bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analytical theory for one‐dimensional consolidation of clayey soils exhibiting rheological characteristics under time‐dependent loading
Authors: Xie Kang‐He , Xie Xin‐Yu , Li Xi‐Bin 
Published: February 2008

AbstractThis paper presents analytical solutions to the one‐dimensional consolidation problem taking into consideration the rheological properties of clayey soil under variable loadings. A four‐element rheological model is introduced, and different loading types are involved, i.e. constant loading, one‐step loading, triangular loading, rectangular loading, and isosceles–trapezoidal cyclic loading. The differential equations governing consolidation are solved by the Laplace transform. Based on the solutions obtained, the influences of the rheological parameters and loading conditions on the consolidation process are investigated. It has been shown that the consolidation behavior is mainly governed by four dimensionless parameters, a1, a2, b, and Tv0. Load shape has a great influence on the rate of consolidation. A decrease either in the modulus of the spring in the Kelvin body or in the viscosity coefficient of independent dashpot will slow down the rate of consolidation. An increase in the viscosity coefficient of the dashpot in the Kelvin body will make the rate of consolidation increase at an early stage but decrease at a later stage. For isosceles–trapezoidal cyclic loading, the consolidation rate in each cycle reaches a maximum at the end of the constant loading phase and the minimum at the end of this cycle. Copyright © 2008 John Wiley & Sons, Ltd.
Influence of size on the constitutive equations of concrete or rock dowels
Authors: Miguel Letícia Fleck Fadel , Riera Jorge Daniel , Iturrioz Ignacio 
Published: February 2008

AbstractThe numerical fracture analysis of non‐homogeneous rock or concrete dowels subjected to shear and compression is described in detail. The method of analysis allows the consideration of scale and rate effects due to material non‐homogeneity and fracture. The proposed approach is verified by comparing numerical predictions with experimental results reported in the literature for a series of small rock samples, since experimental evidence for large bodies is not yet available (2007). Results generated by Monte Carlo simulation using the so‐called discrete element method to model the dowels suggest that a simple three parameters law can be used to predict the relationship between tangential stress at the base and lateral distortion. It is observed that the larger the size of the cubes, the smaller both the peak tangential stress and the rupture distortion. Size effects are also evaluated in samples with vertical restraint. The influence of loading rate is likewise numerically assessed for two sample sizes. The effect is compatible with experimental evidence available for concrete using small samples. Copyright © 2008 John Wiley & Sons, Ltd.
A community‐based stress management programme for an impoverished population in South Africa
Authors: Crouch Rosemary B. 
Published: February 2008

AbstractThe development and evaluation of a programme for the effective management of stress in an impoverished rural community is the subject of this research study. A random sample of 160 participants was selected from the rural population of the Limpopo Province of South Africa. This population resembles in many ways other disadvantaged populations in South Africa, and the outcome may have generalizability. A quantitative, factorial experimental design was used to compare four stress management programmes. Three were conventional stress management programmes derived from the literature, and the fourth programme was a creative activity programme. Data was gathered from two questionnaires. Results from the statistical analyses of data revealed that the participants experienced significant reduction in stress in all four programmes. At post post‐testing, participants in the three conventional programmes experienced a reduction of stress by 39.5, 72.5 and 40.8%, respectively. There was a 41.6% reduction in stress in participants in the creative activity programme. Limitations of the study include differences in the severity of certain psycho‐social stressors experienced by the participants and difficulty in the control of a standardized presentation of the programmes. The most successful and sustainable stress management programme included physical methods of controlling stress such as exercise relaxation and good nutrition. Further research is recommended in combining a stress management programme with a creative activity group in reducing stress in a disadvantaged population. Copyright © 2008 John Wiley & Sons, Ltd.
Proteasome subunit proteins and neuropathology in tauopathies and synucleinopathies: Consequences for proteomic analyses
Authors: Zouambia Mohamed , Fischer David F. , Hobo Barbara , De Vos Rob A. I. , Hol Elly M. , Varndell Ian M. , Sheppard Paul W. , Van Leeuwen Fred W. 
Published: February 2008

AbstractAccumulation of proteins in inclusions in neurological disorders is partly due to dysfunction of the ubiquitin–proteasome system. Proteasomal dysfunction may be caused by misexpression of one or more of its subunits. A large number of antibodies reactive with proteasome subunits were screened on material from patients exhibiting tau‐ and synucleinopathies. Many antisera against proteasomal subunits (11S activator, 19S regulator ATPase/non‐ATPase, and 20S α and β resulted in a distinct nuclear and/or cytoplasmic staining of the entorhinal‐hippocampal area and the temporal cortex of Alzheimer's disease (AD) patients. In particular an antibody directed against 19S regulator ATPase subunit 6b (S6b) specifically stained the neurofibrillary tangles and dystrophic neurites in AD, Down syndrome and aged nondemented controls. In other tauopathies (Pick's disease, frontotemporal dementia, progressive supranuclear palsy and argyrophilic grain disease), neuronal and/or glial inclusions were also S6b immunoreactive. In contrast, in synucleinopathies (Lewy body disease (LBD) and multiple system atrophy) no S6b staining was seen. Real time quantitative PCR on the temporal cortex of AD patients revealed a significant increase in S6b subunit mRNA. This increase was not found in the gyrus cinguli anterior of patients with LBD. This differential expression of S6b most likely will result in different proteomic patterns. Here we present evidence to show that S6b coexists with a reporter for proteasomal dysfunction (ubiquitin+1), and we conclude that S6b transcript up‐regulation and the dysfunction in tauopathies may be functionally related.
The myth of automated, high‐throughput two‐dimensional gel analysis
Authors: Clark Brittan N. , Gutstein Howard B. 
Published: February 2008

AbstractMany software packages have been developed to process and analyze 2‐D gel images. Some programs have been touted as automated, high‐throughput solutions. We tested five commercially available programs using 18 replicate gels of a rat brain protein extract. We determined computer processing time, approximate spot editing time, time required to correct spot mismatches, as well as total processing time. We also determined the number of spots automatically detected, number of spots kept after manual editing, and the percentage of automatically generated correct matches. We also determined the effect of increasing the number of replicate gels on spot matching efficiency for two of the programs. We found that for all programs tested, less than 3% of the total processing time was automated. The remainder of the time was spent in manual, subjective editing of detected spots and computer generated matches. Total processing time for 18 gels varied from 22 to 84 h. The percentage of correct matches generated automatically varied from 1 to 62%. Increasing the number of gels in an experiment dramatically reduced the percentage of automatically generated correct matches. Our results demonstrate that these 2‐D gel analysis programs are not automatic or rapid, and also suggest that matching accuracy decreases as experiment size increases.
Transcriptome and proteome analysis of early embryonic mouse brain development
Authors: Hartl Daniela , Irmler Martin , Römer Irmgard , Mader Michael T. , Mao Lei , Zabel Claus , de Angelis Martin Hrabé , Beckers Johannes , Klose Joachim 
Published: February 2008

AbstractMouse embryonic brain development involves sequential differentiation of multipotent progenitors into neurons and glia cells. Using microarrays and large 2‐DE, we investigated the mouse brain transcriptome and proteome of embryonic days 9.5, 11.5, and 13.5. During this developmental period, neural progenitor cells shift from proliferation to neuronal differentiation. As expected, we detected numerous expression changes between all time points investigated, but interestingly, the rate of alteration remained in a similar range within 2 days of development. Furthermore, up‐ and down‐regulation of gene products was balanced at each time point which was also seen at embryonic days 16–18. We hypothesize that during embryonic development, the rate of gene expression alteration is rather constant due to limited cellular resources such as energy, space, and free water. A similar complexity in terms of expressed genes and proteins suggests that changes in relative concentrations rather than an increase in the number of gene products dominate cellular differentiation. In general, expression of metabolism and cell cycle related gene products was down‐regulated when precursor cells switched from proliferation to neuronal differentiation (days 9.5–11.5), whereas neuron specific gene products were up‐regulated. A detailed functional analysis revealed their implication in differentiation related processes such as rearrangement of the actin cytoskeleton as well as Notch‐ and Wnt‐signaling pathways.
Assessing quantitative post‐mortem changes in the gray matter of the human frontal cortex proteome by 2‐D DIGE
Authors: Crecelius Anna , Götz Andrea , Arzberger Thomas , Fröhlich Thomas , Arnold Georg J. , Ferrer Isidro , Kretzschmar Hans A. 
Published: February 2008

AbstractThe number of proteomics studies concerning human brain samples has been increasing in recent years, in particular in the discovery of biomarkers for neurological diseases. The human brain samples are obtained from brain banks, which are interested in providing high quality human nervous tissue. In order to provide brain banks as well as scientists working in the proteomics field with measures for tissue quality, the critical factors after death, the effect of post‐mortem interval (PMI) and storage temperature on the human brain proteome were investigated. This study was focused on the gray matter of the frontal cortex. The PMI was artificially prolonged from the time of autopsy (2 h after death) by storing samples at 4°C or room temperature over 18, 24, and 48 h. The samples were analyzed by 2‐D DIGE using a pH 4–7 gradient, revealing a time course of quantitative protein changes. The degradation of three proteins, peroxiredoxin‐1, stathmin, and glial fibrillary acidic protein were further confirmed by Western‐blot analysis. Proteins vulnerable to PMI were analyzed by the 2‐D DIGE analysis of cortex samples from three donors, and were derived from a variety of functional groups, including metabolic, structural, stress response, antioxidants, synaptosomal, and neuronal proteins.
An approach to handling and interpretation of ambiguous data in transcriptome and proteome comparisons
Authors: Irmler Martin , Hartl Daniela , Schmidt Thorsten , Schuchhardt Johannes , Lach Christiane , Meyer Helmut E. , Hrabé de Angelis Martin , Klose Joachim , Beckers Johannes 
Published: February 2008

AbstractA major challenge towards a comprehensive analysis of biological systems is the integration of data from different “omics” sources and their interpretation at a functional level. Here we address this issue by analysing transcriptomic and proteomic datasets from mouse brain tissue at embryonic days 9.5 and 13.5. We observe a high concordance between transcripts and their corresponding proteins when they were compared at the level of expression ratios between embryonic stages. Absolute expression values show marginal correlation. We show in examples, that poor concordance between protein and transcript expression is in part explained by the fact, that single genes give rise to multiple transcripts and protein variants. The integration of transcriptomic and proteomic data therefore requires proper handling of such ambiguities. A closer inspection of such cases in our datasets suggests, that comparing gene expression at exon level instead of gene level could improve the comparability. To address the biological relevance of differences in expression profiles, literature‐data mining and analysis of gene ontology terms are widely used. We show here, that this can be complemented by the inspection of physical properties of genes, transcripts, and proteins.
Interlocking transcriptomics, proteomics and toponomics technologies for brain tissue analysis in murine hippocampus
Authors: Bode Marcus , Irmler Martin , Friedenberger Manuela , May Caroline , Jung Klaus , Stephan Christian , Meyer Helmut E. , Lach Christiane , Hillert Reyk , Krusche Andreas , Beckers Johannes , Marcus Katrin , Schubert Walter 
Published: February 2008

AbstractWe have correlated transcriptomics, proteomics and toponomics analyses of hippocampus tissue of inbred C57BL/6 mice to analyse the interrelationship of expressed genes and proteins at different levels of organization. We find that transcriptome and proteome levels of function as well as the topological organization of synaptic protein clusters, detected by toponomics at physiological sites of hippocampus CA3 region, are all largely conserved between different mice. While the number of different synaptic states, characterized by distinct synaptic protein clusters, is enormous (>155 000), these states together form synaptic networks defining distinct and mutually exclusive territories in the hippocampus tissue. The findings provide insight in the systems biology of gene expression on transcriptome, proteome and toponome levels of function in the same brain subregion. The approach will lay the ground for designing studies of neurodegeneration in mouse models and human brains.
BrainProfileDB – a platform for integration of functional genomics data
Authors: Schuchhardt Johannes , Glintschert Alexander , Hartl Daniela , Irmler Martin , Beckers Johannes , Stephan Christian , Marcus Katrin , Klose Joachim , Meyer Helmut E. , Malik Arif 
Published: February 2008

AbstractBrainProfileDB is a database system for integrating large sets of high throughput functional genomics data of the Human Brain Proteome Project (HBPP). Within HBPP (http://www.smp‐proteomics.de/) the molecular pathology of neurodegenerative diseases is investigated, using complementary methods from transcriptomics, proteomics, toponomics and interaction measurements. Aim of the database system is to provide a broad spectrum of scientific users joined in the consortium with a practical integrated view on their data. Employing appropriate mapping techniques and levels of data representation the user is relieved from technical details of gene identification or experimental measurement technique.
Island clustering analysis for the comparison of the membrane and the soluble protein fractions of human brain proteome
Authors: Kwon Kyung‐Hoon , Park Gun Wook , Kim Jin Young , Lee Sang Kwang , Lee Jeong Hwa , Kim Young Hye , Kim Se‐Young , Park Young Mok , Yoo Jong Shin 
Published: February 2008

AbstractA protein identified in multiple separate bands of a 1‐D gel reflects variation in the molecular weight caused by alternative splicing, endoproteolytic cleavage, or PTMs, such as glycosylation or ubiquitination. To characterize such a protein distribution over the bands, we defined an entity called an ‘island’ as the band region including the bands of the same protein identified sequentially. We quantified the island distribution using a new variable called an Iscore. Previously, as described in Park et al.. (Proteomics 2006, 6, 4978–4986.), we analyzed human brain tissue using a multidimensional MS/MS separation method. Here, the new method of island analysis was applied to the previous proteome data. The soluble and membrane protein fractions of human brain tissue were reanalyzed using the island distribution. The proteome of the soluble fraction exhibited more variation in island positions than that of the membrane fraction. Through the island analysis, we identified protein modifications and protein complexes over the 1‐D gel bands.
Fluorescence and bioluminescence procedures for functional proteomics
Authors: Prinz Anke , Reither Gregor , Diskar Mandy , Schultz Carsten 
Published: February 2008

AbstractThis review aims to provide an overview of current optical procedures used in functional proteomics, investigating protein localization, protein–protein interaction, intracellular signaling events, and second messenger generation in living cells. Reporter assays using proteins tagged with fluorescent or bioluminescent moieties are discussed. Recently, intracellular biosensor assays, flow cytometry‐based techniques (fluorescent cell barcoding), as well as transfected cell microarray assays involving RNA interference coupled with automated imaging were introduced and have been adopted as screening platforms for annotating small molecules, investigating signaling events, or in phenotype analysis. These novel methodological advances include improved image acquisition and processing techniques and help linking in vitro observations to in vivo processes. In addition, the acquired data are increasingly quantitative in nature and will therefore pave the way for modeling of signaling cascades and other complex cellular events, an important step toward systems biology.
Inside SMP proteomics: Six years German Human Brain Proteome Project (HBPP) – A summary
Authors: Hamacher Michael , Hardt Tanja , van Hall Andre , Stephan Christian , Marcus Katrin , Meyer Helmut E. 
Published: February 2008

AbstractIn 2001, the German Federal Ministry of Education and Research (BMBF) initiated the National Genome Research Network (NGFN; www.ngfn.de) as a nation‐wide multidisciplinary networking platform aiming at the analysis of common human diseases and aging. Within the NGFN the Human Brain Proteome Project (HBPP; www.smp‐proteomics.de) focuses on the analysis of the human brain in health and disease. The concept is based on two consecutive steps: (i) Elaborating and establishing the necessary technology platforms. (ii) Application of the established technologies for research in Alzheimer's disease and Parkinson's disease. In the first funding period, HBPP1, running from 2001 to 2004, necessary technologies were established and optimized. In HBPP2, which started 2004 and will end in May 2008, the developed technologies are used for large‐scale experiments, offering new links for disease related research and therapies. The following overview describes structure, aims and outcome of this unique German Brain Proteome Project.
Crop losses due to olive moth mediated by ethylene
Authors: Ramos Pedro , Rosales Raquel , Sabouni Ibrahim , Garrido Dolores , Ramos Jose M 
Published: February 2008

AbstractBACKGROUND:Studies for nine years in southern Spain on the olive moth, Prays oleae Bern., have tested the possibility of altering oviposition behaviour on newly formed olive fruits by means of a single ethylene application.RESULTS:A single spraying of ethylene on the olive trees at the beginning of fruiting significantly decreased the olive moth egg populations and consequent the olive fruit fall. At the same time, no negative effect was found in the activity of natural oophagous predators of the olive moth.CONCLUSIONS:The ethylene treatments against P. oleae yielded substantial economical benefits each year (a mean of €526 ha−1), benefits that fluctuated depending on the olive crop and on the annual fruit fall caused by this major pest. Copyright © 2008 Society of Chemical Industry
EPR study of low symmetry Er centers in congruent lithium niobate
Authors: Bodziony T. , Kaczmarek S. M. 
Published: February 2008

AbstractElectron paramagnetic resonance study of congruent LiNbO3 single crystal weakly doped (0.1 wt%) with erbium is reported. The EPR lines originating both from the 167Er isotope with a hyperfine structure, as well as from the evenEr isotopes causing fine structure, are identified. Angular dependence of the EPR lines reveals the presence of several non‐equivalent centers. Deconvolution of the EPR line into several Lorentzian components in a plane perpendicular to the z‐axis (optical c‐axis) allowed us to show the Er3+ center with the lowest (C1) point group symmetry and estimate the values of g‐tensor. The obtained results confirmed the model of non‐ equivalent centers of the rare‐earth ions in lithium niobate having the lowest C1 symmetry due to the presence of intrinsic defects in the near‐neighborhood of RE3+. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Silicon nano particles: Surface characterization, defects and electronic properties
Authors: Hahn Torsten , Heimfarth Jan P. , Roewer Gerhard , Kroke Edwin 
Published: February 2008

AbstractNano scaled silicon particles (nc‐Si) having a diameter of about 3 to 9 nm were synthesized by direct reduction of SiCl4 with H2 in a LaCl3 matrix by a vapour deposition (CVD) route. The particles were characterized by diffuse reflection fourier transform spectroscopy (DR/FT‐IR), photoluminescence (PL), electron paramagnetic resonance (EPR) and microwave detected photo induced current transient spectroscopy (MD‐PICTS). EPR measurements identified dangling bond defects on the surface of as‐prepared nc‐Si particles in the LaCl3 matrix. The number of dangling bonds significantly decreases upon extraction of the nc‐Si with ethanol. As expected, the dangling bonds disappear completely after treatment with 1% HF solution. A strong correlation between presence of dangling bond defects and electronic properties was found. The temperature dependent photoconductivity in conjunction with the EPR and PL results allowed us to analyze the defect structure of the nc‐Si particles. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effects of hydrostatic pressure on the donor binding energy and intra donor transition matrix elements in GaAs–GaAlAs quantum wells
Authors: Panahi H. , Maleki M. 
Published: February 2008

AbstractThe effects of hydrostatic pressure on the donor binding energy in GaAs–Ga0.7Al0.3As quantum wells have been studied in the effective mass approximation, using a variational approach for hydrogenic ground state 1s and excited states 2s, 2px, 3px. Results obtained show that the donor binding energy variation with the well width and the position of impurity under pressure is similar to that without pressure. The intra donor squared transition matrix elements are calculated as functions of impurity position in the presence of hydrostatic pressure. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photophysics of J‐aggregate microcavities
Authors: Michetti P. , La Rocca G. C. 
Published: February 2008

AbstractWe have developed a model in order to account for the photo‐excitation dynamics of J‐aggregate films and strongly coupled J‐aggregate microcavities. The J‐aggregates are described as a disordered Frenkel exciton system in which relaxation occurs due to the presence of a thermal bath of molecular vibrations. The link between the J‐aggregate film and the microcavities is obtained introducing a model polariton wavefunction mixing cavity photon modes and J‐aggregate superradiant excitons. With the same approach we have calculated both absorption and luminescence spectra for the J‐aggregate film and the photoluminescence of strongly coupled organic microcavities. The model is able to explain the organic microcavities fast relaxation dynamics and polariton luminescence following non resonant pumping starting from the excitonic properties of the optically active layer. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)