818 research outputs found

    Interspecific Genetic Differences and Historical Demography in South American Arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum)

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    The South American arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum) are emblematic species widely distributed in the Amazon and surrounding basins. Arowana species are under strong anthropogenic pressure as they are extensively exploited for ornamental and food purposes. Until now, limited genetic and cytogenetic information has been available, with only a few studies reporting to their genetic diversity and population structure. In the present study, cytogenetic and DArTseq-derived single nucleotide polymorphism (SNP) data were used to investigate the genetic diversity of the two Osteoglossum species, the silver arowana O. bicirrhosum, and the black arowana O. ferreirai. Both species differ in their 2n (with 2n = 54 and 56 for O. ferreirai and O. bicirrhosum, respectively) and in the composition and distribution of their repetitive DNA content, consistent with their taxonomic status as different species. Our genetic dataset was coupled with contemporary and paleogeographic niche modeling, to develop concurrent demographic models that were tested against each other with a deep learning approach in O. bicirrhosum. Our genetic results reveal that O. bicirrhosum colonized the Tocantins-Araguaia basin from the Amazon basin about one million years ago. In addition, we highlighted a higher genetic diversity of O. bicirrhosum in the Amazon populations in comparison to those from the Tocantins-Araguaia basin. © 2019 by the authors. Licensee MDPI, Basel, Switzerland

    Molecular Evolution of Vasopressin and Oxytocin Receptor Genes in Owl Monkeys (aotus Azarai) of Northern Argentina

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    The arginine vasopressin (AVP) and oxytocin (OT) hormone pathways are involved in a multitude of physiological processes, and their receptor genes (AVPR1A and OXTR) have been implicated in increased partner preference and pair bonding behavior in mammalian lineages. This observation is of considerable importance for understanding social monogamy in primates, which is present in only a small subset of primate taxa, including Azara\u27s owl monkeys (Aotus azarai). Thus, it is the goal of this dissertation to examine the molecular evolution of AVPR1A and OXTR in owl monkeys to better understand how the pro-social behaviors related to those loci may have evolved. However, in order to properly contextualize functional neurogenetic variation related to such sociobehavioral pattterns, it is necessary to first establish the range of molecular variation occurring at non-related genetic loci. To address this issue, we sequenced the entire mitochondrial genome of two species of Aotus (A. azarai and A. nancymaae), and analyzed 39 haplotypes of the mitochondrial COII gene from ten different owl monkey taxa. Next, to understand the recent evolutionary history and genetic structure of our focal owl monkey population, we assessed variation of the mtDNA control region (D-loop) in 118 wild individuals. Furthermore, to establish our knowledge of genetic kinship and individual identity within the wild population, we investigated autosomal variation in the form of 24 short tandem repeat (STR) microsatellite loci. In concert with these analyses, we characterized the molecular features of AVPR1A and OXTR in A. azarai and other platyrrhines through direct sequencing, and demonstrated that there are substantial sequence differences at both loci across primate species. These data provide new clues on the possible basis of pair bonding in New World species, and may help to explain the sporadic appearance of monogamy in this infraorder. Specifically, despite a common molecular origin, we argue that the AVP and OT pathways have evolved in markedly different ways, due in part to their chromosomal locations and their relative proximity to regions of molecular instability. This study reinforces the notion that neurogenetic loci in primates have undergone significant evolutionary changes, and suggests that monogamy has arisen multiple times in the primate order through different molecular mechanisms

    Metaheuristic Optimization Techniques for Articulated Human Tracking

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    Four adaptive metaheuristic optimization algorithms are proposed and demonstrated: Adaptive Parameter Particle Swarm Optimization (AP-PSO), Modified Artificial Bat (MAB), Differential Mutated Artificial Immune System (DM-AIS) and hybrid Particle Swarm Accelerated Artificial Immune System (PSO-AIS). The algorithms adapt their search parameters on the basis of the fitness of obtained solutions such that a good fitness value favors local search, while a poor fitness value favors global search. This efficient feedback of the solution quality, imparts excellent global and local search characteristic to the proposed algorithms. The algorithms are tested on the challenging Articulated Human Tracking (AHT) problem whose objective is to infer human pose, expressed in terms of joint angles, from a continuous video stream. The Particle Filter (PF) algorithms, widely applied in generative model based AHT, suffer from the 'curse of dimensionality' and 'degeneracy' challenges. The four proposed algorithms show stable performance throughout the course of numerical experiments. DM-AIS performs best among the proposed algorithms followed in order by PSO-AIS, AP-PSO, and MBA in terms of Most Appropriate Pose (MAP) tracking error. The MAP tracking error of the proposed algorithms is compared with four heuristic approaches: generic PF, Annealed Particle Filter (APF), Partitioned Sampled Annealed Particle Filter (PSAPF) and Hierarchical Particle Swarm Optimization (HPSO). They are found to outperform generic PF with a confidence level of 95%, PSAPF and HPSO with a confidence level of 85%. While DM-AIS and PSO-AIS outperform APF with a confidence level of 80%. Further, it is noted that the proposed algorithms outperform PSAPF and HPSO using a significantly lower number of function evaluations, 2500 versus 7200. The proposed algorithms demonstrate reduced particle requirements, hence improving computational efficiency and helping to alleviate the 'curse of dimensionality'. The adaptive nature of the algorithms is found to guide the whole swarm towards the optimal solution by sharing information and exploring a wider solution space which resolves the 'degeneracy' challenge. Furthermore, the decentralized structure of the algorithms renders them insensitive to accumulation of error and allows them to recover from catastrophic failures due to loss of image data, sudden change in motion pattern or discrete instances of algorithmic failure. The performance enhancements demonstrated by the proposed algorithms, attributed to their balanced local and global search capabilities, makes real-time AHT applications feasible. Finally, the utility of the proposed algorithms in low-dimensional system identification problems as well as high-dimensional AHT problems demonstrates their applicability in various problem domains

    Chemometric Approaches for Systems Biology

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    The present Ph.D. thesis is devoted to study, develop and apply approaches commonly used in chemometrics to the emerging field of systems biology. Existing procedures and new methods are applied to solve research and industrial questions in different multidisciplinary teams. The methodologies developed in this document will enrich the plethora of procedures employed within omic sciences to understand biological organisms and will improve processes in biotechnological industries integrating biological knowledge at different levels and exploiting the software packages derived from the thesis. This dissertation is structured in four parts. The first block describes the framework in which the contributions presented here are based. The objectives of the two research projects related to this thesis are highlighted and the specific topics addressed in this document via conference presentations and research articles are introduced. A comprehensive description of omic sciences and their relationships within the systems biology paradigm is given in this part, jointly with a review of the most applied multivariate methods in chemometrics, on which the novel approaches proposed here are founded. The second part addresses many problems of data understanding within metabolomics, fluxomics, proteomics and genomics. Different alternatives are proposed in this block to understand flux data in steady state conditions. Some are based on applications of multivariate methods previously applied in other chemometrics areas. Others are novel approaches based on a bilinear decomposition using elemental metabolic pathways, from which a GNU licensed toolbox is made freely available for the scientific community. As well, a framework for metabolic data understanding is proposed for non-steady state data, using the same bilinear decomposition proposed for steady state data, but modelling the dynamics of the experiments using novel two and three-way data analysis procedures. Also, the relationships between different omic levels are assessed in this part integrating different sources of information of plant viruses in data fusion models. Finally, an example of interaction between organisms, oranges and fungi, is studied via multivariate image analysis techniques, with future application in food industries. The third block of this thesis is a thoroughly study of different missing data problems related to chemometrics, systems biology and industrial bioprocesses. In the theoretical chapters of this part, new algorithms to obtain multivariate exploratory and regression models in the presence of missing data are proposed, which serve also as preprocessing steps of any other methodology used by practitioners. Regarding applications, this block explores the reconstruction of networks in omic sciences when missing and faulty measurements appear in databases, and how calibration models between near infrared instruments can be transferred, avoiding costs and time-consuming full recalibrations in bioindustries and research laboratories. Finally, another software package, including a graphical user interface, is made freely available for missing data imputation purposes. The last part discusses the relevance of this dissertation for research and biotechnology, including proposals deserving future research.Esta tesis doctoral se centra en el estudio, desarrollo y aplicación de técnicas quimiométricas en el emergente campo de la biología de sistemas. Procedimientos comúnmente utilizados y métodos nuevos se aplican para resolver preguntas de investigación en distintos equipos multidisciplinares, tanto del ámbito académico como del industrial. Las metodologías desarrolladas en este documento enriquecen la plétora de técnicas utilizadas en las ciencias ómicas para entender el funcionamiento de organismos biológicos y mejoran los procesos en la industria biotecnológica, integrando conocimiento biológico a diferentes niveles y explotando los paquetes de software derivados de esta tesis. Esta disertación se estructura en cuatro partes. El primer bloque describe el marco en el cual se articulan las contribuciones aquí presentadas. En él se esbozan los objetivos de los dos proyectos de investigación relacionados con esta tesis. Asimismo, se introducen los temas específicos desarrollados en este documento mediante presentaciones en conferencias y artículos de investigación. En esta parte figura una descripción exhaustiva de las ciencias ómicas y sus interrelaciones en el paradigma de la biología de sistemas, junto con una revisión de los métodos multivariantes más aplicados en quimiometría, que suponen las pilares sobre los que se asientan los nuevos procedimientos aquí propuestos. La segunda parte se centra en resolver problemas dentro de metabolómica, fluxómica, proteómica y genómica a partir del análisis de datos. Para ello se proponen varias alternativas para comprender a grandes rasgos los datos de flujos metabólicos en estado estacionario. Algunas de ellas están basadas en la aplicación de métodos multivariantes propuestos con anterioridad, mientras que otras son técnicas nuevas basadas en descomposiciones bilineales utilizando rutas metabólicas elementales. A partir de éstas se ha desarrollado software de libre acceso para la comunidad científica. A su vez, en esta tesis se propone un marco para analizar datos metabólicos en estado no estacionario. Para ello se adapta el enfoque tradicional para sistemas en estado estacionario, modelando las dinámicas de los experimentos empleando análisis de datos de dos y tres vías. En esta parte de la tesis también se establecen relaciones entre los distintos niveles ómicos, integrando diferentes fuentes de información en modelos de fusión de datos. Finalmente, se estudia la interacción entre organismos, como naranjas y hongos, mediante el análisis multivariante de imágenes, con futuras aplicaciones a la industria alimentaria. El tercer bloque de esta tesis representa un estudio a fondo de diferentes problemas relacionados con datos faltantes en quimiometría, biología de sistemas y en la industria de bioprocesos. En los capítulos más teóricos de esta parte, se proponen nuevos algoritmos para ajustar modelos multivariantes, tanto exploratorios como de regresión, en presencia de datos faltantes. Estos algoritmos sirven además como estrategias de preprocesado de los datos antes del uso de cualquier otro método. Respecto a las aplicaciones, en este bloque se explora la reconstrucción de redes en ciencias ómicas cuando aparecen valores faltantes o atípicos en las bases de datos. Una segunda aplicación de esta parte es la transferencia de modelos de calibración entre instrumentos de infrarrojo cercano, evitando así costosas re-calibraciones en bioindustrias y laboratorios de investigación. Finalmente, se propone un paquete software que incluye una interfaz amigable, disponible de forma gratuita para imputación de datos faltantes. En la última parte, se discuten los aspectos más relevantes de esta tesis para la investigación y la biotecnología, incluyendo líneas futuras de trabajo.Aquesta tesi doctoral es centra en l'estudi, desenvolupament, i aplicació de tècniques quimiomètriques en l'emergent camp de la biologia de sistemes. Procediments comúnment utilizats i mètodes nous s'apliquen per a resoldre preguntes d'investigació en diferents equips multidisciplinars, tant en l'àmbit acadèmic com en l'industrial. Les metodologies desenvolupades en aquest document enriquixen la plétora de tècniques utilitzades en les ciències òmiques per a entendre el funcionament d'organismes biològics i milloren els processos en la indústria biotecnològica, integrant coneixement biològic a distints nivells i explotant els paquets de software derivats d'aquesta tesi. Aquesta dissertació s'estructura en quatre parts. El primer bloc descriu el marc en el qual s'articulen les contribucions ací presentades. En ell s'esbossen els objectius dels dos projectes d'investigació relacionats amb aquesta tesi. Així mateix, s'introduixen els temes específics desenvolupats en aquest document mitjançant presentacions en conferències i articles d'investigació. En aquesta part figura una descripació exhaustiva de les ciències òmiques i les seues interrelacions en el paradigma de la biologia de sistemes, junt amb una revisió dels mètodes multivariants més aplicats en quimiometria, que supossen els pilars sobre els quals s'assenten els nous procediments ací proposats. La segona part es centra en resoldre problemes dins de la metabolòmica, fluxòmica, proteòmica i genòmica a partir de l'anàlisi de dades. Per a això es proposen diverses alternatives per a compendre a grans trets les dades de fluxos metabòlics en estat estacionari. Algunes d'elles estàn basades en l'aplicació de mètodes multivariants propostos amb anterioritat, mentre que altres són tècniques noves basades en descomposicions bilineals utilizant rutes metabòliques elementals. A partir d'aquestes s'ha desenvolupat software de lliure accés per a la comunitat científica. Al seu torn, en aquesta tesi es proposa un marc per a analitzar dades metabòliques en estat no estacionari. Per a això s'adapta l'enfocament tradicional per a sistemes en estat estacionari, modelant les dinàmiques dels experiments utilizant anàlisi de dades de dues i tres vies. En aquesta part de la tesi també s'establixen relacions entre els distints nivells òmics, integrant diferents fonts d'informació en models de fusió de dades. Finalment, s'estudia la interacció entre organismes, com taronges i fongs, mitjançant l'anàlisi multivariant d'imatges, amb futures aplicacions a la indústria alimentària. El tercer bloc d'aquesta tesi representa un estudi a fons de diferents problemes relacionats amb dades faltants en quimiometria, biologia de sistemes i en la indústria de bioprocessos. En els capítols més teòrics d'aquesta part, es proposen nous algoritmes per a ajustar models multivariants, tant exploratoris com de regressió, en presencia de dades faltants. Aquests algoritmes servixen ademés com a estratègies de preprocessat de dades abans de l'ús de qualsevol altre mètode. Respecte a les aplicacions, en aquest bloc s'explora la reconstrucció de xarxes en ciències òmiques quan apareixen valors faltants o atípics en les bases de dades. Una segona aplicació d'aquesta part es la transferència de models de calibració entre instruments d'infrarroig proper, evitant així costoses re-calibracions en bioindústries i laboratoris d'investigació. Finalment, es proposa un paquet software que inclou una interfície amigable, disponible de forma gratuïta per a imputació de dades faltants. En l'última part, es discutixen els aspectes més rellevants d'aquesta tesi per a la investigació i la biotecnologia, incloent línies futures de treball.Folch Fortuny, A. (2016). Chemometric Approaches for Systems Biology [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/77148TESISPremios Extraordinarios de tesis doctorale

    Real-time people tracking in a camera network

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    Visual tracking is a fundamental key to the recognition and analysis of human behaviour. In this thesis we present an approach to track several subjects using multiple cameras in real time. The tracking framework employs a numerical Bayesian estimator, also known as a particle lter, which has been developed for parallel implementation on a Graphics Processing Unit (GPU). In order to integrate multiple cameras into a single tracking unit we represent the human body by a parametric ellipsoid in a 3D world. The elliptical boundary can be projected rapidly, several hundred times per subject per frame, onto any image for comparison with the image data within a likelihood model. Adding variables to encode visibility and persistence into the state vector, we tackle the problems of distraction and short-period occlusion. However, subjects may also disappear for longer periods due to blind spots between cameras elds of view. To recognise a desired subject after such a long-period, we add coloured texture to the ellipsoid surface, which is learnt and retained during the tracking process. This texture signature improves the recall rate from 60% to 70-80% when compared to state only data association. Compared to a standard Central Processing Unit (CPU) implementation, there is a signi cant speed-up ratio

    Statistical Modelling

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    The book collects the proceedings of the 19th International Workshop on Statistical Modelling held in Florence on July 2004. Statistical modelling is an important cornerstone in many scientific disciplines, and the workshop has provided a rich environment for cross-fertilization of ideas from different disciplines. It consists in four invited lectures, 48 contributed papers and 47 posters. The contributions are arranged in sessions: Statistical Modelling; Statistical Modelling in Genomics; Semi-parametric Regression Models; Generalized Linear Mixed Models; Correlated Data Modelling; Missing Data, Measurement of Error and Survival Analysis; Spatial Data Modelling and Time Series and Econometrics

    Stochastic spatial modelling of DNA methylation patterns and moment-based parameter estimation

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    In the first part of this thesis, we introduce and analyze spatial stochastic models for DNA methylation, an epigenetic mark with an important role in development. The underlying mechanisms controlling methylation are only partly understood. Several mechanistic models of enzyme activities responsible for methylation have been proposed. Here, we extend existing hidden Markov models (HMMs) for DNA methylation by describing the occurrence of spatial methylation patterns with stochastic automata networks. We perform numerical analysis of the HMMs applied to (non-)hairpin bisulfite sequencing KO data and accurately predict the wild-type data from these results. We find evidence that the activities of Dnmt3a/b responsible for de novo methylation depend on the left but not on the right CpG neighbors. The second part focuses on parameter estimation in chemical reaction networks (CRNs). We propose a generalized method of moments (GMM) approach for inferring the parameters of CRNs based on a sophisticated matching of the statistical moments of the stochastic model and the sample moments of population snapshot data. The proposed parameter estimation method exploits recently developed moment-based approximations and provides estimators with desirable statistical properties when many samples are available. The GMM provides accurate and fast estimations of unknown parameters of CRNs. The accuracy increases and the variance decreases when higher-order moments are considered.Im ersten Teil der Arbeit führen wir eine Analyse für spatielle stochastische Modelle der DNA Methylierung, ein wichtiger epigenetischer Marker in der Entwicklung, durch. Die zugrunde liegenden Mechanismen der Methylierung werden noch nicht vollständig verstanden. Mechanistische Modelle beschreiben die Aktivität der Methylierungsenzyme. Wir erweitern bestehende Hidden Markov Models (HMMs) zur DNA Methylierung durch eine Stochastic Automata Networks Beschreibung von spatiellen Methylierungsmustern. Wir führen eine numerische Analyse der HMMs auf bisulfit-sequenzierten KO Datens¨atzen aus und nutzen die Resultate, um die Wildtyp-Daten erfolgreich vorherzusagen. Unsere Ergebnisse deuten an, dass die Aktivitäten von Dnmt3a/b, die überwiegend für die de novo Methylierung verantwortlich sind, nur vom Methylierungsstatus des linken, nicht aber vom rechten CpG Nachbarn abhängen. Der zweite Teil befasst sich mit Parameterschätzung in chemischen Reaktionsnetzwerken (CRNs). Wir führen eine Verallgemeinerte Momentenmethode (GMM) ein, die die statistischen Momente des stochastischen Modells an die Momente von Stichproben geschickt anpasst. Die GMM nutzt hier kürzlich entwickelte, momentenbasierte Näherungen, liefert Schätzer mit wünschenswerten statistischen Eigenschaften, wenn genügend Stichproben verfügbar sind, mit schnellen und genauen Schätzungen der unbekannten Parameter in CRNs. Momente höherer Ordnung steigern die Genauigkeit des Schätzers, während die Varianz sinkt

    2019 IMSAloquium: Student Inquiry and Research Program and IMSA Internship Program

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    Welcome to IMSAloquium 2019! This is IMSA’s 32nd year of leading in educational innovation, the 31st year of the IMSA Student Inquiry and Research (SIR) Program, and the first year of the newly imagined IMSA Internship Program.https://digitalcommons.imsa.edu/archives_sir/1029/thumbnail.jp

    Raman scattering of single photons and its use for quantum networks and high-precision measurements

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    This work concerns the interaction of single atoms and light as a platform for quantum-communication networks, both experimentally and simulative. It treats, at its kernel, the calcium ion as a node of such a network, i. e. as storage of a quantum bit. Especially the quantum interface of this ion with the light field and its experimental implementation are addressed in detail. Thereby spontaneous Raman scattering is used to transfer the polarisation state of a single photon onto the ion’s electronic state and vice versa. On the way to this interface the Raman scattering process of single photons was investigated intensively. This led to a high-precision experiment measuring the phase shift of such photons as well as a detailed theoretical study of the spectral and temporal structure of the photons. The experiments used and expanded an existing hybrid quantum-optical set-up consisting of two identical ion traps and a light source of entangled photon pairs.Diese Arbeit behandelt die Wechselwirkung einzelner Atome mit Licht als Plattform für Quantenkommunikationsnetzwerke, sowohl experimentell als auch simulativ. Im Kern befasst sie sich mit dem Calciumion als Knotenpunkt eines solchen Netzwerks, d. h. als Speicher eines Quantenbits. Insbesondere wird die Quantenschnittstelle dieses Ions mit dem Lichtfeld und ihre experimentelle Umsetzung detailliert behandelt. Dabei wird durch spontane Raman-Streuung der Polarisationszustand eines einzelnen Photons auf den elektronischen Zustand des Ions übertragen und umgekehrt. Auf dem Weg zur Umsetzung dieser Schnittstelle wurde der Raman’sche Streuprozess einzelner Photonen genau untersucht. Dies mündete in einem Hochpräzisionsexperiment zur Messung des Phasengangs solcher Photonen sowie zu einer detaillierten theoretischen Studie der spektralen und temporalen Struktur der Photonen. Zur Verwirklichung dieser Experimente wurde ein bestehender hybrider quantenoptischer Aufbau, bestehend aus zwei identischen Ionenfallen sowie einer Lichtquelle verschränkter Photonenpaare, genutzt und erweitert.Die dò Ahwett hannelt vun de Weggselwirgung ähnselner Atome mim Licht als Arwettsplatt fa e Quandenetzwerk – unn zwar experimendell unn simmuleert. In de Hauptsach geht’s um’s Calciumion als Knibbelche vun some Netzwerk, das häßt, es dud e Quandebit speichere. Insbesonnere gebt die Quandeschnittstell vum Ion mim Lichtfeld unn die experimendell Umsetzung dòdevun genau beschrieb. Dòdebei werd mit spondaner Raman-Streiung de Polarisationszustand vumme ähnselne Phoddòn uff de elegdronische Zustand vum Ion iwwertrah odder annersch’erum. Uffem Wäh zu der dò Schnittstell is ’em Raman sei Streiprozess genau unnersucht wòr. Das hat zum ähne zuner scheen Messung vum Phasegang vun so Phodone gefihrt unn zum annere zuner deddaijiert theoredisch Ahwett iwwer die spegdral unn zeitlich Strugdur vun denne Phodone. Fa die dò Experimende ze mache, is amme voorischer Quandeobdik-Uffbau geknoddelt wòr unn aach noch meh draangebaut wòr. Bestehn duder aus zwä Ionefalle vun ähn unn de selb Sort unn’er Quell vun veschrängde Phodonepaare
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