Compelling transgenetic evidence for transmission of bovine spongiform encephalopathy prions to humans

There is growing concern that bovine spongiform encephalopathy (BSE) may have passed from cattle to humans. We report here that transgenic (Tg) mice expressing bovine (Bo) prion protein (PrP) serially propagate BSE prions and that there is no species barrier for transmission from cattle to Tg(BoPrP) mice. These same mice were also highly susceptible to a new variant of Creutzfeldt–Jakob disease (nvCJD) and natural sheep scrapie. The incubation times (≈250 days), neuropathology, and disease-causing PrP isoforms in Tg(BoPrP)Prnp0/0 mice inoculated with nvCJD and BSE brain extracts were indistinguishable and differed dramatically from those seen in these mice injected with natural scrapie prions. Our findings provide the most compelling evidence to date that prions from cattle with BSE have infected humans and caused fatal neurodegeneration.

Metodologia estatística na solução do problema do caixeiro viajante e na avaliação de algoritmos : um estudo aplicado à transgenética computacional

The problems of combinatory optimization have involved a large number of researchers in search of approximative solutions for them, since it is generally accepted that they are unsolvable in polynomial time. Initially, these solutions were focused on heuristics. Currently, metaheuristics are used more for this task, especially those based on evolutionary algorithms. The two main contributions of this work are: the creation of what is called an -Operon- heuristic, for the construction of the information chains necessary for the implementation of transgenetic (evolutionary) algorithms, mainly using statistical methodology - the Cluster Analysis and the Principal Component Analysis; and the utilization of statistical analyses that are adequate for the evaluation of the performance of the algorithms that are developed to solve these problems. The aim of the Operon is to construct good quality dynamic information chains to promote an -intelligent- search in the space of solutions. The Traveling Salesman Problem (TSP) is intended for applications based on a transgenetic algorithmic known as ProtoG. A strategy is also proposed for the renovation of part of the chromosome population indicated by adopting a minimum limit in the coefficient of variation of the adequation function of the individuals, with calculations based on the population. Statistical methodology is used for the evaluation of the performance of four algorithms, as follows: the proposed ProtoG, two memetic algorithms and a Simulated Annealing algorithm. Three performance analyses of these algorithms are proposed. The first is accomplished through the Logistic Regression, based on the probability of finding an optimal solution for a TSP instance by the algorithm being tested. The second is accomplished through Survival Analysis, based on a probability of the time observed for its execution until an optimal solution is achieved. The third is accomplished by means of a non-parametric Analysis of Variance, considering the Percent Error of the Solution (PES) obtained by the percentage in which the solution found exceeds the best solution available in the literature. Six experiments have been conducted applied to sixty-one instances of Euclidean TSP with sizes of up to 1,655 cities. The first two experiments deal with the adjustments of four parameters used in the ProtoG algorithm in an attempt to improve its performance. The last four have been undertaken to evaluate the performance of the ProtoG in comparison to the three algorithms adopted. For these sixty-one instances, it has been concluded on the grounds of statistical tests that there is evidence that the ProtoG performs better than these three algorithms in fifty instances. In addition, for the thirty-six instances considered in the last three trials in which the performance of the algorithms was evaluated through PES, it was observed that the PES average obtained with the ProtoG was less than 1% in almost half of these instances, having reached the greatest average for one instance of 1,173 cities, with an PES average equal to 3.52%. Therefore, the ProtoG can be considered a competitive algorithm for solving the TSP, since it is not rare in the literature find PESs averages greater than 10% to be reported for instances of this size.

O problema do caixeiro viajante alugador : um estudo algorítmico

The Car Rental Salesman Problem (CaRS) is a variant of the classical Traveling Salesman Problem which was not described in the literature where a tour of visits can be decomposed into contiguous paths that may be performed in different rental cars. The aim is to determine the Hamiltonian cycle that results in a final minimum cost, considering the cost of the route added to the cost of an expected penalty paid for each exchange of vehicles on the route. This penalty is due to the return of the car dropped to the base. This paper introduces the general problem and illustrates some examples, also featuring some of its associated variants. An overview of the complexity of this combinatorial problem is also outlined, to justify their classification in the NPhard class. A database of instances for the problem is presented, describing the methodology of its constitution. The presented problem is also the subject of a study based on experimental algorithmic implementation of six metaheuristic solutions, representing adaptations of the best of state-of-the-art heuristic programming. New neighborhoods, construction procedures, search operators, evolutionary agents, cooperation by multi-pheromone are created for this problem. Furtermore, computational experiments and comparative performance tests are conducted on a sample of 60 instances of the created database, aiming to offer a algorithm with an efficient solution for this problem. These results will illustrate the best performance reached by the transgenetic algorithm in all instances of the dataset

O problema biobjetivo da árvore geradora quadrática em adjacência de arestas

The Quadratic Minimum Spanning Tree Problem (QMST) is a version of the Minimum Spanning Tree Problem in which, besides the traditional linear costs, there is a quadratic structure of costs. This quadratic structure models interaction effects between pairs of edges. Linear and quadratic costs are added up to constitute the total cost of the spanning tree, which must be minimized. When these interactions are restricted to adjacent edges, the problem is named Adjacent Only Quadratic Minimum Spanning Tree (AQMST). AQMST and QMST are NP-hard problems that model several problems of transport and distribution networks design. In general, AQMST arises as a more suitable model for real problems. Although, in literature, linear and quadratic costs are added, in real applications, they may be conflicting. In this case, it may be interesting to consider these costs separately. In this sense, Multiobjective Optimization provides a more realistic model for QMST and AQMST. A review of the state-of-the-art, so far, was not able to find papers regarding these problems under a biobjective point of view. Thus, the objective of this Thesis is the development of exact and heuristic algorithms for the Biobjective Adjacent Only Quadratic Spanning Tree Problem (bi-AQST). In order to do so, as theoretical foundation, other NP-hard problems directly related to bi-AQST are discussed: the QMST and AQMST problems. Bracktracking and branch-and-bound exact algorithms are proposed to the target problem of this investigation. The heuristic algorithms developed are: Pareto Local Search, Tabu Search with ejection chain, Transgenetic Algorithm, NSGA-II and a hybridization of the two last-mentioned proposals called NSTA. The proposed algorithms are compared to each other through performance analysis regarding computational experiments with instances adapted from the QMST literature. With regard to exact algorithms, the analysis considers, in particular, the execution time. In case of the heuristic algorithms, besides execution time, the quality of the generated approximation sets is evaluated. Quality indicators are used to assess such information. Appropriate statistical tools are used to measure the performance of exact and heuristic algorithms. Considering the set of instances adopted as well as the criteria of execution time and quality of the generated approximation set, the experiments showed that the Tabu Search with ejection chain approach obtained the best results and the transgenetic algorithm ranked second. The PLS algorithm obtained good quality solutions, but at a very high computational time compared to the other (meta)heuristics, getting the third place. NSTA and NSGA-II algorithms got the last positions

Algoritomos transgenéticos aplicados ao problema da árvore geradora biobjetivo

The Multiobjective Spanning Tree is a NP-hard Combinatorial Optimization problem whose application arises in several areas, especially networks design. In this work, we propose a solution to the biobjective version of the problem through a Transgenetic Algorithm named ATIS-NP. The Computational Transgenetic is a metaheuristic technique from Evolutionary Computation whose inspiration relies in the conception of cooperation (and not competition) as the factor of main influence to evolution. The algorithm outlined is the evolution of a work that has already yielded two other transgenetic algorithms. In this sense, the algorithms previously developed are also presented. This research also comprises an experimental analysis with the aim of obtaining information related to the performance of ATIS-NP when compared to other approaches. Thus, ATIS-NP is compared to the algorithms previously implemented and to other transgenetic already presented for the problem under consideration. The computational experiments also address the comparison to two recent approaches from literature that present good results, a GRASP and a genetic algorithms. The efficiency of the method described is evaluated with basis in metrics of solution quality and computational time spent. Considering the problem is within the context of Multiobjective Optimization, quality indicators are adopted to infer the criteria of solution quality. Statistical tests evaluate the significance of results obtained from computational experiments

Um estudo algorítmico de problemas logísticos na indústria de petróleo e gás natural

This work consists on the study of two important problems arising from the operations of petroleum and natural gas industries. The first problem the pipe dimensioning problem on constrained gas distribution networks consists in finding the least cost combination of diameters from a discrete set of commercially available ones for the pipes of a given gas network, such that it respects minimum pressure requirements at each demand node and upstream pipe conditions. On its turn, the second problem the piston pump unit routing problem comes from the need of defining the piston pump unit routes for visiting a number of non-emergent wells in on-shore fields, i.e., wells which don t have enough pressure to make the oil emerge to surface. The periodic version of this problem takes into account the wells re-filling equation to provide a more accurate planning in the long term. Besides the mathematical formulation of both problems, an exact algorithm and a taboo search were developed for the solution of the first problem and a theoretical limit and a ProtoGene transgenetic algorithm were developed for the solution of the second problem. The main concepts of the metaheuristics are presented along with the details of their application to the cited problems. The obtained results for both applications are promising when compared to theoretical limits and alternate solutions, either relative to the quality of the solutions or to associated running time

Algoritmo treansgenético na solução do problema do Caixeiro Viajante

The Traveling Purchaser Problem is a variant of the Traveling Salesman Problem, where there is a set of markets and a set of products. Each product is available on a subset of markets and its unit cost depends on the market where it is available. The objective is to buy all the products, departing and returning to a domicile, at the least possible cost defined as the summation of the weights of the edges in the tour and the cost paid to acquire the products. A Transgenetic Algorithm, an evolutionary algorithm with basis on endosymbiosis, is applied to the Capacited and Uncapacited versions of this problem. Evolution in Transgenetic Algorithms is simulated with the interaction and information sharing between populations of individuals from distinct species. The computational results show that this is a very effective approach for the TPP regarding solution quality and runtime. Seventeen and nine new best results are presented for instances of the capacited and uncapacited versions, respectively

O problema do caixeiro alugador com coleta de bonus: um estudo algoritmico

This paper introduces a new variant of the Traveling Car Renter Problem, named Prizecollecting Traveling Car Renter Problem. In this problem, a set of vertices, each associated with a bonus, and a set of vehicles are given. The objective is to determine a cycle that visits some vertices collecting, at least, a pre-defined bonus, and minimizing the cost of the tour that can be traveled with different vehicles. A mathematical formulation is presented and implemented in a solver to produce results for sixty-two instances. The proposed problem is also subject of an experimental study based on the algorithmic application of four metaheuristics representing the best adaptations of the state of the art of the heuristic programming.We also provide new local search operators which exploit the neighborhoods of the problem, construction procedures and adjustments, created specifically for the addressed problem. Comparative computational experiments and performance tests are performed on a sample of 80 instances, aiming to offer a competitive algorithm to the problem. We conclude that memetic algorithms, computational transgenetic and a hybrid evolutive algorithm are competitive in tests performed

Subcellular colocalization of the cellular and scrapie prion proteins in caveolae-like membranous domains

Results of transgenetic studies argue that the scrapie isoform of the prion protein (PrPSc) interacts with the substrate cellular PrP (PrPC) during conversion into nascent PrPSc. While PrPSc appears to accumulate primarily in lysosomes, caveolae-like domains (CLDs) have been suggested to be the site where PrPC is converted into PrPSc. We report herein that CLDs isolated from scrapie-infected neuroblastoma (ScN2a) cells contain PrPC and PrPSc. After lysis of ScN2a cells in ice-cold Triton X-100, both PrP isoforms and an N-terminally truncated form of PrPC (PrPC-II) were found concentrated in detergent-insoluble complexes resembling CLDs that were isolated by flotation in sucrose gradients. Similar results were obtained when CLDs were purified from plasma membranes by sonication and gradient centrifugation; with this procedure no detergents are used, which minimizes artifacts that might arise from redistribution of proteins among subcellular fractions. The caveolar markers ganglioside GM1 and H-ras were found concentrated in the CLD fractions. When plasma membrane proteins were labeled with the impermeant reagent sulfo-N-hydroxysuccinimide-biotin, both PrPC and PrPSc were found biotinylated in CLD fractions. Similar results on the colocalization of PrPC and PrPSc were obtained when CLDs were isolated from Syrian hamster brains. Our findings demonstrate that both PrPC and PrPSc are present in CLDs and, thus, support the hypothesis that the PrPSc formation occurs within this subcellular compartment.

Prions

Prions are unprecedented infectious pathogens that cause a group of invariably fatal neurodegenerative diseases by an entirely novel mechanism. Prion diseases may present as genetic, infectious, or sporadic disorders, all of which involve modification of the prion protein (PrP). Bovine spongiform encephalopathy (BSE), scrapie of sheep, and Creutzfeldt–Jakob disease (CJD) of humans are among the most notable prion diseases. Prions are transmissible particles that are devoid of nucleic acid and seem to be composed exclusively of a modified protein (PrPSc). The normal, cellular PrP (PrPC) is converted into PrPSc through a posttranslational process during which it acquires a high β-sheet content. The species of a particular prion is encoded by the sequence of the chromosomal PrP gene of the mammals in which it last replicated. In contrast to pathogens carrying a nucleic acid genome, prions appear to encipher strain-specific properties in the tertiary structure of PrPSc. Transgenetic studies argue that PrPSc acts as a template upon which PrPC is refolded into a nascent PrPSc molecule through a process facilitated by another protein. Miniprions generated in transgenic mice expressing PrP, in which nearly half of the residues were deleted, exhibit unique biological properties and should facilitate structural studies of PrPSc. While knowledge about prions has profound implications for studies of the structural plasticity of proteins, investigations of prion diseases suggest that new strategies for the prevention and treatment of these disorders may also find application in the more common degenerative diseases.

Prion protein (PrP) synthetic peptides induce cellular PrP to acquire properties of the scrapie isoform.

Conversion of the cellular isoform of prion protein (PrPC) into the scrapie isoform (PrPSc) involves an increase in the beta-sheet content, diminished solubility, and resistance to proteolytic digestion. Transgenetic studies argue that PrPC and PrPSc form a complex during PrPSc formation; thus, synthetic PrP peptides, which mimic the conformational pluralism of PrP, were mixed with PrPC to determine whether its properties were altered. Peptides encompassing two alpha-helical domains of PrP when mixed with PrPC produced a complex that displayed many properties of PrPSc. The PrPC-peptide complex formed fibrous aggregates and up to 65% of complexed PrPC sedimented at 100,000 x g for 1 h, whereas PrPC alone did not. These complexes were resistant to proteolytic digestion and displayed a high beta-sheet content. Unexpectedly, the peptide in a beta-sheet conformation did not form the complex, whereas the random coil did. Addition of 2% Sarkosyl disrupted the complex and rendered PrPC sensitive to protease digestion. While the pathogenic A117V mutation increased the efficacy of complex formation, anti-PrP monoclonal antibody prevented interaction between PrPC and peptides. Our findings in concert with transgenetic investigations argue that PrPC interacts with PrPSc through a domain that contains the first two putative alpha-helices. Whether PrPC-peptide complexes possess prion infectivity as determined by bioassays remains to be established.

Distribuição de derivados de petróleo por redes de polidutos: uma abordagem através de algoritmos evolucionários híbridos para um problema triobjetivo

An important problem faced by the oil industry is to distribute multiple oil products through pipelines. Distribution is done in a network composed of refineries (source nodes), storage parks (intermediate nodes), and terminals (demand nodes) interconnected by a set of pipelines transporting oil and derivatives between adjacent areas. Constraints related to storage limits, delivery time, sources availability, sending and receiving limits, among others, must be satisfied. Some researchers deal with this problem under a discrete viewpoint in which the flow in the network is seen as batches sending. Usually, there is no separation device between batches of different products and the losses due to interfaces may be significant. Minimizing delivery time is a typical objective adopted by engineers when scheduling products sending in pipeline networks. However, costs incurred due to losses in interfaces cannot be disregarded. The cost also depends on pumping expenses, which are mostly due to the electricity cost. Since industrial electricity tariff varies over the day, pumping at different time periods have different cost. This work presents an experimental investigation of computational methods designed to deal with the problem of distributing oil derivatives in networks considering three minimization objectives simultaneously: delivery time, losses due to interfaces and electricity cost. The problem is NP-hard and is addressed with hybrid evolutionary algorithms. Hybridizations are mainly focused on Transgenetic Algorithms and classical multi-objective evolutionary algorithm architectures such as MOEA/D, NSGA2 and SPEA2. Three architectures named MOTA/D, NSTA and SPETA are applied to the problem. An experimental study compares the algorithms on thirty test cases. To analyse the results obtained with the algorithms Pareto-compliant quality indicators are used and the significance of the results evaluated with non-parametric statistical tests.

Algoritmos experimentais para o problema biobjetivo da árvore geradora quadrática em adjacência de arestas

The Quadratic Minimum Spanning Tree (QMST) problem is a generalization of the Minimum Spanning Tree problem in which, beyond linear costs associated to each edge, quadratic costs associated to each pair of edges must be considered. The quadratic costs are due to interaction costs between the edges. When interactions occur between adjacent edges only, the problem is named Adjacent Only Quadratic Minimum Spanning Tree (AQMST). Both QMST and AQMST are NP-hard and model a number of real world applications involving infrastructure networks design. Linear and quadratic costs are summed in the mono-objective versions of the problems. However, real world applications often deal with conflicting objectives. In those cases, considering linear and quadratic costs separately is more appropriate and multi-objective optimization provides a more realistic modelling. Exact and heuristic algorithms are investigated in this work for the Bi-objective Adjacent Only Quadratic Spanning Tree Problem. The following techniques are proposed: backtracking, branch-and-bound, Pareto Local Search, Greedy Randomized Adaptive Search Procedure, Simulated Annealing, NSGA-II, Transgenetic Algorithm, Particle Swarm Optimization and a hybridization of the Transgenetic Algorithm with the MOEA-D technique. Pareto compliant quality indicators are used to compare the algorithms on a set of benchmark instances proposed in literature.

Algoritmos experimentais para o problema biobjetivo da árvore geradora quadrática em adjacência de arestas

The Quadratic Minimum Spanning Tree (QMST) problem is a generalization of the Minimum Spanning Tree problem in which, beyond linear costs associated to each edge, quadratic costs associated to each pair of edges must be considered. The quadratic costs are due to interaction costs between the edges. When interactions occur between adjacent edges only, the problem is named Adjacent Only Quadratic Minimum Spanning Tree (AQMST). Both QMST and AQMST are NP-hard and model a number of real world applications involving infrastructure networks design. Linear and quadratic costs are summed in the mono-objective versions of the problems. However, real world applications often deal with conflicting objectives. In those cases, considering linear and quadratic costs separately is more appropriate and multi-objective optimization provides a more realistic modelling. Exact and heuristic algorithms are investigated in this work for the Bi-objective Adjacent Only Quadratic Spanning Tree Problem. The following techniques are proposed: backtracking, branch-and-bound, Pareto Local Search, Greedy Randomized Adaptive Search Procedure, Simulated Annealing, NSGA-II, Transgenetic Algorithm, Particle Swarm Optimization and a hybridization of the Transgenetic Algorithm with the MOEA-D technique. Pareto compliant quality indicators are used to compare the algorithms on a set of benchmark instances proposed in literature.