bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longest biased interval and longest non-negative sum interval
Authors: Allison Lloyd 
Published: June 2003

Abstract
Summary: Described is an algorithm to find the longest interval having at least a specified minimum bias in a sequence of characters (bases, amino acids), e.g. ‘at least 0.95 (A+T)-rich’. It is based on an algorithm to find the longest interval having a non-negative sum in a sequence of positive and negative numbers. In practice, it runs in linear time; this can be guaranteed if the bias is rational.
Availability: Java code of the algorithm can be found at http://www.csse.monash.edu.au/~lloyd/tildeProgLang/Java2/Biased/
Contact: lloyd@bruce.cs.monash.edu.au
Supplementary information: Examples of applications to Plasmodium falciparum genomic DNA can be found at the above URL.
* To whom correspondence should be addressed.
TableView: portable genomic data visualization
Authors: Johnson James E. , Stromvik Martina V. , Silverstein Kevin A.T. , Crow John A. , Shoop Elizabeth , Retzel Ernest F. 
Published: June 2003

Abstract
Summary: TableView is a generalized scientific visualization program for exploration of various biological data, including EST, SAGE, microarray and annotation data. Written in Java, TableView is portable, is easily used together with other software including DBMSs and is versatile enough to be applied to any tabular data
Availability: TableView is freely available at: http://ccgb.umn.edu/software/java/apps/TableView/
Contact: tableview@ccgb.umn.edu
* To whom correspondence should be addressed.
† Present address: Macalester College, Mathematics and Computer Science, St Paul, MN 55105, USA.
The DynDom database of protein domain motions
Authors: Lee Richard A. , Razaz Moe , Hayward Steven 
Published: June 2003

Abstract
Summary: A relational database has been developed based on the results from the application of the DynDom program to a number of proteins for which multiple X-ray conformers are available. The database is populated via a web-based tool that allows visitors to the website to run the DynDom program server-side by selecting pairs of X-ray conformers by Protein Data Bank code and chain identifier.
Availability: The website can be found at: http://www.sys.uea.ac.uk/dyndom
Contact: sjh@sys.uea.ac.uk
* To whom correspondence should be addressed.
HaploBlockFinder: haplotype block analyses
Authors: Zhang Kun , Jin Li 
Published: June 2003

Abstract
Summary: Recent studies have unveiled discrete block-like structures of linkage disequilibrium (LD) in the human genome. We have developed a set of computer programs to analyze the block-like LD structures (haplotype blocks) based on haplotype data. Three definitions of haplotype block are supported, including minimal LD range, no historic recombination, and chromosome coverage. Tagged SNPs that uniquely distinguish common haplotypes are identified. A greedy algorithm was used to improve the efficiency. Two separate utilities were also provided to assist visual inspection of haplotype block structure and pattern of linkage disequilibrium.
Availability: A web interface for the HaploBlockFinder is available at http://cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.cgi the source codes are also freely available on the web site.
Contact: jinl@ucmail.uc.edu
* To whom correspondence should be addressed.
Local structure prediction with local structure-based sequence
profiles
Authors: Yang An-Suei , Wang Lu-yong 
Published: June 2003

Abstract
Motivation: A large body of experimental and theoretical evidence suggests that local structural determinants are frequently encoded in short segments of protein sequence. Although the local structural information, once recognized, is particularly useful in protein structural and functional analyses, it remains a difficult problem to identify embedded local structural codes based solely on sequence information.
Results: In this paper, we describe a local structure prediction method aiming at predicting the backbone structures of nine-residue sequence segments. Two elements are the keys for this local structure prediction procedure. The first key element is the LSBSP1 database, which contains a large number of non-redundant local structure-based sequence profiles for nine-residue structure segments. The second key element is the consensus approach, which identifies a consensus structure from a set of hit structures. The local structure prediction procedure starts by matching a query sequence segment of nine consecutive amino acid residues to all the sequence profiles in the local structure-based sequence profile database (LSBSP1). The consensus structure, which is at the center of the largest structural cluster of the hit structures, is predicted to be the native state structure adopted by the query sequence segment. This local structure prediction method is assessed with a large set of random test protein structures that have not been used in constructing the LSBSP1 database. The benchmark results indicate that the prediction capacities of the novel local structure prediction procedure exceed the prediction capacities of the local backbone structure prediction methods based on the I-sites library by a significant margin.
Availability: All the computational and assessment procedures have been implemented in the integrated computational system PrISM.1 (Protein Informatics System for Modeling). The system and associated databases for LINUX systems can be downloaded from the website: http://www.columbia.edu/~ay1/
Contact: ay1@columbia.edu
* To whom correspondence should be addressed.
p210 BCR/ABL kinase regulates nucleotide excision repair (NER) and resistance to UV radiation
Authors: Canitrot Yvan , Falinski Rafal , Louat Thierry , Laurent Guy , Cazaux Christophe , Hoffmann Jean-Sébastien , Lautier Dominique , Skorski Tomasz 
Published: June 2003

Abstract
Both clinical and experimental evidence illustrate that p190 and p210 BCR/ABL oncogenic tyrosine kinases induce resistance to DNA damage and confer an intrinsic genetic instability. Here, we investigated whether BCR/ABL expression could modulate nucleotide excision repair (NER). We found that ectopic expression of p210 BCR/ABL in murine lymphoid BaF3 cell line inhibited NER activity in vitro, promoting hypersensitivity of these cells to ultraviolet (UV) treatment and facilitating a mutator phenotype. However, expression of p210 BCR/ABL in human and murine myeloid cell lines and primary bone marrow cells resulted in the increased NER activity and resistance to UV irradiation. The ABL tyrosine kinase inhibitor STI571 reversed these effects, showing that p210 BCR/ABL tyrosine kinase activity is responsible for deregulation of NER. Hypoactivity of NER in p210 BCR/ABL-positive lymphoid cells was accompanied by the decreased interaction between proliferating cell nuclear antigen (PCNA) and xeroderma pigmentosum group B (XPB); conversely, this interaction was enhanced in p210 BCR/ABL-positive myeloid cells. p190 BCR/ABL did not affect NER in lymphoid and myeloid cells. In summary, our study suggests that p210 BCR/ABL reduced NER activity in lymphoid cells, leading to hypersensitivity to UV and mutagenesis. In contrast, p210 BCR/ABL expression in myeloid cells facilitated NER and induced resistance to UV. (Blood. 2003;102:2632-2637)
Pain, anxiety and insomnia – a global perspective on the relief of suffering
Authors: Ghodse Hamid 
Published: June 2003

BackgroundThe unavailability of psychotropic and analgesic drugs for medical purposes results in suffering that goes unrelieved. Their excessive availability results in overmedication and suffering of a different kind.AimsTo highlight the discrepancies between the demand for and supply of controlled drugs for licit purposes by different communities, and to promote their rational utilisation.MethodReview of the United Nations, World Health Organization and other literature on the licit use of narcotic analgesics and psychotropic substances.ResultsThereare large differences in the use of psychotropics and analgesics by different countries. The differences between industrialised and non-industrialised countries are particularly striking. There is evidence of unmet need in some countries and overutilisation in others.ConclusionsGovernments, international organisations, health professionals and the pharmaceutical industry must work together to ensure an adequate supply of psychotropic and analgesic drugs for medical and scientific purposes, and to implement appropriate measures to minimise the development of misuse and dependence.
Developing a local shared care protocol for managing people with psychotic illness in primary care
Authors: Snowden Helen , Marriott Sarah 
Published: June 2003

Aims and MethodThe National Service Framework sets standards to improve the treatment of mental health on a national level, and requires the development of localised shared care protocols. We aimed to develop a shared care protocol for use in local National Health Service (NHS) services, based on best practice guidelines and local consensus. A systematic literature search used three databases and the advice of a clinical expert. Articles satisfying the search inclusion criteria were retrieved and appraised. Clinical recommendations from well-designed regional and national documents relevant to all aspects of the management of psychotic illness in primary care were compared and contrasted by a facilitated group involving primary and secondary care clinicians who drafted the final recommendations. A multi-agency steering group guided the work.ResultsTwenty-two articles were retrieved, of which nine reached the criteria for inclusion. The protocol provided a comprehensive range of recommendations regarding detection, assessment, management, referral and shared working with local mental health services.Clinical ImplicationsUsing local clinical consensus to resolve uncertainty about conflicting clinical recommendations from a series of well-designed guidelines was an effective method for adapting clinical guidelines to local circumstances.
Cytochrome P450 CYP3A4/5 Expression as a Biomarker of Outcome in Osteosarcoma
Authors: Dhaini Hassan R. , Thomas Dafydd G. , Giordano Thomas J. , Johnson Timothy D. , Biermann J. Sybil , Leu Kirsten , Hollenberg Paul F. , Baker Laurence H. 
Published: June 2003

Purpose: Osteosarcoma, the most common pediatric primary bone tumor, is an aggressive malignancy with a tendency for early pulmonary metastasis. A reliable biomarker to predict clinical outcome at diagnosis has not yet been identified. To date, pathological review of neoadjuvant chemotherapy–induced necrosis is the most useful determinant of which patients are likely to develop metastatic disease. There is a clinical need to identify patients who will benefit from more aggressive preoperative therapy or perhaps require less aggressive chemotherapy. More than 30 human P450 isoenzymes have been characterized, with at least nine possessing some clinical relevance. One of these, CYP3A4/5 is involved in metabolic activation and detoxification of a wide number of carcinogens and chemotherapeutic agents, including many drugs that are useful in the treatment of osteosarcomas. Materials and Methods: Osteosarcoma tissue microarray blocks containing biopsies from 18 primary tumors were used to analyze the expression of P450s 1A1/2, 1B1, 2B6, 2D6, and 3A4/5 by enzyme-linked avidin-biotin complexed immunohistochemistry. The frequencies of expression were 83%, 67%, and 83% for P450s 1A1/2, 1B1, and 3A4/5, respectively. P450s 2B6 and 2D6 were not detectable. Results: These results were extended by developing a fluorescent-based quantitative immunocytochemistry technique to assess the levels of CYP3A4/5 in 18 paraffin-embedded primary biopsy sections. Expression of CYP3A4/5 was found to be significantly higher in primary biopsies of patients who developed distant metastatic disease compared with biopsies from patients with nonmetastatic disease (P = 0.0004). Conclusion: High cytochrome P450 CYP3A4/5 expression may predict metastasis and poor prognosis in osteosarcomas. Its use as a biomarker of therapeutic response will have implications for the treatment of these tumors.
Correlation of Early Metastatic Response by123I-Metaiodobenzylguanidine Scintigraphy With Overall Response and Event-Free Survival in Stage IV Neuroblastoma
Authors: Matthay Katherine K. , Edeline Veronique , Lumbroso Jean , Tanguy Marie Laure , Asselain Bernard , Zucker Jean Michel , Valteau-Couanet Dominique , Hartmann Olivier , Michon Jean 
Published: June 2003

Purpose: Metaiodobenzylguanidine (MIBG), specifically taken up in cells of sympathetic origin, provides a highly sensitive and specific indicator for the detection of metastases in neuroblastoma. The aim of this study was to correlate early response to therapy by MIBG scan, using a semiquantitative scoring method, with the end induction response and event-free survival (EFS) rate in stage IV neuroblastoma. Patients and Methods: Seventy-five children older than 1 year and with stage IV neuroblastoma had 123I-MIBG scans at diagnosis, after two and four cycles of induction therapy, and before autologous stem-cell transplantation. The scans were read by two independent observers (concordance > 95%) using a semiquantitative method. Absolute and relative (score divided by initial score) MIBG scores were then correlated with overall pretransplantation response, bone marrow response, and EFS. Results: The pretransplantation response rate was 81%, and the 3-year EFS rate was 32%, similar to a concomitant group of 375 stage IV patients. The median relative MIBG scores after two, four, and six cycles were 0.5, 0.24, and 0.12, respectively. The probability of having a complete response or very good partial response before transplantation was significantly higher if the relative score after two cycles was ≤ 0.5, or, if after four cycles, the relative score was ≤ 0.24. Patients with a relative score of ≤ 0.5 after two cycles or a score of ≤ 0.24 after four cycles had an improved EFS rate (P = .053 and .045, respectively). Conclusion: Semiquantitative MIBG score early in therapy provides valuable prognostic information for overall response and EFS, which may be useful in tailoring treatment.
High Response Rates and Lasting Remissions After Low-Dose Involved Field Radiotherapy in Indolent Lymphomas
Authors: Haas R.L.M. , Poortmans Ph. , de Jong D. , Aleman B.M.P. , Dewit L.G.H. , Verheij M. , Hart A.A.M. , van Oers M.H.J. , van der Hulst M. , Baars J.W. , Bartelink H. 
Published: June 2003

Purpose: To study the response rates and duration of response after low-dose (4 Gy) involved field radiotherapy (LD-IF-RT) in patients with recurrent indolent lymphoma. Patients and Methods: A total of 109 assessable patients (304 symptomatic sites) were irradiated (53 males and 56 females; median age, 62 years; range, 35 to 93), including 98 patients with follicular lymphoma (43 grade 1 and 55 grade 2), nine extranodal marginal zone lymphomas of mucosa-associated lymphoid tissue-type and two patients with lymphoplasmacytoid lymphoma. Bulky disease (≥5 cm) was present in 52% of all patients. A median of two prior regimens (range, 0 to 11) preceded LD-IF-RT. The median time since diagnosis was 41 months (range, 2 to 358 months). Time to (local) progression was calculated according to the Kaplan-Meier method. Differences in response rates between treatments within the same patient were compared using the McNemar test. Results: The overall response rate was 92%; complete response was reached in 67 patients (61%), partial response in 34 patients (31%), stable disease in six patients (6%), and progressive disease in two patients (2%). The median time to progression was 14 months. The median time to local progression was 25 months. The 67 patients with complete response showed a median time to progression of 25 months and a median time to local progression of 42 months. None of the factors studied (age, sex, follicular lymphoma grade, radiotherapy regimen, number of previous regimens and previous history, number of positive sites or largest lymphoma diameter) were found to be related to response rate. Conclusion: LD-IF-RT is a valuable asset in the management of patients with follicular lymphoma and should be considered in patients with recurrent disease.
Phase II Study of First-Line Chemotherapy With Temozolomide in Recurrent Oligodendroglial Tumors: The European Organization for Research and Treatment of Cancer Brain Tumor Group Study 26971
Authors: van den Bent M.J. , Taphoorn M.J.B. , Brandes A.A. , Menten J. , Stupp R. , Frenay M. , Chinot O. , Kros J.M. , van der Rijt C.C.D. , Vecht Ch.J. , Allgeier A. , Gorlia T. 
Published: June 2003

Purpose: Oligodendroglial tumors are chemotherapy-sensitive tumors, with two thirds of patients responding to combination chemotherapy with procarbazine, lomustine, and vincristine (PCV). Temozolomide (TMZ), a new alkylating and methylating agent, has demonstrated high response rates in patients with recurrent anaplastic astrocytoma. We investigated TMZ as first-line chemotherapy in recurrent oligodendroglial tumors (OD) and mixed oligoastrocytomas (OA) after surgery and radiation therapy. Patients and Methods: In a prospective, nonrandomized, multicenter, phase II trial, patients were treated with 200 mg/m2 of TMZ on days 1 through 5 in 28-day cycles for 12 cycles. Patients with a recurrence after prior surgery and radiotherapy, and with measurable and enhancing disease on magnetic resonance imaging (MRI) were eligible for this study. Patients with large lesions and mass effect or with new clinical deficits were not eligible. Pathology and the MRI scans of all responding patients were centrally reviewed. Results: Thirty-eight eligible patients were included. In three patients, pathology review did not confirm the presence of an OD or OA. TMZ was generally well tolerated. The most frequent side effects were hematologic; only one patient discontinued treatment for toxicity. In 20 (52.6%) of 38 patients (95% exact confidence interval, 35.8% to 69.0%), a complete (n = 10) or partial response to TMZ was observed. The median time to progression was 10.4 months for all patients and 13.2 months for responding patients. At 12 months from the start of treatment, 40% of patients were still free from progression. Conclusion: TMZ provides an excellent response rate with good tolerability in chemotherapy-naive patients with recurrent OD. A randomized phase III study comparing PCV with TMZ is warranted.
Free‐rider effects of generic advertising: The case of salmon
Authors: Kinnucan Henry W. , Myrland Øystein 
Published: June 2003

AbstractThe free‐rider effects of commodity promotion are a neglected issue in the empirical literature. This study addresses the lacuna by considering the salmon promotion program conducted by the Norwegian Seafood Export Council. Specifically, a model of the world salmon market is used to indicate returns to Norwegian producers from NSEC's marketing activities, but also returns to Norway's international competitors. Results suggest program intensification would have a positive effect on total (worldwide) producer surplus in the short run, but the gain's distribution is uneven. Specifically, Norway would receive 23% of the gain compared to 48% for United Kingdom producers. By way of comparison, Norway and UK world trade shares are 47 and 16%, respectively. The disproportionate gains to UK producers are due to a double free ride: from the export tax used to fund the advertising increase, and from the advertising itself. [EconLit citations: L660, Q130, Q170]. © 2003 Wiley Periodicals, Inc. Agribusiness 19: 315–324, 2003.
Performance of an acrylic acid grafted polycaprolactone/starch composite: Characterization and mechanical properties
Authors: Wu Chin‐San 
Published: June 2003

AbstractIn this article, the properties of a polycaprolactone and starch composite (PCL/starch) and an acrylic acid grafted polycaprolactone and starch composite (PCL‐g‐AA/starch) were examined by Fourier transform infrared spectroscopy, nuclear magnetic resonance, differential scanning calorimetry, Instron mechanical testing, and scanning electron microscopy. Mechanical properties of PCL became significantly worse when it was blended with starch, due to the poor compatibility between the two phases. Much better dispersion and homogeneity of starch in the polymer matrix was obtained when PCL‐g‐AA was used in place of PCL in the composite. Improved mechanical and thermal properties of the PCL‐g‐AA/starch composite, notably an increase in tensile strength at breakpoint, evidenced its superiority to the PCL/starch one. Furthermore, PCL‐g‐AA/starch was more easily processed than PCL/starch because the former had lower melt viscosity. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 2888–2895, 2003
Synthesis of Na+‐montmorillonite/amphiphilic polyurethane nanocomposite via bulk and coalescence emulsion polymerization
Authors: Kim Ju‐Young , Jung Woo‐Chul , Park Kang‐Yeol , Suh Kyung‐Do 
Published: June 2003

AbstractPolyurethane/clay nanocomposites have been synthesized using Na+‐montmorillonite (Na+‐MMT)/amphiphilic urethane precursor (APU) chains that have hydrophilic polyethylene oxide (PEO) chains and hydrophobic segments at the same molecules. Nanocomposites were synthesized through two different crosslinking polymerization methods. One is UV curing of melt mixed APU/Na+‐MMT mixtures; the other is coalescence polymerization of APU/Na+‐MMT emulsions. These two kinds of composites had intercalated silicate layers of Na+‐montmorillonite by insertion of PEO chains in APU chains, which was confirmed by X‐ray diffraction measurement and transmission electron microscopy. These composite films also showed improved mechanical properties compared to pristine APU films. Although the two kinds of nanocomposites exhibited the same degree of intercalation and were synthesized based on the same precursor chains, these nanocomposite films had the different mechanical properties. Nanocomposites synthesized using APU/Na+‐MMT emulsions, having microphase‐separated structure, had greater tensile strength than those prepared with melt‐mixed APU/Na+‐MMT mixtures. Location of intercalated Na+‐MMT by PEO chains at the oil–water interface also could be confirmed by rheological behavior of the APU/Na+‐MMT/water mixture. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 3130–3136, 2003
Preparation and characterization of acrylonitrile–styrene–methylmethacrylate terpolymer as a compatibilizer for rubber blends
Authors: Botros S. H. , Moustafa A. F. 
Published: June 2003

AbstractAcrylonitrile‐co‐styrene‐co‐methylmethacrylate (AN‐S‐MMA) terpolymer was prepared by bulk and emulsifier‐free emulsion polymerization techniques. The bulk and emulsion terpolymers were characterized by means of Fourierr transform infrared spectroscopy, 13C nuclear magnetic resonance (NMR) spectroscopy, gel permeation chromatography, thermal gravimetric analysis, and elemental analysis. The kinetics of the terpolymerization were studied. The terpolymers were then incorporated into butadiene—acrylonitrile rubber (NBR)/ethylene propylene diene monomer rubber (EPDM) blends and into chloroprene rubber (CR)/EPDM blend. The terpolymers were then tested for potential as compatibilizers by using scanning electron microscopy and differential scanning calorimetry. The terpolymers improved the compatibility of CR/EPDM and NBR/EPDM blends. The physicomechanical properties of CR/EPDM and NBR/EPDM blend vulcanizates revealed that the incorporation of terpolymers was advantageous, since they resulted in blend vulcanizates with higher 100% moduli and with more thermally stable mechanical properties than the individual rubbers. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 3143–3153, 2003