Probabilistic abstract interpretation: From trace semantics to DTMC’s and linear regression

In order to perform probabilistic program analysis we need to consider probabilistic languages or languages with a probabilistic semantics, as well as a corresponding framework for the analysis which is able to accommodate probabilistic properties and properties of probabilistic computations. To this purpose we investigate the relationship between three different types of probabilistic semantics for a core imperative language, namely Kozen’s Fixpoint Semantics, our Linear Operator Semantics and probabilistic versions of Maximal Trace Semantics. We also discuss the relationship between Probabilistic Abstract Interpretation (PAI) and statistical or linear regression analysis. While classical Abstract Interpretation, based on Galois connection, allows only for worst-case analyses, the use of the Moore-Penrose pseudo inverse in PAI opens the possibility of exploiting statistical and noisy observations in order to analyse and identify various system properties

Loss of paraplegin drives spasticity rather than ataxia in a cohort of 241 patients with SPG7

Objective : We took advantage of a large multinational recruitment to delineate genotype-phenotype correlations in a large, trans-European multicenter cohort of patients with spastic paraplegia gene 7 (SPG7). Methods : We analyzed clinical and genetic data from 241 patients with SPG7, integrating neurologic follow-up data. One case was examined neuropathologically. Results : Patients with SPG7 had a mean age of 35.5 +/- 14.3 years (n = 233) at onset and presented with spasticity (n = 89), ataxia (n = 74), or both (n = 45). At the first visit, patients with a longer disease duration (> 20 years, n = 62) showed more cerebellar dysarthria (p < 0.05), deep sensory loss (p < 0.01), muscle wasting (p < 0.01), ophthalmoplegia (p < 0.05), and sphincter dysfunction (p < 0.05) than those with a shorter duration (< 10 years, n = 93). Progression, measured by Scale for the Assessment and Rating of Ataxia evaluations, showed a mean annual increase of 1.0 +/- 1.4 points in a subgroup of 30 patients. Patients homozygous for loss of function (LOF) variants (n = 65) presented significantly more often with pyramidal signs (p < 0.05), diminished visual acuity due to optic atrophy (p < 0.0001), and deep sensory loss (p < 0.0001) than those with at least 1 missense variant (n = 176). Patients with at least 1 Ala510Val variant (58%) were older (age 37.6 +/- 13.7 vs 32.8 +/- 14.6 years, p < 0.05) and showed ataxia at onset (p < 0.05). Neuropathologic examination revealed reduction of the pyramidal tract in the medulla oblongata and moderate loss of Purkinje cells and substantia nigra neurons. Conclusions : This is the largest SPG7 cohort study to date and shows a spasticity-predominant phenotype of LOF variants and more frequent cerebellar ataxia and later onset in patients carrying at least 1 Ala510Val variant

The Ciliate Paramecium Shows Higher Motility in Non-Uniform Chemical Landscapes

We study the motility behavior of the unicellular protozoan Paramecium tetraurelia in a microfluidic device that can be prepared with a landscape of attracting or repelling chemicals. We investigate the spatial distribution of the positions of the individuals at different time points with methods from spatial statistics and Poisson random point fields. This makes quantitative the informal notion of “uniform distribution” (or lack thereof). Our device is characterized by the absence of large systematic biases due to gravitation and fluid flow. It has the potential to be applied to the study of other aquatic chemosensitive organisms as well. This may result in better diagnostic devices for environmental pollutants.University of Wisconsin--Milwaukee (SURF (Salary for Undergraduate Research Fellows) Award)National Science Foundation (U.S.) (grant DMS-016214

Size Evolution of Ordered SiGe Islands Grown by Surface Thermal Diffusion on Pit-Patterned Si(100) Surface

The ordered growth of self-assembled SiGe islands by surface thermal diffusion in ultra high vacuum from a lithographically etched Ge stripe on pit-patterned Si(100) surface has been experimentally investigated. The total surface coverage of Ge strongly depends on the distance from the source stripe, as quantitatively verified by Scanning Auger Microscopy. The size distribution of the islands as a function of the Ge coverage has been studied by coupling atomic force microscopy scans with Auger spectro-microscopy data. Our observations are consistent with a physical scenario where island positioning is essentially driven by energetic factors, which predominate with respect to the local kinetics of diffusion, and the growth evolution mainly depends on the local density of Ge atoms

Nano-Stenciled RGD-Gold Patterns That Inhibit Focal Contact Maturation Induce Lamellipodia Formation in Fibroblasts

Cultured fibroblasts adhere to extracellular substrates by means of cell-matrix adhesions that are assembled in a hierarchical way, thereby gaining in protein complexity and size. Here we asked how restricting the size of cell-matrix adhesions affects cell morphology and behavior. Using a nanostencil technique, culture substrates were patterned with gold squares of a width and spacing between 250 nm and 2 µm. The gold was functionalized with RGD peptide as ligand for cellular integrins, and mouse embryo fibroblasts were plated. Limiting the length of cell-matrix adhesions to 500 nm or less disturbed the maturation of vinculin-positive focal complexes into focal contacts and fibrillar adhesions, as indicated by poor recruitment of α5-integrin. We found that on sub-micrometer patterns, fibroblasts spread extensively, but did not polarize. Instead, they formed excessive numbers of lamellipodia and a fine actin meshwork without stress fibers. Moreover, these cells showed aberrant fibronectin fibrillogenesis, and their speed of directed migration was reduced significantly compared to fibroblasts on 2 µm square patterns. Interference with RhoA/ROCK signaling eliminated the pattern-dependent differences in cell morphology. Our results indicate that manipulating the maturation of cell-matrix adhesions by nanopatterned surfaces allows to influence morphology, actin dynamics, migration and ECM assembly of adhering fibroblasts