Methods for Modeling and Analyzing Concurrent Software

Concurrent software executes multiple threads or processes to achieve high performance. However, concurrency results in a huge number of different system behaviors that are difficult to test and verify. The aim of this dissertation is to develop new methods and tools for modeling and analyzing concurrent software systems at design and code levels. This dissertation consists of several related results. First, a formal model of Mondex, an electronic purse system, is built using Petri nets from user requirements, which is formally verified using model checking. Second, Petri nets models are automatically mined from the event traces generated from scientific workflows. Third, partial order models are automatically extracted from some instrumented concurrent program execution, and potential atomicity violation bugs are automatically verified based on the partial order models using model checking. Our formal specification and verification of Mondex have contributed to the world wide effort in developing a verified software repository. Our method to mine Petri net models automatically from provenance offers a new approach to build scientific workflows. Our dynamic prediction tool, named McPatom, can predict several known bugs in real world systems including one that evades several other existing tools. McPatom is efficient and scalable as it takes advantage of the nature of atomicity violations and considers only a pair of threads and accesses to a single shared variable at one time. However, predictive tools need to consider the tradeoffs between precision and coverage. Based on McPatom, this dissertation presents two methods for improving the coverage and precision of atomicity violation predictions: 1) a post-prediction analysis method to increase coverage while ensuring precision; 2) a follow-up replaying method to further increase coverage. Both methods are implemented in a completely automatic tool.

Analyzing the Effect of Soiling on the Performance of a Photovoltaic System of Different Module Technologies in Kalkbult, South Africa

The fact that most of the large scale solar PV plants are built in arid and semi-arid areas where land availability and solar radiation is high, it is expected the performance of the PV plants in such locations will be affected significantly due to high cell temperature as well as due to soiling. Therefore, it is essential to study how the different PV module technologies will perform in such geographical locations to ensure a consistent and reliable power delivery over the lifetime of the PV power plants. As soiling is strongly dependent on the climatic conditions of a particular location a test station, consisted of about 24 PV modules and a well-equipped weather station, was built within the fences of Scatec’s 75 MW Kalkbult solar PV plant in South Africa. This study was performed to a better understand the effect of soiling by comparing the relative power generation by the cleaned modules to the un-cleaned modules. Such knowledge can enable more quantitative evaluations of the cleaning strategies that are going to be implemented in bigger solar PV power plants. The data collected and recorded from the test station has been analyzed at IFE, Norway using a MatLab script written for this thesis project. This thesis work has been done at IFE, Norway in collaboration with Stellenbosch University in South Africa and Scatec Solar a Norwegian independent power producer company. Generally for the polycrystalline modules it is found that the average temperature corrected efficiency during the period of the experiment has been 15.00±0.08 % and for the thin film-CdTe with ARC is 11.52% and for the thin film without ARC is about 11.13% with standard uncertainty of ±0.01 %. Besides, by comparing the initial relative average efficiency of the polycrystalline-Si modules when all the modules have been cleaned for the first time and the final relative efficiency; after the last cleaning schedule which is when all the reference modules E, F, G, and H have been cleaned for the last time it is found that poly3 performs 2 % and 3 % better than poly1 and poly16 respectively, poly13 performs 1 % better than poly15 as well as poly5 and poly12 performs 1 % and 2 % better than poly10 respectively. Besides, poly5 and poly12 performs a 9 % and 11 % better than poly7. Furthermore, there is no change in performance between poly6 and poly9 as well as poly4 and poly15. However, the increase in performance of poly3 to poly1, poly13 to poly15 as well as poly5 and poly12 to poly10 is insignificant. In addition, it is found that TF22 perform 7% better than the reference un-cleaned module TF24 and similarly; TF21 performs 7% higher than TF23. Furthermore, modules with ARC glass (TF17, TF18, TF19, and TF20) shows that cleaning the modules with only distilled water (TF19) or dry-cleaned after cleaned with distilled water(TF20) decreases the performance of the modules by 5 % and 4 % comparing to its respective reference uncleanedmodules TF17 and TF18 respectively.

A SHORTENED RNA-FISH PROTOCOL FOR ANALYZING ARTWORKS’ MICROCOLONIZERS

Microorganisms are involved in the deterioration of Cultural Heritage. Thus, there is a need to enhance the techniques used for their detection and identification. RNA Fluorescent In Situ Hybridization (RNA-FISH) has been successfully applied for phylogenetic identification of the viable components of the microbial communities colonizing artworks both in situ and ex situ. Until recently, it was time-consuming, taking not less than 6 h for the analysis. We have developed an RNA-FISH in suspension protocol that allowed ex situ analysis of microorganisms involved in artworks’ biodeterioration in 5 h. In this work, three modified protocols, involving microwave heating, were evaluated for further shortening two of the four main critical steps in RNA-FISH: hybridization and washing. The original and modified protocols were applied in cellular suspensions of bacteria and yeast isolates. The results obtained were evaluated and compared in terms of detectability and specificity of the signals detected by epifluorescence microscopy. One of the methods tested showed good and specific FISH signals for all the microorganisms selected and did not produce signals evidencing non-specific or fixation-induced fluorescence. This 3 h protocol allows a remarkable reduction of the time usually required for performing RNA-FISH analysis in Cultural Heritage samples. Thus, a rapid alternative for analyzing yeast and bacteria cells colonizing artworks’ surfaces by RNA-FISH is presented in this work.

Analyzing consumer-based brand equity on Facebook: the impact of brand gender

In recent years, Facebook and other social media have become key players in branding activities. However, empirical research is still needed about the way in which consumer-based brand equity is created on social media. The purpose of this paper is to study the relationship between masculine and feminine brand personality and brand equity, on Facebook, and to analyze the mediating role of consumer-brand engagement and brand love on this relationship. Data were collected using an online survey with 614 valid responses. The hypotheses were tested using structural equation modeling. Results support 7 of the 11 hypotheses with significant relationship between analyzed constructs. This study confirms the advantages of a clear gender positioning and extends prior research by suggesting that brands with a strong brand gender identity will encourage brand love. Results also highlight that brand love has a mediating role on the relationship between brand gender and overall brand equity.

Analyzing urban green adaptation opportunities: concepts, approaches, & strategies for existing neighborhoods

Over the last decades, the growing evidence of human-caused climate change has raised awareness of the consequences of exceeding global temperature by 2˚C. This awareness has led to a contemporary approach to the conceptualization and management of green adaptation policies in spatial planning. This thesis aims to develop a comprehensive methodology for assessing the adaptability of existing neighborhoods to green strategies. The reliability of the proposed method is examined in the cities of Bologna and Imola and proved to be applicable in other geoghraphical locations. This thesis integrates three key themes of conceptual and implementation principles for urban green adaptation. This thesis initially defines methods for narrowing uncertainties in urban planning energy forecasting modeling by exploring the roles of integrated energy planning. The second is by exploring green retrofitting strategies in building, this thesis examines the effects of various energy-saving factors in roofing scenarios including a green roof, rooftop greenhouse, and insolated roof. Lastly, this thesis analyzes green strategies in urban spaces to enhance thermal comfort through facing urban heat exposure related to urban heat island effects. The roles of integrated energy policies and green strategic thinking are discussed to highlight various aspects of green adaptation on the neighborhood scale. This thesis develops approaches by which cities can face the challenges of current green urban planning and connect the conceptual and practical aspects of green spatial planning. Another point that this thesis highlight is that due to the interdependency of individuals and places, it is difficult to assure whether all the adaptation policies on a large scale are enhancing the resiliency of the neighborhood or they are simply shuffling the vulnerability through the individuals and places. Besides, it asserts that neglecting to reflect on these reallocations of the effects generates serious complications, and will result in long-term dysfunctional consequences.

Interpretable Convolutional Neural Networks for Decoding and Analyzing Neural Time Series Data

Machine learning is widely adopted to decode multi-variate neural time series, including electroencephalographic (EEG) and single-cell recordings. Recent solutions based on deep learning (DL) outperformed traditional decoders by automatically extracting relevant discriminative features from raw or minimally pre-processed signals. Convolutional Neural Networks (CNNs) have been successfully applied to EEG and are the most common DL-based EEG decoders in the state-of-the-art (SOA). However, the current research is affected by some limitations. SOA CNNs for EEG decoding usually exploit deep and heavy structures with the risk of overfitting small datasets, and architectures are often defined empirically. Furthermore, CNNs are mainly validated by designing within-subject decoders. Crucially, the automatically learned features mainly remain unexplored; conversely, interpreting these features may be of great value to use decoders also as analysis tools, highlighting neural signatures underlying the different decoded brain or behavioral states in a data-driven way. Lastly, SOA DL-based algorithms used to decode single-cell recordings rely on more complex, slower to train and less interpretable networks than CNNs, and the use of CNNs with these signals has not been investigated. This PhD research addresses the previous limitations, with reference to P300 and motor decoding from EEG, and motor decoding from single-neuron activity. CNNs were designed light, compact, and interpretable. Moreover, multiple training strategies were adopted, including transfer learning, which could reduce training times promoting the application of CNNs in practice. Furthermore, CNN-based EEG analyses were proposed to study neural features in the spatial, temporal and frequency domains, and proved to better highlight and enhance relevant neural features related to P300 and motor states than canonical EEG analyses. Remarkably, these analyses could be used, in perspective, to design novel EEG biomarkers for neurological or neurodevelopmental disorders. Lastly, CNNs were developed to decode single-neuron activity, providing a better compromise between performance and model complexity.

It's a matter of culture: analyzing worldbuilding in Avatar: The Last Airbender.

This dissertation is going to analyze culture in media and the role it plays in worldbuilding, taking into account one of the most-loved franchises in western animation, Avatar: The Last Airbender. Moreover, it wants to provide a different perspective on culture, posing the focus on the products consumed by many on a daily basis. First of all, this dissertation will start by trying to give “culture” itself a definition, focusing on two works of literature from which it will draw its analysis related to worldbuilding: Agar’s cultures in comparison and Hofstede’s model of culture. Then, it will move on to the concept of worldbuilding – what we define as worldbuilding, and how it mixes with culture. We will comment on how worldbuilding has gotten more attention with growing online communities and how it could make or break a franchise, with the example of the Divergent saga. Finally, it will move on to the main case study, Avatar: The Last Airbender, which will be analyzed from a cultural standpoint, underlining the role worldbuilding plays in it, and there will be a focus on nonverbal communication in animated media.

The Cratylia Mollis Seed Lectin Induces Membrane Permeability Transition In Isolated Rat Liver Mitochondria And A Cyclosporine A-insensitive Permeability Transition In Trypanosoma Cruzi Mitochondria.

Previous results provided evidence that Cratylia mollis seed lectin (Cramoll 1,4) promotes Trypanosoma cruzi epimastigotes death by necrosis via a mechanism involving plasma membrane permeabilization to Ca(2+) and mitochondrial dysfunction due to matrix Ca(2+) overload. In order to investigate the mechanism of Ca(2+) -induced mitochondrial impairment, experiments were performed analyzing the effects of this lectin on T. cruzi mitochondrial fraction and in isolated rat liver mitochondria (RLM), as a control. Confocal microscopy of T. cruzi whole cell revealed that Cramoll 1,4 binding to the plasma membrane glycoconjugates is followed by its internalization and binding to the mitochondrion. Electrical membrane potential (∆Ψm ) of T. cruzi mitochondrial fraction suspended in a reaction medium containing 10 μM Ca(2+) was significantly decreased by 50 μg/ml Cramoll 1,4 via a mechanism insensitive to cyclosporine A (CsA, membrane permeability transition (MPT) inhibitor), but sensitive to catalase or 125 mM glucose. In RLM suspended in a medium containing 10 μM Ca(2+) this lectin, at 50 μg/ml, induced increase in the rate of hydrogen peroxide release, mitochondrial swelling, and ∆Ψm disruption. All these mitochondrial alterations were sensitive to CsA, catalase, and EGTA. These results indicate that Cramoll 1, 4 leads to inner mitochondrial membrane permeabilization through Ca(2+) dependent mechanisms in both mitochondria. The sensitivity to CsA in RLM characterizes this lectin as a MPT inducer and the lack of CsA effect identifies a CsA-insensitive MPT in T. cruzi mitochondria.

Profile Of The Use Of Disease Modifying Drugs In The Brazilian Registry Of Spondyloarthritides.

Few studies have evaluated the profile of use of disease modifying drugs (DMD) in Brazilian patients with spondyloarthritis (SpA). A common research protocol was applied prospectively in 1505 patients classified as SpA by criteria of the European Spondyloarthropathies Study Group (ESSG), followed at 29 referral centers in Rheumatology in Brazil. Demographic and clinical variables were obtained and evaluated, by analyzing their correlation with the use of DMDs methotrexate (MTX) and sulfasalazine (SSZ). At least one DMD was used by 73.6% of patients: MTX by 29.2% and SSZ by 21.7%, while 22.7% used both drugs. The use of MTX was significantly associated with peripheral involvement, and SSZ was associated with axial involvement, and the two drugs were more administered, separately or in combination, in the mixed involvement (p < 0.001). The use of a DMD was significantly associated with Caucasian ethnicity (MTX , p = 0.014), inflammatory back pain (SSZ, p = 0.002) , buttock pain (SSZ, p = 0.030), neck pain (MTX, p = 0.042), arthritis of the lower limbs (MTX, p < 0.001), arthritis of the upper limbs (MTX, p < 0.001), enthesitis (p = 0.007), dactylitis (MTX, p < 0.001), inflammatory bowel disease (SSZ, p < 0.001) and nail involvement (MTX, p < 0.001). The use of at least one DMD was reported by more than 70% of patients in a large cohort of Brazilian patients with SpA, with MTX use more associated with peripheral involvement and the use of SSZ more associated with axial involvement.

High Diagnostic Accuracy And Reproducibility Of Fine-needle Aspiration Cytology For Diagnosing Salivary Gland Tumors: Cytohistologic Correlation In 182 Cases.

The purpose of this study was to assess the efficacy and reproducibility of the cytologic diagnosis of salivary gland tumors (SGTs) using fine-needle aspiration cytology (FNAC). The study aimed to determine diagnostic accuracy, sensitivity, and specificity and to evaluate the extent of interobserver agreement. We retrospectively evaluated SGTs from the files of the Division of Pathology at the Clinics Hospital of São Paulo and Piracicaba Dental School between 2000 and 2006. We performed cytohistologic correlation in 182 SGTs. The sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy were 94%, 100%, 100%, 100%, and 99%, respectively. The interobserver cytologic reproducibility showed significant statistical concordance (P < .0001). FNAC is an effective tool for performing a reliable preoperative diagnosis in SGTs and shows high diagnostic accuracy and consistent interobserver reproducibility. Further FNAC studies analyzing large samples of malignant SGTs and reactive salivary lesions are needed to confirm their accuracy.

Photoelastic Analysis Of All-on-four Concept Using Different Implants Angulations For Maxilla.

Conventional tilted implants are used in oral rehabilitation for heavily absorbed maxilla to avoid bone grafts; however, few research studies evaluate the biomechanical behavior when different angulations of the implants are used. The aim of this study was evaluate, trough photoelastic method, two different angulations and length of the cantilever in fixed implant-supported maxillary complete dentures. Two groups were evaluated: G15 (distal tilted implants 15°) and G35 (distal tilted implants 35°) n = 6. For each model, 2 distal tilted implants (3.5 x 15 mm long cylindrical cone) and 2 parallel tilted implants in the anterior region (3.5 x 10 mm) were installed. Photoelastic models were submitted to three vertical load tests: in the end of cantilever, in the last pillar and in the all pillars at the same time. We obtained the shear stress by Fringes software and found values for total, cervical and apical stress. The quantitative analysis was performed using the Student tests and Mann-Whitney test; p ≥ 0.05. There is no difference between G15 and G35 for total stress regardless of load type. Analyzing the apical region, G35 reduced strain values considering the distal loads (in the cantilever p = 0.03 and in the last pillar p = 0.02), without increasing the stress level in the cervical region. Considering the load in all pillars, G35 showed higher stress concentration in the cervical region (p = 0.04). For distal loads, G15 showed increase of tension in the apical region, while for load in all pillars, G35 inclination increases stress values in the cervical region.

Graded Meshes In Bio-thermal Problems With Transmission-line Modeling Method.

In this study, the transmission-line modeling (TLM) applied to bio-thermal problems was improved by incorporating several novel computational techniques, which include application of graded meshes which resulted in 9 times faster in computational time and uses only a fraction (16%) of the computational resources used by regular meshes in analyzing heat flow through heterogeneous media. Graded meshes, unlike regular meshes, allow heat sources to be modeled in all segments of the mesh. A new boundary condition that considers thermal properties and thus resulting in a more realistic modeling of complex problems is introduced. Also, a new way of calculating an error parameter is introduced. The calculated temperatures between nodes were compared against the results obtained from the literature and agreed within less than 1% difference. It is reasonable, therefore, to conclude that the improved TLM model described herein has great potential in heat transfer of biological systems.

Sim-xl: A Powerful And User-friendly Tool For Peptide Cross-linking Analysis.

Chemical cross-linking has emerged as a powerful approach for the structural characterization of proteins and protein complexes. However, the correct identification of covalently linked (cross-linked or XL) peptides analyzed by tandem mass spectrometry is still an open challenge. Here we present SIM-XL, a software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). Our software introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. Moreover, our search engine is the first to capitalize on reporter ions for selecting tandem mass spectra derived from cross-linked peptides. It also makes available a 2D interaction map and a spectrum-annotation tool unmatched by any of its kind. We show SIM-XL to be more sensitive and faster than a competing tool when analyzing a data set obtained from the human HSP90. The software is freely available for academic use at http://patternlabforproteomics.org/sim-xl. A video demonstrating the tool is available at http://patternlabforproteomics.org/sim-xl/video. SIM-XL is the first tool to support XL data in the mzIdentML format; all data are thus available from the ProteomeXchange consortium (identifier PXD001677).

Correlation Between The Friedman Staging System And The Upper Airway Volume In Patients With Obstructive Sleep Apnea.

This study was designed to evaluate the correlation between computed tomography findings and data from the physical examination and the Friedman Staging System (FSS) in patients with obstructive sleep apnea (OSA). We performed a retrospective evaluation by reviewing the medical records of 33 patients (19 male and 14 female patients) with a mean body mass index of 30.38 kg/m(2) and mean age of 49.35 years. Among these patients, 14 presented with severe OSA, 7 had moderate OSA, 7 had mild OSA, and 5 were healthy. The patients were divided into 2 groups according to the FSS: Group A comprised patients with FSS stage I or II, and group B comprised patients with FSS stage III. By use of the Fisher exact test, a positive relationship between the FSS stage and apnea-hypopnea index (P = .011) and between the FSS stage and body mass index (P = .012) was found. There was no correlation between age (P = .55) and gender (P = .53) with the FSS stage. The analysis of variance test comparing the upper airway volume between the 2 groups showed P = .018. In this sample the FSS and upper airway volume showed an inverse correlation and were useful in analyzing the mechanisms of airway collapse in patients with OSA.

Avaliação de perdas invisíveis na colheita mecanizada em dois fluxos de massa de cana-de-açúcar

In this work the performance of a sugar cane chopped harvester was analysed when fed with two sugar cane mass flows, measuring the invisible losses, which are impossible to measure in the field, harvester sugar cane cleaning efficiency and air velocity on extractors exit. The trial was done under controlled conditions at Copersucar Technology Center in January 2000. The results showed that the flow of sugar cane through the harvester doesn't influence the magnitudes of total invisible losses and raw material cleaning efficiency. The mean air velocity on the primary extractors exit was 12.0 m s-1, and 9.2 m s-1 on the secondary extractor, with a coefficient of variation of 21%, indicating that the poor cleaning performance of the harvester could be related to air velocity difference inside the extractor. Analyzing the data collected in the trials, it was possible to conclude that invisible losses in sugar cane harvester were 10% and the cleaning efficiency was 87%.