CPLOP: The Cal Poly Library of Pyroprints

To date, microbial source tracking (MST), i.e. determining the source of microbial contamination based on the specific strains observed in the environment, often uses methods that are time-consuming, expensive and not always reliable. The biology department at Cal Poly, San Luis Obispo has developed a new method for MST called pyroprinting. Pyroprints can be used as DNA fingerprints for identifying sources of fecal contamination and studying bacterial populations in host animals. The MST method consists of two parts: the pyroprinting process and a database of pyroprints. The Cal Poly Library of Pyroprints (CPLOP) was developed to provide a database application for automating the storage and analysis of pyroprints. The initial version of CPLOP provided support for storing and organizing data related to microbes and their sources. This thesis describes the additional analytical tools needed to fully support pyroprinting as an MST method. This includes the ability to organize pyroprints into dataets, detect erroneous pyroprint data, run analyses to find similarities between bacterial isolates, and cluster isolates into bacterial strains

Towards identifying salient patterns in genetic programming individuals

This thesis addresses the problem of offline identification of salient patterns in genetic programming individuals. It discusses the main issues related to automatic pattern identification systems, namely that these (a) should help in understanding the final solutions of the evolutionary run, (b) should give insight into the course of evolution and (c) should be helpful in optimizing future runs. Moreover, it proposes an algorithm, Extended Pattern Growing Algorithm ([E]PGA) to extract, filter and sort the identified patterns so that these fulfill as many as possible of the following criteria: (a) they are representative for the evolutionary run and/or search space, (b) they are human-friendly and (c) their numbers are within reasonable limits. The results are demonstrated on six problems from different domains

Asteroid lightcurves from the Palomar Transient Factory survey: Rotation periods and phase functions from sparse photometry

We fit 54,296 sparsely-sampled asteroid lightcurves in the Palomar Transient Factory to a combined rotation plus phase-function model. Each lightcurve consists of 20+ observations acquired in a single opposition. Using 805 asteroids in our sample that have reference periods in the literature, we find the reliability of our fitted periods is a complicated function of the period, amplitude, apparent magnitude and other attributes. Using the 805-asteroid ground-truth sample, we train an automated classifier to estimate (along with manual inspection) the validity of the remaining 53,000 fitted periods. By this method we find 9,033 of our lightcurves (of 8,300 unique asteroids) have reliable periods. Subsequent consideration of asteroids with multiple lightcurve fits indicate 4% contamination in these reliable periods. For 3,902 lightcurves with sufficient phase-angle coverage and either a reliably-fit period or low amplitude, we examine the distribution of several phase-function parameters, none of which are bimodal though all correlate with the bond albedo and with visible-band colors. Comparing the theoretical maximal spin rate of a fluid body with our amplitude versus spin-rate distribution suggests that, if held together only by self-gravity, most asteroids are in general less dense than 2 g/cm$^3$, while C types have a lower limit of between 1 and 2 g/cm$^3$, in agreement with previous density estimates. For 5-20km diameters, S types rotate faster and have lower amplitudes than C types. If both populations share the same angular momentum, this may indicate the two types' differing ability to deform under rotational stress. Lastly, we compare our absolute magnitudes and apparent-magnitude residuals to those of the Minor Planet Center's nominal $G=0.15$, rotation-neglecting model; our phase-function plus Fourier-series fitting reduces asteroid photometric RMS scatter by a factor of 3.Comment: 35 pages, 29 figures. Accepted 15-Apr-2015 to The Astronomical Journal (AJ). Supplementary material including ASCII data tables will be available through the publishing journal's websit

Ab Initio Derived Force Fields for Zeolitic Imidazolate Frameworks: MOF-FF for ZIFs

International audienceIn this paper, we parametrized in a consistent way a new force field for a range of different zeolitic imidazolate framework systems (ZIF-8, ZIF-8(H), ZIF-8(Br), and ZIF-8(Cl)), extending the MOF-FF parametrization methodology in two aspects. First, we implemented the possibility to use periodic reference data in order to prevent the difficulty of generating representative finite clusters. Second, a new optimizer based on the covariance matrix adaptation evolutionary strategy (CMA-ES) was employed during the parametrization process. We confirmed that CMA-ES, as a state-of-the-art black box optimizer for problems on continuous variables, is more efficient and versatile for force field optimization than the previous genetic algorithm. The obtained force field was then validated with respect to some static and dynamic properties. Much effort was spent to ensure that the FF is able to describe the crucial linker swing effect in a large number of ZIF-8 derivatives. For this reason, we compared our force field to ab initio molecular dynamic simulations and found an accuracy comparable to those obtained by different exchange–correlation functionals

Methods for Analysing Endothelial Cell Shape and Behaviour in Relation to the Focal Nature of Atherosclerosis

The aim of this thesis is to develop automated methods for the analysis of the spatial patterns, and the functional behaviour of endothelial cells, viewed under microscopy, with applications to the understanding of atherosclerosis. Initially, a radial search approach to segmentation was attempted in order to trace the cell and nuclei boundaries using a maximum likelihood algorithm; it was found inadequate to detect the weak cell boundaries present in the available data. A parametric cell shape model was then introduced to fit an equivalent ellipse to the cell boundary by matching phase-invariant orientation fields of the image and a candidate cell shape. This approach succeeded on good quality images, but failed on images with weak cell boundaries. Finally, a support vector machines based method, relying on a rich set of visual features, and a small but high quality training dataset, was found to work well on large numbers of cells even in the presence of strong intensity variations and imaging noise. Using the segmentation results, several standard shear-stress dependent parameters of cell morphology were studied, and evidence for similar behaviour in some cell shape parameters was obtained in in-vivo cells and their nuclei. Nuclear and cell orientations around immature and mature aortas were broadly similar, suggesting that the pattern of flow direction near the wall stayed approximately constant with age. The relation was less strong for the cell and nuclear length-to-width ratios. Two novel shape analysis approaches were attempted to find other properties of cell shape which could be used to annotate or characterise patterns, since a wide variability in cell and nuclear shapes was observed which did not appear to fit the standard parameterisations. Although no firm conclusions can yet be drawn, the work lays the foundation for future studies of cell morphology. To draw inferences about patterns in the functional response of cells to flow, which may play a role in the progression of disease, single-cell analysis was performed using calcium sensitive florescence probes. Calcium transient rates were found to change with flow, but more importantly, local patterns of synchronisation in multi-cellular groups were discernable and appear to change with flow. The patterns suggest a new functional mechanism in flow-mediation of cell-cell calcium signalling

Foveated object recognition by corner search

textHere we describe a gray scale object recognition system based on foveated corner finding, the computation of sequential fixation points, and elements of Lowe’s SIFT transform. The system achieves rotational, transformational, and limited scale invariant object recognition that produces recognition decisions using data extracted from sequential fixation points. It is broken into two logical steps. The first is to develop principles of foveated visual search and automated fixation selection to accomplish corner search. The result is a new algorithm for finding corners which is also a corner-based algorithm for aiming computed foveated visual fixations. In the algorithm, long saccades move the fovea to previously unexplored areas of the image, while short saccades improve the accuracy of putative corner locations. The system is tested on two natural scenes. As an interesting comparison study we compare fixations generated by the algorithm with those of subjects viewing the same images, whose eye movements are being recorded by an eyetracker. The comparison of fixation patterns is made using an information-theoretic measure. Results show that the algorithm is a good locator of corners, but does not correlate particularly well with human visual fixations. The second step is to use the corners located, which meet certain goodness criteria, as keypoints in a modified version of the SIFT algorithm. Two scales are implemented. This implementation creates a database of SIFT features of known objects. To recognize an unknown object, a corner is located and a feature vector created. The feature vector is compared with those in the database of known objects. The process is continued for each corner in the unknown object until enough information has been accumulated to reach a decision. The system was tested on 78 gray scale objects, hand tools and airplanes, and shown to perform well.Electrical and Computer Engineerin

Measurement of the W → ev cross section with early data from the CMS experiment at CERN

The Compact Muon Solenoid (CMS) is a general purpose detector designed to study proton-proton collisions, and heavy ion collisions, delivered by the Large Hadron Collider (LHC) at the European Laboratory for High Energy Physics (CERN). This thesis describes a measurement of the inclusive W → ev cross section at 7 TeV centre of mass energy with 2:88 ± 0:32 pb-1 of LHC collision data recorded by CMS between March and September 2010. W boson decays are identified by the presence of a high-pT electron that satisfies selection criteria in order to reject electron candidates due to background processes. Electron selection variables are studied with collision data and found to be in agreement with expectations from simulation. A fast iterative technique is developed to tune electron selections based on these variables. Electron efficiency is determined from simulation and it is corrected from data using an electron sample from Z decays. The number of W candidates is corrected for remaining background events using a fit to the missing transverse energy distribution. The measured value for the inclusive W production cross section times the branching ratio of the W decay in the electron channel is: σ(pp → W+X)xBR(W → ev) = 10.04±0.10(stat)±0.52(syst)±1.10(luminosity) nb; which is in excellent agreement with theoretical expectations