bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Vaccine-Induced Effector CD8 T Cell Responses Directed against Self- and Non–Self-Tumor Antigens: Implications for Cancer Immunotherapy
Authors: Pedersen Sara R. , Sørensen Maria R. , Buus Søren , Christensen Jan P. , Thomsen Allan R. 
Published: September 2013

Abstract
It is generally accepted that CD8 T cells play a major role in tumor control, yet vaccination aimed at eliciting potent CD8 T cell responses are rarely efficient in clinical trials. To try and understand why this is so, we have generated potent adenoviral vectors encoding the endogenous tumor Ags (TA) tyrosinase-related protein-2 (TRP-2) and glycoprotein 100 (GP100) tethered to the invariant chain (Ii). Using these vectors, we sought to characterize the self-TA–specific CD8 T cell response and compare it to that induced against non–self-Ags expressed from a similar vector platform. Prophylactic vaccination with adenoviral vectors expressing either TRP-2 (Ad-Ii-TRP-2) or GP100 (Ad-Ii-GP100) had little or no effect on the growth of s.c. B16 melanomas, and only Ad-Ii-TRP-2 was able to induce a marginal reduction of B16 lung metastasis. In contrast, vaccination with a similar vector construct expressing a foreign (viral) TA induced efficient tumor control. Analyzing the self-TA–specific CD8 T cells, we observed that these could be activated to produce IFN-γ and TNF-α. In addition, surface expression of phenotypic markers and inhibitory receptors, as well as in vivo cytotoxicity and degranulation capacity matched that of non–self-Ag–specific CD8 T cells. However, the CD8 T cells specific for self-TAs had a lower functional avidity, and this impacted on their in vivo performance. On the basis of these results and a low expression of the targeted TA epitopes on the tumor cells, we suggest that low avidity of the self-TA–specific CD8 T cells may represent a major obstacle for efficient immunotherapy of cancer.
Induction of Cyclooxygenase-2 Signaling by Stomatococcus mucilaginosus Highlights the Pathogenic Potential of an Oral Commensal
Authors: Yuan Zhihong , Panchal Dipti , Syed Mansoor Ali , Mehta Hiren , Joo Myungsoo , Hadid Walid , Sadikot Ruxana T. 
Published: September 2013

Abstract
Stomatococcus mucilaginosus is an oral commensal that has been occasionally reported to cause severe infections in immunocompromised patients. There is no information about the pathogenic role of S. mucilaginosus in airway infections. In a cohort of 182 subjects with bronchiectasis, we found that 9% were colonized with S. mucilaginosus in their lower airways by culture growth from bronchoalveolar lavage. To address the pathogenic potential of S.mucilaginosus, we developed a murine model of S. mucilaginosus lung infection. Intratracheal injection of S. mucilaginosus in C57BL/6 mice resulted in a neutrophilic influx with production of proinflammatory cytokines, chemokines, and lipid mediators, mainly PGE2 with induction of cyclooxygenase-2 (COX-2) in the lungs. Presence of TLR2 was necessary for induction of COX-2 and production of PGE2 by S. mucilaginosus. TLR2-deficient mice showed an enhanced clearance of S. mucilaginosus compared with wild-type mice. Administration of PGE2 to TLR2−/− mice resulted in impaired clearance of S. mucilaginosus, suggesting a key role for COX-2–induced PGE2 production in immune response to S. mucilaginosus. Mechanistically, induction of COX-2 in macrophages was dependent on the p38-ERK/MAPK signaling pathway. Furthermore, mice treated with S. mucilaginosus and Pseudomonas aeruginosa showed an increased mortality compared with mice treated with PA103 or S. mucilaginosus alone. Inhibition of COX-2 significantly improved survival in mice infected with PA103 and S. mucilaginosus. These data provide novel insights into the bacteriology and personalized microbiome in patients with bronchiectasis and suggest a pathogenic role for S. mucilaginosus in patients with bronchiectasis.
Patients’ Experience of a Regional Allergy Service
Authors: Jones Ray , O'Connor Anita , Kaminski Edward 
Published: September 2013

Background The principle reason for referral to specialist allergy clinics is to establish diagnoses and provide treatment plans to help patients manage their allergy. If patients do not accept, understand, or remember diagnoses or treatment, clinic visits may have been a waste of time. Few specialist allergy clinics follow up patients after diagnosis. Design and Methods This was a postal survey to assess patients’ i) perception of usefulness of specialist allergy clinic visits, ii) understanding of their allergy, iii) confidence in managing it, and iv) response to joining a regional online forum. Data for patients with confirmed allergy who attended the Peninsula Allergy Service (PAS) from 1998-2009 were extracted from consultant letters to general practitioners. Postal questionnaires were sent to 933 patients; 39% (336) responded. Results Two-thirds (63%) thought their clinic visit useful and resulted in them being more in control of their allergy; 9% thought it useful but they still had problems, 26% thought it had not been much use. One in six (16%, 55) respondents had major differences in their view of their allergy compared to that recorded by PAS. Over half (56%) had had further symptoms since their clinic visit and 120 patients, who were not confident in coping with their allergy, listed aspects of their lives that gave concern. Conclusions Specialist clinics need routine feedback from patients if they are to monitor their effectiveness and some better form of follow up for patients is needed to reinforce education and support patients. Public education is important.
Learning Environments’ Activity Potential for Preschoolers (LEAPP): Study Rationale and Design
Authors: Tucker Patricia , Vanderloo Leigh M. , Newnham-Kanas Courtney , Burke Shauna M. , Irwin Jennifer D. , Johnson Andrew M. , van Zandvoort Melissa M. 
Published: September 2013

Background The purpose of this paper is to provide an overview of the study protocol for the Learning Environments’ Activity Potential for Preschoolers (LEAPP) study, the goal of which is to describe the activity levels of preschoolers attending various early learning venues and explore which attributes of these facilities (e.g. curriculum, policies, equipment, etc.) support activity participation. Design and Methods This cross-sectional study aimed to recruit approximately 30 early learning environments requesting participation from preschoolers aged 2.5-5 years. Data collection included: Actical accelerometers (MiniMitter, Oregon, USA) to measure the activity levels of children for five consecutive days (15-second epoch length) while in care; the Environment and Policy Assessment and Observation tool to explore the early learning environment's impact on activity; anthropometric data; the Child Temperament Questionnaire to assess the influence of preschoolers’ temperament on physical activity; and demographic information from parents/guardians and early learning staff. ANOVA and linear regression analyses will be conducted to assess variances in activity levels among preschoolers attending different early learning types and to explore the impact of early learning environments on their activity levels. Independent sample t-tests will be used to examine differences in activity levels based on sex and weight status. Expected impact of the study for public health This research will provide the first Canadian data to address environmental influences on preschoolers’ activity levels in differing early learning environments. Additionally, this work will highlight the extent to which activity levels vary among preschoolers enrolled in full-day kindergarten, centre-, and home-based childcare.
Crisis Communication in the Area of Risk Management: The CriCoRM Project
Authors: Scarcella Carmelo , Antonelli Laura , Orizio Grazia , Rossmann Costanze , Ziegler Lena , Meyer Lisa , Garcia-Jimenez Leonarda , Losada Jose Carlos , Correia Joao , Soares Joana , Covolo Loredana , Lirangi Enrico , Gelatti Umberto 
Published: September 2013

Background During the last H1N1 pandemic has emerged the importance of crisis communication as an essential part of health crisis management. The Project aims specifically to improve the understanding of crisis communication dynamics and effective tools and to allow public health institutions to communicate better with the public during health emergencies. Design and Methods The Project will perform different activities: i) state of the art review; ii) identification of key stakeholders; iii) communicational analysis performed using data collected on stakeholder communication activities and their outcomes considering the lessons learnt from the analysis of the reasons for differing public reactions during pandemics; iv) improvement of the existing guidelines; v) development of Web 2.0 tools as web-platform and feed service and implementation of impact assessment algorithms; vi) organization of exercises and training on this issues. Expected impact of the study for public health In the context of health security policies at an EU level, the project aims to find a common and innovative approach to health crisis communication that was displayed by differing reactions to the H1N1 pandemic policies. The focus on new social media tools aims to enhance the role of e-health, and the project aims to use these tools in the specific field of health institutions and citizens. The development of Web 2.0 tools for health crisis communication will allow an effective two-way exchange of information between public health institutions and citizens. An effective communication strategy will increase population compliance with public health recommendations.
Correlation of stroke Volume Measurement between sonosite portable Echocardiogram and Edwards Flotrac sensor-Vigileo Monitor in an Intensive care Unit
Authors: Behnia Mehrdad , Powell Sherry , Fallen Linda , Tamaddon Houman , Behnia Masud 
Published: September 2013

Purpose Stroke volume (SV) is a parameter that is being recognized as an endpoint in fluid resuscitation algorithms. Its role is now being realized as an important variable in hemodynamic assessment in various clinical scenarios such as septic and cardiogenic shocks. Direct measurement of stroke volume (SV) and its novel corollary, stroke volume variation (SVV) derived by proprietary software, are preferred over mean cardiac output (CO) measurements because they render a more accurate reflection of hemodynamic status independent of heart rate. Flotrac-Vigileo monitor (FTV) (Edwards Lifesciences, Irvine, CA, USA) is a system that uses a complex algorithm analyzing arterial waveform to calculate SV, SVV, and CO. We assessed the feasibility of obtaining SV measurements with a portable echocardiogram and validated its accuracy with the FTV system in mechanically ventilated patients in our intensive care unit (ICU). Furthermore, we emphasized the importance of hemodynamic measurements and familiarity with critical care echocardiography for the intensivists. Methods Ten patients who were on mechanical ventilation were studied. A femoral arterial line was connected to the FTV system monitoring SV and CO. A portable echocardiogram (M-Turbo; Sonosite, Bothell, WA) was used to measure SV. CO was calculated by multiplying SV by heart rate. No patient had arrhythmia. We used biplane Simpson's method of discs to calculate SV in which subtraction of end-systolic volume from end-diastolic volume yields the SV Results The comparison of simultaneous SV and CO measurements by echocardiography with FTV showed a strong correlation between the 2. (For SV, y = 0.9545x + 3.3, R2 = 0.98 and for CO, y = 0.9104x + 7.7074, R2 = 0.97). Conclusions In our small cohort, the SV and CO measured by a portable echocardiogram (Sonosite M-Turbo) appears to be closely correlated with their respective values measured by FTV. Portable echocardiography is a reliable noninvasive tool for the hemodynamic assessment of the critically ill. Its results need further validation with gold standard measures in a larger cohort of patients. However, our results suggest portable echocardiography could be an attractive tool in assessment of different hemodynamic scenarios in the critically ill.
Mathematical Modelling of Malaria with Treatment
Authors: Ghosh Mini 
Published: September 2013

AbstractThis paper proposes a Susceptible-Infective-Susceptible (SIS) model to study the malaria transmission with treatment by considering logistic growth of mosquito population. In this work, it is assumed that the treatment rate is proportional to the number of infectives below the capacity and is constant when the number of infectives is greater than the capacity. We find that the system exhibits backward bifurcation if the capacity is small and it gives bi-stable equilibria which makes the system more sensitive to the initial conditions. The existence and stability of the equilibria of the model are discussed in-detail and numerical simulations are presented to illustrate the numerical results.
A Solver for Helmholtz System Generated by the Discretization of Wave Shape Functions
Authors: Yuan Long , Hu Qiya 
Published: September 2013

AbstractAn interesting discretization method for Helmholtz equations was introduced in B. Després [1]. This method is based on the ultra weak variational formulation (UWVF) and the wave shape functions, which are exact solutions of the governing Helmholtz equation. In this paper we are concerned with fast solver for the system generated by the method in [1]. We propose a new preconditioner for such system, which can be viewed as a combination between a coarse solver and the block diagonal preconditioner introduced in [13]. In our numerical experiments, this preconditioner is applied to solve both two-dimensional and three-dimensional Helmholtz equations, and the numerical results illustrate that the new preconditioner is much more efficient than the original block diagonal preconditioner.
Analyses of the Dispersion Overshoot and Inverse Dissipation of the High-Order Finite Difference Scheme
Authors: Li Qin , Guo Qilong , Zhang Hanxin 
Published: September 2013

AbstractAnalyses were performed on the dispersion overshoot and inverse dissipation of the high-order finite difference scheme using Fourier and precision analysis. Schemes under discussion included the pointwise- and staggered-grid type, and were presented in weighted form using candidate schemes with third-order accuracy and three-point stencil. All of these were commonly used in the construction of difference schemes. Criteria for the dispersion overshoot were presented and their critical states were discussed. Two kinds of instabilities were studied due to inverse dissipation, especially those that occur at lower wave numbers. Criteria for the occurrence were presented and the relationship of the two instabilities was discussed. Comparisons were made between the analytical results and the dispersion/dissipation relations by Fourier transformation of typical schemes. As an example, an application of the criteria was given for the remedy of inverse dissipation in Weirs &amp; Martín’s third-order scheme.
A Meshless Regularization Method for a Two-Dimensional Two-Phase Linear Inverse Stefan Problem
Authors: Tomas Johansson B. , Lesnic Daniel , Reeve Thomas 
Published: September 2013

AbstractIn this paper, a meshless regularization method of fundamental solutions is proposed for a two-dimensional, two-phase linear inverse Stefan problem. The numerical implementation and analysis are challenging since one needs to handle composite materials in higher dimensions. Furthermore, the inverse Stefan problem is ill-posed since small errors in the input data cause large errors in the desired output solution. Therefore, regularization is necessary in order to obtain a stable solution. Numerical results for several benchmark test examples are presented and discussed.
A Constrained Cauchy-Born Elasticity Accelerated Multigrid Method for Nanoindentation
Authors: Chen Jingrun , Ming Pingbing , Yang Jerry Zhijian 
Published: September 2013

AbstractWe introduce a new multigrid method to study the lattice statics model arising from nanoindentation. A constrained Cauchy-Born elasticity model is used as the coarse-grid operator. This method accelerates the relaxation process and considerably reduces the computational cost. In particular, it saves quite a bit when dislocations nucleate and move, as demonstrated by the simulation results.
An Entropic Scheme for an Angular Moment Model for the Classical Fokker-Planck-Landau Equation of Electrons
Authors: Mallet Jessy , Brull Stéphane , Dubroca Bruno 
Published: September 2013

AbstractIn plasma physics domain, the electron transport is described with the Fokker-Planck-Landau equation. The direct numerical solution of the kinetic equation is usually intractable due to the large number of independent variables. That is why we propose in this paper a new model whose derivation is based on an angular closure in the phase space and retains only the energy of particles as kinetic dimension. To find a solution compatible with physics conditions, the closure of the moment system is obtained under a minimum entropy principle. This model is proved to satisfy the fundamental properties like a H theorem. Moreover an entropic discretization in the velocity variable is proposed on the semi-discrete model. Finally, we validate on numerical test cases the fundamental properties of the full discrete model.
A Survey on Parallel Computing and its Applications in Data-Parallel Problems Using GPU Architectures
Authors: Navarro Cristóbal A. , Hitschfeld-Kahler Nancy , Mateu Luis 
Published: September 2013

AbstractParallel computing has become an important subject in the field of computer science and has proven to be critical when researching high performance solutions. The evolution of computer architectures (multi-coreandmany-core) towards a higher number of cores can only confirm that parallelism is the method of choice for speeding up an algorithm. In the last decade, the graphics processing unit, or GPU, has gained an important place in the field of high performance computing (HPC) because of its low cost and massive parallel processing power. Super-computing has become, for the first time, available to anyone at the price of a desktop computer. In this paper, we survey the concept of parallel computing and especially GPU computing. Achieving efficient parallel algorithms for the GPU is not a trivial task, there are several technical restrictions that must be satisfied in order to achieve the expected performance. Some of these limitations are consequences of the underlying architecture of the GPU and the theoretical models behind it. Our goal is to present a set of theoretical and technical concepts that are often required to understand the GPU and itsmassive parallelismmodel. In particular, we show how this new technology can help the field ofcomputational physics,especially when the problem isdata-parallel.We present four examples of computational physics problems;n-body, collision detection, Potts modelandcellular automatasimulations. These examples well represent the kind of problems that are suitable for GPU computing. By understanding the GPU architecture and its massive parallelism programming model, one can overcome many of the technical limitations found along the way, design better GPU-based algorithms for computational physics problems and achieve speedups that can reach up to two orders of magnitude when compared to sequential implementations.
A Multi-Material CCALE-MOF Approach in Cylindrical Geometry
Authors: Friess Marie Billaud , Breil Jérôme , Maire Pierre-Henri , Shashkov Mikhail 
Published: September 2013

AbstractIn this paper we present recent developments concerning a Cell-Centered Arbitrary Lagrangian Eulerian (CCALE) strategy using the Moment Of Fluid (MOF) interface reconstruction for the numerical simulation of multi-material compressible fluid flows on unstructured grids in cylindrical geometries. Especially, our attention is focused here on the following points. First, we propose a new formulation of the scheme used during the Lagrangian phase in the particular case of axisymmetric geometries. Then, the MOF method is considered for multi-interface reconstruction in cylindrical geometry. Subsequently, a method devoted to the rezoning of polar meshes is detailed. Finally, a generalization of the hybrid remapping to cylindrical geometries is presented. These explorations are validated by mean of several test cases using unstructured grid that clearly illustrate the robustness and accuracy of the new method.
A Parallel Adaptive Treecode Algorithm for Evolution of Elastically Stressed Solids
Authors: Feng Hualong , Barua Amlan , Li Shuwang , Li Xiaofan 
Published: September 2013

AbstractThe evolution of precipitates in stressed solids is modeled by coupling a quasi-steady diffusion equation and a linear elasticity equation with dynamic boundary conditions. The governing equations are solved numerically using a boundary integral method (BIM). A critical step in applying BIM is to develop fast algorithms to reduce the arithmetic operation count of matrix-vector multiplications. In this paper, we develop a fast adaptive treecode algorithm for the diffusion and elasticity problems in two dimensions (2D). We present a novel source dividing strategy to parallelize the treecode. Numerical results show that the speedup factor is nearly perfect up to a moderate number of processors. This approach of parallelization can be readily implemented in other treecodes using either uniform or non-uniform point distribution. We demonstrate the effectiveness of the treecode by computing the long-time evolution of a complicated microstructure in elastic media, which would be extremely difficult with a direct summation method due to CPU time constraint. The treecode speeds up computations dramatically while fulfilling the stringent precision requirement dictated by the spectrally accurate BIM.
A Coupled Immersed Interface and Level Set Method for Three-Dimensional Interfacial Flows with Insoluble Surfactant
Authors: Xu Jian-Jun , Huang Yunqing , Lai Ming-Chih , Li Zhilin 
Published: September 2013

AbstractIn this paper, a numerical method is presented for simulating the 3D interfacial flows with insoluble surfactant. The numerical scheme consists of a 3D immersed interface method (IIM) for solving Stokes equations with jumps across the interface and a 3D level-set method for solving the surfactant convection-diffusion equation along a moving and deforming interface. The 3D IIM Poisson solver modifies the one in the literature by assuming that the jump conditions of the solution and the flux are implicitly given at the grid points in a small neighborhood of the interface. This assumption is convenient in conjunction with the level-set techniques. It allows standard Lagrangian interpolation for quantities at the projection points on the interface. The interface jump relations are re-derived accordingly. A novel rotational procedure is given to generate smooth local coordinate systems and make effective interpolation. Numerical examples demonstrate that the IIM Poisson solver and the Stokes solver achieve second-order accuracy. A 3D drop with insoluble surfactant under shear flow is investigated numerically by studying the influences of different physical parameters on the drop deformation.