Theories of anterior cingulate cortex function : opportunity cost

The target article highlights the role of the anterior cingulate cortex (ACC) in conflict monitoring, but ACC function may be better understood in terms of the hierarchical organization of behavior. This proposal suggests that the ACC selects extended goal-directed actions according to their learned costs and benefits and executes those behaviors subject to depleting resources

Genome-scale metabolic modelling of an extremophile microbial community

Dissertação de mestrado em BioinformaticsBiomining offers an ecological alternative to the standard mining practices by using ex tremophiles that can endure elevated temperatures and low pH values. Several studies have been performed using Acidithiobacillus caldus SM-1 and Acidimicrobium ferrooxidans DSM 10331, suggesting that these bacteria in a community offer several advantages in bioleaching environ ments. Genome-Scale Metabolic (GSM) models simulate the organisms’ metabolism through constraint based approaches. Therefore, the reconstruction of GSM models for A. caldus and A. ferroox idans and their integration into a community will offer, besides valuable insights into their metabolism, a unique perspective on the potential interaction mechanisms between the two organisms within the community. In this work, we developed manually curated GSM models for A. caldus with 416 genes, 846 reactions and 646 metabolites, and A. ferrooxidans with 408 genes, 817 reactions and 640 metabolites. Both models were reconstructed using the user-friendly software merlin. We performed the functional annotation of both organisms’ genomes to identify their metabolic characteristics, which allowed generating a draft of the metabolic network. Manual curation efforts through literature, genomic information, phylogenetically close organisms and biological databases allowed refining the metabolic network. Furthermore, the models were validated using Cobrapy and Mewpy which allowed analysing flux distribution and interactions in different environmental conditions, and the results were compared with the literature and experimental data. Lastly, the community model was built using the organisms’ validated GSM models. In silico phenotypic simulations of the community model revealed that A. caldus exchanged lipid-production related compounds whilst A. ferrooxidans donated hydrogen sulfide assisting the former with its more complex sulfur metabolism. Moreover, the results suggest a more significant influence of A. ferrooxidans in the community’s growth rate whilst A. caldus assists A. ferrooxidans in biomass production. These models can serve as a starting point to study and model the community’s behaviour in several bioleaching conditions.A biomineração oferece uma alternativa ecológica às práticas de mineração comuns através do uso de extremófilos que são capazes suportar elevadas temperaturas e baixos valores de pH. Vários estudos foram realizados usando os microrganismos Acidithiobacillus caldus SM-1 e Acidimicrobium ferrooxidans DSM 10331 em comunidade, sugerindo várias vantagens em ambientes de biolixiviação. Os modelos metabólicos à escala genómica permitem a modelação do metabolismo através de abordagens baseadas em restrições. Portanto, a construção de uma comunidade com contendo o modelo da A. caldus e outro da A. ferrooxidans poderá oferecer novas perspetivas sobre os seus respetivos metabolismos, assim como sobre os mecanismos de interação entre os dois organismos dentro da comunidade. Neste trabalho, foram reconstruídos dois modelos metabólicos à escala genómica com um elevado nível de curação manual utilizando a ferramenta merlin. O modelo da A. caldus conta com 416 genes e 846 reações enquanto que o da A. ferrooxidans possuí 408 genes e 817 reações. Os modelos foram funcionalmente anotados a fim de identificar as características metabólicas dos organismos, gerando um esboço da rede metabólica. Esta rede metabólica foi depois curada manualmente a fim de a refinar. Para isto foi usado informação presente na literatura, dados genómicos, organismos filogeneticamente próximos e bases de dados biológicas. Posteriormente, os modelos foram validados através de uma análise da distribuição de fluxo com diferentes condições ambientais e os resultados foram comparados com a literatura e dados experimentais. Por fim, o modelo da comunidade foi construído usando os modelos validados dos dois organismos. Simulações fenotípicas in silico do modelo da comunidade revelaram uma troca de compostos relacionados com produção de lípidios por parte da A. caldus, enquanto A. ferrooxidans doou sulfato de hidrogénio, auxiliando o primeiro no seu metabolismo de enxofre mais complexo. Por fim, os resultados sugerem uma maior influência de A. ferrooxidans na taxa de crescimento da comunidade enquanto que A. caldus auxilia o primeiro na produção de biomassa

Method and System for Identification of Metabolites Using Mass Spectra

A method and system is provided for mass spectrometry for identification of a specific elemental formula for an unknown compound which includes but is not limited to a metabolite. The method includes calculating a natural abundance probability (NAP) of a given isotopologue for isotopes of non-labelling elements of an unknown compound. Molecular fragments for a subset of isotopes identified using the NAP are created and sorted into a requisite cache data structure to be subsequently searched. Peaks from raw spectrum data from mass spectrometry for an unknown compound. Sample-specific peaks of the unknown com- pound from various spectral artifacts in ultra-high resolution Fourier transform mass spectra are separated. A set of possible isotope-resolved molecular formula (IMF) are created by iteratively searching the molecular fragment caches and combining with additional isotopes and then statistically filtering the results based on NAP and mass-to-charge (m/2) matching probabilities. An unknown compound is identified and its corresponding elemental molecular formula (EMF) from statistically-significant caches of isotopologues with compatible IMFs

The computer revolution in science: steps towards the realization of computer-supported discovery environments

The tools that scientists use in their search processes together form so-called discovery environments. The promise of artificial intelligence and other branches of computer science is to radically transform conventional discovery environments by equipping scientists with a range of powerful computer tools including large-scale, shared knowledge bases and discovery programs. We will describe the future computer-supported discovery environments that may result, and illustrate by means of a realistic scenario how scientists come to new discoveries in these environments. In order to make the step from the current generation of discovery tools to computer-supported discovery environments like the one presented in the scenario, developers should realize that such environments are large-scale sociotechnical systems. They should not just focus on isolated computer programs, but also pay attention to the question how these programs will be used and maintained by scientists in research practices. In order to help developers of discovery programs in achieving the integration of their tools in discovery environments, we will formulate a set of guidelines that developers could follow