Langevin Trajectories between Fixed Concentrations

We consider the trajectories of particles diffusing between two infinite baths of fixed concentrations connected by a channel, e.g. a protein channel of a biological membrane. The steady state influx and efflux of Langevin trajectories at the boundaries of a finite volume containing the channel and parts of the two baths is replicated by termination of outgoing trajectories and injection according to a residual phase space density. We present a simulation scheme that maintains averaged fixed concentrations without creating spurious boundary layers, consistent with the assumed physics

On central tendency and dispersion measures for intervals and hypercubes

The uncertainty or the variability of the data may be treated by considering, rather than a single value for each data, the interval of values in which it may fall. This paper studies the derivation of basic description statistics for interval-valued datasets. We propose a geometrical approach in the determination of summary statistics (central tendency and dispersion measures) for interval-valued variables

Dynamics and Efficiency of Brownian Rotors

Brownian rotors play an important role in biological systems and in future nano-technological applications. However the mechanisms determining their dynamics, efficiency and performance remain to be characterized. Here the F0 portion of the F-ATP synthase is considered as a paradigm of a Brownian rotor. In a generic analytical model we analyze the stochastic rotation of F0-like motors as a function of the driving free energy difference and of the free energy profile the rotor is subjected to. The latter is composed of the rotor interaction with its surroundings, of the free energy of chemical transitions, and of the workload. The dynamics and mechanical efficiency of the rotor depends on the magnitude of its stochastic motion driven by the free energy energy difference and its rectification on the reaction-diffusion path. We analyze which free energy profiles provide maximum flow and how their arrangement on the underlying reaction-diffusion path affects rectification and -- by this -- the efficiency.Comment: 22 pages, 11 figures, pdflatex, JCP in pres

Finite size scaling in neural networks

We demonstrate that the fraction of pattern sets that can be stored in single- and hidden-layer perceptrons exhibits finite size scaling. This feature allows to estimate the critical storage capacity \alpha_c from simulations of relatively small systems. We illustrate this approach by determining \alpha_c, together with the finite size scaling exponent \nu, for storing Gaussian patterns in committee and parity machines with binary couplings and up to K=5 hidden units.Comment: 4 pages, RevTex, 5 figures, uses multicol.sty and psfig.st

Simulations of grafted polymers in a good solvent

We present improved simulations of three-dimensional self avoiding walks with one end attached to an impenetrable surface on the simple cubic lattice. This surface can either be a-thermal, having thus only an entropic effect, or attractive. In the latter case we concentrate on the adsorption transition, We find clear evidence for the cross-over exponent to be smaller than 1/2, in contrast to all previous simulations but in agreement with a re-summed field theoretic $\epsilon$-expansion. Since we use the pruned-enriched Rosenbluth method (PERM) which allows very precise estimates of the partition sum itself, we also obtain improved estimates for all entropic critical exponents.Comment: 5 pages with 9 figures included; minor change

Benefits of biomarker selection and clinico-pathological covariate inclusion in breast cancer prognostic models

Introduction: Multi-marker molecular assays have impacted management of early stage breast cancer, facilitating adjuvant chemotherapy decisions. We generated prognostic models that incorporate protein-based molecular markers and clinico-pathological variables to improve survival prediction. Methods: We used a quantitative immunofluorescence method to study protein expression of 14 markers included in the Oncotype DX™ assay on a 638 breast cancer patient cohort with 15-year follow-up. We performed cross-validation analyses to assess performance of multivariate Cox models consisting of these markers and standard clinico-pathological covariates, using an average time-dependent Area Under the Receiver Operating Characteristic curves and compared it to nested Cox models obtained by robust backward selection procedures. Results: A prognostic index derived from of a multivariate Cox regression model incorporating molecular and clinico-pathological covariates (nodal status, tumor size, nuclear grade, and age) is superior to models based on molecular studies alone or clinico-pathological covariates alone. Performance of this composite model can be further improved using feature selection techniques to prune variables. When stratifying patients by Nottingham Prognostic Index (NPI), the most prognostic markers in high and low NPI groups differed. Similarly, for the node-negative, hormone receptor-positive sub-population, we derived a compact model with three clinico-pathological variables and two protein markers that was superior to the full model. Conclusions: Prognostic models that include both molecular and clinico-pathological covariates can be more accurate than models based on either set of features alone. Furthermore, feature selection can decrease the number of molecular variables needed to predict outcome, potentially resulting in less expensive assays.This work was supported by a grant from the Susan G Komen Foundation (to YK)

Reconstruction of a first-order phase transition from computer simulations of individual phases and subphases

We present a new method for investigating first-order phase transitions using Monte Carlo simulations. It relies on the multiple-histogram method and uses solely histograms of individual phases. In addition, we extend the method to include histograms of subphases. The free energy difference between phases, necessary for attributing the correct statistical weights to the histograms, is determined by a detour in control parameter space via auxiliary systems with short relaxation times. We apply this method to a recently introduced model for structure formation in polypeptides for which other methods fail.Comment: 13 pages in preprint mode, REVTeX, 2 Figures available from the authors ([email protected], [email protected]

Plagiorchis sp. in small mammals of Senegal and the potential emergence of a zoonotic trematodiasis

Trematodes of the genus Plagiorchis have a wide geographical distribution and can exploit a variety of hosts. The occurrence and zoonotic potential of Plagiorchis spp. have been characterised across several countries in Asia; in contrast, information on Plagiorchis parasites in Africa remains anecdotal. We isolated a previously undescribed Plagiorchis species from the biliary tract and small intestine of 201 out of 427 small mammals collected in the region of Lake Guiers, Senegal, with local prevalence ranging from 38.6% to 77.0%. Conversely, Plagiorchis isolates were not observed in the 244 small mammals sampled in and around the town of Richard Toll, Senegal. Molecular phylogenetics of the internal transcribed spacer region, nuclear ribosomal DNA, and of the cytochrome c oxidase subunit 1 gene, mitochondrial DNA, supported the monophyly and multi-host spectrum of this newly discovered West African Plagiorchis species. Sequencing of individual cercariae shed by Radix natalensis (Gastropoda: Lymnaeidae) suggested that these freshwater snails may act as suitable first intermediate hosts. Phylogenetic analysis yielded a highly resolved topology indicating two different clades, one composed by Plagiorchis spp. infecting rodents, insectivores, and birds, while the other included parasites of bats. Our findings showed the low host specificity and high prevalence of the isolated Plagiorchis sp. in the Lake Guiers region, with Hubert's multimammate mice (Mastomys huberti) appearing to play a primary role in the epidemiology of this parasite. The results raise concern about the zoonotic potential of Plagiorchis sp. in local communities of the Lake Guiers region, and highlight food-borne trematodiases and their link to land-use change as a neglected public health issue in regions of West Africa

When the world collapses : Changed worldview and social reconstruction in a traumatized community

Background: Traumatic experience can affect the individual’s basic beliefs about the world as a predictable and safe place. One of the cornerstones in recovery from trauma is reestablishment of safety, connectedness, and the shattered schema of a worldview. Objective: This study explored the role of negatively changed worldview in the relationship between war-related traumatization and readiness for social reconstruction of intergroup relations in a post-conflict community measured by three processes: intergroup rapprochement, rebuilding trust, and need for apology. It was hypothesized that more traumatized people are less supportive of social reconstruction and that this relationship is mediated by the changed worldview. Method: The study included a community random sample of 333 adults in the city of Vukovar, Croatia, that was most devastated during the 1991–1995 war. Six instruments were administered: Stressful Events Scale, Impact of Event Scale-Revised, Changed Worldview Scale, and three scales measuring the post-conflict social reconstruction processes: Intergroup Rapprochement, Intergroup Trust and Need for Apology. Results: Mediation analyses showed that the worldview change fully mediated between traumatization and all three aspects of social reconstruction. Conclusions: In a population exposed to war traumatization the worldview change mediates post-conflict social recovery of community relations