Aplicação do Building Information Modeling na gestão de projetos de construção

Dissertação de mestrado em Construção e Reabilitação Sustentáveis

A integração do Building Information Modeling (BIM) num projeto de reabilitação

Dissertação de mestrado integrado em Engenharia Civil

The MIGCLIM R package - seamless integration of dispersal constraints into projections of species distribution models

The MIGCLIM R package is a function library for the open source R software that enables the implementation of species-specific dispersal constraints into projections of species distribution models under environmental change and/or landscape fragmentation scenarios. The model is based on a cellular automaton and the basic modeling unit is a cell that is inhabited or not. Model parameters include dispersal distance and kernel, long distance dispersal, barriers to dispersal, propagule production potential and habitat invasibility. The MIGCLIM R package has been designed to be highly flexible in the parameter values it accepts, and to offer good compatibility with existing species distribution modeling software. Possible applications include the projection of future species distributions under environmental change conditions and modeling the spread of invasive species.

Modeling stochasticity and robustness in gene regulatory networks.

MOTIVATION: Understanding gene regulation in biological processes and modeling the robustness of underlying regulatory networks is an important problem that is currently being addressed by computational systems biologists. Lately, there has been a renewed interest in Boolean modeling techniques for gene regulatory networks (GRNs). However, due to their deterministic nature, it is often difficult to identify whether these modeling approaches are robust to the addition of stochastic noise that is widespread in gene regulatory processes. Stochasticity in Boolean models of GRNs has been addressed relatively sparingly in the past, mainly by flipping the expression of genes between different expression levels with a predefined probability. This stochasticity in nodes (SIN) model leads to over representation of noise in GRNs and hence non-correspondence with biological observations. RESULTS: In this article, we introduce the stochasticity in functions (SIF) model for simulating stochasticity in Boolean models of GRNs. By providing biological motivation behind the use of the SIF model and applying it to the T-helper and T-cell activation networks, we show that the SIF model provides more biologically robust results than the existing SIN model of stochasticity in GRNs. AVAILABILITY: Algorithms are made available under our Boolean modeling toolbox, GenYsis. The software binaries can be downloaded from http://si2.epfl.ch/ approximately garg/genysis.html.

Study and implementation of some quantitative trading models

Quantitative or algorithmic trading is the automatization of investments decisions obeying a fixed or dynamic sets of rules to determine trading orders. It has increasingly made its way up to 70% of the trading volume of one of the biggest financial markets such as the New York Stock Exchange (NYSE). However, there is not a signi cant amount of academic literature devoted to it due to the private nature of investment banks and hedge funds. This projects aims to review the literature and discuss the models available in a subject that publications are scarce and infrequently. We review the basic and fundamental mathematical concepts needed for modeling financial markets such as: stochastic processes, stochastic integration and basic models for prices and spreads dynamics necessary for building quantitative strategies. We also contrast these models with real market data with minutely sampling frequency from the Dow Jones Industrial Average (DJIA). Quantitative strategies try to exploit two types of behavior: trend following or mean reversion. The former is grouped in the so-called technical models and the later in the so-called pairs trading. Technical models have been discarded by financial theoreticians but we show that they can be properly cast into a well defined scientific predictor if the signal generated by them pass the test of being a Markov time. That is, we can tell if the signal has occurred or not by examining the information up to the current time; or more technically, if the event is F_t-measurable. On the other hand the concept of pairs trading or market neutral strategy is fairly simple. However it can be cast in a variety of mathematical models ranging from a method based on a simple euclidean distance, in a co-integration framework or involving stochastic differential equations such as the well-known Ornstein-Uhlenbeck mean reversal ODE and its variations. A model for forecasting any economic or financial magnitude could be properly defined with scientific rigor but it could also lack of any economical value and be considered useless from a practical point of view. This is why this project could not be complete without a backtesting of the mentioned strategies. Conducting a useful and realistic backtesting is by no means a trivial exercise since the \laws" that govern financial markets are constantly evolving in time. This is the reason because we make emphasis in the calibration process of the strategies' parameters to adapt the given market conditions. We find out that the parameters from technical models are more volatile than their counterpart form market neutral strategies and calibration must be done in a high-frequency sampling manner to constantly track the currently market situation. As a whole, the goal of this project is to provide an overview of a quantitative approach to investment reviewing basic strategies and illustrating them by means of a back-testing with real financial market data. The sources of the data used in this project are Bloomberg for intraday time series and Yahoo! for daily prices. All numeric computations and graphics used and shown in this project were implemented in MATLAB^R scratch from scratch as a part of this thesis. No other mathematical or statistical software was used.

Genetic and genomic analysis modeling of germline c-MYC overexpression and cancer susceptibility

Background: Germline genetic variation is associated with the differential expression of many human genes. The phenotypic effects of this type of variation may be important when considering susceptibility to common genetic diseases. Three regions at 8q24 have recently been identified to independently confer risk of prostate cancer. Variation at 8q24 has also recently been associated with risk of breast and colorectal cancer. However, none of the risk variants map at or relatively close to known genes, with c-MYC mapping a few hundred kilobases distally. Results: This study identifies cis-regulators of germline c-MYC expression in immortalized lymphocytes of HapMap individuals. Quantitative analysis of c-MYC expression in normal prostate tissues suggests an association between overexpression and variants in Region 1 of prostate cancer risk. Somatic c-MYC overexpression correlates with prostate cancer progression and more aggressive tumor forms, which was also a pathological variable associated with Region 1. Expression profiling analysis and modeling of transcriptional regulatory networks predicts a functional association between MYC and the prostate tumor suppressor KLF6. Analysis of MYC/Myc-driven cell transformation and tumorigenesis substantiates a model in which MYC overexpression promotes transformation by down-regulating KLF6. In this model, a feedback loop through E-cadherin down-regulation causes further transactivation of c-MYC.Conclusion: This study proposes that variation at putative 8q24 cis-regulator(s) of transcription can significantly alter germline c-MYC expression levels and, thus, contribute to prostate cancer susceptibility by down-regulating the prostate tumor suppressor KLF6 gene.

Financial integration, productivity and capital accumulation

Understanding the mechanism through which financial globalization affect economic performance is crucial for evaluating the costs and benefits of opening financial markets. This paper is a first attempt at disentangling the effects of financial integration on the two main determinants of economic performance: productivity (TFP)and investments. I provide empirical evidence from a sample of 93 countries observed between 1975 and 1999. The results suggest that financial integration has a positive direct effect on productivity, while it spurs capital accumulation only with some delay and indirectly, since capital follows the rise in productivity. I control for indirect effects of financial globalization through banking crises. Such episodes depress both investments and TFP, though they are triggered by financial integration only to a minor extent. The paper also provides a discussion of a simple model on the effects of financial integration, and shows additional empirical evidence supporting it.

Physical properties and particle-size fractions of soil organic matter in crop-livestock integration

Crop-livestock integration represents an interesting alternative of soil management, especially in regions where the maintenance of cover crops in no-tillage systems is difficult. The objective of this study was to evaluate soil physical and chemical properties, based on the hypothesis that a well-managed crop-livestock integration system improves the soil quality and stabilizes the system. The experiment was set up in a completely randomized design, with five replications. The treatments were arranged in a 6 x 4 factorial design, to assess five crop rotation systems in crop-livestock integration, and native forest as reference of soil undisturbed by agriculture, in four layers (0.0-0.05; 0.05-0.10; 0.10-0.15 and 0.15-0.20 m). The crop rotation systems in crop-livestock integration promoted changes in soil physical and chemical properties and the effects of the different systems were mainly detected in the surface layer. The crops in integrated crop-livestock systems allowed the maintenance of soil carbon at levels equal to those of the native forest, proving the efficiency of these systems in terms of soil conservation. The systems influenced the environmental stability positively; the soil quality indicator mineral-associated organic matter was best related to aggregate stability.

Modeling of Pressurizer Using APROS and TRACE Thermal Hydraulic Codes

Diplomityön tavoitteena on paineistimen yksityiskohtainen mallintaminen APROS- ja TRACE- termohydrauliikkaohjelmistoja käyttäen. Rakennetut paineistinmallit testattiin vertaamalla laskentatuloksia paineistimen täyttymistä, tyhjentymistä ja ruiskutusta käsittelevistä erilliskokeista saatuun mittausdataan. Tutkimuksen päätavoitteena on APROSin paineistinmallin validoiminen käyttäen vertailuaineistona PACTEL ATWS-koesarjan sopivia paineistinkokeita sekä MIT Pressurizer- ja Neptunus- erilliskokeita. Lisäksi rakennettiin malli Loviisan ydinvoimalaitoksen paineistimesta, jota käytettiin turbiinitrippitransientin simulointiin tarkoituksena selvittää mahdolliset voimalaitoksen ja koelaitteistojen mittakaavaerosta johtuvat vaikutukset APROSin paineistinlaskentaan. Kokeiden simuloinnissa testattiin erilaisia noodituksia ja mallinnusvaihtoehtoja, kuten entalpian ensimmäisen ja toisen kertaluvun diskretisointia, ja APROSin sekä TRACEn antamia tuloksia vertailtiin kattavasti toisiinsa. APROSin paineistinmallin lämmönsiirtokorrelaatioissa havaittiin merkittävä puute ja laskentatuloksiin saatiin huomattava parannus ottamalla käyttöön uusi seinämälauhtumismalli. Työssä tehdyt TRACE-simulaatiot ovat osa United States Nuclear Regulatory Commissionin kansainvälistä CAMP-koodinkehitys-ja validointiohjelmaa.

Novel Genome-Editing Tools to Model and Correct Primary Immunodeficiencies.

Severe combined immunodeficiency (SCID) and other severe non-SCID primary immunodeficiencies (non-SCID PID) can be treated by allogeneic hematopoietic stem cell (HSC) transplantation, but when histocompatibility leukocyte antigen-matched donors are lacking, this can be a high-risk procedure. Correcting the patient's own HSCs with gene therapy offers an attractive alternative. Gene therapies currently being used in clinical settings insert a functional copy of the entire gene by means of a viral vector. With this treatment, severe complications may result due to integration within oncogenes. A promising alternative is the use of endonucleases such as ZFNs, TALENs, and CRISPR/Cas9 to introduce a double-stranded break in the DNA and thus induce homology-directed repair. With these genome-editing tools a correct copy can be inserted in a precisely targeted "safe harbor." They can also be used to correct pathogenic mutations in situ and to develop cellular or animal models needed to study the pathogenic effects of specific genetic defects found in immunodeficient patients. This review discusses the advantages and disadvantages of these endonucleases in gene correction and modeling with an emphasis on CRISPR/Cas9, which offers the most promise due to its efficacy and versatility.

Dual and Opposite Effects of hRAD51 Chemical Modulation on HIV-1 Integration.

The cellular DNA repair hRAD51 protein has been shown to restrict HIV-1 integration both in vitro and in vivo. To investigate its regulatory functions, we performed a pharmacological analysis of the retroviral integration modulation by hRAD51. We found that, in vitro, chemical activation of hRAD51 stimulates its integration inhibitory properties, whereas inhibition of hRAD51 decreases the integration restriction, indicating that the modulation of HIV-1 integration depends on the hRAD51 recombinase activity. Cellular analyses demonstrated that cells exhibiting high hRAD51 levels prior to de novo infection are more resistant to integration. On the other hand, when hRAD51 was activated during integration, cells were more permissive. Altogether, these data establish the functional link between hRAD51 activity and HIV-1 integration. Our results highlight the multiple and opposite effects of the recombinase during integration and provide new insights into the cellular regulation of HIV-1 replication.

Synergy Sources, Target Autonomy and Integration in Acquisitions

Determining the appropriate level of integration is crucial to realizing value from acquisitions. Most prior research assumes that higher integration implies the removal of autonomy from target managers, which in turn undermines the functioning of the target firm if it entails unfamiliar elements for the acquirer. Using a survey of 86 acquisitions to obtain the richness of detail necessary to distinguish integration from autonomy, the authors argue and find that integration and autonomy are not the opposite ends of a single continuum. Certain conditions (e.g., when complementarity rather than similarity is the primary source of synergy) lead to high levels of both integration and autonomy. In addition, similarity negatively moderates the relationship between complementarity and autonomy when the target offers both synergy sources. In contrast, similarity does not moderate the link between complementarity and integration. The authors' findings advance scholarly understanding about the drivers of implementation strategy and in particular the different implementation strategies acquiring managers deploy when they attempt to leverage complementarities, similarities, or both.

Introducing Continuous Integration for C and C++ Software Development Projects on Linux Platform

Software integration is a stage in a software development process to assemble separate components to produce a single product. It is important to manage the risks involved and being able to integrate smoothly, because software cannot be released without integrating it first. Furthermore, it has been shown that the integration and testing phase can make up 40 % of the overall project costs. These issues can be mitigated by using a software engineering practice called continuous integration. This thesis work presents how continuous integration is introduced to the author's employer organisation. This includes studying how the continuous integration process works and creating the technical basis to start using the process on future projects. The implemented system supports software written in C and C++ programming languages on Linux platform, but the general concepts can be applied to any programming language and platform by selecting the appropriate tools. The results demonstrate in detail what issues need to be solved when the process is acquired in a corporate environment. Additionally, they provide an implementation and process description suitable to the organisation. The results show that continuous integration can reduce the risks involved in a software process and increase the quality of the product as well.

Sensor Fusion of Proprioception, Force and Vision in Estimation and Robot

Sensor-based robot control allows manipulation in dynamic environments with uncertainties. Vision is a versatile low-cost sensory modality, but low sample rate, high sensor delay and uncertain measurements limit its usability, especially in strongly dynamic environments. Force is a complementary sensory modality allowing accurate measurements of local object shape when a tooltip is in contact with the object. In multimodal sensor fusion, several sensors measuring different modalities are combined to give a more accurate estimate of the environment. As force and vision are fundamentally different sensory modalities not sharing a common representation, combining the information from these sensors is not straightforward. In this thesis, methods for fusing proprioception, force and vision together are proposed. Making assumptions of object shape and modeling the uncertainties of the sensors, the measurements can be fused together in an extended Kalman filter. The fusion of force and visual measurements makes it possible to estimate the pose of a moving target with an end-effector mounted moving camera at high rate and accuracy. The proposed approach takes the latency of the vision system into account explicitly, to provide high sample rate estimates. The estimates also allow a smooth transition from vision-based motion control to force control. The velocity of the end-effector can be controlled by estimating the distance to the target by vision and determining the velocity profile giving rapid approach and minimal force overshoot. Experiments with a 5-degree-of-freedom parallel hydraulic manipulator and a 6-degree-of-freedom serial manipulator show that integration of several sensor modalities can increase the accuracy of the measurements significantly.