Theory blending: extended algorithmic aspects and examples

In Cognitive Science, conceptual blending has been proposed as an important cognitive mechanism that facilitates the creation of new concepts and ideas by constrained combination of available knowledge. It thereby provides a possible theoretical foundation for modeling high-level cognitive faculties such as the ability to understand, learn, and create new concepts and theories. Quite often the development of new mathematical theories and results is based on the combination of previously independent concepts, potentially even originating from distinct subareas of mathematics. Conceptual blending promises to offer a framework for modeling and re-creating this form of mathematical concept invention with computational means. This paper describes a logic-based framework which allows a formal treatment of theory blending (a subform of the general notion of conceptual blending with high relevance for applications in mathematics), discusses an interactive algorithm for blending within the framework, and provides several illustrating worked examples from mathematics

Molecular Systematic of Three Species of Oithona (Copepoda, Cyclopoida) from the Atlantic Ocean: Comparative Analysis Using 28S rDNA

Species of Oithona (Copepoda, Cyclopoida) are highly abundant, ecologically important, and widely distributed throughout the world oceans. Although there are valid and detailed descriptions of the species, routine species identifications remain challenging due to their small size, subtle morphological diagnostic traits, and the description of geographic forms or varieties. This study examined three species of Oithona (O. similis, O. atlantica and O. nana) occurring in the Argentine sector of the South Atlantic Ocean based on DNA sequence variation of a 575 base-pair region of 28S rDNA, with comparative analysis of these species from other North and South Atlantic regions. DNA sequence variation clearly resolved and discriminated the species, and revealed low levels of intraspecific variation among North and South Atlantic populations of each species. The 28S rDNA region was thus shown to provide an accurate and reliable means of identifying the species throughout the sampled domain. Analysis of 28S rDNA variation for additional species collected throughout the global ocean will be useful to accurately characterize biogeographical distributions of the species and to examine phylogenetic relationships among them

Ectomycorrhizal fungal diversity and community structure associated with cork oak in different landscapes

Cork oak (Quercus suber L.) forests play an important ecological and economic role. Ectomycorrhizal fungi (ECMF) are key components for the sustainability and functioning of these ecosystems. The community structure and composition of ECMF associated with Q. suber in different landscapes of distinct Mediterranean bioclimate regions have not previously been compared. In this work, soil samples from cork oak forests residing in different bioclimates (arid, semi-arid, sub-humid, and humid) were collected and surveyed for ectomycorrhizal (ECM) root tips. A global analysis performed on 3565 ECM root tips revealed that the ECMF community is highly enriched in Russula, Tomentella, and Cenoccocum, which correspond to the ECMF genera that mainly contribute to community differences. The ECMF communities from the rainiest and the driest cork oak forests were distinct, with soils from the rainiest climates being more heterogeneous than those from the driest climates. The analyses of several abiotic factors on the ECMF communities revealed that bioclimate, precipitation, soil texture, and forest management strongly influenced ECMF structure. Shifts in ECMF with different hyphal exploration types were also detected among forests, with precipitation, forest system, and soil texture being the main drivers controlling their composition. Understanding the effects of environmental factors on the structuring of ECM communities could be the first step for promoting the sustainability of this threatened ecosystem.This work was supported by Fundacao Ciencia e Tecnologia (FCT/MCTES/PIDDAC, Portugal), under the project (PEst-OE/BIA/UI4046/2014; UID/MULTI/04046/2013) and PhD grant to F.R. (SFRH/BD/86519/2012)

New Algorithm to Determine True Colocalization in Combination with Image Restoration and Time-Lapse Confocal Microscopy to Map Kinases in Mitochondria

The subcellular localization and physiological functions of biomolecules are closely related and thus it is crucial to precisely determine the distribution of different molecules inside the intracellular structures. This is frequently accomplished by fluorescence microscopy with well-characterized markers and posterior evaluation of the signal colocalization. Rigorous study of colocalization requires statistical analysis of the data, albeit yet no single technique has been established as a standard method. Indeed, the few methods currently available are only accurate in images with particular characteristics. Here, we introduce a new algorithm to automatically obtain the true colocalization between images that is suitable for a wide variety of biological situations. To proceed, the algorithm contemplates the individual contribution of each pixel's fluorescence intensity in a pair of images to the overall Pearsońs correlation and Manders' overlap coefficients. The accuracy and reliability of the algorithm was validated on both simulated and real images that reflected the characteristics of a range of biological samples. We used this algorithm in combination with image restoration by deconvolution and time-lapse confocal microscopy to address the localization of MEK1 in the mitochondria of different cell lines. Appraising the previously described behavior of Akt1 corroborated the reliability of the combined use of these techniques. Together, the present work provides a novel statistical approach to accurately and reliably determine the colocalization in a variety of biological images

Eficácia do exercício físico na fadiga dos pacientes com câncer durante o tratamento ativo: revisão sistemática e meta-análise

El objetivo del estudio fue determinar la efectividad del ejercicio físico en la fatiga de pacientes con cáncer durante el tratamiento activo. Las bases de datos de PubMed Central, EMBASE y OVID fueron consultadas hasta abril de 2014 para identificar ensayos clínicos aleatorizados, que evaluaran el efecto del ejercicio en la fatiga de pacientes con cáncer sometidos a tratamiento activo. Once estudios (n = 1.407) fueron incluidos. La quimioterapia fue el tratamiento más común (n = 1.028). Los estudios tuvieron bajo riesgo de sesgo y alta calidad metodológica. Las estimaciones de efecto mostraron que el ejercicio físico mejoró significativamente la fatiga (SMD = -3,0; IC95%: -5,21; -0,80), p < 0,0001. Se encontraron efectos similares para el entrenamiento de resistencia (SMD = -4,5; IC95%: -7,24; -1,82), p = 0,001. Se encontraron mejoras significativas en pacientes con cáncer de mama y de próstata (p < 0,05). El ejercicio es una intervención segura y eficaz en el control de la fatiga en pacientes sometidos a tratamiento activoThis study aimed to determine the effectiveness of physical exercise in decreasing fatigue in cancer patients during active treatment. The PubMed Central, EMBASE, and OVID databases were consulted up to April 2014 to identify randomized clinical trials that evaluated the effect of exercise on fatigue in cancer patients undergoing active treatment. Eleven studies (n = 1,407) were included. Chemotherapy was the most common form of treatment (n = 1,028). The studies showed a low risk of bias and high methodological quality. Effect estimates showed that physical exercise significantly improved fatigue (SMD = -3.0; 95%CI: -5.21; -0.80), p < 0.0001. Similar effects were found for resistance training (SMD = -4.5; 95%CI: -7.24; -1.82), p = 0.001. Significant improvements were found in breast and prostate cancer patients (p < 0.05). Exercise is a safe and effective intervention in the management fatigue in cancer patients undergoing active treatmentO objetivo foi determinar a efetividade do exercício físico sobre a fadiga em pacientes com câncer durante o tratamento ativo. As bases de dados PubMed Central, EMBASE e OVID foram consultadas até abril de 2014 para identificar ensaios clínicos randomizados que avaliaram o efeito do exercício sobre a fadiga em pacientes com câncer em tratamento ativo. Onze estudos (n = 1.407) foram incluídos. A quimioterapia foi o tratamento mais comum (n = 1.028). Os estudos tiveram baixo risco de viés e alta qualidade metodológica. As estimativas de efeito mostraram que o exercício melhorou significativamente a fadiga (DMP = -3,0; IC95%: -5,21; -0,80), p < 0,0001. Efeitos semelhantes sobre o treinamento de resistência (DMP = -4,5; IC95%: -7,24; -1,82), p = 0,001 foram encontrados. O exercício físico é uma intervenção segura e eficaz contra a fadiga em pacientes submetidos ao tratamento ativoEl presente trabajo forma parte del Proyecto Práctica del autoexamen de seno y los conocimientos, factores de riesgo y estilos de vida relacionados con el cáncer de mama en mujeres jóvenes de la Universidad Santo Tomás de Bogotá: un análisis transversal (9ª Convocatoria FODEIN- Código del proyecto 4110060001 - 008)

Carbon uptake by mature Amazon forests has mitigated Amazon nations' carbon emissions

BACKGROUND: Several independent lines of evidence suggest that Amazon forests have provided a significant carbon sink service, and also that the Amazon carbon sink in intact, mature forests may now be threatened as a result of different processes. There has however been no work done to quantify non-land-use-change forest carbon fluxes on a national basis within Amazonia, or to place these national fluxes and their possible changes in the context of the major anthropogenic carbon fluxes in the region. Here we present a first attempt to interpret results from ground-based monitoring of mature forest carbon fluxes in a biogeographically, politically, and temporally differentiated way. Specifically, using results from a large long-term network of forest plots, we estimate the Amazon biomass carbon balance over the last three decades for the different regions and nine nations of Amazonia, and evaluate the magnitude and trajectory of these differentiated balances in relation to major national anthropogenic carbon emissions. RESULTS: The sink of carbon into mature forests has been remarkably geographically ubiquitous across Amazonia, being substantial and persistent in each of the five biogeographic regions within Amazonia. Between 1980 and 2010, it has more than mitigated the fossil fuel emissions of every single national economy, except that of Venezuela. For most nations (Bolivia, Colombia, Ecuador, French Guiana, Guyana, Peru, Suriname) the sink has probably additionally mitigated all anthropogenic carbon emissions due to Amazon deforestation and other land use change. While the sink has weakened in some regions since 2000, our analysis suggests that Amazon nations which are able to conserve large areas of natural and semi-natural landscape still contribute globally-significant carbon sequestration. CONCLUSIONS: Mature forests across all of Amazonia have contributed significantly to mitigating climate change for decades. Yet Amazon nations have not directly benefited from providing this global scale ecosystem service. We suggest that better monitoring and reporting of the carbon fluxes within mature forests, and understanding the drivers of changes in their balance, must become national, as well as international, priorities

Analysis of Biological Features Associated with Meiotic Recombination Hot and Cold Spots in Saccharomyces cerevisiae

Meiotic recombination is not distributed uniformly throughout the genome. There are regions of high and low recombination rates called hot and cold spots, respectively. The recombination rate parallels the frequency of DNA double-strand breaks (DSBs) that initiate meiotic recombination. The aim is to identify biological features associated with DSB frequency. We constructed vectors representing various chromatin and sequence-based features for 1179 DSB hot spots and 1028 DSB cold spots. Using a feature selection approach, we have identified five features that distinguish hot from cold spots in Saccharomyces cerevisiae with high accuracy, namely the histone marks H3K4me3, H3K14ac, H3K36me3, and H3K79me3; and GC content. Previous studies have associated H3K4me3, H3K36me3, and GC content with areas of mitotic recombination. H3K14ac and H3K79me3 are novel predictions and thus represent good candidates for further experimental study. We also show nucleosome occupancy maps produced using next generation sequencing exhibit a bias at DSB hot spots and this bias is strong enough to obscure biologically relevant information. A computational approach using feature selection can productively be used to identify promising biological associations. H3K14ac and H3K79me3 are novel predictions of chromatin marks associated with meiotic DSBs. Next generation sequencing can exhibit a bias that is strong enough to lead to incorrect conclusions. Care must be taken when interpreting high throughput sequencing data where systematic biases have been documented

Widespread Genomic Signatures of Natural Selection in Hominid Evolution

Selection acting on genomic functional elements can be detected by its indirect effects on population diversity at linked neutral sites. To illuminate the selective forces that shaped hominid evolution, we analyzed the genomic distributions of human polymorphisms and sequence differences among five primate species relative to the locations of conserved sequence features. Neutral sequence diversity in human and ancestral hominid populations is substantially reduced near such features, resulting in a surprisingly large genome average diversity reduction due to selection of 19–26% on the autosomes and 12–40% on the X chromosome. The overall trends are broadly consistent with “background selection” or hitchhiking in ancestral populations acting to remove deleterious variants. Average selection is much stronger on exonic (both protein-coding and untranslated) conserved features than non-exonic features. Long term selection, rather than complex speciation scenarios, explains the large intragenomic variation in human/chimpanzee divergence. Our analyses reveal a dominant role for selection in shaping genomic diversity and divergence patterns, clarify hominid evolution, and provide a baseline for investigating specific selective events