Recycling workflows and services through discovery and reuse

Scientific workflows are becoming a valuable tool for scientists to capture and automate e-Science procedures. Their success brings the opportunity to publish, share, reuse and repurpose this explicitly captured knowledge. Within the myGrid project, we have identified key resources that can be shared including complete workflows, fragments of workflows and constituent services. We have examined the alternative ways these can be described by their authors (and subsequent users), and developed a unified descriptive model to support their later discovery. By basing this model on existing standards, we have been able to extend existing Web Service and Semantic Web Service infrastructure whilst still supporting the specific needs of the e-Scientist. myGrid components enable a workflow life-cycle that extends beyond execution, to include discovery of previous relevant designs, reuse of those designs, and subsequent publication. Experience with example groups of scientists indicates that this cycle is valuable. The growing number of workflows and services mean more work is needed to support the user in effective ranking of search results, and to support the repurposing process.

Assessing the performance of private equity investments

This study presents an alternative investment projection model to estimate the future values of Private Equity (PE) investments. The performance of PE investments is assessed by analyzing the risk-return relationship relative to simulated Public Market (PM) investments that mimic the cash flow patterns of PE investments. The model allows for a quantified analysis of the underlying inputs that outline the PE performance and risks, and accounts for survivorship bias. These inputs include the fund manager’s decisions regarding the selection, leverage, size, duration and timing of investment and divestments.

Using Neo4J geospatial data storage and integration

Online geographic-databases have been growing increasingly as they have become a crucial source of information for both social networks and safety-critical systems. Since the quality of such applications is largely related to the richness and completeness of their data, it becomes imperative to develop adaptable and persistent storage systems, able to make use of several sources of information as well as enabling the fastest possible response from them. This work will create a shared and extensible geographic model, able to retrieve and store information from the major spatial sources available. A geographic-based system also has very high requirements in terms of scalability, computational power and domain complexity, causing several difficulties for a traditional relational database as the number of results increases. NoSQL systems provide valuable advantages for this scenario, in particular graph databases which are capable of modeling vast amounts of inter-connected data while providing a very substantial increase of performance for several spatial requests, such as finding shortestpath routes and performing relationship lookups with high concurrency. In this work, we will analyze the current state of geographic information systems and develop a unified geographic model, named GeoPlace Explorer (GE). GE is able to import and store spatial data from several online sources at a symbolic level in both a relational and a graph databases, where several stress tests were performed in order to find the advantages and disadvantages of each database paradigm.

PUPSI :uma proposta de processo unificado para políticas de segurança da informação

The way to deal with information assets means nowadays the main factor not only for the success but also for keeping the companies in the global world. The number of information security incidents has grown for the last years. The establishment of information security policies that search to keep the security requirements of assets in the desired degrees is the major priority for the companies. This dissertation suggests a unified process for elaboration, maintenance and development of information security policies, the Processo Unificado para Políticas de Segurança da Informação - PUPSI. The elaboration of this proposal started with the construction of a structure of knowledge based on documents and official rules, published in the last two decades, about security policies and information security. It's a model based on the examined documents which defines the needed security policies to be established in the organization, its work flow and identifies the sequence of hierarchy among them. It's also made a model of the entities participating in the process. Being the problem treated by the model so complex, which involves all security policies that the company must have. PUPSI has an interative and developing approach. This approach was obtained from the instantiation of the RUP - Rational Unified Process model. RUP is a platform for software development object oriented, of Rational Software (IBM group). Which uses the best practice known by the market. PUPSI got from RUP a structure of process that offers functionality, diffusion capacity and comprehension, performance and agility for the process adjustment, offering yet capacity of adjustment to technological and structural charges of the market and the company

Visualização 3D de uma imagem digital

Pós-graduação em Ciências Cartográficas - FCT

Modelagem fotogramétrica e calibração de um sistema de visão omnidirecional

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Functional polymer coatings — My-Patterning and My-Analysis

In dieser Arbeit werden Strukturen beschrieben, die mit Polymeren auf Oberflächen erzeugt wurden. Die Anwendungen reichen von PMMA und PNIPAM Polymerbürsten, über die Restrukturierung von Polystyrol durch Lösemittel bis zu 3D-Strukturen, die aus PAH/ PSS Polyelektrolytmultischichten bestehen. Im ersten Teil werden Polymethylmethacrylat (PMMA) Bürsten in der ionischen Flüssigkeit 1-Butyl-3-Methylimidazolium Hexafluorophospat ([Bmim][PF6]) durch kontrollierte radikalische Polymerisation (ATRP) hergestellt. Kinetische Untersuchungen zeigten ein lineares und dichtes Bürstenwachstum mit einer Wachstumsrate von 4600 g/mol pro nm. Die durchschnittliche Pfropfdichte betrug 0.36 µmol/m2. Als Anwendung wurden Mikrotropfen bestehend aus der ionischen Flüssigkeit, Dimethylformamid und dem ATRP-Katalysator benutzt, um in einer definierten Geometrie Polymerbürsten auf Silizium aufzubringen. Auf diese Weise lässt sich eine bis zu 13 nm dicke Beschichtung erzeugen. Dieses Konzept ist durch die Verdampfung des Monomers Methylmethacrylat (MMA) limitiert. Aus einem 1 µl großen Tropfen aus ionischer Flüssigkeit und MMA (1:1) verdampft MMA innerhalb von 100 s. Daher wurde das Monomer sequentiell zugegeben. Der zweite Teil konzentriert sich auf die Strukturierung von Oberflächen mit Hilfe einer neuen Methode: Tintendruck. Ein piezoelektrisch betriebenes „Drop-on-Demand“ Drucksystem wurde verwendet, um Polystyrol mit 0,4 nl Tropfen aus Toluol zu strukturieren. Die auf diese Art und Weise gebildeten Mikrokrater können Anwendung als Mikrolinsen finden. Die Brennweite der Mikrolinsen kann über die Anzahl an Tropfen, die für die Strukturierung verwendet werden, eingestellt werden. Theoretisch und experimentell wurde die Brennweite im Bereich von 4,5 mm bis 0,21 mm ermittelt. Der zweite Strukturierungsprozess nutzt die Polyelektrolyte Polyvinylamin-Hydrochlorid (PAH) und Polystyrolsulfonat (PSS), um 3D-Strukturen wie z.B. Linien, Schachbretter, Ringe, Stapel mit einer Schicht für Schicht Methode herzustellen. Die Schichtdicke für eine Doppelschicht (DS) liegt im Bereich von 0.6 bis 1.1 nm, wenn NaCl als Elektrolyt mit einer Konzentration von 0,5 mol/l eingesetzt wird. Die Breite der Strukturen beträgt im Mittel 230 µm. Der Prozess wurde erweitert, um Nanomechanische Cantilever Sensoren (NCS) zu beschichten. Auf einem Array bestehend aus acht Cantilevern wurden je zwei Cantilever mit fünf Doppelschichten PAH/ PSS und je zwei Cantilever mit zehn Doppelschichten PAH/ PSS schnell und reproduzierbar beschichtet. Die Massenänderung für die individuellen Cantilever war 0,55 ng für fünf Doppelschichten und 1,08 ng für zehn Doppelschichten. Der daraus resultierende Sensor wurde einer Umgebung mit definierter Luftfeuchtigkeit ausgesetzt. Die Cantilever verbiegen sich durch die Ausdehnung der Beschichtung, da Wasser in das Polymer diffundiert. Eine maximale Verbiegung von 442 nm bei 80% Luftfeuchtigkeit wurde für die mit zehn Doppelschichten beschichteten Cantilever gefunden. Dies entspricht einer Wasseraufnahme von 35%. Zusätzlich konnte aus den Verbiegungsdaten geschlossen werden, dass die Elastizität der Polyelektrolytmultischichten zunimmt, wenn das Polymer gequollen ist. Das thermische Verhalten in Wasser wurde im nächsten Teil an nanomechanischen Cantilever Sensoren, die mit Poly(N-isopropylacrylamid)bürsten (PNIPAM) und plasmapolymerisiertem N,N-Diethylacrylamid beschichtet waren, untersucht. Die Verbiegung des Cantilevers zeigte zwei Bereiche: Bei Temperaturen kleiner der niedrigsten kritischen Temperatur (LCST) ist die Verbiegung durch die Dehydration der Polymerschicht dominiert und bei Temperaturen größer der niedrigsten kritischen Temperatur (LCST) reagiert der Cantilever Sensor überwiegend auf Relaxationsprozesse innerhalb der kollabierten Polymerschicht. Es wurde gefunden, dass das Minimum in der differentiellen Verbiegung mit der niedrigsten kritischen Temperatur von 32°C und 44°C der ausgewählten Polymeren übereinstimmt. Im letzten Teil der Arbeit wurden µ-Reflektivitäts- und µ-GISAXS Experimente eingeführt als neue Methoden, um mikrostrukturierte Proben wie NCS oder PEM Linien mit Röntgenstreuung zu untersuchen. Die Dicke von jedem individuell mit PMMA Bürsten beschichtetem NCS ist im Bereich von 32,9 bis 35,2 nm, was mit Hilfe von µ-Reflektivitätsmessungen bestimmt wurde. Dieses Ergebnis kann mit abbildender Ellipsometrie als komplementäre Methode mit einer maximalen Abweichung von 7% bestätigt werden. Als zweites Beispiel wurde eine gedruckte Polyelektrolytmultischicht aus PAH/PSS untersucht. Die Herstellungsprozedur wurde so modifiziert, dass Goldnanopartikel in die Schichtstruktur eingebracht wurden. Durch Auswertung eines µ-GISAXS Experiments konnte der Einbau der Partikel identifiziert werden. Durch eine Anpassung mit einem Unified Fit Modell wurde herausgefunden, dass die Partikel nicht agglomeriert sind und von einer Polymermatrix umgeben sind.

Hip2Norm: an object-oriented cross-platform program for 3D analysis of hip joint morphology using 2D pelvic radiographs

We developed an object-oriented cross-platform program to perform three-dimensional (3D) analysis of hip joint morphology using two-dimensional (2D) anteroposterior (AP) pelvic radiographs. Landmarks extracted from 2D AP pelvic radiographs and optionally an additional lateral pelvic X-ray were combined with a cone beam projection model to reconstruct 3D hip joints. Since individual pelvic orientation can vary considerably, a method for standardizing pelvic orientation was implemented to determine the absolute tilt/rotation. The evaluation of anatomically morphologic differences was achieved by reconstructing the projected acetabular rim and the measured hip parameters as if obtained in a standardized neutral orientation. The program had been successfully used to interactively objectify acetabular version in hips with femoro-acetabular impingement or developmental dysplasia. Hip(2)Norm is written in object-oriented programming language C++ using cross-platform software Qt (TrollTech, Oslo, Norway) for graphical user interface (GUI) and is transportable to any platform.

Enabling the evolution of J2EE applications through reverse engineering and quality assurance

Enterprise Applications are complex software systems that manipulate much persistent data and interact with the user through a vast and complex user interface. In particular applications written for the Java 2 Platform, Enterprise Edition (J2EE) are composed using various technologies such as Enterprise Java Beans (EJB) or Java Server Pages (JSP) that in turn rely on languages other than Java, such as XML or SQL. In this heterogeneous context applying existing reverse engineering and quality assurance techniques developed for object-oriented systems is not enough. Because those techniques have been created to measure quality or provide information about one aspect of J2EE applications, they cannot properly measure the quality of the entire system. We intend to devise techniques and metrics to measure quality in J2EE applications considering all their aspects and to aid their evolution. Using software visualization we also intend to inspect to structure of J2EE applications and all other aspects that can be investigate through this technique. In order to do that we also need to create a unified meta-model including all elements composing a J2EE application.

Trying to make sense in nonsense-mediated mRNA decay

Despite over 30 years of research, the molecular mechanisms of nonsense-mediated mRNA decay (NMD) are still not well understood. NMD appears to exist in most eukaryotes and is intensively studied in S. cerevisiae, C. elegans, D. melanogaster and in mammalian cells. Current evidence suggests that the core of NMD – involving UPF1, UPF2 and UPF3 – is evolutionarily conserved, but that different species may have evolved slightly different ways to identify target mRNAs for NMD and to degrade them. Our lab has shown that the exon junction complex (EJC) is not absolutely required for NMD in human cells (Bühler et al., NSMB 2006) and that it is neither restricted to CBP80-bound mRNAs as classical models claim (Rufener & Mühlemann, NSMB 2013). Together with the finding that long 3’ UTRs often are an NMD-inducing feature (Eberle et al, PLoS Biol 2008; Yepiskoposyan et al., RNA 2011), our data is consistent with much of the data from other species and hence has led to a “unified” working model for NMD (Stalder & Mühlemann, Trends Cell Biol 2008; Schweingruber et al., Biochim Biophys Acta 2013). Our recent iCLIP experiments with endogenous UPF1 indicate that UPF1 binds mRNAs indiscriminately with respect to being an NMD target or not before they engage with ribosomes (Zünd et al., NSMB 2013). After onset of translation, UPF1 is cleared from the coding region but remains bound to the 3’ UTR of mRNAs. Why this 3’ UTR-associated in some cases induces NMD and in others not is currently being investigated and not yet understood. Following assembly of a phospho-UPF1-containing NMD complex, decay adaptors (SMG5, SMG7, PNRC2) and/or the endonuclease SMG6 are recruited. While the latter cleaves the mRNA in the vicinity of the termination codon, the former proteins induce deadenylation, decapping and exonucleolytic degradation of the mRNA. In my talk, I will give an overview about the latest developments in NMD – with a focus on our own work – and try to integrate the bits and pieces into a somewhat coherent working model.

Superspace description of wagnerite-group minerals (Mg,Fe,Mn) 2 (PO 4 )(F,OH)

Reinvestigation of more than 40 samples of minerals belonging to the wagnerite group (Mg, Fe, Mn)2(PO4)(F,OH) from diverse geological environments worldwide, using single-crystal X-ray diffraction analysis, showed that most crystals have incommensurate structures and, as such, are not adequately described with known polytype models (2b), (3b), (5b), (7b) and (9b). Therefore, we present here a unified superspace model for the structural description of periodically and aperiodically modulated wagnerite with the (3+1)-dimensional superspace group C2/c(0[beta]0)s0 based on the average triplite structure with cell parameters a [asymptotically equal to] 12.8, b [asymptotically equal to] 6.4, c [asymptotically equal to] 9.6 Å, [beta] [asymptotically equal to] 117° and the modulation vectors q = [beta]b*. The superspace approach provides a way of simple modelling of the positional and occupational modulation of Mg/Fe and F/OH in wagnerite. This allows direct comparison of crystal properties.

Outcomes of Active Surveillance for Ductal Carcinoma in Situ: A Computational Risk Analysis.

BACKGROUND Ductal carcinoma in situ (DCIS) is a noninvasive breast lesion with uncertain risk for invasive progression. Usual care (UC) for DCIS consists of treatment upon diagnosis, thus potentially overtreating patients with low propensity for progression. One strategy to reduce overtreatment is active surveillance (AS), whereby DCIS is treated only upon detection of invasive disease. Our goal was to perform a quantitative evaluation of outcomes following an AS strategy for DCIS. METHODS Age-stratified, 10-year disease-specific cumulative mortality (DSCM) for AS was calculated using a computational risk projection model based upon published estimates for natural history parameters, and Surveillance, Epidemiology, and End Results data for outcomes. AS projections were compared with the DSCM for patients who received UC. To quantify the propagation of parameter uncertainty, a 95% projection range (PR) was computed, and sensitivity analyses were performed. RESULTS Under the assumption that AS cannot outperform UC, the projected median differences in 10-year DSCM between AS and UC when diagnosed at ages 40, 55, and 70 years were 2.6% (PR = 1.4%-5.1%), 1.5% (PR = 0.5%-3.5%), and 0.6% (PR = 0.0%-2.4), respectively. Corresponding median numbers of patients needed to treat to avert one breast cancer death were 38.3 (PR = 19.7-69.9), 67.3 (PR = 28.7-211.4), and 157.2 (PR = 41.1-3872.8), respectively. Sensitivity analyses showed that the parameter with greatest impact on DSCM was the probability of understaging invasive cancer at diagnosis. CONCLUSION AS could be a viable management strategy for carefully selected DCIS patients, particularly among older age groups and those with substantial competing mortality risks. The effectiveness of AS could be markedly improved by reducing the rate of understaging.

Information bias and lifetime mortality risks of radiation-induced cancer

Additive and multiplicative models of relative risk were used to measure the effect of cancer misclassification and DS86 random errors on lifetime risk projections in the Life Span Study (LSS) of Hiroshima and Nagasaki atomic bomb survivors. The true number of cancer deaths in each stratum of the cancer mortality cross-classification was estimated using sufficient statistics from the EM algorithm. Average survivor doses in the strata were corrected for DS86 random error ($\sigma$ = 0.45) by use of reduction factors. Poisson regression was used to model the corrected and uncorrected mortality rates with covariates for age at-time-of-bombing, age at-time-of-death and gender. Excess risks were in good agreement with risks in RERF Report 11 (Part 2) and the BEIR-V report. Bias due to DS86 random error typically ranged from $-$15% to $-$30% for both sexes, and all sites and models. The total bias, including diagnostic misclassification, of excess risk of nonleukemia for exposure to 1 Sv from age 18 to 65 under the non-constant relative projection model was $-$37.1% for males and $-$23.3% for females. Total excess risks of leukemia under the relative projection model were biased $-$27.1% for males and $-$43.4% for females. Thus, nonleukemia risks for 1 Sv from ages 18 to 85 (DRREF = 2) increased from 1.91%/Sv to 2.68%/Sv among males and from 3.23%/Sv to 4.02%/Sv among females. Leukemia excess risks increased from 0.87%/Sv to 1.10%/Sv among males and from 0.73%/Sv to 1.04%/Sv among females. Bias was dependent on the gender, site, correction method, exposure profile and projection model considered. Future studies that use LSS data for U.S. nuclear workers may be downwardly biased if lifetime risk projections are not adjusted for random and systematic errors. (Supported by U.S. NRC Grant NRC-04-091-02.) ^

Alpine permafrost index map

The objective of this study is the production of an Alpine Permafrost Index Map (APIM) covering the entire European Alps. A unified statistical model that is based on Alpine-wide permafrost observations is used for debris and bedrock surfaces across the entire Alps. The explanatory variables of the model are mean annual air temperatures, potential incoming solar radiation and precipitation. Offset terms were applied to make model predictions for topographic and geomorphic conditions that differ from the terrain features used for model fitting. These offsets are based on literature review and involve some degree of subjective choice during model building. The assessment of the APIM is challenging because limited independent test data are available for comparison and these observations represent point information in a spatially highly variable topography. The APIM provides an index that describes the spatial distribution of permafrost and comes together with an interpretation key that helps to assess map uncertainties and to relate map contents to their actual expression in terrain. The map can be used as a first resource to estimate permafrost conditions at any given location in the European Alps in a variety of contexts such as research and spatial planning. Results show that Switzerland likely is the country with the largest permafrost area in the Alps, followed by Italy, Austria, France and Germany. Slovenia and Liechtenstein may have marginal permafrost areas. In all countries the permafrost area is expected to be larger than the glacier-covered area.