very small probabilities during the construction of the transition probability matrix. An error analysis of this approximation method is given and theoretical result on the distribution of BNs in a PBN with at most two Boolean functions for one gene is also presented. These give a foundation and support for the approximation method. Numerical experiments based on a genetic network are given to demonstrate the efficiency of the proposed method.Contact: sqzhang@hkusua.hku.hkSupplementary information: Supplementary data are available at Bioinformatics online.
iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences
Authors: Gaëta Bruno A. , Malming Harald R. , Jackson Katherine J.L. , Bain Michael E. , Wilson Patrick , Collins Andrew M. 
Published: April 2007

Abstract
Motivation: Immunoglobulin heavy chain (IGH) genes in mature B lymphocytes are the result of recombination of IGHV, IGHD and IGHJ germline genes, followed by somatic mutation. The correct identification of the germline genes that make up a variable VH domain is essential to our understanding of the process of antibody diversity generation as well as to clinical investigations of some leukaemias and lymphomas.
Results: We have developed iHMMune-align, an alignment program that uses a hidden Markov model (HMM) to model the processes involved in human IGH gene rearrangement and maturation. The performance of iHMMune-align was compared to that of other immunoglobulin gene alignment utilities using both clonally related and randomly selected IGH sequences. This evaluation suggests that iHMMune-align provides a more accurate identification of component germline genes than other currently available IGH gene characterization programs.
Availability: iHMMune-align cross-platform Java executable and web interface are freely available to academic users and can be accessed at http://www.emi.unsw.edu.au/~ihmmune/
Contact: bgaeta@cse.unsw.edu.au
Meta-analysis of gene expression data: a predictor-based approach
Authors: Fishel Irit , Kaufman Alon , Ruppin Eytan 
Published: April 2007

Abstract
Motivation: With the increasing availability of cancer microarray data sets there is a growing need for integrative computational methods that evaluate multiple independent microarray data sets investigating a common theme or disorder. Meta-analysis techniques are designed to overcome the low sample size typical to microarray experiments and yield more valid and informative results than each experiment separately.
Results: We propose a new meta-analysis technique that aims at finding a set of classifying genes, whose expression level may be used to answering the classification question in hand. Specifically, we apply our method to two independent lung cancer microarray data sets and identify a joint core subset of genes which putatively play an important role in tumor genesis of the lung. The robustness of the identified joint core set is demonstrated on a third unseen lung cancer data set, where it leads to successful classification using very few top-ranked genes. Identifying such a set of genes is of significant importance when searching for biologically meaningful biomarkers.
Contact: ruppin@post.tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
A network-based method for target selection in metabolic networks
Authors: Guimerà R. , Sales-Pardo M. , Amaral L.A.N. 
Published: April 2007

Abstract
Motivation: The lack of new antimicrobials, combined with increasing microbial resistance to old ones, poses a serious threat to public health. With hundreds of genomes sequenced, systems biology promises to help in solving this problem by uncovering new drug targets.
Results: Here, we propose an approach that is based on the mapping of the interactions between biochemical agents, such as proteins and metabolites, onto complex networks. We report that nodes and links in complex biochemical networks can be grouped into a small number of classes, based on their role in connecting different functional modules. Specifically, for metabolic networks, in which nodes represent metabolites and links represent enzymes, we demonstrate that some enzyme classes are more likely to be essential, some are more likely to be species-specific and some are likely to be both essential and specific. Our network-based enzyme classification scheme is thus a promising tool for the identification of drug targets.
Contact: rguimera@northwestern.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method
Authors: Fujita A. , Sato J.R. , Garay-Malpartida H.M. , Morettin P.A. , Sogayar M.C. , Ferreira C.E. 
Published: April 2007

AbstractMotivation: A variety of biological cellular processes are achieved through a variety of extracellular regulators, signal transduction, protein–protein interactions and differential gene expression. Understanding of the mechanisms underlying these processes requires detailed molecular description of the protein and gene networks involved. To better understand these molecular networks, we propose a statistical method to estimate time-varying gene regulatory networks from time series microarray data. One well known problem when inferring connectivity in gene regulatory networks is the fact that the relationships found constitute correlations that do not allow inferring causation, for which, a priori biological knowledge is required. Moreover, it is also necessary to know the time period at which this causation occurs. Here, we present the Dynamic Vector Autoregressive model as a solution to these problems.Results: We have applied the Dynamic Vector Autoregressive model to estimate time-varying gene regulatory networks based on gene expression profiles obtained from microarray experiments. The network is determined entirely based on gene expression profiles data, without any prior biological knowledge. Through construction of three gene regulatory networks (of p53, NF-κB and c-myc) for HeLa cells, we were able to predict the connectivity, Granger-causality and dynamics of the information flow in these networks.Contact: cef@ime.usp.brSupplementary information: Additional figures may be found at http://mariwork.iq.usp.br/dvar/
OSLay: optimal syntenic layout of unfinished assemblies
Authors: Richter Daniel C. , Schuster Stephan C. , Huson Daniel H. 
Published: April 2007

Abstract
Summary: The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight matching. The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure.
Motivation: To enhance efficiency in the gap closure phase of a genome project it is crucial to know which contigs are adjacent in the target genome. Related genome sequences can be used to layout contigs in an assembly.
Availability: OSLay is freely available from: http://www-ab.informatik.unituebingen.de/software/oslay
Contact: drichter@informatik.uni-tuebingen.de
SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates
Authors: Hayes Ben J. , Nilsen Kjetil , Berg Paul R. , Grindflek Eli , Lien Sigbjørn 
Published: April 2007

Abstract
Motivation: Single nucleotide polymorphism (SNP) detection exploiting redundancy in expressed sequence tag (EST) collections that arises from the presence of transcripts of the same gene from different individuals has been used to generate large collections of SNPs for many species. A second source of redundancy, namely that EST collections can contain multiple transcripts of the same gene from the same individual, can be exploited to distinguish true SNPs from sequencing error. In this article, we demonstrate with Atlantic salmon and pig EST collections that splitting the EST collection in two, detecting SNPs in both subsets, then accepting only cross-validated SNPs increases validation rates.
Results: In the pig data set, 676 cross-validated putative SNPs were detected in a collection of 160 689 ESTs. When validating a subset of these by genotyping on MassARRAY 85.1% of SNPs were polymorphic in successful assays. In the salmon data set, 856 cross-validated putative SNPs were detected in a collection of 243 674 ESTs. Validation by genotyping showed that 81.0% of the cross-validated putative SNPs were polymorphic in successful assays.
Availability: Cross-validated SNPs are available at dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/), ss69371838-ss69372575 for the salmon SNPs and ss69372587-ss69373226 for the pig SNPs.
Contact: ben.hayes@dpi.vic.gov.au
The qualitative and time-dependent character of spatial relations in biomedical ontologies
Authors: Bittner Thomas , Goldberg Louis J. 
Published: April 2007

Abstract
Motivation: The formal representation of mereological aspects of canonical anatomy (parthood relations) is relatively well understood. The formal representation of other aspects of canonical anatomy, such as connectedness and adjacency relations between anatomical parts, their shape and size as well as the spatial arrangement of anatomical parts within larger anatomical structures are, however, much less well understood and represented in existing computational anatomical and bio-medical ontologies only insufficiently.
Results: In this article, we provide a methodology of how to incorporate this kind of information into anatomical and bio-medical ontologies by applying techniques of representing qualitative spatial information from Artificial Intelligence. In particular, we focus on how to explicitly take into account the qualitative and time-dependent character of these relations. As a running example, we use the human temporomandibular joint (TMJ).
Availability: Using the presented methodology, a formal ontology was developed which is accessible on http://www.ifomis.org/bfo/fol. This ontology may help to improve the logical and ontological rigor of bio-medical ontologies such as the OBO relation ontology.
Contact: bittner3@buffalo.edu
SciRoKo: a new tool for whole genome microsatellite search and investigation
Authors: Kofler Robert , Schlötterer Christian , Lelley Tamas 
Published: April 2007

Abstract
Summary: SciRoKo is a user-friendly software tool for the identification of microsatellites in genomic sequences. The combination of an extremely fast search algorithm with a built-in summary statistic tool makes SciRoKo an excellent tool for full genome analysis. Compared to other already existing tools, SciRoKo also allows the analysis of compound microsatellites.
Availability: free for use: www.kofler.or.at/Bioinformatics
Contact: robert.kofler@boku.ac.at
Supplementary information: Supplementary data are available at Bioinformatics online.
Faspad: fast signaling pathway detection
Authors: Hüffner Falk , Wernicke Sebastian , Zichner Thomas 
Published: April 2007

Abstract
Summary: Faspad is a user-friendly tool that detects candidates for linear signaling pathways in protein interaction networks based on an approach by Scott et al. (Journal of Computational Biology, 2006). Using recent algorithmic insights, it can solve the underlying NP-hard problem quite fast: for protein networks of typical size (several thousand nodes), pathway candidates of length up to 13 proteins can be found within seconds and with a 99.9% probability of optimality. Faspad graphically displays all candidates that are found; for evaluation and comparison purposes, an overlay of several candidates and the surrounding network context can also be shown.
Availability: Faspad is available as free software under the GPL license at http://theinf1.informatik.uni-jena.de/faspad/ and runs under Linux and Windows.
Contact: hueffner@minet.uni-jena.de
Improved seawater depth determination using corrected helicopter time‐domain electromagnetic data
Authors: Vrbancich Julian , Fullagar Peter K. 
Published: April 2007

ABSTRACTTwo areas within Sydney Harbour were surveyed in 2002 with a helicopter‐borne time‐domain electromagnetic system to test its potential for bathymetric mapping in shallow seawater. As delivered, the data were improperly calibrated. Therefore a re‐calibration was performed to reconcile the measured data with ‘ground truth’. Synthetic electromagnetic transients were computed for two‐layer models representing the seawater and the sediment overlying bedrock at a number of locations within the survey area. The seawater depth in the models varied between 3 m and 70 m. The measured and calculated data were compared at each delay time, and were found to be linearly related. The slope and intercept of the line of best fit were used to correct all the measured data. Inversion of the corrected time‐domain electromagnetic data generally resolved the bathymetry to submetre accuracy down to depths of about 55 m.
Orchids of the West Indies: predictability of diversity and endemism
Authors: Ackerman J. D. , Trejo‐Torres J. C. , Crespo‐Chuy Y. 
Published: April 2007

AbstractAim We examined phytogeographical patterns of West Indian orchids, and related island area and maximum elevation with orchid species richness and endemism. We expected strong species–area relationships, but that these would differ between low and montane island groups. In so far as maximum island elevation is a surrogate for habitat diversity, we anticipated a strong relationship with maximum elevation and both species richness and endemism for montane islands.Location The West Indies.Methods Our data included 49 islands and 728 species. Islands were classified as either montane (≥ 300 m elevation) or low (< 300 m). Linear and multivariate regression analyses were run to detect relationships between either area or maximum island elevation and species richness or the number of island endemic species.Results For all 49 islands, the species–area relationship was strong, producing az‐value of 0.47 (slope of the regression line) and explaining 46% of the variation. For 18 relatively homogeneous, low islands we found a non‐significant slope ofz = −0.01 that explained only 0.1% of the variation. The 31 montane islands had a highly significant species–area relationship, withz = 0.49 and accounting for 65% of the variation. Species numbers were also strongly related to maximum island elevation. For all islands < 750 km2, we found a small‐island effect, which reduced the species–area relationship to a non‐significantz = 0.16, with only 5% of the variation explained by the model. Species–area relationships for montane islands of at least 750 km2were strong and significant, but maximum elevation was the best predictor of species richness and accounted for 79% of the variation. The frequency of single‐island endemics was high (42%) but nearly all occurred on just nine montane islands (300 species). The taxonomic distribution of endemics was also skewed, suggesting that seed dispersability, while remarkable in some taxa, is very limited in others. Montane island endemics showed strong species–area and species–elevation relationships.Main conclusions Area and elevation are good predictors of orchid species diversity and endemism in the West Indies, but these associations are driven by the extraordinarily strong relationships of large, montane islands. The species richness of low islands showed no significant relationship with either variable. A small‐island effect exists, but the montane islands had a significant relationship between species diversity and maximum elevation. Thus, patterns of Caribbean orchid diversity are dependent on an interplay between area and topographic diversity.
Different mechanisms can lead to the same altered HLA class I phenotype in tumors
Authors: Rodriguez T. , Aptsiauri N. , Méndez R. , Jimenez P. , Ruiz‐Cabello F. , Garrido F 
Published: April 2007

AbstractHuman leukocyte antigen (HLA) class I plays an important role in tumor recognition and rejection. Total or selective losses of HLA class I antigens (classified into seven HLA class I altered phenotypes) represent one of the main routes of tumor escape from immune surveillance. Abnormal expression of HLA class I has been reported in different human tumor samples with distinct underlying mechanisms. Notably, different molecular mechanisms can generate the same altered HLA class I phenotype. Here, we describe various molecular mechanisms that can lead to HLA total loss or downregulation (phenotype I) in melanoma, colorectal carcinoma and bladder cancer.
Clinical significance of donor–recipient HLA matching on survival after myeloablative hematopoietic cell transplantation from unrelated donors
Authors: Petersdorf E. W. , Gooley T. , Malkki M. , Horowitz M. ,   for The International Histocompatibility Working Group in Hematopoietic Cell Transplantation
Published: April 2007

AbstractThe application of unrelated donor hematopoietic cell transplantation can be expanded with the use of mismatched donors if human leukocyte antigen (HLA) disparity does not lead to increased morbidity and mortality. The rules that govern permissibility of HLA mismatches are not well defined. The International Histocompatibility Working Group in hematopoietic cell transplantation measured the risks associated with locus‐specific disparity in 4796 patients transplanted for low, intermediate, or high‐risk hematologic diseases. The permissibility of a given HLA mismatch is in part defined by the locus and by disease risk.
Cloning and sequencing alleles of the KIR2DL4 gene from genomic DNA samples
Authors: Roberts C. H. , Madrigal J. A. , Marsh S. G. E. 
Published: April 2007

AbstractKiller‐cell immunoglobulin‐like receptor (KIR) genes are highly polymorphic and polymorphisms have been found in all KIR exons. Although less is known of the introns, these also appear to be polymorphic. To generate a comprehensive database of KIR genomic sequences, which will aid in the design of KIR typing reagents, we have established a method for cloning and sequencing of KIR genes from genomic DNA. We cloned and sequenced the entire KIR2DL4 gene from genomic DNA using long template touchdown PCR and high capacity cloning vectors. Overlapping secondary amplicons were modified to include a nucleotide analogue that reduced sequencing problems associated with secondary structure formation in the KIR sequence. Using a modified sequencing chemistry we were able to sequence approximately 11,000 bases confirming the previously published KIR2DL4*005 allele sequence.
Functions of HLA‐G in the immune system
Authors: Favier B. , LeMaoult J. , Carosella E. D. 
Published: April 2007

AbstractHuman leukocyte antigen (HLA)‐G is a nonclassical HLA class I molecule that has tolerogenic functions and acts on cells of both innate and adaptive immunity. The molecular mechanism leading to tolerance involves the interaction between HLA‐G and inhibitory receptors that are expressed at the surface of immune cells. In this review, we will briefly summarize the key advances on the relationships between HLA‐G and the immune system and their consequences in pathology.
14th International HLA and Immunogenetics Workshop: Report on joint study on MHC and infection
Authors: Mehra N. K. , Kaur G. 
Published: April 2007

AbstractThe ‘MHC and Infection’ study of the 14th International HLA and Immunogenetics Workshop was undertaken to evaluate the contribution of specific variants of major histocompatibility complex (MHC) and non‐MHC genes that are specifically associated with higher probabilities of infection, disease severity, and progression in different populations.
Schirmer tear test, phenol red thread tear test, eye blink frequency and corneal sensitivity in the guinea pig
Authors: Trost Katrin , Skalicky M. , Nell Barbara 
Published: April 2007

AbstractObjective To establish reference values for Schirmer tear tests (STT) I and II, phenol red thread (PRT) tear test and eye blink frequency, and to determine corneal sensitivity for normal guinea pigs.Animals studied One hundred and eight eyes of 54 adult Duncan‐Hartley guinea pigs.Procedure Schirmer tear test (STT) I and then STT II were performed in 36 guinea pigs. PRT and STT I were compared in 18 adult Duncan‐Hartley guinea pigs. Corneal sensitivity was determined in 23 guinea pigs by evaluating the corneal touch threshold (CTT) of five different regions using a Cochet‐Bonnet esthesiometer. Eye blink frequency was measured in 10 guinea pigs over a period of 20 min and in 17 guinea pigs over a period of 10 min.Results Mean STT I was 0.36 mm ± 1.09 mm (wetting/min) and mean STT II was 0.43 mm ± 1.29 mm (wetting/min). There was no significant difference between mean STT I and mean STT II (P = 0.79). The mean PRT‐value was 16 ± 4.7 mm (wetting/15 s), and the mean STT I‐value in the same guinea pigs was 0.6 ± 1.83 mm (wetting/min). Corneal sensitivity was significantly higher in the center than in the four limbal regions. The mean CTT for central, ventral, nasal, temporal and dorsal regions was 2, 1.7, 1.7, 1.7 and 1.6 cm or 3.7, 5.2, 5.6, 5.7 and 6.4 g/mm2, respectively. Eye blink frequency was between two to five (mean 3.4 ± 1.04) blinks per eye over 20 min in guinea pigs in their home environment, while in handheld and restrained guinea pigs eye blink frequency showed a variation between 0 and 17 blinks per eye (mean 3.24 ± 3.64 blinks per eye) over 10 min.Conclusions As there were no significant differences between STT I and STT II results, reflex tear secretion in the guinea pig may not exist. The most likely explanation is a lower corneal sensitivity in the guinea pig than in other species, such as cats, dogs and horses. Because of the small amount of tears, PRT is the preferred test for tear measurement in the guinea pig.
International Trade with a Public Intermediate Good and the Gains from Trade*
Authors: Suga Nobuhito , Tawada Makoto 
Published: April 2007

AbstractThis paper presents a one‐primary factor, two‐consumer good, and two‐country model of international trade where each country’s government supplies a country‐specific public intermediate good so as to attain efficient production. By introducing the Marshallian adjustment process, it is demonstrated that the country with larger factor endowment exports the good whose productivity is more sensitive to the public intermediate good. Our normative analysis of free trade shows the following results. First, at least one country gains from trade. Secondly, if a country incompletely specializes in the trading equilibrium, the country necessarily loses from trade.