10,319 research outputs found

    Revisão taxonómica do género Calendula L. (Asteraceae - Calenduleae) na Península Ibérica e Marrocos

    Get PDF
    The genus Calendula L. (Asteraceae - Calenduleae) includes, depending on the author, 10 to 25 species, distributed mainly in the Mediterranean basin. The taxonomy of this genus is considered to be extremely difficult, due to a great morphological variability, doubtfull relevance of some of the characters used to distinguish its species (e.g. the life form: annual or perennial; the habit: erect or diffuse, shape of the leaves, indumentum, relative size of the capitula and colour of disc or ray florets, achene morphology), but also due to the hybridization and polyploidization. Despite the numerous studies that have been published, no agreement on the classification and characters used to discriminate between taxa has been reached. A taxonomic study of the genus Calendula was conducted for the Iberian Peninsula and Morocco, aiming at (1) access the morphological variability between and within taxa, (2) confirm the chromosome numbers, (3) increase the nuclear DNA content estimations, (4) re-evaluate taxa delimitations and circumscription, and (5) reassess, and redefine, the descriptions and characters useful to distinguish taxa. In order to achieve a satisfying taxonomic core, extensive fieldwork, detailed morphometric analysis, chorological, karyological and genome size studies were conducted. For the Iberian Peninsula, four species were recognized, including nine subspecies (between these two new subspecies were described). For Morocco, including some taxa from Algeria and Tunisia 13 species were recognized (two new species and a nomenclatural change), including 15 subspecies (among these eight new subspecies were described). To corroborate the results obtained and to evaluate the evolutionary relationships among taxa, phylogenetic studies using molecular methods, such as ITS, microsatellites or other molecular markers, should be used.O género Calendula L. (Asteraceae - Calenduleae) inclui, dependendo do autor, 10 a 25 espécies, distribuídas essencialmente na bacia do Mediterrâneo. A taxonomia deste género é considerada extremamente difícil, devido à grande variabilidade morfológica, discutivel relevância de alguns dos caracteres utilizados para distinguir suas espécies (por exemplo, a forma de vida: anual ou perene, o hábito: erecto ou difuso, a forma das folhas, o indumento, o tamanho e a cor dos capítulos e a morfologia dos aquénios), mas também devido à hibridização e poliploidização. Apesar dos inúmeros estudos que foram publicados, não foi alcançado um acordo sobre a classificação e os caracteres utilizados para discriminar as suas espécies. Um estudo taxonómico do género Calendula foi realizado para a Península Ibérica e Marrocos, com o objectivo de (1) verificar a variabilidade morfológica, (2) confirmar o número de cromossomas, (3) aumentar as estimativas de conteúdo em ADN, (4) reavaliar a delimitação e a circunscrição dos taxa, e (5) reavaliar e redefinir as descrições e caracteres úteis para os distinguir. Para alcançar uma robustês taxonómica satisfatória, foram realizados extensos trabalhos de campo, análise morfométrica detalhada, abordagens corológicas, cariológicas e quanto ao conteúdo em ADN. Para a Península Ibérica, quatro espécies foram reconhecidas, incluindo nove subespécies (entre essas duas novas subespécies foram descritas). Para Marrocos, incluindo alguns taxa da Argelia e Tunisia, foram reconhecidas 13 espécies (duas novas e uma mudança nomenclatural), incluindo 15 subespécies (entre essas oito novas subespécies foram descritas). Para corroborar os resultados obtidos e avaliar as relações evolutivas e filogenéticas entre os taxa, estudos que utilizem diferentes métodos moleculares, tais como ITS, microsatélites ou outros marcadores moleculares, devem ser utilizados.Apoio financeiro do Laboratório Associado CESAM - Centro de Estudos do Ambiente e do Mar (AMB/50017) financiado por fundos nacionais através da FCT/MCTES e cofinanciado pelo FEDER (POCI-01-0145-FEDER-007638), no âmbito do Acordo de Parceria PT2020, e Compete 2020Programa Doutoral em Biologi

    UMSL Bulletin 2023-2024

    Get PDF
    The 2023-2024 Bulletin and Course Catalog for the University of Missouri St. Louis.https://irl.umsl.edu/bulletin/1088/thumbnail.jp

    Ultra High Strength Steels for Roll Formed Automotive Body in White

    Get PDF
    One of the more recent steel developments is the quenching and partitioning process, first proposed by Speer et al. in 2003 on developing 3rd generation advanced high-strength steel (AHSS). The quenching and partitioning (Q&P) process set a new way of producing martensitic steels with enhanced austenite levels, realised through controlled thermal treatments. The main objective of the so-called 3rd generation steels was to realise comparable properties to the 2nd generation but without high alloying additions. Generally, Q&P steels have remained within lab-scale environments, with only a small number of Q&P steels produced industrially. Q&P steels are produced either by a one-step or two-step process, and the re-heating mechanism for the two-step adds additional complexities when heat treating the material industrially. The Q&P steels developed and tested throughout this thesis have been designed to achieve the desired microstructural evolution whilst fitting in with Tata’s continuous annealing processing line (CAPL) capabilities. The CALPHAD approach using a combination of thermodynamics, kinetics, and phase transformation theory with software packages ThermoCalc and JMatPro has been successfully deployed to find novel Q&P steels. The research undertaken throughout this thesis has led to two novel Q&P steels, which can be produced on CAPL without making any infrastructure changes to the line. The two novel Q&P steels show an apparent reduction in hardness mismatch, illustrated visually and numerically after nano-indentation experiments. The properties realised after Q&P heat treatments on the C-Mn-Si alloy with 0.2 Wt.% C and the C-Mn-Si alloy with the small Cr addition is superior to the commercially available QP980/1180 steels by BaoSteel. Both novel alloys had comparable levels of elongation and hole expansion ratio to QP1180 but are substantially stronger with a > 320MPa increase in tensile stress. The heat treatment is also less complex as there is no requirement to heat the steel back up after quenching due to one-step quenching and partitioning being employed on the novel alloys

    Using machine learning to predict pathogenicity of genomic variants throughout the human genome

    Get PDF
    Geschätzt mehr als 6.000 Erkrankungen werden durch Veränderungen im Genom verursacht. Ursachen gibt es viele: Eine genomische Variante kann die Translation eines Proteins stoppen, die Genregulation stören oder das Spleißen der mRNA in eine andere Isoform begünstigen. All diese Prozesse müssen überprüft werden, um die zum beschriebenen Phänotyp passende Variante zu ermitteln. Eine Automatisierung dieses Prozesses sind Varianteneffektmodelle. Mittels maschinellem Lernen und Annotationen aus verschiedenen Quellen bewerten diese Modelle genomische Varianten hinsichtlich ihrer Pathogenität. Die Entwicklung eines Varianteneffektmodells erfordert eine Reihe von Schritten: Annotation der Trainingsdaten, Auswahl von Features, Training verschiedener Modelle und Selektion eines Modells. Hier präsentiere ich ein allgemeines Workflow dieses Prozesses. Dieses ermöglicht es den Prozess zu konfigurieren, Modellmerkmale zu bearbeiten, und verschiedene Annotationen zu testen. Der Workflow umfasst außerdem die Optimierung von Hyperparametern, Validierung und letztlich die Anwendung des Modells durch genomweites Berechnen von Varianten-Scores. Der Workflow wird in der Entwicklung von Combined Annotation Dependent Depletion (CADD), einem Varianteneffektmodell zur genomweiten Bewertung von SNVs und InDels, verwendet. Durch Etablierung des ersten Varianteneffektmodells für das humane Referenzgenome GRCh38 demonstriere ich die gewonnenen Möglichkeiten Annotationen aufzugreifen und neue Modelle zu trainieren. Außerdem zeige ich, wie Deep-Learning-Scores als Feature in einem CADD-Modell die Vorhersage von RNA-Spleißing verbessern. Außerdem werden Varianteneffektmodelle aufgrund eines neuen, auf Allelhäufigkeit basierten, Trainingsdatensatz entwickelt. Diese Ergebnisse zeigen, dass der entwickelte Workflow eine skalierbare und flexible Möglichkeit ist, um Varianteneffektmodelle zu entwickeln. Alle entstandenen Scores sind unter cadd.gs.washington.edu und cadd.bihealth.org frei verfügbar.More than 6,000 diseases are estimated to be caused by genomic variants. This can happen in many possible ways: a variant may stop the translation of a protein, interfere with gene regulation, or alter splicing of the transcribed mRNA into an unwanted isoform. It is necessary to investigate all of these processes in order to evaluate which variant may be causal for the deleterious phenotype. A great help in this regard are variant effect scores. Implemented as machine learning classifiers, they integrate annotations from different resources to rank genomic variants in terms of pathogenicity. Developing a variant effect score requires multiple steps: annotation of the training data, feature selection, model training, benchmarking, and finally deployment for the model's application. Here, I present a generalized workflow of this process. It makes it simple to configure how information is converted into model features, enabling the rapid exploration of different annotations. The workflow further implements hyperparameter optimization, model validation and ultimately deployment of a selected model via genome-wide scoring of genomic variants. The workflow is applied to train Combined Annotation Dependent Depletion (CADD), a variant effect model that is scoring SNVs and InDels genome-wide. I show that the workflow can be quickly adapted to novel annotations by porting CADD to the genome reference GRCh38. Further, I demonstrate the integration of deep-neural network scores as features into a new CADD model, improving the annotation of RNA splicing events. Finally, I apply the workflow to train multiple variant effect models from training data that is based on variants selected by allele frequency. In conclusion, the developed workflow presents a flexible and scalable method to train variant effect scores. All software and developed scores are freely available from cadd.gs.washington.edu and cadd.bihealth.org

    Surface-Based tools for Characterizing the Human Brain Cortical Morphology

    Get PDF
    Tesis por compendio de publicacionesThe cortex of the human brain is highly convoluted. These characteristic convolutions present advantages over lissencephalic brains. For instance, gyrification allows an expansion of cortical surface area without significantly increasing the cranial volume, thus facilitating the pass of the head through the birth channel. Studying the human brain’s cortical morphology and the processes leading to the cortical folds has been critical for an increased understanding of the pathological processes driving psychiatric disorders such as schizophrenia, bipolar disorders, autism, or major depression. Furthermore, charting the normal developmental changes in cortical morphology during adolescence or aging can be of great importance for detecting deviances that may be precursors for pathology. However, the exact mechanisms that push cortical folding remain largely unknown. The accurate characterization of the neurodevelopment processes is challenging. Multiple mechanisms co-occur at a molecular or cellular level and can only be studied through the analysis of ex-vivo samples, usually of animal models. Magnetic Resonance Imaging can partially fill the breach, allowing the portrayal of the macroscopic processes surfacing on in-vivo samples. Different metrics have been defined to measure cortical structure to describe the brain’s morphological changes and infer the associated microstructural events. Metrics such as cortical thickness, surface area, or cortical volume help establish a relation between the measured voxels on a magnetic resonance image and the underlying biological processes. However, the existing methods present limitations or room for improvement. Methods extracting the lines representing the gyral and sulcal morphology tend to over- or underestimate the total length. These lines can provide important information about how sulcal and gyral regions function differently due to their distinctive ontogenesis. Nevertheless, some methods label every small fold on the cortical surface as a sulcal fundus, thus losing the perspective of lines that travel through the deeper zones of a sulcal basin. On the other hand, some methods are too restrictive, labeling sulcal fundi only for a bunch of primary folds. To overcome this issue, we have proposed a Laplacian-collapse-based algorithm that can delineate the lines traversing the top regions of the gyri and the fundi of the sulci avoiding anastomotic sulci. For this, the cortex, represented as a 3D surface, is segmented into gyral and sulcal surfaces attending to the curvature and depth at every point of the mesh. Each resulting surface is spatially filtered, smoothing the boundaries. Then, a Laplacian-collapse-based algorithm is applied to obtain a thinned representation of the morphology of each structure. These thin curves are processed to detect where the extremities or endpoints lie. Finally, sulcal fundi and gyral crown lines are obtained by eroding the surfaces while preserving the structure topology and connectivity between the endpoints. The assessment of the presented algorithm showed that the labeled sulcal lines were close to the proposed ground truth length values while crossing through the deeper (and more curved) regions. The tool also obtained reproducibility scores better or similar to those of previous algorithms. A second limitation of the existing metrics concerns the measurement of sulcal width. This metric, understood as the physical distance between the points on opposite sulcal banks, can come in handy in detecting cortical flattening or complementing the information provided by cortical thickness, gyrification index, or such features. Nevertheless, existing methods only provided averaged measurements for different predefined sulcal regions, greatly restricting the possibilities of sulcal width and ignoring the intra-region variability. Regarding this, we developed a method that estimates the distance from each sulcal point in the cortex to its corresponding opposite, thus providing a per-vertex map of the physical sulcal distances. For this, the cortical surface is sampled at different depth levels, detecting the points where the sulcal banks change. The points corresponding to each sulcal wall are matched with the closest point on a different one. The distance between those points is the sulcal width. The algorithm was validated against a simulated sulcus that resembles a simple fold. Then the tool was used on a real dataset and compared against two widely-used sulcal width estimation methods, averaging the proposed algorithm’s values into the same region definition those reference tools use. The resulting values were similar for the proposed and the reference methods, thus demonstrating the algorithm’s accuracy. Finally, both algorithms were tested on a real aging population dataset to prove the methods’ potential in a use-case scenario. The main idea was to elucidate fine-grained morphological changes in the human cortex with aging by conducting three analyses: a comparison of the age-dependencies of cortical thickness in gyral and sulcal lines, an analysis of how the sulcal and gyral length changes with age, and a vertex-wise study of sulcal width and cortical thickness. These analyses showed a general flattening of the cortex with aging, with interesting findings such as a differential age-dependency of thickness thinning in the sulcal and gyral regions. By demonstrating that our method can detect this difference, our results can pave the way for future in vivo studies focusing on macro- and microscopic changes specific to gyri or sulci. Our method can generate new brain-based biomarkers specific to sulci and gyri, and these can be used on large samples to establish normative models to which patients can be compared. In parallel, the vertex-wise analyses show that sulcal width is very sensitive to changes during aging, independent of cortical thickness. This corroborates the concept of sulcal width as a metric that explains, in the least, the unique variance of morphology not fully captured by existing metrics. Our method allows for sulcal width vertex-wise analyses that were not possible previously, potentially changing our understanding of how changes in sulcal width shape cortical morphology. In conclusion, this thesis presents two new tools, open source and publicly available, for estimating cortical surface-based morphometrics. The methods have been validated and assessed against existing algorithms. They have also been tested on a real dataset, providing new, exciting insights into cortical morphology and showing their potential for defining innovative biomarkers.Programa de Doctorado en Ciencia y Tecnología Biomédica por la Universidad Carlos III de MadridPresidente: Juan Domingo Gispert López.- Secretario: Norberto Malpica González de Vega.- Vocal: Gemma Cristina Monté Rubi

    Graduate Council Minutes - February 16, 2023

    Get PDF

    Mixed-Integer Programming Approaches to Generalized Submodular Optimization and its Applications

    Full text link
    Submodularity is an important concept in integer and combinatorial optimization. A classical submodular set function models the utility of selecting homogenous items from a single ground set, and such selections can be represented by binary variables. In practice, many problem contexts involve choosing heterogenous items from more than one ground set or selecting multiple copies of homogenous items, which call for extensions of submodularity. We refer to the optimization problems associated with such generalized notions of submodularity as Generalized Submodular Optimization (GSO). GSO is found in wide-ranging applications, including infrastructure design, healthcare, online marketing, and machine learning. Due to the often highly nonlinear (even non-convex and non-concave) objective function and the mixed-integer decision space, GSO is a broad subclass of challenging mixed-integer nonlinear programming problems. In this tutorial, we first provide an overview of classical submodularity. Then we introduce two subclasses of GSO, for which we present polyhedral theory for the mixed-integer set structures that arise from these problem classes. Our theoretical results lead to efficient and versatile exact solution methods that demonstrate their effectiveness in practical problems using real-world datasets

    optimización da planificación de adquisición de datos LIDAR cara ó modelado 3D de interiores

    Get PDF
    The main objective of this doctoral thesis is the design, validation and implementation of methodologies that allow the geometric and topological modelling of navigable spaces, whether inside buildings or urban environments, to be integrated into three-dimensional geographic information systems (GIS-3D). The input data of this work will consist mainly of point clouds (which can be classified) acquired by LiDAR systems both indoors and outdoors. In addition, the use of BIM infrastructure models and cadastral maps is proposed depending on their availability. Point clouds provide a large amount of environmental information with high accuracy compared to data offered by other acquisition technologies. However, the lack of data structure and volume requires a great deal of processing effort. For this reason, the first step is to structure the data by dividing the input cloud into simpler entities that facilitate subsequent processes. For this first division, the physical elements present in the cloud will be considered, since they can be walls in the case of interior environments or kerbs in the case of exteriors. In order to generate navigation routes adapted to different mobile agents, the next objective will try to establish a semantic subdivision of space according to the functionalities of space. In the case of internal environments, it is possible to use BIM models to evaluate the results and the use of cadastral maps that support the division of the urban environment. Once the navigable space is divided, the design of topologically coherent navigation networks will be parameterized both geometrically and topologically. For this purpose, several spatial discretization techniques, such as 3D tessellations, will be studied to facilitate the establishment of topological relationships, adjacency, connectivity and inclusion between subspaces. Based on the geometric characterization and the topological relations established in the previous phase, the creation of three-dimensional navigation networks with multimodal support will be addressed and different levels of detail will be considered according to the mobility specifications of each agent and its purpose. Finally, the possibility of integrating the networks generated in a GIS-3D visualization system will be considered. For the correct visualization, the level of detail can be adjusted according to geometry and semantics. Aspects such as the type of user or transport, mobility, rights of access to spaces, etc. They must be considered at all times.El objetivo principal de esta tesis doctoral es el diseño, la validación y la implementación de metodologías que permitan el modelado geométrico y topológico de espacios navegables, ya sea de interiores de edificios o entornos urbanos, para integrarse en sistemas de información geográfica tridimensional (SIG). -3D). Los datos de partida de este trabajo consistirán principalmente en nubes de puntos (que pueden estar clasificados) adquiridas por sistemas LiDAR tanto en interiores como en exteriores. Además, se propone el uso de modelos BIM de infraestructuras y mapas catastrales en función de su disponibilidad. Las nubes de puntos proporcionan una gran cantidad de información del entorno con gran precisión con respecto a los datos ofrecidos por otras tecnologías de adquisición. Sin embargo, la falta de estructura de datos y su volumen requiere un gran esfuerzo de procesamiento. Por este motivo, el primer paso que se debe realizar consiste en estructurar los datos dividiendo la nube de entrada en entidades más simples que facilitan los procesos posteriores. Para esta primera división se considerarán los elementos físicos presentes en la nube, ya que pueden ser paredes en el caso de entornos interiores o bordillos en el caso de los exteriores. Con el propósito de generar rutas de navegación adaptadas a diferentes agentes móviles, el próximo objetivo intentará establecer una subdivisión semántica del espacio de acuerdo con las funcionalidades del espacio. En el caso de entornos internos, es posible utilizar modelos BIM para evaluar los resultados y el uso de mapas catastrales que sirven de apoyo en la división del entorno urbano. Una vez que se divide el espacio navegable, se parametrizará tanto geométrica como topológicamente al diseño de redes de navegación topológicamente coherentes. Para este propósito, se estudiarán varias técnicas de discretización espacial, como las teselaciones 3D, para facilitar el establecimiento de relaciones topológicas, la adyacencia, la conectividad y la inclusión entre subespacios. A partir de la caracterización geométrica y las relaciones topológicas establecidas en la fase anterior, se abordará la creación de redes de navegación tridimensionales con soporte multimodal y se considerarán diversos niveles de detalle según las especificaciones de movilidad de cada agente y su propósito. Finalmente, se contemplará la posibilidad de integrar las redes generadas en un sistema de visualización tridimensional 3D SIG 3D. Para la correcta visualización, el nivel de detalle se puede ajustar en función de la geometría y la semántica. Aspectos como el tipo de usuario o transporte, movilidad, derechos de acceso a espacios, etc. Deben ser considerados en todo momento.O obxectivo principal desta tese doutoral é o deseño, validación e implementación de metodoloxías que permitan o modelado xeométrico e topolóxico de espazos navegables, ben sexa de interiores de edificios ou de entornos urbanos, ca fin de seren integrados en Sistemas de Información Xeográfica tridimensionais (SIX-3D). Os datos de partida deste traballo constarán principalmente de nubes de puntos (que poden estar clasificadas) adquiridas por sistemas LiDAR tanto en interiores como en exteriores. Ademáis plantease o uso de modelos BIM de infraestruturas e mapas catastrais dependendo da súa dispoñibilidade. As nubes de puntos proporcionan unha gran cantidade de información do entorno cunha gran precisión respecto os datos que ofrecen outras tecnoloxías de adquisición. Sen embargo, a falta de estrutura dos datos e a seu volume esixe un amplo esforzo de procesado. Por este motivo o primeiro paso a levar a cabo consiste nunha estruturación dos datos mediante a división da nube de entrada en entidades máis sinxelas que faciliten os procesos posteriores. Para esta primeira división consideraranse elementos físicos presentes na nube como poden ser paredes no caso de entornos interiores ou bordillos no caso de exteriores. Coa finalidade de xerar rutas de navegación adaptadas a distintos axentes móbiles, o seguinte obxectivo tratará de establecer unha subdivisión semántica do espazo de acordo as funcionalidades do espazo. No caso de entornos interiores plantease a posibilidade de empregar modelos BIM para avaliar os resultados e o uso de mapas catastrais que sirvan de apoio na división do entorno urbano. Unha vez divido o espazo navigable parametrizarase tanto xeométricamente como topolóxicamene de cara ao deseño de redes de navegación topolóxicamente coherentes. Para este fin estudaranse varias técnicas de discretización de espazos como como son as teselacións 3D co obxectivo de facilitar establecer relacións topolóxicas, de adxacencia, conectividade e inclusión entre subespazos. A partir da caracterización xeométrica e das relación topolóxicas establecidas na fase previa abordarase a creación de redes de navegación tridimensionais con soporte multi-modal e considerando varios niveis de detalle de acordo as especificacións de mobilidade de cada axente e a súa finalidade. Finalmente comtemplarase a posibilidade de integrar as redes xeradas nun sistema SIX 3D visualización tridimensional. Para a correcta visualización o nivel de detalle poderá axustarse en base a xeometría e a semántica. Aspectos como o tipo de usuario ou transporte, mobilidade, dereitos de acceso a espazos, etc. deberán ser considerados en todo momento
    corecore