bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of polyunsaturated phosphatidyl‐choline on lipid transport system in alcoholic liver injury
Authors: CHIRKIN ALEXANDER A. , KONEVALOVA NATALYA YU. , GREBENNIKOV IGOR N. , KULIKOV VYACHESLAV A. , SARAEV YURY V. , BUKO VLADYMIR U. , CHIRKINA IRINA A. , DANCHENKO ELENA O. , GUNDERMANN KARL‐J.
Published: July 2002

The aim of this study was to determine whether serum lipid composition and lipolytic activities in alcoholinduced liver dystrophy were modified by the co‐administration of polyunsaturated phosphatidylcholine (PPC). Chronic alcohol intoxication was induced in rats by intragastric ethanol administration of 3.5 g/kg body weight per day over 56 days. Aqueous PPC suspension was given intragastrally in doses of 100 and 300 mg/kg body weight. Chronic alcohol intoxication led to the development of protein and lipid dystrophy of hepatocytes. PPC partially prevented alcoholic injury of the liver cells and had a normalizing effect on cholesterol esterification, lipolysis of lipoproteins and on the fatty acid composition of the main lipoprotein classes.
Wound Complications Following Resection of Adductor Compartment Tumours
Authors: Grainger Melvin F. , Grimer Robert J. , Carter Simon R. , Tillman Roger M.
Published: July 2002

Purpose Limb salvage surgery of soft tissue sarcomas is associated with both a risk of local recurrence and wound complications.
Although the lower limb appears to be at greater risk of wound‐related morbidity, few studies separate anatomical
compartments. We believe that the adductor compartment of the thigh has a particularly high rate of complications and so
performed a retrospective analysis of all soft tissue sarcomas arising in this region undergoing limb salvage.

Patients Patients with intermediate and high grade adductor compartment tumours were identified from our database and
the case notes were reviewed for patient, tumour, surgical and wound variables, identifying those with wound complications
both before and after discharge.

Results Of 49 patients who underwent limb salvage surgery, 22 (42.9%) developed complications. Twelve patients (24.5%)
required further surgery prior to wound healing and 10 patients had delays in post‐operative radiotherapy. There were significant
differences in the rates of preceding surgery, open biopsy performed at other centres and previous radiotherapy to this
region between the complicated and uncomplicated groups.

Discussion The management of these difficult tumours carries a high rate of wound complications and requires careful planning
prior to tissue biopsy. Open biopsies should be performed by the tumour surgeon to allow easy inclusion of this site in
the definitive procedure. In previously irradiated or operated limbs, alternative strategies for wound management may need
to be considered.
Real or Imaginary? Human Metabolism through Nuclear Magnetism
Authors: Ross Brian D.
Published: July 2002

This account of the beginnings and later applications of the use of nuclear magnetic resonance for noninvasive medical diagnosis was presented at a Symposium held in Oxford, UK, during September 13‐15, 2000 to mark the centenary of the birth of Hans Krebs, on August 25, 1900.
Transfer of Free Polymannose-type Oligosaccharides from the Cytosol to Lysosomes in Cultured Human Hepatocellular Carcinoma HEPG2 Cells
Authors: Saint-Pol Agnès , Bauvy Chantal , Codogno Patrice , Moore Stuart E.H.
Published: July 2002

Large, free polymannose oligosaccharides generated during glycoprotein biosynthesis rapidly appear in the cytosol of HepG2 cells where they undergo processing by a cytosolic endo H–like enzyme and a mannosidase to yield the linear isomer of Man5GlcNAc (Man[α1-2]Man[α1-2]Man[α1-3][Man α1-6]Man[β14]GlcNAc). Here we have examined the fate of these partially trimmed oligosaccharides in intact HepG2 cells. Subsequent to pulse–chase incubations with d-[2- 3H]mannose followed by permeabilization of cells with streptolysin O free oligosaccharides were isolated from the resulting cytosolic and membrane-bound compartments. Control pulse–chase experiments revealed that total cellular free oligosaccharides are lost from HepG2 cells with a half-life of 3–4 h. In contrast use of the vacuolar H+/ATPase inhibitor, concanamycin A, stabilized total cellular free oligosaccharides and enabled us to demonstrate a translocation of partially trimmed oligosaccharides from the cytosol into a membrane-bound compartment. This translocation process was unaffected by inhibitors of autophagy but inhibited if cells were treated with either 100 μM swainsonine, which provokes a cytosolic accumulation of large free oligosaccharides bearing 8-9 residues of mannose, or agents known to reduce cellular ATP levels which lead to the accumulation of the linear isomer of Man5GlcNAc in the cytosol. Subcellular fractionation studies on Percoll density gradients revealed that the cytosol-generated linear isomer of Man5GlcNAc is degraded in a membrane-bound compartment that cosediments with lysosomes.
A Three-dimensional Collagen Lattice Activates NF-κB in Human Fibroblasts: Role in Integrin α2 Gene Expression and Tissue Remodeling
Authors: Xu Jiahua , Zutter Mary M. , Santoro Samuel A. , Clark Richard A.F.
Published: July 2002

Normal adult human dermal fibroblasts grown in a three-dimensional collagen lattice increase mRNA level of collagen receptor integrin subunit α2 (Xu, J., and R.A.F. Clark. 1996. J. Cell Biol. 132:239– 249.) and DNA binding activity of a nuclear transcription factor, NF-κB (Xu, J., and R.A.F. Clark. 1997. J. Cell Biol. 136:473–483.). Here we present evidence that the collagen lattice induced the nuclear translocation of p50, one member of NF-κB family, and the degradation of an NF-κB inhibitor protein, IκB-α. The inhibition of NF-κB activity by SN50, a peptide inhibitor targeted at nuclear translocation of NF-κB, significantly reduced the induction of integrin α2 mRNA and protein by the collagen lattice. A region located between −549 and −351 bp in the promoter of integrin α2 gene conferred the inducibility by three-dimensional collagen lattice. The presence of either SN50 or IκB-α32, 36, a stable mutant of IκB-α, abrogated this inducibility, indicating that the activation of integrin α2 gene expression was possibly mediated by NF-κB through this region. Although there were three DNA–protein binding complexes forming in this region that are sensitive to the inhibition of NF-κB nuclear translocation, NF-κB was not directly present in the binding complexes. Therefore, an indirect regulatory mechanism by NF-κB in integrin α2 gene expression induced by three-dimensional collagen lattice is suggested. The involvement of NF-κB in reorganization and contraction of three-dimensional collagen lattice, a process that requires the presence of abundant integrin α2β1, was also examined. The inhibition of NF-κB activity by SN50 greatly blocked the contraction, suggesting its critical role in not only the induction of integrin α2 gene expression by three- dimensional collagen lattice, but also α2β1-mediated tissue-remodeling process.
Snarepins Are Functionally Resistant to Disruption by Nsf and αSNAP
Authors: Weber Thomas , Parlati Francesco , McNew James A. , Johnston Robert J. , Westermann Benedikt , Söllner Thomas H. , Rothman James E.
Published: July 2002

SNARE (SNAP [soluble NSF {N-ethylmaleimide–sensitive fusion protein} attachment protein] receptor) proteins are required for many fusion processes, and recent studies of isolated SNARE proteins reveal that they are inherently capable of fusing lipid bilayers. Cis-SNARE complexes (formed when vesicle SNAREs [v-SNAREs] and target membrane SNAREs [t-SNAREs] combine in the same membrane) are disrupted by the action of the abundant cytoplasmic ATPase NSF, which is necessary to maintain a supply of uncombined v- and t-SNAREs for fusion in cells. Fusion is mediated by these same SNARE proteins, forming trans-SNARE complexes between membranes. This raises an important question: why doesn't NSF disrupt these SNARE complexes as well, preventing fusion from occurring at all? Here, we report several lines of evidence that demonstrate that SNAREpins (trans-SNARE complexes) are in fact functionally resistant to NSF, and they become so at the moment they form and commit to fusion. This elegant design allows fusion to proceed locally in the face of an overall environment that massively favors SNARE disruption.
The Roles of Integrin-Linked Kinase in the Regulation of Myogenic Differentiation
Authors: Huang Yao , Li Ji , Zhang Yongjun , Wu Chuanyue
Published: July 2002

Myogenic differentiation is a highly orchestrated, multistep process that is coordinately regulated by growth factors and cell adhesion. We show here that integrin-linked kinase (ILK), an intracellular integrin– and PINCH-binding serine/threonine protein kinase, is an important regulator of myogenic differentiation. ILK is abundantly expressed in C2C12 myoblasts, both before and after induction of terminal myogenic differentiation. However, a noticeable amount of ILK in the Triton X-100–soluble cellular fractions is significantly reduced during terminal myogenic differentiation, suggesting that ILK is involved in cellular control of myogenic differentiation. To further investigate this, we have overexpressed the wild-type and mutant forms of ILK in C2C12 myoblasts. Overexpression of ILK in the myoblasts inhibited the expression of myogenic proteins (myogenin, MyoD, and myosin heavy chain) and the subsequent formation of multinucleated myotubes. Furthermore, mutations that eliminate either the PINCH-binding or the kinase activity of ILK abolished its ability to inhibit myogenic protein expression and allowed myotube formation. Although overexpression of the ILK mutants is permissive for the initiation of terminal myogenic differentiation, the myotubes derived from myoblasts overexpressing the ILK mutants frequently exhibited an abnormal morphology (giant myotubes containing clustered nuclei), suggesting that ILK functions not only in the initial decision making process, but also in later stages (fusion or maintaining myotube integrity) of myogenic differentiation. Additionally, we show that overexpression of ILK, but not that of the PINCH-binding defective or the kinase-deficient ILK mutants, prevents inactivation of MAP kinase, which is obligatory for the initiation of myogenic differentiation. Finally, inhibition of MAP kinase activation reversed the ILK-induced suppression of myogenic protein expression. Thus, ILK likely influences the initial decision making process of myogenic differentiation by regulation of MAP kinase activation.
The Cytokinesis Gene KEULE Encodes a Sec1 Protein That Binds the Syntaxin Knolle
Authors: Assaad Farhah F. , Huet Yoann , Mayer Ulrike , Jürgens Gerd
Published: July 2002

KEULE is required for cytokinesis in Arabidopsis thaliana. We have positionally cloned the KEULE gene and shown that it encodes a Sec1 protein. KEULE is expressed throughout the plant, yet appears enriched in dividing tissues. Cytokinesis-defective mutant sectors were observed in all somatic tissues upon transformation of wild-type plants with a KEULE–green fluorescent protein gene fusion, suggesting that KEULE is required not only during embryogenesis, but at all stages of the plant's life cycle. KEULE is characteristic of a Sec1 protein in that it appears to exist in two forms: soluble or peripherally associated with membranes. More importantly, KEULE binds the cytokinesis-specific syntaxin KNOLLE. Sec1 proteins are key regulators of vesicle trafficking, capable of integrating a large number of intra- and/or intercellular signals. As a cytokinesis-related Sec1 protein, KEULE appears to represent a novel link between cell cycle progression and the membrane fusion apparatus.
Laminin-1 redistributes postsynaptic proteins and requires rapsyn, tyrosine phosphorylation, and Src and Fyn to stably cluster acetylcholine receptors
Authors: Marangi P. Angelo , Wieland Simon T. , Fuhrer Christian
Published: July 2002

Clustering of acetylcholine receptors (AChRs) is a critical step in neuromuscular synaptogenesis, and is induced by agrin and laminin which are thought to act through different signaling mechanisms. We addressed whether laminin redistributes postsynaptic proteins and requires key elements of the agrin signaling pathway to cause AChR aggregation. In myotubes, laminin-1 rearranged dystroglycans and syntrophins into a laminin-like network, whereas inducing AChR-containing clusters of dystrobrevin, utrophin, and, to a marginal degree, MuSK. Laminin-1 also caused extensive coclustering of rapsyn and phosphotyrosine with AChRs, but none of these clusters were observed in rapsyn −/− myotubes. In parallel with clustering, laminin-1 induced tyrosine phosphorylation of AChR β and δ subunits. Staurosporine and herbimycin, inhibitors of tyrosine kinases, prevented laminin-induced AChR phosphorylation and AChR and phosphotyrosine clustering, and caused rapid dispersal of clusters previously induced by laminin-1. Finally, laminin-1 caused normal aggregation of AChRs and phosphotyrosine in myotubes lacking both Src and Fyn kinases, but these clusters dispersed rapidly after laminin withdrawal. Thus, laminin-1 redistributes postsynaptic proteins and, like agrin, requires tyrosine kinases for AChR phosphorylation and clustering, and rapsyn for AChR cluster formation, whereas cluster stabilization depends on Src and Fyn. Therefore, the laminin and agrin signaling pathways overlap intracellularly, which may be important for neuromuscular synapse formation.
Rho is Required for the Initiation of Calcium Signaling and Phagocytosis by Fcγ Receptors in Macrophages
Authors: Hackam David J. , Rotstein Ori D. , Schreiber Alan , Zhang Wei-jian , Grinstein Sergio
Published: July 2002

Phagocytosis of bacteria by macrophages and neutrophils is an essential component of host defense against infection. The mechanism whereby the interaction of opsonized particles with Fcγ receptors triggers the engulfment of opsonized particles remains incompletely understood, although activation of tyrosine kinases has been recognized as an early step. Recent studies in other systems have demonstrated that tyrosine kinases can in turn signal the activation of small GTPases of the ras superfamily. We therefore investigated the possible role of Rho in Fc receptor–mediated phagocytosis. To this end we microinjected J774 macrophages with C3 exotoxin from Clostridium botulinum, which ADP-ribosylates and inactivates Rho. C3 exotoxin induced the retraction of filopodia, the disappearance of focal complexes, and a global decrease in the F-actin content of J774 cells. In addition, these cells exhibited increased spreading and the formation of vacuolar structures. Importantly, inactivation of Rho resulted in the complete abrogation of phagocytosis. Inhibition of Fcγ receptor–mediated phagocytosis by C3 exotoxin was confirmed in COS cells, which become phagocytic upon transfection of the FcγRIIA receptor. Rho was found to be essential for the accumulation of phosphotyrosine and of F-actin around phagocytic cups and for Fcγ receptor–mediated Ca2+ signaling. The clustering of receptors in response to opsonin, an essential step in Fcγ-induced signaling, was the earliest event shown to be inhibited by C3 exotoxin. The effect of the toxin was specific, since clustering and internalization of transferrin receptors were unaffected by microinjection of C3. These data identify a role for small GTPases in Fcγ receptor–mediated phagocytosis by leukocytes.
Tolerization of Anti–Galα1-3Gal Natural Antibody–forming B Cells by Induction of Mixed Chimerism
Authors: Yang Yong-Guang , deGoma Emil , Ohdan Hideki , Bracy Jennifer L. , Xu Yuanxin , Iacomini John , Thall Aron D. , Sykes Megan
Published: July 2002

Xenotransplantation could overcome the severe shortage of allogeneic organs, a major factor limiting organ transplantation. Unfortunately, transplantation of organs from pigs, the most suitable potential donor species, results in hyperacute rejection in primate recipients, due to the presence of anti–Galα1-3Gal (Gal) natural antibodies (NAbs) in their sera. We evaluated the ability to tolerize anti-Gal NAb–producing B cells in α1,3-galactosyltransferase knockout (GalT KO) mice using bone marrow transplantation (BMT) from GalT+/+ wild-type (WT) mice. Lasting mixed chimerism was achieved in KO mice by cotransplantation of GalT KO and WT marrow after lethal irradiation. The levels of anti-Gal NAb in sera of mixed chimeras were reduced markedly 2 wk after BMT, and became undetectable at later time points. Immunization with Gal+/+ xenogeneic cells failed to stimulate anti-Gal antibody production in mixed chimeras, whereas the production of non–Gal-specific antixenoantigen antibodies was stimulated. An absence of anti-Gal–producing B cells was demonstrated by enzyme-linked immunospot assays in mixed KO+WT→ KO chimeras. Thus, mixed chimerism efficiently induces anti-Gal–specific B cell tolerance in addition to T cell tolerance, providing a single approach to overcoming both the humoral and the cellular immune barriers to discordant xenotransplantation.
Evidence That the Autoimmune Antigen Myelin Basic Protein (MBP) Ac1-9 Binds Towards One End of the Major Histocompatibility Complex (MHC) Cleft
Authors: Lee Christopher , Liang Michael N. , Tate Keri M. , Rabinowitz Joshua D. , Beeson Craig , Jones Patricia P. , McConnell Harden M.
Published: July 2002

The NH2-terminal peptide of myelin basic protein (MBP) bound to the class II major histocompatibility complex (MHC) protein I-Au is an immunodominant epitope in experimental autoimmune encephalomyelitis, a murine model of multiple sclerosis. However, the MBP–I-Au complex is very unstable. To investigate this, we performed site-directed mutagenesis of the I-Au MHC protein and the MBP peptide. Biochemical, T cell activation, and molecular modeling studies of mutant complexes demonstrate that the MBP peptide's key residue for MHC binding, lysine 4, is buried in the P6 pocket of I-Au, which is predominantly hydrophobic. This implies that the MBP–I-Au complex differs from more stable complexes in two respects: (a) the peptide leaves the NH2-terminal region of the MHC peptide-binding cleft unoccupied; (b) the peptide is not anchored by typical favorable interactions between peptide side chains and MHC pockets. To test these hypotheses, a modified MBP peptide was designed based on molecular modeling, with the aim of producing strong I-Au binding. Extension of the NH2 terminus of MBP with six amino acids from the ova peptide, and replacement of the lysine side chain in the P6 pocket with an aromatic anchor, results in >1,000-fold increased binding stability. These results provide an explanation for the unusual peptide–MHC-binding kinetics of MBP, and should facilitate an understanding of why mice are not tolerant to this self-peptide– MHC complex.
Anergy and Cytokine-Mediated Suppression as Distinct Superantigen-Induced Tolerance Mechanisms in Vivo
Authors: Miller Carla , Ragheb Jack A. , Schwartz Ronald H.
Published: July 2002

Recombinant-activating gene 2 (RAG-2−/−) T cell receptor–transgenic mice repeatedly injected with the superantigen staphylococcal enterotoxin A entered a tolerant state in which splenic CD4+ T cells produced little interleukin (IL)-2, interferon γ, or IL-4. This state resulted from a combination of both clonal anergy and cytokine-mediated immunosuppression. The anergy persisted for at least 3 wk and could be distinguished from the suppression by a decrease in IL-2 production per cell, a block in the activation of early response kinases, and a failure to be reversed with anti–transforming growth factor (TGF)-β. Full suppression lasted for only 1 wk and involved both IL-10 and TGF-β, but required additional unknown molecules for optimal effect. These experiments show that complex in vivo interactions of multiple peripheral tolerance mechanisms can now be dissected at both the cellular and molecular levels.
Self-Renewal of Multipotent Long-Term Repopulating Hematopoietic Stem Cells Is Negatively Regulated by FAS and Tumor Necrosis Factor Receptor Activation
Authors: Bryder David , Ramsfjell Veslemøy , Dybedal Ingunn , Theilgaard-Mönch Kim , Högerkorp Carl-Magnus , Adolfsson Jörgen , Borge Ole Johan , Jacobsen Sten Eirik W.
Published: July 2002

Multipotent self-renewing hematopoietic stem cells (HSCs) are responsible for reconstitution of all blood cell lineages. Whereas growth stimulatory cytokines have been demonstrated to promote HSC self-renewal, the potential role of negative regulators remains elusive. Receptors for tumor necrosis factor (TNF) and Fas ligand have been implicated as regulators of steady-state hematopoiesis, and if overexpressed mediate bone marrow failure. However, it has been proposed that hematopoietic progenitors rather than stem cells might be targeted by Fas activation. Here, murine Lin−Sca1+c-kit+ stem cells revealed little or no constitutive expression of Fas and failed to respond to an agonistic anti-Fas antibody. However, if induced to undergo self-renewal in the presence of TNF-α, the entire short and long-term repopulating HSC pool acquired Fas expression at high levels and concomitant activation of Fas suppressed in vitro growth of Lin−Sca1+c-kit+ cells cultured at the single cell level. Moreover, Lin−Sca1+c-kit+ stem cells undergoing self-renewal divisions in vitro were severely and irreversibly compromised in their short- and long-term multilineage reconstituting ability if activated by TNF-α or through Fas, providing the first evidence for negative regulators of HSC self-renewal.
Estimating the number of asymptotic degrees of freedom for nonlinear dissipative systems
Authors: Cockburn Bernardo , Jones Don , Titi Edriss
Published: July 2002

We show that the long-time behavior of the projection of the exact solutions to the Navier-Stokes equations and other dissipative evolution equations on the finite-dimensional space of interpolant polynomials determines the long-time behavior of the solution itself provided that the spatial mesh is fine enough. We also provide an explicit estimate on the size of the mesh. Moreover, we show that if the evolution equation has an inertial manifold, then the dynamics of the evolution equation is equivalent to the dynamics of the projection of the solutions on the finite-dimensional space spanned by the approximating polynomials. Our results suggest that certain numerical schemes may capture the essential dynamics of the underlying evolution equation.
Estimating the significance of sequence order in protein
secondary structure and prediction
Authors: Park Jong , Dietmann Sabine , Heger Andreas , Holm Liisa
Published: July 2002

Motivation: How critical is the sequence order information in predicting protein secondary structure segments? We tried to get a rough insight on it from a theoretical approach using both a prediction algorithm and structural fragments from Protein Databank (PDB).

Results: Using reverse protein sequences and PDB structural fragments, we theoretically estimated the significance of the order for protein secondary structure and prediction. On average: (1) 79% of protein sequence segments resulted in the same prediction in both normal and reverse directions, which indicated a relatively high conservation of secondary structure propensity in the reverse direction; (2) the reversed sequence prediction alone performed less accurately than the normal forward sequence prediction, but comparably high (2% difference); (3) the commonly predicted regions showed a slightly higher prediction accuracy (4%) than the normal sequences prediction; and (4) structural fragments which have counterparts in reverse direction in the same protein showed a comparable degree of secondary structure conservation (73% identity with reversed structures on average for pentamers).

Contact: jong@biosophy.org; dietmann@ebi.ac.uk; heger@ebi.ac.uk; holm@ebi.ac.uk

*** Present address: EBI, Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. To whom correspondence should be addressed.
EDIBLE: experimental design and information calculations in
phylogenetics
Authors: Massingham T. , Goldman N.
Published: July 2002

*Present address: University Museum of Zoology, Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK.

Summary: Although evolutionary inference from molecular sequences is a statistical problem, little attention has been paid to questions of experimental design. A computer program, EDIBLE, has been developed to perform likelihood calculations based on Markov process models of nucleotide substitution allied with phylogenetic trees, and from these to compute Fisher information measures under different experimental designs. These calculations can be used to answer questions of optimal experimental design in molecular phylogenetics.

Availability: Source code (ANSI C), executables and documentation for EDIBLE are available from http://ng-dec1.gen.cam.ac.uk/info/index.htmland ‘downstream’ Web pages.

Contact: N.Goldman@gen.cam.ac.uk
Prediction of genetic structure in eukaryotic DNA using
reference point logistic regression and sequence alignment
Authors: Hooper Peter M. , Zhang Haiyan , Wishart David S.
Published: July 2002

* To whom correspondence should be addressed.

Motivation: Current software tools are moderately effective in predicting genetic structure (exons, introns, intergenic regions, and complete genes) from raw DNA sequence data. Improvements in accuracy and speed are needed to deal with the increasing volume of data from large scale sequencing projects.

Results: We present a two-stage computer program to predict genetic structure in eukaryotic DNA. The first stage makes use of a novel statistical technique, called reference point logistic (RPL) regression, to calculate scores for potential functional sites. These site scores are combined with interval content, length, and state scores, via a Generalized Hidden Markov Model, to determine a combined score for each possible parse of a given DNA sequence into exons, introns, and intergenic regions. An optimal parse is found using a dynamic programming algorithm. In the second stage, protein sequence alignment methods are applied to improve the accuracy of the initial parse. Computation in the first stage of the program is very fast (1 s on a 360 MHz CPU for a 16 kb sequence) and its predictive accuracy typically matches or exceeds the best results reported for other methods (Sensitivity = 0.93 and Specificity = 0.93 for the Burset/Guigótest set). Computation in the second stage is slower, but the final predictions are more accurate (Sn = 0.97, Sp = 0.97). The program (called GRPL) can handle partial, single, and multi-gene sequences. The program is also capable of predicting the genetic structure of vertebrate, invertebrate, and plant DNA with nearly equal accuracy. Statistical techniques have also been introduced to model the effects of varying C+G content in a continuous manner and to control overfitting of parameters for smaller training sets.

Availability: An academic implementation of GRPL, compiled for SUN workstations, is available by anonymous ftp from snipe.pharmacy.ualberta.ca/pub. The training and test sets used in this work, together with supplementary material, can be found at the same location. A commercial implementation is available as a component of GeneTool (BioTools Inc., http://biotools.com).

Contact: hooper@stat.ualberta.ca
RadCon: phylogenetic tree comparison and consensus
Authors: Thorley Joseph L. , Page Roderic D. M.
Published: July 2002

* To whom correspondence should be addressed.

Summary: RadCon is a Macintosh® program for manipulating and analysing phylogenetic trees. The program can determine the Cladistic Information Content of individual trees, the stability of leaves across a set of bootstrap trees, produce the strict basic Reduced Cladistic Consensus profile of a set of trees and convert a set of trees into its matrix representation for supertree construction.

Availability: The program is free and available at http://taxonomy.zoology.gla.ac.uk/~jthorley/radcon/radcon.html.

Contact: j.l.thorley@bris.ac.uk
A cross-comparison of a large dataset of genes
Authors: Cannarozzi G. , Hallett M. T. , Norberg J. , Zhou X.
Published: July 2002

Summary: We make available a large cross-comparison for 16 of the completely sequenced genomes and additional eukaryotic genes. The alignments were performed at the protein level using liberal similarity bounds in order to capture as many significant alignments as possible. This dataset will be updated as new genomes become available.

Availability: The dataset is accessible at http://cbrg.inf.ethz.ch/AllAllGeneAlign.html

Contact: hallett@inf.ethz.ch

* To whom correspondence should be addressed.
EASY—an Expert Analysis SYstem for interpreting database
search outputs
Authors: Selley J. N. , Swift J. , Attwood T. K.
Published: July 2002

Summary: With the ever-increasing need to handle large volumes of sequence data efficiently and reliably, we have developed the EASY system for performing combined protein sequence and pattern database searches. EASY runs searches simultaneously and distils results into a concise 1-line diagnosis. By bringing together results of several different analyses, EASY provides a rapid means of evaluating biological significance, minimising the risk of inferring false relationships, for example from relying exclusively on top BLAST hits. The program has been tested using a variety of protein families and was instrumental in resolving family assignments in a major update of the PRINTS database.

Availability: http://www.bioinf.man.ac.uk/dbbrowser/easy/

Contact: selley@bioinf.man.ac.uk

* To whom correspondence should be addressed.
Detection of conserved physico-chemical characteristics of
proteins by analyzing clusters of positions with co-ordinated
substitutions
Authors: Afonnikov D. A. , Oshchepkov D. Yu. , Kolchanov N. A.
Published: July 2002

Motivation: It is known that the physico-chemical characteristics of proteins underlying specific folding of the polypeptide chain and the protein function are evolutionary conserved. Detection of such characteristics while analyzing homologous sequences would expand essentially the knowledge on protein function, structure, and evolution. These characteristics are maintained constant, in particular, by co-ordinated substitutions. In this process, the destabilizing effect of a substitution may be compensated by another substitution at a different position within the same protein, making the overall change in this protein characteristic insignificant. Consequently, the patterns of co-ordinated substitutions contain important information on conserved physico-chemical properties of proteins, requiring their investigation and development of the corresponding methods and software for correlation analysis of protein sequences available to a wide range of users.

Results: A software package for analyzing correlated amino acid substitutions at different positions within aligned protein sequences was developed. The approach implies searching for evolutionary conserved physico-chemical characteristics of proteins based on the information on the pairwise correlations of amino acid substitutions at different protein positions. The software was applied to analyze DNA-binding domains of the homeodomain class. As a result, two conservative physico-chemical characteristics preserved due to the co-ordinated substitutions at certain groups of positions in the protein sequence. Possible functional roles of these characteristics are discussed.

Availability: The program package is available at http://wwwmgs.bionet.nsc.ru/programs/CRASP/

Contact: ada@bionet.nsc.ru

* To whom correspondence should be addressed.
Taxonomy workbench
Authors: Wildpaner Michael , Schneider Georg , Schleiffer Alexander , Eisenhaber Frank
Published: July 2002

Summary: At advanced stages of working with user-defined protein and gene sequence collections, it is frequently necessary to link these data to the taxonomic tree and to extract subsets in accordance with taxonomic considerations. Since no general automatic tools had been available, this was a tedious manual effort. Our taxonomy workbench allows processing of sequence sets, mapping of these sets onto the taxonomic tree, collection of taxonomic subsets from them and printing of the whole tree or some part of it. As a side effect, the system enables queries to and navigation within the taxonomy database.

Availability: An implementation of the taxonomy workbench is accessible for public use as a www-service at http://mendel.imp.univie.ac.at/taxonomy/. Software components for the command-line and for the www-version are available on request.

Contact: Georg.Schneider@nt.imp.univie.ac.at; Frank.Eisenhaber@nt.imp.univie.ac.at

Supplementary information: Documentation for the taxonomy workbench can be accessed at http://mendel.imp.univie.ac.at/taxonomy/help.html.

* To whom correspondence should be addressed.
ToolShop: prerelease inspections for protein structure
prediction servers
Authors: Rychlewski Leszek
Published: July 2002

Summary: The ToolShop server offers a possibility to compare a protein tertiary structure prediction server with other popular servers before releasing it to the public. The comparison is conducted on a set of 203 proteins and the collected models are compared with over 20 other programs using various assessment procedures. The evaluation lasts ca one week.

Availability: The ToolShop server is available at http://BioInfo.PL/ToolShop/. The administrator should be contacted to couple the tested server to the evaluation suite.

Contact: leszek@bioinfo.pl

Supplementary information: The evaluation procedures are similar to those implemented in the continuous online server evaluation program, LiveBench. Additional information is available from its homepage (http://BioInfo.PL/LiveBench/).
MutaProt: a web interface for structural analysis of point

mutations
Authors: Eyal Eran , Najmanovich Rafael , Sobolev Vladimir , Edelman Marvin
Published: July 2002

Summary: A web-based tool, termed ‘MutaProt’, is described which analyses pairs of PDB files whose members differ in one, or two, amino acids. MutaProt examines the micro environment surrounding the exchanged residue(s) and can be searched by specifying a PDB ID, keywords, or any pair of amino acids. Detailed information about accessibility of the exchanged residue(s) and its atomic contacts are provided based on CSU software (Sobolev et al. , Bioinformatics , 15, 327–332, 1999). An interactive 3D presentation of the superimposed regions around the mutation(s) is included. MutaProt is updated weekly.

Availability: http://www.bioinfo.weizmann.ac.il/MutaProt

Contact: eran.eyal@weizmann.ac.il

* To whom correspondence should be addressed.
Mixture modelling of gene expression data from microarray
experiments
Authors: Ghosh Debashis , Chinnaiyan Arul M.
Published: July 2002

Motivation: Hierarchical clustering is one of the major analytical tools for gene expression data from microarray experiments. A major problem in the interpretation of the output from these procedures is assessing the reliability of the clustering results. We address this issue by developing a mixture model-based approach for the analysis of microarray data. Within this framework, we present novel algorithms for clustering genes and samples. One of the byproducts of our method is a probabilistic measure for the number of true clusters in the data.

Results: The proposed methods are illustrated by application to microarray datasets from two cancer studies; one in which malignant melanoma is profiled (Bittner et al. , Nature , 406, 536–540, 2000), and the other in which prostate cancer is profiled (Dhanasekaran et al. , 2001, submitted).

Availability: Macros written in the R language implementing the methods in this report can be obtained at the first author’s website: http://www.sph.umich.edu/~ghoshd/COMPBIO/mixture1/index.html.

Contact: ghoshd@umich.edu
D-ASSIRC: distributed program for finding sequence similarities
in genomes
Authors: Vincens Pierre , Badel-Chagnon Anne , André Cécile , Hazout Serge
Published: July 2002

Motivation: Locating the regions of similarity in a genome requires the availability of appropriate tools such as ‘Accelerated Search for SImilar Regions in Chromosomes’ (assirc; Vincens et al. , Bioinformatics , 14, 715–725, 1998). The aim of this paper is to present different strategies for improving this program by distributing the operations and data to multiple processing units and to assess the efficiency of the different implementations in terms of running time as a function of the number of processing units.

Results: The new version d-assircis based on three alternative strategies of task sharing: (1) a distributed search using the splitting of studied sequences into large overlapping subsequences (strategy ass); (2) two distributed searches for repeated exact motifs of fixed size either managed by a central processor (strategy agd) or locally managed by numerous processors (strategy ald). The result is that the strategy assis suitable for a large number of processing units (the time was divided by a factor of 12 when the number of processing units was increased from 1 to 16) wheras the strategy aldis better for a small set of processors (typically for four or six).The different proposed strategies are efficient for various applications in genomic research, particularly for locating similarities of nucleic sequences in large genomes.

Availability: d-assircis freely available by anonymous FTP at ftp://ftp.ens.fr/pub/molbio/dassirc.tar.gz. Sources and binaries for Solaris and Linux are included in the distribution.

Contact: vincens@biologie.ens.fr

* To whom correspondence should be addressed.
The p53 tumour suppressor inhibits glucocorticoid‐induced proliferation of erythroid progenitors
Authors: Ganguli Gitali , Back Jonathan , Sengupta Sagar , Wasylyk Bohdan
Published: July 2002

Hypoxia encountered at high altitude, blood loss and erythroleukemia instigate stress erythropoiesis, which involves glucocorticoid‐induced proliferation of erythroid progenitors (ebls). The tumour suppressor p53 stimulates hematopoietic cell maturation and antagonizes glucocorticoid receptor (GR) activity in hypoxia, suggesting that it may inhibit stress erythropoiesis. We report that mouse fetal liver ebls that lack p53 proliferate better than wild‐type cells in the presence of the GR agonist dexamethasone. An important mediator of GR‐induced ebl self‐renewal, the c‐myb gene, is induced to higher levels in p53−/− ebls by dexamethasone. The stress response to anemia is faster in the spleens of p53−/− mice, as shown by the higher levels of colony forming units erythroids and the increase in the CD34/c‐kit double positive population. Our results show that p53 antagonizes GR‐mediated ebl expansion and demonstrate for the first time that p53–GR cross‐talk is important in a physiological process in vivo: stress erythropoiesis.
In-vitro activity of moxifloxacin against fluoroquinolone-resistant strains of aerobic Gram-negative bacilli and Enterococcus faecalis
Authors: Tankovic Jacques , Bachoual Rafik , Ouabdesselam Saliha , Boudjadja Azzedine , Soussy Claude-James
Published: July 2002

MICs of the new fluoroquinolone, moxifloxacin, and those of ciprofloxacin, ofloxacin and sparfloxacin for 19 genetically characterized fluoroquinolone-resistant strains were determined by the agar dilution method. The MICs of moxifloxacin for Escherichia isolates with one mutation in gyrA (corresponding to Ser83→Leu or Asp87→Gly substitution) were 0.25–0.5 mg/L, while those of ciprofloxacin, ofloxacin and sparfloxacin were 0.06–0.25, 1 and 0.12–0.5 mg/L, respectively. These values were four- to 16-fold higher than those of the same antibiotics for the wild-type strain, E. coli KL16. Similar results were observed with clinical isolates of Salmonella spp. harbouring one mutation in gyrA leading to the substitution of Ser83 by Phe or Tyr. In the presence of two mutations in the E. coligyrA gene, the MICs of moxifloxacin ciprofloxacin, ofloxacin and sparfloxacin were 2, 0.5, 4 and 1 mg/L, respectively; these were 32 times higher than the MICs of these agents for E. coli KL16. The MICs of the four quinolones for triple mutants with two mutations in gyrA and one in parC were even higher, i.e. 8, 8, 16 and 8–16 mg/L, respectively. The MICs of moxifloxacin for Campylobacter coli and Campylobacter jejuni strains with a gyrA mutation leading to Thr86→Ile substitution ranged from 1 to 2 mg/L, while the MICs of ciprofloxacin, ofloxacin and sparfloxacin were 16–32 mg/L, 8–16 and 4–8 mg/L, respectively. For high-level ciprofloxacin-resistant (MICs of 32 mg/L) clinical isolates of Enterococcus faecalis with one substitution at position 83 in GyrA (E. coli coordinates), the MICs of moxifloxacin, ofloxacin and sparfloxacin were 8–16, ≥128 and 32 mg/L respectively. In conclusion, moxifloxacin and other fluoroquinolones exhibit cross-resistance against aerobic Gram-negative bacilli and enterococci. The in-vitro activity of moxifloxacin was greater than that of ofloxacin and slightly less than that of ciprofloxacin and sparfloxacin against Enterobacteriaceae, but greater than those of the three other compounds tested against Campylobacter spp and E. faecalis.
Safety, efficacy and effectiveness of cold-adapted, live, attenuated, trivalent, intranasal influenza vaccine in adults and children
Authors: Belshe Robert B. , Gruber William C.
Published: July 2002

Studies in children and adults revealed cold–adapted, live, attenuated, trivalent, intranasal influenza vaccine (CAIV–T) to be well accepted, well tolerated and highly protective against culture–confirmed influenza, and to provide significant health benefits. A 2 year, multicentre, double–blind, placebo–controlled efficacy field trial of CAIV–T in children aged 15–71 months with annual re–immunization revealed the vaccine to be highly protective against culture–confirmed influenza. Vaccine induced serum and secretory antibodies in vaccinated children. Overall, during 2 years of study, vaccine was 92% protective against culture–confirmed influenza. During the second year of study the vaccine was 86% protective against influenza A/Sydney/5/97–like virus, a significantly drifted strain not well matched to the vaccine. Antibody studies on children given CAIV–T revealed that high titres of cross–reacting antibodies to influenza A/Sydney/5/97 were induced with vaccination by live attenuated influenza A/Wuhan/359/95–like vaccine. Effectiveness measures revealed significant reductions in febrile illness (21% reduction in year 1, 19% reduction in year 2), febrile otitis media (33% reduction in year 1, 16% reduction in year 2) and associated antibiotic use among vaccinated children compared with placebo recipients. In adults, vaccination with CAIV–T resulted in protection during experimental challenge with virulent wild–type viruses. An effectiveness trial in adults demonstrated significant benefits of CAIV–T vaccine (28% reduction in days of missed work for febrile upper respiratory illness days with associated 45% reduction in days taking antibiotics). General use of CAIV–T has the potential to significantly reduce the impact of influenza in children and adults.
Electron pencil‐beam redefinition algorithm dose calculations in the presence of heterogeneities
Authors: Boyd Robert A. , Hogstrom Kenneth R. , Starkschall George
Published: July 2002

The electron pencil‐beam redefinition algorithm (PBRA) is currently being refined and evaluated for clinical use. The purpose of this work was to evaluate the accuracy of PBRA‐calculated dose in the presence of heterogeneities and to benchmark PBRA dose accuracy for future improvements to the algorithm. The PBRA was evaluated using a measured electron beam dose algorithm verification data set developed at The University of Texas M. D. Anderson Cancer Center. The data set consists of measurements made using 9 and 20 MeV beams in a water phantom with air gaps, internal air and bone heterogeneities, and irregular surfaces. Refinements to the PBRA have enhanced the speed of the dose calculations by a factor of approximately 7 compared to speeds previously reported in published data; a 20 MeV, field electron‐beam dose distribution took approximately 10 minutes to calculate. The PBRA showed better than 4% accuracy in most experiments. However, experiments involving the low‐energy (9 MeV) electron beam and irregular surfaces showed dose differences as great as 22%, in albeit a small fractional region. The geometries used in this study, particularly those in the irregular surface experiments, were extreme in the sense that they are not seen clinically. A more appropriate clinical evaluation in the future will involve comparisons to Monte Carlo generated patient dose distributions using actual computed tomography scan data. The present data also serve as a benchmark against which future enhancements to the PBRA can be evaluated.
A stereotactic radiation therapy device for retinoblastoma using a noncircular collimator and intensity filter
Authors: Cormack R. A. , Kooy H. M. , Bellerive M. R. , Loeffler J. S. , Petersen R. A. , Tarbell N. J.
Published: July 2002

The proximity of the lens to the retina makes the treatment of retinoblastoma a challenge for external beam radiation therapy. The ∼1 mm separation between the posterior edge of the lens and the anterior region of the retina causes a trade‐off between coverage of the entire retina and excessive dose to the lens. A stereotactic, LINAC based, lens sparing technique for treating retinoblastoma is presented. The technique uses noncoplanar arcs with the lens at isocenter. A special noncircular collimator blocks the lens but it also causes the dose distribution to vary across the retina. A fluence modulation filter is used to reduce the dose inhomogeneity across the target. The resulting dose distribution is roughly hemispheric, providing both anterior coverage of the retina and lens blocking unlike conventional techniques. The method used to develop the collimator and filter assembly is presented. Dosimetry of the assembly was carried out using radiochromic film, and the results were entered in a treatment planning system. The dose distribution as measured in a phantom is provided and compared to calculations.
High temporal resolution for multislice helical computed tomography
Authors: Taguchi Katsuyuki , Anno Hirofumi
Published: July 2002

Multislice helical computed tomography (CT) substantially reduces scanning time. However, the temporal resolution of individual images is still insufficient for imaging rapidly moving organs such as the heart and adjacent pulmonary vessels. It may, in some cases, be worse than with current single‐slice helical CT. The purpose of this study is to describe a novel image reconstruction algorithm to improve temporal resolution in multislice helical CT, and to evaluate its performance against existing algorithms. The proposed image reconstruction algorithm uses helical interpolation followed by data weighting based on the acquisition time. The temporal resolution, the longitudinal (z‐axis) spatial resolution, the image noise, and the in‐plane image artifacts created by a moving phantom were compared with those from the basic multislice helical reconstruction (helical filter interpolation, HFI) algorithm and the basic single‐slice helical reconstruction algorithm (180° linear interpolation, 180LI) using computer simulations. Computer simulation results were verified with CT examinations of the heart and lung vasculature using a 0.5 second multislice scanner. The temporal resolution of HFI algorithm varies from 0.28 and 0.86 s, depending on helical pitch. The proposed method improves the resolution to a constant value of 0.29 s, independent of pitch, allowing moving objects to be imaged with reduced blurring or motion artifacts. The spatial (z) resolution was slightly worse than with the HFI algorithm; the image noise was worse than with the HFI algorithm but was comparable to axial (step‐and‐shoot) CT. The proposed method provided sharp images of the moving objects, portraying the anatomy accurately. The proposed algorithm for multislice helical CT allowed us to obtain CT images with high temporal resolution. It may improve the image quality of clinical cardiac, lung, and vascular CT imaging.