Academic literature on the topic 'Plant singals'

Les bactéries pectinolytiques des genres Pectobacterium (ancien nom Erwinia carotovora) et Dickeya (ancien nom Erwinia chrysanthemi) sont les agents des maladies de la jambe noire et de la pourriture molle. Ils provoquent des dommages aux cultures et des pertes économiques élevées. Les pertes causées par les bactéries pectinolytiques sont évaluées à environ 2 à 10% du rendement de pommes de terre, en fonction de l'année. En 2009, les pertes en pommes de terre en Europe ont été estimées à 250 millions d'euros. Au cours des dernières années, des souches de Dickeya ont été de plus en plus souvent isolées de plantes malades en Pologne, en France et d'autres pays européens. Le genre Dickeya est un groupe très diversifié, qui, selon la nomenclature actuelle contient sept espèces: D. aquatica, D. chrysanthemi, D. dadantii, D. dianthicola, D. paradisiaca, D. solani et D. zeae. Les résultats récents, obtenus dans différents pays européens, indiquent qu'un nouveau groupe de souches de Dickeya peut infecter efficacement les plantes de pomme de terre et causer des symptômes de la maladie en climat tempéré. Les souches de D. solani sont considérés comme plus agressives que les autres bactéries causant la jambe noire. Une analyse préliminaire a suggéré qu’elles ont besoin de plus faibles températures optimales pour le développement de la maladie ainsi que de niveaux d'inoculum inférieurs pour la propagation de l'infection. Elles semblent avoir une plus forte capacité à coloniser les racines de plantes de pomme de terre et à se propager à travers le système vasculaire de la plante. Les souches de D. solani produisent une large gamme d’enzymes dégradant de la paroi cellulaire végétale, qui sont les principaux facteurs de virulence. Les objectifs de l'étude étaient les suivants: 1) la caractérisation phénotypique et génotypique des souches de D. solani isolées dans des pays ayant des conditions climatiques différentes: Pologne, Finlande et Israël, 2) l'étude de l’influence d'extraits de pomme de terre sur l'expression de quelques gènes sélectionnés de D. solani: pelD, pelL, tssk, lfaA, 3) la génomique comparative de dix souches de D. solani, basée sur 4 génomes séquencés pour cette étude et 6 séquences génomiques disponibles dans la base de données GenBank. En conclusion, toutes les études génomiques ont montré que les souches de D. solani forment un groupe très homogène. Cependant, leur analyse phénotypique révèle une certaine variabilité entre les souches provenant de différentes conditions climatiques. La raison des variations observées dans les traits phénotypiques peut être liée à la régulation de l'expression des gènes codant les facteurs de virulence qui peuvent être influencés par la température, le pH, la carence en fer ou en oxygène et la disponibilité en azote, ainsi que par la présence de composés spécifiques des tissus végétaux<br>Dickeya solani is a species consisting of newly emerged plant pathogenic bacteria that cause blackleg and soft rot diseases. They are responsible for great damages to potato plantations in most of European countries. D. solani strains produce a wide range of plant cell-wall degrading enzymes which are the main virulence factors. The aims of the study were: 1) phenotypic and genotypic characterizations of the D. solani strains isolated in countries with different climatic conditions: Poland, Finland and Israel, 2) study of the potato tuber extract influence on the expression of a few selected D. solani genes : pelD, pelL, tssK, lfaA,3) comparative genomics of ten D. solani strains, performed on 4 genomes sequenced for this study and 6 genome sequences available in the GenBank databases. The results showed that the strains from different climatic conditions have identical profiles in rep-PCR (with three different primers) and in Restriction Fragments Lenght Polymorphism-Pulse Field Gel Electrophoresis. However, they do differ phenotypically, especially in the activity of plant cell-wall degrading enzymes. Polish strains have higher activities of pectinolytic, cellulolytic and proteolytic enzymes than Finnish and Israeli strains. D. solani mutants in the pelD, pelL, tssK, lfaA genes were constructed by site-specific mutagenesis. The highest induction by plant extracts was observed for the lfaA gene. The expression of pelL is also induced by plant derived signal(s), but not that of pelD and tssK. Comparative genomics helped to elucidate the D. solani pangenome. The 10 D. solani strains genomes are coding for a total of 41 947 proteins which were grouped into 5 045 Orthologous Groups, 3 809 belonging to the core genome, 413 to the accessory genome and 823 to the unique genome. Some pathogenicity-related genes as well as their regulators were selected on the basis of the knowledge available for D. dadantii 3937, the most studied Dickeya strain, which belongs to a closely related species. Analysis of their protein sequence showed no difference in the sequence of those genes within the 10 genomes. All the genetic studies proved that D. solani strains form a very homogenous group. On the other hand, the phenotypic analysis showed some variability among strains from different climatic conditions. The observed variations in the phenotypic traits can results from a different regulation of the expression of the genes encoding virulence factors which are influenced by temperature, pH, iron deprivation, oxygen and nitrogen availability, as well as by the presence of plant compounds

Mestrado em Engenharia Electrónica e Telecomunicações<br>As actuais normas para codificação de vídeo, tais como os MPEG2/4 ou H.263/4, foram desenvolvidas para codificação de vídeo com cor. A informação de cor é representada usando um espaço apropriado, como, por exemplo, o YCbCr. Estes espaços de cor são constituídos por três planos: um para a dominância (no exemplo dado, o Y) e dois para a informação de crominância (neste caso, o Cb e o Cr). Contudo, há aplicações onde a informação a codificar é composta apenas por um plano de informação que pode, por exemplo, representar níveis de cinzento em imagem médica, ou índices para tabelas de cores. A motivação desta tese prende-se com dois factos: a produção de imagens médicas em formato digital estar a crescer, impondo técnicas eficazes para o tratamento e a compressão de dados e, embora os modelos de cor indexada sejam há muito utilizados para representar imagens, não têm sido convenientemente explorados em vídeo. Com esta dissertação pretende-se investigar novas estratégias de compressão sem perdas que explorem a redundância entre imagens consecutivas que caracterizam estas modalidades de imagem. Portanto, ao longo do trabalho implementou-se dois codificadores de vídeo para um só plano de informação, baseados num modelo híbrido. Um deles utiliza codificação de Golomb e o outro codificação aritmética, estudando-se assim a eficácia de cada um, quer para a escala de cinzentos, quer para vídeos com tabela de cores indexadas. Adicionalmente, para vídeos de cor indexada, implementou-se um algoritmo de reordenação da tabela de cores, o que torna a codificação mais eficaz. ABSTRACT: The current standards for video encoding, such as MPEG2/4 or H.263/4, have been developed for encoding video with color. The color information is represented using an appropriate space, such as YCbCr. These color spaces are made of three planes: one for luminance (in the given example, the Y) and two for the chrominance information (in this case, the Cb and Cr). However, there are applications where the information lies in a single information plane that may, for example, represent shades of gray (medical imaging) or indexes to color tables (color indexed video). The motivation of this thesis is related with two points: the production of medical images in digital format has been growing, imposing efficient techniques for the treatment and compression of data and, although color indexed models have been used for a long time to represent images, it has not been adequately explored in video. With this thesis, we intended to investigate new strategies for lossless compression which exploits the redundancy between consecutive images that characterize these types of images. Therefore, during this work, it has been implemented two video encoders with one information plane, based on a hybrid model. One of them uses Golomb codes and the other arithmetic coding. It has been studied the efficiency of each one, both using gray scale and color indexed videos. In addition, for color indexed videos, it has been implemented a palette reordering algorithm, making the encoding more efficient.

Extreme haustorial parasites have long captured the interest of naturalists and scientists with their greatly reduced and highly specialized morphology. Along with the reduction or loss of photosynthesis, the plastid genome often decays as photosynthetic genes are released from selective constraint. This makes it challenging to use traditional plastid genes for parasitic plant phylogenetics, and has driven the search for alternative phylogenetic and molecular evolutionary markers. Thus, evolutionary studies, such as molecular clock-based age estimates, are not yet available for all parasitic lineages. In the present study, we extracted 14 nuclear single copy genes (nSCG) from Illumina transcriptome data from one of the “strangest plants in the world”, Hydnora visseri (Hydnoraceae). A ~15,000 character molecular dataset, based on all three genomic compartments, shows the utility of nSCG for reconstructing phylogenetic relationships in parasitic lineages. A relaxed molecular clock approach with the same multi-locus dataset, revealed an ancient age of ~91 MYA for Hydnoraceae. We then estimated the stem ages of all independently originated parasitic angiosperm lineages using a published dataset, which also revealed a Cretaceous origin for Balanophoraceae, Cynomoriaceae and Apodanthaceae. With the exception of Santalales, older parasite lineages tend to be more specialized with respect to trophic level and have lower species diversity. We thus propose the “temporal specialization hypothesis” (TSH) implementing multiple independent specialization processes over time during parasitic angiosperm evolution.

This research addresses sourcing decisions and how those decisions can affect the management of a company's assets. The study begins with a single-plant problem, in which one facility chooses, from a list of parts, which parts to bring in-house. The selection is based on maximizing the value of the selected parts, while remaining within the plant's capacity. This problem is defined as the insourcing problem and modeled as a multidimensional knapsack problem (MKP). The insourcing model is extended to address outsourcing and multiple plants. This multi-plant model, also modeled as an MKP, enables the movement of parts from one plant to another and consideration of a company-wide objective function (as opposed to a single-plant objective function as in the insourcing model). The sourcing problem possesses characteristics that distinguish it from the standard MKP. One such characteristic is what we define as multiple attributes. To understand the multiple attribute characteristic, we compare the various dimensions in the multidimensional knapsack problem. A classification is given for an MKP as either having a single attribute (SA) or multiple attributes (MA). Mathematically, the problems of each attribute classification can be modeled in the same way with simply a different interpretation of the knapsack constraints. However, experimentation indicates that the MA-MKP is more difficult to solve than the SA-MKP. For small problems, with 100 variables and 5 constraints, the CPU time required to find the optimal solution for MA-MKP to SA-MKP problems has a ratio of 32:1. To determine effective methods for addressing the MA-MKP, standard mixed integer programming techniques are tested. The results of this testing are that the exact approaches are not successful in dramatically reducing the solution time to the level of the SA problems. However, a simple heuristic that performs very well on the MA-MKP is presented. The heuristic utilizes variations on the benefit-to-cost ratio and strongest surrogate constraints. The results from experimentation for MA-MKP problem sets, generated using the methods for standard MKP test data sets in the literature, are presented and indicate that the heuristic performs well and improves with larger problems. The average gap between the heuristic solution and the optimal solution is 1.39% for 200-part problems and is reduced to 0.69% when the size of the problem is increased to 298 parts. Although the MA characteristic reflects the sourcing problem, the actual data used in the eperimentation is generated with techniques presented in the literature for standard MKP test problems. Therefore, to more accurately represent the sourcing problem, industry data from a manufacturing facility is studied to identify further sourcing problem characteristics. As a result, industry-motivated data sets are generated that reflect the characteristics of industry data, yet maintain the structure of literature data sets to allow for easy comparison. It is found that both industry and industry-motivated data sets, although possessing the MA characteristic, are much easier to solve than SA problems. Indicators of difficulty appear to be the constraint tightness and a measure of the matrix sparsity. The sparsity is a significant factor because industry data tends to be very sparse, while data sets generated in the literature are completely dense. Another interesting result from the industry-motivated data sets with the single-plant problem is the tendency for a facility to prefer currently produced parts over insourcing new parts from outside the facility. It is not uncommon for a company to have more than one facility with a particular capability. Therefore, the sourcing model is extended to include multiple facilities. With multiple-facilities, effectively all the parts are removed to form one list, and then each part is assigned to one of the facilities or outsourced externally. The multi-facility model is similar to the single-facility model with the addition of assignment constraints enforcing that each part can be assigned to only one facility. Experimentation is performed for the two-, three-, and four-facility models. The problem gets easier to solve as the number of facilities increases. With a greater number of facilities, it is likely that for each part one of facilities will dominate as the best option. Therefore, other solutions can quickly be eliminated and the problem solved more quickly. The two-facility problem is the most difficult; however, the heuristic performs well with an average gap of 0.06% between the heuristic and optimal solutions. We conclude with a summary on experiences with modeling and solving the sourcing problem for a sheet metal fabrication facility. The model solved for this problem had over 1857 parts with 19 machines, which translates to over 70,000 variables and 38 constraints. Although extremely large compared to problems solved in the literature, this problem was solvable because of the unique structure of industry data. Our work with the facility saved the parent organization up to $4.16M per year and provided a tool that encourages a systematic and quantitative process for evaluating decisions related to sheet metal fabrication capacity.<br>Ph. D.

We consider the problem of Adaptive Control of finite-dimensional, stable, Linear Time Invariant (LTI) plants. Amongst such plants, the subclass regarding which an upper bound on the order is not known or which are known to be nonminimum phase (zeros in the unstable region) pose formidable problems in their own right. On one hand, if an upper bound on the order of the plant is not known, adaptive control usually involves some form of order estimation. On the other hand, when the plant is allowed to be either minimum phase or nonminimum phase, the adaptive control problem, as is well-known, becomes considerably-less tractable. In this study, the class of unknown plants considered is such that no information is available on the upper bound of the plant order and, further, the plant may be either minimum phase or nonminimum phase. Albeit known to be stable, such plants throw myriads of challenges in the context of adaptive control. Adaptive control involving such plants has been addressed [79] in a Model Reference Adaptive Control (MRAC) framework. There, the inputs and outputs of the unknown plant are the only quantities available by measurement in terms of which any form of modeling of the unknown plant may be made. Inputs to the reference model have been taken from certain restricted classes of bounded signals. In particular, the three classes of inputs considered are piecewise continuous bounded functions which asymptotically approach • a nonzero constant, • a sinusoid, and • a sinusoid with a nonzero shift. Moreover, the control law is such that adaptation is carried out at specific instants separated by progressively larger intervals of time. The schemes there have been proved to be e-optimal in the sense of a suitably formulated optimality criterion. If, however, the reference model inputs be extended to the class of piecewise continuous bounded functions, that would compound the complexity of the adaptive control problem. Only one attempt [78] in adaptive control in such a setting has come to our notice. The problem there has been tackled by an application of the theory of Pade Approximations to time moments of an LTI system. Based on a time moments estimation procedure, a simple adaptive scheme for Single-Input Single-Output (SISO) systems with only a cascade compensator has been reported. The first chapter is essentially meant to ensure that the problem we seek to address in the field of adaptive control indeed has scope for research. Having defined Adaptive Control, we selectively scan through the literature on LTI systems, with focus on MRAC. We look out in particular for studies involving plants of which not much is known regarding their order and systems which are possibly nonminimum phase. We found no evidence to assert that the problem of adaptive control of stable LTI systems, not necessarily minimum phase and of unknown upper bound on the order, was explored enough, save two attempts involving SISO systems. Taking absence of evidence (of in-depth study) for evidence of absence, we make a case for the problem and formally state it. We preview the thesis. We set two targets before us in Chapter 2. The first is to review one of the existing procedures attacking the problem we intend to address. Since the approach is based on the notion of time moments of an LTI system, and as we are to employ Pade Approximations as a tool, we uncover these concepts to the limited extent of our requirement. The adaptive procedure, Plant Command Modifier Scheme (PCMS) [78], for SISO plants is reported in some detail. It stands supported on an algorithm specially designed to estimate the time moments of an LTI system given no more than its input and output. Model following there has been sought to be achieved by matching the first few time moments of the reference model by the corresponding ones of the overall compensated plant. The plant time moment estimates have been taken to represent the unknown plant. The second of the goals is to analyze PCMS critically so that it may serve as a forerunner to our work. We conclude the chapter after accomplishing these goals. In Chapter 3, we devise a time moment estimator for SISO systems from a perspective which is conceptually equivalent to, yet functionally different from, that appropriated in [78]. It is a recipe to obtain estimates of time moments of a system by computing time moment estimates of system input and output signals measured up to current time. Pade approximations come by handy for this purpose. The lacunae exposed by a critical examination of PCMS in Chapter 2 guide us to progressively refine the estimator. Infirmities in the control part of PCMS too have come to light on our probing into it. A few of these will be fixed by way of fabricating two exclusively cascade compensators. We encounter some more issues, traceable to the estimator, which need redressal. Instead of directly fine-tuning the estimator itself, as is the norm, we propose the idea of 'estimating' the lopsidedness of the estimator by using it on the fully known reference model. This will enable us to effect corrections and obtain admissible estimates. Next, we explore the possibility of incorporating feedback compensation in addition to the existing cascade compensation. With output error minimization in mind, we come up with three schemes in this category. In the process, we anticipate the risk of instability due to feedback and handle it by means of an instability preventer with an inbuilt instability detector. Extensive simulations with minimum and rionminimum phase unknown plants employing the various schemes proposed are presented. A systematic study of simulation results reveals a dyad of hierarchies of progressively enhanced overall performance. One is in the sequence of the proposed schemes and the other in going for matching more and more moments. Based on our experiments we pick one of the feedback schemes as the best. Chapter 4 is conceived of as a bridge between SISO and multivariable systems. A transition from SISO to Multi-Input Multi-Output (MIMO) adaptive control is not a proposition confined to the mathematics of dimension-enhancement. A descent from the MIMO to the SISO case is expected to be relatively simple, though. So to transit as smoothly and gracefully as possible, some issues have to be placed in perspective before exploring multivariable systems. We succinctly debate on the efforts in pursuit of the exact vis-a-vis the accurate, and their implications. We then set some notations and formulate certain results which serve to unify and simplify the development in the subsequent three chapters. We list a few standard results from matrix theory which are to be of frequent use in handling multivariable systems. We derive control laws for Single-Input Multi-Output (SIMO) systems in Chapter 5. Expectedly, SIMO systems display traits of observability and uncontrollability. Results of illustrative simulations are furnished. In Chapter 6, we formulate control laws for Multi-Input Single-Output (MISO) systems. Characteristics of unobservability and controllability stand out there. We present case studies. Before actually setting foot onto MIMO systems, we venture to conjecture on what to expect there. We work out all the cascade and feedback adaptive schemes for square and nonsquare MIMO systems in Chapter 7. We show that MIMO laws when projected to MISO, SIMO and SISO cases agree with the corresponding laws in the respective cases. Thus the generality of our treatment of MIMO systems over other multivariable and scalar systems is established. We report simulations of instances depicting satisfactory performance and highlight the limitations of the schemes in tackling the family of plants of unknown upper bound on the order and possibly nonminimum phase. This forms the culmination of our exercise which took off from the reported work involving SISO systems [78]. Up to the end of the 7th chapter, we are in pursuit of solutions for the problem as general as in §1.4. For SISO systems, with input restrictions, the problem has been addressed in [79]. The laws proposed there carry out adaptation only at certain discrete instants; with respect to a suitably chosen cost, the final laws are proved to be e>optimal. In Chapter 8, aided by initial suboptimal control laws, we finally devise two algorithms with continuous-time adaptation and prove their optimality. Simulations with minimum and nonminimum phase plants reveal the effectiveness of the various laws, besides throwing light on the bootstrapping and auto-rectifying features of the algorithms. In the tail-piece, we summarize the work and wind up matters reserved for later deliberation. As we critically review the present work, we decant the take-home message. A short note on applications followed by some loud thinking as a spin-off of this report will take us to finis.

Extreme haustorial parasites have long captured the interest of naturalists and scientists with their greatly reduced and highly specialized morphology. Along with the reduction or loss of photosynthesis, the plastid genome often decays as photosynthetic genes are released from selective constraint. This makes it challenging to use traditional plastid genes for parasitic plant phylogenetics, and has driven the search for alternative phylogenetic and molecular evolutionary markers. Thus, evolutionary studies, such as molecular clock-based age estimates, are not yet available for all parasitic lineages. In the present study, we extracted 14 nuclear single copy genes (nSCG) from Illumina transcriptome data from one of the “strangest plants in the world”, Hydnora visseri (Hydnoraceae). A ~15,000 character molecular dataset, based on all three genomic compartments, shows the utility of nSCG for reconstructing phylogenetic relationships in parasitic lineages. A relaxed molecular clock approach with the same multi-locus dataset, revealed an ancient age of ~91 MYA for Hydnoraceae. We then estimated the stem ages of all independently originated parasitic angiosperm lineages using a published dataset, which also revealed a Cretaceous origin for Balanophoraceae, Cynomoriaceae and Apodanthaceae. With the exception of Santalales, older parasite lineages tend to be more specialized with respect to trophic level and have lower species diversity. We thus propose the “temporal specialization hypothesis” (TSH) implementing multiple independent specialization processes over time during parasitic angiosperm evolution.