bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intrinsic disorder explains diverse nuclear roles of chromatin remodeling proteins
Authors: Sandhu Kuljeet Singh 
Published: September 2008

AbstractChromatin remodelers, a group of proteins involved in nucleosome re‐positioning and modification, have extensive range of interacting partners. They form multimeric complexes and interact with modified histones, transcription, splicing, and replication factors, DNA, RNA, and the factors related to the maintenance of chromosome structure. Such diverse range of interactions is hard to explain with the presumed highly structured form of the protein. In the current analysis, the conformations of chromatin remodelers were explored using protein disorder prediction algorithms. The study revealed that a significant proportion (p < 2.2e‐16) of these proteins harbor at least one long region of intrinsic disorder (>70 aa). These unstructured regions do not exhibit any preference to the N/C terminal or middle of the protein. They do not show any significant representation in the Protein Data Bank (PDB) structure repository. Limited examples from PDB indicate direct involvement of disordered regions in binding of chromatin remodeling proteins to naked or modified DNA, histones, and other chromatin‐related factors. Furthermore, intrinsic disorder seen in these proteins correlates to the presence of low sequence complexity regions (p = 1.851e‐10) particularly the tandem repeats of hydrophilic and charged amino acids. This probably hints at their evolutionary origin via repeat expansion. The disordered regions may enable these proteins to reversibly bind to various interacting partners and eventually contribute to functional diversity and specialization of chromatin remodeling complexes. These could also endow combinatorial action of multiple domains within a protein. We further discuss the prominent association of intrinsic disorder with other chromatin‐related proteins and its functional relevance therein. Copyright © 2008 John Wiley & Sons, Ltd.
Gallbladder cancer (GBC): 10‐year experience at Memorial Sloan‐Kettering Cancer Centre (MSKCC)
Authors: Duffy A. , Capanu M. , Abou‐Alfa G.K. , Huitzil D. , Jarnagin W. , Fong Y. , D'Angelica M. , DeMatteo R.P. , Blumgart L.H. , O'Reilly E.M. 
Published: September 2008

AbstractBackgroundThe incidence of gallbladder cancer (GBC) in the US is 1.2/100,000. This report examines the patterns of presentation, adjuvant treatment and survival of a large cohort of patients with GBC evaluated at MSKCC over a 10‐year period.MethodsA retrospective analysis of patients referred to MSKCC with a diagnosis of GBC between January 1995 and December 2005 was performed. Patients were identified from the MSKCC cancer registry. Information extracted included, demographics, clinical and pathological stage, surgical management, pathology, adjuvant and palliative therapy, date of relapse, death or last follow‐up. Date of diagnosis was defined as date of surgery or biopsy. Survival curves were estimated using the Kaplan–Meier method and compared using the log‐rank test.ResultsFour hundred thirty‐five GBC cases were identified: 285 (65.5%) females,150 (34.5%) males. Median age 67 years (range 28–100). Pathology: 88% adenocarcinoma, 4% squamous, 3% neuroendocrine, 2% sarcoma. 36.6% presented as AJCC Stage IV. 47% were discovered incidentally at laparoscopic cholecystectomy. One hundred thirty‐six of these were re‐explored, of whom 100 (73.5%) had residual disease. Of those who underwent curative resections (N = 123), 8 (6.5%) received adjuvant chemotherapy, 8 (6.5%) chemoradiation alone and 8 (6.5%) both chemoradiation and systemic chemotherapy. Median overall survival for the cohort was 10.3 months (95% CI 8.8–11.8) with a median follow up of 26.6 months. The median survival for those presenting with stage Ia–III disease was 12.9 months (95% CI 11.7–15.8 months) and 5.8 months (95% CI 4.5–6.7) for those presenting with stage IV disease. Median survival was 15.7 months (95% CI 12.4–18.4) for those discovered incidentally at laparoscopic cholecystectomy. For those who underwent re‐exploration, median survival was 14.6 months (95% CI 12.6–18.3) if residual disease was present, and 72 months (95% CI 34 to infinity) if no evidence of disease. The median survival for those who received adjuvant therapy was 23.4 months (95% CI 15.7–47).ConclusionsGBC is commonly diagnosed incidentally (47%). Re‐exploration reveals a high incidence of residual disease (74%). Median survival is better for patients who have no evidence of disease on re‐exploration (72 months) compared to those with residual disease detected (P < 0.0001). Overall prognosis is poor. Although we did not observe a survival benefit for those who received adjuvant therapy, the study did not have sufficient power to address this question. In addition, the number of patients who received adjuvant therapy was small with marked heterogeneity in clinical and therapeutic details, precluding any definitive conclusions being drawn. Prospective randomized trials of adjuvant therapy are needed in this disease. J. Surg. Oncol. 2008;98:485–489. © 2008 Wiley‐Liss, Inc.
A network management tool for resource‐partition based layer 1 virtual private networks
Authors: Wu Jing , Savoie Michel , Campbell Scott , Zhang Hanxi 
Published: September 2008

AbstractA Layer 1 Virtual Private Network (L1‐VPN) has two models for service management: the resource‐partition based model and the domain‐service based model. In this paper, we present a network management tool for resource‐partition based L1‐VPNs. A Transaction Language One (TL1) proxy is designed to achieve resource partitioning at the network element level. Building on top of a TL1 proxy, we implemented a User‐Controlled LightPath (UCLP) system to support physical network brokers to assign and allocate virtually dedicated resources to customers, and to enable customers to directly manage their resources. With such a capability, customers are able to create wide area networks based on their traffic pattern, and to adjust their traffic pattern based on available resources. Copyright © 2008 Crown in the right of Canada. Published by John Wiley & Sons, Ltd.
Testing the psychometric properties of a Chinese version of the Level of Expressed Emotion scale
Authors: Chien Wai‐Tong , Chan Sally W.C. 
Published: September 2008

AbstractExpressed emotion of families of people with schizophrenia is useful and important to evaluate the effects of family interventions. This study tested the reliability and validity of a Chinese version of the Level of Expressed Emotion scale. This psychometric analysis included tests of content validity and reliability, and an exploratory factor analysis. Results indicated that the Chinese version had a high level of equivalence with the original English version and demonstrated good internal consistency and test–retest reliability. The refined 52‐item Chinese version consisted of four factors, indicating satisfactory correlation with two theoretically relevant scales. The Chinese version appears psychometrically sound as a measure of schizophrenic patients' perceptions of their family members' expressed emotion. © 2008 Wiley Periodicals, Inc. Res Nurs Health 32:59–70, 2009
Locally divergence‐preserving schemes of higher order
Authors: Artebrant Robert 
Published: September 2008

AbstractViolation of the divergence constraint on the magnetic flux density in magnetohydrodynamical (MHD) simulations leads to stability problems. It is therefore of great importance to numerically respect this intrinsic constraint. Since the divergence preservation is a local phenomenon inherent in the MHD‐system it is appealing to mimic this property numerically by a locally divergence‐preserving scheme.A common numerical technique for simulation of the MHD‐system of conservation laws is the finite volume (FV) method. In [SISC 26 2005 pp. 1166] a local procedure to redistribute the numerical fluxes in a FV‐scheme so that a discrete divergence operator vanishes was presented. This procedure stabilizes the base scheme and respects the accuracy to the second order level.The present note describes a development of the above procedure that complies with the finite volume framework, preserves a fourth order discrete divergence operator locally and retains the accuracy of a generic semi‐discrete finite volume scheme up to fourth order. The redistribution of the numerical magnetic field fluxes is formulated in a standard conservative setting, making it trivial to implement the divergence‐preserving modification in an existing FV‐scheme; see [JCP 227 2008 pp.3405] for the details. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Jamming, plasticity and diffusion in dense granular materials
Authors: Behringer R.P. 
Published: September 2008

AbstractIn this paper, we present experimental results based on photoelastic techniques that allow us to obtain complete details of processes in dense granular materials. This work focuses in particular on the jamming transition and on the nature of affine and non‐affine deformations in the shear band occuring in granular Couette flow. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Applications on variational inequalities involving multivalued maps
Authors: Benedetti Irene , Zecca Pietro 
Published: September 2008

AbstractWe present a connection between variational inequalities of Stampacchia's type involving multivalued maps and partial differential inclusions. We solve the variational inequalities considered and, as a consequence, the differential inclusion associated, using the topological degree theory. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The balance of material momentum at a shock wave propagating in a thermo‐elastic material
Authors: Braun Manfred 
Published: September 2008

AbstractAt a surface of discontinuity, the mechanical balance laws are represented by jump conditions. It is shown how the balance of material momentum at an adiabatic shock propagating in a thermo‐elastic material is obtained from the discontinuous balances of physical momentum and energy. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Some software aspects of DAE simulation & optimization software
Authors: Campbel S. L. , Betts J. T. , Engelsone A. , Nikoukhah R. , Najafi M. 
Published: September 2008

AbstractConsiderable numerical software has been written for simulation and optimization of dynamical systems. From the beginning of their development, differential algebraic equations (DAEs) have often been proposed as a way to make modeling easier. The modeler need only write down equations relating the variables in the model. However, much DAE software requires at least as much user numerical and mathematical expertise as explicit methods. An important aspect of our research has been working toward helping the idea of DAEs achieve its promise in modeling and simulation by both pushing the software to handle more general problems and to also allow for less user expertise. Some recent examples are presented where this research impacts on software and their underlying algorithms. Space necessitates we assume the reader has a rough idea of what a DAE is. The examples are implicit Scicos, and optimization of DAE models. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Blind source separation and automatic transcription of music using tensor decompositions
Authors: FitzGerald Derry 
Published: September 2008

AbstractRecent advances in the use of tensor decompositions for the analysis of music are described. In particular, the use of such decompositions for sound source separation and the automatic transcription of music are explored. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Global instability computations of separated flows
Authors: Logue R.P. , Gajjar J. , Ruban A. 
Published: September 2008

AbstractThe primary motivation for the current work is to develop suitable techniques for studying the global instability in many different flows such as that occuring in the subsonic flow past a corner. In this paper we will discuss the methodology and some of the results obtained. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The cosymmetric bifurcations in the planar filtrational convection problem: numerical results
Authors: Govorukhin V.N. , Shevchenko I.V. 
Published: September 2008

AbstractHere we present survey of our numerical results concerning possible bifurcation in cosymmetric filtrational convection problem. We study bifurcations connected with existence of cycles of equilibria and scenarios for onset of unsteady regimes. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interaction of point defects in ferroelectrics ‐parameter identification and simulation
Authors: Goy Oliver , Mueller Ralf , Gross Dietmar 
Published: September 2008

AbstractFerroelectric materials are used in a wide field of applications, where they are exposed to a high number of mechanical and electrical load cycles. This involves degradation of the material and a decrease of the electromechanical coupling capability, which is usually called electric fatigue. The causes are assumed to be ionic and electronic charge carriers, which interact with each other, with microstructural elements in the bulk and with interfaces. Accumulation of defects can lead to degradation, mechanical damage and dissociation reactions, for more details see e.g. [3].In order to get a better understanding of the defect accumulation processes, a model based on material forces is used in [6] to simulate the interaction of defects in periodic and in infinite cells. Applying thermodynamically reasonable kinetic laws, defect migration is simulated in a deterministic way in order to understand the general tendency of defect formations. The transversally isotropic material is modelled with linear electromechanical coupling. Here, the defect parameters used in the continuum model are obtained by fitting the results of molecular dynamics (MD) simulations to the continuous spatial fields. Transferring data from the atomic to the continuum level is a field of active research and no unique solution can be presented. On the atomic level, Coulomb–interaction causes a displacement field incompatible to an elastic solution. To address this difficulty, the volume change of a domain around the defect is used to determine defect parameters. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
One‐shot multigrid method for aerodynamic shape optimization
Authors: Hazra Subhendu Bikash 
Published: September 2008

AbstractThis paper presents a numerical method for aerodynamic shape optimization problems. It is based on simultaneous pseudotime‐stepping in which the optimality is reached simultaneously with the state and costate feasibility. An optimization‐based multigrid strategy results in efficient convergence of the method. The total effort of optimization is less than two forward simulation runs. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Amplitude‐dependent phenomena of filler‐reinforced rubber: Experiments, modelling and simulation
Authors: Höfer Philipp , Lion Alexander 
Published: September 2008

AbstractIt's a matter of common knowledge, that carbon black‐or silica‐loaded elastomers show a pronounced nonlinearity when excited with dynamic deformation amplitudes, namely the Payne‐effect. Furthermore, several experiments prove a very complex history‐dependence and significant recovery‐behaviour of this effect. In the present paper, a few experimental results of dynamical measurements on filler‐loaded rubber are shown with importance attached to the complicated history dependence. In order to describe the depicted phenomena, a model, based on intrinsic time scales is presented with corresponding simulation results. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Energy functionals for microstructured multi‐phase materials
Authors: Langhoff T.‐A. , Böhlke T. , Schnack E. 
Published: September 2008

AbstractFor describing the influence of multi‐phase materials with microstructure on different length scales as well as the evolution of phase changes under thermomechanical loading, an energetic model is developed. Relying on the incremental formulation of the energetic model, a new solution procedure for the coupled thermomechanical problem is proposed. This model can be applied to describe e.g. the macroscopic response of carbon fibre reinforced carbon. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Jamming in attractive granular media
Authors: Lois Gregg , Blawzdziewicz Jerzy , O'Hern Corey S. 
Published: September 2008

AbstractThe jamming transition is studied numerically in systems of particles with attraction. Unlike the purely repulsive case where a single transition separates the jammed from unjammed phase, the presence of even an infinitesimal amount of attraction yields two distinct transitions: connectivity and rigidity percolation. We measure critical exponents of these two percolation transitions and find that they are different than the corresponding lattice values. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Blow‐up and regularity problems of hypoviscous fluid equations
Authors: Ohkitani Koji 
Published: September 2008

AbstractWe consider 1D Burgers equation with hypoviscosity at a critical exponent under periodic boundary conditions. Assuming global (in time) regularity, we derive an asymptotic equation by a simple transformation. It turned out that it has exactly the same form as the one obtained by applying Moore's asymptotic analysis, originally developed for the Birkhoff‐Rott equation, to the inviscid Burgers equation. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
δ ‐ and δ ′‐shocks and the transportation and concentration processes
Authors: Shelkovich V.M. 
Published: September 2008

AbstractUsing the definitions of δ ‐ and δ ′‐shocks for some systems of conservation laws, the corresponding Rankine–Hugoniot conditions are derived. We also derive the balance laws describing area, volume, mass and momentum transportation between the area outside the wave front and the wave front. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An improved scheme for accelerating the convergence of the simulated annealing algorithm applied to real world problems
Authors: Verdiell Adriana Beatriz , Maciel María Cristina , Vidal Marta Cecilia 
Published: September 2008

AbstractWhen formulated in mathematical terms, the problem of zoning a protected natural area subject to both box and spatial constraints results in a large combinatorial optimization problem belonging to the NP‐hard class. These facts suggest the need to apply a heuristic approach. In this contribution a new proposal to decrease the control parameter, known as temperature, in the simulated annealing algorithm is presented. The strategy is based on that proposed by Lundy and Mees [4], and developed in order to decrease the running time of the algorithm applied to large scale problems. When applied to solving small‐size simulated problems, results were indistinguishable from those obtained via an exact, enumerative method.A coarse‐scale zoning of Talampaya National Park (Argentina) rendered maps remarkably similar to those produced by subject area experts using a non‐quantitative consensus‐seeking approach. Results are encouraging and show particular potential for the periodical update of zoning of protected natural areas. Such a capability is crucial for application in developing countries where both human and financial resources are usually scarce but still critical for updating zoning and management plans. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optimal design of frames under stochastic uncertainties
Authors: Zier Simone 
Published: September 2008

AbstractIn the following the design of frames is treated where the load is supposed to be stochastic. The recourse problem will be formulated in the standard form of stochastic linear programming (SLP). After this formulation the recourse problem with discretization and the expected value problem are introduced as representatives of substitute problems. Subsequently, optimization results using these methods for the robust optimal design of a two‐storey frame are presented. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Transdermal buprenorphine in children with cancer‐related pain
Authors: Attinà Giorgio , Ruggiero Antonio , Maurizi Palma , Arlotta Annalisa , Chiaretti Antonio , Riccardi Riccardo 
Published: September 2008

AbstractWe present three cases of children (aged 3–5 years) in which cancer‐related pain was adequately controlled by Transdermal Buprenorphine. The endpoints for evaluating analgesic efficacy consisted of the assessment of pain using a visual scale and the possibility of reducing other pain treatment. Improvement of pain level was demonstrated by the decrease in pain scores, by reduction of the overall amount of medications, especially opioids, and by improvement of uninterrupted sleep. Only limited data is available on the use of Transdermal Buprenorphine in children. In our experience, Transdermal Buprenorphine allowed good analgesia without significant side effects in these three children with cancer‐related pain. Pediatr Blood Cancer 2009;52:125–127. © 2008 Wiley‐Liss, Inc.
The prognostic value of tumor markers in newly diagnosed patients with primary central nervous system germ cell tumors
Authors: Kim AeRang , Ji Lingyun , Balmaceda Casilda , Diez Blanca , Kellie Stewart J. , Dunkel Ira J. , Gardner Sharon L. , Sposto Richard , Finlay Jonathan L. 
Published: September 2008

AbstractBackgroundTo determine the impact of diagnostic serum and/or cerebrospinal fluid (CSF) alpha‐fetoprotein (AFP) and beta‐human chorionic gonadotropin (b‐HCG) elevations on survival in newly diagnosed patients with central nervous system germ cell tumors (CNS GCT) treated with chemotherapy with the intent to avoid irradiation.ProcedureSeventy‐five patients with newly diagnosed CNS GCT enrolled in two sequential internationally conducted clinical trials with serum and CSF AFP and b‐HCG levels available from initial diagnosis were retrospectively analyzed. Subjects received platinum based chemotherapy and were followed with serial imaging and tumor marker evaluations.ResultsThe 5‐year overall survival (OS) and event free survival (EFS) for patients with normal tumor markers compared with those with elevated markers at diagnosis was 78% (95% CI 51–91%) versus 60% (95% CI 46–72%) (P = 0.08) and 22% (95% CI 7–43%) versus 28% (95% CI 16–40%) (P = 0.68). The hazard ratio of death for patients with elevated markers was 1.9 times as high as that for those with normal markers (95% CI 0.58–6.5) after adjusting for other baseline characteristics. There was no observed difference in survival among patients with histologically confirmed germinomas, irrespective of level of b‐HCG.ConclusionsPatients with elevated tumor markers appear to have poorer OS independent of tumor histology, although these differences do not reach statistical significance (P ≤ 0.05). No differences were observed in EFS between groups likely due to the poor response of chemotherapy only approach to patients with normal markers. b‐HCG elevations in biopsy proven germinomas do not seem to alter a patient's prognosis. Pediatr Blood Cancer 2008;51:768–773. © 2008 Wiley‐Liss, Inc.