Process algebra modelling styles for biomolecular processes

We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed

A criterion for separating process calculi

We introduce a new criterion, replacement freeness, to discern the relative expressiveness of process calculi. Intuitively, a calculus is strongly replacement free if replacing, within an enclosing context, a process that cannot perform any visible action by an arbitrary process never inhibits the capability of the resulting process to perform a visible action. We prove that there exists no compositional and interaction sensitive encoding of a not strongly replacement free calculus into any strongly replacement free one. We then define a weaker version of replacement freeness, by only considering replacement of closed processes, and prove that, if we additionally require the encoding to preserve name independence, it is not even possible to encode a non replacement free calculus into a weakly replacement free one. As a consequence of our encodability results, we get that many calculi equipped with priority are not replacement free and hence are not encodable into mainstream calculi like CCS and pi-calculus, that instead are strongly replacement free. We also prove that variants of pi-calculus with match among names, pattern matching or polyadic synchronization are only weakly replacement free, hence they are separated both from process calculi with priority and from mainstream calculi.Comment: In Proceedings EXPRESS'10, arXiv:1011.601

The use of FDG-PET in the initial staging of 142 patients with follicular lymphoma: a retrospective study from the FOLL05 randomized trial of the Fondazione Italiana Linfomi

BACKGROUND: The role of [(18)F] fluorodeoxyglucose (FDG)-positron emission tomography (PET) in follicular lymphoma (FL) staging is not yet determined. PATIENTS AND METHODS: The aim of the present study was to investigate the role of PET in the initial staging of FL patients enrolled in the FOLL05-phase-III trial that compared first-line regimens (R-CVP, R-CHOP and R-FM). Patients should have undergone conventional staging and have available PET baseline to be included. RESULTS: A total of 142 patients were analysed. PET identified a higher number of nodal areas in 32% (46 of 142) of patients and more extranodal (EN) sites than computed tomography (CT) scan. Also, the Follicular Lymphoma International Prognostic Index (FLIPI) score increased in 18% (26 of 142) and decreased in 6% (9 of 142) of patients. Overall, the impact of PET on modifying the stage was highest in patients with limited stage. Actually, 62% (15 of 24) of cases with limited disease were upstaged with PET. CONCLUSIONS: The inclusion of PET among staging procedures makes the evaluation of patients with FL more accurate and has the potential to modify therapy decision and prognosis in a moderate proportion of patients. Further prospective clinical trials on FL should incorporate PET at different moments, and the therapeutic criteria to start therapy should be re-visited in the views of this new tool

The ANTARES Collaboration: Contributions to ICRC 2017 Part II: The multi-messenger program

Papers on the ANTARES multi-messenger program, prepared for the 35th International Cosmic Ray Conference (ICRC 2017, Busan, South Korea) by the ANTARES Collaboratio

KM3NeT and ANTARES status and results

The latest results from the ANTARES neutrino telescope will be presented regarding the search for a diffuse high energy neutrino flux, the analysis to identify astrophysical neutrino point sources and the various searches for multimessenger coincidences between neutrinos and other cosmic probes, like photons or gravitational waves. KM3NeT, the new generation of underwater neutrino telescopes, is currently under construction in the Mediterranean sea. Thanks to its large size and improved detection capabilities, KM3NeT will open new perspectives in neutrino astronom

The ANTARES Collaboration: Contributions to ICRC 2017 Part I: Neutrino astronomy (diffuse fluxes and point sources)

Papers on neutrino astronomy (diffuse fluxes and point sources, prepared for the 35th International Cosmic Ray Conference (ICRC 2017, Busan, South Korea) by the ANTARES Collaboratio

The prognostic role of post-induction FDG-PET in patients with follicular lymphoma: a subset analysis from the FOLL05 trial of the Fondazione Italiana Linfomi (FIL)

BACKGROUND: [18F]fluorodeoxyglucose-positron emission tomography (PET) is emerging as a strong diagnostic and prognostic tool in follicular lymphoma (FL) patients. PATIENTS AND METHODS: In a subset analysis of the FOLL05 trial (NCT00774826), we investigated the prognostic role of post-induction PET (PI-PET) scan. Patients were eligible to this study if they had a PI-PET scan carried out within 3 months from the end of induction immunochemotherapy. Progression-free survival (PFS) was the primary study end point. RESULTS: A total of 202 patients were eligible and analysed for this study. The median age was 55 years (range 33-75). Overall, PI-PET was defined as positive in 49 (24%) patients. Conventional response assessment with CT scan was substantially modified by PET: 15% (22/145) of patients considered as having a complete response (CR) after CT were considered as having partial response (PR) after PI-PET and 53% (30/57) patients considered as having a PR after CT were considered as a CR after PI-PET. With a median follow-up of 34 months, the 3-year PFS was 66% and 35%, respectively, for patients with negative and positive PI-PET (P<0.001). At multivariate analysis, PI-PET (hazard ratio 2.57, 95% confidence interval 1.52-4.34, P<0.001) was independent of conventional response, FLIPI and treatment arm. Also, the prognostic role of PI-PET was maintained within each FLIPI risk group. CONCLUSIONS: In FL patients, PI-PET substantially modifies response assessment and is strongly predictive for the risk of progression. PET should be considered in further updates of response criteria

The ANTARES Collaboration: Contributions to ICRC 2017 Part III: Searches for dark matter and exotics, neutrino oscillations and detector calibration

Papers on the searches for dark matter and exotics, neutrino oscillations and detector calibration, prepared for the 35th International Cosmic Ray Conference (ICRC 2017, Busan, South Korea) by the ANTARES Collaboratio

Concentration of apricot juice using complex membrane technology

In this study, pressed apricot (Prunus armeniaca L.) juice was concentrated using complex membrane technology with different module combinations: UF-RO-OD, UF-RO-MD, UF-NF-OD and UF-NF-MD. In case of the best combination a cross-flow polyethylene ultrafiltration membrane (UF) was applied for clarification, after which preconcentration was done using reverse osmosis (RO) with a polyamide membrane, and the final concentration was completed by osmotic distillation (OD) using a polypropylene module. The UF-RO-OD procedure resulted in a final concentrate with a 65-70 °Brix dry solid content and an excellent quality juice with high polyphenol content and high antioxidant capacity.Nanofiltration (NF) and membrane distillation (MD) were not proper economic solutions.The influence of certain operation parameters was examined experimentally. Temperatures of UF and RO were: 25, 30, and 35 °C, and of OD 25 °C. Recycle flow rates were: UF: 1, 1.5, and 2 m3 h−1; RO: 200, 400, and 600 l h−1; OD: 20, 30 and 40 l h−1. The flow rates in the module were expressed by the Reynolds number, as well. Based on preliminary experiments, the transmembrane pressures of UF and RO filtration were 4 bar and 50 bar, respectively. Each experimental run was performed three times. The following optimal operation parameters provided the lowest total cost: UF: 35 °C, 2 m3 h−1, 4 bar; RO: 35 °C, 600 l h−1, 50 bar; OD: 20, 30 and 40 l h−1; temperature 25 °C.In addition, experiments were performed for apricot juice concentration by evaporation, which technique is widely applied in the industry using vacuum and low temperature.For description the UF filtration, a dynamic model and regression by SPSS 14.0 statistics software were applied

Inertial bioluminescence rhythms at the Capo Passero (KM3NeT-Italia) site, Central Mediterranean Sea

In the deep sea, the sense of time is dependent on geophysical fluctuations, such as internal tides and atmospheric-related inertial currents, rather than day-night rhythms. Deep-sea neutrino telescopes instrumented with light detecting Photo-Multiplier Tubes (PMT) can be used to describe the synchronization of bioluminescent activity of abyssopelagic organisms with hydrodynamic cycles. PMT readings at 8 different depths (from 3069 to 3349 m) of the NEMO Phase 2 prototype, deployed offshore Capo Passero (Sicily) at the KM3NeT-Italia site, were used to characterize rhythmic bioluminescence patterns in June 2013, in response to water mass movements. We found a significant (p < 0.05) 20.5 h periodicity in the bioluminescence signal, corresponding to inertial fluctuations. Waveform and Fourier analyses of PMT data and tower orientation were carried out to identify phases (i.e. the timing of peaks) by subdividing time series on the length of detected inertial periodicity. A phase overlap between rhythms and cycles suggests a mechanical stimulation of bioluminescence, as organisms carried by currents collide with the telescope infrastructure, resulting in the emission of light. A bathymetric shift in PMT phases indicated that organisms travelled in discontinuous deep-sea undular vortices consisting of chains of inertially pulsating mesoscale cyclones/anticyclones, which to date remain poorly known