The numerical solution of nonlinear two-point boundary value problems using iterated deferred correction - a survey

The use of iterated deferred correction has proved to be a very efficient approach to the numerical solution of general first order systems of nonlinear two-point boundary value problems. In particular the two high order codes TWPBVP.f, based on mono-implicit Runge-Kutta (MIRK) formulae, and TWPBVPL.f based on Lobatto Runge-Kutta formulae as well as the continuation codes ACDC.f and COLMOD.f are now widely used. In this survey we describe some of the problems involved in the derivation of efficient deferred correction schemes. In particular we consider the construction of high order methods which preserve the stability of the underlying formulae, the choice of the mesh choosing algorithm which is based both on local accuracy and conditioning, and the computation of continuous solutions

Folliculin interacts with p0071 (plakophilin-4) and deficiency is associated with disordered rhoa signalling, epithelial polarization and cytokinesis

Inherited mutations in the folliculin (FLCN) gene cause the Birt-Hogg-Dubé syndrome of familial hair follicle tumours (fibrofolliculomas), lung cysts and kidney tumours. Though folliculin has features of a tumour suppressor, the precise function of the FLCN gene product is not well characterized. We identified plakophilin-4 (p0071) as a potential novel folliculin interacting protein by yeast two-hybrid analysis. We confirmed the interaction of folliculin with p0071 by co-immunoprecipitation studies and, in view of previous studies linking p0071 to the regulation of rho-signalling, cytokinesis and intercellular junction formation, we investigated the effect of cell folliculin status on p0071-related functions. Folliculin and p0071 partially co-localized at cell junctions and in mitotic cells, at the midbody during cytokinesis. Previously, p0071 has been reported to regulate RhoA signalling during cytokinesis and we found that folliculin deficiency was associated with increased expression and activity of RhoA and evidence of disordered cytokinesis. Treatment of folliculin-deficient cells with a downstream inhibitor of RhoA signalling (the ROCK inhibitor Y-27632) reversed the increased cell migration phenotype observed in folliculin-deficient cells. Deficiency of folliculin and of p0071 resulted in tight junction defects and mislocalization of E-cadherin in mouse inner medullary collecting duct-3 renal tubular cells. These findings suggest that aspects of folliculin tumour suppressor function are linked to interaction with p0071 and the regulation of RhoA signalling

The numerical solution of nonlinear two-point boundary value problems using iterated deferred correction - a survey

Tyt. z nagłówka.Bibliografia s. 285-286.Dostępny również w formie drukowanej.ABSTRACT: The use of iterated deferred correction has proved to be a very efficient approach to the numerical solution of general first order systems of nonlinear two-point boundary value problems. In particular the two high order codes TWPBVP.f, based on mono-implicit Runge–Kutta (MIRK) formulae, and TWPBVPL.f based on Lobatto Runge–Kutta formulae as well as the continuation codes ACDC.f and COLMOD.f are now widely used. In this survey we describe some of the problems involved in the derivation of efficient deferred correction schemes. In particular we consider the construction of high order methods which preserve the stability of the underlying formulae, the choice of the mesh choosing algorithm which is based both on local accuracy and conditioning, and the computation of continuous solutions. KEYWORDS: Deferred Correction, boundary value problems, conditioning, mesh selection

Solving boundary value problems in the open source software R: package bvpSolve

The R package bvpSolve for the numerical solution of Boundary Value Problems (BVPs) is presented. This package is free software which is distributed under the GNU General Public License, as part of the R open source software project. It includes some well known codes to solve boundary value problems of ordinary differential equations (ODEs) and differential algebraic equations (DAEs). In addition to the packages already available for solving initial value problems, the new package now allows non expert users to efficiently solve boundary value problems in the problem solving environment R

Malignancy validation in a United States registry of rheumatoid arthritis patients

<p>Abstract</p> <p>Background</p> <p>Physician reporting is commonly used to ascertain adverse events or outcomes measured in epidemiologic studies. However, little is known on the accuracy of physician reported malignancies compared to pertinent medical record review in large cohort studies.</p> <p>Methods</p> <p>The Consortium of Rheumatology Researchers of North America (CORRONA) registry gathers physician-completed questionnaires for rheumatoid arthritis (RA) patients, including request for information on incident malignancies, approximately every three months. For incident malignancies reported from October 1st, 2001, through December 31st, 2007, we retrospectively requested completion of a Targeted Adverse Event (TAE) form for additional information as well as primary source documents to adjudicate the malignancy reports. CORRONA has employed a prospective request for source documentation for these events since 2008. We classified each malignancy as definite, probable, possible, or not a malignancy.</p> <p>Results</p> <p>From 20,837 RA patients enrolled in CORRONA, 461 incident malignancies were initially reported on physician questionnaires. After review of returned source documents with adjudication, 234 were deemed definite, 69 probable, 101 possible, and 57 not an incident malignancy. The positive predictive value (PPV) of initial physician report of a malignancy <it>versus</it> “definite or probable” malignancy based on adjudication was 0.66 (95% CI 0.61 - 0.70). The PPV was 0.68 (95% CI 0.63 – 0.72) when the subsequent TAE form also confirmed the presence of malignancy. When possible malignancies were included, the PPV of physician-reported malignancies without a subsequent TAE form increased to 0.86 (0.83 – 0.89), and with a subsequent TAE form, 0.89 (0.85-0.91).</p> <p>Conclusion</p> <p>Twelve percent of initial physician reports of incident malignancy could not be confirmed with review of source documents. The most common reason for lack of confirmation was inability to obtain documents or insufficient data in source materials. These results suggest that timely collection of relevant medical records and an adjudication process are required to improve the accuracy of cancer reporting in epidemiologic studies.</p