bluuebunny/crossref_metadata_2025_split huggingface dataset:
A finite volume method for large strain analysis of incompressible hyperelastic materials
Authors: Bijelonja I. , Demirdžić I. , Muzaferija S. 
Published: July 2005

AbstractThis paper describes development of a displacement–pressure based finite volume formulation for modelling of large strain problems involving incompressible hyperelastic materials. The method is based on the solution of the integral conservation equations governing momentum balance in total Lagrangian description. The incompressibility constraint is enforced by employing the integral form of the mass conservation equation in deformed configurations of the body. A Mooney–Rivlin incompressible material model is used for material description. A collocated variable arrangement is used and the spatial domain is discretized using finite volumes of an arbitrary polyhedral shape. A segregated approach is employed to solve resulting set of coupled non‐linear algebraic equations, utilizing a SIMPLE based algorithm for displacement–pressure coupling. Comparisons of numerical and analytical results show a very good agreement. For the limited range of cell topologies tested the developed method appears to be locking free. Copyright © 2005 John Wiley & Sons, Ltd.
Up‐regulated expression of ADAM17 in human colon carcinoma: co‐expression with EGFR in neoplastic and endothelial cells
Authors: Blanchot‐Jossic Frédérique , Jarry Anne , Masson Damien , Bach‐Ngohou Kalyane , Paineau Jacques , Denis Marc G , Laboisse Christian L , Mosnier Jean‐François 
Published: July 2005

AbstractThe ADAM17 metalloproteinase (a disintegrin and metalloprotease 17) controls epidermal growth factor receptor (EGFR) activation through regulated shedding of EGFR ligands. With the advent of new therapeutic options targeting EGFR signalling in colon carcinoma, it was decided to determine ADAM17 status in relation to clinico‐pathological parameters and EGFR status. To this end, a series of 39 colon carcinomas were analysed.Immunohistochemistry and immunofluorescence were used to localize ADAM17, EGFR, and the activated forms of EGFR. The activated form of ADAM17 was assessed in primary cancers and colon cell lines by immunoblotting. ADAM17 and EGFR mRNA levels were assessed by quantitative RT‐PCR. Chromogenic in situ hybridization (CISH) was used to quantify the HER1 gene. ADAM17 was strongly expressed in all tumours, by both neoplastic and endothelial cells. It was expressed both as a pro‐ and as an active form in tumours and colonic cancer cell lines. ADAM17 mRNA was up‐regulated in 90% of colon carcinomas relative to the paired normal mucosa, whatever the tumour grade or stage. When present, activated EGFR was co‐expressed with ADAM17 by colon carcinomas, although at a variable level among tumour cells, and by endothelial cells. EGFR mRNA was overexpressed in 77% of colon carcinomas compared with the paired normal mucosa. One case showed high‐level amplification of HER1. In conclusion, this study is the first demonstration that ADAM17 is overexpressed in human primary colon carcinoma, whatever the tumour stage and differentiation and whatever the level of EGFR expression. Its co‐expression with EGFR, in both neoplastic and endothelial cells, suggests a role for ADAM17 in tumour growth and angiogenesis. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Prognostic value of MYCN and ID2 overexpression in neuroblastoma
Authors: Alaminos Miguel , Gerald William L. , Cheung Nai‐Kong V. 
Published: July 2005

AbstractBackgroundThe molecular mechanisms driven by overexpression of the MYCN gene in neuroblastoma are not well known. Whether MYCN overexpression in the absence of genomic amplification, or ID2 overexpression has prognostic value remains controversial.ProcedureNinety‐nine neuroblastic tumors from Memorial Sloan‐Kettering Cancer Center and 12 neuroblastoma cell lines were analyzed by Affymetrix U95v2 Microarray System. The expression levels of the genes MYCN and ID2 were determined by RT‐PCR and immunohistochemistry and the clinical value of the overexpression of both genes was determined.ResultsMYCN genomic amplification with overexpression was prognostic for survival (P = 0.0005). Stage 4 patients with MYCN amplification but without overexpression, had no increased likelihood of death, whereas cases with MYCN overexpression but no genomic amplification showed a low survival (P = 0.0096). ID2 did not correlate with MYCN expression (R = −0.23 for tumors and −0.27 for cell lines) or with survival (P = 0.8746).ConclusionsMYCN amplification was not related to clinical outcome in the absence of overexpression in neuroblastoma tumors. ID2 expression appears to be independent of MYCN expression and lacks prognostic value. © 2005 Wiley‐Liss, Inc.
Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: Systematic variation between sample types and calibration of mass spectrometry data
Authors: Haab Brian B. , Geierstanger Bernhard H. , Michailidis George , Vitzthum Frank , Forrester Sara , Okon Ryan , Saviranta Petri , Brinker Achim , Sorette Martin , Perlee Lorah , Suresh Shubha , Drwal Garry , Adkins Joshua N. , Omenn Gilbert S. 
Published: July 2005

AbstractFour different immunoassay and antibody microarray methods performed at four different sites were used to measure the levels of a broad range of proteins (N = 323 assays; 39, 88, 168, and 28 assays at the respective sites; 237 unique analytes) in the human serum and plasma reference specimens distributed by the Plasma Proteome Project (PPP) of the HUPO. The methods provided a means to (1) assess the level of systematic variation in protein abundances associated with blood preparation methods (serum, citrate‐anticoagulated‐plasma, EDTA‐anticoagulated‐plasma, or heparin‐anticoagulated‐plasma) and (2) evaluate the dependence on concentration of MS‐based protein identifications from data sets using the HUPO specimens. Some proteins, particularly cytokines, had highly variable concentrations between the different sample preparations, suggesting specific effects of certain anticoagulants on the stability or availability of these proteins. The linkage of antibody‐based measurements from 66 different analytes with the combined MS/MS data from 18 different laboratories showed that protein detection and the quality of MS data increased with analyte concentration. The conclusions from these initial analyses are that the optimal blood preparation method is variable between analytes and that the discovery of blood proteins by MS can be extended to concentrations below the ng/mL range under certain circumstances. Continued developments in antibody‐based methods will further advance the scientific goals of the PPP.
Immunoaffinity separation of plasma proteins by IgY microbeads: Meeting the needs of proteomic sample preparation and analysis
Authors: Huang Lei , Harvie Gulia , Feitelson Jerald S. , Gramatikoff Kosi , Herold David A. , Allen David L. , Amunngama Ravi , Hagler Rachel A. , Pisano Michael R. , Zhang Wei‐Wei , Fang Xiangming 
Published: July 2005

AbstractSeparation of complex protein mixtures that have a wide dynamic range of concentration, such as plasma or serum, is a challenge for proteomic analysis. Sample preparation to remove high‐abundant proteins is essential for proteomics analysis. Immunoglobulin yolk (IgY) antibodies have unique and advantageous features that enable specific protein removal to aid in the detection of low‐abundant proteins and biomarker discovery. This report describes the efficiency and effectiveness of IgY microbeads in separating 12 abundant proteins from plasma with an immunoaffinity spin column or LC column. The protein separation and sample preparation process was monitored via SDS‐PAGE, 2‐DE, LC‐MS/MS, or clinical protein assays. The data demonstrate the high specificity of the protein separation, with removal of 95–99.5% of the abundant proteins. IgY microbeads against human proteins can also selectively remove orthologous proteins of other mammals such as mouse, rat, etc. Besides the specificity and reproducibility of the IgY microbeads, the report discusses the factors that may cause potential variations in protein separation such as protein–protein interactions (known as “Interactome”), binding and washing conditions of immunoaffinity reagents, etc. A novel concept of Seppromics is introduced to address methodologies and science of protein separation in a context of proteomics.
A novel strategy using MASCOT Distiller for analysis of cleavable isotope‐coded affinity tag data to quantify protein changes in plasma
Authors: Leung Kit‐Yi , Lescuyer Pierre , Campbell James , Byers Helen L. , Allard Laure , Sanchez Jean‐Charles , Ward Malcolm A. 
Published: July 2005

AbstractA novel strategy consisting of cleavable Isotope‐Coded Affinity Tag (cICAT) combined with MASCOT Distiller was evaluated as a tool for the quantification of proteins in ‘abnormal’ patient plasma, prepared by pooling samples from patients with acute stroke. Quantification of all light and heavy cICAT‐labelled peptide ion pairs was obtained using MASCOT Distiller combined with a proprietary software. Peptides displaying differences were selected for identification by MS. These preliminary results show the promise of our approach to identify potential biomarkers.
Web‐based data warehouse on gene expression in human colorectal cancer
Authors: Sagynaliev Emil , Steinert Ralf , Nestler Gerd , Lippert Hans , Knoch Manfred , Reymond Marc‐André 
Published: July 2005

AbstractBased on biomedical literature databases, we tried a first step for constructing a gene expression “data warehouse” specific to human colorectal cancer (CRC). Results of genome‐wide transcriptomic research were available from 12 studies, using various technologies, namely, SAGE, cDNA and oligonucleotide arrays, and adaptor‐tagged amplification. Three studies analyzed CRC cell lines and nine studies of human samples. The total number of patients was 144. Out of 982 up‐ or down‐regulated genes, 863 (88%) were found to be differentially expressed in a single study, 88 in two studies, 22 in three studies, 7 in four studies, and only 2 genes in six studies. Eight large‐scale proteomics studies were published in CRC, using 2‐D‐, SDS‐ or free‐flow electrophoresis, involving only 11 patients. Out of 408 differentially expressed proteins, 339 (83%) were found to be differentially expressed only in a single study, 16 in three studies, 10 in four studies, 3 in five, and 1 in eight studies. Confirmation at proteome level of results obtained with large‐scale transcriptomics studies was possible in 25%. This proportion was higher (67%) for reproducing proteome results using transcriptomics technologies. Obviously, reproducibility and overlapping between published gene expression results at proteome and transcriptome level are low in human CRC. Thus, the development of standardized processes for collecting samples, storing, retrieving, and querying gene expression data obtained with different technologies is of central importance in translational research.
A wide range of protein isoforms in serum and plasma uncovered by a quantitative intact protein analysis system
Authors: Misek David E. , Kuick Rork , Wang Hong , Galchev Vladimir , Deng Bin , Zhao Rong , Tra John , Pisano Michael R. , Amunugama Ravi , Allen David , Walker Angela K. , Strahler John R. , Andrews Philip , Omenn Gilbert S. , Hanash Samir M. 
Published: July 2005

AbstractWe have implemented an orthogonal 3‐D intact protein analysis system (IPAS) to quantitatively profile protein differences between human serum and plasma. Reference specimens consisting of pooled Caucasian‐American serum, citrate‐anticoagulated plasma, and EDTA‐anticoagulated plasma were each depleted of six highly abundant proteins, concentrated, and labeled with a different Cy dye (Cy5, Cy3, or Cy2). A mixture consisting of each of the labeled samples was subjected to three dimensions of separation based on charge, hydrophobicity, and molecular mass. Differences in the abundance of proteins between each of the three samples were determined. More than 5000 bands were found to have greater than two‐fold difference in intensity between any pair of labeled specimens by quantitative imaging. As expected, some of the differences in band intensities between serum and plasma were attributable to proteins related to coagulation. Interestingly, many proteins were identified in multiple fractions, each exhibiting different pI, hydrophobicity, or molecular mass. This is likely reflective of the expression of different protein isoforms or specific protein cleavage products, as illustrated by complement component 3 precursor and clusterin. IPAS provides a high resolution, high sensitivity, and quantitative approach for the analysis of serum and plasma proteins, and allows assessment of PTMs as a potential source of biomarkers.
Novel block–comb/graft copolymers with the macromonomer strategy and anionic polymerization
Authors: Koutalas Giorgos , Lohse David J. , Hadjichristidis Nikos 
Published: July 2005

AbstractThe following block–comb/graft copolymers of styrene (S), isoprene (I), and butadiene (B)—PS‐b‐(PB‐g‐PB), PS‐b‐(PB‐g‐PB)‐b‐PS, (PB‐g‐PB)‐b‐P2VP, (PS‐g‐PB)‐b‐(PI‐g‐PS), (PS‐g‐PB)‐b‐(PI‐g‐PS)‐b‐(PB‐g‐PI), (PS‐g‐PB)‐b‐(PI‐g‐PS)‐b‐(PB‐g‐PI)‐b‐(PI‐g‐PS)‐b‐(PS‐g‐PB), and (PS)2(PB‐g‐PB) [where PS is polystyrene, PB is polybutadiene, P2VP is poly(2‐vinylpyridine) (2VP), and PI is polyisoprene]—were synthesized with the macromonomer strategy and anionic polymerization high‐vacuum techniques. The synthetic approach involves the synthesis and block copolymerization of styrenic macromonomers in situ without isolation. The prepared samples were characterized by size exclusion chromatography with a differential refractometer detector, size exclusion chromatography with a two‐angle laser light scattering detector, and NMR spectroscopy. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4040–4049, 2005
Effect of freezing and thawing on microbial activity and glyphosate degradation in two Norwegian soils
Authors: Stenrød Marianne , Eklo Ole Martin , Charnay Marie‐Paule , Benoit Pierre 
Published: July 2005

AbstractLittle research has been done on pesticide dissipation in cold climates and there is a need to focus on the influence of climate on pesticide degradation in soil. Glyphosate, N‐(phosphonomethyl)glycine, is a herbicide frequently used for controlling perennial weeds through application after harvest and was used as a model compound for this study. The effect of freeze–thaw activity on the availability of glyphosate in soil, and consequently its mineralization by soil microorganisms, was studied through laboratory incubations of repacked soil cores treated with 14C‐labelled glyphosate and subjected to different freeze–thaw treatments. Winter simulation regimes applied were constant thaw (+5 °C), constant freezing (−5 °C), unstable conditions with short fluctuations (24 h of −5 °C followed by 24 h of +5 °C), and long duration fluctuations (3 weeks of −5 °C followed by 3 weeks of +5 °C). Distribution of 14C‐glyphosate was followed during the incubation through measurements of the mineralized fraction (14CO2), soil water fraction, KOH extractable fraction, and non‐extractable fraction. Microbial parameters used to characterize the soils were estimates of size of microbial biomass, overall microbial activity and microbial diversity. The constant freezing treatment exhibited the lowest amount of glyphosate mineralization. The constant thawed treatment and the treatments with fluctuating temperature exhibited significantly increased mineralization. These results were in accordance with the observed concentration of glyphosate in soil water; the higher the activity, the lower the concentration. The amount of glyphosate extractable with KOH and the resulting non‐extractable fraction, however, were not significantly affected by soil type or temperature regime. The glyphosate mineralization pattern was comparable with the overall microbial activity in the soils. Observed different levels of diversity might explain some of the difference in total glyphosate mineralization between soils. Copyright © 2005 Society of Chemical Industry
Treatment methods for the determination of δ2H and δ18O of hair keratin by continuous‐flow isotope‐ratio mass spectrometry
Authors: Bowen Gabriel J. , Chesson Lesley , Nielson Kristine , Cerling Thure E. , Ehleringer James R. 
Published: July 2005

AbstractThe structural proteins that comprise ∼90% of animal hair have the potential to record environmentally and physiologically determined variation in δ2H and δ18O values of body water. Broad, systematic, geospatial variation in stable hydrogen and oxygen isotopes of environmental water and the capacity for rapid, precise measurement via methods such as high‐temperature conversion elemental analyzer/isotope ratio mass spectrometry (TC/EA‐IRMS) make these isotope systems particularly well suited for applications requiring the geolocation of hair samples. In order for such applications to be successful, however, methods must exist for the accurate determination of hair δ2H and δ18O values reflecting the primary products of biosynthesis. Here, we present the results of experiments designed to examine two potential inaccuracies affecting δ2H and δ18O measurements of hair: the contribution of non‐biologic hydrogen and oxygen to samples in the form of sorbed molecular water, and the exchange of hydroxyl‐bound hydrogen between hair keratin and ambient water vapor. We show that rapid sorption of molecular water from the atmosphere can have a substantial effect on measured δ2H and δ18O values of hair (comprising ∼7.7% of the measured isotopic signal for H and up to ∼10.6% for O), but that this contribution can be effectively removed through vacuum‐drying of samples for 6 days. Hydrogen exchange between hair keratin and ambient vapor is also rapid (reaching equilibrium within 3–4 days), with 9–16% of the total hydrogen available for exchange at room temperature. Based on the results of these experiments, we outline a recommended sample treatment procedure for routine measurement of δ2H and δ18O in mammal hair. Copyright © 2005 John Wiley & Sons, Ltd.
Sustainable development (1987–2005): an oxymoron comes of age
Authors: Redclift Michael 
Published: July 2005

AbstractThe paper examines the conceptual history of ‘sustainable development’, from the Brundtland Commission's definition in 1987 to the present day. It argues that the superficial consensus that has characterized much of the early debate has given way to a series of parallel but distinct discourses around sustainability. The underlying assumptions behind much of the discussion are assessed, as is the move, after the first Earth Summit (1992), to focus on rights, rather than needs, as the principal line of enquiry. This analytical attention to rights is linked to the neo‐liberal economic agendas of the 1990s, and the growth of interest in congruent areas, including human security and the environment, social capital, critical natural capital and intellectual property rights. The paper argues that increasing attention to questions of biology and science studies has strengthened this ‘rights‐based’ approach, as well as interest in the linkages between ‘natural’ and ‘human’ systems, including attention to questions of environmental justice. It is clear that issues of global environmental justice are as important as they were when the concept of ‘sustainable development’ was in its infancy, but the new material realities of science and the environment in the 21st century demand a re‐engagement with their social consequences, something which is largely ignored by the (market) liberal consensus. Copyright © 2005 John Wiley & Sons, Ltd and ERP Environment.
Enzyme inhibitors as chemical tools to study enzyme catalysis: rational design, synthesis, and applications
Authors: Hiratake Jun 
Published: July 2005

AbstractCarefully designed molecules that are intimately related to the reaction mechanism of enzymes are often highly selective and potent inhibitors that serve as extremely useful chemical probes for understanding the reaction mechanism and structure of enzymes. This article describes the design, synthesis, and applications of specific inhibitors of two mechanistically distinct groups of enzymes, ATP‐dependent amide ligases and Ser‐ and Thr‐hydrolases. Our strategy is based on the premise that stable analogues of the transition state (transition‐state analogues) are highly potent inhibitors that serve as good mechanistic probes, and that a key structure of a good inhibitor of one enzyme is also utilized for the inhibitors of other enzymes that share the same chemistry in their catalyzed reactions, irrespective of the degree of structural similarity and evolutionary link between the enzymes. According to these principles, we designed and synthesized a series of phosphinate‐ and sulfoximine‐based transition‐state analogue inhibitors of glutathione synthetase, γ‐glutamylcysteine synthetase and asparagine synthetase. For the second group of enzymes, we synthesized a γ‐monofluorophosphono glutamate analogue for mechanism‐based affinity labeling of γ‐glutamyltranspeptidase and fluorescent phosphonic acid esters for the active‐site titration of lipase. These inhibitors were used successfully as ligands for detailed kinetic analyses, X‐ray crystallography, and mass analysis of the enzymes to identify the key amino acid residues responsible for catalysis and substrate recognition in the transition state. © 2005 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 5: 209–228; 2005: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20045
Monoamniotic twins discordant for anencephaly managed conservatively with good outcomes: two case reports and a review of the literature
Authors: Lim K. I. , Dy C. , Pugash D. , Williams K. P. 
Published: July 2005

AbstractMonoamniotic twin pregnancy discordant for anencephaly (MATDA) is a rare occurrence with only seven prior reported cases. Selective termination has been advocated in managing discordant monoamniotic twins. We report two cases managed expectantly with good outcomes and review other previously reported cases. The first case was a primigravid woman diagnosed with MATDA at 18 weeks. She was managed expectantly until 32 + 5 weeks when a Cesarean section was performed for preterm labor. The surviving female infant weighed 1610 g. The second case was a multigravid woman who was diagnosed with MATDA at 17 + 5 weeks and was managed as an outpatient. An emergency Cesarean section was performed at 31 weeks for non‐reassuring monitoring and the surviving male infant weighed 1790 g. In both cases, the survivors were discharged home in good condition. A review of these two cases and those in the literature suggests that expectant management should be considered among management options for this rare condition. Copyright © 2005 ISUOG. Published by John Wiley & Sons, Ltd.