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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
Epidemiology and human genetics of Buruli ulcer
No full textL'ulcère de Buruli (UB), infection à Mycobacterium ulcerans, troisième mycobactériose mondiale, connait une émergence rapide depuis 1980, essentiellement dans les pays d'Afrique subsaharienne. Jusqu’ici, les connaissances épidémiologiques sur l’UB étaient fondées sur des séries de cas cliniques non confirmés par laboratoire. Nous avons constitué la plus grande cohorte de cas confirmés à ce jour rassemblant plus de 1200 patients traités au CDTUB de Pobè au Bénin entre 2005 et 2011, afin de décrire l'épidémiologie clinique de la maladie et d'explorer l’architecture génétique de la susceptibilité à cette maladie. Les patients atteints d’UB sont des enfants (âge médian au diagnostic de 12 ans), présentant une lésion unique (96%), large (plus de 15 cm, 36%), ulcérative (66%) du membre inférieur (60%). Nous rapportons une présentation clinique atypique de l’UB, dans laquelle les patients présentent exclusivement une ostéomyélite à M. ulcerans. Le sex-ratio varie avec l’âge : les garçons sont majoritaires parmi les enfants (57% de patients masculins chez les moins de 15 ans), et les femmes parmi les adultes (33% de patients masculins). La présentation clinique dépend de l’âge et du sexe. 9% des patients masculins ont présenté une ostéomyélite contre 4% des patients féminins. Un an après la fin du traitement, 22% des patients présentent des séquelles fonctionnelles fixées. Une présentation clinique comportant une lésion oedémateuse, osseuse, de grande taille ou plusieurs lésions est significativement associée avec le développement de séquelles fonctionnelles (OR 7.64, IC95% [5.29-11.31]). Les patients coinfectés par le VIH ont un risque significativement plus élevé de développer un UB sévère (OR 2.77, IC95% [1.32-6.33]). Nous avons exploré l’architecture génétique de la susceptibilité à l’UB dans une perspective mendélienne et une perspective complexe. Le cas le plus sévère de la maladie observé dans ce centre appartient à une famille consanguine dans laquelle la ségrégation du phénotype suggère un défaut génétique mendélien récessif. Une analyse de liaison génétique par cartographie d'homozygotie suggère l’implication du locus des béta-défensines sur le chromosome 8 dans la pathogénèse de l'UB, et mène à l’identification d’une délétion homozygote ségrégeant parfaitement avec la maladie. Dans une perspective complexe, une étude d’association pangénomique a été réalisée après génotypage d’une cohorte de 400 cas et 400 témoins exposés sur plus de 2 millions de SNPs par la puce Illumina Omni2.5 et a permis l’identification de nombreux signaux d’intérêt. L’étude de réplication est en cours. La compréhension de la physiopathologie de l'infection à M. ulcerans est cruciale pour générer de nouvelles pistes thérapeutiques et vaccinales. La dissection du contrôle génétique de l'infection par l'hôte est en ce sens indispensable.Buruli ulcer (BU), caused by Mycobacterium ulcerans, is the third most frequent mycobacteriosis worldwide. It has been rapidly emerging in sub-Saharan African countries since 1980. Until now, knowledge of BU epidemiology relied on series of non laboratory-confirmed clinical cases. From 2005-2011, we recruited the current largest cohort of laboratory-confirmed cases (more than 1,200 patients) at the Pobe CDTUB, Benin, to describe the clinical epidemiology of the disease and to explore the genetic architecture of human susceptibility to BU. Typically, patients with BU were children (median age at diagnosis 12 years) presenting with a unique (96%) large (≥15 cm, 36%) ulcerative (66%) lesion of the lower limb (60%). Atypical clinical presentation of BU included osteomyelitis with no identifiable present or past BU skin lesions. The sex ratio of BU widely varied with age, with male patients accounting for 57% of patients aged 15 years and younger, but only 33% of those older than 15 years. Clinical presentation of BU was significantly dependent on age and sex. 9% male patients had BU osteomyelitis, whereas only 4% of female patients did. 1 year after treatment, 22% of patients with follow-up information presented with permanent functional sequelae. Presentation with oedema, osteomyelitis, or large (≥15 cm in diameter), or multifocal lesions was significantly associated with occurrence of permanent functional sequelae (OR 7•64, 95% CI 5•29–11•31) and operationally defines severe BU. When coinfected with HIV, patients had a significantly higher risk to develop severe BU (OR 2.77, IC95% [1.32-6.33]). We explored the genetic architecture of susceptibility to BU in both mendelian and complex genetic frameworks. The most severe case of the disease to have been treated at the Pobe CDTUB belonged to a consanguineous family in which the segregation of the phenotype was indicative of a recessive mendelian genetic defect. Genetic linkage analysis by homozygosity mapping suggested the implication of the beta-defensin locus on chromosome 8 in BU pathogenesis and lead to the identification of a homozygous deletion, which co-segregated perfectly with the disease in the family. In a complex genetics approach, we undertook a genome-wide association study, which involved the genotyping of more than 2 million SNPs (Illumina Omni2.5) in a cohort of 400 cases and 400 exposed controls. We identified many signals of interest. The replication study is ongoing. Understanding BU physiopathology is crucial to the development of efficient vaccines and drugs. Dissection of the genetic control of the infection by M. ulcerans by its human host therefore constitutes an indispensable step
Human genetics of leprosy in Vietnam : a family affair
No full textLa lèpre, maladie infectieuse chronique causée par Mycobacterium leprae, affecte principalement la peau, les nerfs et les yeux avec des séquelles majeures en l’absence de traitement. Avec 200 000 nouveaux cas diagnostiqués chaque année (1 toutes les 2 minutes), il s’agit de la mycobactériose la plus commune après la tuberculose et requalifiée « maladie tropicale négligée » en 2017 par l’Organisation Mondiale de la Santé (OMS). Si la contribution génétique de l’hôte dans l’histoire naturelle de la maladie est maintenant bien établie, son architecture reste lacunaire. Dans cette continuité et afin de la préciser, nous avons, pour la première fois, utilisé une approche de génétique épidémiologique familiale. Plus précisément, nous avons réalisé la première étude d’association pangénomique (Genome-Wide Association Study, GWAS) familiale sur la lèpre. Ainsi, au cours des 20 dernières années, un échantillon de 481 familles nucléaires, parents et enfants, sélectionnées à partir d’un enfant atteint, a été constitué au Vietnam. Sur cet échantillon primaire de 1749 individus incluant 622 enfants atteints, nous avons testé l’association de près de 6 millions de variants bi-alléliques (Single Nucleotide Polymorphism, SNP), génotypés ou imputés, avec la lèpre. Dans un second temps, nous avons testé les signaux les plus prometteurs dans un échantillon de réplication, c’est-à-dire, indépendant et issu de la même population, constitué de 1 181 cas et 668 contrôles. Les résultats les plus significatifs ont été observés au sein de la région HLA et l’analyse multivariée a permis d’identifier trois signaux indépendants. Deux dans la région HLA classe I : rs1265048 [Odds-ratio (OR) = 0,69 ; p-val = 5,5.10⁻¹¹] et rs114598080 [OR = 1,47 ; p-val = 8,8.10⁻¹³] ; Et un dans la région HLA classe II : rs3187964 [OR = 1,67 ; p-val = 8,4.10⁻¹⁶]. Nous avons également identifié deux signaux hors HLA : un variant faux-sens dans le gène LACC1 (rs3764147 : OR = 1,52 ; p-val = 5,1.10⁻¹⁴), et un variant à proximité du gène IL12B (rs6871626 : OR = 0,73 ; p-val = 6.4.10⁻⁸). Les contraintes de coûts des études pangénomiques imposent une réduction majeure du nombre de SNPs à tester dans d’autres échantillons. Dans les études familiales, les parents sont de fait génotypés et pourraient permettre une réplication immédiate sans coûts ajoutés. Au moyen d’une large étude de simulation, nous avons montré que cette approche était pertinente. Une étude cas-contrôle chez les parents de l’échantillon primaire est une réplication valide, statistiquement indépendante de l’étude d’association familiale. C’est un argument fort en faveur des approches familiales pour l’exploration pangénomique de la contribution génétique de l’hôte dans les phénotypes complexes. La compréhension de la physiopathologie de l'infection à M. leprae est cruciale pour optimiser les approches préventives selon les profils génétiques à plus haut risque, et ouvrir de nouvelles pistes thérapeutiques en précisant les cascades fonctionnelles pertinentes. En ce sens, la dissection du contrôle génétique de l'infection par l'hôte est indispensable. Enfin, remettre la famille au cœur de la quête génétique, c’est remettre la génétique dans son milieu naturel.Leprosy is a chronic infectious disease caused by Mycobacterium leprae. It primarily affects the skin and peripheral nerves, and can cause an irreversible impairment of nerve function, often leading to severe disabilities and social stigma if left untreated. The disease, re-qualified by WHO (World Health Organization) as a “Neglected Tropical Disease” in 2017, remains a major public health problem in regions of endemic countries, with over 200,000 new cases per year (one every two minutes). It is ranked second as the most common mycobacterial infectious disease, right after tuberculosis. While it has been well established that there is a genetic contribution to this disease, the underlying genetic causes remains unknown. In our study, we sought to reveal the host´s genetic architecture of leprosy by taking of a familial epidemiological approach. We conducted the first Family-Based Genome-Wide Association Study (GWAS) of leprosy in 481 Vietnamese nuclear families (parents and children) selected based on one affected child and collected over the past 20 years. Using this sample of 1,749 individuals, including 622 affected offspring, we performed association tests between six million biallelic genetic variants (Single-Nucleotide Polymorphism, genotyped or imputed) and the binary phenotype of disease status. Following this first analysis, we conducted a replication analysis of the most promising results in an independent sample of the same ethnic origin, accounting for 1,181 cases and 668 controls. The most significant results were observed within the HLA (Human Leukocyte Antigen) region, in which 3 independent SNPs displayed genome-wide significant associations. Among these, two were for the HLA class I region and one for the HLA class II (rs1265048 [OR = 0.69; p-value = 5.5x10⁻¹¹], rs114598080 [OR = 1.47; p-value = 8.8x10⁻¹³] and rs3187964 [OR = 1.67; p-value = 8.4x10⁻¹⁶] respectively). We also identified a missense variant in the LACC1 gene (rs3764147: OR = 1.52; p-value = 5.1x10⁻¹⁴) and an intergenic variant located close to the IL12B gene (rs6871626: OR = 0.73; p-value = 6.4x10⁻⁸). LACC1 encodes a central regulator of the metabolic function and bioenergetic state of macrophages and IL12B encodes IL-12p40, which is common to two interleukins, IL-12 and IL-23. Large GWAS are expensive, strongly limiting the number of variants to test in a replication set. Here, we took advantage of the available parental phenotypic and genotypic information to perform a classical case-control study among the parents of the family-based sample. Indeed, using of extensive computer simulations, we demonstrated that this population-based parental study is a valid, powerful and costless replication strategy to confirm family-based associations. Overall, our observations add to the attractiveness of family-based designs and should provide valuable help for investigators planning to perform GWA studies. Understanding leprosy pathophysiology infection is crucial to optimize preventive approaches based on genetic profiles. Dissection of the genetic control of the infection by M. leprae by its human host, therefore, constitutes an indispensable step. Finally, repositioning the family at the heart of the genetic quest means repositioning genetics into its natural environment
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
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
Human genetics of clinical forms of leprosy
No full textLa lèpre est une maladie tropicale négligée qui atteint près de 200 000 personnes chaque année et dont l’agent causal est Mycobacterium leprae. La susceptibilité génétique de l’hôte à la maladie est bien établie, et a permis de comprendre certains mécanismes de la physiopathologie de la maladie. Il existe par ailleurs une grande variabilité inter-individuelle des manifestions cliniquesde la maladie, qui s’étendent d’un pôle dit tuberculoïde à un pôle dit lépromateux. Nous avons cherché à identifier les facteurs de susceptibilité génétique à cette polarisation de la maladie. Nous avons tout d’abord décrit que le sexe et l’âge sont des facteurs non-génétiques associés à ce phénotype.Notre travail s’est ensuite appuyé sur les outils classiques de l’épidémiologie génétique, c’est à dire les études de liaison et d’association, pour identifier des variants génétiques qui influencent la polarisation de la lèpre. Nous avons utilisé une puce à ADN pangénomique avec plus de 500 000 marqueurs pour génotyper un échantillon de familles vietnamiennes comprenant 939 malades, dont 692 enfants. Nous avons identifié une liaison de la région 19p12 avec la polarisation de la lèpre. L’étude d’association n’a pas permis d’identifier de signal significatif à l’échelle du génome. Nous avons développé un nouveau test d’association pour des données familiales qui a permis d’améliorer les résultats sans atteindre la significativité. Notre travail sera prolongé par des études d’association dans deux populations cas-témoins du Vietnam et du Brésil. Nous chercherons à identifier les marqueurs causaux au sein de la région de liaison 19p12 d’une part, et à découvrir de nouveaux variants d’autre part. L’identification de marqueurs associés à la polarisation de la lèpre permettra de mieux prévoir l’évolution de la maladie et de proposer des traitements plus ciblés selon le risque génétique individuel.Leprosy is a neglected tropical disease that affects nearly 200,000 people each year and caused byMycobacterium leprae. Genetic host susceptibility to the disease is well established, and helped to understand some of the mechanisms of the disease’s physiopathology. There is also a wide inter-individual variability of the clinical manifestations of the disease, which runs from a so-said tuberculoid to a so-said lepromatous pole. We sought to identify genetic susceptibility factors for this polarization of the disease. We initially described gender and age as non-genetic factors associated with this phenotype. We then based our analysis on the classical tools from thefield of genetic epidemiology, namely linkage and association studies, to identify genetic variants that influence leprosy polarization. We used a DNA-microarray with 500,000 markers spanning over the whole genome to genotype a sample of Vietnamese families including 939 patients, of which 692 were children. We have found a region linked to leprosy polarization on chromosome 19p12. The association study could not identify a significant signal across the genome. We developed a new test for association designed for familial data that improved the results without reaching significance. Our work will be pursued by association studies in two case-control populations from Vietnam and Brazil. We will try to identify the causal markers within the 19p12 linkage region on the one hand, and to discover new variants on theother hand. The identification of markers associated with leprosy polarization could help us to better predict the evolution of the disease, and to offer more targeted treatments to patients, based on their individual genetic risk
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
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