1st INCF Workshop on Sustainability of Neuroscience Databases

The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability

The Evolutionary Dynamics of Discursive Knowledge

This open access book addresses three themes which have been central to Leydesdorff's research: (1) the dynamics of science, technology, and innovation; (2) the scientometric operationalization of these concept; and (3) the elaboration in terms of a Triple Helix of university-industry-government relations. In this study, I discuss the relations among these themes. Using Luhmann's social-systems theory for modelling meaning processing and Shannon's theory for information processing, I show that synergy can add new options to an innovation system as redundancy. The capacity to develop new options is more important for innovation than past performance. Entertaining a model of possible future states makes a knowledge-based system increasingly anticipatory. The trade-off between the incursion of future states on the historical developments can be measured using the Triple-Helix synergy indicator. This is shown, for example, for the Italian national and regional systems of innovation

Towards Lifelong Reasoning with Sparse and Compressive Memory Systems

Humans have a remarkable ability to remember information over long time horizons. When reading a book, we build up a compressed representation of the past narrative, such as the characters and events that have built up the story so far. We can do this even if they are separated by thousands of words from the current text, or long stretches of time between readings. During our life, we build up and retain memories that tell us where we live, what we have experienced, and who we are. Adding memory to artificial neural networks has been transformative in machine learning, allowing models to extract structure from temporal data, and more accurately model the future. However the capacity for long-range reasoning in current memory-augmented neural networks is considerably limited, in comparison to humans, despite the access to powerful modern computers. This thesis explores two prominent approaches towards scaling artificial memories to lifelong capacity: sparse access and compressive memory structures. With sparse access, the inspection, retrieval, and updating of only a very small subset of pertinent memory is considered. It is found that sparse memory access is beneficial for learning, allowing for improved data-efficiency and improved generalisation. From a computational perspective - sparsity allows scaling to memories with millions of entities on a simple CPU-based machine. It is shown that memory systems that compress the past to a smaller set of representations reduce redundancy and can speed up the learning of rare classes and improve upon classical data-structures in database systems. Compressive memory architectures are also devised for sequence prediction tasks and are observed to significantly increase the state-of-the-art in modelling natural language

Towards an engineering theory of evolution

Effective biological engineering requires the acknowledgement of evolution and its consideration during the design process. In this perspective, the authors present the concept of the evotype to reason about and shape the evolutionary potential of natural and engineered biosystems

The Community Ecology of Herbivore Regulation in an Agroecosystem: Lessons from Complex Systems

AbstractWhether an ecological community is controlled from above or below remains a popular framework that continues generating interesting research questions and takes on especially important meaning in agroecosystems. We describe the regulation from above of three coffee herbivores, a leaf herbivore (the green coffee scale, Coccus viridis), a seed predator (the coffee berry borer, Hypothenemus hampei), and a plant pathogen (the coffee rust disease, caused by Hemelia vastatrix) by various natural enemies, emphasizing the remarkable complexity involved. We emphasize the intersection of this classical question of ecology with the burgeoning field of complex systems, including references to chaos, critical transitions, hysteresis, basin or boundary collision, and spatial self-organization, all aimed at the applied question of pest control in the coffee agroecosystem

Deficiency of annexins A5 and A6 induces complex changes in the transcriptome of growth plate cartilage but does not inhibit the induction of mineralization

Initiation of mineralization during endochondral ossification is a multistep process and has been assumed to correlate with specific interactions of annexins A5 and A6 and collagens. However, skeletal development appears to be normal in mice deficient for either A5 or A6, and the highly conserved structures led to the assumption that A5 and A6 may fulfill redundant functions. We have now generated mice deficient of both proteins. These mice were viable and fertile and showed no obvious abnormalities. Assessment of skeletal elements using histologic, ultrastructural, and peripheral quantitative computed tomographic methods revealed that mineralization and development of the skeleton were not significantly affected in mutant mice. Otherwise, global gene expression analysis showed subtle changes at the transcriptome level of genes involved in cell growth and intermediate metabolism. These results indicate that annexins A5 and A6 may not represent the essential annexins that promote mineralization in vivo

Ecological indicators as tools to monitor the effects of climate change on Tropical dry forest

As terras secas (hiper-áridas, áridas, semi-áridas e sub-húmidas secas) cobrem cerca de 47% do globo terrestre e abrigam cerca de 39% da população mundial. Ocorrem maioritariamente em países menos desenvolvidos, mais pobres e altamente dependentes dos recursos naturais. A necessidade de antecipar os impactos das alterações climáticas nas terras secas é indiscutível devido à sua alta vulnerabilidade a alterações climáticas e ambientais (tendo como consequência a desertificação), já que ambas constituem importantes ameaças para a biodiversidade e para a prestação de serviços de ecossistema essenciais para o bem-estar humano. Métricas de diversidade (taxonómicas e funcionais) são usadas de forma complementar para monitorizar a resposta dos ecossistemas ao clima. Assim, o principal objetivo desta tese é identificar potenciais indicadores ecológicos, baseados métricas taxonómicas e funcionais, que possam ser usados como ferramentas para monitorizar os efeitos das alterações climáticas na Floresta tropical seca. A Caatinga, um dos ecossistemas mais diversos das Florestas Neotropicais sazonalmente secas, mas também dos mais vulneráveis às alterações climáticas no Brasil foi a área estudada. O índice de aridez foi considerado uma variável adequada para avaliar os efeitos das alterações climáticas na vegetação. Para este estudo, utilizamos um banco de dados muito rico com informações sobre a ocorrência de cerca de 1 000 espécies de plantas neste ecossistema, obtida a partir de dados provenientes de diferentes fontes, recolhidos com diferentes metodologias e esforços de amostragem no espaço e ao longo do tempo. Aplicando uma metodologia de reamostragem, a abundância de espécies de plantas foi estimada ao longo de um gradiente espacial de clima. Tais informações são essenciais para avaliar a resposta das métricas de diversidade, especialmente aquelas que requerem dados de abundância, como métricas funcionais. Foram estudadas 13 características funcionais da planta (CFP), que determinam as respostas das espécies ao meio ambiente e permitem avaliar a resposta das métricas ao clima. Das 13 CFP estudadas, oito responderam à aridez, que por sua vez afetou a estrutura funcional da vegetação da Caatinga. A análise de agrupamento com base nos 13 CFP foi usada para agrupar espécies em sete grupos funcionais principais que respondem à aridez. Os grupos caracterizados pela presença de defesas químicas e via fotossintética CAM (metabolismo ácido das crassuláceas) foram aqueles cuja abundância relativa aumentou mais com o aumento da aridez. Assim, estes foram propostos como indicadores ecológicos para rastrear os efeitos a aridez na estrutura funcional da comunidade vegetal. Com base nos resultados descritos anteriormente, foi feita uma análise global de métricas complementares de diversidade para avaliar a suscetibilidade da comunidade de plantas, do ponto de vista taxonómico e funcional, ao longo do gradiente de aridez. Em locais mais áridos, verificou-se uma maior diversidade funcional suportada por algumas espécies de plantas (baixa riqueza de espécies) com funções únicas, sugerindo baixa resiliência. Em contraste, locais menos áridos mostraram menor diversidade funcional, mas maior redundância funcional entre as espécies. No geral, as conclusões deste trabalho apoiam o uso de métricas complementares de diversidade vegetal como indicadores ecológicos de alerta dos impactos das mudanças climáticas no ecossistema da Caatinga. Além disso, a resposta da comunidade vegetal ao longo do gradiente espacial do clima fornece indicações sobre possíveis alterações ao longo do tempo sob um aumento da aridez global, contribuindo para melhorar as previsões sobre os efeitos das alterações climáticas. Como as projeções não são muito animadoras, é fundamental que conservemos e restauremos taxonómica e funcionalmente estas florestas secas, a fim de mitigar os impactos negativos previstos das alterações climáticas no ecossistema da Caatinga.Drylands (hyper-arid, arid, semi-arid and dry sub-humid areas) cover about 47% of global land surface and harbour about 39% of the world´s population, encompassing the least developed countries, poorest and highly dependent on natural resources. The need to anticipate the impacts of climate change on drylands is indisputable due to their high vulnerability to climate and environmental changes (leading to desertification), as both disturbances are key threats to biodiversity and to ecolosystem services delivery, essential to human well-being. Diversity metrics (taxonomic and functional) are complementarily used to monitoring ecosystems’ response to climate. With this in mind the main aim of this thesis was to identify potential ecological indicators based on both taxonomic and functional plant diversity metrics, to be used as tools to monitor the effects of climate change on Tropical dry forest. Caatinga, one of the most diverse ecosystems in Neotropical seasonally dry forests, and more vulnerable to climate change in Brazil, was used as a case study. The aridity index was considered as an adequate variable to assess the effects of climate change on vegetation. In this study, a very rich database with information on the occurrence of around 1 000 plant species in this ecosystem was used. It contained data derived from different sources, collected with different sampling methodologies and sampling efforts in space and over time. By applying a re-sampling methodology, plant species abundance was estimated along a spatial climate gradient. This information is essential to assess the response of diversity metrics, especially those that require abundance data, such as functional metrics. Thirteen plant functional traits (PFT) were studied, which determine species’ responses to the environment, and allow to assess the response of functional metrics to climate. Of the 13 PFT studied, eight responded to aridity, which affected the functional structure of Caatinga vegetation. Clustering analysis based on the 13 PFT was used to group species into seven main functional groups responding to aridity. Functional groups with the presence of chemical defense and CAM (crassulacean acid metabolism) photosynthetic pathway were those whose relative abundance increased most with increasing aridity. Thus, they were proposed as ecological indicators to track aridity effects on the plant community functional structure. Based on the previously described results, a global analysis of complementary diversity metrics was made to assess the susceptibility of the plant community, from a taxonomic and functional point of view, along the aridity gradient. In more arid sites, there was a higher functional diversity supported by a few plant species (low species richness) with unique functions, suggesting low resilience to environmental change. Contrastingly, less arid sites showed lower functional diversity but higher functional redundancy among species. Overall, this work’s findings support the use of complementary plant diversity metrics as warning ecological indicators of climate change impacts on the Caatinga ecosystem. In adition, the response of the plant community along the spatial climate gradient provides indications on how it might change over time under a global aridity increase, contributing to improve predictions on the effects of climate change. As projections are not very encouraging, it is crucial that we taxonomically and functionally conserve and restore these dry forests in order to mitigate the predicted negative impacts of climate change in the Caatinga ecosystem.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq - bolsa: 206444/2014-1)Ministério do Desenvolvimento Regional junto ao Projeto de Integração do Rio São Francisco (PISF

The Evolutionary Dynamics of Discursive Knowledge

This open access book addresses three themes which have been central to Leydesdorff's research: (1) the dynamics of science, technology, and innovation; (2) the scientometric operationalization of these concept; and (3) the elaboration in terms of a Triple Helix of university-industry-government relations. In this study, I discuss the relations among these themes. Using Luhmann's social-systems theory for modelling meaning processing and Shannon's theory for information processing, I show that synergy can add new options to an innovation system as redundancy. The capacity to develop new options is more important for innovation than past performance. Entertaining a model of possible future states makes a knowledge-based system increasingly anticipatory. The trade-off between the incursion of future states on the historical developments can be measured using the Triple-Helix synergy indicator. This is shown, for example, for the Italian national and regional systems of innovation

Spatial clarity form structural idea.

Lau Hing Ching."Architecture Department, Chinese University of Hong Kong, Master of Architecture Programme 2010-2011, design report."Includes bibliographical references (leaves 33).Prolog --- p.4Preliminary Study - Tree & Human Body --- p.5Case Studies - Christian Kerez --- p.7"""Function""" --- p.12Program --- p.13Site --- p.17Structural Idea --- p.18Museum Design --- p.20Epilogue --- p.27Appendix --- p.28Reference --- p.3

Applying Hypervisor-Based Fault Tolerance Techniques to Safety-Critical Embedded Systems

This document details the work conducted through the development of this thesis, and it is structured as follows: • Chapter 1, Introduction, has briefly presented the motivation, objectives, and contributions of this thesis. • Chapter 2, Fundamentals, exposes a series of concepts that are necessary to correctly understand the information presented in the rest of the thesis, such as the concepts of virtualization, hypervisors, or software-based fault tolerance. In addition, this chapter includes an exhaustive review and comparison between the different hypervisors used in scientific studies dealing with safety-critical systems, and a brief review of some works that try to improve fault tolerance in the hypervisor itself, an area of research that is outside the scope of this work, but that complements the mechanism presented and could be established as a line of future work. • Chapter 3, Problem Statement and Related Work, explains the main reasons why the concept of Hypervisor-Based Fault Tolerance was born and reviews the main articles and research papers on the subject. This review includes both papers related to safety-critical embedded systems (such as the research carried out in this thesis) and papers related to cloud servers and cluster computing that, although not directly applicable to embedded systems, may raise useful concepts that make our solution more complete or allow us to establish future lines of work. • Chapter 4, Proposed Solution, begins with a brief comparison of the work presented in Chapter 3 to establish the requirements that our solution must meet in order to be as complete and innovative as possible. It then sets out the architecture of the proposed solution and explains in detail the two main elements of the solution: the Voter and the Health Monitoring partition. • Chapter 5, Prototype, explains in detail the prototyping of the proposed solution, including the choice of the hypervisor, the processing board, and the critical functionality to be redundant. With respect to the voter, it includes prototypes for both the software version (the voter is implemented in a virtual machine) and the hardware version (the voter is implemented as IP cores on the FPGA). • Chapter 6, Evaluation, includes the evaluation of the prototype developed in Chapter 5. As a preliminary step and given that there is no evidence in this regard, an exercise is carried out to measure the overhead involved in using the XtratuM hypervisor versus not using it. Subsequently, qualitative tests are carried out to check that Health Monitoring is working as expected and a fault injection campaign is carried out to check the error detection and correction rate of our solution. Finally, a comparison is made between the performance of the hardware and software versions of Voter. • Chapter 7, Conclusions and Future Work, is dedicated to collect the conclusions obtained and the contributions made during the research (in the form of articles in journals, conferences and contributions to projects and proposals in the industry). In addition, it establishes some lines of future work that could complete and extend the research carried out during this doctoral thesis.Programa de Doctorado en Ciencia y Tecnología Informática por la Universidad Carlos III de MadridPresidente: Katzalin Olcoz Herrero.- Secretario: Félix García Carballeira.- Vocal: Santiago Rodríguez de la Fuent