Bayesian Methods for Inferring Gene Regulatory Networks

Thesis (Ph.D.)--University of Washington, 2016-08

Trois essais sur les banques et le pouvoir de marché

Cette thèse examine le rôle du pouvoir de marché dans le marché bancaire. L’emphase est mis sur la prise de risque, les économies d’échelle, l’efficacité économique du marché et la transmission des chocs. Le premier chapitre présente un modèle d’équilibre général dynamique stochastique en économie ouverte comprenant un marché bancaire en concurrence monopolistique. Suivant l’hypothèse de Krugman (1979, 1980) sur la relation entre les économies d’échelle et les exportations, les banques doivent défrayer un coût de transaction pour échanger à l’étranger qui diminue à mesure que le volume de leurs activités locales augmente. Cela incite les banques à réduire leur marge locale afin de profiter davantage du marché extérieur. Le modèle est solutionné et simulé pour divers degrés de concentration dans le marché bancaire. Les résultats obtenus indiquent que deux forces contraires, les économies d’échelle et le pouvoir de marché, s’affrontent lorsque le marché se concentre. La concentration permet aussi aux banques d’accroître leurs activités étrangères, ce qui les rend en contrepartie plus vulnérables aux chocs extérieurs. Le deuxième chapitre élabore un cadre de travail semblable, mais à l’intérieur duquel les banques font face à un risque de crédit. Celui-ci est partiellement assuré par un collatéral fourni par les entrepreneurs et peut être limité à l’aide d’un effort financier. Le modèle est solutionné et simulé pour divers degrés de concentration dans le marché bancaire. Les résultats montrent qu’un plus grand pouvoir de marché réduit la taille du marché financier et de la production à l’état stationnaire, mais incite les banques à prendre moins de risques. De plus, les économies dont le marché bancaire est fortement concentré sont moins sensibles à certains chocs puisque les marges plus élevés donnent initialement de la marge de manoeuvre aux banques en cas de chocs négatifs. Cet effet modérateur est éliminé lorsqu’il est possible pour les banques d’entrer et de sortir librement du marché. Une autre extension avec économies d’échelle montre que sous certaines conditions, un marché moyennement concentré est optimal pour l’économie. Le troisième chapitre utilise un modèle en analyse de portefeuille de type Moyenne-Variance afin de représenter une banque détenant du pouvoir de marché. Le rendement des dépôts et des actifs peut varier selon la quantité échangée, ce qui modifie le choix de portefeuille de la banque. Celle-ci tend à choisir un portefeuille dont la variance est plus faible lorsqu’elle est en mesure d’obtenir un rendement plus élevé sur un actif. Le pouvoir de marché sur les dépôts amène un résultat sembable pour un pouvoir de marché modéré, mais la variance finit par augmenter une fois un certain niveau atteint. Les résultats sont robustes pour différentes fonctions de demandes.

Solar magnetic carpet I: simulation of synthetic magnetograms

This paper describes a new 2D model for the photospheric evolution of the magnetic carpet. It is the first in a series of papers working towards constructing a realistic 3D non-potential model for the interaction of small-scale solar magnetic fields. In the model, the basic evolution of the magnetic elements is governed by a supergranular flow profile. In addition, magnetic elements may evolve through the processes of emergence, cancellation, coalescence and fragmentation. Model parameters for the emergence of bipoles are based upon the results of observational studies. Using this model, several simulations are considered, where the range of flux with which bipoles may emerge is varied. In all cases the model quickly reaches a steady state where the rates of emergence and cancellation balance. Analysis of the resulting magnetic field shows that we reproduce observed quantities such as the flux distribution, mean field, cancellation rates, photospheric recycle time and a magnetic network. As expected, the simulation matches observations more closely when a larger, and consequently more realistic, range of emerging flux values is allowed (4×1016 - 1019 Mx). The model best reproduces the current observed properties of the magnetic carpet when we take the minimum absolute flux for emerging bipoles to be 4×1016 Mx. In future, this 2D model will be used as an evolving photospheric boundary condition for 3D non-potential modeling.

Coupled CFD Shape Optimization for aerodynamic profiles

The present document deals with the optimization of shape of aerodynamic profiles -- The objective is to reduce the drag coefficient on a given profile without penalising the lift coefficient -- A set of control points defining the geometry are passed and parameterized as a B-Spline curve -- These points are modified automatically by means of CFD analysis -- A given shape is defined by an user and a valid volumetric CFD domain is constructed from this planar data and a set of user-defined parameters -- The construction process involves the usage of 2D and 3D meshing algorithms that were coupled into own- code -- The volume of air surrounding the airfoil and mesh quality are also parametrically defined -- Some standard NACA profiles were used by obtaining first its control points in order to test the algorithm -- Navier-Stokes equations were solved for turbulent, steady-state ow of compressible uids using the k-epsilon model and SIMPLE algorithm -- In order to obtain data for the optimization process an utility to extract drag and lift data from the CFD simulation was added -- After a simulation is run drag and lift data are passed to the optimization process -- A gradient-based method using the steepest descent was implemented in order to define the magnitude and direction of the displacement of each control point -- The control points and other parameters defined as the design variables are iteratively modified in order to achieve an optimum -- Preliminary results on conceptual examples show a decrease in drag and a change in geometry that obeys to aerodynamic behavior principles

Shock Train/Boundary-Layer Interaction in Rectangular Scramjet Isolators

Numerous studies of the dual-mode scramjet isolator, a critical component in preventing inlet unstart and/or vehicle loss by containing a collection of flow disturbances called a shock train, have been performed since the dual-mode propulsion cycle was introduced in the 1960s. Low momentum corner flow and other three-dimensional effects inherent to rectangular isolators have, however, been largely ignored in experimental studies of the boundary layer separation driven isolator shock train dynamics. Furthermore, the use of two dimensional diagnostic techniques in past works, be it single-perspective line-of-sight schlieren/shadowgraphy or single axis wall pressure measurements, have been unable to resolve the three-dimensional flow features inside the rectangular isolator. These flow characteristics need to be thoroughly understood if robust dual-mode scramjet designs are to be fielded. The work presented in this thesis is focused on experimentally analyzing shock train/boundary layer interactions from multiple perspectives in aspect ratio 1.0, 3.0, and 6.0 rectangular isolators with inflow Mach numbers ranging from 2.4 to 2.7. Secondary steady-state Computational Fluid Dynamics studies are performed to compare to the experimental results and to provide additional perspectives of the flow field. Specific issues that remain unresolved after decades of isolator shock train studies that are addressed in this work include the three-dimensional formation of the isolator shock train front, the spatial and temporal low momentum corner flow separation scales, the transient behavior of shock train/boundary layer interaction at specific coordinates along the isolator's lateral axis, and effects of the rectangular geometry on semi-empirical relations for shock train length prediction. A novel multiplane shadowgraph technique is developed to resolve the structure of the shock train along both the minor and major duct axis simultaneously. It is shown that the shock train front is of a hybrid oblique/normal nature. Initial low momentum corner flow separation spawns the formation of oblique shock planes which interact and proceed toward the center flow region, becoming more normal in the process. The hybrid structure becomes more two-dimensional as aspect ratio is increased but corner flow separation precedes center flow separation on the order of 1 duct height for all aspect ratios considered. Additional instantaneous oil flow surface visualization shows the symmetry of the three-dimensional shock train front around the lower wall centerline. Quantitative synthetic schlieren visualization shows the density gradient magnitude approximately double between the corner oblique and center flow normal structures. Fast response pressure measurements acquired near the corner region of the duct show preliminary separation in the outer regions preceding centerline separation on the order of 2 seconds. Non-intrusive Focusing Schlieren Deflectometry Velocimeter measurements reveal that both shock train oscillation frequency and velocity component decrease as measurements are taken away from centerline and towards the side-wall region, along with confirming the more two dimensional shock train front approximation for higher aspect ratios. An updated modification to Waltrup \& Billig's original semi-empirical shock train length relation for circular ducts based on centerline pressure measurements is introduced to account for rectangular isolator aspect ratio, upstream corner separation length scale, and major- and minor-axis boundary layer momentum thickness asymmetry. The latter is derived both experimentally and computationally and it is shown that the major-axis (side-wall) boundary layer has lower momentum thickness compared to the minor-axis (nozzle bounded) boundary layer, making it more separable. Furthermore, it is shown that the updated correlation drastically improves shock train length prediction capabilities in higher aspect ratio isolators. This thesis suggests that performance analysis of rectangular confined supersonic flow fields can no longer be based on observations and measurements obtained along a single axis alone. Knowledge gained by the work performed in this study will allow for the development of more robust shock train leading edge detection techniques and isolator designs which can greatly mitigate the risk of inlet unstart and/or vehicle loss in flight.

Experimental and analytical investigation of refrigerant and lubricant migration

The off-cycle refrigerant mass migration has a direct influence on the on-cycle performance since compressor energy is necessary to redistribute the refrigerant mass. No studies, as of today, are available in the open literature which experimentally measured the lubricant migration within a refrigeration system during cycling or stop/start transients. Therefore, experimental procedures measuring the refrigerant and lubricant migration through the major components of a refrigeration system during stop/start transients were developed and implemented. Results identifying the underlying physics are presented. The refrigerant and lubricant migration of an R134a automotive A/C system-utilizing a fixed orifice tube, minichannel condenser, plate and fin evaporator, U-tube type accumulator and fixed displacement compressor-was measured across five sections divided by ball valves. Using the Quick-Closing Valve Technique (QCVT) combined with the Remove and Weigh Technique (RWT) using liquid nitrogen as the condensing agent resulted in a measurement uncertainty of 0.4 percent regarding the total refrigerant mass in the system. The determination of the lubricant mass distribution was achieved by employing three different techniques-Remove and Weigh, Mix and Sample, and Flushing. To employ the Mix and Sample Technique a device-called the Mix and Sample Device-was built. A method to separate the refrigerant and lubricant was developed with an accuracy-after separation-of 0.04 grams of refrigerant left in the lubricant. When applying the three techniques, the total amount of lubricant mass in the system was determined to within two percent. The combination of measurement results-infrared photography and high speed and real time videography-provide unprecedented insight into the mechanisms of refrigerant and lubricant migration during stop-start operation. During the compressor stop period, the primary refrigerant mass migration is caused by, and follows, the diminishing pressure difference across the expansion device. The secondary refrigerant migration is caused by a pressure gradient as a result of thermal nonequilibrium within the system and causes only vapor phase refrigerant migration. Lubricant migration is proportional to the refrigerant mass during the primary refrigerant mass migration. During the secondary refrigerant mass migration lubricant is not migrating. The start-up refrigerant mass migration is caused by an imbalance of the refrigerant mass flow rates across the compressor and expansion device. The higher compressor refrigerant mass flow rate was a result of the entrainment of foam into the U-tube of the accumulator. The lubricant mass migration during the start-up was not proportional to the refrigerant mass migration. The presence of water condensate on the evaporator affected the refrigerant mass migration during the compressor stop period. Caused by an evaporative cooling effect the evaporator held 56 percent of the total refrigerant mass in the system after three minutes of compressor stop time-compared to 25 percent when no water condensate was present on the evaporator coil. Foam entrainment led to a faster lubricant and refrigerant mass migration out of the accumulator than liquid entrainment through the hole at the bottom of the U-tube. The latter was observed for when water condensate was present on the evaporator coil because-as a result of the higher amount of refrigerant mass in the evaporator before start-up-the entrainment of foam into the U-tube of the accumulator ceased before the steady state refrigerant mass distribution was reached.

Renewable energy scenarios for South Karelia – non-industrial energy demands

Tässä diplomityössä tarkastellaan täysin uusiutuvaa energiajärjestelmää Etelä-Karjalan maakunnan alueella, mikä onkin jo tällä hetkellä Suomen uusiutuvin maakunta. Diplomityössä tarkastellaan julkisen sektorin, liikenteen ja rakennusten energian kulutusta mutta teollisuuden energiankäyttö jätetään tarkastelun ulkopuolelle. Työssä tutustutaan tämän hetken Etelä-Karjalan energiajärjestelmään ja sen perusteella tehdään referenssi-skenaario. Tulevaisuuden skenaariot tehdään vuosille 2030 ja 2050. Tulevaisuuden skenaarioissa muutos keskittyy järjestelmän sähköistymiseen ja uusiutuvien tuotantomuotojen integroimiseen järjestelmään. Sähköistyminen kasvattaa sähkönkulutusta, joka pyritään kattamaan uusiutuvilla tuotantomuodoilla, lähinnä tuuli- ja aurinkovoimalla. Liikennesektori rajataan kumipyöräliikenteeseen ja sen muutos tulee olemaan haastavin ja aikaa vievin. Muutokseen pyritään liikennepolttoaineiden tuotannolla maakunnassa sekä sähköautoilulla. Uusiutuva energiajärjestelmä tarvitsee tuotannon ja kysynnän joustoa sekä älyä järjestelmältä. Työssä tarkastellaan myös järjestelmän kustannuksia sekä työllisyysvaikutuksia.

Understanding and validating accelerometry as a measure of physical activity in children with intellectual disabilities

Background Physical activity in children with intellectual disabilities is a neglected area of study, which is most apparent in relation to physical activity measurement research. Although objective measures, specifically accelerometers, are widely used in research involving children with intellectual disabilities, existing research is based on measurement methods and data interpretation techniques generalised from typically developing children. However, due to physiological and biomechanical differences between these populations, questions have been raised in the existing literature on the validity of generalising data interpretation techniques from typically developing children to children with intellectual disabilities. Therefore, there is a need to conduct population-specific measurement research for children with intellectual disabilities and develop valid methods to interpret accelerometer data, which will increase our understanding of physical activity in this population. Methods Study 1: A systematic review was initially conducted to increase the knowledge base on how accelerometers were used within existing physical activity research involving children with intellectual disabilities and to identify important areas for future research. A systematic search strategy was used to identify relevant articles which used accelerometry-based monitors to quantify activity levels in ambulatory children with intellectual disabilities. Based on best practice guidelines, a novel form was developed to extract data based on 17 research components of accelerometer use. Accelerometer use in relation to best practice guidelines was calculated using percentage scores on a study-by-study and component-by-component basis. Study 2: To investigate the effect of data interpretation methods on the estimation of physical activity intensity in children with intellectual disabilities, a secondary data analysis was conducted. Nine existing sets of child-specific ActiGraph intensity cut points were applied to accelerometer data collected from 10 children with intellectual disabilities during an activity session. Four one-way repeated measures ANOVAs were used to examine differences in estimated time spent in sedentary, moderate, vigorous, and moderate to vigorous intensity activity. Post-hoc pairwise comparisons with Bonferroni adjustments were additionally used to identify where significant differences occurred. Study 3: The feasibility on a laboratory-based calibration protocol developed for typically developing children was investigated in children with intellectual disabilities. Specifically, the feasibility of activities, measurements, and recruitment was investigated. Five children with intellectual disabilities and five typically developing children participated in 14 treadmill-based and free-living activities. In addition, resting energy expenditure was measured and a treadmill-based graded exercise test was used to assess cardiorespiratory fitness. Breath-by-breath respiratory gas exchange and accelerometry were continually measured during all activities. Feasibility was assessed using observations, activity completion rates, and respiratory data. Study 4: Thirty-six children with intellectual disabilities participated in a semi-structured school-based physical activity session to calibrate accelerometry for the estimation of physical activity intensity. Participants wore a hip-mounted ActiGraph wGT3X+ accelerometer, with direct observation (SOFIT) used as the criterion measure. Receiver operating characteristic curve analyses were conducted to determine the optimal accelerometer cut points for sedentary, moderate, and vigorous intensity physical activity. Study 5: To cross-validate the calibrated cut points and compare classification accuracy with existing cut points developed in typically developing children, a sub-sample of 14 children with intellectual disabilities who participated in the school-based sessions, as described in Study 4, were included in this study. To examine the validity, classification agreement was investigated between the criterion measure of SOFIT and each set of cut points using sensitivity, specificity, total agreement, and Cohen’s kappa scores. Results Study 1: Ten full text articles were included in this review. The percentage of review criteria met ranged from 12%−47%. Various methods of accelerometer use were reported, with most use decisions not based on population-specific research. A lack of measurement research, specifically the calibration/validation of accelerometers for children with intellectual disabilities, is limiting the ability of researchers to make appropriate and valid accelerometer use decisions. Study 2: The choice of cut points had significant and clinically meaningful effects on the estimation of physical activity intensity and sedentary behaviour. For the 71-minute session, estimations for time spent in each intensity between cut points ranged from: sedentary = 9.50 (± 4.97) to 31.90 (± 6.77) minutes; moderate = 8.10 (± 4.07) to 40.40 (± 5.74) minutes; vigorous = 0.00 (± .00) to 17.40 (± 6.54) minutes; and moderate to vigorous = 8.80 (± 4.64) to 46.50 (± 6.02) minutes. Study 3: All typically developing participants and one participant with intellectual disabilities completed the protocol. No participant met the maximal criteria for the graded exercise test or attained a steady state during the resting measurements. Limitations were identified with the usability of respiratory gas exchange equipment and the validity of measurements. The school-based recruitment strategy was not effective, with a participation rate of 6%. Therefore, a laboratory-based calibration protocol was not feasible for children with intellectual disabilities. Study 4: The optimal vertical axis cut points (cpm) were ≤ 507 (sedentary), 1008−2300 (moderate), and ≥ 2301 (vigorous). Sensitivity scores ranged from 81−88%, specificity 81−85%, and AUC .87−.94. The optimal vector magnitude cut points (cpm) were ≤ 1863 (sedentary), ≥ 2610 (moderate) and ≥ 4215 (vigorous). Sensitivity scores ranged from 80−86%, specificity 77−82%, and AUC .86−.92. Therefore, the vertical axis cut points provide a higher level of accuracy in comparison to the vector magnitude cut points. Study 5: Substantial to excellent classification agreement was found for the calibrated cut points. The calibrated sedentary cut point (ĸ =.66) provided comparable classification agreement with existing cut points (ĸ =.55−.67). However, the existing moderate and vigorous cut points demonstrated low sensitivity (0.33−33.33% and 1.33−53.00%, respectively) and disproportionately high specificity (75.44−.98.12% and 94.61−100.00%, respectively), indicating that cut points developed in typically developing children are too high to accurately classify physical activity intensity in children with intellectual disabilities. Conclusions The studies reported in this thesis are the first to calibrate and validate accelerometry for the estimation of physical activity intensity in children with intellectual disabilities. In comparison with typically developing children, children with intellectual disabilities require lower cut points for the classification of moderate and vigorous intensity activity. Therefore, generalising existing cut points to children with intellectual disabilities will underestimate physical activity and introduce systematic measurement error, which could be a contributing factor to the low levels of physical activity reported for children with intellectual disabilities in previous research.

Dynamic instabilities in scalar neural field equations with space-dependent delays

In this paper we consider a class of scalar integral equations with a form of space-dependent delay. These non-local models arise naturally when modelling neural tissue with active axons and passive dendrites. Such systems are known to support a dynamic (oscillatory) Turing instability of the homogeneous steady state. In this paper we develop a weakly nonlinear analysis of the travelling and standing waves that form beyond the point of instability. The appropriate amplitude equations are found to be the coupled mean-field Ginzburg-Landau equations describing a Turing-Hopf bifurcation with modulation group velocity of O(1). Importantly we are able to obtain the coefficients of terms in the amplitude equations in terms of integral transforms of the spatio-temporal kernels defining the neural field equation of interest. Indeed our results cover not only models with axonal or dendritic delays but those which are described by a more general distribution of delayed spatio-temporal interactions. We illustrate the predictive power of this form of analysis with comparison against direct numerical simulations, paying particular attention to the competition between standing and travelling waves and the onset of Benjamin-Feir instabilities.

Transformada wavelet aplicada a análise automática de oscilografias de curta duração em unidades geradoras

The focus of this work is the automatic analysis of disturbance records for electrical power generating units. The main proposition is a method based on wavelet transform applied to short-term disturbance records (waveform records). The goal of the method is to detect the time instants of recorded disturbances and extract meaningful information that characterize the faults. The result is a set of representative information of the monitored signals in power generators. This information can be further classified by an expert system (or other classification method) in order to classify the faults and other abnormal operating conditions. The large amount of data produced by digital fault recorders during faults justify the research of methods to assist the analysts in their task of analysing the disturbances. The literature review pointed out the state of the art and possible applications for oscillography records. The review of the COMTRADE standard and wavelet transform underlines the choice of the method for solving the problem. The conducted tests lead to the determination of the best mother wavelet for the segmentation process. The application of the proposed method to five case studies with real oscillographic records confirmed the accuracy and efficiency of the proposed scheme. With this research, the post-operation analysis of occurrences is improved and as a direct result is the reduction of the time that generators are offline.

Modeling electrocortical activity through improved local approximations of integral neural field equations

Neural field models of firing rate activity typically take the form of integral equations with space-dependent axonal delays. Under natural assumptions on the synaptic connectivity we show how one can derive an equivalent partial differential equation (PDE) model that properly treats the axonal delay terms of the integral formulation. Our analysis avoids the so-called long-wavelength approximation that has previously been used to formulate PDE models for neural activity in two spatial dimensions. Direct numerical simulations of this PDE model show instabilities of the homogeneous steady state that are in full agreement with a Turing instability analysis of the original integral model. We discuss the benefits of such a local model and its usefulness in modeling electrocortical activity. In particular we are able to treat "patchy'" connections, whereby a homogeneous and isotropic system is modulated in a spatially periodic fashion. In this case the emergence of a "lattice-directed" traveling wave predicted by a linear instability analysis is confirmed by the numerical simulation of an appropriate set of coupled PDEs. Article published and (c) American Physical Society 2007

Cardiac T2-mapping using a fast gradient echo spin echo sequence - first in vitro and in vivo experience

Background: The aim of this study was the evaluation of a fast Gradient Spin Echo Technique (GraSE) for cardiac T2-mapping, combining a robust estimation of T2 relaxation times with short acquisition times. The sequence was compared against two previously introduced T2-mapping techniques in a phantom and in vivo. Methods: Phantom experiments were performed at 1.5 T using a commercially available cylindrical gel phantom. Three different T2-mapping techniques were compared: a Multi Echo Spin Echo (MESE; serving as a reference), a T2-prepared balanced Steady State Free Precession (T2prep) and a Gradient Spin Echo sequence. For the subsequent in vivo study, 12 healthy volunteers were examined on a clinical 1.5 T scanner. The three T2-mapping sequences were performed at three short-axis slices. Global myocardial T2 relaxation times were calculated and statistical analysis was performed. For assessment of pixel-by-pixel homogeneity, the number of segments showing an inhomogeneous T2 value distribution, as defined by a pixel SD exceeding 20 % of the corresponding observed T2 time, was counted. Results: Phantom experiments showed a greater difference of measured T2 values between T2prep and MESE than between GraSE and MESE, especially for species with low T1 values. Both, GraSE and T2prep resulted in an overestimation of T2 times compared to MESE. In vivo, significant differences between mean T2 times were observed. In general, T2prep resulted in lowest (52.4 +/- 2.8 ms) and GraSE in highest T2 estimates (59.3 +/- 4.0 ms). Analysis of pixel-by-pixel homogeneity revealed the least number of segments with inhomogeneous T2 distribution for GraSE-derived T2 maps. Conclusions: The GraSE sequence is a fast and robust sequence, combining advantages of both MESE and T2prep techniques, which promises to enable improved clinical applicability of T2-mapping in the future. Our study revealed significant differences of derived mean T2 values when applying different sequence designs. Therefore, a systematic comparison of different cardiac T2-mapping sequences and the establishment of dedicated reference values should be the goal of future studies.

AUXIN-BINDING-PROTEIN1 (ABP1) in phytochrome-B-controlled responses

The auxin receptor ABP1 directly regulates plasma membrane activities including the number of PIN-formed (PIN) proteins and auxin efflux transport. Red light (R) mediated by phytochromes regulates the steady-state level of ABP1 and auxin-inducible growth capacity in etiolated tissues but, until now, there has been no genetic proof that ABP1 and phytochrome regulation of elongation share a common mechanism for organ elongation. In far red (FR)-enriched light, hypocotyl lengths were larger in the abp1-5 and abp1/ABP1 mutants, but not in tir1-1, a null mutant of the TRANSPORT-INHIBITOR-RESPONSE1 auxin receptor. The polar auxin transport inhibitor naphthylphthalamic acid (NPA) decreased elongation in the low R: FR light-enriched white light (WL) condition more strongly than in the high red: FR light-enriched condition WL suggesting that auxin transport is an important condition for FR-induced elongation. The addition of NPA to hypocotyls grown in R-and FR-enriched light inhibited hypocotyl gravitropism to a greater extent in both abp1 mutants and in phyB-9 and phyA-211 than the wild-type hypocotyl, arguing for decreased phytochrome action in conjunction with auxin transport in abp1 mutants. Transcription of FR-enriched light-induced genes, including several genes regulated by auxin and shade, was reduced 3-5-fold in abp1-5 compared with Col and was very low in abp1/ABP1. In the phyB-9 mutant the expression of these reporter genes was 5-15-fold lower than in Col. In tir1-1 and the phyA-211 mutants shade-induced gene expression was greatly attenuated. Thus, ABP1 directly or indirectly participates in auxin and light signalling.

Práticas de ensino supervisionada e a importância da creche na transição para o Jardim-de-Infância

O presente Relatório Final de Estágio foi desenvolvido no âmbito da unidade curricular de Prática de Ensino Supervisionada III (PES III) do 2.º Ciclo de Estudos, do Mestrado em Educação Pré-Escolar e Ensino do 1.º Ciclo do Ensino Básico e inclui duas partes distintas. A primeira parte diz respeito às práticas de estágio desenvolvidas no decorrer da unidade curricular Prática de Ensino Supervisionada (PES). Aí, proceder-se-á a uma reflexão crítica acerca do trabalho desenvolvido nos referidos contextos e das experiências de aprendizagem que daí resultaram. A segunda parte do relatório final de estágio está relacionada com a execução de um trabalho de investigação centrado nos seguintes objetivos: compreender a importância da frequência da creche no desenvolvimento e aprendizagem das crianças, identificar a opinião dos profissionais sobre a creche e as suas atividades e conhecer a relação pais/Jardim-de-Infância/Creche. O estudo em causa segue uma metodologia qualitativa, mais concretamente o estudo de caso e envolve duas educadoras de creche, três educadoras do jardim-de-infância, nove pais das crianças da creche e sessenta e uma crianças (9 responderam às entrevistas acerca da frequência da creche e 52 executaram o desenho alusivo à visita à sala de creche). Com a realização deste trabalho de investigação pretende-se acima de tudo obter resposta à seguinte questão: “Qual a importância da frequência da Creche na transição para o Jardim-de-Infância?” Tendo em conta o estudo realizado foi possível obter determinadas conclusões de acordo com as perpetivas dos profissionais (educadoras de creche e educadoras do jardim-de-infância), pais e crianças do jardim-de-infância. No parecer dos profissionais a creche é importante no sentido de autonomia (gerir a separação dos pais), em termos de regras, altruísmo e partilha de brinquedos, bem como o desenvolvimento global das crianças. Os pais consideram que a creche proporciona o desenvolvimento pessoal e aprendizagem das crianças. Para além disto, a mesma permite educar os seus filhos e é a primeira etapa da educação escolar. Porém, existem pais que referem que o facto de deixarem os seus filhos na referida instituição está relacionado com a inexistência de tempo da sua parte.De acordo com as entrevistas realizadas às crianças do jardim-de-infância podemos verificar que a frequência da creche foi fundamental para o crescimento saudável das crianças, sendo que 89% das crianças têm lembranças positivas sobre o primeiro dia de creche, 57% das crianças menciona como atividades que mais gostavam brincar com as bolas, 100% mencionaram que preferem brincar com outras crianças, 78% revelaram a existência de uma interação positiva entre as mesmas e a educadora, bem como 100% afirmou existir reações positivas à participação dos pais nas suas atividades.

Solid-liquid interactions in microscale structures and devices

Liquid-solid interactions become important as dimensions approach mciro/nano-scale. This dissertation focuses on liquid-solid interactions in two distinct applications: capillary driven self-assembly of thin foils into 3D structures, and droplet wetting of hydrophobic micropatterned surfaces. The phenomenon of self-assembly of complex structures is common in biological systems. Examples include self-assembly of proteins into macromolecular structures and self-assembly of lipid bilayer membranes. The principles governing this phenomenon have been applied to induce self-assembly of millimeter scale Si thin films into spherical and other 3D structures, which are then integrated into light-trapping photovoltaic (PV) devices. Motivated by this application, we present a generalized analytical study of the self-folding of thin plates into deterministic 3D shapes, through fluid-solid interactions, to be used as PV devices. This study consists of developing a model using beam theory, which incorporates the two competing components — a capillary force that promotes folding and the bending rigidity of the foil that resists folding into a 3D structure. Through an equivalence argument of thin foils of different geometry, an effective folding parameter, which uniquely characterizes the driving force for folding, has been identified. A criterion for spontaneous folding of an arbitrarily shaped 2D foil, based on the effective folding parameter, is thus established. Measurements from experiments using different materials and predictions from the model match well, validating the assumptions used in the analysis. As an alternative to the mechanics model approach, the minimization of the total free energy is employed to investigate the interactions between a fluid droplet and a flexible thin film. A 2D energy functional is proposed, comprising the surface energy of the fluid, bending energy of the thin film and gravitational energy of the fluid. Through simulations with Surface Evolver, the shapes of the droplet and the thin film at equilibrium are obtained. A critical thin film length necessary for complete enclosure of the fluid droplet, and hence successful self-assembly into a PV device, is determined and compared with the experimental results and mechanics model predictions. The results from the modeling and energy approaches and the experiments are all consistent. Superhydrophobic surfaces, which have unique properties including self-cleaning and water repelling are desired in many applications. One excellent example in nature is the lotus leaf. To fabricate these surfaces, well designed micro/nano- surface structures are often employed. In this research, we fabricate superhydrophobic micropatterned Polydimethylsiloxane (PDMS) surfaces composed of micropillars of various sizes and arrangements by means of soft lithography. Both anisotropic surfaces, consisting of parallel grooves and cylindrical pillars in rectangular lattices, and isotropic surfaces, consisting of cylindrical pillars in square and hexagonal lattices, are considered. A novel technique is proposed to image the contact line (CL) of the droplet on the hydrophobic surface. This technique provides a new approach to distinguish between partial and complete wetting. The contact area between droplet and microtextured surface is then measured for a droplet in the Cassie state, which is a state of partial wetting. The results show that although the droplet is in the Cassie state, the contact area does not necessarily follow Cassie model predictions. Moreover, the CL is not circular, and is affected by the micropatterns, in both isotropic and anisotropic cases. Thus, it is suggested that along with the contact angle — the typical parameter reported in literature quantifying wetting, the size and shape of the contact area should also be presented. This technique is employed to investigate the evolution of the CL on a hydrophobic micropatterned surface in the cases of: a single droplet impacting the micropatterned surface, two droplets coalescing on micropillars, and a receding droplet resting on the micropatterned surface. Another parameter which quantifies hydrophobicity is the contact angle hysteresis (CAH), which indicates the resistance of the surface to the sliding of a droplet with a given volume. The conventional methods of using advancing and receding angles or tilting stage to measure the resistance of the micropatterned surface are indirect, without mentioning the inaccuracy due to the discrete and stepwise motion of the CL on micropillars. A micronewton force sensor is utilized to directly measure the resisting force by dragging a droplet on a microtextured surface. Together with the proposed imaging technique, the evolution of the CL during sliding is also explored. It is found that, at the onset of sliding, the CL behaves as a linear elastic solid with a constant stiffness. Afterwards, the force first increases and then decreases and reaches a steady state, accompanied with periodic oscillations due to regular pinning and depinning of the CL. Both the maximum and steady state forces are primarily dependent on area fractions of the micropatterned surfaces in our experiment. The resisting force is found to be proportional to the number of pillars which pin the CL at the trailing edge, validating the assumption that the resistance mainly arises from the CL pinning at the trailing edge. In each pinning-and-depinning cycle during the steady state, the CL also shows linear elastic behavior but with a lower stiffness. The force variation and energy dissipation involved can also be determined. This novel method of measuring the resistance of the micropatterned surface elucidates the dependence on CL pinning and provides more insight into the mechanisms of CAH.