Replicability of data collected for empirical estimation of relative pollen productivity

The effects of repeated survey and fieldwork timing on data derived from a recently proposed standard field methodology for empirical estimation of Relative Pollen Productivity have been tested. Seasonal variations in vegetation and associated pollen assemblages were studied in three contrasting cultural habitat types; semi-natural ancient woodlands, lowland heaths, and unimproved, traditionally managed hay meadows. Results show that in woodlands and heathlands the standard method generates vegetation data with a reasonable degree of similarity throughout the field season, though in some instances additional recording of woodland canopy cover should be undertaken, and differences were greater for woodland understorey taxa than for arboreal taxa. Large differences in vegetation cover were observed over the field season in the grassland community, and matching the phenological timing of surveys within and between studies is clearly important if RPP estimates from these sites are to be comparable. Pollen assemblages from closely co-located moss polsters collected on different visits are shown to be variable in all communities, to a greater degree than can be explained by the sampling error associated with pollen counting, and further study of moss polsters as pollen traps is recommended.

Operator and replicability bias in comparative taphonomic studies

The operator effect is a well-known methodological bias already quantified in some taphonomic studies. However, the replicability effect, i.e., the use of taphonomic attributes as a replicable scientific method, has not been taken into account to the present. Here, we quantified for the first time this replicability bias using different multivariate statistical techniques, testing if the operator effect is related to the replicability effect. We analyzed the results reported by 15 operators working on the same dataset. Each operator analyzed 30 biological remains (bivalve shells) from five different sites, considering the attributes fragmentation, edge rounding, corrasion, bioerosion and secondary color. The operator effect followed the same pattern reported in previous studies, characterized by a worse correspondence for those attributes having more than two levels of damage categories. However, the effect did not appear to have relation with the replicability effect, because nearly all operators found differences among sites. Despite the binary attribute bioerosion exhibited 83% of correspondence among operators it was the taphonomic attributes that showed the highest dispersion among operators (28%). Therefore, we conclude that binary attributes (despite showing a reduction of the operator effect) diminish replicability, resulting in different interpretations of concordant data. We found that a variance value of nearly 8% among operators, was enough to generate a different taphonomic interpretation, in a Q-mode cluster analysis. The results reported here showed that the statistical method employed influences the level of replicability and comparability of a study and that the availability of results may be a valid alternative to reduce bias.

A context sensitive model for querying linked scientific data

This thesis provides a query model suitable for context sensitive access to a wide range of distributed linked datasets which are available to scientists using the Internet. The model is designed based on scientific research standards which require scientists to provide replicable methods in their publications. Although there are query models available that provide limited replicability, they do not contextualise the process whereby different scientists select dataset locations based on their trust and physical location. In different contexts, scientists need to perform different data cleaning actions, independent of the overall query, and the model was designed to accommodate this function. The query model was implemented as a prototype web application and its features were verified through its use as the engine behind a major scientific data access site, Bio2RDF.org. The prototype showed that it was possible to have context sensitive behaviour for each of the three mirrors of Bio2RDF.org using a single set of configuration settings. The prototype provided executable query provenance that could be attached to scientific publications to fulfil replicability requirements. The model was designed to make it simple to independently interpret and execute the query provenance documents using context specific profiles, without modifying the original provenance documents. Experiments using the prototype as the data access tool in workflow management systems confirmed that the design of the model made it possible to replicate results in different contexts with minimal additions, and no deletions, to query provenance documents.

Faster than the speed of print : reconciling ‘big data’ social media analysis and academic scholarship

The promise of ‘big data’ has generated a significant deal of interest in the development of new approaches to research in the humanities and social sciences, as well as a range of important critical interventions which warn of an unquestioned rush to ‘big data’. Drawing on the experiences made in developing innovative ‘big data’ approaches to social media research, this paper examines some of the repercussions for the scholarly research and publication practices of those researchers who do pursue the path of ‘big data’–centric investigation in their work. As researchers import the tools and methods of highly quantitative, statistical analysis from the ‘hard’ sciences into computational, digital humanities research, must they also subscribe to the language and assumptions underlying such ‘scientificity’? If so, how does this affect the choices made in gathering, processing, analysing, and disseminating the outcomes of digital humanities research? In particular, is there a need to rethink the forms and formats of publishing scholarly work in order to enable the rigorous scrutiny and replicability of research outcomes?

Selective Review of Proton Magnetic Resonance Spectroscopy in Schizophrenia

Magnetic Resonance Spectroscopy (MRS) offers a unique opportunity to measure brain metabolites in-vivo, and in doing so enables one to understand the brain function and cellular processes implicated in the pathophysiology of psychiatric disorders. MRS, in addition to being non-invasive, is devoid of radioactive tracers and ionizing radiation, a distinct advantage over other imaging modalities like positron emission tomography and single photon emission computed tomography. With advances in MRS technique it is now possible to quantify concentrations of relevant compounds like neurotransmitters, neuronal viability markers and pharmacological compounds. Majority of the MRS studies have examined the neurometabolites in schizophrenia, a common and debilitating psychiatric disorder. Abnormalities in N Acetyl aspartate and Glutamate are consistently reported while the reports regarding the myoinsoitol and choline are inconsistent. These abnormalities are not changed across the illness stages and despite treatment. However, multiple technical challenges have limited the widespread use of MRS in psychiatric disorders. Guidelines for uniform acquisition and preprocessing are need of the hour, which. would increase the replicability and validity of MRS measures in psychiatry. Finally long term, prospective, longitudinal studies are required in different psychiatric disorders for potential clinical applications.

Interações entre anuros, bromélias e a comunidade bromelícola associada em três unidades de conservação no Estado do Rio de Janeiro

Bromeliaceae é uma família vegetal com distribuição essencialmente neotropical frequentemente utilizada em estudos ecológicos devido às suas características de armazenar água livre, sustentar uma biota própria, apresentar tamanho relativamente reduzido e ter fácil replicabilidade por serem abundantes. Estas características conferem às bromélias o status de microcosmos natural e, dentro do ambiente bromelícola as espécies também interagem entre si. Anuros são habitantes comumente encontrados em bromélias sendo que algumas espécies têm estreita relação com estes vegetais ao ponto de passarem todo seu ciclo de vida associados a bromélias. Na presente tese foram estudados distintos organismos que habitam bromélias (e.g. ostracodas, protozoários, helmintos e artrópodes em geral) com ênfase em anuros do gênero Scinax (Hylidae). Foi realizado um experimento controlado em casa de vegetação para testar diferentes aspectos da relação entre anuros e bromélias usando como modelo S. perpusillus e Neoregelia sp. Foram também realizados estudos de campo em três unidades de conservação do estado do Rio de Janeiro, a saber: Monumento Natural do Morro da Urca e Pão-de-Açúcar; Parque Estadual da Serra da Tiririca; e Parque Nacional da Serra dos Órgãos onde, respectivamente, ocorrem os anuros S. perpusillus, S. littoreus e S. v-signatus. A tese está dividida em seis capítulos que abordam diferentes interações interespecíficas como predação, parasitismo, foresia e mutualismo.

What are the local impacts of energy systems on marine ecosystem services: a systematic map protocol

Background: Increasing concentrations of atmospheric greenhouse gases (GHG) and its impact on the climate has resulted in many international governments committing to reduce their GHG emissions. The UK, for example, has committed to reducing its carbon emissions by 80% by 2050. Suggested ways of reaching such a target are to increase dependency on offshore wind, offshore gas and nuclear. It is not clear, however, how the construction, operation and decommissioning of these energy systems will impact marine ecosystem services, i.e. the services obtained by people from the natural environment such as food provisioning, climate regulation and cultural inspiration. Research on ecosystem service impacts associated with offshore energy technologies is still in its infancy. The objective of this review is to bolster the evidence base by firstly, recording and describing the impacts of energy technologies at the marine ecosystems and human level in a consistent and transparent way; secondly, to translate these ecosystem and human impacts into ecosystem service impacts by using a framework to ensure consistency and comparability. The output of this process will be an objective synthesis of ecosystem service impacts comprehensive enough to cover different types of energy under the same analysis and to assist in informing how the provision of ecosystem services will change under different energy provisioning scenarios. Methods: Relevant studies will be sourced using publication databases and selected using a set of selection criteria including the identification of: (i) relevant subject populations such as marine and coastal species, marine habitat types and the general public; (ii) relevant exposure types including offshore wind farms, offshore oil and gas platforms and offshore structures connected with nuclear; (iii) relevant outcomes including changes in species structure and diversity; changes in benthic, demersal and pelagic habitats; and changes in cultural services. The impacts will be synthesised and described using a systematic map. To translate these findings into ecosystem service impacts, the Common International Classification of Ecosystem Services (CICES) and Millennium Ecosystem Assessment (MEA) frameworks are used and a detailed description of the steps taken provided to ensure transparency and replicability.

Sistema de deteção de eventos adversos baseado num data warehouse

RESUMO - A Segurança do Doente tem assumido uma relevância crescente nas organizações de saúde, resultado da divulgação de diversos estudos que revelaram a magnitude deste problema e simultaneamente, de uma maior pressão por parte da opinião pública e da comunicação social. Este estudo pretende desenvolver e avaliar a performance de um sistema eletrónico de deteção de eventos adversos, baseado num Data Warehouse, por comparação com os resultados obtidos pela metodologia tradicional de revisão dos registos clínicos. O objetivo principal do trabalho consistiu em identificar um conjunto de triggers / indicadores de alerta que permitam detetar potenciais eventos adversos mais comuns. O sistema desenvolvido apresentou um Valor Preditivo Positivo de 18.2%, uma sensibilidade de 65.1% e uma especificidade de 68.6%, sendo constituído por nove indicadores baseados em informação clínica e 445 códigos do ICD-9-CM, relativos a diagnósticos e procedimentos. Apesar de terem algumas limitações, os sistemas eletrónicos de deteção de eventos adversos apresentam inúmeras potencialidades, nomeadamente a utilização em tempo real e em complemento a metodologias já existentes. Considerando a importância da problemática em análise e a necessidade de aprofundar os resultados obtidos neste trabalho de projeto, seria relevante a sua extensão a um universo mais alargado de instituições hospitalares, estando a sua replicabilidade facilitada, uma vez que o Data Warehouse tem por base um conjunto de aplicações disseminadas a nível nacional. O desenvolvimento e a consolidação dos sistemas eletrónicos de deteção de eventos adversos constitui inegavelmente uma área de futuro, com reflexos ao nível da melhoria da informação existente nas organizações e que contribuirá decisivamente para a melhoria dos cuidados de saúde prestados aos doentes.

Genetic variant rs17225178 in the ARNT2 gene is associated with Asperger Syndrome

Background Autism Spectrum Conditions (ASC) are neurodevelopmental conditions characterized by difficulties in communication and social interaction, alongside unusually repetitive behaviours and narrow interests. Asperger Syndrome (AS) is one subgroup of ASC and differs from classic autism in that in AS there is no language or general cognitive delay. Genetic, epigenetic and environmental factors are implicated in ASC and genes involved in neural connectivity and neurodevelopment are good candidates for studying the susceptibility to ASC. The aryl-hydrocarbon receptor nuclear translocator 2 (ARNT2) gene encodes a transcription factor involved in neurodevelopmental processes, neuronal connectivity and cellular responses to hypoxia. A mutation in this gene has been identified in individuals with ASC and single nucleotide polymorphisms (SNPs) have been nominally associated with AS and autistic traits in previous studies. Methods In this study, we tested 34 SNPs in ARNT2 for association with AS in 118 cases and 412 controls of Caucasian origin. P values were adjusted for multiple comparisons, and linkage disequilibrium (LD) among the SNPs analysed was calculated in our sample. Finally, SNP annotation allowed functional and structural analyses of the genetic variants in ARNT2. We tested the replicability of our result using the genome-wide association studies (GWAS) database of the Psychiatric Genomics Consortium (PGC). Results We report statistically significant association of rs17225178 with AS. This SNP modifies transcription factor binding sites and regions that regulate the chromatin state in neural cell lines. It is also included in a LD block in our sample, alongside other genetic variants that alter chromatin regulatory regions in neural cells. Conclusions These findings demonstrate that rs17225178 in the ARNT2 gene is associated with AS and support previous studies that pointed out an involvement of this gene in the predisposition to ASC.

Changes of a mutualistic network over time: reanalysis over a 10-year period

We analyzed the structure of a multispecific network or interacting ants and plants bearing extrafloral nectaries recorded in 1990 and again in 2000 in La Mancha, Veracruz, Mexico. We assessed the replicability of the number of interactions found among species and also whether there had been changes in the network structure associated with appearance of new ant and plant species during. that 10-year period. Our results show that the nested topology of the network was similar between sampling dates, group dissimilarity increased, mean number of interactions for ant species increased, the frequency distribution of standardized degrees reached higher values for plant species, more ant species and fewer plant species constituted the core of the more recent network, and the presence of new ant and plant species increased while their contribution to nestedness remained the same. Generalist species (i.e., those with the most links or interactions) appeared to maintain the stability of the network because the new species incorporated into the communities were linked to this core of generalists. Camponotus planatus was the most extreme generalist ant species (the one with the most links) in both networks, followed by four other ant species; but other species changed either their position along the continuum of generalists relative to specialists or their presence or absence within the network. Even though new species moved into the area during the decade between the surveys, the overall network structure remained unmodified.

Innovating, gaining market share and fostering social inclusion: success stories in SME development

Includes bibliography

Imagem digital em movimento

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Information and communication technologies for agricultural development in Latin America: trends, barriers and policies

Includes bibliography