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.

MILITARY VEHICLE OPTIMIZATION AND CONTROL

It is remarkable that there are no deployed military hybrid vehicles since battlefield fuel is approximately 100 times the cost of civilian fuel. In the commercial marketplace, where fuel prices are much lower, electric hybrid vehicles have become increasingly common due to their increased fuel efficiency and the associated operating cost benefit. An absence of military hybrid vehicles is not due to a lack of investment in research and development, but rather because applying hybrid vehicle architectures to a military application has unique challenges. These challenges include inconsistent duty cycles for propulsion requirements and the absence of methods to look at vehicle energy in a holistic sense. This dissertation provides a remedy to these challenges by presenting a method to quantify the benefits of a military hybrid vehicle by regarding that vehicle as a microgrid. This innovative concept allowed for the creation of an expandable multiple input numerical optimization method that was implemented for both real-time control and system design optimization. An example of each of these implementations was presented. Optimization in the loop using this new method was compared to a traditional closed loop control system and proved to be more fuel efficient. System design optimization using this method successfully illustrated battery size optimization by iterating through various electric duty cycles. By utilizing this new multiple input numerical optimization method, a holistic view of duty cycle synthesis, vehicle energy use, and vehicle design optimization can be achieved.

Enotourism – more than a life style

Enotourism is a relatively new form of sustainable tourism. But is more than a lifestyle. The Douro landscape reflects its ancient and deep connection with the culture of wine, creating a picture of Man and Nature working side by side in search of the perfect wine. Lifestyle typically reflects: an individual's attitude, a way of life, values, or world view. Practical implications - the results suggest that there is scope for developing wine tourism products to attract tourists and which could be used to promote the Douro Valley region as a centre for enotourism. The beautifully unique landscape of the Douro was one of the reasons that made it a World Heritage site in 2001. There isn´t in Portugal an autonomous strategy process to define enotourism. Is a legal problem when we try to analyse the process or a data base to find information about enotourism players. So, how do winery operators, particularly those running small or family businesses, cope with the new developments occurring in the world of wines? The present study examines these issues from the perspective of a group of Portuguese winery operators. Our proposal in this research, is to analyse how many wineris or enotecas are hable to develop enotourism with a legal process. The results of the study reflect the level of education of employees, the seasonal nature of tourism, the improvements in its promotion and the need for greater support from local government. A key aspect is respect for the people who call the location home, the culture and customs of the area, and the socio-economic system. Design/methodology/approach - The methodology employed for this study consisted of a combination of surveys, interviews and field observations with the suppliers in the traditional wine‐producing region, Douro Valley, or Porto wine region, in the north of Portugal. The results of this investigation are almost analisys made inside the villages and also us wineries and enotecas. From the 30 winemakers that we visited, only 2 have an enotourism service acording to legislation and have a certificate that allows to pratices. It was very hard but it is an open field to future researchs (TOMÁS López‐Guzmán,et al, 2011). From the 30 wineries we have analysed only 2 were enotourism with a legal basis. Enotourism is on the travel agencies department and most of the wineries don´t have the legal licenses. Despite of most tourism agencies see enoturism as a segment of the industry with tremendous growth potential, stating that in some regions, it's only functioning at 20% of its full potential. Enotourism development guidelines and management practices are applicable to all forms of tourism in all destination types, including mass tourism and the various niche tourism segments.

Constructs in Knowledge Organization Systems: Rhythm in Time, Intention, and Form

In the context of the International Society for Knowledge Organization, we often consider knowledge organization systems to comprise catalogues, thesauri, and bibliothecal classification schemes – schemes for library arrangement. In recent years we have added ontologies and folksonomies to our sphere of study. In all of these cases it seems we are concerned with improving access to information. We want a good system.And much of the literature from the late 19th into the late 20th century took that as their goal – to analyze the world of knowledge and the structures of representing it as its objects of study; again, with the ethos for creating a good system. In most cases this meant we had to be correct in our assertions about the universe of knowledge and the relationships that obtain between its constituent parts. As a result much of the literature of knowledge organization is prescriptive – instructing designers and professionals how to build or use the schemes correctly – that is to maximize redundant success in accessing information.In 2005, there was a turn in some of the knowledge organization literature. It has been called the descriptive turn. This is in relation to the otherwise prescriptive efforts of researchers in KO. And it is the descriptive turn that makes me think of context, languages, and cultures in knowledge organization–the theme of this year’s conference.Work in the descriptive turn questions the basic assumptions about what we want to do when we create, implement, maintain, and evaluate knowledge organization systems. Following on these assumptions researchers have examined a wider range of systems and question the motivations behind system design. Online websites that allow users to curate their own collections are one such addition, for example Pinterest (cf., Feinberg, 2011). However, researchers have also looked back at other lineages of organizing to compare forms and functions. For example, encyclopedias, catalogues raisonnés, archival description, and winter counts designed and used by Native Americans.In this case of online curated collections, Melanie Feinberg has started to examine the craft of curation, as she calls it. In this line of research purpose, voice, and rhetorical stance surface as design considerations. For example, in the case of the Pinterest, users are able and encouraged to create boards. The process of putting together these boards is an act of curation in contemporary terminology. It is describing this craft that comes from the descriptive turn in KO.In the second case, when researchers in the descriptive turn look back at older and varied examples of knowledge organization systems, we are looking for a full inventory of intent and inspiration for future design. Encyclopedias, catalogues raisonnés, archival description, and works of knowledge organization in other cultures provide a rich world for the descriptive turn. And researchers have availed themselves of this.

Improving magnetic coupling for battery charging through 3D magnetic flux

The spatial distribution of the magnetic field and the coupling between the coils in the Wireless Power Transfer (WPT) systems is an important aspect to consider in the system design and efficiency optimization. The presented study in this paper is based on tests performed on a physical model. The transmitting (primary) equipment, is an electrical three-phase system, capable to be connected in star or delta (both electrically and geometrically). The measured results allow to describe graphically the magnetic field distribution in three dimensions. The analytical formulas aim to help to understand and to quantify the physical phenomena but they cannot be considered a universal approach and the measurement results help to understand better the observable facts. In the WPT, the key issues that will influence the efficiency, are the alignment of the coils, the spatial orientation of the magnetic field, the detachment and the tilt between the windings, all they changing the magnetic coupling between the transmitter and the receiver of energy. This research is directed not only to the magnetic field distribution but finally, to optimize the energy transfer efficiency.

The Impacts of Climate Change on Irrigated Agriculture in Southern Portugal

Climate change projections point to increasing air temperature and reduced precipitation in southern Portugal, which would affect farming systems. This study aims to assess the impacts of climate change on irrigated agriculture in southern Portugal. These impacts were assessed by combining climate model data with a soil water balance model and a numerical model for the design of irrigation systems. Meteorological data from two weather stations were used along with three climate models (HadRM3P, HIRHAMh and HIRHAMhh; 2071–2100). The crop rotations studied included sugar beet–maize–tomato–wheat and sunflower–wheat–barley. Two adaptation measures were considered: (i) maintaining the current crop varieties; (ii) using new crop varieties. The results from the considered climate change scenarios indicated that the impacts of climate change on irrigation requirements depend on the adopted adaptation measures. On average, the seasonal irrigation requirements increased by 13–70% when new crop varieties were used and by −13 to 7% when the current crop varieties were maintained. The impacts of climate change on irrigation system design were considerable, with the design flow rate increasing by 5–24%.

RF energy harvesting solutions for electromagnetic harsh environments: from industrial plants to wearable/implantable devices

The presented Thesis describes the design of RF-energy harvesting systems with applications on different environments, from the biomedical side to the industrial one, tackling the common thread problem which is the design of complete energy autonomous tags each of them with its dedicated purpose. This Thesis gathers a work of three years in the field of energy harvesting system design, a combination of full-wave electromagnetic designs to optimize not only the antenna performance but also to fulfill the requirements given by each case study such as dimensions, insensitivity from the surrounding environment, flexibility and compliance with regulations. The research activity has been based on the development of highly-demanded ideas and real-case necessities which are in line with the environment in which modern IoT applications can really make a positive contribution. The Thesis is organized as follows: the first application, described in Chapter 2, regards the design and experimental validations of a rotation-insensitive WPT system for implantable devices. Chapter 3 presents the design of a wearable energy autonomous detector to identify the presence of ethanol on the body surface. Chapter 4 describes investigations in the use of Bessel Beam launchers for creating a highly-focused energy harvesting link for wearable applications. Reduced dimensions, high focusing and decoupling from the human body are the key points to be addressed during the full-wave design and nonlinear optimization of the receiver antenna. Finally, Chapter 5 presents an energy autonomous system exploiting LoRa (Long Range) nodes for tracking trailers in industrial plants. The novelty behind this design lies on the aim of obtaining a perfectly scalable system that exploits not only EH basic operating system but embeds a seamless solution for collecting a certain amount of power that varies with respect the received power level on the antenna, without the need of additional off-the-shelf components.

Grant-free protocols for massive multiple access

In next generation Internet-of-Things, the overhead introduced by grant-based multiple access protocols may engulf the access network as a consequence of the proliferation of connected devices. Grant-free access protocols are therefore gaining an increasing interest to support massive multiple access. In addition to scalability requirements, new demands have emerged for massive multiple access, including latency and reliability. The challenges envisaged for future wireless communication networks, particularly in the context of massive access, include: i) a very large population size of low power devices transmitting short packets; ii) an ever-increasing scalability requirement; iii) a mild fixed maximum latency requirement; iv) a non-trivial requirement on reliability. To this aim, we suggest the joint utilization of grant-free access protocols, massive MIMO at the base station side, framed schemes to let the contention start and end within a frame, and succesive interference cancellation techniques at the base station side. In essence, this approach is encapsulated in the concept of coded random access with massive MIMO processing. These schemes can be explored from various angles, spanning the protocol stack from the physical (PHY) to the medium access control (MAC) layer. In this thesis, we delve into both of these layers, examining topics ranging from symbol-level signal processing to succesive interference cancellation-based scheduling strategies. In parallel with proposing new schemes, our work includes a theoretical analysis aimed at providing valuable system design guidelines. As a main theoretical outcome, we propose a novel joint PHY and MAC layer design based on density evolution on sparse graphs.

Numerical simulation of the flow and performance evaluation of an aerospike engine

The main focus of this work is to define a numerical methodology to simulate an aerospike engine and then to analyse the performance of DemoP1, which is a small aerospike demonstrator built by Pangea Aerospace. The aerospike is a promising solution to build more efficient engine than the actual one. Its main advantage is the expansion adaptation that allows to reach the optimal expansion in a wide range of ambient pressures delivering more thrust than an equivalent bell-shaped nozzle. The main drawbacks are the cooling system design and the spike manufacturing but nowadays, these issues seem to be overcome with the use of the additive manufacturing method. The simulations are performed with dbnsTurbFoam which is a solver of OpenFOAM. It has been designed to simulate a supersonic compressible turbulent flow. This work is divided in four chapters. The first one is a short introduction. The second one shows a brief summary of the theoretical performance of the aerospike. The third one introduces the numerical methodology to simulate a compressible supersonic flow. In the fourth chapter, the solver has been verified with an experiment found in literature. And in the fifth chapter, the simulations on DemoP1 engine are illustrated.

Grant-Free Access for Massive IoT Based on Interference Cancellation and Massive MIMO

Recent years have witnessed an increasing evolution of wireless mobile networks, with an intensive research work aimed at developing new efficient techniques for the future 6G standards. In the framework of massive machine-type communication (mMTC), emerging Internet of Things (IoT) applications, in which sensor nodes and smart devices transmit unpredictably and sporadically short data packets without coordination, are gaining an increasing interest. In this work, new medium access control (MAC) protocols for massive IoT, capable of supporting a non-instantaneous feedback from the receiver, are studied. These schemes guarantee an high time for the acknowledgment (ACK) messages to the base station (BS), without a significant performance loss. Then, an error floor analysis of the considered protocols is performed in order to obtain useful guidelines for the system design. Furthermore, non-orthogonal multiple access (NOMA) coded random access (CRA) schemes based on power domain are here developed. The introduction of power diversity permits to solve more packet collision at the physical (PHY) layer, with an important reduction of the packet loss rate (PLR) in comparison to the number of active users in the system. The proposed solutions aim to improve the actual grant-free protocols, respecting the stringent constraints of scalability, reliability and latency requested by 6G networks.

Design, construction and evaluation of a simple pressurized solvent extraction system

This work describes the construction and testing of a simple pressurized solvent extraction (PSE) system. A mixture of acetone:water (80:20), 80 ºC and 103.5 bar, was used to extract two herbicides (Diuron and Bromacil) from a sample of polluted soil, followed by identification and quantification by high-performance liquid chromatography coupled with diode array detector (HPLC-DAD). The system was also used to extract soybean oil (70 ºC and 69 bar) using pentane. The extracted oil was weighed and characterized through the fatty acid methyl ester analysis (myristic (< 0.3%), palmitic (16.3%), stearic (2.8%), oleic (24.5%), linoleic (46.3%), linolenic (9.6%), araquidic (0.3%), gadoleic (< 0.3%), and behenic (0.3%) acids) using high-resolution gas chromatography with flame ionization detection (HRGC-FID). PSE results were compared with those obtained using classical procedures: Soxhlet extraction for the soybean oil and solid-liquid extraction followed by solid-phase extraction (SLE-SPE) for the herbicides. The results showed: 21.25 ± 0.36% (m/m) of oil in the soybeans using the PSE system and 21.55 ± 0.65% (m/m) using the soxhlet extraction system; extraction efficiency (recovery) of herbicides Diuron and Bromacil of 88.7 ± 4.5% and 106.6 ± 8.1%, respectively, using the PSE system, and 96.8 ± 1.0% and 94.2 ± 3.9%, respectively, with the SLP-SPE system; limit of detection (LOD) and limit of quantification (LOQ) for Diuron of 0.012 mg kg-1 and 0.040 mg kg-1, respectively; LOD and LOQ for Bromacil of 0.025 mg kg-1 and 0.083 mg kg-1, respectively. The linearity used ranged from 0.04 to 1.50 mg L-1 for Diuron and from 0.08 to 1.50 mg L-1 for Bromacil. In conclusion, using the PSE system, due to high pressure and temperature, it is possible to make efficient, fast extractions with reduced solvent consumption in an inert atmosphere, which prevents sample and analyte decomposition.

Automatic tuning method for the design of supplementary damping controllers for flexible alternating current transmission system devices

The design of supplementary damping controllers to mitigate the effects of electromechanical oscillations in power systems is a highly complex and time-consuming process, which requires a significant amount of knowledge from the part of the designer. In this study, the authors propose an automatic technique that takes the burden of tuning the controller parameters away from the power engineer and places it on the computer. Unlike other approaches that do the same based on robust control theories or evolutionary computing techniques, our proposed procedure uses an optimisation algorithm that works over a formulation of the classical tuning problem in terms of bilinear matrix inequalities. Using this formulation, it is possible to apply linear matrix inequality solvers to find a solution to the tuning problem via an iterative process, with the advantage that these solvers are widely available and have well-known convergence properties. The proposed algorithm is applied to tune the parameters of supplementary controllers for thyristor controlled series capacitors placed in the New England/New York benchmark test system, aiming at the improvement of the damping factor of inter-area modes, under several different operating conditions. The results of the linear analysis are validated by non-linear simulation and demonstrate the effectiveness of the proposed procedure.

Design and assembly of an experimental laboratory for the study of atmosphere-plant interactions in the system of fumigation chambers

An experimental laboratory was designed and assembled at the Botanical Institute of So Paulo, Brazil, in order to research atmosphere-plant interactions through the use of a system of fumigation chambers. A system of three ""closed"" fumigation chambers was designed to be used inside or outside the laboratory. The system was built to be used with a single pollutant or a mix of them. The innovation in this system is to allow chemical reactions inside the chambers that simulate atmospheric chemistry, especially photochemical processes involving high levels of ozone. Assessment of the performance and applicability of the system was based on the response of Nicotiana tabacum Bel W3 exposed to ozone produced alternatively by a generator and inside the chamber by reactions of its precursors. The results showed that the system can be well applied to the study of atmospheric chemistry interactions and the effects on plants.

Pressure-Frequency Sensing Subxiphoid Access System for Use in Percutaneous Cardiac Electrophysiology: Prototype Design and Pilot Study Results

We have designed, built, and tested an early prototype of a novel subxiphoid access system intended to facilitate epicardial electrophysiology, but with possible applications elsewhere in the body. The present version of the system consists of a commercially available insertion needle, a miniature pressure sensor and interconnect tubing, read-out electronics to monitor the pressures measured during the access procedure, and a host computer with user-interface software. The nominal resolution of the system is <0.1 mmHg, and it has deviations from linearity of <1%. During a pilot series of human clinical studies with this system, as well as in an auxiliary study done with an independent method, we observed that the pericardial space contained pressure-frequency components related to both the heart rate and respiratory rate, while the thorax contained components related only to the respiratory rate, a previously unobserved finding that could facilitate access to the pericardial space. We present and discuss the design principles, details of construction, and performance characteristics of this system.