Dielectrophoresis (dep) and electrowetting (ewod) as an anti-fouling process for antibacterial surfaces

Nowadays the medical field is struggling to decrease bacteria biofilm formation which leads to infection. Biomedical devices sterilization has not changed over a long period of time. This results in high costs for hospitals healthcare managements. The objective of this project is to investigate electric field effects and surface energy manipulation as solutions for preventing bacteria biofilm for future devices. Based on electrokinectic environments 2 different methods were tested: feasibility of electric gradient through mediums (DEP) reinforced by numerical simulations; and EWOD by the fabrication of golden interdigitated electrodes on silicon glass substrates, standard ~480 nm Teflon (PTFE) layer and polymeric gasket to contain the bacteria medium. In the first experiment quantitative analysis was carried out to achieve forces required to reject bacteria without considering dielectric environment limitations as bacteria and medium frequency dependence. In the second experiment applied voltages was characterized by droplets contact angle measurements and put to the live bacteria tests. The project resulted on promising results for DEP application due to its wide range of frequency that can be used to make a “general” bacteria rejecting; but in terms of practicality, EWOD probably have higher potential for success but more experiments are needed to verify if can prevent biofilm adhesion besides the Teflon non-adhesive properties (including limitations as Teflon breakthrough, layer sensitivity) at incubation times larger than 24 hours.

Efficient calculation of gluon amplitudes with n legs and an implementation of parton showers using the dipole formalism

The conventional way to calculate hard scattering processes in perturbation theory using Feynman diagrams is not efficient enough to calculate all necessary processes - for example for the Large Hadron Collider - to a sufficient precision. Two alternatives to order-by-order calculations are studied in this thesis.rnrnIn the first part we compare the numerical implementations of four different recursive methods for the efficient computation of Born gluon amplitudes: Berends-Giele recurrence relations and recursive calculations with scalar diagrams, with maximal helicity violating vertices and with shifted momenta. From the four methods considered, the Berends-Giele method performs best, if the number of external partons is eight or bigger. However, for less than eight external partons, the recursion relation with shifted momenta offers the best performance. When investigating the numerical stability and accuracy, we found that all methods give satisfactory results.rnrnIn the second part of this thesis we present an implementation of a parton shower algorithm based on the dipole formalism. The formalism treats initial- and final-state partons on the same footing. The shower algorithm can be used for hadron colliders and electron-positron colliders. Also massive partons in the final state were included in the shower algorithm. Finally, we studied numerical results for an electron-positron collider, the Tevatron and the Large Hadron Collider.

Tracking, b-tagging and measurement of the b-jet production cross section with the ATLAS detector

The Standard Model of elementary particle physics was developed to describe the fundamental particles which constitute matter and the interactions between them. The Large Hadron Collider (LHC) at CERN in Geneva was built to solve some of the remaining open questions in the Standard Model and to explore physics beyond it, by colliding two proton beams at world-record centre-of-mass energies. The ATLAS experiment is designed to reconstruct particles and their decay products originating from these collisions. The precise reconstruction of particle trajectories plays an important role in the identification of particle jets which originate from bottom quarks (b-tagging). This thesis describes the step-wise commissioning of the ATLAS track reconstruction and b-tagging software and one of the first measurements of the b-jet production cross section in pp collisions at sqrt(s)=7 TeV with the ATLAS detector. The performance of the track reconstruction software was studied in great detail, first using data from cosmic ray showers and then collisions at sqrt(s)=900 GeV and 7 TeV. The good understanding of the track reconstruction software allowed a very early deployment of the b-tagging algorithms. First studies of these algorithms and the measurement of the b-tagging efficiency in the data are presented. They agree well with predictions from Monte Carlo simulations. The b-jet production cross section was measured with the 2010 dataset recorded by the ATLAS detector, employing muons in jets to estimate the fraction of b-jets. The measurement is in good agreement with the Standard Model predictions.

Portfolio Approaches in Constraint Programming

Recent research has shown that the performance of a single, arbitrarily efficient algorithm can be significantly outperformed by using a portfolio of —possibly on-average slower— algorithms. Within the Constraint Programming (CP) context, a portfolio solver can be seen as a particular constraint solver that exploits the synergy between the constituent solvers of its portfolio for predicting which is (or which are) the best solver(s) to run for solving a new, unseen instance. In this thesis we examine the benefits of portfolio solvers in CP. Despite portfolio approaches have been extensively studied for Boolean Satisfiability (SAT) problems, in the more general CP field these techniques have been only marginally studied and used. We conducted this work through the investigation, the analysis and the construction of several portfolio approaches for solving both satisfaction and optimization problems. We focused in particular on sequential approaches, i.e., single-threaded portfolio solvers always running on the same core. We started from a first empirical evaluation on portfolio approaches for solving Constraint Satisfaction Problems (CSPs), and then we improved on it by introducing new data, solvers, features, algorithms, and tools. Afterwards, we addressed the more general Constraint Optimization Problems (COPs) by implementing and testing a number of models for dealing with COP portfolio solvers. Finally, we have come full circle by developing sunny-cp: a sequential CP portfolio solver that turned out to be competitive also in the MiniZinc Challenge, the reference competition for CP solvers.

Closed-loop investigation of the dynamical properties of cardiomyocyte electrophysiology by means of Dynamic clamp and Mathematical modelling

The research field of my PhD concerns mathematical modeling and numerical simulation, applied to the cardiac electrophysiology analysis at a single cell level. This is possible thanks to the development of mathematical descriptions of single cellular components, ionic channels, pumps, exchangers and subcellular compartments. Due to the difficulties of vivo experiments on human cells, most of the measurements are acquired in vitro using animal models (e.g. guinea pig, dog, rabbit). Moreover, to study the cardiac action potential and all its features, it is necessary to acquire more specific knowledge about single ionic currents that contribute to the cardiac activity. Electrophysiological models of the heart have become very accurate in recent years giving rise to extremely complicated systems of differential equations. Although describing the behavior of cardiac cells quite well, the models are computationally demanding for numerical simulations and are very difficult to analyze from a mathematical (dynamical-systems) viewpoint. Simplified mathematical models that capture the underlying dynamics to a certain extent are therefore frequently used. The results presented in this thesis have confirmed that a close integration of computational modeling and experimental recordings in real myocytes, as performed by dynamic clamp, is a useful tool in enhancing our understanding of various components of normal cardiac electrophysiology, but also arrhythmogenic mechanisms in a pathological condition, especially when fully integrated with experimental data.

Bitext alignment: building and evaluating a bilingual corpus and translation memory of academic course descriptions

Following the internationalization of contemporary higher education, academic institutions based in non-English speaking countries are increasingly urged to produce contents in English to address international prospective students and personnel, as well as to increase their attractiveness. The demand for English translations in the institutional academic domain is consequently increasing at a rate exceeding the capacity of the translation profession. Resources for assisting non-native authors and translators in the production of appropriate texts in L2 are therefore required in order to help academic institutions and professionals streamline their translation workload. Some of these resources include: (i) parallel corpora to train machine translation systems and multilingual authoring tools; and (ii) translation memories for computer-aided tools. The purpose of this study is to create and evaluate reference resources like the ones mentioned in (i) and (ii) through the automatic sentence alignment of a large set of Italian and English as a Lingua Franca (ELF) institutional academic texts given as equivalent but not necessarily parallel (i.e. translated). In this framework, a set of aligning algorithms and alignment tools is examined in order to identify the most profitable one(s) in terms of accuracy and time- and cost-effectiveness. In order to determine the text pairs to align, a sample is selected according to document length similarity (characters) and subsequently evaluated in terms of extent of noisiness/parallelism, alignment accuracy and content leverageability. The results of these analyses serve as the basis for the creation of an aligned bilingual corpus of academic course descriptions, which is eventually used to create a translation memory in TMX format.

Algorithmen zur labelfreien quantitativen Proteomanalyse auf Basis datenunabhängig-akquirierter LC-MS-Daten

Moderne ESI-LC-MS/MS-Techniken erlauben in Verbindung mit Bottom-up-Ansätzen eine qualitative und quantitative Charakterisierung mehrerer tausend Proteine in einem einzigen Experiment. Für die labelfreie Proteinquantifizierung eignen sich besonders datenunabhängige Akquisitionsmethoden wie MSE und die IMS-Varianten HDMSE und UDMSE. Durch ihre hohe Komplexität stellen die so erfassten Daten besondere Anforderungen an die Analysesoftware. Eine quantitative Analyse der MSE/HDMSE/UDMSE-Daten blieb bislang wenigen kommerziellen Lösungen vorbehalten. rn| In der vorliegenden Arbeit wurden eine Strategie und eine Reihe neuer Methoden zur messungsübergreifenden, quantitativen Analyse labelfreier MSE/HDMSE/UDMSE-Daten entwickelt und als Software ISOQuant implementiert. Für die ersten Schritte der Datenanalyse (Featuredetektion, Peptid- und Proteinidentifikation) wird die kommerzielle Software PLGS verwendet. Anschließend werden die unabhängigen PLGS-Ergebnisse aller Messungen eines Experiments in einer relationalen Datenbank zusammengeführt und mit Hilfe der dedizierten Algorithmen (Retentionszeitalignment, Feature-Clustering, multidimensionale Normalisierung der Intensitäten, mehrstufige Datenfilterung, Proteininferenz, Umverteilung der Intensitäten geteilter Peptide, Proteinquantifizierung) überarbeitet. Durch diese Nachbearbeitung wird die Reproduzierbarkeit der qualitativen und quantitativen Ergebnisse signifikant gesteigert.rn| Um die Performance der quantitativen Datenanalyse zu evaluieren und mit anderen Lösungen zu vergleichen, wurde ein Satz von exakt definierten Hybridproteom-Proben entwickelt. Die Proben wurden mit den Methoden MSE und UDMSE erfasst, mit Progenesis QIP, synapter und ISOQuant analysiert und verglichen. Im Gegensatz zu synapter und Progenesis QIP konnte ISOQuant sowohl eine hohe Reproduzierbarkeit der Proteinidentifikation als auch eine hohe Präzision und Richtigkeit der Proteinquantifizierung erreichen.rn| Schlussfolgernd ermöglichen die vorgestellten Algorithmen und der Analyseworkflow zuverlässige und reproduzierbare quantitative Datenanalysen. Mit der Software ISOQuant wurde ein einfaches und effizientes Werkzeug für routinemäßige Hochdurchsatzanalysen labelfreier MSE/HDMSE/UDMSE-Daten entwickelt. Mit den Hybridproteom-Proben und den Bewertungsmetriken wurde ein umfassendes System zur Evaluierung quantitativer Akquisitions- und Datenanalysesysteme vorgestellt.

An integrated system for building and running reproducible research

Our generation of computational scientists is living in an exciting time: not only do we get to pioneer important algorithms and computations, we also get to set standards on how computational research should be conducted and published. From Euclid’s reasoning and Galileo’s experiments, it took hundreds of years for the theoretical and experimental branches of science to develop standards for publication and peer review. Computational science, rightly regarded as the third branch, can walk the same road much faster. The success and credibility of science are anchored in the willingness of scientists to expose their ideas and results to independent testing and replication by other scientists. This requires the complete and open exchange of data, procedures and materials. The idea of a “replication by other scientists” in reference to computations is more commonly known as “reproducible research”. In this context the journal “EAI Endorsed Transactions on Performance & Modeling, Simulation, Experimentation and Complex Systems” had the exciting and original idea to make the scientist able to submit simultaneously the article and the computation materials (software, data, etc..) which has been used to produce the contents of the article. The goal of this procedure is to allow the scientific community to verify the content of the paper, reproducing it in the platform independently from the OS chosen, confirm or invalidate it and especially allow its reuse to reproduce new results. This procedure is therefore not helpful if there is no minimum methodological support. In fact, the raw data sets and the software are difficult to exploit without the logic that guided their use or their production. This led us to think that in addition to the data sets and the software, an additional element must be provided: the workflow that relies all of them.

SMARTDIAB: a communication and information technology approach for the intelligent monitoring, management and follow-up of type 1 diabetes patients

SMARTDIAB is a platform designed to support the monitoring, management, and treatment of patients with type 1 diabetes mellitus (T1DM), by combining state-of-the-art approaches in the fields of database (DB) technologies, communications, simulation algorithms, and data mining. SMARTDIAB consists mainly of two units: 1) the patient unit (PU); and 2) the patient management unit (PMU), which communicate with each other for data exchange. The PMU can be accessed by the PU through the internet using devices, such as PCs/laptops with direct internet access or mobile phones via a Wi-Fi/General Packet Radio Service access network. The PU consists of an insulin pump for subcutaneous insulin infusion to the patient and a continuous glucose measurement system. The aforementioned devices running a user-friendly application gather patient's related information and transmit it to the PMU. The PMU consists of a diabetes data management system (DDMS), a decision support system (DSS) that provides risk assessment for long-term diabetes complications, and an insulin infusion advisory system (IIAS), which reside on a Web server. The DDMS can be accessed from both medical personnel and patients, with appropriate security access rights and front-end interfaces. The DDMS, apart from being used for data storage/retrieval, provides also advanced tools for the intelligent processing of the patient's data, supporting the physician in decision making, regarding the patient's treatment. The IIAS is used to close the loop between the insulin pump and the continuous glucose monitoring system, by providing the pump with the appropriate insulin infusion rate in order to keep the patient's glucose levels within predefined limits. The pilot version of the SMARTDIAB has already been implemented, while the platform's evaluation in clinical environment is being in progress.

Postreperfusion cardiac arrest and resuscitation during orthotopic liver transplantation: dynamic visualization and analysis of physiologic recordings

We recently reported on the Multi Wave Animator (MWA), a novel open-source tool with capability of recreating continuous physiologic signals from archived numerical data and presenting them as they appeared on the patient monitor. In this report, we demonstrate for the first time the power of this technology in a real clinical case, an intraoperative cardiopulmonary arrest following reperfusion of a liver transplant graft. Using the MWA, we animated hemodynamic and ventilator data acquired before, during, and after cardiac arrest and resuscitation. This report is accompanied by an online video that shows the most critical phases of the cardiac arrest and resuscitation and provides a basis for analysis and discussion. This video is extracted from a 33-min, uninterrupted video of cardiac arrest and resuscitation, which is available online. The unique strength of MWA, its capability to accurately present discrete and continuous data in a format familiar to clinicians, allowed us this rare glimpse into events leading to an intraoperative cardiac arrest. Because of the ability to recreate and replay clinical events, this tool should be of great interest to medical educators, researchers, and clinicians involved in quality assurance and patient safety.

German validation of the Conners Adult ADHD Rating Scales (CAARS) II: reliability, validity, diagnostic sensitivity and specificity

The German version of the Conners Adult ADHD Rating Scales (CAARS) has proven to show very high model fit in confirmative factor analyses with the established factors inattention/memory problems, hyperactivity/restlessness, impulsivity/emotional lability, and problems with self-concept in both large healthy control and ADHD patient samples. This study now presents data on the psychometric properties of the German CAARS-self-report (CAARS-S) and observer-report (CAARS-O) questionnaires.

Pathogenesis and classification of eosinophil disorders: a review of recent developments in the field

Eosinophils and their products play an essential role in the pathogenesis of various reactive and neoplastic disorders. Depending on the underlying disease, molecular defect and involved cytokines, hypereosinophilia may develop and may lead to organ damage. In other patients, persistent eosinophilia is accompanied by typical clinical findings, but the causative role and impact of eosinophilia remain uncertain. For patients with eosinophil-mediated organ pathology, early therapeutic intervention with agents reducing eosinophil counts can be effective in limiting or preventing irreversible organ damage. Therefore, it is important to approach eosinophil disorders and related syndromes early by using established criteria, to perform all appropriate staging investigations, and to search for molecular targets of therapy. In this article, we review current concepts in the pathogenesis and evolution of eosinophilia and eosinophil-related organ damage in neoplastic and non-neoplastic conditions. In addition, we discuss classifications of eosinophil disorders and related syndromes as well as diagnostic algorithms and standard treatment for various eosinophil-related disorders.

Tests for Comparing Mark-Specific Hazards and Cumulative Incidence Functions

It is of interest in some applications to determine whether there is a relationship between a hazard rate function (or a cumulative incidence function) and a mark variable which is only observed at uncensored failure times. We develop nonparametric tests for this problem when the mark variable is continuous. Tests are developed for the null hypothesis that the mark-specific hazard rate is independent of the mark versus ordered and two-sided alternatives expressed in terms of mark-specific hazard functions and mark-specific cumulative incidence functions. The test statistics are based on functionals of a bivariate test process equal to a weighted average of differences between a Nelson--Aalen-type estimator of the mark-specific cumulative hazard function and a nonparametric estimator of this function under the null hypothesis. The weight function in the test process can be chosen so that the test statistics are asymptotically distribution-free.Asymptotically correct critical values are obtained through a simple simulation procedure. The testing procedures are shown to perform well in numerical studies, and are illustrated with an AIDS clinical trial example. Specifically, the tests are used to assess if the instantaneous or absolute risk of treatment failure depends on the amount of accumulation of drug resistance mutations in a subject's HIV virus. This assessment helps guide development of anti-HIV therapies that surmount the problem of drug resistance.

Bioconductor: Open software development for computational biology and bioinformatics

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software paradigms and operational strategies that have allowed a small number of researchers to provide a wide variety of innovative, extensible, software solutions in a relatively short time. The use of an object oriented programming paradigm, the adoption and development of a software package system, designing by contract, distributed development and collaboration with other projects are elements of this project's success. Individually, each of these concepts are useful and important but when combined they have provided a strong basis for rapid development and deployment of innovative and flexible research software for scientific computation. A primary objective of this initiative is achievement of total remote reproducibility of novel algorithmic research results.