1,721,211 research outputs found
Resolving the scales of plankton ecology and biogeochemical fluxes with the Underwater Vision Profiler
No full textThe Underwater Vision Profiler (UVP) has been developed to study the number, size and shape of particles (size > 80µm) and plankton (size > 700µm) in situ. Over the last decade, thousands of profiles have been collected in the world's oceans by the UVP5 to better understand and quantify processes affecting community compositions of large plankton and the biological carbon pump. These data, used together with modeling approaches helped estimate plankton global carbon biomass and particle vertical flux. The most recent UVP (UVP6) sensors have been developed to be mounted on autonomous platforms, mooring and CTD rosettes down to 6000 m depth. Fully inter-calibrated, they record particles and identify plankton and marine snow after recovery or during deployment using an embedded recognition algorithm. A complete software ecosystem is used to pilot the instrument, record the data, and make them available to fulfill the global need of easy data access expressed by scientists, policy makers and the public. Because of the cost reduction of the UVP6, its capability to be mounted on many platforms including autonomous ones, the Ocean is being quickly populated by this sensor (125 sensors have been in operation in the last 2 years). Recent plankton community composition, particle mass, and flux data from three different basins in the Atlantic will be presented. In the next decade, the massive global monitoring of these key biological Essential Oceanographic Variables will significantly advance our understanding of key aquatic processes including the biological carbon pump
Export and lateral advection of organic matter within the biological carbon pump
No full textThe biological carbon pump (BCP) exports organic carbon from the surface to the deep ocean through which it drives the oceanic carbon storage of atmospheric CO2. The majority of this exported carbon is mediated by sinking marine particles, which are mostly formed by primary producers i.e. phytoplankton, and detrital material including dead zoo- and phytoplankton as well as fecal pellets. The efficiency at which these marine particles are exported is largely dependent on the interplay between their degradation and the duration the particles settle through the water column. Particle and aggregate degradation is largely driven by attached microbes and zooplankton grazing, which is most prominent in the upper few hundred meters of the water column. Settling velocities of particles or aggregates are largely determined by their density and thus composition. Therefore, fast settling aggregates or particles sink more rapidly through the upper water column, which increases the carbon export efficiency. The incorporation of ballasting components, such as sediments or minerals, during particle aggregation may increase the size-specific settling velocities of the aggregates and are thus an important process for carbon export via the biological pump. The manuscripts within this dissertation focus on the impact of aggregate morphology and ballasting on settling velocities and how carbon export is mediated by slow versus fast settling aggregates. We investigated (1) the horizontal relocation of slow vs. fast settling aggregates in form of subsurface particle clouds, (2) aggregate ballasting through the incorporation of minerals which are released by melting sea-ice and (3) the role of the aggregate microstructure on settling
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Variations on the Author
Full text link“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
Full text linkWe 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
Diversity, biogeography and ecology of the Collodaria (Radiolaria) in the global ocean
No full textLes Collodaires (Radiolaires) sont des eucaryotes unicellulaires (protistes) marins appartenant au super-groupe des Rhizaria. Tandis que certains sont caractérisés par un mode de vie colonial, d’autres sont observés sous la forme de larges organismes solitaires. Les Collodaires sont des protistes hétérotrophes, prédateurs de plancton, mais également hôtes systématiques de micro-algues photosynthétiques intracellulaires. Les récentes analyses de leur diversité moléculaire dans l’environnement ont démontré leur importante contribution aux communautés planctoniques ainsi que leur distribution globale dans l’océan mondial. Cependant, nos connaissances sur leur diversité, biogéographie et écologie restent paradoxalement parcellaires. La première partie de cette thèse a été dédiée à des études morphologiques détaillées (en microscopie électronique et optique) et combinées à une phylogénie moléculaire élaborée en séquençant les sous-unités 18S et 28S de l’ADN ribosomal pour 75 spécimens, coloniaux ou solitaires. Ce travail a abouti à la réévaluation de la classification des Collodaires et à l’élaboration d’une base de référence morpho-moléculaire robuste. Par la suite, ce cadre de référence morpho-moléculaire a permis d’explorer la biodiversité des Collodaires grâce à une approche de metabarcoding appliquée à une série d’échantillons collectés dans l’océan mondial pendant l’Expédition Tara Océans. La distribution cosmopolite à la surface des océans des différents taxons qui composent les Collodaires, a révélé une diversité plus importante dans les vastes régions océaniques intertropicales et oligotrophiques. Les Collosphaeridae ont été principalement observés en pleine mer alors que les Sphaerozoidae formaient la famille dominante dans les régions côtières, où la biodiversité des Collodaires était plus faible. Les Collophidiidae, formellement décrits au cours de thèse, ont rarement été rencontrés dans les zones photiques, quelque que soit la latitude, suggérant ainsi qu’ils occupent une niche écologique particulière. Enfin, j’ai également employé la technologie d’imagerie in situ Underwater Vision Profiler (UVP5) afin d’explorer de façon quantitative les abondances et biomasses des Collodaires et des Rhizaria, à travers l’océan mondial. Cette approche a révélé que les Rhizaria forment un composant majeur du méso- et macro-plancton, et représentent jusqu’à 4,5% de la biomasse globale des 200 premiers mètres de l’océan mondial. Plus particulièrement dans les 100 premiers mètres, les Collodaires constituent le groupe le plus important des Rhizaria et leur distribution suggère que la photosymbiose pourrait influencer leur succès dans les régions oligotrophiques où ils sont particulièrement abondants. Au-delà d’améliorer notre compréhension de la diversité, la biogéographie et l’écologie des Collodaires dans l’océan mondial, ce travail de thèse souligne la pertinence de combiner et d’utiliser des approches alternatives d’échantillonnage et d’analyses tel que le séquençage haut-débit et l’imagerie in situ dans l’étude des protistes marins dans leur environnement.Collodaria (Radiolaria) are unicellular marine eukaryotes (protists) belonging to the super-group Rhizaria. Collodarian species contribute to planktonic communities as large solitary cells or can form large gelatinous colonies. They are heterotrophic organisms feeding on other plankton, which also systematically harbour intracellular symbiotic microalgae. Recent environmental molecular diversity surveys demonstrated their important contribution to planktonic communities and their worldwide occurrence in the global ocean. However, knowledge on their diversity, biogeography and ecology is paradoxically very poor. In the first part of this thesis I performed detailed morphological analyses (electron and optical microscopy) combined with a molecular phylogeny based on the 18S and 28S rRNA genes, sequencing for a total of 75 distinct colonial and solitary specimens. Ultimately, this work led to the revision of the Collodaria classification and to the construction of a robust morpho-molecular reference database. Then, this morpho-molecular framework allowed the exploration of Collodaria biodiversity through a metabarcoding approach across samples collected in the global ocean during the Tara Ocean expedition. The cosmopolitan distribution of the different collodarian taxa in the surface oceans revealed a higher biodiversity in the vast oligotrophic inter-tropical open oceans. Collosphaeridae were predominantly found in the open oceans while the Sphaerozoidae were the dominant family in the less diverse coastal regions. The newly defined Collophidiidae were rarely encountered in the photic zones at all latitudes, suggesting that they inhabit a different ecological niche. Finally, I also used the in situ imaging system Underwater Vision Profiler (UVP5) to quantitatively explore the abundances and biomasses of collodarian and rhizarian in the global ocean. This approach revealed that the Rhizaria were a major component of the meso- and macro-plankton, constituting up to 4.5% of the global carbon standing stock in the upper 200 m of the world oceans. More specifically, Collodaria were the most important rhizarian groups in the first 100 m of the oceans, and their distribution suggested that photosymbiosis might be an important factor explaining their success in oligotrophic regions where they are particularly abundant. Besides the improvement of our knowledge on the diversity, biogeography and ecology of Collodaria in the global ocean, this thesis highlights the relevance to combine and/or use alternative sampling and analytical procedures such as high-throughput sequencing and in situ imaging technologies to study marine protists in their environment
Image-based global analysis of the biological carbon pump
No full textLa pompe à carbone biologique (PCB) joue un rôle central dans le cycle global du carbone océanique, en transportant le carbone de la surface vers les profondeurs et en le séquestrant pendant de longues périodes. Ce travail vise à analyser deux acteurs clés de la PCB : le zooplancton et les particules. Pour cela, nous utilisons les données d'imagerie in situ de l'Underwater Vision Profiler (UVP5) pour étudier deux axes principaux : 1) la distribution globale de la biomasse du zooplancton et 2) l'exportation de carbone dans le contexte d'une efflorescence printanière dans l'Atlantique Nord. À l'aide de l'UVP5 et de l'apprentissage automatique par le biais de modèles d'habitat utilisant des arbres de régression boostés, nous étudions la distribution mondiale de la biomasse du zooplancton et ses implications écologiques. Les résultats montrent des valeurs maximales de biomasse autour de 60°N et 55°S et des valeurs minimales au niveau des gyres océaniques, avec une biomasse globale dominée par les crustacés et les rhizaires. En utilisant des techniques d'apprentissage automatique sur des données globalement homogènes, cette étude fournit des informations sur la distribution de 19 grands groupes de zooplancton (1-50 mm de diamètre sphérique équivalent). Ce premier protocole permet d'estimer la biomasse du zooplancton et la composition de la communauté à l'échelle globale à partir d'observations d'imagerie in situ d'organismes individuels. Dans le contexte unique de la campagne EXPORTS 2021, nous analysons les données UVP5 obtenues par le déploiement de trois instruments dans un tourbillon à forte rétention. Après avoir regroupé les 1 720 914 images à l'aide de Morphocluster, un logiciel de classification semi-autonome, nous nous intéressons aux caractéristiques des particules marines, en étudiant leur morphologie à travers un cadre oblique qui suit un panache de particules entre la surface et 800 m. Les résultats montrent que, contrairement aux attentes, les agrégats deviennent de manière inattendue plus grands, plus denses, plus circulaires et plus complexes avec la profondeur. En revanche, l'évolution des pelottes fécales est plus hétérogène et façonnée par l'activité du zooplancton. Ces résultats remettent en question les attentes antérieures et appellent à une réévaluation de notre vision des agrégats et des pelottes fécales. Nous avons également étudié la dynamique des concentrations et des flux de carbone à l'aide d'un cadre 1D plus traditionnel dans lequel nous explorons les trois éléments clés de l'estimation des flux à partir d'imagerie in situ en comparant les estimations de l'UVP5 et des pièges à sédiments: la gamme de tailles couvertes, la vitesse de sédimentation et le contenu en carbone. Selon la littérature, les pièges à sédiments à flottabilité neutre (NBST) et les pièges attachés à la surface (STT) couvrent généralement une gamme de tailles allant de 10 µm à environ 2 mm. Dans notre étude, nous avons constaté qu'en élargissant la gamme de tailles de l'UVP5 à 10 µm et en la limitant à 2 mm, une comparaison plus consistante peut être faite entre le flux issu de l'UVP5 et celui des pièges à sédiments (obtenus par des collègues). Toutefois, il reste une contribution importante du flux au-dessus de ce seuil de taille qui nécessite une étude plus approfondie de ses implications par l'utilisation d'approches complémentaires telles que des pièges à sédiments avec des ouvertures plus grandes. Ce manuscrit ne fait pas seulement progresser nos connaissances, mais il aborde également des défis critiques dans l'estimation de la biomasse du zooplancton et de la dynamique des particules pendant les événements d'export. Les résultats de cette étude ouvrent de nouvelles voies pour la recherche future sur la PCB et approfondissent notre compréhension des écosystèmes marins.The biological carbon pump (BCP) plays a central role in the global ocean carbon cycle, transporting carbon from the surface to the deep ocean and sequestering it for long periods. This work aims to analyse two key players of the BCP: zooplankton and particles. To this end, we use in situ imaging data from the Underwater Vision Profiler (UVP5) to investigate two primary axes: 1) the global distribution of zooplankton biomass and 2) carbon export in the context of a North Atlantic spring bloom. Our objectives includes a quantification of global zooplankton biomass, enhancing our comprehension of the BCP via morphological analysis of particles, and assessing and comparing the gravitational flux of detrital particles during a the North Atlantic spring bloom using high-resolution UVP5 data. With the help of UVP5 imagery and machine learning through habitat models using boosted regression trees, we investigate the global distribution of zooplankton biomass and its ecological implications. The results show maximum zooplankton biomass values around 60°N and 55°S and minimum values within the oceanic gyres, with a global biomass dominated by crustaceans and rhizarians. By employing machine learning techniques on globally homogeneous data, this study provides taxonomical insights into the distribution of 19 large zooplankton groups (1-50 mm equivalent spherical diameter). This first protocol estimates global, spatially resolved zooplankton biomass and community composition from in situ imaging observations of individual organisms. In addition, within the unique context of the EXPORTS 2021 campaign, we analyse UVP5 data obtained by deploying three instruments in a highly retentive eddy. After clustering the 1,720,914 images using Morphocluster, a semi-autonomous classification software, we delve into the characteristics of the marine particles, studying their morphology through an oblique framework that follows a plume of detrital particles between the surface and 800 m depth. The results of the plume following approach show that, contrary to expectations, aggregates become unexpectedly larger, denser, more circular and more complex with depth. In contrast, the evolution of fecal pellets is more heterogeneous and shaped by zooplankton activity. Such results challenge previous expectations and may require a reassessment of our view of sinking aggregates and fecal pellets. We also studied concentration and carbon flux dynamics using a more traditional 1D framework where we explore the three key elements in flux estimation from in situ imaging data by comparing UVP5 and sediment trap flux estimates: size range covered, sinking rate and carbon content. According to the current literature, neutrally buoyant sediment traps (NBST) and surface-tethered traps (STT) usually cover a size range from 10 µm to approximately 2 mm. In our study, we have found that by expanding the UVP size range to 10 µm and limiting it to 2 mm, a more consistent comparison can be made between UVP5-generated flux and sediment trap fluxes (obtained by colleagues). However, it is worth noting that there remains a large flux contribution above this size threshold, necessitating further investigation of its implications through the use of complementary approaches such as the use of sediment traps with larger openings. This manuscript not only advances our knowledge, but also addresses critical challenges in estimating zooplankton biomass and particle dynamics during export events. The findings of this study open up new avenues for future research on the biological carbon pump and deepen our understanding of marine ecosystems
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe 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
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