Is sustainable development a motor or a constraint for the professionalization of the pearl oyster industry in tahiti?

This article reports the results of a survey of the pearl oyster industry in French Polynesia territory. Its purpose is to examine the perceptions of the priorities for the development of this industry towards sustainable development. These perceptions were apprehended by a survey of pearl oyster farmers and other stakeholders of the sector (management authorities, scientists). After describing the methodological protocol of these investigations, it comes to confront the priorities chosen by professionals (i.e. pearl farmers) concerning sustainable development, with the perceptions of others stakeholders in the sector. Secondly it comes to build a typology of the priorities of pearl farmers concerning sustainable development. This analysis enables the assessment of the degree of convergence within the sector, which is the base material for defining a shared action plan at the territory scale. This is the first study compiling data of surveys of various professionals and stakeholders of the pearl farming industry in such a large area in French Polynesia.

Comparison of five popular normalization methods using a spike-in proteomics data set

Mass spectrometry (MS)-based proteomics has seen significant technical advances during the past two decades and mass spectrometry has become a central tool in many biosciences. Despite the popularity of MS-based methods, the handling of the systematic non-biological variation in the data remains a common problem. This biasing variation can result from several sources ranging from sample handling to differences caused by the instrumentation. Normalization is the procedure which aims to account for this biasing variation and make samples comparable. Many normalization methods commonly used in proteomics have been adapted from the DNA-microarray world. Studies comparing normalization methods with proteomics data sets using some variability measures exist. However, a more thorough comparison looking at the quantitative and qualitative differences of the performance of the different normalization methods and at their ability in preserving the true differential expression signal of proteins, is lacking. In this thesis, several popular and widely used normalization methods (the Linear regression normalization, Local regression normalization, Variance stabilizing normalization, Quantile-normalization, Median central tendency normalization and also variants of some of the forementioned methods), representing different strategies in normalization are being compared and evaluated with a benchmark spike-in proteomics data set. The normalization methods are evaluated in several ways. The performance of the normalization methods is evaluated qualitatively and quantitatively on a global scale and in pairwise comparisons of sample groups. In addition, it is investigated, whether performing the normalization globally on the whole data or pairwise for the comparison pairs examined, affects the performance of the normalization method in normalizing the data and preserving the true differential expression signal. In this thesis, both major and minor differences in the performance of the different normalization methods were found. Also, the way in which the normalization was performed (global normalization of the whole data or pairwise normalization of the comparison pair) affected the performance of some of the methods in pairwise comparisons. Differences among variants of the same methods were also observed.

ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

Background: Statistical analysis of DNA microarray data provides a valuable diagnostic tool for the investigation of genetic components of diseases. To take advantage of the multitude of available data sets and analysis methods, it is desirable to combine both different algorithms and data from different studies. Applying ensemble learning, consensus clustering and cross-study normalization methods for this purpose in an almost fully automated process and linking different analysis modules together under a single interface would simplify many microarray analysis tasks. Results: We present ArrayMining.net, a web-application for microarray analysis that provides easy access to a wide choice of feature selection, clustering, prediction, gene set analysis and cross-study normalization methods. In contrast to other microarray-related web-tools, multiple algorithms and data sets for an analysis task can be combined using ensemble feature selection, ensemble prediction, consensus clustering and cross-platform data integration. By interlinking different analysis tools in a modular fashion, new exploratory routes become available, e.g. ensemble sample classification using features obtained from a gene set analysis and data from multiple studies. The analysis is further simplified by automatic parameter selection mechanisms and linkage to web tools and databases for functional annotation and literature mining. Conclusion: ArrayMining.net is a free web-application for microarray analysis combining a broad choice of algorithms based on ensemble and consensus methods, using automatic parameter selection and integration with annotation databases.

Macroglial and retinal changes in hypercholesterolemic rabbits after normalization of cholesterol levels

This study evaluates hypercholesterolemic rabbits, examining the retinal changes in Müller cells and astrocytes as well as their variations after a period of normal blood-cholesterol values induced by a standard diet. New Zealand rabbits were divided into three groups: G0, fed a standard diet; G1A, fed a 0.5% cholesterol-enriched diet for 8 months; and G1B, fed as G1A followed by standard diet for 6 months. Eyes were processed for transmission electron microscopy and immunohistochemistry (GFAP). While G1B resembled G0 more than did G1A, they shared alterations with G1A: a) as in G1A, Müller cells were GFAP+, filled spaces left by axonal degeneration, formed glial scars and their nuclei were displaced to the nerve-fibre layer. The area occupied by the astrocytes associated with the nerve-fibre bundles (AANFB) and by perivascular astrocytes (PVA) in G1A and G1B was significantly lower than in controls. However, no significant differences in PVA were found between G1A and G1B. In G1B, type I PVA was absent and replaced by hypertrophic type II cells; b) Bruch's membrane (BM) was thinner in G1B than in G1A; c) the retinal pigment epithelium (RPE) cytoplasm contained fewer lipids in G1B than in G1A; d) in G1A and G1B choriocapillaris and retinal vessel showed alterations with respect to G0; e) cell death and axonal degeneration in the retina were similar in G1A and G1B. The substitution of a hyperlipemic diet by a standard one normalizes blood-lipid levels. However, the persistence of damage at retinal vessels and BM-RPE could trigger chronic ischemia.

Eficácia dos protocolos modificados de constraint induced movement therapy na função motora e desempenho de atividades diárias

Projeto de Graduação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Licenciada em Fisioterapia

Constraint-Informed Information Systems in Space Management Utilization

Declarative techniques such as Constraint Programming can be very effective in modeling and assisting management decisions. We present a method for managing university classrooms which extends the previous design of a Constraint-Informed Information System to generate the timetables while dealing with spatial resource optimization issues. We seek to maximize space utilization along two dimensions: classroom use and occupancy rates. While we want to maximize the room use rate, we still need to satisfy the soft constraints which model students’ and lecturers’ preferences. We present a constraint logic programming-based local search method which relies on an evaluation function that combines room utilization and timetable soft preferences. Based on this, we developed a tool which we applied to the improvement of classroom allocation in a University. Comparing the results to the current timetables obtained without optimizing space utilization, the initial versions of our tool manages to reach a 30% improvement in space utilization, while preserving the quality of the timetable, both for students and lecturers.

Load balancing for constraint solving with GPUs

Solving a complex Constraint Satisfaction Problem (CSP) is a computationally hard task which may require a considerable amount of time. Parallelism has been applied successfully to the job and there are already many applications capable of harnessing the parallel power of modern CPUs to speed up the solving process. Current Graphics Processing Units (GPUs), containing from a few hundred to a few thousand cores, possess a level of parallelism that surpasses that of CPUs and there are much less applications capable of solving CSPs on GPUs, leaving space for further improvement. This paper describes work in progress in the solving of CSPs on GPUs, CPUs and other devices, such as Intel Many Integrated Cores (MICs), in parallel. It presents the gains obtained when applying more devices to solve some problems and the main challenges that must be faced when using devices with as different architectures as CPUs and GPUs, with a greater focus on how to effectively achieve good load balancing between such heterogeneous devices.

Constraint Programming-based Job Dispatching for Modern HPC Applications

A High-Performance Computing job dispatcher is a critical software that assigns the finite computing resources to submitted jobs. This resource assignment over time is known as the on-line job dispatching problem in HPC systems. The fact the problem is on-line means that solutions must be computed in real-time, and their required time cannot exceed some threshold to do not affect the normal system functioning. In addition, a job dispatcher must deal with a lot of uncertainty: submission times, the number of requested resources, and duration of jobs. Heuristic-based techniques have been broadly used in HPC systems, at the cost of achieving (sub-)optimal solutions in a short time. However, the scheduling and resource allocation components are separated, thus generates a decoupled decision that may cause a performance loss. Optimization-based techniques are less used for this problem, although they can significantly improve the performance of HPC systems at the expense of higher computation time. Nowadays, HPC systems are being used for modern applications, such as big data analytics and predictive model building, that employ, in general, many short jobs. However, this information is unknown at dispatching time, and job dispatchers need to process large numbers of them quickly while ensuring high Quality-of-Service (QoS) levels. Constraint Programming (CP) has been shown to be an effective approach to tackle job dispatching problems. However, state-of-the-art CP-based job dispatchers are unable to satisfy the challenges of on-line dispatching, such as generate dispatching decisions in a brief period and integrate current and past information of the housing system. Given the previous reasons, we propose CP-based dispatchers that are more suitable for HPC systems running modern applications, generating on-line dispatching decisions in a proper time and are able to make effective use of job duration predictions to improve QoS levels, especially for workloads dominated by short jobs.

Il ruolo del controllo posturale per il movimento selettivo degli arti superiori attraverso la facilitazione con trunk constraint nel paziente neurologico: case report

Background Recentemente la letteratura scientifica ha dimostrato come un corretto controllo posturale faciliti i movimenti dell’arto superiore. Ci sono evidenze secondo cui, applicando al paziente dei contenimenti sul tronco, si ha un miglioramento della funzionalità dell’arto superiore. Obiettivi L’obiettivo principale della tesi era quello di verificare come il sostegno del tronco con l’utilizzo di una stabile struttura assiale, attraverso un supporto esterno definito “trunk constraint”, incrementi il controllo posturale, per facilitare i movimenti frazionati degli arti superiori in persone con esiti di patologie neurologiche. Materiali e metodi Il caso clinico riguarda un uomo di 60 anni con esiti di emiparesi sinistra da ictus ischemico destro. E’ stato eseguito un protocollo di dieci sessioni di trattamento, di un’ora ciascuna, in cui veniva applicata la facilitazione attraverso trunk constraint in diversi setting riabilitativi. I dati sono stati raccolti tramite le scale: Trunk Control Test, Trunk Impairment Scale e Fugl-Meyer Assessment. Inoltre, è stata eseguita l’analisi osservazionale, attraverso videoripresa, di un gesto funzionale dell’arto superiore. Risultati I dati rilevati dimostrano degli effetti positivi rispetto alle ipotesi di partenza. Infatti sono stati riscontrati miglioramenti negli item delle scale somministrate e nella valutazione qualitativa dell’arto superiore. In particolare, si è evidenziato un miglioramento nel controllo del tronco nella scala Trunk Control Test e nella Trunk Impairment Scale e della funzione dell’arto superiore alla scala Fugl-Meyer Assessment. L’analisi osservazionale dei video dimostra un miglioramento del timing di attivazione durante la fase di reaching. Conclusioni I risultati ottenuti supportano il fatto che un incremento dell’attività antigravitaria del tronco, anche attraverso supporti esterni come la trunk constraint, possono facilitare un miglioramento funzionale dell’arto superiore.

Machine Learning in Automatic Tabulation for Constraint Model Reformulation

Combinatorial decision and optimization problems belong to numerous applications, such as logistics and scheduling, and can be solved with various approaches. Boolean Satisfiability and Constraint Programming solvers are some of the most used ones and their performance is significantly influenced by the model chosen to represent a given problem. This has led to the study of model reformulation methods, one of which is tabulation, that consists in rewriting the expression of a constraint in terms of a table constraint. To apply it, one should identify which constraints can help and which can hinder the solving process. So far this has been performed by hand, for example in MiniZinc, or automatically with manually designed heuristics, in Savile Row. Though, it has been shown that the performances of these heuristics differ across problems and solvers, in some cases helping and in others hindering the solving procedure. However, recent works in the field of combinatorial optimization have shown that Machine Learning (ML) can be increasingly useful in the model reformulation steps. This thesis aims to design a ML approach to identify the instances for which Savile Row’s heuristics should be activated. Additionally, it is possible that the heuristics miss some good tabulation opportunities, so we perform an exploratory analysis for the creation of a ML classifier able to predict whether or not a constraint should be tabulated. The results reached towards the first goal show that a random forest classifier leads to an increase in the performances of 4 different solvers. The experimental results in the second task show that a ML approach could improve the performance of a solver for some problem classes.

Indole-3-carbinol Attenuates The Deleterious Gestational Effects Of Bisphenol A Exposure On The Prostate Gland Of Male F1 Rats.

Bisphenol A (BPA) is a chemical that has been investigated for it potential to cause prostate diseases. In this study, pregnant Sprague-Dawley rats were treated with 25 or 250 μg/kg BPA from gestational day (GD) 10 to GD21 with or without concurrent indole-3-carbinol (I3C) feeding. I3C is a phytochemical, and it affords chemoprotection against many types of neoplasia. Male F1 rats from different litters were euthanized on post-natal day (PND) 21 and PND180. BPA-treated groups showed a significant increase in histopathological lesions, but I3C feeding reversed many of these changes, mainly at PND180. Maternal I3C feeding increased prostate epithelial apoptosis in the BPA-treated groups and across age groups. Furthermore, I3C induced partial normalization of the prostate histoarchitecture. The results pointed to a protective effect of maternal I3C feeding during pregnancy in the BPA-exposed male offspring, thereby indicating reduction in the harmful effects of gestational BPA imprinting on the prostate.

Selection And Validation Of Reference Genes For Functional Studies In The Calliphoridae Family.

The genera Cochliomyia and Chrysomya contain both obligate and saprophagous flies, which allows the comparison of different feeding habits between closely related species. Among the different strategies for comparing these habits is the use of qPCR to investigate the expression levels of candidate genes involved in feeding behavior. To ensure an accurate measure of the levels of gene expression, it is necessary to normalize the amount of the target gene with the amount of a reference gene having a stable expression across the compared species. Since there is no universal gene that can be used as a reference in functional studies, candidate genes for qPCR data normalization were selected and validated in three Calliphoridae (Diptera) species, Cochliomyia hominivorax Coquerel, Cochliomyia macellaria Fabricius, and Chrysomya albiceps Wiedemann . The expression stability of six genes ( Actin, Gapdh, Rp49, Rps17, α -tubulin, and GstD1) was evaluated among species within the same life stage and between life stages within each species. The expression levels of Actin, Gapdh, and Rp49 were the most stable among the selected genes. These genes can be used as reliable reference genes for functional studies in Calliphoridae using similar experimental settings.

Vagotomy Ameliorates Islet Morphofunction And Body Metabolic Homeostasis In Msg-obese Rats.

The parasympathetic nervous system is important for β-cell secretion and mass regulation. Here, we characterized involvement of the vagus nerve in pancreatic β-cell morphofunctional regulation and body nutrient homeostasis in 90-day-old monosodium glutamate (MSG)-obese rats. Male newborn Wistar rats received MSG (4 g/kg body weight) or saline [control (CTL) group] during the first 5 days of life. At 30 days of age, both groups of rats were submitted to sham-surgery (CTL and MSG groups) or subdiaphragmatic vagotomy (Cvag and Mvag groups). The 90-day-old MSG rats presented obesity, hyperinsulinemia, insulin resistance, and hypertriglyceridemia. Their pancreatic islets hypersecreted insulin in response to glucose but did not increase insulin release upon carbachol (Cch) stimulus, despite a higher intracellular Ca2+ mobilization. Furthermore, while the pancreas weight was 34% lower in MSG rats, no alteration in islet and β-cell mass was observed. However, in the MSG pancreas, increases of 51% and 55% were observed in the total islet and β-cell area/pancreas section, respectively. Also, the β-cell number per β-cell area was 19% higher in MSG rat pancreas than in CTL pancreas. Vagotomy prevented obesity, reducing 25% of body fat stores and ameliorated glucose homeostasis in Mvag rats. Mvag islets demonstrated partially reduced insulin secretion in response to 11.1 mM glucose and presented normalization of Cch-induced Ca2+ mobilization and insulin release. All morphometric parameters were similar among Mvag and CTL rat pancreases. Therefore, the higher insulin release in MSG rats was associated with greater β-cell/islet numbers and not due to hypertrophy. Vagotomy improved whole body nutrient homeostasis and endocrine pancreatic morphofunction in Mvag rats.

Recovery Of The Incretin Effect In Type 2 Diabetic Patients After Biliopancreatic Diversion.

Context: Bariatric surgery often results in remission of the diabetic state in obese patients. Increased incretin effect seems to play an important role in the glycemic improvements after Roux-en-Y gastric bypass, but the impact of biliopancreatic diversion (BPD) remains unexplored. Objective: To elucidate the effect of BPD on the incretin effect and its interplay with beta-cell function and insulin sensitivity (IS) in obese subjects with type 2 diabetes (T2DM). Design, Setting and Patients: Twenty-three women were studied: a control group of 13 lean, normal glucose-tolerant women (lean NGT) studied once and 10 obese patients with T2DM studied before, 1 and 12 months after BPD. Intervention: The ObeseT2DM group underwent BPD. Main Outcome Measures: The change in incretin effect as measured by the isoglycemic intravenous glucose infusion test. Secondary outcomes encompassed IS and beta-cell function. Results: At baseline, the incretin effect was lower in obese T2DM compared to lean NGT (p<0.05). One month after BPD, the incretin effect was not changed, but at 12 months it reached the level of the lean NGT group (p>0.05). IS improved (p<0.05) 1 month after BPD and at 12 months it resembled the levels of the lean NGT group. Insulin secretory rate and beta-cell glucose sensitivity increased after BPD and achieved levels similar to lean NGT group 1 month after BPD and even higher levels at 12 months (p<0.05). Conclusions: BPD has no acute impact on the reduced incretin effect, but 12 months after surgery the incretin effect normalizes alongside normalization of glucose control, IS and beta-cell function.