Using contexts to extract models from code

Behaviour models facilitate the understanding and analysis of software systems by providing an abstract view of their behaviours and also by enabling the use of validation and verification techniques to detect errors. However, depending on the size and complexity of these systems, constructing models may not be a trivial task, even for experienced developers. Model extraction techniques can automatically obtain models from existing code, thus reducing the effort and expertise required of engineers and helping avoid errors often present in manually constructed models. Existing approaches for model extraction often fail to produce faithful models, either because they only consider static information, which may include infeasible behaviours, or because they are based only on dynamic information, thus relying on observed executions, which usually results in incomplete models. This paper describes a model extraction approach based on the concept of contexts, which are abstractions of concrete states of a program, combining static and dynamic information. Contexts merge some of the advantages of using either type of information and, by their combination, can overcome some of their problems. The approach is partially implemented by a tool called LTS Extractor, which translates information collected from execution traces produced by instrumented Java code to labelled transition systems (LTS), which can be analysed in an existing verification tool. Results from case studies are presented and discussed, showing that, considering a certain level of abstraction and a set of execution traces, the produced models are correct descriptions of the programs from which they were extracted. Thus, they can be used for a variety of analyses, such as program understanding, validation, verification, and evolution

New host plant records for Oenomaus ortygnus (Cramer) (Lepidoptera: Lycaenidae) in Mexico

This is the first record of Oenomaus ortygnus (Cramer) damaging fruits of ilama (Annona diversifolia) and extends the butterfly distribution for three states in Mexico.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Pró-Reitoria de Pesquisa of the Universidade de São Paulo (USP

Importância da Deformação Longitudinal na Deteção da Cardiotoxicidade Induzida por Quimioterapia e na Identificação de Padrões Específicos de Afetação Segmentar

INTRODUCTION: Serial echocardiographic assessment of left ventricular ejection fraction (LVEF) is the gold standard in screening for chemotherapy-induced cardiotoxicity (CIC). Measurement of myocardial deformation using speckle tracking enables more detailed assessment of myocardial contractility. The aim of this study was to determine the relationship between global and regional longitudinal strain and CIC. METHODS: This was a prospective study of 158 breast cancer patients undergoing chemotherapy with anthracyclines with or without adjuvant trastuzumab who underwent serial monitoring by transthoracic echocardiography with assessment of myocardial deformation. CIC was defined as a decrease in LVEF to <53%. Global longitudinal strain (GLS) was estimated using EchoPAC BT12 software on a GE Vivid E9 cardiac ultrasound system. Patients were classified according to the 2015 ASE/EACVI criteria as having impaired myocardial deformation when GLS was reduced (less negative), with a cutoff of -18%. RESULTS: During a mean follow-up of 5.4 months (1-48 months), the incidence of CIC was 18.9%. A decrease in GLS was observed during follow-up for the entire cohort (baseline GLS -20.1±3.5% vs. -18.7±3.4% at last follow-up assessment, p=0.001). A total of 97 patients (61.4%) were observed to have impaired myocardial deformation (GLS ≥18%) at some point during follow-up. This decrease was more significant in patients who eventually developed CIC (GLS -17.2±2.5%, p=0.02). On analysis of regional strain, impaired contractility was observed in the septal (6 out of 6) and anterior (2 out of 3) segments. Multivariate logistic regression showed that patients who developed impaired longitudinal strain had a 4.9-fold increased risk of developing CIC (odds ratio 4.88, confidence interval 1.32-18.0, p=0.017). CONCLUSIONS: Worsening of myocardial deformation as assessed by speckle tracking is common in breast cancer patients undergoing chemotherapy, with predominantly septal and anterior wall involvement. Impaired myocardial deformation was independently associated with increased incidence of CIC.info:eu-repo/semantics/publishedVersio

Successful treatment of feline leishmaniosis using an association of allopurinol and N-methyl-glucamine antimoniate

This work describes the diagnosis and successful treatment of a 2-year-old domestic cat infected with Leishmania species and presenting fever, and ulcerative and nodular skin lesions after being treated for pyodermatitis for 1 year without clinical improvement. After anamnesis the cat was submitted to a complete clinical examination. Blood was collected for determination of haematological and biochemical parameters, detection of feline leukaemia virus (FeLV), feline immunodeficiency virus (FIV), feline coronavirus (FCoV) and Leishmania amastigotes. Fine-needle aspiration puncture from the skin nodules was also performed. After definitive diagnosis the animal was treated and followed up over a 2 year period. The animal tested negative for FIV-specific antibodies, FeLV antigen and feline coronavirus RNA. Leishmania amastigotes in the skin nodules were confirmed by cytology and molecular diagnosis. Treatment was initiated with allopurinol, resulting in a slight clinical improvement. Thus, N-methyl-glucamine antimoniate was added and administered for 30 days, with complete closure of the ulcerative lesions in the hindlimbs requiring a surgical approach. Close monitoring of the patient in the following 24 months indicated that combined therapy was safe and clinical cure was achieved without further relapses or side effects.publishersversionpublishe

Epidemiologic aspects of the malaria transmission cycle in an area of very low incidence in Brazil

BACKGROUND: Extra-Amazonian autochthonous Plasmodium vivax infections have been reported in mountainous regions surrounded by the Atlantic Forest in Espírito Santo state, Brazil. METHODS: Sixty-five patients and 1,777 residents were surveyed between April 2001 and March 2004. Laboratory methods included thin and thick smears, multiplex-PCR, immunofluorescent assay (IFA) against P. vivax and Plasmodium malariae crude blood-stage antigens and enzyme-linked immunosorbent assay (ELISA) for antibodies against the P. vivax-complex (P. vivax and variants) and P. malariae/Plasmodium brasilianum circumsporozoite-protein (CSP) antigens. RESULTS: Average patient age was 35.1 years. Most (78.5%) were males; 64.6% lived in rural areas; 35.4% were farmers; and 12.3% students. There was no relevant history of travel. Ninety-five per cent of the patients were experiencing their first episode of malaria. Laboratory data from 51 patients were consistent with P. vivax infection, which was determined by thin smear. Of these samples, 48 were assayed by multiplex-PCR. Forty-five were positive for P. vivax, confirming the parasitological results, while P. malariae was detected in one sample and two gave negative results. Fifty percent of the 50 patients tested had IgG antibodies against the P. vivax-complex or P. malariae CSP as determined by ELISA. The percentages of residents with IgM and IgG antibodies detected by IFA for P. malariae, P. vivax and Plasmodium falciparum who did not complain of malaria symptoms at the time blood was collected were 30.1% and 56.5%, 6.2% and 37.7%, and 13.5% and 13%, respectively. The same sera that reacted to P. vivax also reacted to P. malariae. The following numbers of samples were positive in multiplex-PCR: 23 for P. vivax; 15 for P. malariae; 9 for P. falciparum and only one for P. falciparum and P. malariae. All thin and thick smears were negative. ELISA against CSP antigens was positive in 25.4%, 6.3%, 10.7% and 15.1% of the samples tested for "classical" P. vivax (VK210), VK247, P. vivax-like and P. malariae, respectively. Anopheline captures in the transmission area revealed only zoophilic and exophilic species. CONCLUSION: The low incidence of malaria cases, the finding of asymptomatic inhabitants and the geographic separation of patients allied to serological and molecular results raise the possibility of the existence of a simian reservoir in these areas

Three-Dimensional Speckle-Tracking Echocardiography for the Global and Regional Assessments of Left Ventricle Myocardial Deformation in Breast Cancer Patients Treated with Anthracyclines

Background: Assessment of 2D/3D left ventricular ejection fraction (LVEF) and 2D global longitudinal strain (GLS) is the gold standard for diagnosing cancer therapeutics-related cardiac dysfunction (CTRCD). Although 3D speckle-tracking echocardiography (STE) has several advantages, it is not used in this setting. Methods: 105 breast cancer patients who underwent serial echocardiographic assessment during anthracycline therapy were included. STE was used to estimate 2D GLS, 3D GLS, 3D global circumferential strain (GCS), 3D global radial strain (GRS), and 3D global area strain (GAS). CTRCD was defined as an absolute decrease in 2D/3D LVEF > 10% to a value 15%. Results: 24 patients developed CTRCD. There was a significant worsening of all 3D strain parameters during chemotherapy. 3D strain regional analysis showed impaired contractility in the anterior, inferior, and septal walls. Variations of 3D GRS and 3D GCS were associated with a higher incidence of CTRCD and the variation of 3D GRS was an independent predictor of CTRCD. Variations of 3D GCS and 3D GRS had a good discrimination for predicting CTRCD, with optimal cutoff values of - 34.2% for 3D GCS and - 34.4% for 3D GRS. These variations were observed 45 and 23 days before the diagnosis of CTRCD, respectively. Conclusion: Variations of 3D strain parameters were predictive of and preceded CTRCD, and thus have added value over currently recommended 2D/3D LVEF and 2D GLS. Routine application of this technique should be considered to offer targeted monitoring and timely initiation of cardioprotective treatment.info:eu-repo/semantics/publishedVersio

Helminth infections and gut microbiota - a feline perspective

$\textbf{BACKGROUND}$: Investigations of the relationships between the gut microbiota and gastrointestinal parasitic nematodes are attracting growing interest by the scientific community, driven by the need to better understand the contribution of parasite-associated changes in the composition of the gut flora to both host malnutrition and immune modulation. These studies have however been carried out mainly in humans and experimental animals, while knowledge of the make-up of the gut commensal flora in presence or absence of infection by parasitic nematodes in domestic animals is limited. In this study, we investigate the qualitative and quantitative impact that infections by a widespread parasite of cats (i.e. $\textit{Toxocara cati}$) exert on the gut microbiota of feline hosts. $\textbf{METHODS}$: The faecal microbiota of cats with patent infection by $\textit{T. cati}$ (= $\textit{Tc+}$), as well as that of negative controls (= $\textit{Tc-}$) was examined via high-throughput sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene, followed by bioinformatics and biostatistical analyses of sequence data. $\textbf{RESULTS}$: A total of 2,325,366 useable high-quality sequences were generated from the faecal samples analysed in this study and subjected to further bioinformatics analyses, which led to the identification of 128 OTUs and nine bacterial phyla, respectively. The phylum Firmicutes was predominant in all samples analysed (mean of 53.0%), followed by the phyla Proteobacteria (13.8%), Actinobacteria (13.7%) and Bacteroidetes (10.1%). Among others, bacteria of the order Lactobacillales, the family $\textit{Enterococcaceae}$ and genera $\textit{Enterococcus}$ and $\textit{Dorea}$ showed a trend towards increased abundance in $\textit{Tc+}$ compared with $\textit{Tc-}$ samples, while no significant differences in OTU richness and diversity were recorded between $\textit{Tc+}$ and $\textit{Tc-}$ samples ($\textit{P}$=0.485 and $\textit{P}$=0.581, respectively). However, Canonical Correlation and Redundancy Analyses were able to separate samples by infection status ($\textit{P}$=0.030 and $\textit{P}$=0.015, respectively), which suggests a correlation between the latter and the composition of the feline faecal microbiota. $\textbf{CONCLUSIONS}$: In spite of the relatively small number of samples analysed, subtle differences in the composition of the gut microbiota of $\textit{Tc+}$ vs $\textit{Tc-}$ cats could be identified, some of which in accordance with current data from humans and laboratory animal hosts. Nevertheless, the findings from this study contribute valuable knowledge to the yet little explored area of parasite-microbiota interactions in domestic animals.This work was supported by Merial Pty Ltd (CC, AG, DO) and ESCCAP UK & Ireland (CC). CC is supported by grants from the Isaac Newton Trust/Wellcome Trust ISSF/University of Cambridge and the Royal Society. TPJ is supported by scholarships from the Biotechnology and Biological Sciences Research Council (BBSRC) Doctoral Training Partnerships program