bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the computation of nearly singular integrals in 3D BEM collocation
Authors: Scuderi Letizia 
Published: November 2007

AbstractIn this paper, we propose an efficient strategy to compute nearly singular integrals over planar triangles in R3 arising in boundary element method collocation. The strategy is based on a proper use of various non‐linear transformations, which smooth or move away or quite eliminate all the singularities close to the domain of integration. We will deal with near singularities of the form 1/r, 1/r2 and 1/r3, r=∥x−y∥ being the distance between a fixed near observation point x and a generic point y of a triangular element. Extensive numerical tests and comparisons with some already existing methods show that the approach proposed here is highly efficient and competitive. Copyright © 2007 John Wiley & Sons, Ltd.
A boundary meshless method using Chebyshev interpolation and trigonometric basis function for solving heat conduction problems
Authors: Reutskiy S. Yu. , Chen C. S. , Tian H. Y. 
Published: November 2007

AbstractA boundary meshless method has been developed to solve the heat conduction equations through the use of a newly established two‐stage approximation scheme and a trigonometric series expansion scheme to approximate the particular solution and fundamental solution, respectively. As a result, no fundamental solution is required and the closed form of approximate particular solution is easy to obtain. The effectiveness of the proposed computational scheme is demonstrated by several examples in 2D and 3D. We also compare our proposed method with the finite‐difference method and the other meshless method showed in Šarler and Vertnik (Comput. Math. Appl. 2006; 51:1269–1282). Excellent numerical results have been observed. Copyright © 2007 John Wiley & Sons, Ltd.
Assumed strain finite element methods for conserving temporal integrations in non‐linear solid dynamics
Authors: Armero F. 
Published: November 2007

AbstractThis paper presents a new class of assumed strain finite elements to use in combination with general energy‐momentum‐conserving time‐stepping algorithms so that these conservation properties in time are preserved by the fully discretized system in space and time. The case of interest corresponds to nearly incompressible material responses, in the fully non‐linear finite strain elastic and elastoplastic ranges. The new elements consider the classical scaling of the deformation gradient with an assumed Jacobian (its determinant) defined locally through a weighted averaging procedure at the element level. The key aspect of the newly proposed formulation is the definition of the associated linearized strain operator or B‐bar operator. The developments presented here start by identifying the conditions that this discrete operator must satisfy for the fully discrete system in time and space to inherit exactly the conservation laws of linear and angular momenta, and the conservation/dissipation law of energy for elastic and inelastic problems, respectively. Care is also taken of the preservation of the relative equilibria and the corresponding group motions associated with the momentum conservation laws, and characterized by purely rotational and translational motions superimposed to the equilibrium deformed configuration. With these developments at hand, a new general B‐bar operator is introduced that satisfies these conditions. The new operator not only accounts for the spatial interpolations (e.g. bilinear displacements with piece‐wise constant volume) but also depends on the discrete structure of the equations in time. The aforementioned conservation/dissipation properties of energy and momenta are then proven to hold rigorously for the final numerical schemes, unconditionally of the time step size and the material model (elastic or elastoplastic). Different finite elements are considered in this framework, including quadrilateral and triangular elements for plane problems and brick elements for three‐dimensional problems. Several representative numerical simulations are presented involving, in particular, the use of energy‐dissipating momentum‐conserving time‐stepping schemes recently developed by the author and co‐workers for general finite strain elastoplasticity in order to illustrate the properties of the new finite elements, including these conservation/dissipation properties in time and their locking‐free response in the quasi‐incompressible case. Copyright © 2007 John Wiley & Sons, Ltd.
Utility of microsatellite analysis in evaluation of pregnancies with placental mesenchymal dysplasia
Authors: Schuetzle Marie N. , Uphoff Timothy S. , Hatten Bonnie A. , Dawson D. Brian 
Published: November 2007

AbstractObjectiveTo demonstrate a role for microsatellite analysis in the evaluation of prenatal cases with possible placental mesenchymal dysplasia (PMD).MethodsWe present a case report in which several molecular analyses of amniocytes and products of conception were used in combination with cytogenetic and ultrasound studies to evaluate a pregnancy with a clinical suspicion of PMD. A combination of Southern blotting analysis, methylation‐sensitive polymerase chain reaction (PCR) and multiplex ligation‐dependent probe amplification (MLPA) was utilized to evaluate methylation patterns in the Beckwith–Wiedemann syndrome (BWS) and Prader–Willi/Angelman syndrome (PW/AS) critical regions. A series of microsatellite markers were used to evaluate the possibility of an androgenetic cell line.ResultsMethylation studies performed for the BWS and PW/AS critical regions were abnormal and consistent with a molecular diagnosis of BWS and Angelman syndrome. Further studies of amniocytes using microsatellite markers identified androgenetic and biparental cell lines in approximately a 10:1 ratio, respectively.ConclusionsPrenatal ultrasonography, karyotyping and molecular genetic evaluation for BWS alone were not sufficient to identify the underlying etiology of PMD in this case. The androgenetic cell line was only identified after microsatellite analysis. Copyright © 2007 John Wiley & Sons, Ltd.
Resolution of trisomic mosaicism in prenatal diagnosis: estimated performance of a 50K SNP microarray
Authors: Cross Jillian , Peters Greg , Wu Zhanhe , Brohede Jesper , Hannan Garry N. 
Published: November 2007

AbstractObjectiveTo evaluate the ability of a DNA single nucleotide polymorphism (SNP) microarray to detect chromosome mosaicism for trisomy in prenatal samples in order to compare this with conventional cytogenetics.MethodWe created a dilution series of mock mosaic samples, by mixing measured amounts of fibroblast cells containing trisomy 8 from a male with aliquots of cells with a normal female karyotype. DNAs were extracted from these mosaic mixtures, then analysed on the Affymetrix 50K Xba SNP chip. Duplicate aliquots of each mosaic sample were probed using interphase FISH, with centromeric probes for chromosomes X, Y and 8, to estimate independently the proportion of male trisomy 8 in each sample. Data from the arrays were analysed using publicly available analysis tools. Statistical calculations were then performed using a Student's t‐test to determine if there was a significant difference between the copy numbers of each chromosome.ResultsThese experiments using the Affymetrix 50K Xba SNP microarray showed mosaicism to be obvious at 20% and with additional statistical calculations, the lower limit for detection is about 10%.ConclusionThe SNP microarray platform tested can detect mosaicism for trisomy in prenatal samples at levels comparable with conventional cytogenetic techniques in routine use. Copyright © 2007 John Wiley & Sons, Ltd.
Small intestinal atresia in a defined population: occurrence, prenatal diagnosis and survival
Authors: Hemming Victoria , Rankin Judith 
Published: November 2007

AbstractObjectiveTo describe the prevalence, associated anomalies, prenatal diagnosis, and survival of cases of congenital small intestinal atresia (SIA).MethodData were extracted from the Northern Congenital Abnormality Survey (NorCAS) for cases delivered during 1991 to 2001.ResultsA total of 99 cases of SIA were notified from 372 717 registered births. Twenty‐five (25.8%) SIA cases were associated with a chromosomal anomaly. Of the 72 SIA cases with normal karyotype, 18 (25%) were associated with other structural anomalies. The total prevalence for all SIA cases over the 11 years was 2.66 per 10 000 registered births (95% CI 2.13, 3.18), and the livebirth prevalence was 2.37 per 10 000 livebirths (95% CI 1.88, 2.87). For jejunoileal atresia, the total prevalence increased from 0.54 per 10 000 births during 1991–1995 to 1.11 per 10 000 births during 1996–2001, and livebirth prevalence increased from 0.49 to 1.06 per 10 000 livebirths. The more proximal the lesion the prenatal diagnosis sensitivity was slightly better with 19 (44.2%) cases of duodenal atresia and 3 (42.8%) cases of jejunal atresia diagnosed prenatally by routine ultrasonography.ConclusionThis population‐based study of SIA has confirmed several previous findings but, by considering subtypes separately, it also suggests a trend towards an increase in the prevalence of jejunoileal atresia (JIA). Copyright © 2007 John Wiley & Sons, Ltd.
A high yield of fetal nucleated red blood cells isolated using optimal osmolality and a double‐density gradient system
Authors: Kwon K. H. , Jeon Y. J. , Hwang H. S. , Lee K. A. , Kim Y. J. , Chung H. W. , Pang M. G. 
Published: November 2007

AbstractObjectivesTo increase the yield of fetal nucleated red blood cells (NRBCs) from maternal blood using a discontinuous Percoll gradient and to determine the effects of osmolality on NRBC yield.MethodsFetal NRBCs were isolated from combined umbilical cord blood and adult female blood, or from maternal blood using single or double Percoll gradients with different osmolalities. Magnetic activated cell sorting was used to enrich isolated NRBCs, and morphological differentiation was performed with Kleihauer–Betke stain. We also isolated fetal NRBCs from 25 10 mL samples of maternal blood and determined fetal sex by fluorescence in situ hybridization (FISH), using X‐Y probes.ResultsFor single‐density Percoll columns, the greatest number of NRBCs was isolated using 280 mOsm/kg H2O with 1.077 g/mL Percoll and 520 mOsm/kg H2O with 1.119 g/mL Percoll. Significantly more fetal NRBCs were isolated with double Percoll density gradients than with double‐Histopaque gradients (p = 0.043). FISH analysis on NRBC in 25 cases correctly identified 15 male and 9 female euploid fetuses and one Trisomy 21 fetus.ConclusionThe NRBC enrichment method we present requires less maternal blood and yields more NRBCs compared to previous methods. Copyright © 2007 John Wiley & Sons, Ltd.
Quantitative aberrations of hypermethylated RASSF1A gene sequences in maternal plasma in pre‐eclampsia
Authors: Tsui Dana W. Y. , Chan K. C. Allen , Chim Stephen S. C. , Chan Lin‐wai , Leung Tak‐yeung , Lau Tze‐kin , Lo Y. M. Dennis , Chiu Rossa W. K. 
Published: November 2007

AbstractObjectiveTo study if quantitative aberrations in circulating placental‐derived hypermethylated RASSF1A DNA in maternal plasma are associated with pre‐eclamptic pregnancies.MethodMaternal plasma and placental tissues from third‐trimester pre‐eclamptic women and gestational‐age matched normotensive controls were studied. Real‐time PCR was performed to quantify RASSF1A concentrations before and after methylation‐sensitive restriction digestion in a duplex assay, where ß‐actin concentrations were quantified as an internal control to confirm complete enzyme digestion.ResultsThe median concentrations of hypermethylated RASSF1A were 4.3‐fold higher in maternal plasma of pre‐eclamptic subjects than in controls. There was no significant difference between the extent of RASSF1A hypermethylation in placental tissues obtained from pre‐eclamptic and control pregnancies.ConclusionThis study demonstrated the potential utility of hypermethylated RASSF1A sequences in maternal plasma as a gender‐ and polymorphism‐independent marker for pre‐eclampsia. Copyright © 2007 John Wiley & Sons, Ltd.
Steady state protein levels in Geobacter metallireducens grown with iron (III) citrate or nitrate as terminal electron acceptor
Authors: Ahrendt Angela J. , Tollaksen Sandra L. , Lindberg Carl , Zhu Wenhong , Yates John R. , Nevin Kelly P. , Babnigg György , Lovley Derek R. , Giometti Carol S. 
Published: November 2007

AbstractGeobacter species predominate in aquatic sediments and submerged soils where organic carbon sources are oxidized with the reduction of Fe(III). The natural occurrence of Geobacter in some waste sites suggests this microorganism could be useful for bioremediation if growth and metabolic activity can be regulated. 2‐DE was used to monitor the steady state protein levels of Geobacter metallireducens grown with either Fe(III) citrate or nitrate to elucidate metabolic differences in response to different terminal electron acceptors present in natural environments populated by Geobacter. Forty‐six protein spots varied significantly in abundance (p<0.05) between the two growth conditions; proteins were identified by tryptic peptide mass and peptide sequence determined by MS/MS. Enzymes involved in pyruvate metabolism and the tricarboxylic acid (TCA) cycle were more abundant in cells grown with Fe(III) citrate, while proteins associated with nitrate metabolism and sensing cellular redox status along with several proteins of unknown function were more abundant in cells grown with nitrate. These results indicate a higher level of flux through the TCA cycle in the presence of Fe(III) compared to nitrate. The oxidative stress response observed in previous studies of Geobacter sulfurreducens grown with Fe(III) citrate was not seen in G. metallireducens.
Comparative proteomics of industrial lager yeast reveals differential expression of the cerevisiae and non‐cerevisiae parts of their genomes
Authors: Caesar Robert , Palmfeldt Johan , Gustafsson John S. , Pettersson Ellinor , Hashemi Sayed Hossein , Blomberg Anders 
Published: November 2007

AbstractThe proteomes of three industrial lager beer strains, CMBS33, OG2252 and A15, were analysed under standardised laboratory growth conditions. Protein spots in the 2‐DE pattern of the lager strains were subjected to MS/MS to identify protein variants. We found the protein composition of the three lager strains to be qualitatively rather similar, while being substantially different from the Saccharomyces cerevisiae strain BY4742. Database searches using several fully sequenced genomes from the Saccharomyces genera indicated that the non‐cerevisiae proteins in the 2‐D pattern of lager strains were most closely related to S. bayanus. For many proteins the regulation of the bayanus‐like protein and its cerevisiae counterpart varied in a strain‐dependent manner, e.g. the bayanus‐like form of Tdh3p was roughly eight‐fold more abundant than the cerevisiae form in the OG2252 strain. We also found differential regulation of cerevisiae‐ and bayanus‐like proteins during various stress conditions like low temperature growth, and adaptation to high temperatures or high salinity, e.g. for Arg1p, Sti1p and Pdc1p. Our data on the differential regulation of the two genomes in these hybrid strains may have important industrial implications for strain improvement and strain protection.
Mass spectrometry‐based prokaryote gene annotation
Authors: Ishino Yoko , Okada Hitomi , Ikeuchi Masahiko , Taniguchi Hisaaki 
Published: November 2007

AbstractMS combined with database searching has become the preferred method for identifying proteins present in cell or tissue samples. The technique enables us to execute large‐scale proteome analyses of species whose genomes have already been sequenced. Searching mass spectrometric data against protein databases composed of annotated genes has been widely conducted. However, there are some issues with this technique; wrong annotations in protein databases cause deterioration in the accuracy of protein identification, and only proteins that have already been annotated can be identified. We propose a new framework that can detect correct ORFs by integrating an MS/MS proteomic data mapping and a knowledge‐based system regarding the translation initiation sites. This technique can provide correction of predicted coding sequences, together with the possibility of identifying novel genes. We have developed a computational system; it should first conduct the probabilistic peptide‐matching against all possible translational frames using MS/MS data, then search for discriminative DNA patterns around the detected peptides, and lastly integrate the facts using empirical knowledge stored in knowledge bases to obtain correct ORFs. We used photosynthetic bacteria Synechocystis sp. PCC6803 as a sample prokaryote, resulting in the finding of 14 N‐terminus annotation errors and several new candidate genes.
Identification of intra‐ and intermolecular disulphide bonding in the plant mitochondrial proteome by diagonal gel electrophoresis
Authors: Winger Alison M. , Taylor Nicolas L. , Heazlewood Joshua L. , Day David A. , Millar A. Harvey 
Published: November 2007

AbstractRedox active proteins in plant mitochondria were examined using 2‐D oxidant/reductant diagonal‐SDS‐PAGE to separate and identify proteins with intermolecular or intramolecular disulphide bonds using diamide in the first dimension and DTT in the second dimension. Eighteen proteins spots were resolved either above or below the diagonal and these were in‐gel digested and identified by MS/MS. This analysis revealed intermolecular disulphide bonds in alternative oxidase, O‐acetylserine (thiol) lyase, citrate synthase and between subunits of the ATP synthase. Intramolecular disulphide bonds were observed in a range of mitochondrial dehydrogenases, elongation factor Tu, adenylate kinase and the phosphate translocator. Many of the soluble proteins found were known glutaredoxin/thioredoxin targets in other plants, but the membrane proteins were not found by these methods nor were the nature of the disulphides able to be investigated. The accessibility of thiols involved in disulphide bonds to modification by a lipid derived aldehyde gave an insight into the potential impact of Cys modification on redox‐functions in mitochondria during lipid peroxidation. Comparison of the protein sequences of the identified proteins with homologs from other species has identified specific Cys residues that may be responsible for plant‐specific redox modulations of mitochondrial proteins.
A proteomic kinetic analysis of IGROV1 ovarian carcinoma cell line response to cisplatin treatment
Authors: Le Moguen Karen , Lincet Hubert , Marcelo Paulo , Lemoisson Edwige , Heutte Natacha , Duval Marilyne , Poulain Laurent , Vinh Joëlle , Gauduchon Pascal , Baudin Bruno 
Published: November 2007

AbstractOvarian cancer is one of the leading causes of mortality by gynecological cancer. Despite good response to surgery and initial chemotherapy, essentially based on cisplatin (cis‐diamino‐dichloro‐platinum(II) (CDDP)) compounds, frequent recurrences with chemoresistance acquisition are responsible for poor prognosis. Several mechanisms have been described as implicated in CDDP resistance, however they are not sufficient to exhaustively account for this resistance emergence. We applied a proteomic approach based on 2‐DE coupled with MS (MALDI‐TOF/TOF) to identify proteins associated with chemoresistance induced by CDDP. A kinetic analysis of IGROV1 cell behavior following treatment with CDDP and subsequent statistical analysis revealed time and/or concentration‐dependent modifications in protein expression. We evidenced events such as decreased amino‐acid and nucleotide synthesis potentially associated with cell cycle blockade, and variations that may be related to resistance acquisition, such as possible enhanced glycolysis and increased proliferating potential. Moreover, overexpressions of aldehyde dehydrogenase 1 and both cytokeratins 8 and 18 were consistent with our previous findings, demonstrating that expression of these proteins was increased in cisplatin‐resistant IGROV1‐R10 as compared to IGROV1 parental cells. Identification of such proteins could allow improved understanding of the mechanisms leading to cell death or survival and, thus, to the acquisition of chemoresistance.
Proteomic analysis identified N‐cadherin, clusterin, and HSP27 as mediators of SPARC (secreted protein, acidic and rich in cysteines) activity in melanoma cells
Authors: Sosa María Soledad , Girotti María Romina , Salvatierra Edgardo , Prada Federico , de Olmo Juan Antonio López , Gallango Silvia Juárez , Albar Juan Pablo , Podhajcer Osvaldo Luis , Llera Andrea Sabina 
Published: November 2007

AbstractSecreted protein, acidic and rich in cysteines (SPARC) is a secreted protein associated with increased aggressiveness of different human cancer types. In order to identify downstream mediators of SPARC activity, we performed a 2‐DE proteomic analysis of human melanoma cells following antisense‐mediated downregulation of SPARC expression. We found 23/504 differential spots, 15 of which were identified by peptide fingerprinting analysis. Three of the differential proteins (N‐cadherin (N‐CAD), clusterin (CLU), and HSP27) were validated by immunoblotting, confirming decreased levels of N‐CAD and CLU and increased amounts of HSP27 in conditioned media of cells with diminished SPARC expression. Furthermore, transient knock down of SPARC expression in melanoma cells following adenoviral‐mediated transfer of antisense RNA confirmed these changes. We next developed two different RNAs against SPARC that were able to inhibit in vivo melanoma cell growth. Immunoblotting of the secreted fraction of RNAi‐transfected melanoma cells confirmed that downregulation of SPARC expression promoted decreased levels of N‐CAD and CLU and increased secretion of HSP27. Transient re‐expression of SPARC in SPARC‐downregulated cells reverted extracellular N‐CAD, CLU, and HSP27 to levels similar to those in the control. These results constitute the first evidence that SPARC, N‐CAD, CLU, and HSP27 converge in a unique molecular network in melanoma cells.
Glycosylation profiling of immunoglobulin G (IgG) subclasses from human serum
Authors: Wuhrer Manfred , Stam Jord C. , van de Geijn Fleur E. , Koeleman Carolien A. M. , Verrips C. Theo , Dolhain Radboud J. E. M. , Hokke Cornelis H. , Deelder André M. 
Published: November 2007

AbstractAll four subclasses of human serum IgG contain a single N‐glycosylation site in the constant region of their heavy chain, which is occupied by biantennary, largely core‐fucosylated and partially truncated oligosaccharides, that may carry a bisecting N‐acetylglucosamine and sialic acid residues. IgG glycosylation has been shown to be altered under various physiological and pathological circumstances. IgG N‐glycan profiles vary with age, and galactosylation for example is enhanced during pregnancy. Several diseases including rheumatoid arthritis are associated with a reduction in galactosylation of the IgG N‐glycans. Here, we describe a robust method for the isolation of IgG subclasses using protein A (binds IgG1, IgG2, and IgG4) and protein G (binds additionally IgG3) at the 96‐well plate level, which is suitable for automation. Isolated IgGs were digested with trypsin, and obtained glycopeptides were analyzed by nano‐LC‐MS. Glycopeptides were characterized by CID as well as electron transfer dissociation (ETD). The method provided glycosylation profiles for IgG1, IgG2, IgG3, and IgG4 and revealed distinct differences in N‐glycosylation between the four IgG subclasses. The changes in galactosylation associated with rheumatoid arthritis could readily be monitored. This method is suitable for the subclass‐specific analysis of IgG glycosylation from clinical samples.