Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.

Vibrational spectroscopic and electrochemical investigations of multi-centered heme proteins in biomimetic membrane architectures

Membrane proteins play a major role in every living cell. They are the key factors in the cell’s metabolism and in other functions, for example in cell-cell interaction, signal transduction, and transport of ions and nutrients. Cytochrome c oxidase (CcO), as one of the membrane proteins of the respiratory chain, plays a significant role in the energy transformation of higher organisms. CcO is a multi centered heme protein, utilizing redox energy to actively transport protons across the mitochondrial membrane. One aim of this dissertation is to investigate single steps in the mechanism of the ion transfer process coupled to electron transfer, which are not fully understood. The protein-tethered bilayer lipid membrane is a general approach to immobilize membrane proteins in an oriented fashion on a planar electrode embedded in a biomimetic membrane. This system enables the combination of electrochemical techniques with surface enhanced resonance Raman (SERRS), surface enhanced reflection absorption infrared (SEIRAS), and surface plasmon spectroscopy to study protein mediated electron and ion transport processes. The orientation of the enzymes within the surface confined architecture can be controlled by specific site-mutations, i.e. the insertion of a poly-histidine tag to different subunits of the enzyme. CcO can, thus, be oriented uniformly with its natural electron pathway entry pointing either towards or away from the electrode surface. The first orientation allows an ultra-fast direct electron transfer(ET) into the protein, not provided by conventional systems, which can be leveraged to study intrinsic charge transfer processes. The second orientation permits to study the interaction with its natural electron donor cytochrome c. Electrochemical and SERR measurements show conclusively that the redox site structure and the activity of the surface confined enzyme are preserved. Therefore, this biomimetic system offers a unique platform to study the kinetics of the ET processes in order to clarify mechanistic properties of the enzyme. Highly sensitive and ultra fast electrochemical techniques allow the separation of ET steps between all four redox centres including the determination of ET rates. Furthermore, proton transfer coupled to ET could be directly measured and discriminated from other ion transfer processes, revealing novel mechanistic information of the proton transfer mechanism of cytochrome c oxidase. In order to study the kinetics of the ET inside the protein, including the catalytic center, time resolved SEIRAS and SERRS measurements were performed to gain more insight into the structural and coordination changes of the heme environment. The electrical behaviour of tethered membrane systems and membrane intrinsic proteins as well as related charge transfer processes were simulated by solving the respective sets of differential equations, utilizing a software package called SPICE. This helps to understand charge transfer processes across membranes and to develop models that can help to elucidate mechanisms of complex enzymatic processes.

Requirements definition and testing of the new version of multi-mission generic monitoring system (GEMS) v 4.4 for operations at Eumetsat

EUMETSAT (www.eumetsat.int) e’ l’agenzia europea per operazioni su satelliti per monitorare clima, meteo e ambiente terrestre. Dal centro operativo situato a Darmstadt (Germania), si controllano satelliti meteorologici su orbite geostazionarie e polari che raccolgono dati per l’osservazione dell’atmosfera, degli oceani e della superficie terrestre per un servizio continuo di 24/7. Un sistema di monitoraggio centralizzato per programmi diversi all’interno dell’ambiente operazionale di EUMETSAT, e’ dato da GEMS (Generic Event Monitoring System). Il software garantisce il controllo di diverse piattaforme, cross-monitoring di diverse sezioni operative, ed ha le caratteristiche per potere essere esteso a future missioni. L’attuale versione della GEMS MMI (Multi Media Interface), v. 3.6, utilizza standard Java Server Pages (JSP) e fa uso pesante di codici Java; utilizza inoltre files ASCII per filtri e display dei dati. Conseguenza diretta e’ ad esempio, il fatto che le informazioni non sono automaticamente aggiornate, ma hanno bisogno di ricaricare la pagina. Ulteriori inputs per una nuova versione della GEMS MMI vengono da diversi comportamenti anomali riportati durante l’uso quotidiano del software. La tesi si concentra sulla definizione di nuovi requisiti per una nuova versione della GEMS MMI (v. 4.4) da parte della divisione ingegneristica e di manutenzione di operazioni di EUMETSAT. Per le attivita’ di supporto, i test sono stati condotti presso Solenix. Il nuovo software permettera’ una migliore applicazione web, con tempi di risposta piu’ rapidi, aggiornamento delle informazioni automatico, utilizzo totale del database di GEMS e le capacita’ di filtri, insieme ad applicazioni per telefoni cellulari per il supporto delle attivita’ di reperibilita’. La nuova versione di GEMS avra’ una nuova Graphical User Interface (GUI) che utilizza tecnologie moderne. Per un ambiente di operazioni come e’ quello di EUMETSAT, dove l’affidabilita’ delle tecnologie e la longevita’ dell’approccio scelto sono di vitale importanza, non tutti gli attuali strumenti a disposizione sono adatti e hanno bisogno di essere migliorati. Allo stesso tempo, un’ interfaccia moderna, in termini di visual design, interattivita’ e funzionalita’, e’ importante per la nuova GEMS MMI.

An all-solid state laser system for the laser ion source RILIS and in-source laser spectroscopy of astatine at ISOLDE,CERN

This doctoral thesis describes the extension of the resonance ionization laser ion source RILIS at CERN/ISOLDE by the addition of an all-solid state tunable titanium:sapphire (Ti:Sa) laser system to complement the well-established system of dye lasers. Synchronous operation of the so called Dual RILIS system of Ti:Sa and dye lasers was investigated and the potential for increased ion beam intensity, reliability, and reduced setup time has been demonstrated. In-source resonance ionization spectroscopy was performed at ISOLDE/CERN and at ISAC/TRIUMF radioactive ion beam facilities to develop an efficient and selective three-colour ionization scheme for the purely radioactive element astatine. A LabVIEW based monitoring, control and measurement system was conceived which enabled, in conjunction with Dual RILIS operation, the spectroscopy of high lying Rydberg states, from which the ionization potential of the astatine atom was determined for the first time experimentally.

An implantable carotid sinus baroreflex activating system: surgical technique and short-term outcome from a multi-center feasibility trial for the treatment of resistant hypertension

OBJECTIVES: To assess perioperative outcomes and blood pressure (BP) responses to an implantable carotid sinus baroreflex activating system being investigated for the treatment of resistant hypertension. METHODS: We report on the first seventeen patients enrolled in a multicenter study. Bilateral perivascular carotid sinus electrodes (CSL) and a pulse generator (IPG) are permanently implanted. Optimal placement of the CSL is determined by intraoperative BP responses to test activations. Acute BP responses were tested postoperatively and during the first four months of follow-up. RESULTS: Prior to implant, BP was 189.6+/-27.5/110.7+/-15.3 mmHg despite stable therapy (5.2+/-1.8 antihypertensive drugs). The mean procedure time was 202+/-43 minutes. No perioperative strokes or deaths occurred. System tests performed 1 or up to 3 days postoperatively resulted in significant (all p < or = 0.0001) mean maximum reduction, with standard deviations and 95% confidence limits for systolic BP, diastolic BP and heart rate of 28+/-22 (17, 39) mmHg, 16+/-11 (10, 22) mmHg and 8+/-4 (6, 11) BPM, respectively. Repeated testing during 3 months of therapeutic electrical activation demonstrated a durable response. CONCLUSIONS: These preliminary data suggest an acceptable safety of the procedure with a low rate of adverse events and support further clinical development of baroreflex activation as a new concept to treat resistant hypertension.

Economic efficiency analysis of different strategies to control post-weaning multi-systemic wasting syndrome and porcine circovirus type 2 subclinical infection in 3-weekly batch system farms.

The study assessed the economic efficiency of different strategies for the control of post-weaning multi-systemic wasting syndrome (PMWS) and porcine circovirus type 2 subclinical infection (PCV2SI), which have a major economic impact on the pig farming industry worldwide. The control strategies investigated consisted on the combination of up to 5 different control measures. The control measures considered were: (1) PCV2 vaccination of piglets (vac); (2) ensuring age adjusted diet for growers (diets); (3) reduction of stocking density (stock); (4) improvement of biosecurity measures (bios); and (5) total depopulation and repopulation of the farm for the elimination of other major pathogens (DPRP). A model was developed to simulate 5 years production of a pig farm with a 3-weekly batch system and with 100 sows. A PMWS/PCV2SI disease and economic model, based on PMWS severity scores, was linked to the production model in order to assess disease losses. This PMWS severity scores depends on the combination post-weaning mortality, PMWS morbidity in younger pigs and proportion of PCV2 infected pigs observed on farms. The economic analysis investigated eleven different farm scenarios, depending on the number of risk factors present before the intervention. For each strategy, an investment appraisal assessed the extra costs and benefits of reducing a given PMWS severity score to the average score of a slightly affected farm. The net present value obtained for each strategy was then multiplied by the corresponding probability of success to obtain an expected value. A stochastic simulation was performed to account for uncertainty and variability. For moderately affected farms PCV2 vaccination alone was the most cost-efficient strategy, but for highly affected farms it was either PCV2 vaccination alone or in combination with biosecurity measures, with the marginal profitability between 'vac' and 'vac+bios' being small. Other strategies such as 'diets', 'vac+diets' and 'bios+diets' were frequently identified as the second or third best strategy. The mean expected values of the best strategy for a moderately and a highly affected farm were £14,739 and £57,648 after 5 years, respectively. This is the first study to compare economic efficiency of control strategies for PMWS and PCV2SI. The results demonstrate the economic value of PCV2 vaccination, and highlight that on highly affected farms biosecurity measures are required to achieve optimal profitability. The model developed has potential as a farm-level decision support tool for the control of this economically important syndrome.

A versatile gas interface for routine radiocarbon analysis with a gas ion source

In 2010 more than 600 radiocarbon samples were measured with the gas ion source at the MIni CArbon DAting System (MICADAS) at ETH Zurich and the number of measurements is rising quickly. While most samples contain less than 50 mu g C at present, the gas ion source is attractive as well for larger samples because the time-consuming graphitization is omitted. Additionally, modern samples are now measured down to 5 per-mill counting statistics in less than 30 min with the recently improved gas ion source. In the versatile gas handling system, a stepping-motor-driven syringe presses a mixture of helium and sample CO2 into the gas ion source, allowing continuous and stable measurements of different kinds of samples. CO2 can be provided in four different ways to the versatile gas interface. As a primary method. CO2 is delivered in glass or quartz ampoules. In this case, the CO2 is released in an automated ampoule cracker with 8 positions for individual samples. Secondly, OX-1 and blank gas in helium can be provided to the syringe by directly connecting gas bottles to the gas interface at the stage of the cracker. Thirdly, solid samples can be combusted in an elemental analyzer or in a thermo-optical OC/EC aerosol analyzer where the produced CO2 is transferred to the syringe via a zeolite trap for gas concentration. As a fourth method, CO2 is released from carbonates with phosphoric acid in septum-sealed vials and loaded onto the same trap used for the elemental analyzer. All four methods allow complete automation of the measurement, even though minor user input is presently still required. Details on the setup, versatility and applications of the gas handling system are given. (C) 2012 Elsevier B.V. All rights reserved.

An adjustable focusing system for a 2 MeV H- ion beam line based on permanent magnet quadrupoles

A compact adjustable focusing system for a 2 MeV H- RFQ Linac is designed, constructed and tested based on four permanent magnet quadrupoles (PMQ). A PMQ model is realised using finite element simulations, providing an integrated field gradient of 2.35 T with a maximal field gradient of 57 T/m. A prototype is constructed and the magnetic field is measured, demonstrating good agreement with the simulation. Particle track simulations provide initial values for the quadrupole positions. Accordingly, four PMQs are constructed and assembled on the beam line, their positions are then tuned to obtain a minimal beam spot size of (1.2 x 2.2) mm^2 on target. This paper describes an adjustable PMQ beam line for an external ion beam. The novel compact design based on commercially available NdFeB magnets allows high flexibility for ion beam applications.

Automated low flow pump system for the treatment of refractory ascites: A multi-center safety and efficacy study

BACKGROUND & AIMS: Refractory ascites (RA) affects 10% of patients with advanced cirrhosis and ascites. Usual therapy includes large volume paracentesis, and in selected patients, a transjugular portosystemic shunt (TIPS). These therapies may be associated with increased morbidity: paracentesis may induce circulatory dysfunction and impair quality of life and TIPS may induce encephalopathy and is associated with increased mortality in patients with severe liver dysfunction. We present the results of a multicenter, non-randomized trial to assess the safety and efficacy of a new automated pump system for treatment of RA. METHODS: Forty patients at 9 centers (February 2010-June 2011) received an implanted pump for the automated removal of ascites from the peritoneal cavity into the bladder, from where it was eliminated through normal urination. Patients were followed-up for 6months. The primary study outcome was safety. Secondary outcomes included recurrence of tense ascites and pump performance. RESULTS: Surgical complications occurred early in the study and became less frequent. The pump system removed 90% of the ascites and significantly reduced the median number of large volume paracentesis per month [3.4 (range 1-6) vs. 0.2 (range 0-4); p <0.01]. Cirrhosis-related adverse events decreased along follow-up. CONCLUSIONS: The automated pump seems an efficacious tool to move out ascites from the peritoneal cavity to the bladder. Its safety is still moderate, but a broad use in different countries will improve the surgical technique as well as the medical surveillance. A prospective randomized clinical trial vs. large volume paracentesis is underway to confirm these preliminary results.

Digital multi-text editions from scratch to electronic performance. Transcription and collation routines transformed in a flexible database system

The poster demonstrates the preparatory steps of a digital multi-text edition that are abstracted from the experiences made in the Parzival Project, based at the University of Bern, the Berlin-Brandenburg Academy of Sciences and the University of Erlangen. This edition of Wolfram von Eschenbach’s German Grail novel, written shortly after 1200 and transmitted during several centuries in ca. hundred witnesses, has now been completed by more than a half of the textual corpus.