Positive biotic interactions such as mutualism, commensalism and facilitation are ubiquitous in nature, but historically have received considerably less research attention than negative interactions such as competition, predation and parasitism. The paucity of research on positive interactions is particularly evident in stream ecosystems and in vertebrate communities. Stream fishes clearly provide an ideal system for advancing research on positive interactions. Many minnows (Cyprinidae) of eastern North America engage in a potentially mutualistic reproductive interaction known as nest association, in which individuals of one species (nest associates) spawn in nests constructed by host species. In nest association, hosts provide unsilted gravel substrate for spawning nest associates, and increased parental care to associate broods. High associate: host egg ratios can create a dilution effect, reducing the probability that host eggs will be preyed upon by egg predators. Nest associative interactions are common, but are relatively understudied compared to other interactions among stream fishes. The goals of this study were to apply general ecological models to this novel system to (a) gain new insight into the mechanisms structuring nest associative stream fish communities, and (b) to use inference from stream fish communities to potentially expand and improve the general ecological models. These goals required completion of three objectives, including (1) examining the influence of abiotic and biotic contexts on reproductive behavior and fitness outcomes between a cyprinid host and associate, using the biological markets model to generate predictions; (2) examining the utility of the nest web framework (previously only used for cavity nesting vertebrate communities) and the stress gradient hypothesis (previously applied almost exclusively to plant communities) for predicting which associate species spawn on nests built by various nest building species, and the consequences of these choices, respectively; and (3) using two-species occupancy modeling to determine the relative influence of biotic interactions and habitat covariates on the co-occurrence of a host and two nest associates. To accomplish these goals, I conducted a large-scale experiment to manipulate presence of mutualists (Nocomis leptocephalus, host; Chrosomus oreas, associate), egg predators (biotic context) and habitat quality (abiotic context). I conducted behavioral nest observations and conducted repeated stream fish stream fish community surveys to collect demographic data. I constructed a nest web from observational data, and implemented structural equation modeling through an information-theoretic framework to identify nest web plausibility across a large spatial extent. I tested some predictions of the stress gradient hypothesis by regressing juveniles-per-nest and a metric of cyprinid community structure on a composite measure of physical stress (scaled gradients of catchment-scale agricultural land use and catchment area). I used two-species occupancy modeling to model co-occurrence of N. leptocephalus hosts and two associates, C. oreas and Clinostomus funduloides, and used an information-theoretic framework to compare hypotheses representing the importance of biotic interactions, habitat covariates or both at determining species co-occurrence. Results corroborated some (but not all) model predictions, and identified room for improvement in each of the general models. Nest associative spawning by C. oreas was not context dependent; C. oreas did not spawn in the absence of a reproductively active male N. leptocephalus at any treatment level. However, the net fitness outcome of host and associate species was mutualistic, and the interaction outcome switched from commensalistic to mutualistic with abiotic context. N. leptocephalus reproductive success was improved by C. oreas presence in less-silted habitats, but not in heavily-silted habitats. This is most likely because broods were subject to predation in both habitat types, but were also negatively affected by siltation in silted habitats. Accordingly, egg dilution by associates was not sufficient to support a mutualistic relationship in less favorable habitats. Results suggest that the biological markets model may be a useful tool for predicting fitness outcomes of nest associative mutualism, but may not be as useful for predicting the behavioral outcomes of obligate mutualisms. Future applications of the biological markets model should carefully consider species traits, specifically the degree to which trading behavior is obligate for participants. Future work with this model will yield more insight by considering highly facultative associates. Nest webs constructed from nest observational data suggested an interaction topology in which strong (nearly-obligate) associates relied most frequently on N. leptocephalus nests, and less frequently on nests constructed by Campostoma anomalum. Weak (facultative) associates were seldom associated with nests constructed by either species, and probably spawned before hosts began nesting activity. Structural equation models corroborated this topology throughout the New River basin, although some less-supported model evidence specified some nest association by weak associates. Juveniles-per-nest of strong associates responded positively to physical stress, while this metric for other cyprinid reproductive groups showed no relationship. Proportional representation of Nocomis and strong associates also increased predictably with physical stress. This study suggests that the nest web framework can be informative to systems outside the ones for which it was developed; future studies may be able to use this framework to better understand the role of habitat-modifying species in communities other than cavity nesting terrestrial vertebrates and nest associative stream fishes. This work extended the nest web framework by (a) modeling the outcomes of interactions instead of the interactions themselves, and (b) by using structural equation modeling to test nest web predictions with an information-theoretic framework. This study also suggests that the stress gradient hypothesis can be useful for understanding interaction dynamics in vertebrate communities; this represents the first direct evidence that this model can be used in vertebrate communities. Further, I demonstrate that the stress gradient hypothesis may be extended to predict community structure. However, more research in a diversity of systems will be needed to determine the extent to which this can be applied. This study provides some of the first evidence of large-scale positive co-occurrence patterns in vertebrates. However, the precise roles of habitat covariates and biotic interactions were species-specific. Occupancy results suggest that co-occurrence between N. leptocephalus and nest associate C. funduloides is driven only by reproductive behavioral interactions. Alternatively, evidence suggests that co-occurrence between N. leptocephalus and C. oreas is driven by both nest association and habitat covariates. That two-species occupancy modeling can be a useful tool for comparing difficult-to-test hypotheses involving biotic interactions at large spatial scales. This study represents the first quantitative, multi-scale treatment of positive interactions in stream ecosystems. This study demonstrates that applying general ecological models to stream fish communities can yield new insights about both the study system and the models themselves. While models of negative interactions, food webs and dispersal have been applied to stream fishes, we stand to gain much ground by also considering positive biotic interactions. In doing so, stream fish ecologists will also be able to contribute to the advancement of general ecology, and thus raise awareness for these understudied ecosystems and taxa. / Ph. D.

The accelerating pace of growth of aquaculture in sub-Saharan Africa has received much positive appraisal because of the potential of the industry to contribute to economic development and food security by providing jobs and animal protein. Adoption of best management practices (BMPs) holds the potential to ameliorate the related environmental impacts of aquaculture, such as in the amounts of nutrients and sediment that will enter natural water bodies from earthen pond effluents. The goals of this study were to characterize adoption of aquaculture BMPs on small-scale, pond-based farms in Ghana, and to assess selected economic, social, and environmental outcomes of BMP adoption. Two BMPs: 1) water reuse, and 2) commercial floating feeds, were investigated for adoption by pond-based fish farmers in Ghana. I conducted my study in Ghana using on-farm experiments involving intensive monitoring of water quality and growth of Nile tilapia (Oreochromis niloticus) over two production cycles. Additionally, I administered a baseline survey to 393 (and a follow-up survey to 160) fish farmers. I determined the best model for modelling farmed Nile tilapia growth with multi-model inference based on Akaike information criterion (AIC), the profitability of adopting BMPs with stochastic enterprise budgets and, social welfare impact with the Economic-Surplus model. I used a Markov model to predict the equilibrium rate of adoption of the two BMPs and determined the impact of BMP adoption on the reduction of pollutant loading with the Minimum-Data method of the Tradeoffs Analysis (TOA-MD). My results showed that the logistic model is a better alternative to the von Bertalanffy model for modelling the growth of Oreochromis niloticus under pond aquaculture conditions. There were no significant differences in fish weight between the water re-use BMP and the use of new water. Adoption of the commercial floating feed BMP resulted in a 100% increase in fish final weight and yield, and in higher profitability, compared to the sinking feed type. Probability of making a profit was highest (72%) in the scenario with commercial feed and self-financing. Net present values (NPV) of about US$ 11 million and US$ 375 million could be obtained from the adoption of commercial floating feed and Genetically-Improved Farm Tilapia (GIFT) strain, respectively, in Ghana. Hence, any innovation that has a significant impact on fish yield also will have a significant impact on mean NPV and social welfare. However, I identified a number of potential negative ecological and genetic impacts exist from introducing the GIFT strain into Africa from Asia. Although considered low-intensity production systems, nutrients and solids in study ponds were found to be higher than levels expected in intensive culture ponds by wide margins. Pond water quality was significantly higher with commercial floating feed. The water-reuse BMP also prevented pollutants from leaving ponds altogether for the number of cycles for which pond water was reused, especially if associated BMPs such as rainfall capture and avoidance of water exchange are observed. Significant reductions in the loading of all water quality variables (nitrogen, phosphorus, solids, and BOD5) could be achieved with the adoption of the recommended feed type in Ghana. Adoption of the water reuse BMP has the potential to cause pollution reductions of 200% - 3,200% above that from the floating feed BMP. The strongest influence on the combined adoption of these BMPs were from : farmer's awareness of the feed BMP, perceived necessity and relative profitability of the water reuse BMP, and farmer's years of experience. A combination of central media (workshops), demonstrations, and lateral diffusion was found to be the most effective channel for disseminating these BMPs. Maximum adoption rate of the feed BMPs was estimated to be 38% - 58%. Also, US$ 6,000/year and US$12,000/year need to be paid per 0.6 ha pond surface area to push adoption of the feed BMP to 50% and 70%, respectively. Hence, to ensure the successful adoption of aquaculture BMPs, I recommend that regular well-planned workshops be organized to create awareness and a conducive atmosphere to target farmers at multiple stages of the innovation decision process. Incentives and effective dissemination will encourage the adoption of these and other environmental BMPs. Feed costs need to be lowered in order to encourage the adoption of commercial floating feed in Ghana. Future analyses could quantify the differences in production costs between using the two water types, to reveal the possible higher relative profitability of pond water reuse over draining ponds after each production cycle. Also, African governments are advised to commission rigorous baseline and ecological risk analyses before adoption of the GIFT strain. Improvements in management practices and infrastructure could increase the yield and profitability of the local strains even if genetically-improved strains are not introduced. / Ph. D.

Long-term diet patterns based on stable isotope analysis may be helpful to understand changes in food selection of black bears (Ursus americanus) over time and guide management programs to reduce human-bear conflicts. An enriched stable carbon isotope signature indicates an anthropogenic food source in the diet and an enriched nitrogen signature indicates a higher tropic level for a species. I examined longitudinal feeding patterns from 117 hair samples of black bears live captured in Great Smoky Mountains National Park during 1980–2001 using stable carbon and nitrogen isotope analysis from hair samples. I developed a set of a priori models to examine if sex, age class, year, weight class, total hard mast index, white oak index (Quercus spp.), red oak index (Quercus spp.), nuisance status and hog harvest (Sus scrofa) affected stable isotope signatures. I used model averaging and an estimator of the unconditional variance was used to account for model uncertainty. The δ[delta]13C signatures differed by weight class with above average weight, (ß[Beta] = 0.76‰; 95% CI = 0.28 to 1.23) and average weight (ß[Beta] = 0.42‰; CI = 0.06 to 0.78) showing enriched values compared to below average bears. Bears had enriched δ[delta]15N signatures in years with low white oak mast production (ß[beta] = -0.19, CI = -0.34 to -0.03) and depleted when white oak hard mast was abundant. Sub adult bears had enriched δ[delta]15N signatures compared to adult and older adult bears. Variation of nitrogen values was small during 1980–1991 ( = 2.57, SD = 0.28) but increased substantially during 1992–2000 ( = 2.29, SD = 0.71) when there was substantial variation in hard mast production. Bears in better physical condition appear more likely to access anthropogenic food sources. In years of low white oak acorn production, the larger bears and sub adult bears are more likely to turn to alternative food sources. The long term variation detected in this study is important in identifying which bears are potentially more likely to seek out the anthropogenic food sources when changes occur in availability of natural foods.

In this work, a multilayer security solution for digital communication systems is provided by considering the joint effects of physical-layer security channel codes with application-layer cryptography. We address two problems: first, the cryptanalysis of error-prone ciphertext; second, the design of a practical physical-layer security coding scheme. To our knowledge, the cryptographic attack model of the noisy-ciphertext attack is a novel concept. The more traditional assumption that the attacker has the ciphertext is generally assumed when performing cryptanalysis. However, with the ever-increasing amount of viable research in physical-layer security, it now becomes essential to perform the analysis when ciphertext is unreliable. We do so for the simple substitution cipher using an information-theoretic framework, and for stream ciphers by characterizing the success or failure of fast-correlation attacks when the ciphertext contains errors. We then present a practical coding scheme that can be used in conjunction with cryptography to ensure positive error rates in an eavesdropper's observed ciphertext, while guaranteeing error-free communications for legitimate receivers. Our codes are called stopping set codes, and provide a blanket of security that covers nearly all possible system configurations and channel parameters. The codes require a public authenticated feedback channel. The solutions to these two problems indicate the inherent strengthening of security that can be obtained by confusing an attacker about the ciphertext, and then give a practical method for providing the confusion. The aggregate result is a multilayer security solution for transmitting secret data that showcases security enhancements over standalone cryptography.

Traditional solutions to information security in communication systems act in the application layer and are oblivious to the effects in the physical layer. Physical-layer security methods, of which information-theoretic security is a special case, try to extract security from the random effects in the physical layer. In information-theoretic security, there are two asymptotic notions of secrecy---weak and strong secrecy This dissertation investigates the problem of information-theoretic strong secrecy on the binary erasure wiretap channel (BEWC) with a specific focus on designing practical codes. The codes designed in this work are based on analysis and techniques from error-correcting codes. In particular, the dual codes of certain low-density parity-check (LDPC) codes are shown to achieve strong secrecy in a coset coding scheme. First, we analyze the asymptotic block-error rate of short-cycle-free LDPC codes when they are transmitted over a binary erasure channel (BEC) and decoded using the belief propagation (BP) decoder. Under certain conditions, we show that the asymptotic block-error rate falls according to an inverse square law in block length, which is shown to be a sufficient condition for the dual codes to achieve strong secrecy. Next, we construct large-girth LDPC codes using algorithms from graph theory and show that the asymptotic bit-error rate of these codes follow a sub-exponential decay as the block length increases, which is a sufficient condition for strong secrecy. The secrecy rates achieved by the duals of large-girth LDPC codes are shown to be an improvement over that of the duals of short-cycle-free LDPC codes.

Made available in DSpace on 2016-08-17T14:53:18Z (GMT). No. of bitstreams: 1 Dissertacao Ewaldo.pdf: 1169300 bytes, checksum: fc5d4b9840bbafe39d03cd1221da615e (MD5) Previous issue date: 2012-02-10 / This work derives and evaluates a nonlinear method for Blind Source Extraction (BSE) in a Reproducing Kernel Hilbert Space (RKHS) framework. For extracting the desired signal from a mixture a priori information about the autocorrelation function of that signal translated in a linear transformation of the Gram matrix of the nonlinearly transformed data to the Hilbert space. Our method proved to be more robust than methods presented in the literature of BSE with respect to ambiguities in the available a priori information of the signal to be extracted. The approach here introduced can also be seen as a generalization of Kernel Principal Component Analysis to analyze autocorrelation matrices at specific time lags. Henceforth, the method here presented is a kernelization of Dependent Component Analysis, it will be called Kernel Dependent Component Analysis (KDCA). Also in this dissertation it will be show a Information-Theoretic Learning perspective of the analysis, this will study the transformations in the extracted signals probability density functions while linear operations calculated in the RKHS. / Esta dissertação deriva e avalia um novo método nãolinear para Extração Cega de Sinais através de operações algébricas em um Espaço de Hilbert Reproduzido por Kernel (RKHS, do inglês Reproducing Kernel Hilbert Space). O processo de extração de sinais desejados de misturas é realizado utilizando-se informação sobre a estrutura temporal deste sinal desejado. No presente trabalho, esta informação temporal será utilizada para realizar uma transformação linear na matriz de Gram das misturas transformadas para o espaço de Hilbert. Aqui, mostrarse- á também que o método proposto é mais robusto, com relação a ambigüidades sobre a informação temporal do sinal desejado, que aqueles previamente apresentados na literatura para realizar a mesma operação de extração. A abordagem estudada a seguir pode ser vista como uma generalização da Análise de Componentes Principais utilizando Kerneis para analisar matriz de autocorrelação dos dados para um atraso específico. Sendo também uma kernelização da Análise de Componentes Dependentes, o método aqui desenvolvido é denominado Análise de Componentes Dependentes utilizando Kerneis (KDCA, do inglês Kernel Dependent Component Analysis). Também será abordada nesta dissertação, a perspectiva da Aprendizagem de Máquina utilizando Teoria da Informação do novo método apresentado, mostrando assim, que transformações são realizadas na função densidade de probabilidade do sinal extraído enquanto que operação lineares são calculadas no RKHS.

In this work, we study two problems in information-theoretic security. Firstly, we study a wireless network where two nodes want to securely exchange messages via an honest-but-curious bidirectional relay. There is no direct link between the user nodes, and all communication must take place through the relay. The relay behaves like a passive eavesdropper, but otherwise follows the protocol it is assigned. Our objective is to design a scheme where the user nodes can reliably exchange messages such that the relay gets no information about the individual messages. We first describe a perfectly secure scheme using nested lattices, and show that our scheme achieves secrecy regardless of the distribution of the additive noise, and even if this distribution is unknown to the user nodes. Our scheme is explicit, in the sense that for any pair of nested lattices, we give the distribution used for randomization at the encoders to guarantee security. We then give a strongly secure lattice coding scheme, and we characterize the performance of both these schemes in the presence of Gaussian noise. We then extend our perfectly-secure and strongly-secure schemes to obtain a protocol that guarantees end-to-end secrecy in a multichip line network. We also briefly study the robustness of our bidirectional relaying schemes to channel imperfections. In the second problem, we consider the scenario where multiple terminals have access to private correlated Gaussian sources and a public noiseless communication channel. The objective is to generate a group secret key using their sources and public communication in a way that an eavesdropper having access to the public communication can obtain no information about the key. We give a nested lattice-based protocol for generating strongly secure secret keys from independent and identically distributed copies of the correlated random variables. Under certain assumptions on the joint distribution of the sources, we derive achievable secret key rates. The tools used in designing protocols for both these problems are nested lattice codes, which have been widely used in several problems of communication and security. In this thesis, we also study lattice constructions that permit polynomial-time encoding and decoding. In this regard, we first look at a class of lattices obtained from low-density parity-check (LDPC) codes, called Low-density Construction-A (LDA) lattices. We show that high-dimensional LDA lattices have several “goodness” properties that are desirable in many problems of communication and security. We also present a new class of low-complexity lattice coding schemes that achieve the capacity of the AWGN channel. Codes in this class are obtained by concatenating an inner Construction-A lattice code with an outer Reed-Solomon code or an expander code. We show that this class of codes can achieve the capacity of the AWGN channel with polynomial encoding and decoding complexities. Furthermore, the probability of error decays exponentially in the block length for a fixed transmission rate R that is strictly less than the capacity. To the best of our knowledge, this is the first capacity-achieving coding scheme for the AWGN channel which has an exponentially decaying probability of error and polynomial encoding/decoding complexities.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

L'avènement de l'informatique quantique permet de réétudier les primitives cryptographiques avec une sécurité inconditionnelle, c'est à dire sécurisé même contre des adversaires tout puissants. En 1984, Bennett et Brassard ont construit un protocole quantique de distribution de clé. Dans ce protocole, deux joueurs Alice et Bob coopèrent pour partager une clé secrète inconnue d'une tierce personne Eve. Ce protocole a une sécurité inconditionnelle et n'a pasd'équivalent classique.Dans ma thèse, j'ai étudié les primitives cryptographiques à deux joueurs où ces joueurs ne se font pas confiance. J'étudie principalement le pile ou face quantique et la mise-en-gage quantique de bit. En informatique classique, ces primitivessont réalisables uniquement avec des hypothèses calculatoires, c'est-à-dire en supposant la difficulté d'un problème donné. Des protocoles quantiques ont été construits pour ces primitives où un adversaire peut tricher avec une probabilité constante strictement inférieure à 1, ce qui reste impossible classiquement. Néanmoins, Lo et Chau ont montré l'impossibilité de créer ces primitives parfaitement même en utilisant l'informatique quantique. Il reste donc à déterminer quelles sont les limites physiques de ces primitives.Dans une première partie, je construis un protocole quantique de pile ou face où chaque joueur peut tricher avec probabilité au plus 1/racine(2) + eps pour tout eps > 0. Ce résultat complète un résultat de Kitaev qui dit que dans un jeu de pile ou face quantique, un joueur peut toujours tricher avec probabilité au moins 1/racine(2). J'ai également construit un protocole de mise-en-gage de bit quantique optimal où un joueur peut tricher avec probabilité au plus 0,739 + eps pour tout eps > 0 puis ai montré que ce protocole est en fait optimal. Finalement, j'ai dérivé des bornes inférieures et supérieures pour une autre primitive: la transmission inconsciente, qui est une primitive universelle.Dans une deuxième partie, j'intègre certains aspects pratiques dans ces protocoles. Parfois les appareils de mesure ne donnent aucun résultat, ce sont les pertes dans la mesure. Je construis un protocole de lancer de pièce quantique tolérant aux pertes avec une probabilité de tricher de 0,859. Ensuite, j'étudie le modèle dispositif-indépendant où on ne suppose plus rien sur les appareils de mesure et de création d'état quantique.Finalement, dans une troisième partie, j'étudie ces primitives cryptographiques avec un sécurité computationnelle. En particulier, je fais le lien entre la mise en gage de bit quantique et les protocoles zero-knowledge quantiques. / Quantum computing allows us to revisit the study of quantum cryptographic primitives with information theoretic security. In 1984, Bennett and Brassard presented a protocol of quantum key distribution. In this protocol, Alice and Bob cooperate in order to share a common secret key k, which has to be unknown for a third party that has access to the communication channel. They showed how to perform this task quantumly with an information theoretic security; which is impossible classically.In my thesis, I study cryptographic primitives with two players that do not trust each other. I study mainly coin flipping and bit commitment. Classically, both these primitives are impossible classically with information theoretic security. Quantum protocols for these primitives where constructed where cheating players could cheat with probability stricly smaller than 1. However, Lo, Chau and Mayers showed that these primitives are impossible to achieve perfectly even quantumly if one requires information theoretic security. I study to what extent imperfect protocols can be done in this setting.In the first part, I construct a quantum coin flipping protocol with cheating probabitlity of 1/root(2) + eps for any eps > 0. This completes a result by Kitaev who showed that in any quantum coin flipping protocol, one of the players can cheat with probability at least 1/root(2). I also constructed a quantum bit commitment protocol with cheating probability 0.739 + eps for any eps > 0 and showed that this protocol is essentially optimal. I also derived some upper and lower bounds for quantum oblivious transfer, which is a universal cryptographic primitive.In the second part, I study some practical aspects related to these primitives. I take into account losses than can occur when measuring a quantum state. I construct a Quantum Coin Flipping and Quantum Bit Commitment protocols which are loss-tolerant and have cheating probabilities of 0.859. I also construct these primitives in the device independent model, where the players do not trust their quantum device. Finally, in the third part, I study these cryptographic primitives with information theoretic security. More precisely, I study the relationship between computational quantum bit commitment and quantum zero-knowledge protocols.