A holistic approach to model-based testing of Web service compositions

The behavior of composed Web services depends on the results of the invoked services; unexpected behavior of one of the invoked services can threat the correct execution of an entire composition. This paper proposes an event-based approach to black-box testing of Web service compositions based on event sequence graphs, which are extended by facilities to deal not only with service behavior under regular circumstances (i.e., where cooperating services are working as expected) but also with their behavior in undesirable situations (i.e., where cooperating services are not working as expected). Furthermore, the approach can be used independently of artifacts (e.g., Business Process Execution Language) or type of composition (orchestration/choreography). A large case study, based on a commercial Web application, demonstrates the feasibility of the approach and analyzes its characteristics. Test generation and execution are supported by dedicated tools. Especially, the use of an enterprise service bus for test execution is noteworthy and differs from other approaches. The results of the case study encourage to suggest that the new approach has the power to detect faults systematically, performing properly even with complex and large compositions. Copyright © 2012 John Wiley & Sons, Ltd.

Detailed analysis of sequence changes occurring during vlsE antigenic variation in the mouse model of Borrelia burgdorferi infection.

Lyme disease Borrelia can infect humans and animals for months to years, despite the presence of an active host immune response. The vls antigenic variation system, which expresses the surface-exposed lipoprotein VlsE, plays a major role in B. burgdorferi immune evasion. Gene conversion between vls silent cassettes and the vlsE expression site occurs at high frequency during mammalian infection, resulting in sequence variation in the VlsE product. In this study, we examined vlsE sequence variation in B. burgdorferi B31 during mouse infection by analyzing 1,399 clones isolated from bladder, heart, joint, ear, and skin tissues of mice infected for 4 to 365 days. The median number of codon changes increased progressively in C3H/HeN mice from 4 to 28 days post infection, and no clones retained the parental vlsE sequence at 28 days. In contrast, the decrease in the number of clones with the parental vlsE sequence and the increase in the number of sequence changes occurred more gradually in severe combined immunodeficiency (SCID) mice. Clones containing a stop codon were isolated, indicating that continuous expression of full-length VlsE is not required for survival in vivo; also, these clones continued to undergo vlsE recombination. Analysis of clones with apparent single recombination events indicated that recombinations into vlsE are nonselective with regard to the silent cassette utilized, as well as the length and location of the recombination event. Sequence changes as small as one base pair were common. Fifteen percent of recovered vlsE variants contained "template-independent" sequence changes, which clustered in the variable regions of vlsE. We hypothesize that the increased frequency and complexity of vlsE sequence changes observed in clones recovered from immunocompetent mice (as compared with SCID mice) is due to rapid clearance of relatively invariant clones by variable region-specific anti-VlsE antibody responses.

Detailed analysis of sequence changes occurring during vlsE antigenic variation in the mouse model of Borrelia burgdorferi infection.

Lyme disease Borrelia can infect humans and animals for months to years, despite the presence of an active host immune response. The vls antigenic variation system, which expresses the surface-exposed lipoprotein VlsE, plays a major role in B. burgdorferi immune evasion. Gene conversion between vls silent cassettes and the vlsE expression site occurs at high frequency during mammalian infection, resulting in sequence variation in the VlsE product. In this study, we examined vlsE sequence variation in B. burgdorferi B31 during mouse infection by analyzing 1,399 clones isolated from bladder, heart, joint, ear, and skin tissues of mice infected for 4 to 365 days. The median number of codon changes increased progressively in C3H/HeN mice from 4 to 28 days post infection, and no clones retained the parental vlsE sequence at 28 days. In contrast, the decrease in the number of clones with the parental vlsE sequence and the increase in the number of sequence changes occurred more gradually in severe combined immunodeficiency (SCID) mice. Clones containing a stop codon were isolated, indicating that continuous expression of full-length VlsE is not required for survival in vivo; also, these clones continued to undergo vlsE recombination. Analysis of clones with apparent single recombination events indicated that recombinations into vlsE are nonselective with regard to the silent cassette utilized, as well as the length and location of the recombination event. Sequence changes as small as one base pair were common. Fifteen percent of recovered vlsE variants contained "template-independent" sequence changes, which clustered in the variable regions of vlsE. We hypothesize that the increased frequency and complexity of vlsE sequence changes observed in clones recovered from immunocompetent mice (as compared with SCID mice) is due to rapid clearance of relatively invariant clones by variable region-specific anti-VlsE antibody responses.

Finding negative event oriented patterns in long temporal sequences

Pattern discovery in a long temporal event sequence is of great importance in many application domains. Most of the previous work focuses on identifying positive associations among time stamped event types. In this paper, we introduce the problem of defining and discovering negative associations that, as positive rules, may also serve as a source of knowledge discovery. In general, an event-oriented pattern is a pattern that associates with a selected type of event, called a target event. As a counter-part of previous research, we identify patterns that have a negative relationship with the target events. A set of criteria is defined to evaluate the interestingness of patterns associated with such negative relationships. In the process of counting the frequency of a pattern, we propose a new approach, called unique minimal occurrence, which guarantees that the Apriori property holds for all patterns in a long sequence. Based on the interestingness measures, algorithms are proposed to discover potentially interesting patterns for this negative rule problem. Finally, the experiment is made for a real application.

Finding temporal features of event-oriented patterns

A major task of traditional temporal event sequence mining is to predict the occurrences of a special type of event (called target event) in a long temporal sequence. Our previous work has defined a new type of pattern, called event-oriented pattern, which can potentially predict the target event within a certain period of time. However, in the event-oriented pattern discovery, because the size of interval for prediction is pre-defined, the mining results could be inaccurate and carry misleading information. In this paper, we introduce a new concept, called temporal feature, to rectify this shortcoming. Generally, for any event-oriented pattern discovered under the pre-given size of interval, the temporal feature is the minimal size of interval that makes the pattern interesting. Thus, by further investigating the temporal features of discovered event-oriented patterns, we can refine the knowledge for the target event prediction.

Finding event-oriented patterns in long temporal sequences

A major task of traditional temporal event sequence mining is to find all frequent event patterns from a long temporal sequence. In many real applications, however, events are often grouped into different types, and not all types are of equal importance. In this paper, we consider the problem of efficient mining of temporal event sequences which lead to an instance of a specific type of event. Temporal constraints are used to ensure sensibility of the mining results. We will first generalise and formalise the problem of event-oriented temporal sequence data mining. After discussing some unique issues in this new problem, we give a set of criteria, which are adapted from traditional data mining techniques, to measure the quality of patterns to be discovered. Finally we present an algorithm to discover potentially interesting patterns.

A Visual Analytics Approach to Comparing Cohorts of Event Sequences

Sequences of timestamped events are currently being generated across nearly every domain of data analytics, from e-commerce web logging to electronic health records used by doctors and medical researchers. Every day, this data type is reviewed by humans who apply statistical tests, hoping to learn everything they can about how these processes work, why they break, and how they can be improved upon. To further uncover how these processes work the way they do, researchers often compare two groups, or cohorts, of event sequences to find the differences and similarities between outcomes and processes. With temporal event sequence data, this task is complex because of the variety of ways single events and sequences of events can differ between the two cohorts of records: the structure of the event sequences (e.g., event order, co-occurring events, or frequencies of events), the attributes about the events and records (e.g., gender of a patient), or metrics about the timestamps themselves (e.g., duration of an event). Running statistical tests to cover all these cases and determining which results are significant becomes cumbersome. Current visual analytics tools for comparing groups of event sequences emphasize a purely statistical or purely visual approach for comparison. Visual analytics tools leverage humans' ability to easily see patterns and anomalies that they were not expecting, but is limited by uncertainty in findings. Statistical tools emphasize finding significant differences in the data, but often requires researchers have a concrete question and doesn't facilitate more general exploration of the data. Combining visual analytics tools with statistical methods leverages the benefits of both approaches for quicker and easier insight discovery. Integrating statistics into a visualization tool presents many challenges on the frontend (e.g., displaying the results of many different metrics concisely) and in the backend (e.g., scalability challenges with running various metrics on multi-dimensional data at once). I begin by exploring the problem of comparing cohorts of event sequences and understanding the questions that analysts commonly ask in this task. From there, I demonstrate that combining automated statistics with an interactive user interface amplifies the benefits of both types of tools, thereby enabling analysts to conduct quicker and easier data exploration, hypothesis generation, and insight discovery. The direct contributions of this dissertation are: (1) a taxonomy of metrics for comparing cohorts of temporal event sequences, (2) a statistical framework for exploratory data analysis with a method I refer to as high-volume hypothesis testing (HVHT), (3) a family of visualizations and guidelines for interaction techniques that are useful for understanding and parsing the results, and (4) a user study, five long-term case studies, and five short-term case studies which demonstrate the utility and impact of these methods in various domains: four in the medical domain, one in web log analysis, two in education, and one each in social networks, sports analytics, and security. My dissertation contributes an understanding of how cohorts of temporal event sequences are commonly compared and the difficulties associated with applying and parsing the results of these metrics. It also contributes a set of visualizations, algorithms, and design guidelines for balancing automated statistics with user-driven analysis to guide users to significant, distinguishing features between cohorts. This work opens avenues for future research in comparing two or more groups of temporal event sequences, opening traditional machine learning and data mining techniques to user interaction, and extending the principles found in this dissertation to data types beyond temporal event sequences.

Managing pressure: patterns of appraisals and coping strategies of non-elite and elite athletes during competition

The purpose of this study was to compare moment-to-moment appraisals and coping strategies of 4 non-elite and 2 elite male trap shooters during competitions and in particular during periods of competition perceived as critical to performance. Appraisals and coping patterns of trap shooters were captured via verbal reports of thinking provided between sets of shots during major competitions. Verbal reports were coded according to an appraisal and coping typology. Coded data as well as shooting performance data were subjected to a sequential analysis of probabilities of pairs of events. Fewer reports of negative appraisals (NEGAs) and more frequent reports of problem-focused coping (PFC) were observed among both elite athletes compared to non-elite athletes. After making a NEGA, non-elite shooters often progressed to the next target without attempting to cope, whereas elite shooters used both PFC and emotion-focused coping (EFC) before proceeding to the next target. After missing a target, the non-elite athletes used more EFC than expected. These results indicate that elite athletes are more likely to cope with NEGAs than non-elite athletes using a wider variety of coping strategies. Athletes might benefit from increased awareness of the potentially detrimental impact of NEGAs on performance and by integrating coping strategies within preparatory routines.

The mitochondrial genome of the stingless bee Melipona bicolor (Hymenoptera, Apidae, Meliponini): sequence, gene organization and a unique tRNA translocation event conserved across the tribe Meliponini

At present a complete mtDNA sequence has been reported for only two hymenopterans, the Old World honey bee, Apis mellifera and the sawfly Perga condei. Among the bee group, the tribe Meliponini (stingless bees) has some distinction due to its Pantropical distribution, great number of species and large importance as main pollinators in several ecosystems, including the Brazilian rain forest. However few molecular studies have been conducted on this group of bees and few sequence data from mitochondrial genomes have been described. In this project, we PCR amplified and sequenced 78% of the mitochondrial genome of the stingless bee Melipona bicolor (Apidae, Meliponini). The sequenced region contains all of the 13 mitochondrial protein-coding genes, 18 of 22 tRNA genes, and both rRNA genes (one of them was partially sequenced). We also report the genome organization (gene content and order), gene translation, genetic code, and other molecular features, such as base frequencies, codon usage, gene initiation and termination. We compare these characteristics of M. bicolor to those of the mitochondrial genome of A. mellifera and other insects. A highly biased A+T content is a typical characteristic of the A. mellifera mitochondrial genome and it was even more extreme in that of M. bicolor. Length and compositional differences between M. bicolor and A. mellifera genes were detected and the gene order was compared. Eleven tRNA gene translocations were observed between these two species. This latter finding was surprising, considering the taxonomic proximity of these two bee tribes. The tRNA Lys gene translocation was investigated within Meliponini and showed high conservation across the Pantropical range of the tribe.

Characterization of electrical penetration graphs of Bucephalogonia xanthophis, a vector of Xylella fastidiosa in citrus

The sharpshooter Bucephalogonia xanthophis (Berg) (Homoptera: Cicadellidae) is a vector of the xylem-limited bacterium, Xylella fastidiosa (Wells, Raju, Hung, Weisburg, Mandelco-Paul, and Brenner), which causes citrus variegated chlorosis. Despite the importance of citrus variegated chlorosis, the probing behavior of vectors on citrus and its implications for transmission of X. fastidiosa have not been studied. Here we studied electrical penetration graph (EPG-DC system) waveforms produced by B. xanthophis on Citrus sinensis (L.) Osbeck (Rutaceae), and their relationships with stylet activities and xylem ingestion. Electrical penetration graph waveforms were described based on amplitude, frequency, voltage level, and electrical origin of the observed traces during stylet penetration on plant tissues. The main waveforms were correlated with histological observations of salivary sheaths in plant tissues and excretion analysis, in order to determine stylet activities and their precise position. Six waveforms and associated activities are described: (S) secretion of salivary sheath and intracellular stylet pathway, (R) resting during stylet pathway, (Xc) contact of stylets with xylem vessels, (Xi) active xylem ingestion, (N) interruption within the xylem phase (during Xc or Xi), and (W) withdrawal of stylet from the plant. The sharpshooter spent 91.8% of its probing time with its stylet in the xylem, where the main activity was ingestion (Xi: 97.5%). During a probe, the most likely sequence of events is secretion of salivary sheath and pathway (S) through epidermal and parenchyma cells (all individuals), followed by contact with xylem (Xc) (67.6% of all individuals) and ingestion (Xi) (88.3% of those that exhibit waveform Xc). The mean time to contact the xylem (Xc) and initiate ingestion (Xi) after onset of the first probe was 27.8 and 34.2 min, respectively. However, sustained xylem ingestion (Xi > 5 min) was established after 39.8 min, on average. This information is basic for future studies on the transmission mechanisms of X. fastidiosa and in order to establish control strategies aimed at interfering with this process.

The preparation and execution of self-initiated and externally-triggered movement: A study of event-related fMRI

Studies of functional brain imaging in humans and single cell recordings in monkeys have generally shown preferential involvement of the medially located supplementary motor area (SMA) in self-initiated movement and the lateral premotor cortex in externally cued movement. Studies of event-related cortical potentials recorded during movement preparation, however, generally show increased cortical activity prior to self-initiated movements but little activity at early stages prior to movements that are externally cued at unpredictable times. In this study, the spatial location and relative timing of activation for self-initiated and externally triggered movements were examined using rapid event-related functional MRI. Twelve healthy right-handed subjects were imaged while performing a brief finger sequence movement (three rapid alternating button presses: index-middle-index finger) made either in response to an unpredictably timed auditory cue (between 8 to 24 s after the previous movement) or at self-paced irregular intervals. Both movement conditions involved similar strong activation of medial motor areas including the pre-SMA, SMA proper, and rostral cingulate cortex, as well as activation within contralateral primary motor, superior parietal, and insula cortex. Activation within the basal ganglia was found for self-initiated movements only, while externally triggered movements involved additional bilateral activation of primary auditory cortex. Although the level of SMA and cingulate cortex activation did not differ significantly between movement conditions, the timing of the hemodynamic response within the pre-SMA was significantly earlier for self-initiated compared with externally triggered movements. This clearly reflects involvement of the pre-SMA in early processes associated with the preparation for voluntary movement. (C) 2002 Elsevier Science.

Effect of Gender on Swallow Event Duration Assessed by Videofluoroscopy

There are data suggesting that women swallow liquids at a lower flow rate and ingest smaller volumes in each swallow than men. Our objective in this work was to compare swallowing in asymptomatic men and women by videofluoroscopy. We studied 18 men [age = 33-77 years, mean = 61 (10) years] and 12 women [age = 29-72 years, mean = 53 (15) years] who swallowed in duplicate 5 and 10 ml of liquid and paste barium boluses. None of the volunteers had dysphagia, neurologic diseases, or oral, pharyngeal, or esophageal diseases. The videofluoroscopic examination showed that for the 5-ml bolus, women had a longer oropharyngeal transit [liquid: men, 0.63 (0.21) s, women, 0.88 (0.39) s; paste: men, 0.64 (0.35) s, women, 0.94 (0.58) s], longer oral transit [liquid: men, 0.41 (0.21) s, women, 0.59 (0.35) s; paste: men, 0.39 (0.28) s, women, 0.59 (0.42) s], and longer pharyngeal clearance [liquid: men, 0.36 (0.11) s, women, 0.45 (0.16) s; paste: men, 0.42 (0.25) s, women, 0.56 (0.27) s] compared with men (p < 0.05). We conclude that there are differences in swallowing between men and women, with women having a longer oropharyngeal transit than men for a 5-ml bolus.

Minimization of open orders using interval graphs

In this paper we address an order processing optimization problem known as the Minimization of Open Stacks Problem (MOSP). This problem consists in finding the best sequence for manufacturing the different products required by costumers, in a setting where only one product can be made at a time. The objective is to minimize the maximum number of incomplete orders from costumers that are being processed simultaneously. We present an integer programming model, based on the existence of a perfect elimination order in interval graphs, which finds an optimal sequence for the costumers orders. Among other economic advantages, manufacturing the products in this optimal sequence reduces the amount of space needed to store incomplete orders.

Sequencing cutting patterns with colored interval graphs

The problem addressed here originates in the industry of flat glass cutting and wood panel sawing, where smaller items are cut from larger items accordingly to predefined cutting patterns. In this type of industry the smaller pieces that are cut from the patterns are piled around the machine in stacks according to the size of the pieces, which are moved to the warehouse only when all items of the same size have been cut. If the cutting machine can process only one pattern at a time, and the workspace is limited, it is desirable to set the sequence in which the cutting patterns are processed in a way to minimize the maximum number of open stacks around the machine. This problem is known in literature as the minimization of open stacks (MOSP). To find the best sequence of the cutting patterns, we propose an integer programming model, based on interval graphs, that searches for an appropriate edge completion of the given graph of the problem, while defining a suitable coloring of its vertices.