Synthetic regulation of eukaryotic gene expression by noncoding RNA

Synthetic biological systems promise to combine the spectacular diversity of biological functionality with engineering principles to design new life to address many pressing needs. As these engineered systems advance in sophistication, there is ever-greater need for customizable, situation-specific expression of desired genes. However, existing gene control platforms are generally not modular, or do not display performance requirements required for robust phenotypic responses to input signals. This work expands the capabilities of eukaryotic gene control in two important directions.

For development of greater modularity, we extend the use of synthetic self-cleaving ribozyme switches to detect changes in input protein levels and convey that information into programmed gene expression in eukaryotic cells. We demonstrate both up- and down-regulation of levels of an output transgene by more than 4-fold in response to rising input protein levels, with maximal output gene expression approaching the highest levels observed in yeast. In vitro experiments demonstrate protein-dependent ribozyme activity modulation. We further demonstrate the platform in mammalian cells. Our switch devices do not depend on special input protein activity, and can be tailored to respond to any input protein to which a suitable RNA aptamer can be developed. This platform can potentially be employed to regulate the expression of any transgene or any endogenous gene by 3’ UTR replacement, allowing for more complex cell state-specific reprogramming.

We also address an important concern with ribozyme switches, and riboswitch performance in general, their dynamic range. While riboswitches have generally allowed for versatile and modular regulation, so far their dynamic ranges of output gene modulation have been modest, generally at most 10-fold. We address this shortcoming by developing a modular genetic amplifier for near-digital control of eukaryotic gene expression. We combine ribozyme switch-mediated regulation of a synthetic TF with TF-mediated regulation of an output gene. The amplifier platform allows for as much as 20-fold regulation of output gene expression in response to input signal, with maximal expression approaching the highest levels observed in yeast, yet being tunable to intermediate and lower expression levels. EC50 values are more than 4 times lower than in previously best-performing non-amplifier ribozyme switches. The system design retains the modular-input architecture of the ribozyme switch platform, and the near-digital dynamic ranges of TF-based gene control.

Together, these developments suggest great potential for the wide applicability of these platforms for better-performing eukaryotic gene regulation, and more sophisticated, customizable reprogramming of cellular activity.

Qubit state estimation and enhancement by quantum thermal noise

International audience

A Thermal Management Solution for Compact Power Converters

Regulated Transformer Rectifier Units contain several power electronic boards to facilitate AC to DC power conversion. As these units become smaller, the number of devices on each board increases while their distance from each other decreases, making active cooling essential to maintaining reliable operation. Although it is widely accepted that liquid is a far superior heat transfer medium to air, the latter is still capable of yielding low device operating temperatures with proper heat sink and airflow design. The purpose of this study is to describe the models and methods used to design and build the thermal management system for one of the power electronic boards in a compact, high power regulated transformer rectifier unit. Maximum device temperature, available pressure drop and manufacturability were assessed when selecting the final design for testing. Once constructed, the thermal management system’s performance was experimentally verified at three different power levels.

Impacte da nova regulamentação na certificação energética de edifícios

Dissertação de Mestrado, Engenharia Civil, Especialização em Construção, Instituto Superior de Engenharia, Universidade do Algarve, 2016

Qualificação de edifícios residenciais verticais em Natal/RN à luz do regulamento técnico da qualidade para o nível de eficiência energética de edificações residenciais (RTQ-R)

The goal of the research was to investigate the energy performance of residential vertical buildings envelope in the hot and humid climate of Natal, capital of Rio Grande do Norte, based in the Technical Regulation of Quality for Energy Efficiency Level in Residential Buildings (RTQ -R), launched in 2010. The study pretends to contribute to the development of design strategies appropriate to the specific local climate and the increasing of energy efficiency level of the envelope. The methodological procedures included the survey in 22 (twenty two) residential buildings, the formulation of representative prototypes based on typological and constructives characters researched and the classification of the level of energy efficiency in the envelopment of these prototypes, using as a tool the prescriptive method of the RTQ-R and the parametric analyzes from assigning different values of the following variables: shape of the pavement type; distribution of housing compartments; orientation of the building; area and shading of openings; thermal transmittance, and solar absorptance of opaque materials of the frontage in order to evaluate the influence of these on the envelopment performance. The main results accomplished with this work includes the qualification of vertical residential buildings in Natal/RN; the verification of the adequacy of these buildings to local climate based from the diagnosis of the thermal energy of the envelopment performance, the identification of variables with more significant influence on the prescriptive methodology of RTQ-R and design solutions more favorable to obtain higher levels energy efficiency by this method. Finally, it was verified, that some of these solutions proved contradictory in relation to the recommendations contained in the theoretical approaches regarding environmental comfort in hot and humid weather, which indicates the need for improvement of the prescriptive method RTQ-R and further research on efficient design solutions

Removal of BrO3 − from drinking water samples using newly developed agricultural waste-based activated carbon and its determination by ultra-performance liquid chromatography-mass spectrometry

Activated carbon was prepared from date pits via chemical activation with H3PO4. The effects of activating agent concentration and activation temperature on the yield and surface area were studied. The optimal activated carbon was prepared at 450 °C using 55 % H3PO4. The prepared activated carbon was characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, thermogravimetric-differential thermal analysis, and Brunauer, Emmett, and Teller (BET) surface area. The prepared date pit-based activated carbon (DAC) was used for the removal of bromate (BrO3 −). The concentration of BrO3 − was determined by ultra-performance liquid chromatography-mass tandem spectrometry (UPLC-MS/MS). The experimental equilibrium data for BrO3 − adsorption onto DAC was well fitted to the Langmuir isotherm model and showed maximum monolayer adsorption capacity of 25.64 mg g−1. The adsorption kinetics of BrO3 − adsorption was very well represented by the pseudo-first-order equation. The analytical application of DAC for the analysis of real water samples was studied with very promising results.

A SCR Model based on Reactor and Engine Experimental Studies for a Cu-zeolite Catalyst

A NOx reduction efficiency higher than 95% with NH3 slip less than 30 ppm is desirable for heavy-duty diesel (HDD) engines using selective catalytic reduction (SCR) systems to meet the US EPA 2010 NOx standard and the 2014-2018 fuel consumption regulation. The SCR performance needs to be improved through experimental and modeling studies. In this research, a high fidelity global kinetic 1-dimensional 2-site SCR model with mass transfer, heat transfer and global reaction mechanisms was developed for a Cu-zeolite catalyst. The model simulates the SCR performance for the engine exhaust conditions with NH3 maldistribution and aging effects, and the details are presented. SCR experimental data were collected for the model development, calibration and validation from a reactor at Oak Ridge National Laboratory (ORNL) and an engine experimental setup at Michigan Technological University (MTU) with a Cummins 2010 ISB engine. The model was calibrated separately to the reactor and engine data. The experimental setup, test procedures including a surrogate HD-FTP cycle developed for transient studies and the model calibration process are described. Differences in the model parameters were determined between the calibrations developed from the reactor and the engine data. It was determined that the SCR inlet NH3 maldistribution is one of the reasons causing the differences. The model calibrated to the engine data served as a basis for developing a reduced order SCR estimator model. The effect of the SCR inlet NO2/NOx ratio on the SCR performance was studied through simulations using the surrogate HD-FTP cycle. The cumulative outlet NOx and the overall NOx conversion efficiency of the cycle are highest with a NO2/NOx ratio of 0.5. The outlet NH3 is lowest for the NO2/NOx ratio greater than 0.6. A combined engine experimental and simulation study was performed to quantify the NH3 maldistribution at the SCR inlet and its effects on the SCR performance and kinetics. The uniformity index (UI) of the SCR inlet NH3 and NH3/NOx ratio (ANR) was determined to be below 0.8 for the production system. The UI was improved to 0.9 after installation of a swirl mixer into the SCR inlet cone. A multi-channel model was developed to simulate the maldistribution effects. The results showed that reducing the UI of the inlet ANR from 1.0 to 0.7 caused a 5-10% decrease in NOx reduction efficiency and 10-20 ppm increase in the NH3 slip. The simulations of the steady-state engine data with the multi-channel model showed that the NH3 maldistribution is a factor causing the differences in the calibrations developed from the engine and the reactor data. The Reactor experiments were performed at ORNL using a Spaci-IR technique to study the thermal aging effects. The test results showed that the thermal aging (at 800°C for 16 hours) caused a 30% reduction in the NH3 stored on the catalyst under NH3 saturation conditions and different axial concentration profiles under SCR reaction conditions. The kinetics analysis showed that the thermal aging caused a reduction in total NH3 storage capacity (94.6 compared to 138 gmol/m3), different NH3 adsorption/desorption properties and a decrease in activation energy and the pre-exponential factor for NH3 oxidation, standard and fast SCR reactions. Both reduction in the storage capability and the change in kinetics of the major reactions contributed to the change in the axial storage and concentration profiles observed from the experiments.

CHARACTERIZATION OF THE ATMOSPHERIC EFFECTS ON THE TRANSMISSION OF THERMAL RADIATION

Atmospheric scattering plays a crucial rule in degrading the performance of electro optical imaging systems operating in the visible and infra-red spectral bands, and hence limits the quality of the acquired images, either through reduction of contrast or increase of image blur. The exact nature of light scattering by atmospheric media is highly complex and depends on the types, orientations, sizes and distributions of particles constituting these media, as well as wavelengths, polarization states and directions of the propagating radiation. Here we follow the common approach for solving imaging and propagation problems by treating the propagating light through atmospheric media as composed of two main components: a direct (unscattered), and a scattered component. In this work we developed a detailed model of the effects of absorption and scattering by haze and fog atmospheric aerosols on the optical radiation propagating from the object plane to an imaging system, based on the classical theory of EM scattering. This detailed model is then used to compute the average point spread function (PSF) of an imaging system which properly accounts for the effects of the diffraction, scattering, and the appropriate optical power level of both the direct and the scattered radiation arriving at the pupil of the imaging system. Also, the calculated PSF, properly weighted for the energy contributions of the direct and scattered components is used, in combination with a radiometric model, to estimate the average number of the direct and scattered photons detected at the sensor plane, which are then used to calculate the image spectrum signal to- noise ratio (SNR) in the visible near infra-red (NIR) and mid infra-red (MIR) spectral wavelength bands. Reconstruction of images degraded by atmospheric scattering and measurement noise is then performed, up to the limit imposed by the noise effective cutoff spatial frequency of the image spectrum SNR. Key results of this research are as follows: A mathematical model based on Mie scattering theory for how scattering from aerosols affects the overall point spread function (PSF) of an imaging system was developed, coded in MATLAB, and demonstrated. This model along with radiometric theory was used to predict the limiting resolution of an imaging system as a function of the optics, scattering environment, and measurement noise. Finally, image reconstruction algorithms were developed and demonstrated which mitigate the effects of scattering-induced blurring to within the limits imposed by noise.

AN INVESTIGATION OF VARIABLE VALVE TIMING EFFECTS ON HCCI ENGINE PERFORMANCE

The Homogeneous Charge Compression Ignition (HCCI) engine is a promising combustion concept for reducing NOx and particulate matter (PM) emissions and providing a high thermal efficiency in internal combustion engines. This concept though has limitations in the areas of combustion control and achieving stable combustion at high loads. For HCCI to be a viable option for on-road vehicles, further understanding of its combustion phenomenon and its control are essential. Thus, this thesis has a focus on both the experimental setup of an HCCI engine at Michigan Technological University (MTU) and also developing a physical numerical simulation model called the Sequential Model for Residual Affected HCCI (SMRH) to investigate performance of HCCI engines. The primary focus is on understanding the effects of intake and exhaust valve timings on HCCI combustion. For the experimental studies, this thesis provided the contributions for development of HCCI setup at MTU. In particular, this thesis made contributions in the areas of measurement of valve profiles, measurement of piston to valve contact clearance for procuring new pistons for further studies of high geometric compression ratio HCCI engines. It also consists of developing and testing a supercharging station and the setup of an electrical air heater to extend the HCCI operating region. The HCCI engine setup is based on a GM 2.0 L LHU Gen 1 engine which is a direct injected engine with variable valve timing (VVT) capabilities. For the simulation studies, a computationally efficient modeling platform has been developed and validated against experimental data from a single cylinder HCCI engine. In-cylinder pressure trace, combustion phasing (CA10, CA50, BD) and performance metrics IMEP, thermal efficiency, and CO emission are found to be in good agreement with experimental data for different operating conditions. Effects of phasing intake and exhaust valves are analyzed using SMRH. In addition, a novel index called Fuel Efficiency and Emissions (FEE) index is defined and is used to determine the optimal valve timings for engine operation through the use of FEE contour maps.

THE EFFECT OF ANNEALING ON AMORPHOUS SILICON BASED SOLAR PHOTOVOLTAIC THERMAL SYSTEM (PV/T) AND APPROPRIATE GLOBAL DISPATCH STRATEGIES

Previous work has shown that high-temperature short-term spike thermal annealing of hydrogenated amorphous silicon (a-Si:H) photovoltaic thermal (PVT) systems results in higher electrical energy output. The relationship between temperature and performance of a-Si:H PVT is not simple as high temperatures during thermal annealing improves the immediate electrical performance following an anneal, but during the anneal it creates a marked drop in electrical performance. In addition, the power generation of a-Si:H PVT depends on both the environmental conditions and the Staebler-Wronski Effect kinetics. In order to improve the performance of a-Si:H PVT systems further, this paper reports on the effect of various dispatch strategies on system electrical performance. Utilizing experimental results from thermal annealing, an annealing model simulation for a-Si:Hbased PVT was developed and applied to different cities in the U.S. to investigate potential geographic effects on the dispatch optimization of the overall electrical PVT systems performance and annual electrical yield. The results showed that spike thermal annealing once per day maximized the improved electrical energy generation. In the outdoor operating condition this ideal behavior deteriorates and optimization rules are required to be implemented.

Leakage Temperature Dependency Aware Real-Time Scheduling for Power and Thermal Optimization

Catering to society’s demand for high performance computing, billions of transistors are now integrated on IC chips to deliver unprecedented performances. With increasing transistor density, the power consumption/density is growing exponentially. The increasing power consumption directly translates to the high chip temperature, which not only raises the packaging/cooling costs, but also degrades the performance/reliability and life span of the computing systems. Moreover, high chip temperature also greatly increases the leakage power consumption, which is becoming more and more significant with the continuous scaling of the transistor size. As the semiconductor industry continues to evolve, power and thermal challenges have become the most critical challenges in the design of new generations of computing systems. In this dissertation, we addressed the power/thermal issues from the system-level perspective. Specifically, we sought to employ real-time scheduling methods to optimize the power/thermal efficiency of the real-time computing systems, with leakage/ temperature dependency taken into consideration. In our research, we first explored the fundamental principles on how to employ dynamic voltage scaling (DVS) techniques to reduce the peak operating temperature when running a real-time application on a single core platform. We further proposed a novel real-time scheduling method, “M-Oscillations” to reduce the peak temperature when scheduling a hard real-time periodic task set. We also developed three checking methods to guarantee the feasibility of a periodic real-time schedule under peak temperature constraint. We further extended our research from single core platform to multi-core platform. We investigated the energy estimation problem on the multi-core platforms and developed a light weight and accurate method to calculate the energy consumption for a given voltage schedule on a multi-core platform. Finally, we concluded the dissertation with elaborated discussions of future extensions of our research.

Regulation of bone marrow stem cells through oscillatory shear stresses - A heart valve tissue engineering perspective

Heart valve disease occurs in adults as well as in pediatric population due to age-related changes, rheumatic fever, infection or congenital condition. Current treatment options are limited to mechanical heart valve (MHV) or bio-prosthetic heart valve (BHV) replacements. Lifelong anti-coagulant medication in case of MHV and calcification, durability in case of BHV are major setbacks for both treatments. Lack of somatic growth of these implants require multiple surgical interventions in case of pediatric patients. Advent of stem cell research and regenerative therapy propose an alternative and potential tissue engineered heart valves (TEHV) treatment approach to treat this life threatening condition. TEHV has the potential to promote tissue growth by replacing and regenerating a functional native valve. Hemodynamics play a crucial role in heart valve tissue formation and sustained performance. The focus of this study was to understand the role of physiological shear stress and flexure effects on de novo HV tissue formation as well as resulting gene and protein expression. A bioreactor system was used to generate physiological shear stress and cyclic flexure. Human bone marrow mesenchymal stem cell derived tissue constructs were exposed to native valve-like physiological condition. Responses of these tissue constructs to the valve-relevant stress states along with gene and protein expression were investigated after 22 days of tissue culture. We conclude that the combination of steady flow and cyclic flexure helps support engineered tissue formation by the co-existence of both OSS and appreciable shear stress magnitudes, and potentially augment valvular gene and protein expression when both parameters are in the physiological range. ^

INVESTIGATIVE COMPARISON OF TANK AND RECOVERED ASPHALT SAMPLES THROUGH PHYSICAL PERFORMANCE TESTING AND CHEMICAL ANALYSIS

Despite the development of improved performance test protocols by renowned researchers, there are still road networks which experience premature cracking and failure. One area of major concern in asphalt science and technology, especially in cold regions in Canada is thermal (low temperature) cracking. Usually right after winter periods, severe cracks are seen on poorly designed road networks. Quality assurance tests based on improved asphalt performance protocols have been implemented by government agencies to ensure that roads being constructed are at the required standard but asphalt binders that pass these quality assurance tests still crack prematurely. While it would be easy to question the competence of the quality assurance test protocols, it should be noted that performance tests which are being used and were repeated in this study, namely the extended bending beam rheometer (EBBR) test, double edge-notched tension test (DENT), dynamic shear rheometer (DSR) test and X-ray fluorescence (XRF) analysis have all been verified and proven to successfully predict asphalt pavement behaviour in the field. Hence this study looked to probe and test the quality and authenticity of the asphalt binders being used for road paving. This study covered thermal cracking and physical hardening phenomenon by comparing results from testing asphalt binder samples obtained from the storage ‘tank’ prior to paving (tank samples) and recovered samples for the same contracts with aim of explaining why asphalt binders that have passed quality assurance tests are still prone to fail prematurely. The study also attempted to find out if the short testing time and automated procedure of torsion bar experiments can replace the established but tedious procedure of the EBBR. In the end, it was discovered that significant differences in performance and composition exist between tank and recovered samples for the same contracts. Torsion bar experimental data also indicated some promise in predicting physical hardening.

Self-healing thermal annealing: surface morphological restructuring control of GaN nanorods

With advances in nanolithography and dry etching, top-down methods of nanostructuring have become a widely used tool for improving the efficiency of optoelectronics. These nano dimensions can offer various benefits to the device performance in terms of light extraction and efficiency, but often at the expense of emission color quality. Broadening of the target emission peak and unwanted yellow luminescence are characteristic defect-related effects due to the ion beam etching damage, particularly for III–N based materials. In this article we focus on GaN based nanorods, showing that through thermal annealing the surface roughness and deformities of the crystal structure can be “self-healed”. Correlative electron microscopy and atomic force microscopy show the change from spherical nanorods to faceted hexagonal structures, revealing the temperature-dependent surface morphology faceting evolution. The faceted nanorods were shown to be strain- and defect-free by cathodoluminescence hyperspectral imaging, micro-Raman, and transmission electron microscopy (TEM). In-situ TEM thermal annealing experiments allowed for real time observation of dislocation movements and surface restructuring observed in ex-situ annealing TEM sampling. This thermal annealing investigation gives new insight into the redistribution path of GaN material and dislocation movement post growth, allowing for improved understanding and in turn advances in optoelectronic device processing of compound semiconductors.