bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overview and utilization of the NCI Thesaurus
Authors: Fragoso Gilberto , de Coronado Sherri , Haber Margaret , Hartel Frank , Wright Larry 
Published: February 2005

AbstractThe NCI Thesaurus is a reference terminology covering areas of basic and clinical science, built with the goal of facilitating translational research in cancer. It contains nearly 110 000 terms in approximately 36 000 concepts, partitioned in 20 sub‐domains, which include diseases, drugs, anatomy, genes, gene products, techniques, and biological processes, among others, all with a cancer‐centric focus in content, and originally designed to support coding activities across the National Cancer Institute. Each concept represents a unit of meaning and contains a number of annotations, such as synonyms and preferred name, as well as annotations such as textual definitions and optional references to external authorities. In addition, concepts are modelled with description logic (DL) and defined by their relationships to other concepts; there are currently approximately 90 types of named relations declared in the terminology. The NCI Thesaurus is produced by the Enterprise Vocabulary Services project, a collaborative effort between the NCI Center for Bioinformatics and the NCI Office of Communications, and is part of the caCORE infrastructure stack (http://ncicb.nci.nih.gov/NCICB/core). It can be accessed programmatically through the open caBIO API and browsed via the web (http://nciterms.nci.nih.gov). A history of editing changes is also accessible through the API. In addition, the Thesaurus is available for download in various file formats, including OWL, the web ontology language, to facilitate its utilization by others. Published in 2005 by John Wiley & Sons, Ltd.
Sequence Ontology annotation guide
Authors: Eilbeck Karen , Lewis Suzanna E. 
Published: February 2005

AbstractThis Sequence Ontology (SO) aims to unify the way in which we describe sequence annotations, by providing a controlled vocabulary of terms and the relationships between them. Using SO terms to label the parts of sequence annotations greatly facilitates downstream analyses of their contents, as it ensures that annotations produced by different groups conform to a single standard. This greatly facilitates analyses of annotation contents and characteristics, e.g. comparisons of UTRs, alternative splicing, etc. Because SO also specifies the relationships between features, e.g. part_of, kind_of, annotations described with SO terms are also better substrates for validation and visualization software.This document provides a step‐by‐step guide to producing a SO compliant file describing a sequence annotation. We illustrate this by using an annotated gene as an example. First we show where the terms needed to describe the gene's features are located in SO and their relationships to one another. We then show line by line how to format the file to construct a SO compliant annotation of this gene. Copyright © 2005 John Wiley & Sons, Ltd.
Standardization initiatives in the (eco)toxicogenomics domain: a review
Authors: Sansone Susanna Assunta , Morrison Norman , Rocca‐Serra Philippe , Fostel Jennifer 
Published: February 2005

AbstractThe purpose of this document is to provide readers with a resource of different ongoing standardization efforts within the ‘omics’ (genomic, proteomics, metabolomics) and related communities, with particular focus on toxicological and environmental applications. The review includes initiatives within the research community as well as in the regulatory arena. It addresses data management issues (format and reporting structures for the exchange of information) and database interoperability, highlighting key objectives, target audience and participants. A considerable amount of work still needs to be done and, ideally, collaboration should be optimized and duplication and incompatibility should be avoided where possible. The consequence of failing to deliver data standards is an escalation in the burden and cost of data management tasks. Copyright © 2005 John Wiley & Sons, Ltd.
Syntheses of Seven‐Membered Rings: Ruthenium‐Catalyzed Intramolecular [5+2] Cycloadditions
Authors: Trost Barry M. , Shen Hong C. , Horne Daniel B. , Toste F. Dean , Steinmetz Bernhard G. , Koradin Christopher 
Published: February 2005

AbstractThe Ru‐catalyzed intramolecular [5+2] cycloaddition of cyclopropylenynes is investigated with respect to the regio‐ and diastereoselectivity as well as the functional group compatibility of the reaction. Evidence for the mechanism as occurring through a ruthenacyclopentene intermediate is elucidated from 1) the study of the diastereoselectivity of the cycloaddition; 2) the effect of variation of substituents on the regioselectivity of cyclopropyl bond cleavage in 1,2‐trans‐ and 1,2‐cis‐disubstituted cyclopropanes and 3) examples that clearly do not involve ruthenacyclohexene as intermediates as products still incorporate the cyclopropyl moiety. The scope and limitations of the Ru‐catalyzed cycloaddition are discussed and compared with the Rh‐catalyzed reaction. The potential power of this methodology towards natural product total synthesis is demonstrated by the formation of several polycyclic systems with the chosen reaction conditions and readily available cyclopropylenyne substrates.
Stereoselective Synthesis of cis‐p‐Menth‐8‐ene‐1,7‐diol, cis‐p‐Menthane‐1,7‐diol, and cis‐p‐Menthane‐1,7,8‐triol
Authors: Kobler Christoph , Effenberger Franz 
Published: February 2005

AbstractThe natural products cis‐p‐menthane‐1,7‐diol (cis‐IV), cis‐p‐menth‐8‐ene‐1,7‐diol (cis‐I) and cis‐p‐menthane‐1,7,8‐triol (cis‐II) are obtained starting from the corresponding cis‐cyanohydrins, cis‐2 and cis‐7, respectively, by chemical transformation of the cyano into the hydroxymethyl group. The key step of the synthesis is the very high cis‐selectivity (≥ 96 %) of the MeHNL‐catalyzed HCN addition to 4‐alkylcyclohexanones. From 4‐isopropylcyclohexanone (1) the cyanohydrin cis‐2 and from 4‐(1‐methylvinyl)cyclohexanone (6) the cyanohydrin cis‐7 result almost quantitatively. Regioselective hydroxylation of cis‐I affords the triol cis‐II. X‐ray crystal structure determinations of the final products confirm their cis‐configuration.
Estimated impact of the Prostate Cancer Prevention Trial on population mortality
Authors: Unger Joseph M. , Thompson Ian M. , LeBlanc Michael , Crowley John J. , Goodman Phyllis J. , Ford Leslie G. , Coltman Charles A. 
Published: February 2005

AbstractBACKGROUNDThe potential public health impact of the recently completed Prostate Cancer Prevention Trial (PCPT) is debated. The results indicated that the period prevalence of prostate cancer was reduced by 24.8% due to finasteride, whereas an increase in the rate of high‐grade tumors (Gleason score 8–10) among men who were diagnosed with cancer also was found (5.0% in the PCPT placebo arm vs. 11.9% in the PCPT finasteride arm). Whether the increased Gleason score was valid or was a histologic artifact is under investigation.METHODSThe authors estimated the number of person‐years saved assuming a 24.8% reduction in the incidence of prostate cancer for 5 years among United States males age ≥ 55 years. Scenarios for different proportions of patients with high‐grade Gleason scores also were considered.RESULTSWith a 24.8% reduction in the number of men with newly diagnosed prostate cancer, the authors estimated that 316,760 person‐years would be saved due to finasteride in the United States. An absolute increase of 6.9% in the proportion of men with high‐grade tumors in the United States cancer population (corresponding to the difference between the rates on the placebo and finasteride arms of the PCPT) would reduce the number of person‐years saved to 262,567. For each absolute increase of 5% in the proportion of patients with high‐grade tumors, the number of person‐years saved would be reduced by approximately 39,000.CONCLUSIONSThe results of the PCPT may have a major impact on population mortality from prostate cancer if they are applied clinically. The potential detrimental effects of an increased rate of patients who have prostate cancer with high‐grade Gleason scores would be outweighed by a reduction in incidence. Cancer 2005. © 2005 American Cancer Society.
Osteosarcoma of the pelvis in children and young adults: The St. Jude Children's Research Hospital experience
Authors: Saab Raya , Rao Bhaskar N. , Rodriguez‐Galindo Carlos , Billups Catherine A. , Fortenberry Tamra N. , Daw Najat C. 
Published: February 2005

AbstractBACKGROUNDPelvic osteosarcomas are difficult to resect. The authors reviewed their institution's experience with patients who had such tumors to characterize the patients' clinical findings and to assess the impact of surgical resection on outcome.METHODSA review was conducted of the records from patients with pelvic osteosarcoma who were treated at the authors' institution between January, 1970 and March, 2004.RESULTSAmong 442 patients with osteosarcoma, 19 patients (4%) had high‐grade tumors arising in the pelvic bones, including the ilium in 15 patients, the pubis in 2 patients, and the sacrum in 2 patients. The median patient age at diagnosis was 16.8 years. Four tumors were secondary to radiation therapy. Five patients had metastases in the lung (n = 4 patients) or bone (n = 1 patient) at diagnosis. Ten tumors were chondroblastic. The median greatest tumor dimension for the 13 tumors with known size was 10 cm. Ten patients had unresectable pelvic tumors, and 9 patients underwent hemipelvectomy (2 internal and 7 external); complete resection with negative margins was achieved in 5 patients. Four patients survived, including one patient who survived with disease. Of the three patients who survived disease‐free, one patient underwent complete resection, one patient underwent incomplete resection (nonviable tumor at the soft tissue margin) with a good response to chemotherapy, and one patient with a sacral tumor underwent radiotherapy only for local control. Of the 9 patients who underwent resection, 7 experienced disease recurrence (n = 5 patients) or progression (n = 2 patients) at distant sites and died. All patients with metastatic disease at diagnosis died.CONCLUSIONSPelvic osteosarcomas often were large and unresectable. A high propensity for metastasis contributed to the poor outcome of patients with pelvic osteosarcoma. New therapeutic approaches are needed. Cancer 2005. © 2005 American Cancer Society.
Are seeds suitable for flow cytometric estimation of plant genome size?
Authors: Sliwinska Elwira , Zielinska Elzbieta , Jedrzejczyk Iwona 
Published: February 2005

AbstractBackgroundNuclear DNA content in plants is commonly estimated using flow cytometry (FCM). Plant material suitable for FCM measurement should contain the majority of its cells arrested in the G0/G1 phase of the cell cycle. Usually young, rapidly growing leaves are used for analysis. However, in some cases seeds would be more convenient because they can be easily transported and analyzed without the delays and additional costs required to raise seedlings. Using seeds would be particularly suitable for species that contain leaf cytosol compounds affecting fluorochrome accessibility to the DNA. Therefore, the usefulness of seeds or their specific tissues for FCM genome size estimation was investigated, and the results are presented here.MethodsThe genome size of six plant species was determined by FCM using intercalating fluorochrome propidium iodide for staining isolated nuclei. Young leaves and different seed tissues were used as experimental material. Pisum sativum cv. Set (2C = 9.11 pg) was used as an internal standard. For isolation of nuclei from species containing compounds that interfere with propidium iodide intercalation and/or fluorescence, buffers were used supplemented with reductants.ResultsFor Anethum graveolens, Beta vulgaris, and Zea mays, cytometrically estimated genome size was the same in seeds and leaves. For Helianthus annuus, different values for DNA amounts in seeds and in leaves were obtained when using all but one of four nuclei isolation buffers. For Brassica napus var. oleifera, none of the applied nuclei isolation buffers eliminated differences in genome size determined in the seeds and leaves.ConclusionsThe genome size of species that do not contain compounds that influence fluorochrome accessibility appears to be the same when estimated using specific seed tissues and young leaves. Seeds can be more suitable than leaves, especially for species containing staining inhibitors in the leaf cytosol. Thus, use of seeds for FCM nuclear DNA content estimation is recommended, although for some species a specific seed tissue (usually the radicle) should be used. Protocols for preparation of samples from endospermic and endospermless seeds have been developed. © 2005 Wiley‐Liss, Inc.
Segregation of arterial and venous markers in subpopulations of blood islands before vessel formation
Authors: Herzog Yael , Guttmann‐Raviv Noga , Neufeld Gera 
Published: February 2005

AbstractThe neuropilin‐1 (np1) and the neuropilin‐2 (np2) receptors bind vascular endothelial growth factor (VEGF) and class‐3 semaphorins. They form complexes with VEGF tyrosine‐kinase receptors or alternatively with type‐A plexins to transduce respective VEGF or semaphorin signals. We have compared the expression patterns of np1, np2, plexin‐A1, and plexin‐A2 in the emerging vasculature of chick embryos. Double in situ hybridization reveals that six‐somite embryos contain intermingled extraembryonic blood island (BI) subpopulations that express np1 or np2 as well as a BI subpopulation that coexpresses both neuropilins. In 13‐somite embryos, which already contain an extraembryonic vascular plexus, the expression of np1 and np2 is segregated between the arterial and venous parts of the plexus, despite the absence of blood flow. However, the arterial marker ephrin‐B2 was not yet expressed in the plexus at this stage. In 26‐somite embryos, which possess a functional vascular system, np1 and np2 are differentially expressed in arteries and veins as previously reported. At this stage, posterior BIs expressing np2 appear to undergo fusion to form the posterior sinus vein and its tributaries, suggesting that the venous identity of these veins may be established before their formation. The neuropilin coreceptor plexin‐A2 was expressed in extraembryonic veins but not in extraembryonic arteries. In contrast, within the embryo, plexin‐A2 expression was observed in the dorsal aorta as well as in the cardinal vein. Semaphorin‐3F (s3f), an np2 ligand, bound to np2‐expressing cells in 26‐somite embryos regardless of the presence or absence of plexin‐A1 or plexin‐A2. Of interest, even though s3f binds to np1 in vitro, np1‐expressing arteries fail to bind s3f in whole‐mount binding experiments. Developmental Dynamics 232:1047–1055, 2005. © 2005 Wiley‐Liss, Inc.
Fibrous component of the blastocoelic extracellular matrix shapes epithelia in concert with mesenchyme cells in starfish embryos
Authors: Kaneko Hiroyuki , Okai Murasaki , Murabe Naoyuki , Shimizu Takahiko , Ikegami Susumu , Dan‐Sohkawa Marina 
Published: February 2005

AbstractBy using a monoclonal antibody (4H11 Mab), we have investigated morphogenetic functions of a fibrous component of the blastocoelic extracellular matrix in relation to cellular activities during early development of the starfish Asterina pectinifera. The 4H11 fibers fill the blastocoele from the late‐cleavage to late‐gastrula stage and contain the 370‐kDa proteinaceous molecule secreted only by the epithelial cells. When 4H11 Mab is introduced into the blastocoele of blastulae, the embryos reveal three distinct morphological abnormalities after the mid‐gastrula stage: (1) Distribution of mesenchyme cells confined near the tip of the archenteron, (2) swelling of the posterior ectoderm, and (3) suppressed growth of the mouth, esophagus, and coelomic pouches. These abnormalities occur together with alterations in the distribution of the 4H11 fibers. In embryos recovering from the effect of 4H11 Mab, the mesenchyme cells rearrange the 4H11 fibers. We propose that 4H11 fibers play direct roles in the morphogenesis of starfish embryos by providing a dynamic scaffold not only for the mesenchyme cells but also for the epithelial cells. Moreover, 4H11 fibers have a resist force from within, in concert with the mesenchyme cells, to counter the bulging force intrinsic to the epithelia and hold the epithelia in specific positions, once the positions have been decided. Developmental Dynamics 232:915–927, 2005. © 2005 Wiley‐Liss, Inc.
Genomic, cDNA, and embryonic expression analysis of zebrafish transforming growth factor beta 3 (tgfβ3)
Authors: Cheah Felicia S.H. , Jabs Ethylin Wang , Chong Samuel S. 
Published: February 2005

AbstractTGFβ3, a member of the transforming growth factor β family, regulates a spectrum of biological processes and is involved in mammalian pulmonary and craniofacial development. Homologs of human TGFβ3 have been identified in several vertebrate species. We sequenced a cDNA clone of zebrafish tgfβ3, consisting of a 271‐bp 5′ untranslated region, a 1,233‐bp open reading frame that encodes a predicted 410 amino acid peptide, and a 527‐bp 3′ untranslated region. Using 5′ rapid amplification of cDNA ends, the transcription start site of this gene was determined to lie an additional 29 nucleotides upstream. The gene is composed of seven exons and maps to a segment of linkage group 17 that is syntenic to the human TGFβ3 locus on chromosome 14q24. One stimulating protein 1 (Sp1) and two (TATA binding protein) (TBP) transcription factor binding sites were identified in the putative promoter segment upstream of the transcription start site. Comparative alignment analysis revealed a high degree of tgfβ3 nucleotide and amino acid identity between zebrafish and other species, including complete conservation of the cysteine knot structure that facilitates protein–protein interaction. Also, 9 of 10 amino acid residues critical for ligand/receptor binding in human TGFβ3 are conserved in zebrafish, suggesting a high degree of functional conservation even in lower vertebrates. Zebrafish tgfβ3 transcripts were first detected in the notochord (10 somite to high‐pec stage), followed by expression in the developing pharyngeal arch and neurocranial cartilage (18 somite to protruding mouth stage), lens and heart (21 somite to protruding mouth stage), and pectoral fins (prim‐25 to protruding mouth stage). The strong expression in the pectoral fins, not reported in the orthologous mammalian forelimb, suggests a modified or novel function of tgfβ3 during early fish development. Developmental Dynamics 232:1021–1030, 2005. © 2005 Wiley‐Liss, Inc.
DNA methyltransferase expression in the mouse germ line during periods of de novo methylation
Authors: Lees‐Murdock Diane J. , Shovlin Tanya C. , Gardiner Tom , De Felici Massimo , Walsh Colum P. 
Published: February 2005

AbstractDNA methyltransferase (DNMT) 3A and DNMT3B are both active de novo DNA methyltransferases required for development, whereas DNMT3L, which has no demonstrable methyltransferase activity, is required for methylation of imprinted genes in the oocyte. We show here that different mechanisms are used to restrict access by these proteins to their targets during germ cell development. Transcriptional control of the Dnmt3l promoter guarantees that message is low or absent except during periods of de novo activity. Use of an alternative promoter at the Dnmt3a locus produces the shorter Dnmt3a2 transcript in the germ line and postimplantation embryo only, whereas alternative splicing of the Dnmt3b transcript ensures that Dnmt3b1 is absent in the male prospermatogonia. Control of subcellular protein localization is a common theme for DNMT3A and DNMT3B, as proteins were seen in the nucleus only when methylation was occurring. These mechanisms converge to ensure that the only time that functional products from each locus are present in the germ cell nuclei is around embryonic day 17.5 in males and after birth in the growing oocytes in females. Developmental Dynamics 232:992–1002, 2005. © 2005 Wiley‐Liss, Inc.
Genomic resources for chicken
Authors: Antin Parker B. , Konieczka Jay H. 
Published: February 2005

AbstractThe recent sequencing and draft assembly of a chicken genome has provided biologists with an invaluable research tool that complements a growing list of additional avian genomic resources. For many researchers, finding and using these resources is challenging, because information is presented through an increasing number of Web sites and browser navigation frequently requires specific knowledge and expertise. This primer provides an overview of online genomic resources for the chicken, including the Ensembl, UCSC, and NCBI annotated chicken genome browsers; expressed sequence tag and in situ hybridization databases; and sources for microarrays, cDNAs, and bacterial artificial chromosomes (BACs). Several short tutorials oriented toward the biologist with limited bioinformatics skills outline how to retrieve several types of commonly needed information and reagents. Developmental Dynamics 232:877–882, 2005. © 2005 Wiley‐Liss, Inc.
Magic number silicon dioxide‐based clusters: Laser ablation‐mass spectrometric and density functional theory studies
Authors: Kong Qingyu , Zhao Li , Wang Wenning , Wang Chen , Xu Can , Zhang Wingham , Liu Lei , Fan Kangnian , Li Yufen , Zhuang Jun 
Published: February 2005

AbstractThe magic number silica clusters [(SiO2)nO2H3]− with n = 4 and 8 have been observed in the XeCl excimer laser (308 nm) ablation of various porous siliceous materials. The structural origin of the magic number clusters has been studied by the density functional theoretical calculation at the B3LYP/6‐31G** level, with a genetic algorithm as a supplementary tool for global structure searching. The DFT results of the first magic number cluster are parallel to the corresponding Hartree–Fock results previously reported with only small differences in the structural parameters. Theoretical calculation predicts that the first magic number cluster (SiO2)4O2H4 and its anion [(SiO2)4O2H3]− will most probably take pseudotetrahedral cage‐like structures. To study the structural properties of the second magic number cluster, geometries of the bare cluster (SiO2)8, the neutral complex cluster (SiO2)8O2H4, and the anionic cluster [(SiO2)8O2H3]− are fully optimized at the B3LYP/6‐31G** level, and the corresponding vibrational frequencies are calculated. The DFT calculations predict that the ground state of the bare silica octamer (SiO2)8 has a linear chain structure, whereas the second magic number complex cluster (SiO2)8O2H4 and its anion [(SiO2)8O2H3]− are most probably a mixture of cubic cage‐like structural isomers with an O atom inside the cage and several quasi‐bicage isomers with high intercage interactions. The stabilization of these structures can also be attributed to the active participation of the group of atoms 2O and 4H (3H for the anion) in chemical bonding during cluster formation. Our theoretical calculation gives preliminary structural interpretation of the presence of the first and second magic number clusters and the absence of higher magic numbers. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 584–598, 2005