bluuebunny/crossref_metadata_2025_split huggingface dataset:
SCA db: spinocerebellar ataxia candidate gene database
Authors: Liu Y.-F. , Yang U.-C. 
Published: June 2004

Abstract
Summary: The positional candidate gene approach accelerates the discovery of genes involved in disease. However, the properties of such disease genes are very diverse and the sample size of known disease genes is too small and does not warrant success by the use of a machine-learning approach. A user-defined scoring system may thus help to determine the priority of candidate genes. Spinocerebellar ataxia (SCA) is a good model to test this approach because most SCA subtypes are caused by an expansion of short tandem repeats (STRs). The SCA db is a candidate gene database for SCA, which collected 3185 genes for 17 types of SCA. Those SCA subtypes that have known disease genes can be used as positive controls to optimize the parameters. The users may browse the candidate genes of a given SCA subtype by using the default parameters. The known disease genes were found to be the top three candidates using the default parameters. Alternatively, the users may score the candidate genes by changing the weight or the scores on the basis of their own working hypothesis.
Availability: This database is available at http://ymbc.ym.edu.tw/sca/.
POINT: a database for the prediction of protein–protein interactions based on the orthologous interactome
Authors: Huang Tao-Wei , Tien An-Chi , Huang Wen-Shien , Lee Yuan-Chii G. , Peng Chin-Lin , Tseng Huei-Hun , Kao Cheng-Yan , Huang Chi-Ying F. 
Published: June 2004

Abstract
Summary: One possible path towards understanding the biological function of a target protein is through the discovery of how it interfaces within protein–protein interaction networks. The goal of this study was to create a virtual protein–protein interaction model using the concepts of orthologous conservation (or interologs) to elucidate the interacting networks of a particular target protein. POINT (the prediction of interactome database) is a functional database for the prediction of the human protein–protein interactome based on available orthologous interactome datasets. POINT integrates several publicly accessible databases, with emphasis placed on the extraction of a large quantity of mouse, fruit fly, worm and yeast protein–protein interactions datasets from the Database of Interacting Proteins (DIP), followed by conversion of them into a predicted human interactome. In addition, protein–protein interactions require both temporal synchronicity and precise spatial proximity. POINT therefore also incorporates correlated mRNA expression clusters obtained from cell cycle microarray databases and subcellular localization from Gene Ontology to further pinpoint the likelihood of biological relevance of each predicted interacting sets of protein partners.
Availability: POINT can be freely accessed at http://insilico.csie.ntu.edu.tw:9999/point/.
HumanMSD and MouseMSD: generating genetic maps for human and murine microsatellite markers
Authors: Bahlo M. , Xing L. , Wilkinson C. R. 
Published: June 2004

Abstract
Summary: We present two Web interfaces that generate genetic maps for given sets of human or mouse microsatellite markers. The genetic maps are generated from available databases using linear interpolation of physical map distances to infer genetic map positions for missing markers in these databases.
Availability: http://bioinf.wehi.edu.au/software/MarkerSearch
Supplementary information: http://bioinf.wehi.edu.au/genetics/index.html (further information about microsatellite markers and linkage mapping). http://bioinf.wehi.edu.au/software/MarkerSearch/estimateresult.txt (list of chosen markers with percentage errors for the different bins).
Genetic loci that control the angiogenic response to basic response to basic fibroblast growth factor
Authors: Rogers Michael S. , Rohan Richard M. , Birsner Amy E. , D'amato Robert J. 
Published: June 2004

ABSTRACTAngiogenesis is controlled by a balance between stimulatory growth factors and endogenous inhibitors. We propose that the balance of stimulators and inhibitors, as well as the general sensitivity of the endothelium to these factors, varies from individual to individual. Indeed, we have found that individual mouse strains have dramatically different responses to growth factor‐induced neovascularization. Quantitative trait loci (QTLs), which influence the extent of angiogenesis induced by vascular endothelial growth factor (VEGF), were previously identified by our laboratory. Since genetic susceptibility may vary according to the angiogenic stimulator, we have undertaken a similar mapping approach to identify QTLs that influence basic fibroblast growth factor (FGF2) induced neovascularization in the BXD series of recombinant inbred mouse strains. Composite and multiple interval mapping identified areas of chromosomes 4, 13, 15, and 18. These new angiogenesis QTLs, named AngFq1 through AngFq4 (for angiogenesis due to FGF2), are different from previously identified VEGF QTLs. The mapped regions contain several genes involved in the angiogenic process including matrix metalloproteinase 16, eph receptor A7, angiopoetin 1, endothelial lipase, and autotaxin. Differences in these regions may influence individual susceptibility to angiogenesis related diseases such as cancer, macular degeneration, atherosclerosis, and arthritis.—Rogers, M. S., Rohan, R. M., D'Amato, R. J. Genetic loci that control the angiogenic response to basic fibroblast growth factor. FASEB J. 18, 1050–1059 (2004)
Caveolae compartmentalization of heme oxygenase‐1 in endothelial cells
Authors: Kim Hong Pyo , Wang Xue , Galbiati Ferruccio , Ryter Stefan W. , Choi Augustine M. K. 
Published: June 2004

ABSTRACTThe heme oxygenase (HO) and nitric oxide synthase (NOS) enzymes generate the gaseous signaling molecules carbon monoxide (CO) and nitric oxide, respectively. Constitutive NOSs localize to caveolae, and their activities are modulated by caveo‐ lin‐1. Nothing is known of the localization of the inducible heme oxygenase‐1 (HO‐1) in plasma mem‐ brane caveolae. Thus, we examined the distribution and subcellular localization of HO‐1, biliverdin reduc‐ tase (BVR), and NADPH:cytochrome P450 reductase (NPR) in pulmonary artery endothelial cells. Each of these proteins localized in part to plasma membrane caveolae in endothelial cells. Inducers of HO‐1 or overexpression of HO‐1 increased the content of this protein in a detergent‐resistant fraction containing caveolin‐1. Inducible HO activity appeared in plasma membrane, cytosol, and isolated caveolae. In addition, caveolae contained endogenous BVR activity, supporting the same compartmentalization of both enzymes. Caveolin‐1 physically interacted with HO‐1, as shown by coimmunoprecipitation studies. HO activity dramati‐ cally increased in cells expressing caveolin‐1 antisense transcripts, suggesting a negative regulatory role for caveolin‐1. Conversely, caveolin‐1 expression attenu‐ ated LPS‐inducible HO activity. Since their initial char‐ acterization in 1969, HO enzymes have been described as endoplasmic reticulum‐associated proteins. We dem‐ onstrate for the first time the localization of heme degradation enzymes to plasma membrane caveolae, and present novel evidence that caveolin‐1 interacts with and modulates HO activity.—Kim, H. P., Wang, X., Galbiati, F., Ryter, S. W., Choi, A. M. K. Caveolae compartmentalization of heme oxygenase‐1 in endothe‐ lial cells. FASEB J. 18, 1080–1089 (2004)
Description of Notoernodes stoltzei sp. nov. (Trichoptera: Beraeidae), and of the larva of the genus
Authors: JOHANSON Kjell Arne 
Published: June 2004

Abstract Notoernodes stoltzei sp. nov. is described from the Uzungwa Mountains in Tanzania based on pharate males and larvae. The previously unknown larval stage of the genus is also described. A revised diagnosis to Notoernodes is presented.
Coronavirus Spike Glycoprotein, Extended at the Carboxy Terminus with Green Fluorescent Protein, Is Assembly Competent
Authors: Bosch Berend Jan , de Haan Cornelis A. M. , Rottier Peter J. M. 
Published: June 2004

ABSTRACT
Due to the limited ultrastructural information about the coronavirion, little is known about the interactions acting at the interface between nucleocapsid and viral envelope. Knowing that subtle mutations in the carboxy-terminal endodomain of the M protein are already lethal, we have now probed the equivalent domain of the spike (S) protein by extending it terminally with a foreign sequence of 27 kDa: the green fluorescent protein (GFP). When expressed individually in murine cells, the S-GFP chimeric protein induced the formation of fluorescent syncytia, indicating that it was synthesized and folded properly, trimerized, and transported to the plasma membrane, where it exhibited the two key S protein functions, i.e., interaction with virus receptor molecules and membrane fusion. Incorporation into virus-like particles demonstrated the assembly competence of the chimeric spike protein. The wild-type S gene of mouse hepatitis coronavirus (MHV) was subsequently replaced by the chimeric construct through targeted recombination. A viable MHV-SGFP was obtained, infection by which could be visualized by the fluorescence induced. The efficiency of incorporation of the chimeric protein into particles was, however, reduced relative to that in wild-type particles which may explain, at least in part, the reduced infectivity produced by MHV-SGFP infection. We conclude that the incorporation of spikes carrying the large GFP moiety is apparently impaired by geometrical constraints and selected against during the assembly of virions. Probably due to this disadvantage, deletion mutants, having lost the foreign sequences, rapidly evolved and outcompeted the chimeric viruses during virus propagation. The fluorescent MHV-SGFP will now be a convenient tool to study coronaviral cell entry.
Intrinsic Obstacles to Human Immunodeficiency Virus Type 1 Coreceptor Switching
Authors: Pastore Cristina , Ramos Alejandra , Mosier Donald E. 
Published: June 2004

ABSTRACT
The natural evolution of human immunodeficiency virus type 1 infection often includes a switch in coreceptor preference late in infection from CCR5 to CXCR4, a change associated with expanded target cell range and worsened clinical prognosis. Why coreceptor switching takes so long is puzzling, since it requires as few as one to two mutations. Here we report three obstacles that impede the CCR5-to-CXCR4 switch. Coreceptor switch variants were selected by target cell replacement in vitro. Most switch variants showed diminished replication compared to their parental R5 isolate. Transitional intermediates were more sensitive to both CCR5 and CXCR4 inhibitors than either the parental R5 virus or the final R5X4 (or rare X4) variant. The small number of mutations in viruses selected for CXCR4 use were distinctly nonrandom, with a dominance of charged amino acid substitutions encoded by G-to-A transitions, changes in N-linked glycosylation sites, and isolate-specific mutation patterns. Diminished replication fitness, less-efficient coreceptor use, and unique mutational pathways may explain the long delay from primary infection until the emergence of CXCR4-using viruses.
Interaction of DNA with the Movement Proteins of Geminiviruses Revisited
Authors: Hehnle Stefan , Wege Christina , Jeske Holger 
Published: June 2004

ABSTRACT

Geminiviruses manage the transport of their DNA within plants with the help of three proteins, the coat protein (CP), the nuclear shuttle protein (NSP), and the movement protein (MP). The DNA-binding capabilities of CP, NSP, and MP of
Abutilon mosaic virus
(AbMV; family
Geminiviridae
; genus
Begomovirus
) were scrutinized using gel mobility shift assays and electron microscopy. CP and NSP revealed a sequence-independent affinity for both double-stranded and single-stranded DNA, as has been previously reported for other begomoviruses. MP interacted selectively with dimeric supercoiled plasmid DNA in the electrophoretic assay. Further apparent size- and form-selective binding capacities of MP have been previously reported for another geminivirus (
Bean dwarf mosaic virus
), but in the case of AbMV, they have been identified as the result of electrophoretic interference rather than of complex formation. Without these complications, electron microscopy confirmed the assembly of double-stranded supercoiled DNA with NSP and MP into conspicuous structures and provided the first direct evidence for cooperative interaction of MP, NSP, and DNA. Based on these results and previous ones, a transport model of geminiviruses is discussed in which NSP packages DNA and MP anchors this complex to the protoplasmic leaflets of plasma membranes and microsomes for cell-to-cell movement.
Expression of the Mouse Hepatitis Virus Receptor by Central Nervous System Microglia
Authors: Ramakrishna Chandran , Bergmann Cornelia C. , Holmes Kathryn V. , Stohlman Stephen A. 
Published: June 2004

ABSTRACT

Detection of the mouse hepatitis virus receptor within the central nervous system (CNS) has been elusive. Receptor expression on microglia was reduced during acute infection and restored following immune-mediated virus control. Receptor down regulation was independent of neutrophils, NK cells, gamma interferon, or perforin. Infection of mice devoid of distinct inflammatory cells revealed CD4
+
T cells as the major cell type influencing receptor expression by microglia. In addition to demonstrating receptor expression on CNS resident cells, these data suggest that transient receptor down regulation on microglia aids in establishing persistence in the CNS by assisting virus infection of other glial cell types.
Discrepancies in current practice of pathological evaluation of sentinel lymph nodes in breast cancer. Results of a questionnaire based survey by the European Working Group for Breast Screening Pathology
Authors: Cserni G , Amendoeira I , Apostolikas N , Bellocq J P , Bianchi S , Boecker W , Borisch B , Connolly C E , Decker T , Dervan P , Drijkoningen M , Ellis I O , Elston C W , Eusebi V , Faverly D , Heikkila P , Holland R , Kerner H , Kulka J , Jacquemier J , Lacerda M , Martinez-Penuela J , De Miguel C , Peterse J L , Rank F , Regitnig P , Reiner A , Sapino A , Sigal-Zafrani B , Tanous A M , Thorstenson S , Zozaya E , Fejes G , Wells C A 
Published: June 2004

Aims:To evaluate aspects of the current practice of sentinel lymph node (SLN) pathology in breast cancer via a questionnaire based survey, to recognise major issues that the European guidelines for mammography screening should address in the next revision.Methods:A questionnaire was circulated by mail or electronically by the authors in their respective countries. Replies from pathology units dealing with SLN specimens were evaluated further.Results:Of the 382 respondents, 240 European pathology units were dealing with SLN specimens. Sixty per cent of these units carried out intraoperative assessment, most commonly consisting of frozen sections. Most units slice larger SLNs into pieces and only 12% assess these slices on a single haematoxylin and eosin (HE) stained slide. Seventy one per cent of the units routinely use immunohistochemistry in all cases negative by HE. The terms micrometastasis, submicrometastasis, and isolated tumour cells (ITCs) are used in 93%, 22%, and 71% of units, respectively, but have a rather heterogeneous interpretation. Molecular SLN staging was reported by only 10 units (4%). Most institutions have their own guidelines for SLN processing, but some countries also have well recognised national guidelines.Conclusions:Pathological examination of SLNs throughout Europe varies considerably and is not standardised. The European guidelines should focus on standardising examination. They should recommend techniques that identify metastases > 2 mm as a minimum standard. Uniform reporting of additional findings may also be important, because micrometastases and ITCs may in the future be shown to have clinical relevance.
The prognostic value of the AgNOR parameter in human breast cancer depends on the pRb and p53 status
Authors: Derenzini M , Ceccarelli C , Santini D , Taffurelli M , Treré D 
Published: June 2004

Background:The amount of argyrophilic nucleolar organiser regions (AgNORs) represents a cell kinetics parameter used in tumour pathology for prognostic purposes. AgNOR expression is directly related to the rate of ribosome biogenesis, which has been recently shown to be controlled also by the tumour suppressor proteins pRb and p53.Aims:To ascertain the relative prognostic value of AgNORs and of pRb and p53 expression in breast carcinoma.Methods:This study was carried out on 335 human primary breast carcinomas with a median follow up time of 108 months. AgNORs were measured by morphometric analysis on sections that had been selectively silver stained; expression of p53 and phosphorylated and non-phosphorylated pRb forms was assessed by immunohistochemistry.Results:Patients were divided into groups with low (249) and high (86) AgNOR values; with normal (267) and mutated p53 (68); and with normal (256) and hyperphosphorylated or deleted pRb (79). Univariate analysis of disease free survival showed that AgNORs and the status of pRb and p53 were significantly related to the patients’ clinical outcome. However, among the four groups characterised by different pRb and p53 status, the AgNOR parameter was not capable of distinguishing subgroups of patients with different clinical outcomes.Conclusions:These findings indicate that the prognostic value of the AgNOR parameter depends on the status of the tumour suppressor proteins pRb and p53, and it cannot be ascribed to the relation between AgNORs and the cell proliferation rate.
ALTERNATIVE VEHICLE TECHNOLOGIES AND FUELS IN SCENARIOS FOR ATMOSPHERIC EMISSIONS IN LONDON
Authors: IGLESIAS MARTA , APSIMON HELEN 
Published: June 2004

Alternative fuels and vehicle technologies for road transport are receiving increasing support as a result of climate change mitigation policies and local air quality regulations. This study attempts to estimate the emission reductions of major air pollutants (NOx, PM, HC and CO 2) that might be expected from the introduction of alternative fuels and technologies in London by the year 2020. A number of alternative scenarios for the road transport system have been developed, and their corresponding emissions compared to those arising from a baseline scenario, consisting exclusively of conventional fuels and engines. The results confirmed that by 2020 the emissions of NOx, PM and HC from a conventional vehicle fleet would be greatly decreased as a result of more stringent vehicle emission standards. Significant additional improvements could be achieved by the introduction of hydrogen-fuel cell vehicles, hybrid electric vehicles, natural gas and biofuels. It was found that the emissions of the principal pollutants of concern in London, NOx and PM 10, show similar patterns of reduction. The results also imply that the anticipated increase in conventional vehicle efficiency would only deliver a minimal 2 percent reduction in CO 2 vehicle emissions relative to the present, but greater reductions were achieved in all the alternative scenarios.
STRATEGIC PLANNING, IMPACT ASSESSMENT, AND TECHNICAL AID: THE SOUSS-MASSA INTEGRATED WATER MANAGEMENT PROJECT
Authors: KEITH JOHN E. , OUATTAR SAID 
Published: June 2004

Government agencies, like individuals, can "lose sight" of the impacts of their policies on natural and social systems. Environmental impact analysis (EIA), strategic environmental analysis (SEA), and strategic planning are all aspects of analyzing and projecting the impacts of various management decisions on the public and on natural systems. Integrated river-basin management is another aspect of this type of planning. Integrated management requires several basic conditions. Among these are clear communications among all the actors involved in managing the basin's water resources, one or more sets of data which are shared by all decision-makers, and tools by which the decision-makers can evaluate policies (impact assessment). In the Souss Massa River Basin in Morocco, the result of un-coordinated policies for economic development has led to declining water tables as well as potentially damaging surface and groundwater pollution. The Government of Morocco (GOM), recognizing the need for coordinated and integrated water management, passed a law creating new River Basin Agencies. Aiding those agencies and their partners in developing integrated management is the objective of the USAID-sponsored Souss-Massa Integrated Water Management (SIWM) project. The project activities have been designed to develop and support communications, data sharing and model building within the institutions in the Souss-Massa Basin as a demonstration for all Moroccan river basins but space and time constraints require a more pointed discussion. The focus of this paper is on capacity building for strategic planning and integrated management being undertaken and, to the extent possible, some of the lessons learned.
Low Thymidylate Synthase Expression in the Primary Tumor Predicts Favorable Clinical Outcome in Resected Gastric Cancer Patients Treated with Adjuvant Tegafur
Authors: Grau Juan J. , Domingo-Domenech Josep , Morente Vanesa , Pera Manuel , Garcia-Valdecasas Juan C. , Fuster Josep , Bombí Antoni , Mellado Begoña , Albanell Joan , Gascón Pere 
Published: June 2004

<i>Objective:</i> To assess the thymidylate synthase protein (TS) in tumor cells of resected gastric cancer patients treated with adjuvant tegafur (TG), we reviewed the outcome of 94 randomized patients treated either with adjuvant TG plus mitomycin C (MMC) or MMC alone. <i>Methods:</i> TS was determined in 76 out of 94 patients, previously randomized to receive adjuvant TG, 500 mg/m<sup>2</sup>/day p.o. for 6 months plus four courses of MMC, 10– 20 mg/m<sup>2</sup> i.v. every 6 weeks or MMC alone. An immunohistochemical assessment with the monoclonal antibody TS-106 was performed. <i>Results:</i> Low TS was observed in 38 patients (20 treated with TG-MMC and 18 with MMC) and high TS in the other 38 patients (21 treated with TG-MMC and 17 with MMC). After 10 years’ median follow-up time, 61% of adjuvant TG-MMC patients and 43% of MMC patients were alive and disease-free. Disease-free survival and overall survival were significantly better for patients treated with TG-MMC compared to MMC adjuvant (p = 0.0277 and p = 0.05), and low-TS compared to high-TS patients (p = 0.0184 and p = 0.0198). In 38 low-TS patients we observed an 83% chance to be disease-free in TG-MMC-treated patients and 55% in MMC-treated patients (p = 0.04). <i>Conclusions:</i> A low TS level determines a subset of patients that may benefit from adjuvant oral TG when added to MMC showing a 5-year cure rate of more than 80%.