A Model for Configuration Management of Open Software Systems

The article proposes a model for the configuration management of open systems. The model aims at validation of configurations against given specifications. An extension of decision graphs is proposed to express specifications. The proposed model can be used by software developers to validate their own configurations across different versions of the components, or to validate configurations that include components by third parties. The model can also be used by end-users to validate compatibility among different configurations of the same application. The proposed model is first discussed in some application scenarios and then formally defined. Moreover, a type discipline is given to formally define validation of a configuration against a system specificationComment: 13 page

Thinking digital libraries for preservation as digital cultural heritage: by R to R4 facet of FAIR principles

The Art. 2 of the UE Council conclusions of 21 May 2014 on cultural heritage as a strategic resource for a sustainable Europe (2014/C 183/08) states: “Cultural heritage consists of the resources inherited from the past in all forms and aspects—tangible, intangible and digital (born digital and digitized), including monuments, sites, landscapes, skills, practices, knowledge and expressions of human creativity, as well as collections conserved and managed by public and private bodies such as museums, libraries and archives”. Starting from this assumption, we have to rethink digital and digitization as social and cultural expressions of the contemporary age. We need to rethink digital libraries produced by digitization as cultural entities and no longer as mere dataset for enhancing fruition of cultural heritage, by defining clear and homogeneous criteria to validate and certify them as memory and sources of knowledge for future generations. By expanding R: Re-usable of the FAIR Guiding Principles for scientific data management and stewardship into R4: Re-usable, Relevant, Reliable and Resilient, this paper aims to propose a more reflective approach to creation of descriptive metadata for managing digital resource of cultural heritage, which can guarantee their long term preservation

A Process Calculus for Molecular Interaction Maps

We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are inspired by the reaction symbols used in Molecular Interaction Maps (MIMs), a diagrammatic notation used by biologists. Models of the calculus can be easily derived from MIM diagrams, for which an unambiguous and executable interpretation is thus obtained. We give a formal definition of the syntax and semantics of the MIM calculus, and we study properties of the formalism. A case study is also presented to show the use of the calculus for modeling biomolecular networks.Comment: 15 pages; 8 figures; To be published on EPTCS, proceedings of MeCBIC 200

Uncovering a functional link between CozE proteins and lipoteichoic acid biosynthesis in Staphylococcus aureus

Staphylococcus aureus is a common and successful human pathogen. Infections caused by S aureus have become an urgent challenge in nosocomial and community settings, due to their multiple virulence mechanisms and ability to rapidly evolve resistance to novel antibiotics. Development of new therapeutic approaches to counteract the emergence of (multi) antibiotic resistant S. aureus strains is critical. Antibiotics that target bacterial cell division and teichoic acid biosynthesis has garnered interest in recent years. However, staphylococcal cell division is still not fully understood. In a previous study, the so-called CozE proteins found in S. aureus, CozEa and CozEb, have been demonstrated to play an important role in proper cell division, but the molecular mode of action by which the CozE proteins work are unknown. In this work, the cellular functions of the CozE proteins were investigated further. Construction and characterisation of single and double cozE mutants confirmed that cozEa and cozEb constitute a synthetic lethal gene pair in S. aureus. Based on these results, we hypothesised that CozEa and CozEb possibly had a link to biosynthesis of lipoteichoic acids (LTAs) in S. aureus. By constructing a panel of mutant strains with knockdown of the cozE genes and LTA synthesis/modification genes, followed by growth assays, phase contrast- and transmission electron microscopy, we uncovered that two LTA biosynthesis genes (ugtP and ltaA) have pairwise synthetic genetic interactions with the cozE genes. Knockdown of cozEa and cozEb together is detrimental to wild-type S. aureus cells, and knockdown of these genes in a ΔugtP background perpetuated the cell lysis phenotype observed in wild-type background. On the other hand, knockdown of both cozE genes in ΔltaA background did remarkably not result in any apparent alterations to their growth rate or morphology. Normal cell growth and cell division were re-established in these ΔltaA mutant strains. Anti-LTA immunoblot assays with cell lysates from the different mutants revealed that CozEb play a unique role in controlling LTA polymer length. S. aureus ΔcozEb mutants displayed abnormally long LTA polymers, reminiscent of LTA found in mutants affecting LTA glycolipid anchor synthesis (ΔugtP and ΔltaA). Subcellular localisation analysis by fluorescence microscopy of these proteins were also performed. Together, the results obtained in this work clearly demonstrates a functional link between CozE proteins and LTA biosynthesis in S. aureus, and the CozE proteins are predicted to perform this function upstream of either UgtP or LtaA.Staphylococcus aureus er en vanlig og vellykket human patogen. Infeksjoner forårsaket av S. aureus er en økende utfordring, både i helseinstitusjoner og utenfor, på grunn av deres mangfoldige virulensmekanismer og evne til å utvikle motstandsdyktighet mot nye antibiotika. Utvikling av nye behandlingsmetoder for å motvirke fremveksten av (multi)resistente S. aureus-stammer er svært viktig. Forskere har vist økt interesse for antibiotika som angriper bakteriell celledeling og biosyntese av teikoinsyre de siste årene. Celledelingen hos stafylokokker er imidlertid ikke fullstendig forstått enda. I en tidligere studie har de såkalte CozE-proteinene i S. aureus, CozEa og CozEb, vist seg å spille en viktig rolle i celledeling, men den molekylære virkningsmåten til disse proteinene er ukjent. I dette arbeidet ble funksjonene til CozE-proteinene undersøkt nærmere. Konstruksjon og karakterisering av enkle og doble cozE-mutanter, bekreftet at cozEa og cozEb utgjør et syntetisk letalt genpar i S. aureus. Basert på disse resultatene, formulerte vi en hypotese om at CozEa og CozEb muligens hadde en kobling til biosyntese av lipoteikoinsyrer (LTAer) i S. aureus. Ved å konstruere et panel av mutanter med «knock-down» av cozE-genene og LTAsyntese/modifikasjonsgener, etterfulgt av vekstanalyser, fasekontrast- og transmisjonselektronmikroskopi, avdekket vi at to LTA-syntesegener (ugtP og ltaA) har syntetiske genetiske interaksjoner med cozE-genene. «Knock-down» av cozEa og cozEb sammen er svært skadelig for S. aureus celler, og «knock-down» av disse genene i en ΔugtP bakgrunn forsterket cellelysis-fenotypen observert i villtype bakgrunnen. Derimot «knockdown» av begge cozE-genene i ΔltaA bakgrunn resulterte tilsynelatende ikke i endringer i vekst eller morfologi. Normal cellevekst og -deling ble gjenopprettet i disse ΔltaA mutantene. Anti-LTA immunoblot-analyser med cellelysat fra de forskjellige mutantene avslørte i tillegg at CozEb spiller en unik rolle når det kommer til å kontrollere lengden på LTA-polymerer. S. aureus ΔcozEb-mutanter produserte unormalt lange LTA-polymerer, som minner om LTAene man finner i mutanter med forstyrret LTA glykolipidanker-syntese (ΔugtP og ΔltaA). Subcellulære lokaliseringsanalyser, ved bruk av fluorescensmikroskopi, ble også foretatt med disse proteinene. I sum viser resultatene i dette arbeidet tydelig tilstedeværelsen av en funksjonell kobling mellom CozE-proteiner og LTA-biosyntese i S. aureus, og CozEproteinene ser ut til å utføre denne funksjonen oppstrøms for enten UgtP eller LtaA.M-BIOTE

Modelling the Dynamics of an Aedes albopictus Population

We present a methodology for modelling population dynamics with formal means of computer science. This allows unambiguous description of systems and application of analysis tools such as simulators and model checkers. In particular, the dynamics of a population of Aedes albopictus (a species of mosquito) and its modelling with the Stochastic Calculus of Looping Sequences (Stochastic CLS) are considered. The use of Stochastic CLS to model population dynamics requires an extension which allows environmental events (such as changes in the temperature and rainfalls) to be taken into account. A simulator for the constructed model is developed via translation into the specification language Maude, and used to compare the dynamics obtained from the model with real data.Comment: In Proceedings AMCA-POP 2010, arXiv:1008.314

Ontology of backgrounds in distance learning. Correlations between virtual backgrounds and educational relationship

The paper presents research focused on virtual backgrounds in distance learning (in Italian: DaD) during the first lockdown due to the COVID-19 pandemic by March up to June 2020, and their impact on educational relationships. The research is based on the analysis of the answers that 1283 teachers and 1018 students gave participating in two online surveys. According to data inferred from the analysis, during the online lessons, in most cases, the teachers and students chose a specific setting background, and their choice had a significant impact on attention, motivation, and empathic involvement. So much so, the teachers changed their virtual settings to obtain better results. But the motivations for changing the backgrounds have been very different between teacher and student: 50.6% of teachers changed their background to improve the relationship with students, 44.5% to make their role more authoritative, while 70.9% of students changed the background to fully feel comfortable in watching themselves on screen. Furthermore, the survey asked teachers to choose and explain virtual backgrounds that they think could be used for improving face-to-face learning; students, to choose virtual image backgrounds that they would like behind the teachers in the classroom. More than 1,000 background images with descriptive referred captions were uploaded, which we have classified into five ontological categories. Both in the quantitative and qualitative information inferred by the analysis of such data, real different subcultures between teachers and students bring out. Research in this sense has gathered valuable information on the importance of the visual context even in face-to-face teaching. The research was also an opportunity to investigate the level of the teachers’ and students’ visual culture. The conclusions lead us to question the actual value of virtual backgrounds also in the perspective of Integrated Teaching (in Italian: DID): can they be considered only part of the setting or something more to improve the educational relationship

Fine-tuning anti-tumor immunotherapies via stochastic simulations

Background: Anti-tumor therapies aim at reducing to zero the number of tumor cells in a host within their end or, at least, aim at leaving the patient with a sufficiently small number of tumor cells so that the residual tumor can be eradicated by the immune system. Besides severe side-effects, a key problem of such therapies is finding a suitable scheduling of their administration to the patients. In this paper we study the effect of varying therapy-related parameters on the final outcome of the interplay between a tumor and the immune system.Results: This work generalizes our previous study on hybrid models of such an interplay where interleukins are modeled as a continuous variable, and the tumor and the immune system as a discrete-state continuous-time stochastic process. The hybrid model we use is obtained by modifying the corresponding deterministic model, originally proposed by Kirschner and Panetta. We consider Adoptive Cellular Immunotherapies and Interleukin-based therapies, as well as their combination. By asymptotic and transitory analyses of the corresponding deterministic model we find conditions guaranteeing tumor eradication, and we tune the parameters of the hybrid model accordingly. We then perform stochastic simulations of the hybrid model under various therapeutic settings: constant, piece-wise constant or impulsive infusion and daily or weekly delivery schedules.Conclusions: Results suggest that, in some cases, the delivery schedule may deeply impact on the therapy-induced tumor eradication time. Indeed, our model suggests that Interleukin-based therapies may not be effective for every patient, and that the piece-wise constant is the most effective delivery to stimulate the immune-response. For Adoptive Cellular Immunotherapies a metronomic delivery seems more effective, as it happens for other anti-angiogenesis therapies and chemotherapies, and the impulsive delivery seems more effective than the piece-wise constant. The expected synergistic effects have been observed when the therapies are combined. \ua9 2012 Caravagna et al.; licensee BioMed Central Ltd

A mathematical model for the study of the impact of small commercial fishing on the biodiversity of artificial reefs

Artificial reefs are an essential tool for restoring and maintaining biodiversity in degraded marine areas. They make it possible to prevent trawling and, at the same time, create an environment suitable for restocking of several species of fishes. These submerged structures are compatible with small commercial fishing that could have a negative impact on the biodiversity in the artificial reef environment. Fishing policies should be considered in order to make fishing activities sustainable. We propose a mathematical model of artificial reefs environments. The model can be used to study the impact of small commercial fishing on the biodiversity of an artificial reef and to predict the effects of different fishing policies. The model is developed on the basis of observations made in two protected marine areas located in central Italy where artificial reefs have been realized

On the Interpretation of Delays in Delay Stochastic Simulation of Biological Systems

Delays in biological systems may be used to model events for which the underlying dynamics cannot be precisely observed. Mathematical modeling of biological systems with delays is usually based on Delay Differential Equations (DDEs), a kind of differential equations in which the derivative of the unknown function at a certain time is given in terms of the values of the function at previous times. In the literature, delay stochastic simulation algorithms have been proposed. These algorithms follow a "delay as duration" approach, namely they are based on an interpretation of a delay as the elapsing time between the start and the termination of a chemical reaction. This interpretation is not suitable for some classes of biological systems in which species involved in a delayed interaction can be involved at the same time in other interactions. We show on a DDE model of tumor growth that the delay as duration approach for stochastic simulation is not precise, and we propose a simulation algorithm based on a ``purely delayed'' interpretation of delays which provides better results on the considered model