PETCHA: a Programming Exercises Teaching Assistant

This paper presents a tool called Petcha that acts as an automated Teaching Assistant in computer programming courses. The ultimate objective of Petcha is to increase the number of programming exercises effectively solved by students. Petcha meets this objective by helping both teachers to author programming exercises and students to solve them. It also coordinates a network of heterogeneous systems, integrating automatic program evaluators, learning management systems, learning object repositories and integrated programming environments. This paper presents the concept and the design of Petcha and sets this tool in a service oriented architecture for managing learning processes based on the automatic evaluation of programming exercises. The paper presents also a case study that validates the use of Petcha and of the proposed architecture.

Bridging between programming exercises formats with BabeLO

Assessment plays a vital role in learning. This is certainly the case with assessment of computer programs, both in curricular and competitive learning. The lack of a standard – or at least a widely used format – creates a modern Ba- bel tower made of Learning Objects, of assessment items that cannot be shared among automatic assessment systems. These systems whose interoperability is hindered by the lack of a common format include contest management systems, evaluation engines, repositories of learning objects and authoring tools. A prag- matical approach to remedy this problem is to create a service to convert among existing formats. A kind of translation service specialized in programming prob- lems formats. To convert programming exercises on-the-fly among the most used formats is the purpose of the BabeLO – a service to cope with the existing Babel of Learning Object formats for programming exercises. BabeLO was designed as a service to act as a middleware in a network of systems typically used in auto- matic assessment of programs. It provides support for multiple exercise formats and can be used by: evaluation engines to assess exercises regardless of its format; repositories to import exercises from various sources; authoring systems to create exercises in multiple formats or based on exercises from other sources. This paper analyses several of existing formats to highlight both their differ- ences and their similar features. Based on this analysis it presents an approach to extensible format conversion. It presents also the features of PExIL, the pivotal format in which the conversion is based; and the function definitions of the proposed service – BabeLO. Details on the design and implementation of BabeLO, including the service API and the interfaces required to extend the conversion to a new format, are also provided. To evaluate the effectiveness and efficiency of this approach this paper reports on two actual uses of BabeLO: to relocate exercises to a different repository; and to use an evaluation engine in a network of heterogeneous systems.

Making programming exercises interoperable with PExIL

Several standards have appeared in recent years to formalize the metadata of learning objects, but they are still insufficient to fully describe a specialized domain. In particular, the programming exercise domain requires interdependent resources (e.g. test cases, solution programs, exercise description) usually processed by different services in the programming exercise lifecycle. Moreover, the manual creation of these resources is time-consuming and error-prone, leading to an obstacle to the fast development of programming exercises of good quality. This chapter focuses on the definition of an XML dialect called PExIL (Programming Exercises Interoperability Language). The aim of PExIL is to consolidate all the data required in the programming exercise lifecycle from when it is created to when it is graded, covering also the resolution, the evaluation, and the feedback. The authors introduce the XML Schema used to formalize the relevant data of the programming exercise lifecycle. The validation of this approach is made through the evaluation of the usefulness and expressiveness of the PExIL definition. In the former, the authors present the tools that consume the PExIL definition to automatically generate the specialized resources. In the latter, they use the PExIL definition to capture all the constraints of a set of programming exercises stored in a learning objects repository.

Anaerobic bacteria: an investigation of metabolic important enzymes: a novel type of oxygen reductase and enzymes of the tetrapyrrole biosynthesis

Desulfovibrio desulfuricans was the first species of a sulphatereducing bacterium to be isolated, in 1895. Since that time, many questions were raised in the scientific community regarding the metabolic and ecological aspects of these bacteria. At present, there is still a myriad of open questions remaining to be answered to enlarge our knowledge of the metabolic pathways operative in these bacteria that have implications in the sulfur cycle, in biocorrosion, namely in sewers and in oil and gas systems, and in bioremediation of several toxic metals. The work presented in this dissertation aimed at contributing with new insights of enzymes involved in two different metabolic systems on Desulfovibrio species, namely enzymes that play a role in the response to oxidative stress and that are involved in the haem biosynthetic pathway.(...)

A comprehensive high-throughput FTIR spectroscopy-based method for evaluating the transfection event: estimating the transfection efficiency and extracting associated metabolic responses

Reporter genes are routinely used in every laboratory for molecular and cellular biology for studying heterologous gene expression and general cellular biological mechanisms, such as transfection processes. Although well characterized and broadly implemented, reporter genes present serious limitations, either by involving time-consuming procedures or by presenting possible side effects on the expression of the heterologous gene or even in the general cellular metabolism. Fourier transform mid-infrared (FT-MIR) spectroscopy was evaluated to simultaneously analyze in a rapid (minutes) and high-throughput mode (using 96-wells microplates), the transfection efficiency, and the effect of the transfection process on the host cell biochemical composition and metabolism. Semi-adherent HEK and adherent AGS cell lines, transfected with the plasmid pVAX-GFP using Lipofectamine, were used as model systems. Good partial least squares (PLS) models were built to estimate the transfection efficiency, either considering each cell line independently (R 2 ≥ 0.92; RMSECV ≤ 2 %) or simultaneously considering both cell lines (R 2 = 0.90; RMSECV = 2 %). Additionally, the effect of the transfection process on the HEK cell biochemical and metabolic features could be evaluated directly from the FT-IR spectra. Due to the high sensitivity of the technique, it was also possible to discriminate the effect of the transfection process from the transfection reagent on KEK cells, e.g., by the analysis of spectral biomarkers and biochemical and metabolic features. The present results are far beyond what any reporter gene assay or other specific probe can offer for these purposes.

Assessment of nutritional and metabolic profiles of pea shoots: The new ready-to-eat baby-leaf vegetable

Pea-shoots are a new option as ready-to-eat baby-leaf vegetable. However, data about the nutritional composition and the shelf-life stability of these leaves, especially their phytonutrient composition is scarce. In this work, the macronutrient, micronutrient and phytonutrients profile of minimally processed pea shoots were evaluated at the beginning and at the end of a 10-day storage period. Several physicochemical characteristics (color, pH, total soluble solids, and total titratable acidity) were also monitored. Standard AOAC methods were applied in the nutritional value evaluation, while chromatographic methods with UV–vis and mass detection were used to analyze free forms of vitamins (HPLC-DAD-ESI-MS/MS), carotenoids (HPLC-DAD-APCI-MSn) and flavonoid compounds (HPLC-DAD-ESI-MSn). Atomic absorption spectrometry (HR-CS-AAS) was employed to characterize the mineral content of the leaves. As expected, pea leaves had a high water (91.5%) and low fat (0.3%) and carbohydrate (1.9%) contents, being a good source of dietary fiber (2.1%). Pea shoots showed a high content of vitamins C, E and A, potassium and phosphorous compared to other ready-to-eat green leafy vegetables. The carotenoid profile revealed a high content of β-carotene and lutein, typical from green leafy vegetables. The leaves had a mean flavonoid content of 329 mg/100 g of fresh product, mainly composed by glycosylated quercetin and kaempferol derivatives. Pea shoots kept their fresh appearance during the storage being color maintained throughout the shelf-life. The nutritional composition was in general stable during storage, showing some significant (p < 0.05) variation in certain water-soluble vitamins.

Dynamic programming for a Markov-switching jump–diffusion

We consider an optimal control problem with a deterministic finite horizon and state variable dynamics given by a Markov-switching jump–diffusion stochastic differential equation. Our main results extend the dynamic programming technique to this larger family of stochastic optimal control problems. More specifically, we provide a detailed proof of Bellman’s optimality principle (or dynamic programming principle) and obtain the corresponding Hamilton–Jacobi–Belman equation, which turns out to be a partial integro-differential equation due to the extra terms arising from the Lévy process and the Markov process. As an application of our results, we study a finite horizon consumption– investment problem for a jump–diffusion financial market consisting of one risk-free asset and one risky asset whose coefficients are assumed to depend on the state of a continuous time finite state Markov process. We provide a detailed study of the optimal strategies for this problem, for the economically relevant families of power utilities and logarithmic utilities.

Defective protein folding and function in metabolic disorders: studies on the mitochondrial flavoenzyme ETF

Dissertation presented to obtain the PhD degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

An integer programming framework for sequencing cutting patterns based on interval graph completion

We derived a framework in integer programming, based on the properties of a linear ordering of the vertices in interval graphs, that acts as an edge completion model for obtaining interval graphs. This model can be applied to problems of sequencing cutting patterns, namely the minimization of open stacks problem (MOSP). By making small modifications in the objective function and using only some of the inequalities, the MOSP model is applied to another pattern sequencing problem that aims to minimize, not only the number of stacks, but also the order spread (the minimization of the stack occupation problem), and the model is tested.

An integer programming model for the minimum interval graph completion problem

The minimum interval graph completion problem consists of, given a graph G = ( V, E ), finding a supergraph H = ( V, E ∪ F ) that is an interval graph, while adding the least number of edges |F| . We present an integer programming formulation for solving the minimum interval graph completion problem recurring to a characteri- zation of interval graphs that produces a linear ordering of the maximal cliques of the solution graph.

Increase of the Delivered Power Probability in Distribution Networks using Pareto DC Programming

A methodology to increase the probability of delivering power to any load point through the identification of new investments in distribution network components is proposed in this paper. The method minimizes the investment cost as well as the cost of energy not supplied in the network. A DC optimization model based on mixed integer non-linear programming is developed considering the Pareto front technique in order to identify the adequate investments in distribution networks components which allow increasing the probability of delivering power for any customer in the distribution system at the minimum possible cost for the system operator, while minimizing the energy not supplied cost. Thus, a multi-objective problem is formulated. To illustrate the application of the proposed methodology, the paper includes a case study which considers a 180 bus distribution network

Metabolic and morphogenetic engineering of Bacillus subtilis: biotechnology for industry

Dissertation presented to obtain the Ph.D. degree in “Biology” at the Institute of Chemical and Biological Technology of the New University of Lisbon