MOOGLE: a metamodel-based model search engine

Models are becoming increasingly important in the software development process. As a consequence, the number of models being used is increasing, and so is the need for efficient mechanisms to search them. Various existing search engines could be used for this purpose, but they lack features to properly search models, mainly because they are strongly focused on text-based search. This paper presents Moogle, a model search engine that uses metamodeling information to create richer search indexes and to allow more complex queries to be performed. The paper also presents the results of an evaluation of Moogle, which showed that the metamodel information improves the accuracy of the search.

Missed opportunities for prevention of mother-to-child transmission of HIV-1 in the NISDI Perinatal and LILAC cohorts

Objective: To evaluate cases of mother-to-child transmission of HIV-1 at multiple sites in Latin America and the Caribbean in terms of missed opportunities for prevention. Methods: Pregnant women infected with HIV-1 were eligible for inclusion if they were enrolled in either the NISDI Perinatal or LILAC protocols by October 20, 2009, and had delivered a live infant with known HIV-1 infection status after March 1, 2006. Results: Of 711 eligible mothers, 10 delivered infants infected with HIV-1. The transmission rate was 1.4% (95% CI, 0.7-2.6). Timing of transmission was in utero or intrapartum (n = 5), intrapartum (n = 2), intrapartum or early postnatal (n = 1), and unknown (n = 2). Possible missed opportunities for prevention included poor control of maternal viral load during pregnancy; late initiation of antiretrovirals during pregnancy; lack of cesarean delivery before labor and before rupture of membranes; late diagnosis of HIV-1 infection; lack of intrapartum antiretrovirals; and incomplete avoidance of breastfeeding. Conclusion: Early knowledge of HIV-1 infection status (ideally before or in early pregnancy) would aid timely initiation of antiretroviral treatment and strategies designed to prevent mother-to-child transmission. Use of antiretrovirals must be appropriately monitored in terms of adherence and drug resistance. If feasible, breastfeeding should be completely avoided. Presented in part at the XIX International AIDS Conference (Washington, DC; July 22-27, 2012); abstract WEPE163. (c) 2012 Published by Elsevier Ireland Ltd. on behalf of International Federation of Gynecology and Obstetrics.

Computational simulation of the flow-induced vibration of a circular cylinder subjected to wake interference

In this work, we considered the flow around two circular cylinders of equal diameter placed in tandem with respect to the incident uniform flow. The upstream cylinder was fixed and the downstream cylinder was completely free to move in the cross-stream direction, with no spring or damper attached to it. The centre-to-centre distance between the cylinders was four diameters, and the Reynolds number was varied from 100 to 645. We performed two- and three-dimensional simulations of this flow using a Spectral/hp element method to discretise the flow equations, coupled to a simple Newmark integration routine that solves the equation of the dynamics of the cylinder. The differences of the behaviours observed in the two- and three-dimensional simulations are highlighted and the data is analysed under the light of previously published experimental results obtained for higher Reynolds numbers.

Non-equilibrium molecular dynamics study of an amphiphilic model system

Diese Doktorarbeit untersucht das Verhalten von komplexenFluidenunter Scherung, insbesondere den Einfluss von Scherflüssenauf dieStrukturbildung.Dazu wird ein Modell dieser entworfen, welches imRahmen von Molekulardynamiksimulationen verwendet wird.Zunächst werden Gleichgewichtseigenschaften dieses Modellsuntersucht.Hierbei wird unter anderem die Lage desOrdnungs--Unordnungsübergangs von derisotropen zur lamellaren Phase der Dimere bestimmt.Der Einfluss von Scherflüssen auf diese lamellare Phase wirdnununtersucht und mit analytischen Theorien verglichen. Die Scherung einer parallelen lamellaren Phase ruft eineNeuausrichtung des Direktors in Flussrichtung hervor.Das verursacht eine Verminderung der Schichtdicke mitsteigender Scherrateund führt oberhalb eines Schwellwertes zu Ondulationen.Ein vergleichbares Verhalten wird auch in lamellarenSystemengefunden, an denen in Richtung des Direktors gezogen wird.Allerdings wird festgestellt, dass die Art der Bifurkationenin beidenFällen unterschiedlich ist.Unter Scherung wird ein Übergang von Lamellen parallelerAusrichtung zu senkrechter gefunden.Dabei wird beoachtet, dass die Scherspannung in senkrechterOrientierungniedriger als in der parallelen ist.Dies führt unter bestimmten Bedingungen zum Auftreten vonScherbändern, was auch in Simulationen beobachtet wird. Es ist gelungen mit einem einfachen Modell viele Apsekte desVerhalten vonkomplexen Fluiden wiederzugeben. Die Strukturbildung hängt offensichtlich nurbedingt von lokalen Eigenschaften der Moleküle ab.

Bridging innovation, nature and tradition: assessment of strategies for rural tourism development in Maramureş (Romania)

In the frame of EU rural policy, always more oriented towards environmental concerns and green livelihoods, Romania stands out for the predominance of rural areas and high nature value farming. The country has to face the challenge of joining the modernization process of rural farming systems with the valorization of local assets. Tourism has emerged as one of the main drivers of change and contributors for a sustainable exploitation of local resources. Rural tourism (RT) can foster the enhancement of the territorial capital (TC), the preservation of public goods (PGs) and the promotion of a more environmental oriented livelihood. The research focuses on a case study area, two valleys from Maramureş, where environmental approaches as diversification strategies are partially explored. The work investigates the role of tourism initiatives for the promotion of green oriented practices. The first part of the work is based on a literature review and interdisciplinary analysis of secondary data to identify the key issues: from rural development policy, to the concept of TC, of PGs and RT. The Romanian development programmes and related strategies are investigated; afterwards the characteristics of the County and the role of RT as diversification and valorisation policies is considered. The second part is based on the collection of primary data through interviews to different local stakeholders (farmers owners of rural guesthouses, local administrators, networks and artisans). The main frequencies are analyzed, a cluster analysis is computed to evaluate the similarities within the most representative groups and a comparative analysis is carried out between the two Valleys. The frame of the analysis is based on a set of indicators following the dimensions of the TC, to assess the characteristics of the local stakeholders and to outline the perception about the local PGs and on the adopted strategies to manage the territory. Final considerations are elaborated and few scenarios are outlined, giving relevance to the importance of improving awareness and creating embeddedness among public-private local stakeholders and resources as a tool for a socio-economic and environmental development of the area.

Classical limit of the Nelson model

Since the development of quantum mechanics it has been natural to analyze the connection between classical and quantum mechanical descriptions of physical systems. In particular one should expect that in some sense when quantum mechanical effects becomes negligible the system will behave like it is dictated by classical mechanics. One famous relation between classical and quantum theory is due to Ehrenfest. This result was later developed and put on firm mathematical foundations by Hepp. He proved that matrix elements of bounded functions of quantum observables between suitable coherents states (that depend on Planck's constant h) converge to classical values evolving according to the expected classical equations when h goes to zero. His results were later generalized by Ginibre and Velo to bosonic systems with infinite degrees of freedom and scattering theory. In this thesis we study the classical limit of Nelson model, that describes non relativistic particles, whose evolution is dictated by Schrödinger equation, interacting with a scalar relativistic field, whose evolution is dictated by Klein-Gordon equation, by means of a Yukawa-type potential. The classical limit is a mean field and weak coupling limit. We proved that the transition amplitude of a creation or annihilation operator, between suitable coherent states, converges in the classical limit to the solution of the system of differential equations that describes the classical evolution of the theory. The quantum evolution operator converges to the evolution operator of fluctuations around the classical solution. Transition amplitudes of normal ordered products of creation and annihilation operators between coherent states converge to suitable products of the classical solutions. Transition amplitudes of normal ordered products of creation and annihilation operators between fixed particle states converge to an average of products of classical solutions, corresponding to different initial conditions.

Improvement of photon transport model by including coupled photon-electron transport and kernel refinement

The first part of this work deals with the inverse problem solution in the X-ray spectroscopy field. An original strategy to solve the inverse problem by using the maximum entropy principle is illustrated. It is built the code UMESTRAT, to apply the described strategy in a semiautomatic way. The application of UMESTRAT is shown with a computational example. The second part of this work deals with the improvement of the X-ray Boltzmann model, by studying two radiative interactions neglected in the current photon models. Firstly it is studied the characteristic line emission due to Compton ionization. It is developed a strategy that allows the evaluation of this contribution for the shells K, L and M of all elements with Z from 11 to 92. It is evaluated the single shell Compton/photoelectric ratio as a function of the primary photon energy. It is derived the energy values at which the Compton interaction becomes the prevailing process to produce ionization for the considered shells. Finally it is introduced a new kernel for the XRF from Compton ionization. In a second place it is characterized the bremsstrahlung radiative contribution due the secondary electrons. The bremsstrahlung radiation is characterized in terms of space, angle and energy, for all elements whit Z=1-92 in the energy range 1–150 keV by using the Monte Carlo code PENELOPE. It is demonstrated that bremsstrahlung radiative contribution can be well approximated with an isotropic point photon source. It is created a data library comprising the energetic distributions of bremsstrahlung. It is developed a new bremsstrahlung kernel which allows the introduction of this contribution in the modified Boltzmann equation. An example of application to the simulation of a synchrotron experiment is shown.

The role of SENP1 in B cell development and differentiation

SUMOylation is a highly dynamic and reversible posttranslational protein modification closely related to ubiquitination. SUMOylation regulates a vast array of different cellular functions, such as cell cycle, nuclear transport, DNA damage response, proliferation and transcriptional activation. Several groups have shown in in vitro studies how important SUMOylation is for early B cell development and survival as well as for later plasma cell differentiation. This thesis focuses on the deSUMOylation protease SENP1 and its in vivo effects on B cell development and differentiation. For this a conditional SENP1 knockout mouse model was crossed to the CD19-Cre mouse strain to generate a B cell specific SENP1 knockout mouse.rnIn our conditional SENP1ff CD19-Cre mouse model we observed normal numbers of all B cell subsets in the bone marrow. However in the spleen we observed an impairment of B cell survival, based on a 50% reduction of the follicular B cell compartment, whereas the marginal zone B cell compartment was unchanged. T cell numbers were comparable to control mice. rnFurther, impairments of B cell survival in SENP1ff CD19-Cre mice were analysed after in vivo blocking of IL7R signalling. The αIL7R treatment in mature mice blocked new B cell formation in the bone marrow and increased apoptosis rates could be observed in splenic SENP1 KO B cells. Additionally, a higher turnover rate of B cells was measured by in vivo BrdU incorporation.rnSince it is known that the majority of transcription factors that are important for the maintenance of the germinal centre reaction or for induction of plasma cell development are SUMOylated, the question arose, how defective deSUMOylation will manifest itself in these processes. The majority of in vitro cultured splenic B cells, stimulated to undergo class switch recombination and plasma cell differentiation underwent activation induced cell death. However, the surviving cells increasingly differentiated into IgM expressing plasma cells. Class switch recombination to IgG1 was reduced. These observations stood in line with observation made in in vivo sheep red blood cell immunization experiments, which showed increased amounts of germinal centres and germinal centre B cells, as well as increased amounts of plasma cells differentiation in combination with decreased class switch to IgG1.rnThese results lead to the conclusion that SENP1 KO B cells increasingly undergo apoptosis, however, B cells that survive SENP1 deficiency are more prone to undergo plasma cell differentiation. Further, the precursors of these plasma cells either are not as capable of undergoing class switch recombination or they do switch to IgG1 and succumb to activation induced cell death. One possible explanation for both scenarios could be a defective DNA damage response mechanisms during class switch recombination, caused by impaired deSUMOylation. rn

Clinical applicability of an US model to calculate the head blood outflow through collateral vessels.

Le vene giugulari interne sembrano essere la via principale attraverso cui il sangue defluisce dal cervello verso il cuore, quando siamo in posizione supina. Nel 2008 il professor Paolo Zamboni ha scoperto che una diminuzione dell'attività giugulare può portare allo sviluppo di una condizione emodinamica chiamata CCSVI. Questa può causare ipossia, ritardi nella perfusione cerebrale e riduzione del drenaggio dei cataboliti, oltre ad un'attivazione infiammatoria delle piccole vene e dei tessuti vicini. Questa condizione è stata da subito associata alla sclerosi multipla e su questo argomento si sono dibattuti molti gruppi di ricerca. Inoltre, altre patologie sembrano essere associate alla CCSVI, come il morbo di Parkinson, l'Alzheimer e la sindrome di Meniere. Proprio quest'ultima è uno degli argomenti che attualmente interessa di più il gruppo di lavoro in cui mi sono inserita. Questa patologia comporta problemi uditivi, come sordità e tinnito, vertigini e nausea. Il gruppo Vascolar Disease Center (VDC) dell'Università di Ferrara ha previsto per l'anno 2015 uno studio multicentrico, in cui si cercherà di verificare la correlazione tra CCSVI e sindrome di Meniere. La mia tesi fa parte di un studio preliminare a quello multicentrico. All'inizio del lavoro mi sono dedicata ad un'analisi critica di un modello emodinamico per la quantificazione dei flussi sanguigni: il modello BMC, pubblicato nel 2013 dal gruppo VDC, effettuando in parallelo una ricerca bibliografica sullo stato dell'arte in materia. In seguito ho cominciato a studiare off-line diversi studi patologici e fisiologici, in modo da prendere confidenza con gli strumenti e con le metodologie da utilizzare. Sono stata poi coinvolta dal gruppo VDC per partecipare attivamente al miglioramento del protocollo legato al modello BMC. Infine ho analizzato, con due metodologie differenti, 35 studi effettuati su pazienti otorinolaringoiatrici. Con i risultati ottenuti ho potuto effettuare diverse analisi statistiche al fine di verificare l'equivalenza delle due metodologie. L'obiettivo ultimo era quello di stabilire quale delle due fosse la tecnica migliore da utilizzare, successivamente, nello studio multicentrico.

Qualitatitive and quantitative analysis of fish spoilage processes for development of new food monitoring systems

This study investigates the growth and metabolite production of microorganisms causing spoilage of Atlantic cod (Gadus morhua) fillets packaged under air and modified atmosphere (60 % CO2, 40 % O2). Samples were provided by two different retailers (A and B). Storage of packaged fillets occurred at 4 °C and 8 °C. Microbiological quality and metabolite production of cod fillets stored in MAP 4 °C, MAP 8 °C and air were monitored during 13 days, 7 days and 3 days of storage, respectively. Volatile compounds concentration in the headspace were quantified by Selective ion flow tube mass spectrometry and a correlation with microbiological spoilage was studied. The onset of volatile compounds detection was observed to be mostly around 7 log cfu/g of total psychrotrophic count. Trimethylamine and dimethyl sulfide were found to be the dominant volatiles in all of the tested storage conditions, nevertheless there was no close correlation between concentrations of each main VOC and percentages of rejection based on sensory evaluation. According to results it was concluded that they cannot be considered as only indicators of the quality of cod fillets stored in modified atmosphere and air.  

The Design of XML-Based Model and Experiment Description Languages for Network Simulation

The Simulation Automation Framework for Experiments (SAFE) is a project created to raise the level of abstraction in network simulation tools and thereby address issues that undermine credibility. SAFE incorporates best practices in network simulationto automate the experimental process and to guide users in the development of sound scientific studies using the popular ns-3 network simulator. My contributions to the SAFE project: the design of two XML-based languages called NEDL (ns-3 Experiment Description Language) and NSTL (ns-3 Script Templating Language), which facilitate the description of experiments and network simulationmodels, respectively. The languages provide a foundation for the construction of better interfaces between the user and the ns-3 simulator. They also provide input to a mechanism which automates the execution of network simulation experiments. Additionally,this thesis demonstrates that one can develop tools to generate ns-3 scripts in Python or C++ automatically from NSTL model descriptions.

Antimicrobial use in Swiss dairy farms: quantification and evaluation of data quality

Data on antimicrobial use play a key role in the development of policies for the containment of antimicrobial resistance. On-farm data could provide a detailed overview of the antimicrobial use, but technical and methodological aspects of data collection and interpretation, as well as data quality need to be further assessed. The aims of this study were (1) to quantify antimicrobial use in the study population using different units of measurement and contrast the results obtained, (2) to evaluate data quality of farm records on antimicrobial use, and (3) to compare data quality of different recording systems. During 1 year, data on antimicrobial use were collected from 97 dairy farms. Antimicrobial consumption was quantified using: (1) the incidence density of antimicrobial treatments; (2) the weight of active substance; (3) the used daily dose and (4) the used course dose for antimicrobials for intestinal, intrauterine and systemic use; and (5) the used unit dose, for antimicrobials for intramammary use. Data quality was evaluated by describing completeness and accuracy of the recorded information, and by comparing farmers' and veterinarians' records. Relative consumption of antimicrobials depended on the unit of measurement: used doses reflected the treatment intensity better than weight of active substance. The use of antimicrobials classified as high priority was low, although under- and overdosing were frequently observed. Electronic recording systems allowed better traceability of the animals treated. Recording drug name or dosage often resulted in incomplete or inaccurate information. Veterinarians tended to record more drugs than farmers. The integration of veterinarian and farm data would improve data quality.

Assessment Of Dynamic Properties Of A Crowd Model For Human-Structure Interaction Modeling

As lightweight and slender structural elements are more frequently used in the design, large scale structures become more flexible and susceptible to excessive vibrations. To ensure the functionality of the structure, dynamic properties of the occupied structure need to be estimated during the design phase. Traditional analysis method models occupants simply as an additional mass; however, research has shown that human occupants could be better modeled as an additional degree-of- freedom. In the United Kingdom, active and passive crowd models are proposed by the Joint Working Group as a result of a series of analytical and experimental research. It is expected that the crowd models would yield a more accurate estimation to the dynamic response of the occupied structure. However, experimental testing recently conducted through a graduate student project at Bucknell University indicated that the proposed passive crowd model might be inaccurate in representing the impact on the structure from the occupants. The objective of this study is to provide an assessment of the validity of the crowd models proposed by JWG through comparing the dynamic properties obtained from experimental testing data and analytical modeling results. The experimental data used in this study was collected by Firman in 2010. The analytical results were obtained by performing a time-history analysis on a finite element model of the occupied structure. The crowd models were created based on the recommendations from the JWG combined with the physical properties of the occupants during the experimental study. During this study, SAP2000 was used to create the finite element models and to implement the analysis; Matlab and ME¿scope were used to obtain the dynamic properties of the structure through processing the time-history analysis results from SAP2000. The result of this study indicates that the active crowd model could quite accurately represent the impact on the structure from occupants standing with bent knees while the passive crowd model could not properly simulate the dynamic response of the structure when occupants were standing straight or sitting on the structure. Future work related to this study involves improving the passive crowd model and evaluating the crowd models with full-scale structure models and operating data.

Neonatal hemolytic uremic syndrome after mother-to-child transmission of a low-pathogenic stx2b harboring shiga toxin-producing Escherichia coli

This case describes evidence for a Shiga toxin-producing Escherichia coli (STEC) O146:H28 infection leading to hemolytic uremic syndrome in a neonate. STEC O146:H28 was linked hitherto with asymptomatic carriage in humans. Based on strain characteristics and genotyping data, the mother is a healthy carrier who transmitted the STEC during delivery. STEC strains belonging to the low-pathogenic STEC group must also be considered in the workup of neonatal hemolytic uremic syndrome.