A behavioral analysis tool for models of software systems

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia Informática

The computational role of short-term plasticity and the balance of excitation and inhibition in neural microcircuits: experimental and theoretical analysis

The computations performed by the brain ultimately rely on the functional connectivity between neurons embedded in complex networks. It is well known that the neuronal connections, the synapses, are plastic, i.e. the contribution of each presynaptic neuron to the firing of a postsynaptic neuron can be independently adjusted. The modulation of effective synaptic strength can occur on time scales that range from tens or hundreds of milliseconds, to tens of minutes or hours, to days, and may involve pre- and/or post-synaptic modifications. The collection of these mechanisms is generally believed to underlie learning and memory and, hence, it is fundamental to understand their consequences in the behavior of neurons.(...)

Electrochemical immunosensor for the analysis of the breast cancer biomarker HER2 ECD

Human epidermal growth factor receptor 2 (HER2) is a breast cancer biomarker that plays a major role in promoting breast cancer cell proliferation and malignant growth. The extracellular domain (ECD) of HER2 can be shed into the blood stream and its concentration is measurable in the serum fraction of blood. In this work an electrochemical immunosensor for the analysis of HER2 ECD in human serum samples was developed. To achieve this goal a screen-printed carbon electrode, modified with gold nanoparticles, was used as transducer surface. A sandwich immunoassay, using two monoclonal antibodies, was employed and the detection of the antibody–antigen interaction was performed through the analysis of an enzymatic reaction product by linear sweep voltammetry. Using the optimized experimental conditions the calibration curve (ip vs. log[HER2 ECD]) was established between 15 and 100 ng/mL and a limit of detection (LOD) of 4.4 ng/mL was achieved. These results indicate that the developed immunosensor could be a promising tool in breast cancer diagnostics, patient follow-up and monitoring of metastatic breast cancer since it allows quantification in a useful concentration range and has an LOD below the established cut-off value (15 ng/mL).

The development of the N1 and N2 components in auditory oddball paradigms: a systematic review with narrative analysis and suggested normative values

Auditory event-related potentials (AERPs) are widely used in diverse fields of today’s neuroscience, concerning auditory processing, speech perception, language acquisition, neurodevelopment, attention and cognition in normal aging, gender, developmental, neurologic and psychiatric disorders. However, its transposition to clinical practice has remained minimal. Mainly due to scarce literature on normative data across age, wide spectrumof results, variety of auditory stimuli used and to different neuropsychological meanings of AERPs components between authors. One of the most prominent AERP components studied in last decades was N1, which reflects auditory detection and discrimination. Subsequently, N2 indicates attention allocation and phonological analysis. The simultaneous analysis of N1 and N2 elicited by feasible novelty experimental paradigms, such as auditory oddball, seems an objective method to assess central auditory processing. The aim of this systematic review was to bring forward normative values for auditory oddball N1 and N2 components across age. EBSCO, PubMed, Web of Knowledge and Google Scholarwere systematically searched for studies that elicited N1 and/or N2 by auditory oddball paradigm. A total of 2,764 papers were initially identified in the database, of which 19 resulted from hand search and additional references, between 1988 and 2013, last 25 years. A final total of 68 studiesmet the eligibility criteria with a total of 2,406 participants from control groups for N1 (age range 6.6–85 years; mean 34.42) and 1,507 for N2 (age range 9–85 years; mean 36.13). Polynomial regression analysis revealed thatN1latency decreases with aging at Fz and Cz,N1 amplitude at Cz decreases from childhood to adolescence and stabilizes after 30–40 years and at Fz the decrement finishes by 60 years and highly increases after this age. Regarding N2, latency did not covary with age but amplitude showed a significant decrement for both Cz and Fz. Results suggested reliable normative values for Cz and Fz electrode locations; however, changes in brain development and components topography over age should be considered in clinical practice.

Analysis of Forest Fires by means of Pseudo Phase Plane and Multidimensional Scaling Methods

Forest fires dynamics is often characterized by the absence of a characteristic length-scale, long range correlations in space and time, and long memory, which are features also associated with fractional order systems. In this paper a public domain forest fires catalogue, containing information of events for Portugal, covering the period from 1980 up to 2012, is tackled. The events are modelled as time series of Dirac impulses with amplitude proportional to the burnt area. The time series are viewed as the system output and are interpreted as a manifestation of the system dynamics. In the first phase we use the pseudo phase plane (PPP) technique to describe forest fires dynamics. In the second phase we use multidimensional scaling (MDS) visualization tools. The PPP allows the representation of forest fires dynamics in two-dimensional space, by taking time series representative of the phenomena. The MDS approach generates maps where objects that are perceived to be similar to each other are placed on the map forming clusters. The results are analysed in order to extract relationships among the data and to better understand forest fires behaviour.

Dynamic Analysis and Pattern Visualization of Forest Fires

This paper analyses forest fires in the perspective of dynamical systems. Forest fires exhibit complex correlations in size, space and time, revealing features often present in complex systems, such as the absence of a characteristic length-scale, or the emergence of long range correlations and persistent memory. This study addresses a public domain forest fires catalogue, containing information of events for Portugal, during the period from 1980 up to 2012. The data is analysed in an annual basis, modelling the occurrences as sequences of Dirac impulses with amplitude proportional to the burnt area. First, we consider mutual information to correlate annual patterns. We use visualization trees, generated by hierarchical clustering algorithms, in order to compare and to extract relationships among the data. Second, we adopt the Multidimensional Scaling (MDS) visualization tool. MDS generates maps where each object corresponds to a point. Objects that are perceived to be similar to each other are placed on the map forming clusters. The results are analysed in order to extract relationships among the data and to identify forest fire patterns.

Comparison of Disposable Pipette Extraction and Dispersive Solid-Phase Extraction in the QuEChERS Method for Analysis of Pesticides in Strawberries

In this study, we sought to assess the applicability of GC–MS/MS for the identification and quantification of 36 pesticides in strawberry from integrated pest management (IPM) and organic farming (OF). Citrate versions of QuEChERS (quick, easy, cheap, effective, rugged and safe) using dispersive solid-phase extraction (d-SPE) and disposable pipette extraction (DPX) for cleanup were compared for pesticide extraction. For cleanup, a combination of MgSO4, primary secondary amine and C18 was used for both the versions. Significant differences were observed in recovery results between the two sample preparation versions (DPX and d-SPE). Overall, 86% of the pesticides achieved recoveries (three spiking levels 10, 50 and 200 µg/kg) in the range of 70–120%, with <13% RSD. The matrix effects were also evaluated in both the versions and in strawberries from different crop types. Although not evidencing significant differences between the two methodologies were observed, however, the DPX cleanup proved to be a faster technique and easy to execute. The results indicate that QuEChERS with d-SPE and DPX and GC–MS/MS analysis achieved reliable quantification and identification of 36 pesticide residues in strawberries from OF and IPM.

A framework for memory contention analysis in multi-core platforms

The last decade has witnessed a major shift towards the deployment of embedded applications on multi-core platforms. However, real-time applications have not been able to fully benefit from this transition, as the computational gains offered by multi-cores are often offset by performance degradation due to shared resources, such as main memory. To efficiently use multi-core platforms for real-time systems, it is hence essential to tightly bound the interference when accessing shared resources. Although there has been much recent work in this area, a remaining key problem is to address the diversity of memory arbiters in the analysis to make it applicable to a wide range of systems. This work handles diverse arbiters by proposing a general framework to compute the maximum interference caused by the shared memory bus and its impact on the execution time of the tasks running on the cores, considering different bus arbiters. Our novel approach clearly demarcates the arbiter-dependent and independent stages in the analysis of these upper bounds. The arbiter-dependent phase takes the arbiter and the task memory-traffic pattern as inputs and produces a model of the availability of the bus to a given task. Then, based on the availability of the bus, the arbiter-independent phase determines the worst-case request-release scenario that maximizes the interference experienced by the tasks due to the contention for the bus. We show that the framework addresses the diversity problem by applying it to a memory bus shared by a fixed-priority arbiter, a time-division multiplexing (TDM) arbiter, and an unspecified work-conserving arbiter using applications from the MediaBench test suite. We also experimentally evaluate the quality of the analysis by comparison with a state-of-the-art TDM analysis approach and consistently showing a considerable reduction in maximum interference.

Solid contact PVC membrane electrodes based on neutral or charged carriers for the selective reading of anionic sulfamethoxazole and their application to the analysis of aquaculture water

Sulfamethoxazole (SMX) is among the antibiotics employed in aquaculture for prophylactic and therapeutic reasons. Environmental and food spread may be prevented by controlling its levels in several stages of fish farming. The present work proposes for this purpose new SMX selective electrodes for the potentiometric determination of this sulphonamide in water. The selective membranes were made of polyvinyl chloride (PVC) with tetraphenylporphyrin manganese (III) chloride or cyclodextrin-based acting as ionophores. 2-nitrophenyl octyl ether was employed as plasticizer and tetraoctylammonium, dimethyldioctadecylammonium bromide or potassium tetrakis (4-chlorophenyl) borate was used as anionic or cationic additive. The best analytical performance was reported for ISEs of tetraphenylporphyrin manganese (III) chloride with 50% mol of potassium tetrakis (4-chlorophenyl) borate compared to ionophore. Nersntian behaviour was observed from 4.0 × 10−5 to 1.0 × 10−2 mol/L (10.0 to 2500 µg/mL), and the limit of detection was 1.2 × 10−5 mol/L (3.0 µg/mL). In general, the electrodes displayed steady potentials in the pH range of 6 to 9. Emf equilibrium was reached before 15 s in all concentration levels. The electrodes revealed good discriminating ability in environmental samples. The analytical application to contaminated waters showed recoveries from 96 to 106%.

Novel LTCC-potentiometric microfluidic device for biparametric analysis of organic compounds carrying plastic antibodies as ionophores: Application to sulfamethoxazole and trimethoprim

Monitoring organic environmental contaminants is of crucial importance to ensure public health. This requires simple, portable and robust devices to carry out on-site analysis. For this purpose, a low-temperature co-fired ceramics (LTCC) microfluidic potentiometric device (LTCC/μPOT) was developed for the first time for an organic compound: sulfamethoxazole (SMX). Sensory materials relied on newly designed plastic antibodies. Sol–gel, self-assembling monolayer and molecular-imprinting techniques were merged for this purpose. Silica beads were amine-modified and linked to SMX via glutaraldehyde modification. Condensation polymerization was conducted around SMX to fill the vacant spaces. SMX was removed after, leaving behind imprinted sites of complementary shape. The obtained particles were used as ionophores in plasticized PVC membranes. The most suitable membrane composition was selected in steady-state assays. Its suitability to flow analysis was verified in flow-injection studies with regular tubular electrodes. The LTCC/μPOT device integrated a bidimensional mixer, an embedded reference electrode based on Ag/AgCl and an Ag-based contact screen-printed under a micromachined cavity of 600 μm depth. The sensing membranes were deposited over this contact and acted as indicating electrodes. Under optimum conditions, the SMX sensor displayed slopes of about −58.7 mV/decade in a range from 12.7 to 250 μg/mL, providing a detection limit of 3.85 μg/mL and a sampling throughput of 36 samples/h with a reagent consumption of 3.3 mL per sample. The system was adjusted later to multiple analyte detection by including a second potentiometric cell on the LTCC/μPOT device. No additional reference electrode was required. This concept was applied to Trimethoprim (TMP), always administered concomitantly with sulphonamide drugs, and tested in fish-farming waters. The biparametric microanalyzer displayed Nernstian behaviour, with average slopes −54.7 (SMX) and +57.8 (TMP) mV/decade. To demonstrate the microanalyzer capabilities for real applications, it was successfully applied to single and simultaneous determination of SMX and TMP in aquaculture waters.

Dynamic Analysis and Pattern Visualization of Forest Fires

This paper analyses forest fires in the perspective of dynamical systems. Forest fires exhibit complex correlations in size, space and time, revealing features often present in complex systems, such as the absence of a characteristic length-scale, or the emergence of long range correlations and persistent memory. This study addresses a public domain forest fires catalogue, containing information of events for Portugal, during the period from 1980 up to 2012. The data is analysed in an annual basis, modelling the occurrences as sequences of Dirac impulses with amplitude proportional to the burnt area. First, we consider mutual information to correlate annual patterns. We use visualization trees, generated by hierarchical clustering algorithms, in order to compare and to extract relationships among the data. Second, we adopt the Multidimensional Scaling (MDS) visualization tool. MDS generates maps where each object corresponds to a point. Objects that are perceived to be similar to each other are placed on the map forming clusters. The results are analysed in order to extract relationships among the data and to identify forest fire patterns.

Analysis of UV spectral bands using multidimensional scaling

This study describes the change of the ultraviolet spectral bands starting from 0.1 to 5.0 nm slit width in the spectral range of 200–400 nm. The analysis of the spectral bands is carried out by using the multidimensional scaling (MDS) approach to reach the latent spectral background. This approach indicates that 0.1 nm slit width gives higher-order noise together with better spectral details. Thus, 5.0 nm slit width possesses the higher peak amplitude and lower-order noise together with poor spectral details. In the above-mentioned conditions, the main problem is to find the relationship between the spectral band properties and the slit width. For this aim, the MDS tool is to used recognize the hidden information of the ultraviolet spectra of sildenafil citrate by using a Shimadzu UV–VIS 2550, which is in the world the best double monochromator instrument. In this study, the proposed mathematical approach gives the rich findings for the efficient use of the spectrophotometer in the qualitative and quantitative studies.

Dynamical Analysis and Visualization of Tornadoes Time Series

In this paper we analyze the behavior of tornado time-series in the U.S. from the perspective of dynamical systems. A tornado is a violently rotating column of air extending from a cumulonimbus cloud down to the ground. Such phenomena reveal features that are well described by power law functions and unveil characteristics found in systems with long range memory effects. Tornado time series are viewed as the output of a complex system and are interpreted as a manifestation of its dynamics. Tornadoes are modeled as sequences of Dirac impulses with amplitude proportional to the events size. First, a collection of time series involving 64 years is analyzed in the frequency domain by means of the Fourier transform. The amplitude spectra are approximated by power law functions and their parameters are read as an underlying signature of the system dynamics. Second, it is adopted the concept of circular time and the collective behavior of tornadoes analyzed. Clustering techniques are then adopted to identify and visualize the emerging patterns.

State Space Analysis of Forest Fires

This paper studies forest fires from the perspective of dynamical systems. Burnt area, precipitation and atmospheric temperatures are interpreted as state variables of a complex system and the correlations between them are investigated by means of different mathematical tools. First, we use mutual information to reveal potential relationships in the data. Second, we adopt the state space portrait to characterize the system’s behavior. Third, we compare the annual state space curves and we apply clustering and visualization tools to unveil long-range patterns. We use forest fire data for Portugal, covering the years 1980–2003. The territory is divided into two regions (North and South), characterized by different climates and vegetation. The adopted methodology represents a new viewpoint in the context of forest fires, shedding light on a complex phenomenon that needs to be better understood in order to mitigate its devastating consequences, at both economical and environmental levels.

Clinical Outcome and Morphologic Analysis after Endovascular Aneurysm Repair Using the Excluder Endograft

OBJECTIVE: Long-term follow-up after endovascular aneurysm repair (EVAR) is very scarce, and doubt remains regarding the durability of these procedures. We designed a retrospective cohort study to assess long-term clinical outcome and morphologic changes in patients with abdominal aortic aneurysms (AAAs) treated by EVAR using the Excluder endoprosthesis (W. L. Gore and Associates, Flagstaff, Ariz). METHODS: From 2000 to 2007, 179 patients underwent EVAR in a tertiary institution. Clinical data were retrieved from a prospective database. All patients treated with the Excluder endoprosthesis were included. Computed tomography angiography (CTA) scans were retrospectively analyzed preoperatively, at 30 days, and at the last follow-up using dedicated tridimensional reconstruction software. For patients with complications, all remaining CTAs were also analyzed. The primary end point was clinical success. Secondary end points were freedom from reintervention, sac growth, types I and III endoleak, migration, conversion to open repair, and AAA-related death or rupture. Neck dilatation, renal function, and overall survival were also analyzed. RESULTS: Included were 144 patients (88.2% men; mean age, 71.6 years). Aneurysms were ruptured in 4.9%. American Society of Anesthesiologists classification was III/IV in 61.8%. No patients were lost during a median follow-up of 5.0 years (interquartile range, 3.1-6.4; maximum, 11.2 years). Two patients died of medical complications ≤ 30 days after EVAR. The estimated primary clinical success rates at 5 and 10 years were 63.5% and 41.1%, and secondary clinical success rates were 78.3% and 58.3%, respectively. Sac growth was observed in 37 of 142 patients (26.1%). Cox regression showed type I endoleak during follow-up (hazard ratio, 3.74; P = .008), original design model (hazard ratio, 3.85; P = .001), and preoperative neck diameter (1.27 per mm increase, P = .006) were determinants of sac growth. Secondary interventions were required in 32 patients (22.5%). The estimated 10-year rate of AAA-related death or rupture was 2.1%. Overall life expectancy after AAA repair was 6.8 years. CONCLUSIONS: EVAR using the Excluder endoprosthesis provides a safe and lasting treatment for AAA, despite the need for maintained surveillance and secondary interventions. At up to 11 years, the risk of AAA-related death or postimplantation rupture is remarkably low. The incidences of postimplantation sac growth and secondary intervention were greatly reduced after the introduction of the low-permeability design in 2004.