444 research outputs found
Dynamical features of reaction-diffusion fronts in fractals
The speed of front propagation in fractals is studied by using (i) the reduction of the reaction-transport equation into a Hamilton-Jacobi equation and (ii) the local-equilibrium approach. Different equations proposed for describing transport in fractal media, together with logistic reaction kinetics, are considered. Finally, we analyze the main features of wave fronts resulting from this dynamic process, i.e., why they are accelerated and what is the exact form of this acceleration
Exercise training and detraining modify the morphological and mechanical properties of single cardiac myocytes obtained from spontaneously hypertensive rats
Does backreaction enforce the averaged null energy condition in semiclassical gravity?
The expected stress-energy tensor of quantum fields generically
violates the local positive energy conditions of general relativity. However,
may satisfy some nonlocal conditions such as the averaged null energy
condition (ANEC), which would rule out traversable wormholes. Although ANEC
holds in Minkowski spacetime, it can be violated in curved spacetimes if one is
allowed to choose the spacetime and quantum state arbitrarily, without
imposition of the semiclassical Einstein equation G_{ab} = 8 \pi . In
this paper we investigate whether ANEC holds for solutions to this equation, by
studying a free, massless scalar field with arbitrary curvature coupling in
perturbation theory to second order about the flat spacetime/vacuum solution.
We "reduce the order" of the perturbation equations to eliminate spurious
solutions, and consider the limit in which the lengthscales determined by the
incoming state are much larger than the Planck length. We also need to assume
that incoming classical gravitational radiation does not dominate the first
order metric perturbation. We find that although the ANEC integral can be
negative, if we average the ANEC integral transverse to the geodesic with a
suitable Planck scale smearing function, then a strictly positive result is
obtained in all cases except for the flat spacetime/vacuum solution. This
result suggests --- in agreement with conclusions drawn by Ford and Roman from
entirely independent arguments --- that if traversable wormholes do exist as
solutions to the semiclassical equations, they cannot be macroscopic but must
be ``Planck scale''. A large portion of our paper is devoted to the analysis of
general issues concerning the nature of the semiclassical Einstein equation and
of prescriptions for extracting physically relevant solutions.Comment: 54 pages, 3 figures, uses revtex macros and epsf.tex, to appear in
Phys Rev D. A new appendix has been added showing consistency of our results
with recent results of Visser [gr-qc/9604008]. Some corrections were made to
Appendix A, and several other minor changes to the body of the paper also
were mad
Restarted Q-Arnoldi-type methods exploiting symmetry in quadratic eigenvalue problems
The final publication is available at Springer via http://dx.doi.org/ 10.1007/s10543-016-0601-5.We investigate how to adapt the Q-Arnoldi method for the case of symmetric quadratic eigenvalue problems, that is, we are interested in computing a few eigenpairs of with M, C, K symmetric matrices. This problem has no particular structure, in the sense that eigenvalues can be complex or even defective. Still, symmetry of the matrices can be exploited to some extent. For this, we perform a symmetric linearization , where A, B are symmetric matrices but the pair (A, B) is indefinite and hence standard Lanczos methods are not applicable. We implement a symmetric-indefinite Lanczos method and enrich it with a thick-restart technique. This method uses pseudo inner products induced by matrix B for the orthogonalization of vectors (indefinite Gram-Schmidt). The projected problem is also an indefinite matrix pair. The next step is to write a specialized, memory-efficient version that exploits the block structure of A and B, referring only to the original problem matrices M, C, K as in the Q-Arnoldi method. This results in what we have called the Q-Lanczos method. Furthermore, we define a stabilized variant analog of the TOAR method. We show results obtained with parallel implementations in SLEPc.This work was supported by the Spanish Ministry of Economy and Competitiveness under Grant TIN2013-41049-P. Carmen Campos was supported by the Spanish Ministry of Education, Culture and Sport through an FPU Grant with reference AP2012-0608.Campos, C.; Román Moltó, JE. (2016). Restarted Q-Arnoldi-type methods exploiting symmetry in quadratic eigenvalue problems. BIT Numerical Mathematics. 56(4):1213-1236. https://doi.org/10.1007/s10543-016-0601-5S12131236564Bai, Z., Su, Y.: SOAR: a second-order Arnoldi method for the solution of the quadratic eigenvalue problem. SIAM J. Matrix Anal. Appl. 26(3), 640–659 (2005)Bai, Z., Day, D., Ye, Q.: ABLE: an adaptive block Lanczos method for non-Hermitian eigenvalue problems. SIAM J. Matrix Anal. Appl. 20(4), 1060–1082 (1999)Bai, Z., Ericsson, T., Kowalski, T.: Symmetric indefinite Lanczos method. In: Bai, Z., Demmel, J., Dongarra, J., Ruhe, A., van der Vorst, H. (eds.) Templates for the solution of algebraic eigenvalue problems: a practical guide, pp. 249–260. Society for Industrial and Applied Mathematics, Philadelphia (2000)Balay, S., Abhyankar, S., Adams, M., Brown, J., Brune, P., Buschelman, K., Dalcin, L., Eijkhout, V., Gropp, W., Kaushik, D., Knepley, M., McInnes, L.C., Rupp, K., Smith, B., Zampini, S., Zhang, H.: PETSc users manual. Tech. Rep. ANL-95/11 - Revision 3.6, Argonne National Laboratory (2015)Benner, P., Faßbender, H., Stoll, M.: Solving large-scale quadratic eigenvalue problems with Hamiltonian eigenstructure using a structure-preserving Krylov subspace method. Electron. Trans. Numer. Anal. 29, 212–229 (2008)Betcke, T., Higham, N.J., Mehrmann, V., Schröder, C., Tisseur, F.: NLEVP: a collection of nonlinear eigenvalue problems. ACM Trans. Math. Softw. 39(2), 7:1–7:28 (2013)Campos, C., Roman, J.E.: Parallel Krylov solvers for the polynomial eigenvalue problem in SLEPc (2015, submitted)Day, D.: An efficient implementation of the nonsymmetric Lanczos algorithm. SIAM J. Matrix Anal. Appl. 18(3), 566–589 (1997)Hernandez, V., Roman, J.E., Vidal, V.: SLEPc: a scalable and flexible toolkit for the solution of eigenvalue problems. ACM Trans. Math. Softw. 31(3), 351–362 (2005)Hernandez, V., Roman, J.E., Tomas, A.: Parallel Arnoldi eigensolvers with enhanced scalability via global communications rearrangement. Parallel Comput. 33(7–8), 521–540 (2007)Jia, Z., Sun, Y.: A refined variant of SHIRA for the skew-Hamiltonian/Hamiltonian (SHH) pencil eigenvalue problem. Taiwan J. Math. 17(1), 259–274 (2013)Kressner, D., Roman, J.E.: Memory-efficient Arnoldi algorithms for linearizations of matrix polynomials in Chebyshev basis. Numer. Linear Algebra Appl. 21(4), 569–588 (2014)Kressner, D., Pandur, M.M., Shao, M.: An indefinite variant of LOBPCG for definite matrix pencils. Numer. Algorithms 66(4), 681–703 (2014)Lancaster, P.: Linearization of regular matrix polynomials. Electron. J. Linear Algebra 17, 21–27 (2008)Lancaster, P., Ye, Q.: Rayleigh-Ritz and Lanczos methods for symmetric matrix pencils. Linear Algebra Appl. 185, 173–201 (1993)Lu, D., Su, Y.: Two-level orthogonal Arnoldi process for the solution of quadratic eigenvalue problems (2012, manuscript)Meerbergen, K.: The Lanczos method with semi-definite inner product. BIT 41(5), 1069–1078 (2001)Meerbergen, K.: The Quadratic Arnoldi method for the solution of the quadratic eigenvalue problem. SIAM J. Matrix Anal. Appl. 30(4), 1463–1482 (2008)Mehrmann, V., Watkins, D.: Structure-preserving methods for computing eigenpairs of large sparse skew-Hamiltonian/Hamiltonian pencils. SIAM J. Sci. Comput. 22(6), 1905–1925 (2001)Parlett, B.N.: The symmetric Eigenvalue problem. Prentice-Hall, Englewood Cliffs (1980) (reissued with revisions by SIAM, Philadelphia)Parlett, B.N., Chen, H.C.: Use of indefinite pencils for computing damped natural modes. Linear Algebra Appl. 140(1), 53–88 (1990)Parlett, B.N., Taylor, D.R., Liu, Z.A.: A look-ahead Lánczos algorithm for unsymmetric matrices. Math. Comput. 44(169), 105–124 (1985)de Samblanx, G., Bultheel, A.: Nested Lanczos: implicitly restarting an unsymmetric Lanczos algorithm. Numer. Algorithms 18(1), 31–50 (1998)Sleijpen, G.L.G., Booten, A.G.L., Fokkema, D.R., van der Vorst, H.A.: Jacobi-Davidson type methods for generalized eigenproblems and polynomial eigenproblems. BIT 36(3), 595–633 (1996)Stewart, G.W.: A Krylov-Schur algorithm for large eigenproblems. 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National survey of variations in practice in the prevention of surgical site infections in adult cardiac surgery, United Kingdom and Republic of Ireland
Background: Currently no national standards exist for the prevention of surgical site infection (SSI) in cardiac surgery. SSI rates range from 1% to 8% between centres. Aim: The aim of this study was to explore and characterize variation in approaches to SSI prevention in the UK and the Republic of Ireland (ROI). Methods: Cardiac surgery centres were surveyed using electronic web-based questionnaires to identify variation in SSI prevention at the level of both institution and consultant teams. Surveys were developed and undertaken through collaboration between the Cardiothoracic Interdisciplinary Research Network (CIRN), Public Health England (PHE) and the National Cardiac Benchmarking Collaborative (NCBC) to encompass routine pre-, intra- and postoperative practice. Findings: Nineteen of 38 centres who were approached provided data and included responses from 139 consultant teams. There was no missing data from those centres that responded. The results demonstrated substantial variation in over 40 aspects of SSI prevention. These included variation in SSI surveillance, reporting of SSI infection rates to external bodies, utilization of SSI risk prediction tools, and the use of interventions such as sternal support devices and gentamicin impregnated sponges. Conclusion: Measured variation in SSI prevention in cardiac centres across the UK and ROI is evidence of clinical uncertainty as to best practice, and has identified areas for quality improvement as well as knowledge gaps to be addressed by future research
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990-2015: a systematic analysis for the Global Burden of Disease Study 2015
SummaryBackground The Global Burden of Diseases, Injuries, and Risk Factors Study 2015 provides an up-to-date synthesis of the evidence for risk factor exposure and the attributable burden of disease. By providing national and subnational assessments spanning the past 25 years, this study can inform debates on the importance of addressing risks in context. Methods We used the comparative risk assessment framework developed for previous iterations of the Global Burden of Disease Study to estimate attributable deaths, disability-adjusted life-years (DALYs), and trends in exposure by age group, sex, year, and geography for 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks from 1990 to 2015. This study included 388 risk-outcome pairs that met World Cancer Research Fund-defined criteria for convincing or probable evidence. We extracted relative risk and exposure estimates from randomised controlled trials, cohorts, pooled cohorts, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. We developed a metric that allows comparisons of exposure across risk factors—the summary exposure value. Using the counterfactual scenario of theoretical minimum risk level, we estimated the portion of deaths and DALYs that could be attributed to a given risk. We decomposed trends in attributable burden into contributions from population growth, population age structure, risk exposure, and risk-deleted cause-specific DALY rates. We characterised risk exposure in relation to a Socio-demographic Index (SDI). Findings Between 1990 and 2015, global exposure to unsafe sanitation, household air pollution, childhood underweight, childhood stunting, and smoking each decreased by more than 25%. Global exposure for several occupational risks, high body-mass index (BMI), and drug use increased by more than 25% over the same period. All risks jointly evaluated in 2015 accounted for 57·8% (95% CI 56·6–58·8) of global deaths and 41·2% (39·8–42·8) of DALYs. In 2015, the ten largest contributors to global DALYs among Level 3 risks were high systolic blood pressure (211·8 million [192·7 million to 231·1 million] global DALYs), smoking (148·6 million [134·2 million to 163·1 million]), high fasting plasma glucose (143·1 million [125·1 million to 163·5 million]), high BMI (120·1 million [83·8 million to 158·4 million]), childhood undernutrition (113·3 million [103·9 million to 123·4 million]), ambient particulate matter (103·1 million [90·8 million to 115·1 million]), high total cholesterol (88·7 million [74·6 million to 105·7 million]), household air pollution (85·6 million [66·7 million to 106·1 million]), alcohol use (85·0 million [77·2 million to 93·0 million]), and diets high in sodium (83·0 million [49·3 million to 127·5 million]). From 1990 to 2015, attributable DALYs declined for micronutrient deficiencies, childhood undernutrition, unsafe sanitation and water, and household air pollution; reductions in risk-deleted DALY rates rather than reductions in exposure drove these declines. Rising exposure contributed to notable increases in attributable DALYs from high BMI, high fasting plasma glucose, occupational carcinogens, and drug use. Environmental risks and childhood undernutrition declined steadily with SDI; low physical activity, high BMI, and high fasting plasma glucose increased with SDI. In 119 countries, metabolic risks, such as high BMI and fasting plasma glucose, contributed the most attributable DALYs in 2015. Regionally, smoking still ranked among the leading five risk factors for attributable DALYs in 109 countries; childhood underweight and unsafe sex remained primary drivers of early death and disability in much of sub-Saharan Africa. Interpretation Declines in some key environmental risks have contributed to declines in critical infectious diseases. Some risks appear to be invariant to SDI. Increasing risks, including high BMI, high fasting plasma glucose, drug use, and some occupational exposures, contribute to rising burden from some conditions, but also provide opportunities for intervention. Some highly preventable risks, such as smoking, remain major causes of attributable DALYs, even as exposure is declining. Public policy makers need to pay attention to the risks that are increasingly major contributors to global burden. Funding Bill & Melinda Gates Foundation
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing
molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas
Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN
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