1,721,019 research outputs found
Disentangling ecological networks in marine microbes
Get PDFThere is a myriad of microorganisms on Earth contributing to global biogeochemical cycles, and their interactions are considered pivotal for ecosystem function. Previous studies have already determined relationships between a limited number of microorganisms. Yet, we still need to understand a large number of interactions to increase our knowledge of complex microbiomes. This is challenging because of the vast number of possible interactions. Thus, microbial interactions still remain barely known to date. Networks are a great tool to handle the vast number of microorganisms and their connections, explore potential microbial interactions, and elucidate patterns of microbial ecosystems.
This thesis locates at the intersection of network inference and network analysis. The presented methodology aims to support and advance marine microbial investigations by reducing noise and elucidating patterns in inferred association networks for subsequent biological down-stream analyses. This thesis’s main contribution to marine microbial interactions studies is the development of the program EnDED (Environmentally-Driven Edge Detection), a computational framework to identify environmentally-driven associations inside microbial association networks, inferred from omics datasets. We applied the methodology to a model marine microbial ecosystem at the Blanes Bay Microbial Observatory (BBMO) in the North-Western Mediterranean Sea (ten years of monthly sampling). We also applied the methodology to a dataset compilation covering six global-ocean regions from the surface (3 m) to the deep ocean (down to 4539 m). Thus, our methodology provided a step towards studying the marine microbial distribution in space via the horizontal (ocean regions) and vertical (water column) axes.Hi ha una infinitat de microorganismes a la Terra que contribueixen als cicles biogeoquímics mundials i les seves interaccions es consideren fonamentals pel funcionament dels ecosistemes. Estudis previs ja han determinat les relacions entre un nombre limitat de microorganismes. Tot i això, encara hem d’entendre un gran nombre d’interaccions per augmentar el nostre coneixement dels microbiomes complexos. Això és un repte a causa del gran nombre d'interaccions possibles. Per això, les interaccions microbianes encara són poc conegudes fins ara. Les xarxes són una gran eina per tractar el gran nombre de microorganismes i les seves connexions, explorar interaccions microbianes potencials i dilucidar patrons d’ecosistemes microbians. Aquesta tesi es situa a la intersecció de la inferència de xarxes i l’anàlisi de la xarxes. La metodologia presentada té com a objectiu donar suport i avançar en investigacions microbianes marines reduint el soroll i dilucidant patrons en xarxes d’associació inferides per a posteriors anàlisis biològiques. La principal contribució d’aquesta tesi als estudis d’interaccions microbianes marines és el desenvolupament del programa EnDED (Environmentally-Driven Edge Detection), un marc computacional per identificar associacions impulsades pel medi ambient dins de xarxes d’associació microbiana, inferides a partir de conjunts de dades òmics. S’ha aplicat la metodologia a un model d’ecosistema microbià marí a l’Observatori Microbià de la Badia de Blanes (BBMO) al mar Mediterrani nord-occidental (deu anys de mostreig mensual). També s’ha la metodologia a una recopilació de dades que cobreix sis regions oceàniques globals des de la superfície (3 m) fins a l'oceà profund (fins a 4539 m).Hay una gran cantidad de microorganismos en la Tierra que contribuyen a los ciclos biogeoquímicos globales, y sus interacciones se consideran fundamentales para la función del ecosistema. Estudios previos ya han determinado relaciones entre un número limitado de microorganismos. Sin embargo, todavía necesitamos comprender una gran cantidad de interacciones para aumentar nuestro conocimiento de los microbiomas más complejos. Esto representa un gran desafío debido a la gran cantidad de posibles interacciones. Por lo tanto, las interacciones microbianas son aun poco conocidas. Las redes representan una gran herramienta para analizar la gran cantidad de microorganismos y sus conexiones, explorar posibles interacciones y dilucidar patrones en ecosistemas microbianos. Esta tesis se ubica en la intersección entre la inferencia de redes y el análisis de redes. La metodología presentada tiene como objetivo avanzar las investigaciones sobre interacciones microbianas marinas mediante la reducción del ruido en las inferencias de redes y elucidar patrones en redes de asociación permitiendo análisis biológicos posteriores. La principal contribución de esta tesis a los estudios de interacciones microbianas marinas es el desarrollo del programa EnDED (Environmentally-Driven Edge Detection), un marco computacional para identificar asociaciones generadas por el medio ambiente en redes de asociaciones microbianas, inferidas a partir de datos ómicos. Aplicamos la metodología a un modelo de ecosistema microbiano marino en el Observatorio Microbiano de la Bahía de Blanes (BBMO) en el Mar Mediterráneo Noroccidental (diez años de muestreo mensual). También, aplicamos la metodología a una compilación de conjuntos de datos que cubren seis regiones oceánicas globales desde la superficie (3 m) hasta las profundidades del océano (hasta 4539 m). Por lo tanto, nuestra metodología significa un paso adelante hacia de los patrones temporales microbianos marinos y el estudio de la distribución microbiana marina en el espacio a través de los ejes horizontal (regiones oceánicas) y vertical (columna de agua). Para llegar a hipótesis de interacción precisas, es importante determinar, cuantificar y eliminar las asociaciones generadas por el medio ambiente en las redes de asociaciones microbianas marinas. Además, nuestros resultados subrayaron la necesidad de estudiar la naturaleza dinámica de las redes, en contraste con el uso de redes estáticas únicas agregadas en el tiempo o el espacio. Nuestras nuevas metodologías pueden ser utilizadas por una amplia gama de investigadores que investigan redes e interacciones en diversos microbiomas.Matemàtica aplicadaDOCTORAT EN MATEMÀTICA APLICADA (Pla 2012
RDC National Data Services Summit 2017: Enabling data sharing in the Netherlands
No full textDescription of national data services in the Netherlands. One of a series of presentations delivered at the 2017 Research Data Canada National Data Services Summit
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
A missing link? Connecting data and dissertations in the Netherlands
No full textA doctoral thesis contains by definition ground-breaking new scientific work that expands the current knowledge of a research field. While the importance of guarding and sharing this knowledge is usually well recognized, there are challenges when it comes to finding and accessing research data resulting from dissertations. This poster presentation will focus on the problem of the (often) missing link between a PhD thesis and related data sets. Taking the Netherlands as a use case, we will illustrate the current situation and demonstrate possible ways in which this issue can be overcome. We would like to sketch the current situation in the Netherlands and propose a set of action steps that will to bring us closer to consistent linking of data and dissertations, thereby unlocking the “hidden treasures” of Dutch PhD theses. Of course, a similar approach can be followed elsewhere. The topic of linking data and dissertations will be an interesting feature of the conference, because this linkage will enable the re-use, re-combination and re-purposing of dissertation data. The topic is particularly suited to a poster session because it is relatively well defined, ‘small’ and easy to depict in a poster. Because of these features it will also catch delegates' attention. The Dutch case will show the challenges and possibilities and will inspire others to consider the situation in their own countries
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
The Perceived Value of Acquiring Data Seals of Approval
No full textThe Data Seal of Approval (DSA) is one of the most widely used standards for Trusted Digital Repositories to date. Those who developed this standard have articulated seven main benefits of acquiring DSAs: 1) stakeholder confidence, 2) improvements in communication, 3) improvement in processes, 4) transparency, 5) differentiation from others, 6) awareness raising about digital preservation, and 7) less labor- and time-intensive. Little research has focused on if and how those who have acquired DSAs actually perceive these benefits. Consequently, this study examines the benefits of acquiring DSAs from the point of view of those who have them. In a series of 15 semi-structured interviews with representatives from 16 different organizations, participants described the benefits of having DSAs in their own words. Our findings suggest that participants experience all of the seven benefits that those who developed the standard promised. Additionally, our findings reflect the greater importance of some of those benefits compared to others. For example, participants mentioned the benefits of stakeholder confidence, transparency, improvement in processes and awareness raising about digital preservation more frequently than they discussed less labor- and time-intensive (e.g. it being less labor- and time-intensive to acquire DSAs than becoming certified by other standards), improvements in communication, and differentiation from others. Participants also mentioned two additional benefits of acquiring DSAs that are not explicitly listed on the DSA website that were very important to them: 1) the impact of acquiring the DSA on documentation of their workflows, and 2) assurance that they were following best practice. Implications and future directions for research are discussed
CoreTrustSeal certification: the what, the why and the how
No full textRDA Europe Workshop
Data Stewardship Realized: From Planning to Action
Vienna, 23 November 201
FAIR-IMPACT in a nutshell
No full text23 slides.-- Presentation delivered within Session 3 "EOSC-related projects"FAIR-IMPACT is a DANS-led EU-funded project to develop a web of FAIR data and services, including publications and software. The results of a survey of the European Research Data Landscape are presented showing moderate awareness of FAIR data and associated practices among European researchers. FAIR-IMPACT partially builds on the previous FAIRsFAIR project (2019-2022) to expand FAIR solutions across Europe. Six of the 28 FAIR-IMPACT project partners are also members of the FAIRCORE4EOSC project consortium, which ensures a close collaboration between both projects, among other mechanisms via a technical bridging team. The presentation explains the project activities aimed at meeting the overall FAIR-IMPACT project to realise a FAIR EOSC by supporting the implementation of FAIR-enabling practices across scientific communities and research outputs at a European, national and institutional levels
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