bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational homogenization for heterogeneous thin sheets
Authors: Coenen E. W. C. , Kouznetsova V. G. , Geers M. G. D. 
Published: March 2010

AbstractIn this paper, a computational homogenization technique for thin‐structured sheets is proposed, based on the computational homogenization concepts for first‐ and second‐order continua. The actual three‐dimensional (3D) heterogeneous sheet is represented by a homogenized shell continuum for which the constitutive response is obtained from the nested analysis of a microstructural representative volume element (RVE), incorporating the full thickness of the sheet and an in‐plane representative cell of the macroscopic structure. At an in‐plane integration point of the macroscopic shell, the generalized strains, i.e. the membrane deformation and the curvature, are used to formulate the boundary conditions for the microscale RVE problem. At the RVE scale, all microstructural constituents are modeled as an ordinary 3D continuum, described by the standard equilibrium and the constitutive equations. Upon proper averaging of the RVE response, the macroscopic generalized stress and the moment resultants are obtained. In this way, an in‐plane homogenization is directly combined with a through thickness stress integration. From a macroscopic point of view, a (numerical) generalized stress–strain constitutive response at every macroscopic in‐plane integration point is obtained. Additionally, the simultaneously resolved microscale RVE local deformation and stress fields provide valuable information for assessing the reliability of a particular microstructural design. Copyright © 2010 John Wiley & Sons, Ltd.
A Jacobian‐free‐based IIM for incompressible flows involving moving interfaces with Dirichlet boundary conditions
Authors: Tan Zhijun , Wang Desheng , Wang Yu 
Published: March 2010

AbstractIn this paper, a finite difference marker‐and‐cell (MAC) scheme is presented for the steady Stokes equations with moving interfaces and Dirichlet boundary condition. The moving interfaces are represented by Lagrangian control points and their position is updated implicitly using a Jacobian‐free approach within each time step. The forces at the moving interfaces are calculated from the position of the interfaces and interpolated using cubic splines and then applied to the fluid through the related jump conditions. The proposed Jacobian‐free Newton–generalized minimum residual (GMRES) method avoids the need to form and store the matrix explicitly in the computation of the inverse of the Jacobian and betters numerical stability. The Stokes equations are discretized on a MAC grid via a second‐order finite difference scheme with the incorporation of jump contributions and the resulting saddle point system is solved by the conjugate gradient Uzawa‐type method. Numerical results demonstrate very well the accuracy and effectiveness of the proposed method. The present algorithm has been applied to solve incompressible Navier–Stokes flows with moving interfaces. Copyright © 2010 John Wiley & Sons, Ltd.
A simple dynamical scale‐coupling method for concurrent simulation of hybridized atomistic/coarse‐grained‐particle system
Authors: Kobayashi Ryo , Nakamura Takahide , Ogata Shuji 
Published: March 2010

AbstractWe propose a simple method for dynamical coupling of two sub‐systems with different characteristic scales described with different theoretical models, such as the fine‐scale sub‐system with the atomistic model (AM) such as the empirical inter‐atomic potential and the coarse‐scale sub‐system with the coarse‐grained particle (CGP) method, in a concurrent hybrid simulation scheme. Naive coupling of the different‐scale sub‐systems results in reflection of high wavenumber waves at the interface because of the differences in the phonon Brillouin‐zone and in the dispersion relation. To solve the problem, the present scale‐coupling method introduces (virtual) extra atoms and particles for the AM and the CGP sub‐systems, respectively, beyond the atom–particle interface, and uses the extra atoms and the particles to mutually transfer information of the waves between the two sub‐systems and to suppress the artificial reflection of the incident wave in the whole wavenumber range. As the algorithm in the present scale‐coupling method is local in time and space, it is applicable to hybrid systems with any interface shape at low computation and memory requirement. Accuracy of the present scale‐coupling method is compared with that of the existing methods for a simple model system. The hybrid AM‐CGP simulation of indentation of a graphene nano‐drum using the present scale‐coupling method is performed to demonstrate its accuracy and usefulness through its comparison with the fully atomistic results. Copyright © 2010 John Wiley & Sons, Ltd.
On multiscale non‐equilibrium molecular dynamics simulations
Authors: Li Shaofan , Sheng Ni 
Published: March 2010

AbstractIn this work, we set forth a multiscale non‐equilibrium molecular dynamics (MS‐NEMD) model. The main objectives of MS‐NEMD model are: (1) establishing a rigorous NEMD that provides direct three‐dimensional simulations of thermal–mechanical motions at atomistic scale, and (2) providing a general computational paradigm for non‐equilibrium multiscale simulations. The proposed MS‐NEMD combines a coarse‐grained continuum thermodynamics model with a fine scale NEMD simulation. A novel concept ofMultiscale Canonical Ensembleis put forth, in which we argue that the coarse‐grained field may provide a heat bath within the coarse scale relaxation time interval, while the fine scale motion may reach to a local equilibrium state during that time interval. In this work, we propose to use a Nosé–Hoover thermostat network that is distributed among the local Voronoi cell‐ensembles, and it will then regulate the difference between the coarse scale thermodynamic temperature and kinetic temperature of the fine scale ensemble. The proposed MS‐NEMD algorithm has the following features: (1) the fine scale distribution function is canonical in the sense that it obeys a drifted local Boltzmann distribution and (2) it can spontaneously and automatically return to the equilibrium state. Several numerical examples have been carried out, in which we have simulated the activation of shock waves or dislocations due to thermal fluctuations. Copyright © 2010 John Wiley & Sons, Ltd.
The effect of simvastatin on the proteome of detergent‐resistant membrane domains: Decreases of specific proteins previously related to cytoskeleton regulation, calcium homeostasis and cell fate
Authors: Ponce Jovita , Brea David , Carrascal Montserrat , Guirao Verónica , DeGregorio‐Rocasolano Nuria , Sobrino Tomás , Castillo José , Dávalos Antonio , Gasull Teresa 
Published: March 2010

AbstractCell death induced by over‐activation of glutamate receptors occurs in different neuropathologies. Cholesterol depletors protect from neurotoxic over‐activation of glutamate receptors, and we have recently reported that this neuroprotection is associated with a reduction of the N‐methyl‐D‐aspartate subtype of glutamate receptors in detergent‐resistant membrane domains (DRM). In the present study we used comparative proteomics to further identify which proteins, besides the N‐methyl‐D‐aspartate receptor, change its percentage of association to DRM after treatment of neurons with simvastatin. We detected 338 spots in neuronal DRM subjected to 2‐DE; eleven of these spots changed its intensity after treatment with simvastatin. All 11 differential spots showed reduced intensity in simvastatin‐treated samples and were identified as adipocyte plasma membrane associated protein, enolase, calretinin, coronin 1a, f‐actin capping protein α1, f‐actin capping protein α2, heat shock cognate protein 71, malate dehydrogenase, n‐myc downregulated gene 1, prohibitin 2, Rab GDP dissociation inhibitor, translationally controlled tumor protein and voltage dependent anion selective channel protein 1. The proteins tested colocalized with the lipid raft marker caveolin‐1. Interestingly, the proteins we have identified in the present study had been previously reported to play a role in cell fate and, thus, they might represent novel targets for neuroprotection.
Improved accuracy of cell surface shaving proteomics in Staphylococcus aureus using a false‐positive control
Authors: Solis Nestor , Larsen Martin R. , Cordwell Stuart J. 
Published: March 2010

AbstractProteolytic treatment of intact bacterial cells is an ideal means for identifying surface‐exposed peptide epitopes and has potential for the discovery of novel vaccine targets. Cell stability during such treatment, however, may become compromised and result in the release of intracellular proteins that complicate the final analysis. Staphylococcus aureus is a major human pathogen, causing community and hospital‐acquired infections, and is a serious healthcare concern due to the increasing prevalence of multiple antibiotic resistances amongst clinical isolates. We employed a cell surface “shaving” technique with either trypsin or proteinase‐K combined with LC‐MS/MS. Trypsin‐derived data were controlled using a “false‐positive” strategy where cells were incubated without protease, removed by centrifugation and the resulting supernatants digested. Peptides identified in this fraction most likely result from cell lysis and were removed from the trypsin‐shaved data set. We identified 42 predicted S. aureus COL surface proteins from 260 surface‐exposed peptides. Trypsin and proteinase‐K digests were highly complementary with ten proteins identified by both, 16 specific to proteinase‐K treatment, 13 specific to trypsin and three identified in the control. The use of a subtracted false‐positive strategy improved enrichment of surface‐exposed peptides in the trypsin data set to approximately 80% (124/155 peptides). Predominant surface proteins were those associated with methicillin resistance–surface protein SACOL0050 (pls) and penicillin‐binding protein 2′ (mecA), as well as bifunctional autolysin and the extracellular matrix‐binding protein Ebh. The cell shaving strategy is a rapid method for identifying surface‐exposed peptide epitopes that may be useful in the design of novel vaccines against S. aureus.
QIKS – Quantitative identification of kinase substrates
Authors: Morandell Sandra , Grosstessner‐Hain Karin , Roitinger Elisabeth , Hudecz Otto , Lindhorst Thomas , Teis David , Wrulich Oliver A. , Mazanek Michael , Taus Thomas , Ueberall Florian , Mechtler Karl , Huber Lukas. A. 
Published: March 2010

AbstractSignaling networks regulate cellular responses to external stimuli through post‐translational modifications such as protein phosphorylation. Phosphoproteomics facilitate the large‐scale identification of kinase substrates. Yet, the characterization of critical connections within these networks and the identification of respective kinases remain the major analytical challenge. To address this problem, we present a novel approach for the identification of direct kinase substrates using chemical genetics in combination with quantitative phosphoproteomics. Quantitative identification of kinase substrates (QIKS) is a novel‐screening platform developed for the proteome‐wide substrate‐analysis of specific kinases. Here, we aimed to identify substrates of mitogen‐activated protein kinase/Erk kinase (Mek1), an essential kinase in the mitogen‐activated protein kinase cascade. An ATP analog‐sensitive mutant of Mek1 (Mek1‐as) was incubated with a cell extract from Mek1 deficient cells. Phosphorylated proteins were analyzed by LC‐MS/MS of IMAC‐enriched phosphopeptides, labeled differentially for relative quantification. The identification of extracellular regulated kinase 1/2 as the sole cytoplasmic substrates of MEK1 validates the applicability of this approach and suggests that QIKS could be used to identify substrates of a wide variety of kinases.
The risk of suicide in cancer patients: a review of the literature
Authors: Robson Anna , Scrutton Frances , Wilkinson Liz , MacLeod Fiona 
Published: March 2010

AbstractObjectives: This review investigates the risk of suicide in people diagnosed with cancer.Method: A literature search of PsycINFO, MEDLINE, EMBASE and CINAHL yielded 677 articles of which the abstracts were reviewed for their relevance. Seventy‐one articles were identified as relevant and a further 3 were identified in a search of cited and citing articles; following application of inclusion and exclusion criteria, 39 articles were included in the review.Results: The reported incidence of completed suicide in cancer patients ranged from standardised mortality ratio of 1 to 11. The reported percentages of suicidal ideation in non‐psychiatric populations of cancer patients ranged from 0.8 to 71.4%, compared to a reported prevalence of suicidal ideation in the general population, of between 1.1 and 19.8%. Risk factors identified for completed suicide and suicidal ideation in cancer patients include mental health, socio‐demographic and illness factors. Some of these risk factors extend to the general population; however, some are specific to cancer such as cancer site, physical functioning and prognosis.Conclusions: Despite the prevalence of suicidal ideation in a cancer population being comparable to the general population, the prevalence of completed suicide is elevated. Although suicidal ideation does not necessarily result in completed suicide, it is important that adequate training be provided for cancer professionals on the risk factors for suicide in cancer patients. Copyright © 2010 John Wiley & Sons, Ltd.
Cancer patients' experience of positive and negative changes due to the illness: relationships with psychological well‐being, coping, and goal reengagement
Authors: Schroevers Maya J. , Kraaij Vivian , Garnefski Nadia 
Published: March 2010

AbstractObjective: Most studies in cancer patients on psychological changes focused on positive changes (so‐called ‘posttraumatic growth’), with surprisingly little attention on the possibility that patients may experience both positive and negative changes. This study investigated the relationship between positive and negative changes, and their association with positive and negative affect. We also examined the correlates of positive and negative changes, specifically the role of coping and goal reengagement.Methods: This cross‐sectional study was conducted in 108 patients. We used Pearson correlations and Regression analyses to examine the research questions.Results: Positive and negative changes were relatively unrelated to each other. More positive changes were related to more positive affect, whereas more negative changes were related to more negative affect and less positive affect. Approach coping by more positive reappraisal and goal reengagement was significantly associated with more positive changes. More use of avoidant coping by self‐distraction was related to more negative changes.Conclusions: Patients experienced both positive and negative changes as a result of cancer. These changes were significantly related to patients' well‐being, as well as to their coping and goal reengagement strategies. This knowledge may be incorporated in psychological interventions. Cancer patients can be assisted to learn to acknowledge both positive and negative changes in their life and to approach rather than avoid difficult situations. Patients may also be supported to engage in alternative meaningful goals in life. This is likely to help them find positive meaning. Copyright © 2010 John Wiley & Sons, Ltd.
The Attentional Function Index—a self‐report cognitive measure
Authors: Cimprich Bernadine , Visovatti Moira , Ronis David L. 
Published: March 2010

AbstractObjective: Cognitive assessment in individuals with cancer requires both measured performance on neuropsychological tests and self‐report of effectiveness in functioning. Few instruments are available to assess the perceived impact of cognitive alterations on daily functioning in individuals treated for cancer. In this study, we investigated the psychometric properties of a theoretically based instrument, and the Attentional Function Index (AFI), designed to measure perceived effectiveness in common activities requiring attention and working memory, particularly the ability to formulate plans, carry out tasks, and function effectively in daily life.Methods: Women (N=172), ages 27–86 years, completed the questionnaire before primary treatment for early stage breast cancer. Construct validity was established using exploratory principal component factor analysis with varimax rotation.Results: A 13‐item instrument emerged with 3 subscales, namely effective action, attentional lapses, and interpersonal effectiveness, which explained 74.69% of total variance. The internal consistency coefficients (Cronbach's α) were 0.92 for the total instrument, and ranged from 0.80 to 0.92 for the 3 subscales. Further examination of validity indicated that the scores on the AFI (1) showed expected correlations with established measures of ability to concentrate, cognitive failures, states of confusion, and mental fatigue, and (2) could distinguish differences in perceived cognitive functioning between younger and older age groups. AFI scores were not significantly associated with years of education or presence of comorbid conditions.Conclusion: The brief AFI has demonstrated usefulness for assessment of perceived cognitive functioning in populations with life‐threatening and chronic illness, such as breast cancer. Copyright © 2010 John Wiley & Sons, Ltd.
The High‐Pressure Characterization of Energetic Materials: 1‐Methyl‐5‐Nitramino‐1H‐Tetrazole
Authors: Ciezak Jennifer A. 
Published: March 2010

AbstractPressure–volume relations and optical Raman and Infrared spectra of polycrystalline 1MNT have been obtained under quasi‐hydrostatic conditions up to 16 and 40 GPa, respectively, by using diamond anvil cell, synchrotron‐based angle‐resolved X‐ray diffraction, and microspectroscopy. The X‐ray measurements show that the pressure–volume relations remain smooth up to 16 GPa at room temperature, while vibrational measurements show no evidence of a phase transition to near 40 GPa. Anomalous increases of several vibrational intensities and bandwidths suggest that subtle molecular distortions and structural modifications occur in the crystal as pressure increases. Decompression experiments indicate the structural modifications are reversible.
Analysis of field failure data when modeled Weibull slope increases with time
Authors: Rand Daniel R. , McLinn James A. 
Published: March 2010

AbstractWeibull time‐to‐fail distributions cannot be correctly estimated from field data when manufacturing populations from different vintages have different failure modes. To investigate the pitfalls of ongoing Weibull parameter estimation, two cases, based upon real events, were analyzed. First, a time‐to‐fail distribution was generated assuming the same Weibull shape parameter representing an increasing failure rate for each monthly batch or vintage of production. The shape parameter was estimated from simulated field data at regular periods as the population accumulated service time. Estimates of the shape parameter were not constant, but gradually decreased (as had occurred in a real system) with added service time. In the second case, field reliability performance was modeled to match the actual historical data for one product from a disk drive manufacturer. The actual data was proprietary and was not directly available for analysis. A production schedule was modeled with a mix of two failure characteristics. The population reaching the field in the first 12 months had a low, constant failure rate. For the second and third years of production, higher volumes were introduced that had the higher, increasing failure rates of the first case. Assessment of the mixed population at each month of calendar time resulted in an increasing Weibull shape parameter estimate at each assessment. When the two populations were separated and estimated properly, a better fit with more accurate estimates of Weibull shape parameters resulted. Copyright © 2010 John Wiley & Sons, Ltd.
Quantitative analysis of low‐abundance peptides in HeLa cell cytoplasm by targeted liquid chromatography/mass spectrometry and stable isotope dilution: emphasising the distinction between peptide detection and peptide identification
Authors: Le Bihan Thierry , Grima Ramon , Martin Sarah , Forster Thorsten , Le Bihan Yann 
Published: March 2010

AbstractWe present the application of a targeted liquid chromatography/mass spectrometry (LC/MS) approach developed on a linear ion trap for the evaluation of the abundance of cytoplasmic proteins from a HeLa cell extract. Using a standard data‐dependent approach, we identified some specific peptides from this extract which were also commercially available in their AQUA form (use for absolute quantitation). For some of the peptides, we observed a non‐linear response between the intensity and the added quantity which was then fitted using a quadratic fit. All AQUA peptides spiked into a mix of 3 µg of the HeLa cell digest extract were detected down to 16 fmol. We placed an emphasis on peptide detection which, in this study, is performed using a combination of properties such as three specific Q3‐like ion signatures (for a given Q1‐like selection) and co‐elution with the AQUA peptide counterparts. Detecting a peptide without necessarily identifying it using a search engine imposes less constraint in terms of tandem mass (MS/MS) spectra purity. An example is shown where a peptide is detected using those criteria but could not be identified by Mascot due to its lower abundance. To complement this observation, we used a cross‐correlation analysis approach in order to separate two populations of MS/MS fragments based on differences in their elution patterns. Such an approach opens the door to new strategies to analyse lower intensity peptide fragments. An in silico analysis of the human trypsinosome allows the evaluation of how unique are the sets of features that we are using for peptide detection. Copyright © 2010 John Wiley & Sons, Ltd.
Automated verification and refinement for physical-layer protocols
Authors: Brown Geoffrey M. , Pike Lee 
Published: March 2010

Abstract

This paper demonstrates how to use a
satisfiability modulo theories
(SMT) solver together with a bounded model checker to verify properties of real-time physical layer protocols. The method is first used to verify the Biphase Mark protocol, a protocol that has been verified numerous times previously, allowing for a comparison of results. The techniques are extended to the 8N1 protocol used in universal asynchronous receiver transmitters. We then demonstrate the use of temporal refinement to link a finite state specification of 8N1 with its real-time implementation. This refinement relationship relieves a significant disadvantage of SMT approaches—their inability to scale to large problems. Finally, capturing the impact of metastability on timing requirements is a key issue in modeling physical-layer protocols. Rather than model metastability directly, a contribution of our models is treating its effect as a constraint on non-determinism.