Epigenetics and developmental programming of welfare and production traits in farm animals

Acknowledgements Financial support for composing this article was obtained from the Agriculture and Horticulture Development Board (AHDB, Beef and Lamb), UK. Concept of review was also initiated from discussions originating from EU COST Action FA1201, Epiconcept: Epigenetics and Periconception Environment

Demonstration against Channel 13 for not having more women-oriented programming

General note: Title and date provided by Bettye Lane.

Programming Molecular Devices using Nucleic Acid Hairpins

Nucleic Acid hairpins have been a subject of study for the last four decades. They are composed of single strand that is

hybridized to itself, and the central section forming an unhybridized loop. In nature, they stabilize single stranded RNA, serve as nucleation

sites for RNA folding, protein recognition signals, mRNA localization and regulation of mRNA degradation. On the other hand,

DNA hairpins in biological contexts have been studied with respect to forming cruciform structures that can regulate gene expression.

The use of DNA hairpins as fuel for synthetic molecular devices, including locomotion, was proposed and experimental demonstrated in 2003. They

were interesting because they bring to the table an on-demand energy/information supply mechanism.

The energy/information is hidden (from hybridization) in the hairpin’s loop, until required.

The energy/information is harnessed by opening the stem region, and exposing the single stranded loop section.

The loop region is now free for possible hybridization and help move the system into a thermodynamically favourable state.

The hidden energy and information coupled with

programmability provides another functionality, of selectively choosing what reactions to hide and

what reactions to allow to proceed, that helps develop a topological sequence of events.

Hairpins have been utilized as a source of fuel for many different DNA devices. In this thesis, we program four different

molecular devices using DNA hairpins, and experimentally validate them in the

laboratory. 1) The first device: A

novel enzyme-free autocatalytic self-replicating system composed entirely of DNA that operates isothermally. 2) The second

device: Time-Responsive Circuits using DNA have two properties: a) asynchronous: the final output is always correct

regardless of differences in the arrival time of different inputs.

b) renewable circuits which can be used multiple times without major degradation of the gate motifs

(so if the inputs change over time, the DNA-based circuit can re-compute the output correctly based on the new inputs).

3) The third device: Activatable tiles are a theoretical extension to the Tile assembly model that enhances

its robustness by protecting the sticky sides of tiles until a tile is partially incorporated into a growing assembly.

4) The fourth device: Controlled Amplification of DNA catalytic system: a device such that the amplification

of the system does not run uncontrollably until the system runs out of fuel, but instead achieves a finite

amount of gain.

Nucleic acid circuits with the ability

to perform complex logic operations have many potential practical applications, for example the ability to achieve point of care diagnostics.

We discuss the designs of our DNA Hairpin molecular devices, the results we have obtained, and the challenges we have overcome

to make these truly functional.

Dynamic Programming Approaches for Estimating and Applying Large-scale Discrete Choice Models

People go through their life making all kinds of decisions, and some of these decisions affect their demand for transportation, for example, their choices of where to live and where to work, how and when to travel and which route to take. Transport related choices are typically time dependent and characterized by large number of alternatives that can be spatially correlated. This thesis deals with models that can be used to analyze and predict discrete choices in large-scale networks. The proposed models and methods are highly relevant for, but not limited to, transport applications. We model decisions as sequences of choices within the dynamic discrete choice framework, also known as parametric Markov decision processes. Such models are known to be difficult to estimate and to apply to make predictions because dynamic programming problems need to be solved in order to compute choice probabilities. In this thesis we show that it is possible to explore the network structure and the flexibility of dynamic programming so that the dynamic discrete choice modeling approach is not only useful to model time dependent choices, but also makes it easier to model large-scale static choices. The thesis consists of seven articles containing a number of models and methods for estimating, applying and testing large-scale discrete choice models. In the following we group the contributions under three themes: route choice modeling, large-scale multivariate extreme value (MEV) model estimation and nonlinear optimization algorithms. Five articles are related to route choice modeling. We propose different dynamic discrete choice models that allow paths to be correlated based on the MEV and mixed logit models. The resulting route choice models become expensive to estimate and we deal with this challenge by proposing innovative methods that allow to reduce the estimation cost. For example, we propose a decomposition method that not only opens up for possibility of mixing, but also speeds up the estimation for simple logit models, which has implications also for traffic simulation. Moreover, we compare the utility maximization and regret minimization decision rules, and we propose a misspecification test for logit-based route choice models. The second theme is related to the estimation of static discrete choice models with large choice sets. We establish that a class of MEV models can be reformulated as dynamic discrete choice models on the networks of correlation structures. These dynamic models can then be estimated quickly using dynamic programming techniques and an efficient nonlinear optimization algorithm. Finally, the third theme focuses on structured quasi-Newton techniques for estimating discrete choice models by maximum likelihood. We examine and adapt switching methods that can be easily integrated into usual optimization algorithms (line search and trust region) to accelerate the estimation process. The proposed dynamic discrete choice models and estimation methods can be used in various discrete choice applications. In the area of big data analytics, models that can deal with large choice sets and sequential choices are important. Our research can therefore be of interest in various demand analysis applications (predictive analytics) or can be integrated with optimization models (prescriptive analytics). Furthermore, our studies indicate the potential of dynamic programming techniques in this context, even for static models, which opens up a variety of future research directions.

A green perspective on Structured parallel programming

Structured parallel programming, and in particular programming models using the algorithmic skeleton or parallel design pattern concepts, are increasingly considered to be the only viable means of supporting effective development of scalable and efficient parallel programs. Structured parallel programming models have been assessed in a number of works in the context of performance. In this paper we consider how the use of structured parallel programming models allows knowledge of the parallel patterns present to be harnessed to address both performance and energy consumption. We consider different features of structured parallel programming that may be leveraged to impact the performance/energy trade-off and we discuss a preliminary set of experiments validating our claims.

Commercial and Industrial Network Improvement and Programming Policy, Summary, 1991

The Commercial and Industrial Network improvement and programming policy reflected in this summary report was adopted for use in future highway programming by the Transportation Commission on November 5, 1991. The Iowa Department of Transportation, as directed by the Legislature, has established a 2,331-mile network of commercial and industrial highways and is directing a significant amount of primary construction funding resources toward improvements to this network. This summary outlines the technical needs assessment for improvements on the Commercial and Industrial Network for the next 20-year period. The portions of the network which require four-lane capacity, as well as major improvements to the two-lane sections, are graphically displayed. Detailed improvement needs and costs are listed in tabular form for the first two five-year periods (1992-1996 and 1997-2001). It is essential to note that these improvement needs are the result of a technical assessment and do not imply any funding commitment.

Automatically Evolving Rotation-invariant Texture Image Descriptors by Genetic Programming

In computer vision, training a model that performs classification effectively is highly dependent on the extracted features, and the number of training instances. Conventionally, feature detection and extraction are performed by a domain-expert who, in many cases, is expensive to employ and hard to find. Therefore, image descriptors have emerged to automate these tasks. However, designing an image descriptor still requires domain-expert intervention. Moreover, the majority of machine learning algorithms require a large number of training examples to perform well. However, labelled data is not always available or easy to acquire, and dealing with a large dataset can dramatically slow down the training process. In this paper, we propose a novel Genetic Programming based method that automatically synthesises a descriptor using only two training instances per class. The proposed method combines arithmetic operators to evolve a model that takes an image and generates a feature vector. The performance of the proposed method is assessed using six datasets for texture classification with different degrees of rotation, and is compared with seven domain-expert designed descriptors. The results show that the proposed method is robust to rotation, and has significantly outperformed, or achieved a comparable performance to, the baseline methods.

Type-Aware Programming Models for Distributed Applications

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

Climbing Up the Leaderboard: An Empirical Study of Applying Gamification Techniques to a Computer Programming Class

Conventional taught learning practices often experience difficulties in keeping students motivated and engaged. Video games, however, are very successful at sustaining high levels of motivation and engagement through a set of tasks for hours without apparent loss of focus. In addition, gamers solve complex problems within a gaming environment without feeling fatigue or frustration, as they would typically do with a comparable learning task. Based on this notion, the academic community is keen on exploring methods that can deliver deep learner engagement and has shown increased interest in adopting gamification – the integration of gaming elements, mechanics, and frameworks into non-game situations and scenarios – as a means to increase student engagement and improve information retention. Its effectiveness when applied to education has been debatable though, as attempts have generally been restricted to one-dimensional approaches such as transposing a trivial reward system onto existing teaching materials and/or assessments. Nevertheless, a gamified, multi-dimensional, problem-based learning approach can yield improved results even when applied to a very complex and traditionally dry task like the teaching of computer programming, as shown in this paper. The presented quasi-experimental study used a combination of instructor feedback, real time sequence of scored quizzes, and live coding to deliver a fully interactive learning experience. More specifically, the “Kahoot!” Classroom Response System (CRS), the classroom version of the TV game show “Who Wants To Be A Millionaire?”, and Codecademy’s interactive platform formed the basis for a learning model which was applied to an entry-level Python programming course. Students were thus allowed to experience multiple interlocking methods similar to those commonly found in a top quality game experience. To assess gamification’s impact on learning, empirical data from the gamified group were compared to those from a control group who was taught through a traditional learning approach, similar to the one which had been used during previous cohorts. Despite this being a relatively small-scale study, the results and findings for a number of key metrics, including attendance, downloading of course material, and final grades, were encouraging and proved that the gamified approach was motivating and enriching for both students and instructors.

From Kandinsky to Java (The Use of 20th Century Abstract Art in Learning Programming)

At the University of Worcester we are continually striving to find new approaches to the learning and teaching of programming, to improve the quality of learning and the student experience. Over the past three years we have used the contexts of robotics, computer games, and most recently a study of Abstract Art to this end. This paper discusses our motivation for using Abstract Art as a context, details our principles and methodology, and reports on an evaluation of the student experience. Our basic tenet is that one can view the works of artists such as Kandinsky, Klee and Malevich as Object-Oriented (OO) constructions. Discussion of these works can therefore be used to introduce OO principles, to explore the meaning of classes, methods and attributes and finally to synthesize new works of art through Java code. This research has been conducted during delivery of an “Advanced OOP (Java)” programming module at final-year Undergraduate level, and during a Masters’ OO-Programming (Java) module. This allows a comparative evaluation of novice and experienced programmers’ learning. In this paper, we identify several instructional factors which emerge from our approach, and reflect upon the associated pedagogy. A Catalogue of ArtApplets is provided at the associated web-site.