Enabling a direct path from end-user specifications to executable protocols in a biology laboratory environment

Biomedical analyses are becoming increasingly complex, with respect to both the type of the data to be produced and the procedures to be executed. This trend is expected to continue in the future. The development of information and protocol management systems that can sustain this challenge is therefore becoming an essential enabling factor for all actors in the field. The use of custom-built solutions that require the biology domain expert to acquire or procure software engineering expertise in the development of the laboratory infrastructure is not fully satisfactory because it incurs undesirable mutual knowledge dependencies between the two camps. We propose instead an infrastructure concept that enables the domain experts to express laboratory protocols using proper domain knowledge, free from the incidence and mediation of the software implementation artefacts. In the system that we propose this is made possible by basing the modelling language on an authoritative domain specific ontology and then using modern model-driven architecture technology to transform the user models in software artefacts ready for execution in a multi-agent based execution platform specialized for biomedical laboratories.

Reproductive and post-reproductive life history of wild-caught Drosophila melanogaster under laboratory conditions.

The life history of the fruit fly (Drosophila melanogaster) is well understood, but fitness components are rarely measured by following single individuals over their lifetime, thereby limiting insights into lifetime reproductive success, reproductive senescence and post-reproductive lifespan. Moreover, most studies have examined long-established laboratory strains rather than freshly caught individuals and may thus be confounded by adaptation to laboratory culture, inbreeding or mutation accumulation. Here, we have followed the life histories of individual females from three recently caught, non-laboratory-adapted wild populations of D. melanogaster. Populations varied in a number of life-history traits, including ovariole number, fecundity, hatchability and lifespan. To describe individual patterns of age-specific fecundity, we developed a new model that allowed us to distinguish four phases during a female's life: a phase of reproductive maturation, followed by a period of linear and then exponential decline in fecundity and, finally, a post-ovipository period. Individual females exhibited clear-cut fecundity peaks, which contrasts with previous analyses, and post-peak levels of fecundity declined independently of how long females lived. Notably, females had a pronounced post-reproductive lifespan, which on average made up 40% of total lifespan. Post-reproductive lifespan did not differ among populations and was not correlated with reproductive fitness components, supporting the hypothesis that this period is a highly variable, random 'add-on' at the end of reproductive life rather than a correlate of selection on reproductive fitness. Most life-history traits were positively correlated, a pattern that might be due to genotype by environment interactions when wild flies are brought into a novel laboratory environment but that is unlikely explained by inbreeding or positive mutational covariance caused by mutation accumulation.

Thinking Outside the Box: Enhancing Science Teaching by Combining (Instead of Contrasting) Laboratory and Simulation Activities

The focus of the present work was on 10- to 12-year-old elementary school students’ conceptual learning outcomes in science in two specific inquiry-learning environments, laboratory and simulation. The main aim was to examine if it would be more beneficial to combine than contrast simulation and laboratory activities in science teaching. It was argued that the status quo where laboratories and simulations are seen as alternative or competing methods in science teaching is hardly an optimal solution to promote students’ learning and understanding in various science domains. It was hypothesized that it would make more sense and be more productive to combine laboratories and simulations. Several explanations and examples were provided to back up the hypothesis. In order to test whether learning with the combination of laboratory and simulation activities can result in better conceptual understanding in science than learning with laboratory or simulation activities alone, two experiments were conducted in the domain of electricity. In these experiments students constructed and studied electrical circuits in three different learning environments: laboratory (real circuits), simulation (virtual circuits), and simulation-laboratory combination (real and virtual circuits were used simultaneously). In order to measure and compare how these environments affected students’ conceptual understanding of circuits, a subject knowledge assessment questionnaire was administered before and after the experimentation. The results of the experiments were presented in four empirical studies. Three of the studies focused on learning outcomes between the conditions and one on learning processes. Study I analyzed learning outcomes from experiment I. The aim of the study was to investigate if it would be more beneficial to combine simulation and laboratory activities than to use them separately in teaching the concepts of simple electricity. Matched-trios were created based on the pre-test results of 66 elementary school students and divided randomly into a laboratory (real circuits), simulation (virtual circuits) and simulation-laboratory combination (real and virtual circuits simultaneously) conditions. In each condition students had 90 minutes to construct and study various circuits. The results showed that studying electrical circuits in the simulation–laboratory combination environment improved students’ conceptual understanding more than studying circuits in simulation and laboratory environments alone. Although there were no statistical differences between simulation and laboratory environments, the learning effect was more pronounced in the simulation condition where the students made clear progress during the intervention, whereas in the laboratory condition students’ conceptual understanding remained at an elementary level after the intervention. Study II analyzed learning outcomes from experiment II. The aim of the study was to investigate if and how learning outcomes in simulation and simulation-laboratory combination environments are mediated by implicit (only procedural guidance) and explicit (more structure and guidance for the discovery process) instruction in the context of simple DC circuits. Matched-quartets were created based on the pre-test results of 50 elementary school students and divided randomly into a simulation implicit (SI), simulation explicit (SE), combination implicit (CI) and combination explicit (CE) conditions. The results showed that when the students were working with the simulation alone, they were able to gain significantly greater amount of subject knowledge when they received metacognitive support (explicit instruction; SE) for the discovery process than when they received only procedural guidance (implicit instruction: SI). However, this additional scaffolding was not enough to reach the level of the students in the combination environment (CI and CE). A surprising finding in Study II was that instructional support had a different effect in the combination environment than in the simulation environment. In the combination environment explicit instruction (CE) did not seem to elicit much additional gain for students’ understanding of electric circuits compared to implicit instruction (CI). Instead, explicit instruction slowed down the inquiry process substantially in the combination environment. Study III analyzed from video data learning processes of those 50 students that participated in experiment II (cf. Study II above). The focus was on three specific learning processes: cognitive conflicts, self-explanations, and analogical encodings. The aim of the study was to find out possible explanations for the success of the combination condition in Experiments I and II. The video data provided clear evidence about the benefits of studying with the real and virtual circuits simultaneously (the combination conditions). Mostly the representations complemented each other, that is, one representation helped students to interpret and understand the outcomes they received from the other representation. However, there were also instances in which analogical encoding took place, that is, situations in which the slightly discrepant results between the representations ‘forced’ students to focus on those features that could be generalised across the two representations. No statistical differences were found in the amount of experienced cognitive conflicts and self-explanations between simulation and combination conditions, though in self-explanations there was a nascent trend in favour of the combination. There was also a clear tendency suggesting that explicit guidance increased the amount of self-explanations. Overall, the amount of cognitive conflicts and self-explanations was very low. The aim of the Study IV was twofold: the main aim was to provide an aggregated overview of the learning outcomes of experiments I and II; the secondary aim was to explore the relationship between the learning environments and students’ prior domain knowledge (low and high) in the experiments. Aggregated results of experiments I & II showed that on average, 91% of the students in the combination environment scored above the average of the laboratory environment, and 76% of them scored also above the average of the simulation environment. Seventy percent of the students in the simulation environment scored above the average of the laboratory environment. The results further showed that overall students seemed to benefit from combining simulations and laboratories regardless of their level of prior knowledge, that is, students with either low or high prior knowledge who studied circuits in the combination environment outperformed their counterparts who studied in the laboratory or simulation environment alone. The effect seemed to be slightly bigger among the students with low prior knowledge. However, more detailed inspection of the results showed that there were considerable differences between the experiments regarding how students with low and high prior knowledge benefitted from the combination: in Experiment I, especially students with low prior knowledge benefitted from the combination as compared to those students that used only the simulation, whereas in Experiment II, only students with high prior knowledge seemed to benefit from the combination relative to the simulation group. Regarding the differences between simulation and laboratory groups, the benefits of using a simulation seemed to be slightly higher among students with high prior knowledge. The results of the four empirical studies support the hypothesis concerning the benefits of using simulation along with laboratory activities to promote students’ conceptual understanding of electricity. It can be concluded that when teaching students about electricity, the students can gain better understanding when they have an opportunity to use the simulation and the real circuits in parallel than if they have only the real circuits or only a computer simulation available, even when the use of the simulation is supported with the explicit instruction. The outcomes of the empirical studies can be considered as the first unambiguous evidence on the (additional) benefits of combining laboratory and simulation activities in science education as compared to learning with laboratories and simulations alone.

Architecture for machining process and production monitoring based in open computer numerical control

This paper proposes an architecture for machining process and production monitoring to be applied in machine tools with open Computer numerical control (CNC). A brief description of the advantages of using open CNC for machining process and production monitoring is presented with an emphasis on the CNC architecture using a personal computer (PC)-based human-machine interface. The proposed architecture uses the CNC data and sensors to gather information about the machining process and production. It allows the development of different levels of monitoring systems with mininium investment, minimum need for sensor installation, and low intrusiveness to the process. Successful examples of the utilization of this architecture in a laboratory environment are briefly described. As a Conclusion, it is shown that a wide range of monitoring solutions can be implemented in production processes using the proposed architecture.

Salivary immunoglobulin a response to a match in top-level Brazilian soccer players

Moreira, A, Arsati, F, Cury, PR, Franciscon, C, Oliveira, PR, and Araujo, VC. Salivary immunoglobulin a response to a match in top-level brazilian soccer players. J Strength Cond Res 23(7): 1968-1973, 2009-It has been suggested that several parameters of mucosal immunity, including salivary immunoglobulin A (s-IgA), are affected by heavy exercise either in field sports or in the laboratory environment. Few observations have been made during a true sporting environment, particularly in professional soccer. We tested the hypothesis that salivary IgA levels will be decreased after a 70-minute regulation in a top-level professional soccer friendly match. Saliva samples from 24 male professional soccer players collected before and after the match were analyzed. Salivary immunoglobulin A concentration was measured by enzyme-linked immunosorbent assay and expressed as the absolute concentration (s-IgAabs), s-IgA relative to total protein concentration (IgA-Pro), and the secretion rate of IgA (s-IgArate). Rate of perceived exertion (RPE) was used to monitor the exercise intensity. The paired t-test showed no significant changes in s-IgAabs and s-IgArate (p > 0.05) from PRE to POST match. However, a significant (p < 0.05) increase in total protein concentration (1.46 +/- 0.4 to 2.00 +/- 07) and a decrease in IgA-Pro were observed. The best and most significant correlation was obtained with the RPE and changes in IgA-Pro (rs = -0.43) and could indicate that this expression may be an interesting marker of intensity in a soccer match. However, further investigation regarding exercise intensity, protein concentration, and immune suppression, particularly in team sports, is warranted. From a practical application, the variability of the responses among the players leads us to suggest that there is a need to individually analyze the results with team sports. Some athletes showed a decrease in s-IgA expressions, suggesting the need for taking protective actions to minimize contact with cold viruses or even reducing the training load.

Projecto, optimização e gestão de redes MAIS

Mestrado em Engenharia Electrotécnica e de Computadores

Contribuição para o estudo da combinação de cal com cimento no tratamento de solos

Mestrado em Engenharia Geotécnica e Geoambiente

Experimental characterization of the out-of-plane performance of regular stone masonry walls, including test setups and axial load influence

Stone masonry is one of the oldest and most worldwide used building techniques. Nevertheless, the structural response of masonry structures is complex and the effective knowledge about their mechanical behaviour is still limited. This fact is particularly notorious when dealing with the description of their out-of-plane behaviour under horizontal loadings, as is the case of the earthquake action. In this context, this paper describes an experimental program, conducted in laboratory environment, aiming at characterizing the out-of-plane behaviour of traditional unreinforced stone masonry walls. In the scope of this campaign, six full-scale sacco stone masonry specimens were fully characterised regarding their most important mechanic, geometric and dynamic features and were tested resorting to two different loading techniques under three distinct vertical pre-compression states; three of the specimens were subjected to an out-of-plane surface load by means of a system of airbags and the remaining were subjected to an out-of-plane horizontal line-load at the top. From the experiments it was possible to observe that both test setups were able to globally mobilize the out-of-plane response of the walls, which presented substantial displacement capacity, with ratios of ultimate displacement to the wall thickness ranging between 26 and 45 %, as well as good energy dissipation capacity. Finally, very interesting results were also obtained from a simple analytical model used herein to compute a set of experimental-based ratios, namely between the maximum stability displacement and the wall thickness for which a mean value of about 60 % was found.

Aquisição e registo automático de compradores de massa digitais em calibração de pesos

A presente dissertação foi desenvolvida nas instalações do laboratório de massa da extinta Direção Regional da Economia do Norte (DRE-Norte), no âmbito da unidade curricular de Dissertação/Projeto/Estágio Profissional (DPEPR) do curso de Mestrado de Instrumentação e Metrologia (MEIM) do Instituto Superior de Engenharia do Porto (ISEP). O laboratório de massa da DRE-Norte dedicava-se, entre outras atividades, à calibração de pesos das classes de exatidão F1 e inferior, definidas na recomendação R111-1:2004 da Organização Internacional de Metrologia Legal (OIML), para valores nominais desde 1 mg até 1 000 kg. Foi implementado um sistema real de calibração de pesos utilizando dois comparadores de massa, com interface de comunicação de dados, com fios e sem fios, para o PC (Personal Computer), com aquisição automática dos dados. Desenvolveu-se uma aplicação informática em Visual Basic com o objetivo de ligar os dois comparadores de massa ao PC e automatizar o processo de calibração de pesos com base no método ABBA. O software desenvolvido foi aplicado num caso real de calibração de pesos em ambiente de intercomparação laboratorial com a participação de sete laboratórios nacionais, entre os quais, o laboratório de massa da DRE-Norte.

Spatio-temporal gait analysis in children with cerebral palsy using, foot-worn inertial sensors.

A child's natural gait pattern may be affected by the gait laboratory environment. Wearable devices using body-worn sensors have been developed for gait analysis. The purpose of this study was to validate and explore the use of foot-worn inertial sensors for the measurement of selected spatio-temporal parameters, based on the 3D foot trajectory, in independently walking children with cerebral palsy (CP). We performed a case control study with 14 children with CP aged 6-15 years old and 15 age-matched controls. Accuracy and precision of the foot-worn device were measured using an optical motion capture system as the reference system. Mean accuracy±precision for both groups was 3.4±4.6cm for stride length, 4.3±4.2cm/s for speed and 0.5±2.9° for strike angle. Longer stance and shorter swing phases with an increase in double support were observed in children with CP (p=0.001). Stride length, speed and peak angular velocity during swing were decreased in paretic limbs, with significant differences in strike and lift-off angles. Children with cerebral palsy showed significantly higher inter-stride variability (measured by their coefficient of variation) for speed, stride length, swing and stance. During turning trajectories speed and stride length decreased significantly (p<0.01) for both groups, whereas stance increased significantly (p<0.01) in CP children only. Foot-worn inertial sensors allowed us to analyze gait spatiotemporal data outside a laboratory environment with good accuracy and precision and congruent results with what is known of gait variations during linear walking in children with CP.

Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura

Background: Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes throughout 40 generations of adaptation to a common laboratory environment. Specifically, genetic variability, population differentiation and demographic structure were compared in two replicated groups of Drosophila subobscura populations recently sampled from different wild sources. Results: We found evidence for a decline in genetic variability through time, along with an increase in genetic differentiation between all populations studied. The observed decline in genetic variability was higher during the first 14 generations of laboratory adaptation. The two groups of replicated populations showed overall similarity in variability patterns. Our results also revealed changing demographic structure of the populations during laboratory evolution, with lower effective population sizes in the early phase of the adaptive process. One of the ten microsatellites analyzed showed a clearly distinct temporal pattern of allele frequency change, suggesting the occurrence of positive selection affecting the region around that particular locus. Conclusion: Genetic drift was responsible for most of the divergence and loss of variability between and within replicates, with most changes occurring during the first generations of laboratory adaptation. We also found evidence suggesting a selective sweep, despite the low number of molecular markers analyzed. Overall, there was a similarity of evolutionary dynamics at the molecular level in our laboratory populations, despite distinct genetic backgrounds and some differences in phenotypic evolution.

Goal setting and monetary incentives: when large stakes are not enough

The aim of this paper is to test the effectiveness of wage-irrelevant goal setting policies in a laboratory environment. In our design, managers can assign a goal to their workers by setting a certain level of performance on the work task. We establish our theoretical conjectures by developing a model where assigned goals act as reference points to workers’ intrinsic motivation. Consistent with our model, we find that managers set goals which are challenging but attainable for an average-ability worker. Workers respond to these goals by increasing effort, performance and by decreasing on-the-job leisure activities with respect to the no-goal setting baseline. Finally, we study the interaction between goal setting and monetary rewards and find that goal setting is most effective when monetary incentives are strong. These results suggest that goal setting may produce intrinsic motivation and increase workers’ performance beyond what is achieved using solely monetary incentives.

ENFIN--A European network for integrative systems biology.

Integration of biological data of various types and the development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing an adapted infrastructure to connect databases, and platforms to enable both the generation of new bioinformatics tools and the experimental validation of computational predictions. With the aim of bridging the gap existing between standard wet laboratories and bioinformatics, the ENFIN Network runs integrative research projects to bring the latest computational techniques to bear directly on questions dedicated to systems biology in the wet laboratory environment. The Network maintains internally close collaboration between experimental and computational research, enabling a permanent cycling of experimental validation and improvement of computational prediction methods. The computational work includes the development of a database infrastructure (EnCORE), bioinformatics analysis methods and a novel platform for protein function analysis FuncNet.

Zimbra 8 high availability on Ubuntu 12.04

The purpose of this master thesis is to design and test the setup of a Zimbra 8 Open Source Edition (OSE) High Availability System (HA) in Ubuntu 12.04. A HA system has been proposed and tested in a laboratory environment. Its setup has been documented in its all length. The master thesis shows that thanks to some minor modifications to Zimbra OSE core and thanks to freely available Open Source HA software one can achieve a HA Zimbra OSE system. The proposed HA Zimbra OSE system can be improved in many ways and the author suggests several ways of doing so.