bluuebunny/crossref_metadata_2025_split huggingface dataset:
TIGR Gene Indices clustering tools (TGICL): a software
system for fast clustering of large EST datasets
Authors: Pertea Geo , Huang Xiaoqiu , Liang Feng , Antonescu Valentin , Sultana Razvan , Karamycheva Svetlana , Lee Yuandan , White Joseph , Cheung Foo , Parvizi Babak , Tsai Jennifer , Quackenbush John 
Published: March 2003

Abstract
TGICL is a pipeline for analysis of large Expressed Sequence Tags (EST) and mRNA databases in which the sequences are first clustered based on pairwise sequence similarity, and then assembled by individual clusters (optionally with quality values) to produce longer, more complete consensus sequences. The system can run on multi-CPU architectures including SMP and PVM.
Availability: http://www.tigr.org/tdb/tgi/software/
Contact: johnq@tigr.org; johnq@tigr.org
* To whom correspondence should be addressed.
MINRMS: an efficient algorithm for determining protein structure
similarity using root-mean-squared-distance
Authors: Jewett Andrew I. , Huang Conrad C. , Ferrin Thomas E. 
Published: March 2003

Abstract
Motivation: Existing algorithms for automated protein structure alignment generate contradictory results and are difficult to interpret. An algorithm which can provide a context for interpreting the alignment and uses a simple method to characterize protein structure similarity is needed.
Results: We describe a heuristic for limiting the search space for structure alignment comparisons between two proteins, and an algorithm for finding minimal root-mean-squared-distance (RMSD) alignments as a function of the number of matching residue pairs within this limited search space. Our alignment algorithm uses coordinates of alpha-carbon atoms to represent each amino acid residue and requires a total computation time of O(m3n2), where m and n denote the lengths of the protein sequences. This makes our method fast enough for comparisons of moderate-size proteins (fewer than ∼800 residues) on current workstation-class computers and therefore addresses the need for a systematic analysis of multiple plausible shape similarities between two proteins using a widely accepted comparison metric.
Availability: See http://www.cgl.ucsf.edu/Research/minrms
Contact: tef@cgl.ucsf.edu
* To whom correspondence should be addressed.
Prediction of human protein function according to Gene
Ontology categories
Authors: Jensen L. J. , Gupta R. , Stærfeldt H.-H. , Brunak S. 
Published: March 2003

Abstract
Motivation: The human genome project has led to the discovery of many human protein coding genes which were previously unknown. As a large fraction of these are functionally uncharacterized, it is of interest to develop methods for predicting their molecular function from sequence.
Results: We have developed a method for prediction of protein function for a subset of classes from the Gene Ontology classification scheme. This subset includes several pharmaceutically interesting categories—transcription factors, receptors, ion channels, stress and immune response proteins, hormones and growth factors can all be predicted. Although the method relies on protein sequences as the sole input, it does not rely on sequence similarity, but instead on sequence derived protein features such as predicted post translational modifications (PTMs), protein sorting signals and physical/chemical properties calculated from the amino acid composition. This allows for prediction of the function for orphan proteins where no homologs can be found. Using this method we propose two novel receptors in the human genome, and further demonstrate chromosomal clustering of related proteins.
Availability: Sequences can be submitted to the prediction server via a web interface at http://www.cbs.dtu.dk/services/ProtFun/
Contact: ljj@cbs.dtu.dk
* To whom correspondence should be addressed.
Greedy mixture learning for multiple motif discovery
in biological sequences
Authors: Blekas Konstantinos , Fotiadis Dimitrios I. , Likas Aristidis 
Published: March 2003

Abstract
Motivation: This paper studies the problem of discovering subsequences, known as motifs, that are common to a given collection of related biosequences, by proposing a greedy algorithm for learning a mixture of motifs model through likelihood maximization. The approach adds sequentially a new motif to a mixture model by performing a combined scheme of global and local search for appropriately initializing its parameters. In addition, a hierarchical partitioning scheme based on kd-trees is presented for partitioning the input dataset in order to speed-up the global searching procedure. The proposed method compares favorably over the well-known MEME approach and treats successfully several drawbacks of MEME.
Results: Experimental results indicate that the algorithm is advantageous in identifying larger groups of motifs characteristic of biological families with significant conservation. In addition, it offers better diagnostic capabilities by building more powerful statistical motif-models with improved classification accuracy.
Availability: Source code in Matlab is available at http://www.cs.uoi.gr/~kblekas/greedy/GreedyEM.html
Contact: kblekas@cs.uoi.gr
* To whom correspondence should be addressed.
Gene expression data preprocessing
Authors: Herrero J. , Díaz-Uriarte R. , Dopazo J. 
Published: March 2003

Abstract
Summary: We present an interactive web tool for preprocessing microarray gene expression data. It analyses the data, suggests the most appropriate transformations and proceeds with them after user agreement. The normal preprocessing steps include scale transformations, management of missing values, replicate handling, flat pattern filtering and pattern standardization and they are required before performing any pattern analysis. The processed data set can be sent to other pattern analysis tools.
Availability: The web interface is accessible through http://bioinfo.cnio.es/cgi-bin/tools/dnarray/preprocess
Contact: jdopazo@cnio.es
* To whom correspondence should be addressed.
Cellerator: extending a computer algebra system to include
biochemical arrows for signal transduction simulations
Authors: Shapiro Bruce E. , Levchenko Andre , Meyerowitz Elliot M. , Wold Barbara J. , Mjolsness Eric D. 
Published: March 2003

Abstract
Summary: Cellerator describes single and multi-cellular signal transduction networks (STN) with a compact, optionally palette-driven, arrow-based notation to represent biochemical reactions and transcriptional activation. Multi-compartment systems are represented as graphs with STNs embedded in each node. Interactions include mass-action, enzymatic, allosteric and connectionist models. Reactions are translated into differential equations and can be solved numerically to generate predictive time courses or output as systems of equations that can be read by other programs. Cellerator simulations are fully extensible and portable to any operating system that supports Mathematica, and can be indefinitely nested within larger data structures to produce highly scaleable models.
Availability: Cellerator can be licensed free of charge to noncommercial academic, U.S. government, and nonprofit users. Details and sample notebooks are available at http://www-aig.jpl.nasa.gov/public/mls/cellerator.
Contact: bshapiro@jpl.nasa.gov
* To whom correspondence should be addressed.
MHCBN: a comprehensive database of MHC binding and non-binding
peptides
Authors: Bhasin Manoj , Singh Harpreet , Raghava G. P. S. 
Published: March 2003

Abstract
Summary: MHCBN is a comprehensive database of Major Histocompatibility Complex (MHC) binding and non-binding peptides compiled from published literature and existing databases. The latest version of the database has 19 777 entries including 17 129 MHC binders and 2648 MHC non-binders for more than 400 MHC molecules. The database has sequence and structure data of (a) source proteins of peptides and (b) MHC molecules. MHCBN has a number of web tools that include: (i) mapping of peptide on query sequence; (ii) search on any field; (iii) creation of data sets; and (iv) online data submission. The database also provides hypertext links to major databases like SWISS-PROT, PDB, IMGT/HLA-DB, GenBank and PUBMED.
Availability: MHCBN is available at http://www.imtech.res.in/raghava/mhcbn/. It’s SRS version is available from http://srs.ebi.ac.uk/
Contact: raghava@imtech.res.in
Supplementary information: http://www.imtech.res.in/raghava/mhcbn/supl/
* To whom correspondence should be addressed.
How Bayes tests of molecular phylogenies compare with
frequentist approaches
Authors: Aris-Brosou Stéphane 
Published: March 2003

Abstract
Motivation: The desire to compare molecular phylogenies has stimulated the design of numerous tests. Most of these tests are formulated in a frequentist framework, and it is not known how they compare with Bayes procedures. I propose here two new Bayes tests that either compare pairs of trees (Bayes hypothesis test, BHT), or test each tree against an average of the trees included in the analysis (Bayes significance test, BST).
Results: The algorithm, based on a standard Metropolis–Hastings sampler, integrates nuisance parameters out and estimates the probability of the data under each topology. These quantities are used to estimate Bayes factors for composite vs. composite hypotheses. Based on two data sets, the BHT and BST are shown to construct similar confidence sets to the bootstrap and the Shimodaira Hasegawa test, respectively. This suggests that the known difference among previous tests is mainly due to the null hypothesis considered.
Availability: http://statgen.ncsu.edu/stephane/
Contact: stephane@statgen.ncsu.edu
Supplementary Information: Supplemental material referenced in the text can be found at http://statgen.ncsu.edu/stephane/bayestests.htm
* Present address: Bioinformatics Research Center, North Carolina State University Raleigh, NC 27695-7566, USA
On the Performance of Bond Functions and Basis Set Extrapolation Techniques in High-Accuracy Calculations of Interatomic Potentials. A Helium Dimer Study
Authors: Jeziorska Małgorzata , Bukowski Robert , Cencek Wojciech , Jaszuński Michał , Jeziorski Bogumił , Szalewicz Krzysztof 
Published: March 2003

Helium dimer interaction energies, Eint, obtained recently using the Gaussian geminal implementation of the coupled cluster doubles (CCD) and singles and doubles (CCSD) theory, were employed to evaluate the performance of conventional orbital calculations applying the correlation-consistent polarized valence X-tuple zeta (cc-pVXZ) bases, with X ranging from 4 to 7, and very large sets of bond functions. We found that while the bond functions improve dramatically the convergence of the doubles and triples contribution to the interaction energy, these functions are inefficient or even counterproductive in predicting the effect of the single excitations and the small contribution beyond the CCSD(T) (CCSD model with noniterative account of triple excitations) level of electronic structure theory. We also found that bond functions are very effective in extrapolation techniques. Using simple two-point extrapolations based on the single-power laws X-2 and X-3 for the basis set truncation error, the Gaussian geminal CCSD result for Eint, equal to -9.150 ± 0.001 K at the equilibrium interatomic distance of R = 5.6 bohr, could be reproduced with an error of 2-3 mK. Linear extrapolation of the functional dependence of the CCSD energy on the value of the second-order Møller-Plesset energy and the use of the known accurate value of the latter leads to an even smaller error. Using these extrapolation techniques with basis sets up to doubly augmented septuple-zeta quality and containing large sets of bond functions, we estimated the contribution of triple excitations within the CCSD(T) model to be -1.535 ± 0.002 K, with the error bars reflecting the spread of extrapolated results. The contribution beyond the CCSD(T) model, estimated from full configuration interaction (FCI) calculations with up to 255 orbitals, amounts to -0.323 ± 0.005 K. Combining the Gaussian geminal value of the CCSD energy with the orbital estimations of the CCSD(T) and FCI contributions, we found that Eint = -11.008 ± 0.008 K. This value is consistent with recent high-level orbital computations (van Mourik T., Dunning T. H.: J. Chem. Phys. 1999, 111, 9246; Klopper W.: J. Chem. Phys. 2001, 115, 761) but has substantially tighter error bounds. It differs somewhat, however, from the value of -10.98 ± 0.02 K obtained recently from the "exact" quantum Monte Carlo calculations (Anderson J. B.: J. Chem. Phys. 2001, 115, 4546).
OPEN STRINGS IN THE SL(2,R) WZWN MODEL WITH SOLUTION FOR A RIGIDLY ROTATING STRING
Authors: LOMHOLT M. A. , LARSEN A. L. 
Published: March 2003

Boundary conditions and gluing conditions for open strings and D-branes in the SL (2,R) WZWN model, corresponding to AdS 3, are discussed. Some boundary conditions and gluing conditions previously considered in the literature are shown to be incompatible with the variation principle. We then consider open string boundary conditions corresponding to a certain field-dependent gluing condition. This allows us to consider open strings with constant energy and angular momentum. Classically, these open strings naturally generalize the open strings in flat Minkowski space. For rigidly rotating open strings, we show that the torsion leads to a bending and an unfolding. We also derive the SL (2,R) Regge relation, which generalizes the linear Minkowski Regge relation. For "high" mass, it takes the form L ≈ ± M/H, where H is the scale of the SL (2,R) group manifold.
The chemokine receptor CCR8 mediates rescue from dexamethasone-induced apoptosis via an ERK-dependent pathway
Authors: Spinetti Gaia , Bernardini Giovanni , Camarda Grazia , Mangoni Antonella , Santoni Angela , Capogrossi Maurizio C , Napolitano Monica 
Published: March 2003

Abstract
Several chemokines have been shown to regulate cellular apoptosis following discrete stimuli. It was previously demonstrated that the CC chemokine CCL1 (I-309) rescues thymic lymphoma cells from apoptois by unknown mechanisms. The aim of our study was to characterize the role of the CC chemokine receptor 8 (CCR8), the only described receptor for CCL1, in the rescue of murine thymic lymphoma cells and murine thymocytes from dexamethasone (dex)-induced apoptosis. We show here that the CCR8-restricted agonist Kaposi sarcoma-associated herpesvirus-encoded chemokine viral macrophage-inflammatory protein-1 (vMIP-1) rescues thymic lymphoma cells from dex-induced apoptosis, similar to CCL1, and that such rescue is extracellular-regulated kinase-dependent. Although it has been hypothesized that the rescuing effect of CCL1 from apoptosis could be CCR8-mediated, here, we formally demonstrate the role of such receptor as its selective antagonist encoded by the MC148 gene of molluscum contagiosum virus MC148/vMCC-I inhibits v-MIP-1- and CCL1-induced rescue activity. In addition, CCR8 ligands inhibit dex-induced apoptosis of murine thymocytes with potential implications for thymic selection.
P-selectin mediates IL-13-induced eosinophil transmigration but not eotaxin generation in vivo: a comparative study with IL-4-elicited responses
Authors: Larbi Karen Y , Dangerfield John P , Culley Fiona J , Marshall Diane , Haskard Dorian O , Jose Peter J , Williams Timothy J , Nourshargh Sussan 
Published: March 2003

Abstract
The study investigated the role of P-selectin in the responses of eosinophil transmigration and eotaxin generation in vivo elicited by interleukin (IL)-13, as compared with IL-4. Two murine models of leukocyte transmigration were used, migration into cytokine-stimulated peritoneal cavities and through stimulated cremasteric venules, as observed by intravital microscopy. In mice lacking P-selectin, eosinophil infiltration elicited by the cytokines in the peritonitis model was totally inhibited. In the cremaster muscle, however, although spontaneous leukocyte-rolling flux and stimulated leukocyte firm adhesion were inhibited by ∼97% and ∼48%, respectively, stimulated transmigration was unaffected. However, IL-13-induced leukocyte transmigration was totally blocked in P-selectin-deficient mice treated with an anti-α4 integrin monoclonal antibody (mAb; PS/2). In comparison, treatment of wild-type mice with the anti-α4 integrin mAb resulted in only partial suppression of IL-13-induced leukocyte transmigration. Significant levels of eotaxin were detected in response to IL-13/IL-4 in both tissues in P-selectin-deficient animals. In conclusion, the regulatory role of P-selectin in leukocyte transmigration elicited by IL-13 appears to be tissue-specific, a phenomenon that is independent of the ability of the cytokine to stimulate eotaxin generation.
Peripheral blood-derived bovine dendritic cells promote IgG1-restricted B cell responses in vitro
Authors: Bajer Anna A , Garcia-Tapia David , Jordan Kimberly R , Haas Karen M , Werling Dirk , Howard Chris J , Estes D Mark 
Published: March 2003

Abstract
Regulation of humoral responses involves multiple cell types including the requirements for cognate interactions between T and B cells to drive CD40-dependent responses to T-dependent antigens. A third cell type has also been shown to play an essential role, the dendritic cell (DC). We demonstrate that bovine peripheral blood-derived (PB)-DC are similar in function to features described for human interstitial DC including the production of signature type 2 cytokines [interleukin (IL)-13, IL-10]. PB-DC express moderate-to-high costimulatory molecule expression, and major histocompatibility complex class II is negative for CD14 expression and has low or no expression of CD11c. Consistent with the interstitial phenotype is the ability of PB-DC to influence B cell activation and differentiation via direct expression of CD40L and type 2 cytokines. Collectively, these results suggest that direct B cell-DC interactions may promote an immunoglobulin-isotype expression pattern consistent with type 2 responses, independent of direct T cell involvement.
The role of CCL22 (MDC) for the recruitment of eosinophils during allergic pleurisy in mice
Authors: Pinho Vanessa , Oliveira Sandra H , Souza Danielle G , Vasconcelos Denise , Alessandri Ana Letícia , Lukacs Nicholas W , Teixeira Mauro M 
Published: March 2003

Abstract
Eosinophils are important inflammatory cells in allergic diseases. In the present study, we have investigated the effects of CCL22 on the recruitment of eosinophils in vivo and in vitro. CCL22 induced a dose- and time-dependent recruitment of eosinophils into the pleural cavity of mice, and this was dependent on the release of platelet-activating factor (PAF) and subsequent generation of CCL11. However, in an allergic pleurisy model, an anti-CCL22 polyclonal antibody given during sensitization or before challenge had no significant effect on eosinophil recruitment. CCL22 did not induce eosinophil chemotaxis in vitro but was able to induce eosinophil degranulation in vitro and in vivo. In conclusion, we show that although exogenously added CCL22 may induce eosinophil migration in vivo via release of PAF and CCL11 (eotaxin), endogenous production of CCL22 does not drive eosinophil migration during allergic inflammation. However, CCL22 may be an important activator of eosinophils once these cells have migrated into tissue.
Rational approaches to human cancer immunotherapy
Authors: Davis Ian D , Jefford Michael , Parente Phillip , Cebon Jonathan 
Published: March 2003

Abstract
Over most of the 20th century, immunotherapy for cancer was based on empiricism. Interesting phenomena were observed in the areas of cancer, infectious diseases, or transplantation. Inferences were made and extrapolated into new approaches for the treatment of cancer. If tumors regressed, the treatment approaches could be refined further. However, until the appropriate tools and reagents were available, investigators were unable to understand the biology underlying these observations. In the early 1990s, the first human tumor T cell antigens were defined and dendritic cells were discovered to play a pivotal role in antigen presentation. The current era of cancer immunotherapy is one of translational research based on known biology and rationally designed interventions and has led to a rapid expansion of the field. The beginning of the 21st century brings the possibility of a new era of effective cancer immunotherapy, combining rational, immunological treatments with conventional therapies to improve the outcome for patients with cancer.
Malignant counterpart of myeloid dendritic cell (DC) belonging to acute myelogenous leukemia (AML) exhibits a dichotomous immunoregulatory potential
Authors: Fujii Shin-ichiro , Shimizu Kanako , Koji Fujimoto , Kawano Fumio 
Published: March 2003

Abstract
Dendritic cells (DCs) play a central role in immune regulation. Some leukemic cells are argued to be malignant counterparts of DC because of their ability to differentiate into leukemic DC. We characterize DC-like leukemia homogenously expressing CD11c+CD86+ in acute myelogenous leukemia patients. They express the Wilms’ tumor-1 antigen and common DC phenotypes (i.e., fascin+, CD83+, and DR+) directly. Purified leukemic cells produce interleukin-12 (IL-12) simultaneously with Fas ligand (FasL) and IL-6, which may suppress T cell-mediated immunity. These cells can elicit strong allogeneic T cell responses as well as induce tumor-specific CD8+ cytotoxic T cells, suggesting that they effectively present tumor-associated antigens. In contrast, they drive primary T cells toward apoptosis mediated in a tumor-specific way by a Fas-FasL interaction. Taken together, DC-like leukemia uniquely influences immune surveillance in contadictory ways, some of which may be involved in the mechanism of immune escape.
The unique target specificity of a nonpeptide chemokine receptor antagonist: selective blockade of two Th1 chemokine receptors CCR5 and CXCR3
Authors: Gao Ping , Zhou Xu-Yu , Yashiro-Ohtani Yumi , Yang Yi-Fu , Sugimoto Naotoshi , Ono Shiro , Nakanishi Tsuyoshi , Obika Satoshi , Imanishi Takeshi , Egawa Takeshi , Nagasawa Takashi , Fujiwara Hiromi , Hamaoka Toshiyuki 
Published: March 2003

Abstract
CC chemokine receptor (CCR) 5 and CXC chemokine receptor (CXCR)3 are expressed on T helper cell type 1 cells and have been implicated in their migration to sites of inflammation. Our preceding study demonstrated that a nonpeptide synthetic CCR5 antagonist, TAK-779 {N, N-dimethyl-N-[4-[[[2-(4-methylphenyl)-6, 7-dihydro-5H-benzocyclohepten-8-yl]carbon-yl]amino]benzyl]-tetrahydro-2H-pyran4-aminium chloride, inhibits the development of experimentally induced arthritis by modulating the migration of CCR5+/CXCR3+ T cells to joints. The present study investigated the functional properties of TAK-779, including the effect of this antagonist on CXCR3 function. For this purpose, transfectants expressing mouse CCR5 (mCCR5) or mCXCR3 and expressing mCCR4 or mCXCR4 as controls were established by introducing each relevant gene into 2B4 T cells and were subjected to the following assays. First, the ligand binding to chemokine receptors was assayed by incubating transfectants with [125I]-labeled relevant ligand or with the unlabeled relevant ligand followed by staining with anti-ligand antibody. Second, chemokine-induced lymphocyte function-associated antigen-1 (LFA-1) activation was assayed by measuring the adhesion of cells to microculture plates coated with purified intercellular adhesion molecule-1. Third, chemokine-stimulated chemotaxis was assayed by observing the cell migration through transwells. In these assays, TAK-779 blocked the ligand binding as well as LFA-1 up-regulating and chemotactic function of mCXCR3 and mCCR5 but did not elicit a biologically significant inhibition of those functions of mCCR4 and mCXCR4. These observations indicate the unique target specificity of TAK-779 and explain why this antagonist efficiently blocks the migration of T cells expressing CCR5 and CXCR3 to sites of inflammation.