A Monitoring Language for Run Time and Post-Mortem Behavior Analysis and Visualization

UFO is a new implementation of FORMAN, a declarative monitoring language, in which rules are compiled into execution monitors that run on a virtual machine supported by the Alamo monitor architecture.Comment: In M. Ronsse, K. De Bosschere (eds), proceedings of the Fifth International Workshop on Automated Debugging (AADEBUG 2003), September 2003, Ghent. cs.SE/030902

Community detection in networks without observing edges

We develop a Bayesian hierarchical model to identify communities of time series. Fitting the model provides an end-to-end community detection algorithm that does not extract information as a sequence of point estimates but propagates uncertainties from the raw data to the community labels. Our approach naturally supports multiscale community detection as well as the selection of an optimal scale using model comparison. We study the properties of the algorithm using synthetic data and apply it to daily returns of constituents of the S&P100 index as well as climate data from US cities

Semantic multimedia analysis using knowledge and context

PhDThe difficulty of semantic multimedia analysis can be attributed to the extended diversity in form and appearance exhibited by the majority of semantic concepts and the difficulty to express them using a finite number of patterns. In meeting this challenge there has been a scientific debate on whether the problem should be addressed from the perspective of using overwhelming amounts of training data to capture all possible instantiations of a concept, or from the perspective of using explicit knowledge about the concepts’ relations to infer their presence. In this thesis we address three problems of pattern recognition and propose solutions that combine the knowledge extracted implicitly from training data with the knowledge provided explicitly in structured form. First, we propose a BNs modeling approach that defines a conceptual space where both domain related evi- dence and evidence derived from content analysis can be jointly considered to support or disprove a hypothesis. The use of this space leads to sig- nificant gains in performance compared to analysis methods that can not handle combined knowledge. Then, we present an unsupervised method that exploits the collective nature of social media to automatically obtain large amounts of annotated image regions. By proving that the quality of the obtained samples can be almost as good as manually annotated images when working with large datasets, we significantly contribute towards scal- able object detection. Finally, we introduce a method that treats images, visual features and tags as the three observable variables of an aspect model and extracts a set of latent topics that incorporates the semantics of both visual and tag information space. By showing that the cross-modal depen- dencies of tagged images can be exploited to increase the semantic capacity of the resulting space, we advocate the use of all existing information facets in the semantic analysis of social media

Recommendations for reporting ion mobility Mass Spectrometry measurements

Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method‐dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc

Artificial olfactory system for multi-component analysis of gas mixtures.

Gas analysis is an important part of our world and gas sensing technology is becoming more essential for various aspects of our life. A novel approach for gas mixture analysis by using portable gas chromatography in combination with an array of highly integrated and selective metal oxide (MOX) sensors has been studied. We developed a system with small size (7 x 13 x 16 inches), low power consumption (~10 W) and absence of special carrier gases designed for portable field analysis (assuming apriori calibration). Low ppb and even sub-ppb level of detection for some VOCs was achieved during the analysis of 50 ml of gas samples. A detailed description of our innovative design of multi-sensory platforms based on MOX sensors for multidimensional portable gas chromatography is provided in detail in this work. As a part of this effort, we successfully synthesized nanocomposite gas sensors based on SnO2 for selective detection of hydrogen sulfide, mercaptans, alcohols, ketones and heavy hydrocarbons. The morphology of the prepared sensors was closely studied by scanning electron microscopy (SEM), atomic force microscopy (AFM), transition electron microscopy (TEM) and X-Ray diffraction (XRD). Optical and electrical properties of polycrystalline SnO2 were investigated by using UV-Vis spectroscopy, transmission line measurement (TLM) and four probe resistance measurement techniques. Furthermore, more advanced gas sensing performance for detection of benzene, toluene, ethylbenzene, and O-xylene (BTEX) of polycrystalline SnO2 film (30 nm) coated with bimetal Au:Pd (9:1 molar ratio) nanoclusters was measured. Finally, besides the experimental result, the theoretical validation of the detector’s performance was provided based on high catalytic activity of nanocomposite materials and its superior electronic structure for gas detection compared to the polycrystalline SnO2. The theoretical background of gas chemisorption process at the surface of polycrystalline SnO2 was reviewed in this work. Furthermore, one dimensional Poisson equation relates surface energy states ( and ) and the bulk electronic structure ( and ) of polycrystalline SnO2. The main theory of electronic processes on the surface of semiconductors during the gas chemisorption was further applied in a case of nanocomposite materials

Molecular Response of Retinal Pigment Epithelial Cells to Oxidized Lipoproteins: Global and Targeted Studies

Global-scale examinations of biological systems at the molecular level complement targeted approaches to scientific inquiry that focus on specific subsets of biomolecules, or on a single molecule of interest. In this dissertation, we utilized both the discovery-based approach to evaluate the proteomics workflows centered around mass spectrometry as the key technology, and the targeted approach to examine the molecular response of RPE due to oxidized lipoproteins (oxLDL) treatments. A crucial aspect in proteomics studies is the design of bioanalytical strategies that maximize coverage of the complex repertoire of a proteome. A comprehensive, unbiased examination of the proteome represents a powerful approach toward system-level insights into disease mechanisms. We evaluated the performance of bioanalytical platforms for profiling of the proteome in a biological system. We applied a discovery-based approach to evaluate the global transcriptome and proteome changes due to oxLDL treatment in ARPE-19 cells. We studied the role of scavenger receptors CD36 and CD5L/AIM in ARPE-19 cells when induced with oxLDL. We compared three different multidimensional proteome fractionation platforms: polymeric reversed-phase liquid chromatography at high pH (PLRP), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and isoelectric focusing (IEF) separations. We applied a liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) in a data-dependent setting and used bioinformatics for protein identification. The three platforms identified a total of 1043 proteins altogether. Among the three bioanalytical strategies, SDS-PAGE followed by LC-MS/MS provided the best coverage. We also evaluated another bioanalytical platform which consists of a highresolution mass spectrometer combined with nano-UPLC in a data-independent setting without pre-fractionation for oxLDL mediated proteome alteration in ARPE-19 cells. This platform outperformed the SDS-PAGE based analytical platform in terms of proteome coverage as it identified around 2500 proteins, ca. 3-fold more proteins than the latter. Most importantly, this platform was able to perform label free quantification of differentially expressed proteome alteration. The platforms identified proteins with diverse physicochemical characteristics involved in various functional roles within the biological system. Furthermore, we carried out the first comparative transcriptomic and proteomic study for the evaluation of oxLDL effects on ARPE-19 cells after a 4 h exposure. The treatment with oxLDL affected the regulation of more than 700 genes that were involved in regulation of cell cycle, oxidative stress, cholesterol efflux, circadian rhythm, NRF-2 pathways. However, LDL treatment alone did not induce the regulation of these pathways. The differential proteomic analysis found 41 proteins affected due to the oxLDL treatment. This study provided a foundation for a bioanalytical platform for identification and label-free quantification in the human retinal pigment epithelial cells (ARPE-19) proteome. The list of differentially expressed proteins due to oxLDL treatment identified in this study gives insights to the change in proteins that might be interrogated for their roles in pathogenesis of macular degeneration. These findings could give us targets to intervene in the pathogenesis of AMD progression in human for the development of better treatment and prevention against this degenerative disease. Lastly, we studied the mechanistic role of scavenger receptors CD36 and CD5L/AIM in oxLDL uptake by ARPE-19 cells. We, for the first time, demonstrated the presence of scavenger receptor CD5L in ARPE-19 cell. The oxLDL uptake was primarily dependent on CD36, and both the CD5L/AIM and CD36 were seen to co-localize in the presence of oxLDL. Our results suggest a new dynamics on CD5L/AIM on the oxLDL uptake that was not seen in macrophages. The reduction in intracellular accumulation of oxLDL in the presence of extracellular recombinant CD5L/AIM is an interesting phenomenon as it has been recently shown the involvement of CD5L/AIM in autophagy