Ecological niche modeling, cytogenetics and phylogeography of the genera Geomalacus and Letourneuxia (Gastropoda, Pulmonata) from the Iberian-Moroccan region

First described more that 150 years ago, the systematics of the genera Geomalacus and Letourneuxia (Arionidae, Gastropoda, Pulmonata) is still challenging. The taxonomic classification of arionid species is based on extremely labile characters such as body size or color that depends both on diet and environment, as well as age. Moreover, there is little information on the genetic diversity and population structure of the Iberian slugs that could provide extra clues to disentangle their problematic classification. The present work uses different analytical tools such as habitat suitability (Ecological Niche Modeling - ENM), cytogenetic analysis and phylogeography to establish the geographical distribution and evolutionary history of these pulmonate slugs. The potential distribution of the four Geomalacus species was modeled using ENM, which allowed the identification of new locations for G. malagensis, including a first report in Portugal. Also, it was predicted a much wider distribution for G. malagensis and G. oliveirae than previously known. Classical cytogenetic analyses were assayed with reproductive and a novel use of somatic tissues (mouth and tentacles) returning the number of chromosomes for the four Geomalacus species and L. numidica (n = 31, 2n = 62) and the respective karyotypes. G. malagensis and L. numidica present similar chromosome morphologies and karyotypic formulae, being more similar to each other than the Geomalacus among themselves. We further reconstructed the phylogeny of the genera Geomalacus and Letourneuxia using partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) and the nuclear ribosomal small subunit (18S rRNA), and applied an independent evolutionary rate method, the indicator vectors correlation, to evaluate the existence of cryptic diversity within species. The five nominal species of Geomalacus and Letourneuxia comprise 14 well-supported cryptic lineages. Letourneuxia numidica was retrieved as a sister group of G. malagensis. G. oliveirae is paraphyletic with respect to G. anguiformis. According to our dating estimates, the most recent common ancestor of Geomalacus dates back to the Middle Miocene (end of the Serravallian stage). The major lineage splitting events within Geomalacus occurred during the dry periods of the Zanclean stage (5.3-3.6 million years) and some lineages were confined to more humid mountain areas of the Iberian Peninsula, which lead to a highly geographically structured mitochondrial genetic diversity. The major findings of this are the following: (1) provides updated species distribution maps for the Iberian Geomalacus expanding the known geographic distribution of the concerned species, (2) unravels the cryptic diversity within the genera Geomalacus and Letourneuxia, (3) Geomalacus oliveirae is paraphyletic with G. anguiformis and (4) Letourneuxia numidica is sister group of G. malagensis.

Distributed Diverging Topic Models: A Novel Algorithm for Large Scale Topic Modeling in Spark

Thesis (Master's)--University of Washington, 2014

Modeling Vegetable Fractals by means of Fractional-order Equations

This paper characterizes four ‘fractal vegetables’: (i) cauliflower (brassica oleracea var. Botrytis); (ii) broccoli (brassica oleracea var. italica); (iii) round cabbage (brassica oleracea var. capitata) and (iv) Brussels sprout (brassica oleracea var. gemmifera), by means of electrical impedance spectroscopy and fractional calculus tools. Experimental data is approximated using fractional-order models and the corresponding parameters are determined with a genetic algorithm. The Havriliak-Negami five-parameter model fits well into the data, demonstrating that classical formulae can constitute simple and reliable models to characterize biological structures.

Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression

Affiliation: Institut de recherche en immunologie et en cancérologie, Université de Montréal

MODELING HETEROTACHY IN PHYLOGENETICS

Il a été démontré que l’hétérotachie, variation du taux de substitutions au cours du temps et entre les sites, est un phénomène fréquent au sein de données réelles. Échouer à modéliser l’hétérotachie peut potentiellement causer des artéfacts phylogénétiques. Actuellement, plusieurs modèles traitent l’hétérotachie : le modèle à mélange des longueurs de branche (MLB) ainsi que diverses formes du modèle covarion. Dans ce projet, notre but est de trouver un modèle qui prenne efficacement en compte les signaux hétérotaches présents dans les données, et ainsi améliorer l’inférence phylogénétique. Pour parvenir à nos fins, deux études ont été réalisées. Dans la première, nous comparons le modèle MLB avec le modèle covarion et le modèle homogène grâce aux test AIC et BIC, ainsi que par validation croisée. A partir de nos résultats, nous pouvons conclure que le modèle MLB n’est pas nécessaire pour les sites dont les longueurs de branche diffèrent sur l’ensemble de l’arbre, car, dans les données réelles, le signaux hétérotaches qui interfèrent avec l’inférence phylogénétique sont généralement concentrés dans une zone limitée de l’arbre. Dans la seconde étude, nous relaxons l’hypothèse que le modèle covarion est homogène entre les sites, et développons un modèle à mélanges basé sur un processus de Dirichlet. Afin d’évaluer différents modèles hétérogènes, nous définissons plusieurs tests de non-conformité par échantillonnage postérieur prédictif pour étudier divers aspects de l’évolution moléculaire à partir de cartographies stochastiques. Ces tests montrent que le modèle à mélanges covarion utilisé avec une loi gamma est capable de refléter adéquatement les variations de substitutions tant à l’intérieur d’un site qu’entre les sites. Notre recherche permet de décrire de façon détaillée l’hétérotachie dans des données réelles et donne des pistes à suivre pour de futurs modèles hétérotaches. Les tests de non conformité par échantillonnage postérieur prédictif fournissent des outils de diagnostic pour évaluer les modèles en détails. De plus, nos deux études révèlent la non spécificité des modèles hétérogènes et, en conséquence, la présence d’interactions entre différents modèles hétérogènes. Nos études suggèrent fortement que les données contiennent différents caractères hétérogènes qui devraient être pris en compte simultanément dans les analyses phylogénétiques.

Modeling protein evolution using secondary structures

L’évolution des protéines est un domaine important de la recherche en bioinformatique et catalyse l'intérêt de trouver des outils d'alignement qui peuvent être utilisés de manière fiable et modéliser avec précision l'évolution d'une famille de protéines. TM-Align (Zhang and Skolnick, 2005) est considéré comme l'outil idéal pour une telle tâche, en termes de rapidité et de précision. Par conséquent, dans cette étude, TM-Align a été utilisé comme point de référence pour faciliter la détection des autres outils d'alignement qui sont en mesure de préciser l'évolution des protéines. En parallèle, nous avons élargi l'actuel outil d'exploration de structures secondaires de protéines, Helix Explorer (Marrakchi, 2006), afin qu'il puisse également être utilisé comme un outil pour la modélisation de l'évolution des protéines.

Modeling and Analysis of Some Heavy Tailed Time Series

The thesis has covered various aspects of modeling and analysis of finite mean time series with symmetric stable distributed innovations. Time series analysis based on Box and Jenkins methods are the most popular approaches where the models are linear and errors are Gaussian. We highlighted the limitations of classical time series analysis tools and explored some generalized tools and organized the approach parallel to the classical set up. In the present thesis we mainly studied the estimation and prediction of signal plus noise model. Here we assumed the signal and noise follow some models with symmetric stable innovations.We start the thesis with some motivating examples and application areas of alpha stable time series models. Classical time series analysis and corresponding theories based on finite variance models are extensively discussed in second chapter. We also surveyed the existing theories and methods correspond to infinite variance models in the same chapter. We present a linear filtering method for computing the filter weights assigned to the observation for estimating unobserved signal under general noisy environment in third chapter. Here we consider both the signal and the noise as stationary processes with infinite variance innovations. We derived semi infinite, double infinite and asymmetric signal extraction filters based on minimum dispersion criteria. Finite length filters based on Kalman-Levy filters are developed and identified the pattern of the filter weights. Simulation studies show that the proposed methods are competent enough in signal extraction for processes with infinite variance.Parameter estimation of autoregressive signals observed in a symmetric stable noise environment is discussed in fourth chapter. Here we used higher order Yule-Walker type estimation using auto-covariation function and exemplify the methods by simulation and application to Sea surface temperature data. We increased the number of Yule-Walker equations and proposed a ordinary least square estimate to the autoregressive parameters. Singularity problem of the auto-covariation matrix is addressed and derived a modified version of the Generalized Yule-Walker method using singular value decomposition.In fifth chapter of the thesis we introduced partial covariation function as a tool for stable time series analysis where covariance or partial covariance is ill defined. Asymptotic results of the partial auto-covariation is studied and its application in model identification of stable auto-regressive models are discussed. We generalize the Durbin-Levinson algorithm to include infinite variance models in terms of partial auto-covariation function and introduce a new information criteria for consistent order estimation of stable autoregressive model.In chapter six we explore the application of the techniques discussed in the previous chapter in signal processing. Frequency estimation of sinusoidal signal observed in symmetric stable noisy environment is discussed in this context. Here we introduced a parametric spectrum analysis and frequency estimate using power transfer function. Estimate of the power transfer function is obtained using the modified generalized Yule-Walker approach. Another important problem in statistical signal processing is to identify the number of sinusoidal components in an observed signal. We used a modified version of the proposed information criteria for this purpose.

Interannual and interdecadal oscillations in hydrological variables: Sources and modeling of the persistence in the Elbe River Basin

Wenn man die Existenz von physikalischen Mechanismen ignoriert, die für die Struktur hydrologischer Zeitreihen verantwortlich sind, kann das zu falschen Schlussfolgerungen bzgl. des Vorhandenseins möglicher Gedächtnis (memory) -Effekte, d.h. von Persistenz, führen. Die hier vorgelegte Doktorarbeit spürt der niedrigfrequenten klimatischen Variabilität innerhalb den hydrologischen Zyklus nach und bietet auf dieser "Reise" neue Einsichten in die Transformation der charakteristischen Eigenschaften von Zeitreihen mit einem Langzeitgedächtnis. Diese Studie vereint statistische Methoden der Zeitreihenanalyse mit empirisch-basierten Modelltechniken, um operative Modelle zu entwickeln, die in der Lage sind (1) die Dynamik des Abflusses zu modellieren, (2) sein zukünftiges Verhalten zu prognostizieren und (3) die Abflusszeitreihen an unbeobachteten Stellen abzuschätzen. Als solches präsentiert die hier vorgelegte Dissertation eine ausführliche Untersuchung zu den Ursachen der niedrigfrequenten Variabilität von hydrologischen Zeitreihen im deutschen Teil des Elbe-Einzugsgebietes, den Folgen dieser Variabilität und den physikalisch basierten Reaktionen von Oberflächen- und Grundwassermodellen auf die niedrigfrequenten Niederschlags-Eingangsganglinien. Die Doktorarbeit gliedert sich wie folgt: In Kapitel 1 wird als Hintergrundinformation das Hurst Phänomen beschrieben und ein kurzer Rückblick auf diesbezügliche Studien gegeben. Das Kapitel 2 diskutiert den Einfluss der Präsenz von niedrigfrequenten periodischen Zeitreihen auf die Zuverlässigkeit verschiedener Hurst-Parameter-Schätztechniken. Kapitel 3 korreliert die niedrigfrequente Niederschlagsvariabilität mit dem Index der Nord-Atlantischen Ozillations (NAO). Kapitel 4-6 sind auf den deutschen Teil des Elbe-Einzugsgebietes fokussiert. So werden in Kapitel 4 die niedrigfrequenten Variabilitäten der unterschiedlichen hydro-meteorologischen Parameter untersucht und es werden Modelle beschrieben, die die Dynamik dieser Niedrigfrequenzen und deren zukünftiges Verhalten simulieren. Kapitel 5 diskutiert die mögliche Anwendung der Ergebnisse für die charakteristische Skalen und die Verfahren der Analyse der zeitlichen Variabilität auf praktische Fragestellungen im Wasserbau sowie auf die zeitliche Bestimmung des Gebiets-Abflusses an unbeobachteten Stellen. Kapitel 6 verfolgt die Spur der Niedrigfrequenzzyklen im Niederschlag durch die einzelnen Komponenten des hydrologischen Zyklus, nämlich dem Direktabfluss, dem Basisabfluss, der Grundwasserströmung und dem Gebiets-Abfluss durch empirische Modellierung. Die Schlussfolgerungen werden im Kapitel 7 präsentiert. In einem Anhang werden technische Einzelheiten zu den verwendeten statistischen Methoden und die entwickelten Software-Tools beschrieben.

Downscaling and Modeling the Effects of Climate Change on Hydrology and Water Resources in the Upper Blue Nile River Basin, Ethiopia

The Upper Blue Nile River Basin (UBNRB) located in the western part of Ethiopia, between 7° 45’ and 12° 45’N and 34° 05’ and 39° 45’E has a total area of 174962 km2 . More than 80% of the population in the basin is engaged in agricultural activities. Because of the particularly dry climate in the basin, likewise to most other regions of Ethiopia, the agricultural productivity depends to a very large extent on the occurrence of the seasonal rains. This situation makes agriculture highly vulnerable to the impact of potential climate hazards which are about to inflict Africa as a whole and Ethiopia in particular. To analyze these possible impacts of future climate change on the water resources in the UBNRB, in the first part of the thesis climate projection for precipitation, minimum and maximum temperatures in the basin, using downscaled predictors from three GCMs (ECHAM5, GFDL21 and CSIRO-MK3) under SRES scenarios A1B and A2 have been carried out. The two statistical downscaling models used are SDSM and LARS-WG, whereby SDSM is used to downscale ECHAM5-predictors alone and LARS-WG is applied in both mono-model mode with predictors from ECHAM5 and in multi-model mode with combined predictors from ECHAM5, GFDL21 and CSIRO-MK3. For the calibration/validation of the downscaled models, observed as well as NCEP climate data in the 1970 - 2000 reference period is used. The future projections are made for two time periods; 2046-2065 (2050s) and 2081-2100 (2090s). For the 2050s future time period the downscaled climate predictions indicate rise of 0.6°C to 2.7°C for the seasonal maximum temperatures Tmax, and of 0.5°C to 2.44°C for the minimum temperatures Tmin. Similarly, during the 2090s the seasonal Tmax increases by 0.9°C to 4.63°C and Tmin by 1°C to 4.6°C, whereby these increases are generally higher for the A2 than for the A1B scenario. For most sub-basins of the UBNRB, the predicted changes of Tmin are larger than those of Tmax. Meanwhile, for the precipitation, both downscaling tools predict large changes which, depending on the GCM employed, are such that the spring and summer seasons will be experiencing decreases between -36% to 1% and the autumn and winter seasons an increase of -8% to 126% for the two future time periods, regardless of the SRES scenario used. In the second part of the thesis the semi-distributed, physically based hydrologic model, SWAT (Soil Water Assessment Tool), is used to evaluate the impacts of the above-predicted future climate change on the hydrology and water resources of the UBNRB. Hereby the downscaled future predictors are used as input in the SWAT model to predict streamflow of the Upper Blue Nile as well as other relevant water resources parameter in the basin. Calibration and validation of the streamflow model is done again on 1970-2000 measured discharge at the outlet gage station Eldiem, whereby the most sensitive out the numerous “tuneable” calibration parameters in SWAT have been selected by means of a sophisticated sensitivity analysis. Consequently, a good calibration/validation model performance with a high NSE-coefficient of 0.89 is obtained. The results of the future simulations of streamflow in the basin, using both SDSM- and LARS-WG downscaled output in SWAT reveal a decline of -10% to -61% of the future Blue Nile streamflow, And, expectedly, these obviously adverse effects on the future UBNRB-water availibiliy are more exacerbated for the 2090’s than for the 2050’s, regardless of the SRES.

Modeling, Estimation, and Control of Robot-Soil Interactions

This thesis presents the development of hardware, theory, and experimental methods to enable a robotic manipulator arm to interact with soils and estimate soil properties from interaction forces. Unlike the majority of robotic systems interacting with soil, our objective is parameter estimation, not excavation. To this end, we design our manipulator with a flat plate for easy modeling of interactions. By using a flat plate, we take advantage of the wealth of research on the similar problem of earth pressure on retaining walls. There are a number of existing earth pressure models. These models typically provide estimates of force which are in uncertain relation to the true force. A recent technique, known as numerical limit analysis, provides upper and lower bounds on the true force. Predictions from the numerical limit analysis technique are shown to be in good agreement with other accepted models. Experimental methods for plate insertion, soil-tool interface friction estimation, and control of applied forces on the soil are presented. In addition, a novel graphical technique for inverting the soil models is developed, which is an improvement over standard nonlinear optimization. This graphical technique utilizes the uncertainties associated with each set of force measurements to obtain all possible parameters which could have produced the measured forces. The system is tested on three cohesionless soils, two in a loose state and one in a loose and dense state. The results are compared with friction angles obtained from direct shear tests. The results highlight a number of key points. Common assumptions are made in soil modeling. Most notably, the Mohr-Coulomb failure law and perfectly plastic behavior. In the direct shear tests, a marked dependence of friction angle on the normal stress at low stresses is found. This has ramifications for any study of friction done at low stresses. In addition, gradual failures are often observed for vertical tools and tools inclined away from the direction of motion. After accounting for the change in friction angle at low stresses, the results show good agreement with the direct shear values.

Implementation and application of basis set superposition error-correction schemes to the theoretical modeling of weak intermolecular interactions

This thesis deals with the so-called Basis Set Superposition Error (BSSE) from both a methodological and a practical point of view. The purpose of the present thesis is twofold: (a) to contribute step ahead in the correct characterization of weakly bound complexes and, (b) to shed light the understanding of the actual implications of the basis set extension effects in the ab intio calculations and contribute to the BSSE debate. The existing BSSE-correction procedures are deeply analyzed, compared, validated and, if necessary, improved. A new interpretation of the counterpoise (CP) method is used in order to define counterpoise-corrected descriptions of the molecular complexes. This novel point of view allows for a study of the BSSE-effects not only in the interaction energy but also on the potential energy surface and, in general, in any property derived from the molecular energy and its derivatives A program has been developed for the calculation of CP-corrected geometry optimizations and vibrational frequencies, also using several counterpoise schemes for the case of molecular clusters. The method has also been implemented in Gaussian98 revA10 package. The Chemical Hamiltonian Approach (CHA) methodology has been also implemented at the RHF and UHF levels of theory for an arbitrary number interacting systems using an algorithm based on block-diagonal matrices. Along with the methodological development, the effects of the BSSE on the properties of molecular complexes have been discussed in detail. The CP and CHA methodologies are used for the determination of BSSE-corrected molecular complexes properties related to the Potential Energy Surfaces and molecular wavefunction, respectively. First, the behaviour of both BSSE-correction schemes are systematically compared at different levels of theory and basis sets for a number of hydrogen-bonded complexes. The Complete Basis Set (CBS) limit of both uncorrected and CP-corrected molecular properties like stabilization energies and intermolecular distances has also been determined, showing the capital importance of the BSSE correction. Several controversial topics of the BSSE correction are addressed as well. The application of the counterpoise method is applied to internal rotational barriers. The importance of the nuclear relaxation term is also pointed out. The viability of the CP method for dealing with charged complexes and the BSSE effects on the double-well PES blue-shifted hydrogen bonds is also studied in detail. In the case of the molecular clusters the effect of high-order BSSE effects introduced with the hierarchical counterpoise scheme is also determined. The effect of the BSSE on the electron density-related properties is also addressed. The first-order electron density obtained with the CHA/F and CHA/DFT methodologies was used to assess, both graphically and numerically, the redistribution of the charge density upon BSSE-correction. Several tools like the Atoms in Molecules topologycal analysis, density difference maps, Quantum Molecular Similarity, and Chemical Energy Component Analysis were used to deeply analyze, for the first time, the BSSE effects on the electron density of several hydrogen bonded complexes of increasing size. The indirect effect of the BSSE on intermolecular perturbation theory results is also pointed out It is shown that for a BSSE-free SAPT study of hydrogen fluoride clusters, the use of a counterpoise-corrected PES is essential in order to determine the proper molecular geometry to perform the SAPT analysis.

Top-down systems biology modeling of host metabotype-microbiome associations in obese rodents

Covariation in the structural composition of the gut microbiome and the spectroscopically derived metabolic phenotype (metabotype) of a rodent model for obesity were investigated using a range of multivariate statistical tools. Urine and plasma samples from three strains of 10-week-old male Zucker rats (obese (fa/fa, n = 8), lean (fal-, n = 8) and lean (-/-, n = 8)) were characterized via high-resolution H-1 NMR spectroscopy, and in parallel, the fecal microbial composition was investigated using fluorescence in situ hydridization (FISH) and denaturing gradient gel electrophoresis (DGGE) methods. All three Zucker strains had different relative abundances of the dominant members of their intestinal microbiota (FISH), with the novel observation of a Halomonas and a Sphingomonas species being present in the (fa/fa) obese strain on the basis of DGGE data. The two functionally and phenotypically normal Zucker strains (fal- and -/-) were readily distinguished from the (fa/fa) obese rats on the basis of their metabotypes with relatively lower urinary hippurate and creatinine, relatively higher levels of urinary isoleucine, leucine and acetate and higher plasma LDL and VLDL levels typifying the (fa/fa) obese strain. Collectively, these data suggest a conditional host genetic involvement in selection of the microbial species in each host strain, and that both lean and obese animals could have specific metabolic phenotypes that are linked to their individual microbiomes.

Ecological niche modeling and principal component analysis of Krameria Loefl. (Krameriaceae)

Krameria plants are found in arid regions of the Americas and present a floral system that attracts oil-collecting bees. Niche modeling and multivariate tools were applied to examine ecological and geographical aspects of the 18 species of this genus, using occurrence data obtained from herbaria and literature. Niche modeling showed the potential areas of occurrence for each species and the analysis of climatic variables suggested that North American species occur mostly in deserted or xeric ecoregions with monthly precipitation below 140 mm and large temperature ranges. South American species are mainly found in deserted ecoregions and subtropical savannas where monthly precipitation often exceeds 150 mm and temperature ranges are smaller. Principal Component Analysis (PCA) performed with values of temperature and precipitation showed that the distribution limits of Krameria species are primarily associated with maximum and minimum temperatures. Modeling of Krameria species proved to be a useful tool for analyzing the influence of the ecological niche variables in the geographical distribution of species, providing new information to guide future investigations. (C) 2011 Elsevier Ltd. All rights reserved.

On modeling and evaluating multicomputer transcoding architectures for live-video streams

The pervasive and ubiquitous computing has motivated researches on multimedia adaptation which aims at matching the video quality to the user needs and device restrictions. This technique has a high computational cost which needs to be studied and estimated when designing architectures and applications. This paper presents an analytical model to quantify these video transcoding costs in a hardware independent way. The model was used to analyze the impact of transcoding delays in end-to-end live-video transmissions over LANs, MANs and WANs. Experiments confirm that the proposed model helps to define the best transcoding architecture for different scenarios.

Modeling dialogue with mixed initiative in design space exploration

Exploration with a generative formalism must necessarily account for the nature of interaction between humans and the design space explorer. Established accounts of design interaction are made complicated by two propositions in Woodbury and Burrow's Keynote on design space exploration. First, the emphasis on the primacy of the design space as an ordered collection of partial designs (version, alternatives, extensions). Few studies exist in the design interaction literature on working with multiple threads simultaneously. Second, the need to situate, aid, and amplify human design intentions using computational tools. Although specific research and practice tools on amplification (sketching, generation, variation) have had success, there is a lack of generic, flexible, interoperable, and extensible representation to support amplification. This paper addresses the above, working with design threads and computer-assisted design amplification through a theoretical model of dialogue based on Grice's model of rational conversation. Using the concept of mixed initiative, the paper presents a visual notation for representing dialogue between designer and design space formalism through abstract examples of exploration tasks and dialogue integration.