bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplex Ligation‐dependent Probe Amplification (MLPA) as a stand‐alone test for rapid aneuploidy detection in amniotic fluid cells
Authors: Kooper Angelique J. A. , Faas Brigitte H. W. , Kater‐Baats Ellen , Feuth Ton , Janssen Jasper C. J. A. , van der Burgt Ineke , Lotgering Fred K. , Geurts van Kessel Ad , Smits Arie P. T. 
Published: October 2008

AbstractObjectiveThis study aimed to determine the diagnostic application of multiplex ligation‐dependent probe amplification (MLPA) as a stand‐alone test for targeted detection of common chromosomal aneuploidies (i.e. 13, 18, 21, X and Y) in amniotic fluid cells in routine prenatal clinical practice.MethodsIn this evaluation study, the MLPA test using kit P095 was performed on 1000 consecutive amniotic fluid samples and the results obtained were compared with traditional karyotyping (TK), the gold standard.ResultsThe absolute specificity and sensitivity of the MLPA test were 100%. The test yielded a rapid reporting time: 94% within three working days and 5% within seven working days. The test failure rate was 0.8%. The percentage of abnormalities undetectable using this specific test was 2.4%: abnormal foetal ultrasound (N = 9), increased risk first trimester screening (N = 2), advanced maternal age (N = 3) or other reason for referral (N = 10). These abnormalities can be categorised in clinically significant (N = 8), clinically uncertain (N = 4) and clinically nonsignificant (N = 12).ConclusionsMLPA P095 is suitable as a stand‐alone test for the rapid and efficient detection of the most common chromosomal aneuploidies in routine prenatal clinical practice. A flow chart for integrating the MLPA test into the cytogenetic laboratory workflow is presented. Copyright © 2008 John Wiley & Sons, Ltd.
Influence of ultrasonographers training on prenatal diagnosis of congenital heart diseases: a 12‐year population‐based study
Authors: Pézard Ph. , Bonnemains L. , Boussion F. , Sentilhes L. , Allory P. , Lépinard C. , Guichet A. , Triau S. , Biquard F. , Leblanc M. , Bonneau D. , Descamps Ph. 
Published: October 2008

AbstractObjectiveSince 1998, French multidisciplinary prenatal diagnosis centers (CPDPN) offer a training opportunity to first‐level screening sonographers. This study measures the impact of this training on prenatal detection rates of congenital heart diseases (CHDs).MethodsWe analyzed the sensitivity of screening sonographers by comparing CHD prenatal diagnoses and CHDs observed after birth in the area of Angers from 1994 to 2006. Two groups of sonographers were compared, those who attended the training (n = 19) and those who did not (control group. n = 21). The evolution of CHD detection rate was compared between two successive periods of 6 years each.ResultsOf 947 CHDs, 438 (46%) were detected prenatally. The control group sensitivity was 16 versus 37% for the sonographers who had attended the training course (p < 0.001).Between the two study periods, detection rates for all CHDs and significant CHDs remained unchanged in the control group, whereas they improved significantly in the other group (respectively 54% vs 33% and 75% vs 38%, p < 0.05).ConclusionThis study supports the hypothesis of a beneficial effect of CPDPN on prenatal diagnosis of CHDs. These centers not only fulfill their primary purpose but also operate as learning centers in which screening sonographers may improve their practice. Copyright © 2008 John Wiley & Sons, Ltd.
The utility of detailed first trimester ultrasound examination in abnormal fetal nuchal translucency
Authors: Bronshtein Moshe , Zimmer Etan Z. , Blazer Shraga 
Published: October 2008

AbstractObjectiveTo determine the value of a first trimester fetal ultrasound examination in cases of an increased nuchal translucency (NT).MethodA detailed fetal ultrasound examination was performed within 4 days of a detection of a first trimester increased NT.ResultsAs many as 23 fetuses were evaluated. Severe anomalies were detected in eight and mild anomalies were detected in six fetuses. Two fetuses had trisomy 13, one had trisomy 21, and 16 fetuses had a normal karyotype. A chromosomal analysis was not available in four fetuses with major anomalies due to parental decision. In one fetus, craniosynostosis was detected only at 24 weeks' gestation.ConclusionsThe current study shows that a first trimester targeted scan of fetuses with an increased NT in an experienced center can shorten the parental decision‐making process and spare parents a prolonged period of diagnostic uncertainty and anxiety, particularly when a structural anomaly is clearly diagnosed in the first trimester. Copyright © 2008 John Wiley & Sons, Ltd.
Exfoliation targeted toughness enhancement in polypropylene‐blend‐ montmorillonite nanocomposites
Authors: Bagcioglu Cuneyt , Altuntas Esra , Şen Sinan , Bora İslier M , Ersoy Osman G , Ersoy Nuri , Nugay Turgut , Nugay Nihan 
Published: October 2008

AbstractBACKGROUND: Both exfoliated and toughened polypropylene‐blend‐montmorillonite (PP/MMT) nanocomposites were prepared by melt extrusion in a twin‐screw extruder. Special attention was paid to the enhancement of clay exfoliation and toughness properties of PP by the introduction of a rubber in the form of compatibilizer toughener: ethylene propylene diene‐based rubber grafted with maleic anhydride (EPDM‐g‐MA).RESULTS: The resultant nanocomposites were characterized using X‐ray diffraction, atomic force microscopy, scanning electron microscopy, thermogravimetric analysis, dynamic mechanical analysis and Izod impact testing methods. It was found that the desired exfoliated nanocomposite structure could be achieved for all compatibilizer to organoclay ratios as well as clay loadings. Moreover, a mechanism involving a decreased size of rubber domains surrounded with nanolayers as well as exfoliation of the nanolayers in the PP matrix was found to be responsible for a dramatic increase in impact resistance of the nanocomposites.CONCLUSION: Improved thermal and dynamic mechanical properties of the resultant nanocomposites promise to open the way for highly toughened super PPs via nanocomposite assemblies even with very low degrees of loading. Copyright © 2008 Society of Chemical Industry
Identification of proteins to predict the molecular basis for the observed gender susceptibility in a rat model of alcoholic steatohepatitis by 2‐D gel proteomics
Authors: Banerjee Atrayee , Russell William K. , Jayaraman Arul , Ramaiah Shashi K. 
Published: October 2008

AbstractFemales are reported to be highly susceptible to alcoholic steatohepatitis (ASH) compared to the males. Although a variety of mechanisms have been proposed to explain this higher sensitivity of females, the precise mechanism is not well understood. The objective of this study was to identify changes in global protein expression in liver tissues of male and female rats with pathologically evident ASH by 2‐DE (dimensional electrophoresis). ASH was induced in the SD (Sprague‐Dawley) rats by feeding ethanol (EtOH) containing Lieber‐DeCarli diet for 6 wk followed by a single injection of lipopolysaccharide (LPS, 10 mg/kg, i.p.). Higher liver injury in females in the ASH group as compared to the males was confirmed by HE stained liver sections. As identified by 2‐DE, 22 protein‐spots were differentially expressed in the females in the ASH group as compared to the males. Following identification of these proteins by MALDI‐MS, they were mainly categorized into metabolism and oxidative stress‐related proteins. The expression pattern of a few of these oxidative stress‐related proteins like Ferritin Heavy chain (Ferritin‐H chain), ER stress protein 60 (ER 60) and Heat‐shock protein‐60 (HSP 60) were verified by Western blotting. To conclude, the current study has identified a set of proteins that highlights potential novel mechanisms associated with higher liver injury noted in the female rat ASH model.
Proteomic analysis of circulating monocytes in Chinese premenopausal females with extremely discordant bone mineral density
Authors: Deng Fei‐Yan , Liu Yao‐Zhong , Li Li‐Ming , Jiang Chen , Wu Shan , Chen Yuan , Jiang Hui , Yang Fang , Xiong Ji‐Xian , Xiao Peng , Xiao Su‐Mei , Tan Li‐Jun , Sun Xiao , Zhu Xue‐Zhen , Liu Man‐Yuan , Lei Shu‐Feng , Chen Xiang‐Ding , Xie Jing‐Yun , Xiao Gary G. , Liang Song‐Ping , Deng Hong‐Wen 
Published: October 2008

AbstractOsteoporosis (OP) is a major public health problem, mainly characterized by low bone mineral density (BMD). Circulating monocytes (CMCs) may serve as progenitors of osteoclasts and produce a wide variety of factors important to bone metabolism. However, the specific action mechanism of CMCs in the pathogenesis of OP is far from clear. We performed a comparative protein expression profiling study of CMCs in Chinese premenopausal females with extremely discordant BMD, identified a total of 38 differentially expressed proteins, and confirmed with Western blotting five proteins: ras suppressor protein1 (RSU1), gelsolin (GSN), manganese‐containing superoxide dismutase (SOD2), glutathione peroxidase 1(GPX1), and prolyl 4‐hydroxylase β subunit (P4HB). These proteins might affect CMCs' trans‐endothelium, differentiation, and/or downstream osteoclast functions, thus contribute to differential osteoclastogenesis and finally lead to BMD variation. The findings promote our understanding of the role of CMCs in BMD determination, and provide an insight into the pathogenesis of human OP.
A rapid approach for phenotype‐screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment
Authors: Hoehenwarter Wolfgang , van Dongen Joost T. , Wienkoop Stefanie , Steinfath Matthias , Hummel Jan , Erban Alexander , Sulpice Ronan , Regierer Babette , Kopka Joachim , Geigenberger Peter , Weckwerth Wolfram 
Published: October 2008

AbstractThe dynamics of a proteome can only be addressed with large‐scale, high‐throughput methods. To cope with the inherent complexity, techniques based on targeted quantification using proteotypic peptides are arising. This is an essential systems biology approach; however, for the exploratory discovery of unexpected markers, nontargeted detection of proteins, and protein modifications is indispensable. We present a rapid label‐free shotgun proteomics approach that extracts relevant phenotype‐specific peptide product ion spectra in an automated workflow without prior identification. These product ion spectra are subsequently sequenced with database search andde novoprediction algorithms. We analyzed six potato tuber cultivars grown on three plots of two geographically separated fields in Germany. For data mining about 1.5 million spectra from 107 analyses were aligned and statistically examined in approximately 1 day. Several cultivar‐specific protein markers were detected. Based onde novo‐sequencing a dominant protein polymorphism not detectable in the available EST‐databases was assigned exclusively to a specific potato cultivar. The approach is applicable to organisms with unsequenced or incomplete genomes and to the automated extraction of relevant mass spectra that potentially cannot be identified by genome/EST‐based search algorithms.
In vivo proteome dynamics during early bovine myogenesis
Authors: Chaze Thibault , Meunier Bruno , Chambon Christophe , Jurie Catherine , Picard Brigitte 
Published: October 2008

AbstractMyogenesis is a complex process of which the underlying mechanisms are conserved between species, including birds and mammals. Despite a good understanding of the stages of myogenesis, many of the mechanisms involved in the regulation of proliferation of the successive myoblast generations, the cellular transitions cell proliferation/alignment of myoblasts/fusion of myoblasts into myotubes/differentiation of myofibres and the control of total myofibre number still remain unknown. An in vivo proteomic analysis of the semitendinosus muscle from Charolais foetuses, at three specific stages of myogenesis (60, 110 and 180 days postconception), was conducted using 2‐DE and MS. Expression profiles of more than 170 proteins were revealed and analysed using two way hierarchical clustering and statistical analysis. Our studies identify, for the first time, distinct proteins of varied biological functions and protein clusters with myogenic processes, such as the control of cell cycle activity and apoptosis, the establishment of cellular metabolism and muscle contractile properties and muscle cell reorganisation. These results are of fundamental interest to the field of myogenesis in general, and more specifically to the control of muscle development in meat producing animals.
Quantitative structure activity relationship of IA3‐like peptides as aspartic proteinase inhibitors
Authors: Padrón‐García Juan Alexander , Alonso‐Tarajano Manuel , Alonso‐Becerra Esther , Winterburn Tim J. , Ruiz Yasser , Kay John , Berry Colin 
Published: October 2008

AbstractThe IA3 polypeptide inhibitor from Saccharomyces cerevisiae interacts potently and selectively with its target, the S. cerevisiae vacuolar aspartic proteinase (ScPr). Upon encountering the enzyme, residues 2–32 of the intrinsically unstructured IA3 polypeptide become ordered into an almost‐perfect alpha‐helix. In previous IA3 mutagenesis studies, we identified important characteristics of the enzyme inhibitor interactions and generated a large dataset of variants with Ki values determined experimentally at pH 3.1 and 4.7. Using this information, the three‐dimensional structure of each variant was modelled in silico with the correct protonation for each experimental pH value. A set of descriptors of the inhibitor/ScPr interactions was then calculated and used to establish mathematical models relating the variant sequences to their inhibitory activities at each pH. Cross‐validation, external‐set validation and five separate selections of the training and test samples confirmed the robustness of the equations. A major contributor to the structure‐activity relationship was the free energy of binding calculated by the FoldX program. The mathematical models were challenged further (i) by in silico alanine‐scanning mutagenesis of residues 2–32 in IA3 and relating binding energy to experimentally derived inhibition constants for selected representatives of these variants; and (ii) by predicting inhibitory‐potencies for two novel IA3‐variants. The predictions of the equations for these new IA3‐variants with ScPr matched almost precisely the kinetic data determined experimentally. The models described represent valuable tools for the future design of novel inhibitor variants active against ScPr and other aspartic proteinases. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Local descriptors of protein structure: A systematic analysis of the sequence‐structure relationship in proteins using short‐ and long‐range interactions
Authors: Hvidsten Torgeir R. , Kryshtafovych Andriy , Fidelis Krzysztof 
Published: October 2008

AbstractLocal protein structure representations that incorporate long‐range contacts between residues are often considered in protein structure comparison but have found relatively little use in structure prediction where assembly from single backbone fragments dominates. Here, we introduce the concept of local descriptors of protein structure to characterize local neighborhoods of amino acids including short‐ and long‐range interactions. We build a library of recurring local descriptors and show that this library is general enough to allow assembly of unseen protein structures. The library could on average re‐assemble 83% of 119 unseen structures, and showed little or no performance decrease between homologous targets and targets with folds not represented among domains used to build it. We then systematically evaluate the descriptor library to establish the level of the sequence signal in sets of protein fragments of similar geometrical conformation. In particular, we test whether that signal is strong enough to facilitate correct assignment and alignment of these local geometries to new sequences. We use the signal to assign descriptors to a test set of 479 sequences with less than 40% sequence identity to any domain used to build the library, and show that on average more than 50% of the backbone fragments constituting descriptors can be correctly aligned. We also use the assigned descriptors to infer SCOP folds, and show that correct predictions can be made in many of the 151 cases where PSI‐BLAST was unable to detect significant sequence similarity to proteins in the library. Although the combinatorial problem of simultaneously aligning several fragments to sequence is a major bottleneck compared with single fragment methods, the advantage of the current approach is that correct alignments imply correct long range distance constraints. The lack of these constraints is most likely the major reason why structure prediction methods fail to consistently produce adequate models when good templates are unavailable or undetectable. Thus, we believe that the current study offers new and valuable insight into the prediction of sequence‐structure relationships in proteins. Proteins 2009. © 2008 Wiley‐Liss, Inc.
High pressure reveals structural determinants for globin hexacoordination: Neuroglobin and myoglobin cases
Authors: Capece L. , Marti M. A. , Bidon‐Chanal A. , Nadra A. , Luque F. J. , Estrin D. A. 
Published: October 2008

AbstractThe influence of pressure on the equilibrium between five‐(5c) and six‐coordination (6c) forms in neuroglobin (Ngb) and myoglobin (Mb) has been examined by means of molecular dynamics (MD) simulations at normal and high pressure. The results show that the main effect of high pressure is to reduce the protein mobility without altering the structure in a significant manner. Moreover, our data suggest that the equilibrium between 5c and 6c states in globins is largely controlled by the structure and dynamics of the C‐D region. Finally, in agreement with the available experimental data, the free energy profiles obtained from steered MD for both proteins indicate that high pressure enhances hexacoordination. In Ngb, the shift in equilibrium is mainly related to an increase in the 6c→5c transition barrier, whereas in Mb such a shift is primarily due to a destabilization of the 5c state. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Exciton quantum confinement effect in nanostructures formed by laser radiation on the surface of CdZnTe ternary compound
Authors: Medvid A. , Mychko A. , Strilchyk O. , Litovchenko N. , Naseka Yu. , Onufrijevs P. , Pludonis A. 
Published: October 2008

AbstractSelf‐organizing structures of nanometer size are observed on the surface of CdZnTe crystal irradiated by strongly absorbed Nd:YAG laser radiation (LR) at intensities within 4–12 MW/cm2. The effect of exciton quantum confinement manifested by a shift to higher energies of the A0,X exciton band of the photo‐luminescent spectrum is present in structures of 10–15 nm in diameter at the top of nano‐hills. A graded band gap structure with optical window is formed at the top of nano‐hills. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the relative stability of cobalt‐ and nickel‐based amidinate complexes against β‐migration
Authors: Li Jiaye , Wu Jinping , Zhou Chenggang , Han Bo , Lei Xinjian , Gordon Roy , Cheng Hansong 
Published: October 2008

AbstractWe present a first‐principles study on the relative stability of cobalt‐ and nickel‐based amidinate complexes against β‐migration using density functional theory. Factors that influence the reactivity of these compounds were carefully addressed and the calculated molecular structures are in excellent agreement with the available crystal structural data. Reaction energies as well as activation barriers of β‐migration were evaluated. The predicted relative stability of the selected compounds is consistent with experimental observations. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Coupled cluster response theory in parameter subspaces
Authors: Boman Linus , Koch Henrik 
Published: October 2008

AbstractWe introduce a response function formalism that enables smaller number of parameters than that defined in standard coupled cluster response theory. This is essential in the development of reduced scaling methods. The formalism is general and it applies to all parameterizations at all levels of the coupled cluster hierarchy. We show that to achieve physically reasonable results the parameterization must fulfill certain criteria. The linear response functions are derived and discussed in the context of optimized virtual orbitals and Cholesky decomposition of the cluster amplitudes. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
TCE plume remediation via ISCR‐enhanced bioremediation utilizing EHC® and KB‐1®
Authors: Peale James G. D. , Bakkom Erik , Lakhwala Fayaz , Mueller James , Molin Josephine 
Published: October 2008

AbstractGroundwater below an operating manufacturing facility in Portland, Oregon, was impacted by chlorinated volatile organic compounds (CVOCs), with concentrations indicative of a dense, nonaqueous‐phase liquid (DNAPL) release. The downgradient plume stretched under the adjacent Willamette River, intersecting zones of legacy impacts from a former manufactured gas plant (MGP). An evaluation of source‐area and downgradient plume treatment remedies identified in situ bioremediation as most likely to be effective for the CVOC plume, while leaving the legacy impacts for other responsible parties. With multiple commercially available products to choose from, the team developed and implemented a bench test to identify the most appropriate technology, which was further evaluated in a field pilot study. The results of the testing demonstrated conclusively that bioremediation enhanced by in situ chemical reduction (ISCR) using EHC® and KB‐1® was most appropriate for this site, providing outstanding results. The following describes the implementation and results of the tests. © 2008 Wiley Periodicals, Inc.
Evaluation of the physical stability, groundwater seepage control, and faunal changes associated with an AquaBlok® sediment cap
Authors: Barth Edwin F. , Reible Danny , Bullard Andrew 
Published: October 2008

AbstractActive sediment caps are being considered for addressing contaminated sediment areas in surface‐water bodies. A demonstration of an active cap designed to reduce advective transport of contaminants using AquaBlok® (active cap material) was initiated in a small study area of the Anacostia River in Washington, D.C. The cap remained physically stable, demonstrated the ability to divert groundwater flow, and was recolonized with native organisms after 30 months of monitoring following cap placement. However, the long‐term performance of active caps associated with harsh environmental conditions, hydrogeological settings, and subsurface gas production needs to be further evaluated. © 2008 Wiley Periodicals, Inc.
Remediation of fly ash landfills through plantation
Authors: Ram Lal C. , Jha Sangeet K. , Tripathi Ramesh C. , Masto Reginald E. , Selvi Vetrivel A. 
Published: October 2008

AbstractIn India, a significant area of land is occupied by preexisting coal‐fired thermal power plants (TPPs) for the storage of fly ash slurry in ash ponds. However, the area available for storage of fly ash at these TPPs is limited. In addition, this type of fly ash disposal poses a problem due to restricted land availability and potential contamination issues. A viable alternative is the reclamation of fly ash ponds by plantation. A study at the Ramagundam Super Thermal Power Station (RSTPS) in Andhra Pradesh, India, on reclamation of a portion of an ash‐filled, low‐lying area has been performed. This article describes the characteristics of the RSTPS pond ash, ash leachates, and improvements in the fertility status of the reclaimed area over a three‐year period. Furthermore, morphometric observations of different planted species indicate that these types of ash‐filled, low‐lying areas can be suitably reclaimed and the nutrient‐rich leachate from ash‐filled areas potentially can be used for irrigation purposes. © 2008 Wiley Periodicals, Inc.