1,721,036 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Development of new methods and algorithms for the processing of UMI in high throughput sequencing data
No full textLes objectifs de cette thèse s’inscrivent dans la large problématique du traitement des données issues de séquenceurs à très haut débit, et plus particulièrement des reads courts, issus de séquenceurs de deuxième génération. Les aspects abordés dans cette problématique se concentrent principalement sur le développement de nouvelles méthodologies se basant sur des séquences moléculaires uniques appelées UMI utilisées pour étiqueter les fragments d’ADN initiaux et permettant d’améliorer la précision des résultats obtenus.Tout d’abord, dans le domaine de la transcriptomique, une nouvelle méthode a été développée afin d’améliorer les résultats de mesure de l’expression génique d’une part, et de détecter les transcrits de fusion dans les tumeurs d’autre part. Cette méthode se base sur une RT-MLPA couplée à un séquenceur NGS. Elle permet d’amplifier les fragments d’ARN présents dans un échantillon tumoral et d’obtenir les séquences des fragments récoltés. L’analyse sous-jacente vise à analyser ces séquences une par une pour, dans un premier temps, attribuer chaque séquence à l’échantillon séquencé, et dans un deuxième temps, retrouver le nom du gène qu’il exprime. Pour cela, RT-MiS a été développé. RT-MiS est un outil permettant d’effectuer la totalité de l’analyse commençant par l’extraction et la correction des UMI des séquences jusqu’à la production des résultats sous forme de matrice d’expression par gène pour chaque échantillon. RT-MiS comporte aussi une interface d’analyse dédiée permettant de lancer l’outil facilement par les chercheurs. Cette interface permet d’automatiser le plus possible le processus d’analyse complet et de produire les résultats sous formes de figures et graphiques interactifs rendant l’interprétation biologique plus facile.Ensuite, dans le domaine de la génomique, un nouvel outil de détection de variants somatiques a été développé. L’outil UMI-VarCal est un variant caller basé sur les UMI et donc implémentant une analyse de ces derniers pour appeler efficacement les variants dans les échantillons tumoraux. L’utilité des UMI est mise en évidence par l’amélioration de la précision de détection des variants, surtout quand la fréquence tombe au-dessous de 1%. UMI-VarCal applique un test de Poisson pour filtrer les positions ne présentant pas des variants et puis se sert d’une analyse des UMI et de deux filtres complémentaires pour filtrer les faux positifs. UMI-VarCal a été conçu de façon très optimisée afin d’effectuer son analyse tout en restant plus efficace que les autres outils en termes de détectionde variants et de temps d’exécution.Finalement, et toujours dans le domaine de la détection des variants, un nouveau simulateur de reads a été développé. Cet outil appelé UMI-Gen est le premier simulateur de reads capable de générer des séquences avec des UMI. De plus, UMI-Gen est capable d’insérer des variants somatiques (SNV) ou des variants structuraux (CNV) dans les fichiers simulés. En outre, en analysant un ensemble de fichiers normaux, il est capable d’estimer le bruit de fond dans ces échantillons pour le reproduire dans les reads simulés. Ces fichiers peuvent être utilisés par la suite pour évaluer les variant callers, surtout ceuximplémentant une analyse UMI dans leur algorithme.The objectives of this thesis fall within the broad issue of processing data from next generation sequencers, and more particularly short reads from second-generation sequencers. The aspects addressed in this issue mainly focus on the development of new methodologies based on unique molecular sequences called UMI used to label the initial DNA fragments and to improve the precision of the results.First of all, in the field of transcriptomics, a new method has been developed in order to improve the results of measuring gene expression on the one hand, and to detect fusion transcripts in tumors on the other hand. This method is based on an RT-MLPA coupled to an NGS sequencer. It makes it possible to amplify the RNA fragments from a tumor sample and to obtain the sequences of the analyzed fragments. The underlying analysis aims to analyze these sequences one by one in order, first, to assign each sequence to the corresponding sample, and secondly, to find the name of the gene it expresses. For this, RT-MiS has been developed. RT-MiS is a tool that is able to perform the entire analysis starting with the extraction and correction of the UMI from the sequences until the production of the results in the form of an gene expression matrix for each sample. RT-MiSalso includes a dedicated analysis interface allowing for the tool to be launched easily by the users. This interface automates the entire analysis process as much as possible and produces the results in the form of interactive figures and graphs making biological interpretation much easier.Then, in the field of genomics, a new somatic variant detection tool was developed. The UMI-VarCal tool is a UMI-based variant caller that implements a UMI analysis to efficiently call the variants in tumor samples. The utility of using the information from the UMI is highlighted by the improved accuracy of variant detection, especially when the frequency falls below 1%. UMI-VarCal applies a Poisson test to filter out non-variant positions and then applies a UMI analysis and two complementary filters to remove false positives. UMI-VarCal has been designed in a highly optimized manner allowing it to perform its analysis while remaining more efficient than other tools in terms of variant detection and execution time.Finally, and still in the field of variant detection, a new read simulator was developed. This tool called UMI-Gen is the first read simulator capable of generating sequences with UMI. In addition, UMI-Gen is capable of inserting somatic variants (SNV) or structural variants (CNV) into the simulated files. Furthermore, by analyzing a set of normal files, it is able to estimate the background noise in these samples and reproduce it in the simulated data. These files can be used later to evaluate different variant callers, especially those implementing a UMI analysis in their algorithm
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Characterization of the heterogeneity of B-cell lymphomas and their microenvironment using innovative technologies
No full textLes lymphomes sont les 5èmes cancers les plus fréquents en France avec 22 000 cas diagnostiqués chaque année. Une grande hétérogénéité clinique et biologique existe au sein de ces tumeurs, et la classification de l’Organisation Mondiale de la Santé distingue près de 100 entités différentes. Cette catégorisation en sous-groupes a notamment été rendue possible par le développement de la génétique, permettant de scinder des entités cliniques en fonction des anomalies biologiques retrouvées. L’avènement des thérapies ciblées, ciblant un mécanisme précis de la tumeur, nécessite de disposer de biomarqueurs permettant d’identifier les patients pouvant bénéficier de ces traitements innovants, et de nombreux essais cliniques sont en cours afin de hiérarchiser l’arsenal thérapeutique.Dans ce contexte, il est essentiel de disposer d’outils performants afin de caractériser ces tumeurs. Ce manuscrit présente l’état de l’art de la classification des lymphomes B, des premières descriptions histologiques aux dernières classifications moléculaires. Le développement de nouveaux tests diagnostiques et pronostiques basés sur la RT-MLPA mis au point lors de ce travail de thèse sera décrit, permettant à la fois l’étude exhaustive de plusieurs dizaines de marqueurs d’intérêt et une proposition diagnostique par un algorithme dédié entrainé sur des centaines de cas.Le lymphome folliculaire est le lymphome indolent le plus fréquent. Depuis l’utilisation de l’immunothérapie par anti-CD20, une rémission prolongée est obtenue dans la majorité des cas, cependant les rechutes sont fréquentes et peuvent se produire selon des intervalles de temps très variables. Au cours de ce travail, les répertoires d’immunoglobulines B et T ont été étudiés sur des échantillons tumoraux au diagnostic et à la rechute par une technique couplant 5’-RACE et séquençage haut-débit, permettant une meilleure compréhension des mécanismes d’évolution tumorale au cours du temps.Les outils développés pendant ce travail illustrent l’intérêt des techniques innovantes associant génétique et algorithmique afin de mieux caractériser ces tumeurs complexes..Lymphomas are the 5th most common cancer in France with approximately 22,000 new cases diagnosed each year. There is a considerable clinical and biological heterogeneity in these tumors, and the latest classification of the World Health Organization distinguishes nearly 100 different entities. This categorization into subgroups has been made possible by the development of genetics, allowing clinical entities to be divided according to the biological abnormalities that were highlighted. With the introduction of targeted therapies, targeting a precise mechanism of the tumor, requires biomarkers to identify patients who can benefit from these innovative treatments, and many clinical trials are ongoing to prioritize the therapeutic arsenal.In this context, it is essential to have efficient tools to characterize these tumors. This manuscript presents the state of the art of B-cell lymphoma classification, from the first histological descriptions to the latest molecular classifications. The development of new diagnostic and prognostic tests based on RT-MLPA and developed during this thesis is described in this manuscript, allowing both the exhaustive study of several dozen markers of interest and a diagnostic proposal by a dedicated algorithm trained on hundreds of cases.Follicular lymphoma is the most frequent indolent lymphoma. Since the use of anti-CD20 immunotherapy, a prolonged remission is achieved in the majority of cases, however relapses are frequent and can occur at very variable time intervals. In this manuscript, immunoglobulin B and T repertoires were studied on tumor samples at diagnosis and at relapse by a simple and reliable technique based on 5'-RACE, allowing a better understanding of tumor evolution mechanisms over time.The tools developed during this work illustrate the interest of innovative techniques combining molecular biology and algorithmic to better characterize these complex tumors
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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