CANADA’S GRAIN HANDLING AND TRANSPORTATION SYSTEM: A GIS-BASED EVALUATION OF POLICY CHANGES

Western Canada is in a post Canadian Wheat Board single-desk market, in which grain handlers face policy, allocation, and logistical changes to the transportation of grains. This research looks at the rails transportation problem for allocating wheat from Prairie to port position, offering a new allocation system that fits the evolving environment of Western Canada’s grain market. Optimization and analysis of the transport of wheat by railroads is performed using geographic information system software as well as spatial and historical data. The studied transportation problem searches to minimize the costs of time rather than look purely at locational costs or closest proximity to port. Through optimization three major bottlenecks are found to constrain the transportation problem; 1) an allocation preference towards Thunder Bay and Vancouver ports, 2) small capacity train inefficiency, and 3) a mismatched distribution of supply and demand between the Class 1 railway firms. Through analysis of counterfactual policies and a scaled sensitivity analysis of the transportation problem, the grains transport system of railroads is found to be dynamic and time efficient; specifically when utilizing larger train capacities, offering open access to rail, and under times of increased availability of supplies. Even under the current circumstances of reduced grain movement and inefficiencies, there are policies and logistics that can be implemented to offer grain handlers in Western Canada with the transportation needed to fulfill their export demands

Modeling the Quorum Sensing Signaling Regulatory Network in \u3cem\u3eVibrio fischeri\u3c/em\u3e

Quorum sensing is a mechanism by which bacteria can sense the levels of signaling molecules and respond by controlling the expression of target genes. The marine bacterium, Vibrio fischeri, has been extensively studied as a model for the quorum sensing mechanism in Gram-negative bacteria. In order to systematically investigate the quorum sensing regulatory network in V. fischeri, a conceptual model was first established based on the existing knowledge. Next, molecular microbiology and bioinformatics techniques were employed to both qualitatively and quantitatively characterize the system. These techniques included the quantification of the 3-oxo-C6-HSL concentrations in the cell culture supernatant using a bioluminescent bioreporter strain of E. coli, the measurements of the messenger RNA levels of quorum sensing genes (luxI, luxR, ainS and litR) using the reverse transcription-polymerase chain reaction (RT-PCR), as well as the sequence analysis of the promoter regions of quorum sensing related genes. A mathematical model composed of ordinary differential equations was created to characterize the regulatory process. The simulated annealing method was used to minimize the weighted discrepancy between the modeling output and the experimental data with correlations ranging from 0.85 to 0.99. This study, mathematically modeled the comprehensive quorum sensing regulatory system, which encompasses 3-oxo-C6-HSL, lux operon (luxR and luxICDABEG), C8-HSL, ainS, ainR, luxO, and litR, and can benefit the understanding of dozens of similar quorum sensing regulatory systems

Information processing in biology

To survive, organisms must respond appropriately to a variety of challenges posed by a dynamic and uncertain environment. The mechanisms underlying such responses can in general be framed as input-output devices which map environment states (inputs) to associated responses (output. In this light, it is appealing to attempt to model these systems using information theory, a well developed mathematical framework to describe input-output systems. Under the information theoretical perspective, an organism’s behavior is fully characterized by the repertoire of its outputs under different environmental conditions. Due to natural selection, it is reasonable to assume this input-output mapping has been fine tuned in such a way as to maximize the organism’s fitness. If that is the case, it should be possible to abstract away the mechanistic implementation details and obtain the general principles that lead to fitness under a certain environment. These can then be used inferentially to both generate hypotheses about the underlying implementation as well as predict novel responses under external perturbations. In this work I use information theory to address the question of how biological systems generate complex outputs using relatively simple mechanisms in a robust manner. In particular, I will examine how communication and distributed processing can lead to emergent phenomena which allow collective systems to respond in a much richer way than a single organism could

Polymer Brush Force Modeling and Experimentation

Atomic force microscope (AFM) force measurements were taken on an alginate-polymer brush in varying pH buffer solutions in order to determine the meaning of the variable s in the force model. The current understanding is that s is the root spacing of the polymers, but this experiment suggests that s is the mesh spacing. The force curves were fit in order to determine the brush parameters. It was found that all parameters increased as a function of pH

Negative feedback and transcriptional overshooting in a regulatory network for horizontal gene transfer

This is an open-access article distributed under the terms of the Creative Commons Attribution License.Horizontal gene transfer (HGT) is a major force driving bacterial evolution. Because of their ability to cross inter-species barriers, bacterial plasmids are essential agents for HGT. This ability, however, poses specific requisites on plasmid physiology, in particular the need to overcome a multilevel selection process with opposing demands. We analyzed the transcriptional network of plasmid R388, one of the most promiscuous plasmids in Proteobacteria. Transcriptional analysis by fluorescence expression profiling and quantitative PCR revealed a regulatory network controlled by six transcriptional repressors. The regulatory network relied on strong promoters, which were tightly repressed in negative feedback loops. Computational simulations and theoretical analysis indicated that this architecture would show a transcriptional burst after plasmid conjugation, linking the magnitude of the feedback gain with the intensity of the transcriptional burst. Experimental analysis showed that transcriptional overshooting occurred when the plasmid invaded a new population of susceptible cells. We propose that transcriptional overshooting allows genome rebooting after horizontal gene transfer, and might have an adaptive role in overcoming the opposing demands of multilevel selection.Work was financed by the Spanish Ministry of Economy and Competitivity (BFU2011–26608) and the European Seventh Framework Program (289326/FP7-KBBE-2011-5 and 282004/FP7–HEALTH-2011-2.3.1–2) to FdlC.Peer Reviewe

Negative feedback and transcriptional overshooting in a regulatory network for horizontal gene transfer

Horizontal gene transfer (HGT) is a major force driving bacterial evolution. Because of their ability to cross inter-species barriers, bacterial plasmids are essential agents for HGT. This ability, however, poses specific requisites on plasmid physiology, in particular the need to overcome a multilevel selection process with opposing demands. We analyzed the transcriptional network of plasmid R388, one of the most promiscuous plasmids in Proteobacteria. Transcriptional analysis by fluorescence expression profiling and quantitative PCR revealed a regulatory network controlled by six transcriptional repressors. The regulatory network relied on strong promoters, which were tightly repressed in negative feedback loops. Computational simulations and theoretical analysis indicated that this architecture would show a transcriptional burst after plasmid conjugation, linking the magnitude of the feedback gain with the intensity of the transcriptional burst. Experimental analysis showed that transcriptional overshooting occurred when the plasmid invaded a new population of susceptible cells. We propose that transcriptional overshooting allows genome rebooting after horizontal gene transfer, and might have an adaptive role in overcoming the opposing demands of multilevel selection

Certitex: a Textile Certified Supply Chain

The appearance of blockchain technologies and their growth and development have led to the exploration of applications of the technology in new areas, in addition to the original, cryptocurrencies, areas such as product management and traceability in supply chains are being explored. Initially, this technology was explored with the aim of providing food supply chains with traceability and transparency for the consumer. Currently, solutions for a larger variety of supply chains are being studied and developed. Current studies have proven that the technology has powerful properties to promote traceability and nonrepudiation of information related to products in a supply chain, as well as providing liability of entities for damages caused to products, which in the past has been notoriously difficult. The current structure of these supply chains, several different entities located in different physical spaces, is prone to the application of blockchain solutions as it also fits the architecture of the technology itself. All of this leads to a strong interest in applying blockchain technology to supply chains. Unfortunately, all the blockchain based solutions found to solve similar problems in the research phase of this project were developed by private entities, with little to no divulgation about their development and many times not even about how they function. This led to this project being mainly about researching the base technology and developing a solution from scratch. The problems of currently used traditional solutions are related to the use of non-standardized information registration strategies and ease of repudiation of information, but current consumer demands for knowledge of the origin of products has led to the exploration of new solutions to overcome this. Additionally, it is common for products, at the end of their production cycle, to be damaged and it is practically impossible to locate where the damage occurred in the chain. The idea of adapting blockchain technology as a solution for product traceability in the supply chain presents some points of concern, as blockchains are generally associated with distributed and public systems to maintain a given cryptocurrency, thus making information public. Although this is the initial purpose of its creation, other blockchain technologies oriented to data storage in a business to business model have emerged. These blockchains have access control measures, and are therefore called private. Only allowing access by a select group of entities. Additionally, information stored on a blockchain is also often associated with high costs, and when we refer to public blockchains like Ethereum this is a reality, but by using private solutions we can mitigate this cost. It is also often a concern the computational costs associated with cryptocurrency blockchains like Bitcoin and Etherum. Again, it is possible to get around this limitation by using private solutions where we can use more light weight algorithms, because the environment in which the system will be inserted, does not benefit from the properties of such algorithms. With the usage of blockchain to certify and record the progress of products as they travel through the supply chain, it is also interesting to explore the collected data, and how it could be used to make the supply chain itself more efficient. The purpose of this dissertation is to study how blockchain technology can be combined with a supply chain to offer product traceability and information collection. To achieve this goal, a prototype of a blockchain-based application was developed to collect data in a supply chain, as well as a prototype of an application for remote viewing of the data entered and a prototype of a Machine Learning module able to make use of the information collected by the blockchain.O aparecimento das tecnologias blockchain e o seu crescimento e desenvolvimento, têm levado à exploração de aplicações da tecnologia em novas áreas. Inicialmente, e relativamente ao tema desta tese, esta tecnologia foi explorada com o objetivo de prover cadeias de fornecimento alimentícias de rastreabilidade e transparência para o consumidor. Estudos atuais têm provado que a tecnologia apresenta propriedades poderosas para promover a rastreabilidade e não repúdio de informação. Infelizmente todas as soluções baseadas em blockchain encontradas na fase de pesquisa são soluções desenvolvidas por entidades privadas não havendo qualquer divulgação de informação relativa ao seu desenvolvimento, e também na maioria esmagadora dos casos sobre o seu funcionamento. Isto levou a que esta dissertação fosse maioritariamente um trabalho de investigação da tecnologia base, e desenvolvimento de raiz de uma solução funcional. Os problemas das soluções tradicionais, prendem-se com o uso de estratégias de registo de informação não estandardizadas e facilidade de repúdio de informação isto porque cada entidade por norma age independentemente das outras e apenas comunica com aquelas que lhe estão diretamente ligadas. Adicionalmente, é comum verificar que produtos no final da sua cadeia de produção estão danificados e de ser praticamente impossível localizar onde na cadeia os danos ocorreram. A ideia de adaptar a tecnologia blockchain como uma solução para a rastreabilidade de produtos na cadeia de fornecimento apresenta alguns pontos preocupantes, pois as blockchains são geralmente associadas a sistemas distribuídos e públicos para manter uma dada criptomoeda. Apesar de este ser o propósito inicial para a sua criação têm vindo a surgir outras tecnologias blockchain orientadas para o armazenamento e processamento de dados num modelo business to business. Estas blockchains possuem medidas de controlo de acesso, e são, portanto chamadas de privadas permitindo apenas acesso por parte de um grupo seleto de entidades. Adicionalmente, o armazenamento de informação numa blockchain é também muitas vezes associado a custos elevados, e quando nos referimos a blockchains públicas como a Ethereum isto é uma realidade, mas pelo uso de soluções privadas podemos colmatar este custo. É também uma preocupação os custos computacionais associados a blockchains de criptomoeadas como a Bitcoin e Etherum. Novamente é possível contornar esta limitação pelo uso de soluções privativas onde podemos usar algoritmos mais leves, pois o ambiente em que o sistema se vai inserir, não carece de tantos cuidados. Através do uso de blockchain para certificar a origem e percurso de produtos numa cadeia de fornecimento é também interessante explorar os dados recolhidos no processo e como estes podem ser utilizados para tornar a própria cadeia de fornecimentos mais eficiente. O objetivo desta dissertação é estudar como a tecnologia blockchain pode ser conjugada com uma cadeia de fornecimento para oferecer rastreabilidade de produtos e recolha de informação. Para alcançar este objetivo foi desenvolvido um protótipo de uma aplicação baseada em blockchain para recolha de dados numa cadeia de fornecimento, bem como um protótipo de uma aplicação para a visualização e interação remota com os dados e também um protótipo de um módulo de Machine Learning capaz de fazer uso da informação recolhida pela blockchain