3,763 research outputs found

    Computational Analyses of Metagenomic Data

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    Metagenomics studies the collective microbial genomes extracted from a particular environment without requiring the culturing or isolation of individual genomes, addressing questions revolving around the composition, functionality, and dynamics of microbial communities. The intrinsic complexity of metagenomic data and the diversity of applications call for efficient and accurate computational methods in data handling. In this thesis, I present three primary projects that collectively focus on the computational analysis of metagenomic data, each addressing a distinct topic. In the first project, I designed and implemented an algorithm named Mapbin for reference-free genomic binning of metagenomic assemblies. Binning aims to group a mixture of genomic fragments based on their genome origin. Mapbin enhances binning results by building a multilayer network that combines the initial binning, assembly graph, and read-pairing information from paired-end sequencing data. The network is further partitioned by the community-detection algorithm, Infomap, to yield a new binning result. Mapbin was tested on multiple simulated and real datasets. The results indicated an overall improvement in the common binning quality metrics. The second and third projects are both derived from ImMiGeNe, a collaborative and multidisciplinary study investigating the interplay between gut microbiota, host genetics, and immunity in stem-cell transplantation (SCT) patients. In the second project, I conducted microbiome analyses for the metagenomic data. The workflow included the removal of contaminant reads and multiple taxonomic and functional profiling. The results revealed that the SCT recipients' samples yielded significantly fewer reads with heavy contamination of the host DNA, and their microbiomes displayed evident signs of dysbiosis. Finally, I discussed several inherent challenges posed by extremely low levels of target DNA and high levels of contamination in the recipient samples, which cannot be rectified solely through bioinformatics approaches. The primary goal of the third project is to design a set of primers that can be used to cover bacterial flagellin genes present in the human gut microbiota. Considering the notable diversity of flagellins, I incorporated a method to select representative bacterial flagellin gene sequences, a heuristic approach based on established primer design methods to generate a degenerate primer set, and a selection method to filter genes unlikely to occur in the human gut microbiome. As a result, I successfully curated a reduced yet representative set of primers that would be practical for experimental implementation

    Generalized network-based dimensionality analysis

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    Network analysis opens new horizons for data analysis methods, as the results of ever-developing network science can be integrated into classical data analysis techniques. This paper presents the generalized version of network-based dimensionality reduction and analysis (NDA). The main contributions of this paper are as follows: (1) The proposed generalized dimensionality reduction and analysis (GNDA) method already handles low-dimensional high-sample-size (LDHSS) and high-dimensional and low-sample-size (HDLSS) at the same time. In addition, compared with existing methods, we show that only the proposed GNDA method adequately estimates the number of latent variables (LVs). (2) The proposed GNDA already considers any symmetric and nonsymmetric similarity functions between indicators (i.e., variables or observations) to specify LVs. (3) The proposed prefiltering and resolution parameters provide the hierarchical version of GNDA to check the robustness of LVs. The proposed GNDA method is compared with traditional dimensionality reduction methods on various simulated and real-world datasets

    Multilayer analysis of dynamic network reconfiguration in pediatric posttraumatic stress disorder.

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    Neuroimage studies have reported functional connectome abnormalities in posttraumatic stress disorder (PTSD), especially in adults. However, these studies often treated the brain as a static network, and time-variance of connectome topology in pediatric posttraumatic stress disorder remain unclear. To explore case-control differences in dynamic connectome topology, resting-state functional magnetic resonance imaging data were acquired from 24 treatment-naïve non-comorbid pediatric posttraumatic stress disorder patients and 24 demographically matched trauma-exposed non-posttraumatic stress disorder controls. A graph-theoretic analysis was applied to construct time-varying modular structure of whole-brain networks by maximizing the multilayer modularity. Network switching rate at the global, subnetwork, and nodal levels were calculated and compared between posttraumatic stress disorder and trauma-exposed non-posttraumatic stress disorder groups, and their associations with posttraumatic stress disorder symptom severity and sex interactions were explored. At the global level, individuals with posttraumatic stress disorder exhibited significantly lower network switching rates compared to trauma-exposed non-posttraumatic stress disorder controls. This difference was mainly involved in default-mode and dorsal attention subnetworks, as well as in inferior temporal and parietal brain nodes. Posttraumatic stress disorder symptom severity was negatively correlated with switching rate in the global network and default mode network. No significant differences were observed in the interaction between diagnosis and sex/age. Pediatric posttraumatic stress disorder is associated with dynamic reconfiguration of brain networks, which may provide insights into the biological basis of this disorder

    Une méthode de mesure du mouvement humain pour la programmation par démonstration

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    Programming by demonstration (PbD) is an intuitive approach to impart a task to a robot from one or several demonstrations by the human teacher. The acquisition of the demonstrations involves the solution of the correspondence problem when the teacher and the learner differ in sensing and actuation. Kinesthetic guidance is widely used to perform demonstrations. With such a method, the robot is manipulated by the teacher and the demonstrations are recorded by the robot's encoders. In this way, the correspondence problem is trivial but the teacher dexterity is afflicted which may impact the PbD process. Methods that are more practical for the teacher usually require the identification of some mappings to solve the correspondence problem. The demonstration acquisition method is based on a compromise between the difficulty of identifying these mappings, the level of accuracy of the recorded elements and the user-friendliness and convenience for the teacher. This thesis proposes an inertial human motion tracking method based on inertial measurement units (IMUs) for PbD for pick-and-place tasks. Compared to kinesthetic guidance, IMUs are convenient and easy to use but can present a limited accuracy. Their potential for PbD applications is investigated. To estimate the trajectory of the teacher's hand, 3 IMUs are placed on her/his arm segments (arm, forearm and hand) to estimate their orientations. A specific method is proposed to partially compensate the well-known drift of the sensor orientation estimation around the gravity direction by exploiting the particular configuration of the demonstration. This method, called heading reset, is based on the assumption that the sensor passes through its original heading with stationary phases several times during the demonstration. The heading reset is implemented in an integration and vector observation algorithm. Several experiments illustrate the advantages of this heading reset. A comprehensive inertial human hand motion tracking (IHMT) method for PbD is then developed. It includes an initialization procedure to estimate the orientation of each sensor with respect to the human arm segment and the initial orientation of the sensor with respect to the teacher attached frame. The procedure involves a rotation and a static position of the extended arm. The measurement system is thus robust with respect to the positioning of the sensors on the segments. A procedure for estimating the position of the human teacher relative to the robot and a calibration procedure for the parameters of the method are also proposed. At the end, the error of the human hand trajectory is measured experimentally and is found in an interval between 28.528.5 mm and 61.861.8 mm. The mappings to solve the correspondence problem are identified. Unfortunately, the observed level of accuracy of this IHMT method is not sufficient for a PbD process. In order to reach the necessary level of accuracy, a method is proposed to correct the hand trajectory obtained by IHMT using vision data. A vision system presents a certain complementarity with inertial sensors. For the sake of simplicity and robustness, the vision system only tracks the objects but not the teacher. The correction is based on so-called Positions Of Interest (POIs) and involves 3 steps: the identification of the POIs in the inertial and vision data, the pairing of the hand POIs to objects POIs that correspond to the same action in the task, and finally, the correction of the hand trajectory based on the pairs of POIs. The complete method for demonstration acquisition is experimentally evaluated in a full PbD process. This experiment reveals the advantages of the proposed method over kinesthesy in the context of this work.La programmation par démonstration est une approche intuitive permettant de transmettre une tâche à un robot à partir d'une ou plusieurs démonstrations faites par un enseignant humain. L'acquisition des démonstrations nécessite cependant la résolution d'un problème de correspondance quand les systèmes sensitifs et moteurs de l'enseignant et de l'apprenant diffèrent. De nombreux travaux utilisent des démonstrations faites par kinesthésie, i.e., l'enseignant manipule directement le robot pour lui faire faire la tâche. Ce dernier enregistre ses mouvements grâce à ses propres encodeurs. De cette façon, le problème de correspondance est trivial. Lors de telles démonstrations, la dextérité de l'enseignant peut être altérée et impacter tout le processus de programmation par démonstration. Les méthodes d'acquisition de démonstration moins invalidantes pour l'enseignant nécessitent souvent des procédures spécifiques pour résoudre le problème de correspondance. Ainsi l'acquisition des démonstrations se base sur un compromis entre complexité de ces procédures, le niveau de précision des éléments enregistrés et la commodité pour l'enseignant. Cette thèse propose ainsi une méthode de mesure du mouvement humain par capteurs inertiels pour la programmation par démonstration de tâches de ``pick-and-place''. Les capteurs inertiels sont en effet pratiques et faciles à utiliser, mais sont d'une précision limitée. Nous étudions leur potentiel pour la programmation par démonstration. Pour estimer la trajectoire de la main de l'enseignant, des capteurs inertiels sont placés sur son bras, son avant-bras et sa main afin d'estimer leurs orientations. Une méthode est proposée afin de compenser partiellement la dérive de l'estimation de l'orientation des capteurs autour de la direction de la gravité. Cette méthode, appelée ``heading reset'', est basée sur l'hypothèse que le capteur passe plusieurs fois par son azimut initial avec des phases stationnaires lors d'une démonstration. Cette méthode est implémentée dans un algorithme d'intégration et d'observation de vecteur. Des expériences illustrent les avantages du ``heading reset''. Cette thèse développe ensuite une méthode complète de mesure des mouvements de la main humaine par capteurs inertiels (IHMT). Elle comprend une première procédure d'initialisation pour estimer l'orientation des capteurs par rapport aux segments du bras humain ainsi que l'orientation initiale des capteurs par rapport au repère de référence de l'humain. Cette procédure, consistant en une rotation et une position statique du bras tendu, est robuste au positionnement des capteurs. Une seconde procédure est proposée pour estimer la position de l'humain par rapport au robot et pour calibrer les paramètres de la méthode. Finalement, l'erreur moyenne sur la trajectoire de la main humaine est mesurée expérimentalement entre 28.5 mm et 61.8 mm, ce qui n'est cependant pas suffisant pour la programmation par démonstration. Afin d'atteindre le niveau de précision nécessaire, une nouvelle méthode est développée afin de corriger la trajectoire de la main par IHMT à partir de données issues d'un système de vision, complémentaire des capteurs inertiels. Pour maintenir une certaine simplicité et robustesse, le système de vision ne suit que les objets et pas l'enseignant. La méthode de correction, basée sur des ``Positions Of Interest (POIs)'', est constituée de 3 étapes: l'identification des POIs dans les données issues des capteurs inertiels et du système de vision, puis l'association de POIs liées à la main et de POIs liées aux objets correspondant à la même action, et enfin, la correction de la trajectoire de la main à partir des paires de POIs. Finalement, la méthode IHMT corrigée est expérimentalement évaluée dans un processus complet de programmation par démonstration. Cette expérience montre l'avantage de la méthode proposée sur la kinesthésie dans le contexte de ce travail

    The present and future status of heavy neutral leptons

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    Artículo escrito por un elevado número de autores, solo se referencian el que aparece en primer lugar, los autores pertenecientes a la UAM y el nombre del grupo de colaboración, si lo hubiereThe existence of nonzero neutrino masses points to the likely existence of multiple Standard Model neutral fermions. When such states are heavy enough that they cannot be produced in oscillations, they are referred to as heavy neutral leptons (HNLs). In this white paper, we discuss the present experimental status of HNLs including colliders, beta decay, accelerators, as well as astrophysical and cosmological impacts. We discuss the importance of continuing to search for HNLs, and its potential impact on our understanding of key fundamental questions, and additionally we outline the future prospects for next-generation future experiments or upcoming accelerator run scenario

    Sampling unknown large networks restricted by low sampling rates

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    Graph sampling plays an important role in data mining for large networks. Specifically, larger networks often correspond to lower sampling rates. Under the situation, traditional traversal-based samplings for large networks usually have an excessive preference for densely-connected network core nodes. Aim at this issue, this paper proposes a sampling method for unknown networks at low sampling rates, called SLSR, which first adopts a random node sampling to evaluate a degree threshold, utilized to distinguish the core from periphery, and the average degree in unknown networks, and then runs a double-layer sampling strategy on the core and periphery. SLSR is simple that results in a high time efficiency, but experimental evaluation confirms that the proposed method can accurately preserve many critical structures of unknown large networks at sampling rates not exceeding 10%.Comment: 19 pages,14 figure
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