An automated approach for performance deviation analysis of evolving software systems

A manutenção e evolução de sistemas de software tornou-se uma tarefa bastante crítica ao longo dos últimos anos devido à diversidade e alta demanda de funcionalidades, dispositivos e usuários. Entender e analisar como novas mudanças impactam os atributos de qualidade da arquitetura de tais sistemas é um pré-requisito essencial para evitar a deterioração de sua qualidade durante sua evolução. Esta tese propõe uma abordagem automatizada para a análise de variação do atributo de qualidade de desempenho em termos de tempo de execução (tempo de resposta). Ela é implementada por um framework que adota técnicas de análise dinâmica e mineração de repositório de software para fornecer uma forma automatizada de revelar fontes potenciais – commits e issues – de variação de desempenho em cenários durante a evolução de sistemas de software. A abordagem define quatro fases: (i) preparação – escolher os cenários e preparar os releases alvos; (ii) análise dinâmica – determinar o desempenho de cenários e métodos calculando seus tempos de execução; (iii) análise de variação – processar e comparar os resultados da análise dinâmica para releases diferentes; e (iv) mineração de repositório – identificar issues e commits associados com a variação de desempenho detectada. Estudos empíricos foram realizados para avaliar a abordagem de diferentes perspectivas. Um estudo exploratório analisou a viabilidade de se aplicar a abordagem em sistemas de diferentes domínios para identificar automaticamente elementos de código fonte com variação de desempenho e as mudanças que afetaram tais elementos durante uma evolução. Esse estudo analisou três sistemas: (i) SIGAA – um sistema web para gerência acadêmica; (ii) ArgoUML – uma ferramenta de modelagem UML; e (iii) Netty – um framework para aplicações de rede. Outro estudo realizou uma análise evolucionária ao aplicar a abordagem em múltiplos releases do Netty, e dos frameworks web Wicket e Jetty. Nesse estudo foram analisados 21 releases (sete de cada sistema), totalizando 57 cenários. Em resumo, foram encontrados 14 cenários com variação significante de desempenho para Netty, 13 para Wicket e 9 para Jetty. Adicionalmente, foi obtido feedback de oito desenvolvedores desses sistemas através de um formulário online. Finalmente, no último estudo, um modelo de regressão para desempenho foi desenvolvido visando indicar propriedades de commits que são mais prováveis a causar degradação de desempenho. No geral, 997 commits foram minerados, sendo 103 recuperados de elementos de código fonte degradados e 19 de otimizados, enquanto 875 não tiveram impacto no tempo de execução. O número de dias antes de disponibilizar o release e o dia da semana se mostraram como as variáveis mais relevantes dos commits que degradam desempenho no nosso modelo. A área de característica de operação do receptor (ROC – Receiver Operating Characteristic) do modelo de regressão é 60%, o que significa que usar o modelo para decidir se um commit causará degradação ou não é 10% melhor do que uma decisão aleatória.

Efeitos do treino de marcha em esteira com adição de carga ao membro inferior não parético de indivíduos com acidente vascular cerebral: ensaio clínico controlado e randomizado

Introduction: Gait after stroke is characterized by a significant asymmetry between the lower limbs, with predominant use of the non-paretic lower limb (NPLL) over using the paretic lower limb. Accordingly, it has been suggested that adding load/weight to the NPLL as a form of restricting the movement of this limb may favor the use of the paretic limb, reducing interlimb asymmetry. However, few studies have been conducted up to this moment, which only investigated the immediate effects of this practice. Objectives: 1) Investigating whether there is an influence of adding load to the NPLL during treadmill training on cardiovascular parameters and on gait performance of individuals with stroke, compared to treadmill training without load addition; 2) Analyzing the effects of treadmill training with and without load added to the NPLL on kinematic parameters of each lower limb during gait; 3) Analyzing the effects of treadmill training with and without load added to the NPLL on measurements of functional mobility and postural balance of these patients. Materials and Methods: This is a randomized single blinded clinical trial involving 38 subjects, with a mean age of 56.5 years, at the subacute post-stroke phase (with mean time since stroke of 4.5 months). Participants were randomly assigned into an experimental group (EG) or control group (CG). EG (n= 19) was submitted to gait training on a treadmill with the addition of load to the NPLL by ankle weights equivalent to 5% of body weight. CG (n= 19) was only submitted to gait training on a treadmill. Behavioral strategies which included home exercises were also applied to both groups. The interventions occurred daily for two consecutive weeks (Day 1 to Day 9), being of 30 minutes duration each. Outcome measures: postural balance (Berg Functional Balance Scale – BBS), functional mobility (Timed Up and Go – TUG; kinematic variables of 180° turning) and kinematic gait variables were assessed at baseline (Day 0), after four training sessions (Day 4), after nine training sessions (Day 9), and 40 days after completion of training (Follow-up). Cardiovascular parameters (mean arterial pressure and heart rate) were evaluated at four moments within each training session. Analysis of variance (ANOVA) was used to compare outcomes between EG and CG in the course of the study (Day 0, Day 4, Day 9 and Follow-up). Unpaired t-tests allowed for intergroup comparison at each training session. 5% significance was used for all tests. Results: 1) Cardiovascular parameters (systemic arterial pressure, heart rate and derivated variables) did not change after the interventions and there were no differences between groups within each training session. There was an improvement in gait performance, with increased speed and distance covered, with no statistically significant difference between groups. 2) After the interventions, patients had increased paretic and non-paretic step lengths, in addition to exhibiting greater hip and knee joint excursion on both lower limbs. The gains were observed in the EG and CG, with no statistical difference between the groups and (mostly) maintained at follow-up. 3) After the interventions, patients showed better postural balance (higher scores on BBS) and functional mobility (reduced time spent on the TUG test and better performance on the 180° turning). All gains were observed in the EG and CG, with no statistically significant difference between groups and were maintained at follow-up. Conclusions: The addition of load to the NPLL did not affect cardiovascular parameters in patients with subacute stroke, similar to treadmill training without load, thus seemingly a safe training to be applied to these patients. However, the use of the load did not bring any additional benefits to gait training. The gait training program (nine training sessions on a treadmill + strategies and exercises for paretic limb stimulation) was useful for improving gait performance and kinematics, functional mobility and postural balance, and its use is suggested to promote the optimization of these outcomes in the subacute phase after stroke.

Age determination and paleotemperatures of western Mediterranean Sea sediments

Sea surface temperature (SST) profiles over the last 25 kyr derived from alkenone measurements are studied in four cores from a W-E latitudinal transect encompassing the Gulf of Cadiz (Atlantic Ocean), the Alboran Sea, and the southern Tyrrhenian Sea (western Mediterranean). The results document the sensitivity of the Mediterranean region to the short climatic changes of the North Atlantic Ocean, particularly those involving the latitudinal position of the polar front. The amplitude of the SST oscillations increases toward the Tyrrhenian Sea, indicating an amplification effect of the Atlantic signal by the climatic regime of the Mediterranean region. All studied cores show a shorter cooling phase (700 years) for the Younger Dryas (YD) than that observed in the North Atlantic region (1200 years). This time diachroneity is related to an intra-YD climatic change documented in the European continent. Minor oscillations in the southward displacement of the North Atlantic polar front may also have driven this early warming in the studied area. During the Holocene a regional diachroneity propagating west to east is observed for the SST maxima, 11.5-10.2 kyr B.P. in the Gulf of Cadiz, 10-9 kyr B.P. in the Alboran Sea, and 8.9-8.4 kyr B.P. in the Thyrrenian Sea. A general cooling trend from these SST maxima to present day is observed during this stage, which is marked by short cooling oscillations with a periodicity of 730±40 years and its harmonics.

Diadenosine polyphosphates after laser in situ keratomileusis and photorefractive keratectomy refractive techniques

Purpose:  To study the concentrations of diadenosine polyphosphates in the ocular surface after PRK and LASIK. Methods:  Sixty-one patients (30 males and 31 females) with ages ranging from 20 to 63 (34.04 ± 9.13 years) were recruited in Balear Institute of Ophthalmology, Palma de Mallorca, Spain. LASIK was performed in 92 eyes of 46 patients and PRK in 25 eyes of 15 patients. Variations in the levels of diadenosine polyphosphate (Ap4A and Ap5A), Schirmer I (Jones test), TBUT, corneal staining together with the Dry Eye Questionnaire to evaluate discomfort and dryness were studied. All tests were performed at the preoperative visit and at 1-day, 2-week, 1-month and 3-month postoperative visits. Results:  Ap4A showed a 5 and 3.5 fold increase at the 1-day visit for LASIK and PRK, respectively. LASIK patients continued having higher statistically significant concentrations (p = 0.01) all over the follow-up. Ap5A showed no significant differences at any visit. Tear volume decreased during the 3 months in LASIK. The PRK cases had a normal volume at 1 month. TBUT in LASIK increased at the 1-day visit (p = 0,002) and decreased from the 2 weeks onwards and for the PRK, decreased by a 35% at the 1-day visit and kept reduced for a month. Discomfort only increased at the 1-day visit (p = 0.007). Dryness frequency was similar in all visits. Conclusions:  Ap4A levels only are increased in refractive surgery patients during the first day after the surgery. This increasing suggests that Ap4A may help accelerating the healing process.

Introduction of novel video-based tasks to clinical fMRI: Comparing traditional fMRI tasks with novel video-based tasks for mapping brain language areas

Recently, blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI) has become a routine clinical procedure for localization of language and motor brain regions and has been replacing more invasive preoperative procedures. However, the fMRI results from these tasks are not always reproducible even from the same patient. Evaluating the reproducibility of language and speech mapping is especially complicated due to the complex brain circuitry that may become activated during the functional task. Non-language areas such as sensory, attention, decision-making, and motor brain regions may also be activated in addition to the specific language regions during a traditional sentence-completion task. In this study, I test a new approach, which utilizes 4-minute video-based tasks, to map language and speech brain regions for patients undergoing brain surgery. Results from 35 subjects have shown that the video-based task activates Wernicke’s area, as well as Broca’s area in most subjects. The computed laterality indices, which indicate the dominant hemisphere from that functional task, have indicated left dominance from the video-based tasks. This study has shown that the video-based task may be an alternative method for localization of language and speech brain regions for patients who are unable to complete the sentence-completion task.

Alkenone unsaturation index and alkenones in ODP Hole 161-977A

A number of essential elements closely related to each other are involved in the Earth's climatic system. The temporal and spatial distribution of insolation determines wind patterns and the ocean's thermohaline pump. In turn, these last two are directly linked to the extension and retreat of marine and continental ice and to the chemistry of the atmosphere and the ocean. The variability of these elements may trigger, amplify, sustain or globalize rapid climatic changes. Paleoclimatic oscillations have been identified in this thesis by using fossil organic compounds synthesized by marine and terrestrial flora. High sedimentation rate deposits at the Barents and the Iberian peninsula continental margins were chosen in order to estimate the climatic changes on centennial time resolution. At the Barents margin, the sediment recovered was up to 15,000 years old (unit ''a'', from latin ''annos'') (M23258; west of the Bjørnøya island). At the Iberian margin, the sediment cores studied covered a wide range of time spans: up to 115,000 a (MD99-2343; north of the Minorca island), up to 250,000 a (ODP-977A; Alboran basin) and up to 420,000 a (MD01-2442, MD01-2443, MD01-2444, MD01-2445; close to the Tagus abyssal plain). At the northern site, inputs containing marine, continental and ancient reworked organic matter provided a detailed reconstruction of climate history at the time of the final retreat of the Barents ice sheet. At the western Barents continental slope, warm climatic conditions were observed during the early Holocene (~from 8,650 a to 5,240 a ago); in contrast, an apparent long-term cooling trend occurred in the late Holocene (~from 5,240 a to 760 a ago), in consistence with other paleoarchives from northern and southern European latitudes. The Iberian margin sites, which were never covered with large ice sheets, preserved exceptionally complete sequences of rapid events during ice ages hitherto not studied in such great detail: during the last glacial (~from 70,900 a to 11,800 a ago), the second glacial (~from 189,300 a to 127,500 a ago), the third ice age (~from 278,600 a to 244,800 a ago) and the fourth (~from 376,300 a to 337,500 a ago). In this thesis, crucial research questions were brought up concerning the severity of different glacial periods, the intensity and rates of the recorded oscillations and the long distance connections related to rapid climate change. The data obtained provide a sound basis to further research on the mechanisms involved in this rapid climate variability. An essential point of the research was the evidence that, over the past 420,000 a, at the whole Iberian margin, warm and stable long periods similar to the Holocene always ended abruptly in few centuries after a gradual deterioration of climate conditions. The detailed estimate of past climate variability provides clues to the natural end of the present warm period. Returning to an ice age in European lands would be exacerbated by a number of factors: a lack of differential solar heating between northern and southern north Atlantic latitudes, enhanced evaporation at low latitudes, and an increase in snowfall or iceberg discharges at northern regions. It must be emphasized that all climatic oscillations observed in this thesis were caused by forces of nature, i.e. the last two centuries were not taken into consideration.

Sea surface temperatures, alkenones and sedimentation rate from ODP Hole 161-977A

A continuous high-resolution Western Mediterranean sea surface temperature (SST) alkenone record spanning the past 250,000 years shows that abrupt changes were more common at warming than at cooling. During marine isotope stage (MIS) 6, SST oscillated following a stadial-interstadial pattern but at lower intensities and rates of change than in the Dansgaard/Oeschger events of MIS 3. Some of the most prominent events occurred over MISs 5 and 7, after prolonged warm periods of high stability. Climate during the whole period was predominantly maintained in interglacial-interstadial conditions, whereas the duration of stadials was much shorter.

Sea surface temperature (TEX86), marine GDGTs and BIT index from ODP Hole 161-977A

The TEX86H temperature proxy is a relatively new proxy based on crenarchaeotal lipids and has rarely been applied together with other temperature proxies. In this study, we applied the TEX86H on a sediment core from the Alboran Sea (western Mediterranean, core ODP-977A) covering the penultimate climate cycle, that is, from 244 to 130 ka, and compared this with previously published sea surface temperatures derived from the Uk'37 of alkenones of haptophyta and Mg/Ca records of planktonic foraminifera. The TEX86H temperature record shows remarkably similar stadial-interstadial patterns and abrupt temperature changes to those observed with the Uk'37 palaeothermometer. Absolute TEX86H temperature estimates are generally higher than those of Uk'37, though this difference (<3°C in 81% of the data points) is mainly within the temperature calibration error for both proxies, suggesting that crenarchaeota and haptophyta experienced similar temperature variations. During occasional events (<5% of the analyzed time span), however, the TEX86H exhibits considerably higher absolute temperature estimates than the Uk'37. Comparison with Mg/Ca records of planktonic foraminifera as well as other Mediterranean TEX86 and Uk'37 records suggests that part of this divergence may be attributed to seasonal differences, that is, with TEX86H reflecting mainly the warm summer season while Uk'37 would show annual mean. Biases in the global calibration of both proxies or specific biases in the Mediterranean are an alternative, though less likely, explanation. Despite differences between absolute TEX86H and Uk'37 temperatures, the correlation between the two proxies (r**2 = 0.59, 95% significance) provides support for the occurrence of abrupt temperature variations in the western Mediterranean during the penultimate interglacial-to-glacial cycle.

(Fig. 11c) Alkenones (di and tri alkenones of 37 carbons) from sediment core MD95-2043

The present paper is a synopsis of the research on the climatic evolution of the Western Mediterranean Sea developed within the MATER programme. The sea surface temperature (SST) evolution during the last glacial period, deglaciation and present interglacial have been examined in detail. Special attention has been focussed to millennial-centennial scale changes related to rapid global climatic oscillations. The results have shown the extreme sensitivity of the Western Mediterranean oceanography to this rapid climatic variability giving rise to amplified climatic signals, e.g. strong SST oscillation, that follow the changes recorded in the North Atlantic Ocean or in Greenland ice. Overall, the Western Mediterranean Sea appears to be an ideal environment for the study of the climatic processes occurring at high and intermediate latitudes.