Product line architecture recovery with outlier filtering in software families: the Apo-Games case study

Software product line (SPL) approach has been widely adopted to achieve systematic reuse in families of software products. Despite its benefits, developing an SPL from scratch requires high up-front investment. Because of that, organizations commonly create product variants with opportunistic reuse approaches (e.g., copy-and-paste or clone-and-own). However, maintenance and evolution of a large number of product variants is a challenging task. In this context, a family of products developed opportunistically is a good starting point to adopt SPLs, known as extractive approach for SPL adoption. One of the initial phases of the extractive approach is the recovery and definition of a product line architecture (PLA) based on existing software variants, to support variant derivation and also to allow the customization according to customers’ needs. The problem of defining a PLA from existing system variants is that some variants can become highly unrelated to their predecessors, known as outlier variants. The inclusion of outlier variants in the PLA recovery leads to additional effort and noise in the common structure and complicates architectural decisions. In this work, we present an automatic approach to identify and filter outlier variants during the recovery and definition of PLAs. Our approach identifies the minimum subset of cross-product architectural information for an effective PLA recovery. To evaluate our approach, we focus on real-world variants of the Apo-Games family. We recover a PLA taking as input 34 Apo-Game variants developed by using opportunistic reuse. The results provided evidence that our automatic approach is able to identify and filter outlier variants, allowing to eliminate exclusive packages and classes without removing the whole variant. We consider that the recovered PLA can help domain experts to take informed decisions to support SPL adoption.This research was partially funded by INES 2.0; CNPq grants 465614/2014-0 and 408356/2018-9; and FAPESB grants JCB0060/2016 and BOL2443/201

First record of Polyprion oxygeneios (Perciformes: Polyprionidae) for the southwest Atlantic Ocean and a northernmost range extension.

Copyright © 2004 The Fisheries Society of the British Isles.The hapuka Polyprion oxygeneios (Schneider & Foster) (Fig. 1) is an important deep-water commercial fish species, caught mainly off Australia, New Zealand, Juan Fernandez Archipelago off Chile, the Tristan da Cunha Group of the South Atlantic (Sepúlveda & Pequeño, 1986; May & Maxwell, 1986; Paulin et al., 1989; Paxton et al., 1989; Andrew et al., 1995) and incidentally caught off Chilean Patagonia (Nakamura et al., 1986). The distribution of P. oxygeneios is exclusively southern circum-global, intemperate-cold waters from 28_ to 43_ S (Paxton et al., 1989). Polyprion oxygeneios (Polyprionidae; Nelson, 1994) is mainly a demersal species with a depth range of 50–450 m, occurring over ‘rough’ ground from the central shelf to the upper slope (Paxton et al., 1989). It reaches 150 cm total length (LT) and may weigh up to 100 kg, its juveniles being found near the surface, probably associated with drifting material in a way similar to that recorded for Polyprion americanus (Bloch & Schneider) (Paxton et al., 1989; Saldanha, 1995). This paper reports the first record of P. oxygeneios from the south-west Atlantic

Profiling the circulating miRnome reveals a temporal regulation of the bone injury response

Bone injury healing is an orchestrated process that starts with an inflammatory phase followed by repair and remodelling of the bone defect. The initial inflammation is characterized by local changes in immune cell populations and molecular mediators, including microRNAs (miRNAs). However, the systemic response to bone injury remains largely uncharacterized. Thus, this study aimed to profile the changes in the plasma miRnome after bone injury and determine its biological implications. Methods: A rat model of femoral bone defect was used, and animals were evaluated at days 3 and 14 after injury. Non-operated (NO) and sham operated animals were used as controls. Blood and spleen were collected and peripheral blood mononuclear cells (PBMC) and plasma were separated. Plasma miRnome was determined by RT-qPCR array and bioinformatics Ingenuity pathway analysis (IPA) was performed. Proliferation of bone marrow mesenchymal stem/stromal cells (MSC) was evaluated by Ki67 staining and high-throughput cell imaging. Candidate miRNAs were evaluated in splenocytes by RT-qPCR, and proteins found in the IPA analysis were analysed in splenocytes and PBMC by Western blot. Results: Bone injury resulted in timely controlled changes to the miRNA expression profile in plasma. At day 3 there was a major down-regulation of miRNA levels, which was partially recovered by day 14 post-injury. Interestingly, bone injury led to a significant up-regulation of let-7a, let-7d and miR-21 in plasma and splenocytes at day 14 relative to day 3 after bone injury, but not in sham operated animals. IPA predicted that most miRNAs temporally affected were involved in cellular development, proliferation and movement. MSC proliferation was analysed and found significantly increased in response to plasma of animals days 3 and 14 post-injury, but not from NO animals. Moreover, IPA predicted that miRNA processing proteins Ago2 and Dicer were specifically inhibited at day 3 post-injury, with Ago2 becoming activated at day 14. Protein levels of Ago2 and Dicer in splenocytes were increased at day 14 relative to day 3 post-bone injury and NO animals, while in PBMC, levels were reduced at day 3 (albeit Dicer was not significant) and remained low at day 14. Ephrin receptor B6 followed the same tendency as Ago2 and Dicer, while Smad2/3 was significantly decreased in splenocytes from day 14 relative to NO and day 3 post-bone injury animals. Conclusion: Results show a systemic miRNA response to bone injury that is regulated in time and is related to inflammation resolution and the start of bone repair/regeneration, unravelling candidate miRNAs to be used as biomarkers in the monitoring of healthy bone healing and as therapeutic targets for the development of improved bone regeneration therapies.This work was funded by project NORTE-01-0145-FEDER-000012, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and AO Foundation-Switzerland (project S-15-83S). AMS, MIA, CC and JHT were supported by FCT-Fundação para a Ciência e a Tecnologia, through fellowships SFRH/BD/ 85968/2012, SFRH/BPD/91011/2012, SFRH/BDP/ 87071/2012 and SFRH/BD/112832/2015, respecttively. Work in Dr. Calin's laboratory is supported by National Institutes of Health (NIH/NCATS) grant UH3TR00943-01 through the NIH Common Fund, Office of Strategic Coordination (OSC), the NIH/NCI grant 1R01CA182905-01, a U54 grant-UPR/MDACC Partnership for Excellence in Cancer Research 2016 Pilot Project, a Team DOD (CA160445P1) grant, a Ladies Leukemia League grant, a CLL Moonshot Flagship project, a SINF 2017 grant, and the Estate of C. G. Johnson, J

Description of an optic spine on the sphenoid bone of camels and dromedaries

Objective To describe the presence of an intraorbital cylindrical osseous structure (a spine) in two animal species: camel (Camelus bactrianus) and dromedary (Camelus dromedaries). A homologous osseous structure was previously observed in the large fruit-eating bat (Artibeus lituratus). Procedures The bony anatomy of the orbital cavity was studied and quantified on macerated skulls of 3 camels and 2 dromedaries. Additionally, one macerated skull of a large fruit-eating bat (Artibeus lituratus) was used for comparative purposes. Results The anatomic description of these unique intraorbital spine was made while studying the bony orbit of macerated skulls, and was considered homologous to that of the bat based on the same anatomic position (at the bone bridge that separates the optic canal and the sphenorbital fissure) and similarities in shape. We suggest the name optic spine of the sphenoid bone. Discussion The novel observation of an optic spine on the sphenoid bone in camels and dromedaries (Artiodactyla), when combined with the previous finding of a similar anatomic structure in a bat (Chiroptera) suborder Microchiroptera, may provide further support to the close proximity of these two apparently very distinct animal orders in the phylogenetic tree, and may contribute to the understanding of bat evolution and provide new directions for future research. The function of this osseous spine remains to be investigated, although we hypothesize that the optic spine of the camelids may serve as an attachment site for extraocular muscles

Description of an optic spine on the sphenoid bone of camels and dromedaries

Objective To describe the presence of an intraorbital cylindrical osseous structure (a spine) in two animal species: camel (Camelus bactrianus) and dromedary (Camelus dromedaries). A homologous osseous structure was previously observed in the large fruit-eating bat (Artibeus lituratus). Procedures The bony anatomy of the orbital cavity was studied and quantified on macerated skulls of 3 camels and 2 dromedaries. Additionally, one macerated skull of a large fruit-eating bat (Artibeus lituratus) was used for comparative purposes. Results The anatomic description of these unique intraorbital spine was made while studying the bony orbit of macerated skulls, and was considered homologous to that of the bat based on the same anatomic position (at the bone bridge that separates the optic canal and the sphenorbital fissure) and similarities in shape. We suggest the name optic spine of the sphenoid bone. Discussion The novel observation of an optic spine on the sphenoid bone in camels and dromedaries (Artiodactyla), when combined with the previous finding of a similar anatomic structure in a bat (Chiroptera) suborder Microchiroptera, may provide further support to the close proximity of these two apparently very distinct animal orders in the phylogenetic tree, and may contribute to the understanding of bat evolution and provide new directions for future research. The function of this osseous spine remains to be investigated, although we hypothesize that the optic spine of the camelids may serve as an attachment site for extraocular muscles

Design and protocol of the multimorbidity and mental health cohort study in frailty and aging (MiMiCS-FRAIL):unraveling the clinical and molecular associations between frailty, somatic disease burden and late life depression

BACKGROUND: To explore the mutual relationship between multimorbidity, mental illness and frailty, we have set-up the Multimorbidity and Mental health Cohort Study in FRAILty and Aging (MiMiCS-FRAIL) cohort. At the population level, multimorbidity, frailty and late-life depression are associated with similar adverse outcomes (i.e. falls, disability, hospitalization, death), share the same risk factors, and partly overlap in their clinical presentation. Moreover, these three variables may share a common underlying pathophysiological mechanism like immune-metabolic dysregulation. The overall objectives of MiMiCS-FRAIL are 1) to explore (determinants of) the cross-sectional and longitudinal relationship between multimorbidity, depression, and frailty among non-demented geriatric outpatients; 2) to evaluate molecular levels of senoinflammation as a broad pathophysiological process underlying these conditions; and 3) to examine adverse outcomes of multimorbidity, frailty and depression and their interconnectedness. METHODS: MiMiCS-FRAIL is an ongoing observational cohort study of geriatric outpatients in Brazil, with an extensive baseline assessment and yearly follow-up assessments. Each assessment includes a comprehensive geriatric assessment to identify multimorbidity and geriatric syndromes, a structured psychiatric diagnostic interview and administration of the PHQ-9 to measure depression, and several frailty measures (FRAIL, Physical Phenotype criteria, 36-item Frailty Index). Fasten blood samples are collected at baseline to assess circulating inflammatory and anti-inflammatory cytokines, leukocytes' subpopulations, and to perform immune-metabolic-paired miRome analyses. The primary outcome is death and secondary outcomes are the number of falls, hospital admissions, functional ability, well-being, and dementia. Assuming a 5-year mortality rate between 25 and 40% and a hazard rate varying between 1.6 and 2.3 for the primary determinants require a sample size between 136 and 711 patients to detect a statistically significant effect with a power of 80% (beta = 0.2), an alpha of 5% (0.05), and an R2 between the predictor (death) and all covariates of 0.20. Local ethical board approved this study. DISCUSSION: Frailty might be hypothesized as a final common pathway by which many clinical conditions like depression and chronic diseases (multimorbidity) culminate in many adverse effects. The MiMiCS-FRAIL cohort will help us to understand the interrelationship between these variables, from a clinical perspective as well as their underlying molecular signature

Nutritional Status and Adverse Outcomes in Older Depressed Inpatients:A Prospective Study

OBJECTIVES: Significant weight loss and/or loss of appetite is a criterion of a depressive episode. While malnutrition is associated with many adverse health outcomes, the impact of malnutrition in late-life depression has hardly been examined. The present study aims to (1) evaluate the prevalence of malnutrition in depressed older inpatients, and (2) whether and which indices of malnutrition predict adverse health outcomes in late-life depression. DESIGN: A prospective study at 6 months follow-up. SETTING: A University-based psychiatric hospital. PARTICIPANTS: 105 older adults (psychiatric inpatients suffering from unipolar MDD). MEASUREMENTS: Participants were evaluated according the Mini Nutritional Assessment (MNA) and anthropometric measures to assess their nutritional status. Multiple regression analyses were used to evaluate the association between the MNA score as well as anthropometric measures with either falls or rehospitalization for any reason. RESULTS: Based on the MNA score, 78 (74.3%) patients were at risk of malnutrition and 13 (12.4%) actually presented malnutrition. Malnutrition was associated with a higher age, frailty, lower body mass index, and smaller calf circumference. During follow-up, 21 (20%) patients fell, 27 (25.7%) were rehospitalized, and 3 died (2.9%). The MNA score was associated with adverse health outcomes, but a low calf circumference predicted falling (OR 4.93 [95% CI: 1.42-17.2], p=.012) and a higher calf circumference rehospitalization (OR 1.17 [95% CI: 1.01-1.35], p=.032). CONCLUSION: Malnutrition is prevalent in older depressed inpatients. In contrast to subjective proxies for malnutrition, which are common in depression, only objective measures of malnutrition predict adverse health outcomes such as falls and rehospitalization

The crown pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species' unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.A.G.-d.-S. was funded by the Portuguese Foundation for Science and Technology (FCT) under the grants SFRH/BD/137935/2018, EF (CEECIND/00627/2017) and MLL (2020.03608.CEECIND). This research was developed under ConBiomics: the missing approach for the Conservation of freshwater Bivalves Project No. NORTE-01-0145-FEDER- 030286, co-financed by COMPETE 2020, Portugal 2020 and the European Union through the ERDF, and by FCT through national funds. Additional strategic funding was provided by FCT UIDB/04423/2020 and UIDP/04423/2020. Authors’ interaction and writing of the article was promoted and facilitated by the COST Action CA18239: CONFREMU—Conservation of freshwater mussels: a pan- European approach.info:eu-repo/semantics/publishedVersio

Quantitative analysis of cardiac lesions in chronic canine chagasic cardiomyopathy.

Lesions observed in chronic chagasic cardiopathy frequently produce electrocardiographic alterations and affect cardiac function. Through a computerized morphometrical analysis we quantified the areas occupied by cardiac muscle, connective and adipose tissues in the right atrium of dogs experimentally infected with Trypanosoma cruzi. All of the infected dogs showed chronic myocarditis with variable reduction levels of cardiac muscle, fibrosis and adipose tissue replacement. In the atrial myocardium of dogs infected with Be78 and Be62 cardiac muscle represented 34 and 50%, fibrosis 28 and 32% and adipose tissue 38 and 18%, respectively. The fibrosis observed was both diffuse and focal and mostly intrafascicular, either partially or completely interrupting the path of muscle bundles. Such histological alterations probably contributed to the appearance of electrocardiographic disturbances verified in 10 out 11 dogs which are also common in human chronic chagasic cardiopathy. Fibrosis was the most important microscopic occurrence found since it produces rearrangements of collagen fibers in relation to myocardiocytes which causes changes in anatomical physiognomy and mechanical behavior of the myocardium. These abnormalities can contribute to the appearance of cardiac malfunction, arrhythmias and congestive cardiac insufficiency as observed in two of the analyzed dogs. Strain Be78 caused destruction of atrial cardiac muscle higher than that induced by strain Be62