Detecting and visualizing differences in brain structures with SPHARM and functional data analysis

A new procedure for classifying brain structures described by SPHARM is presented. We combine a dimension reduction technique (functional principal component analysis or functional independent component analysis) with stepwise variable selection for linear discriminant classification. This procedure is compared with many well-known methods in a novel classification problem in neuroeducation, where the reversal error (a common error in mathematical problem solving) is analyzed by using the left and right putamens of 33 participants. The comparison shows that our proposal not only provides outstanding performance in terms of predictive power, but it is also valuable in terms of interpretation, since it yields a linear discriminant function for 3D structures

Ordinal classification of 3D brain structures by functional data analysis

We introduce several ordinal classification methods for functional data, specificallymultiargument and multivariate functional data. Their performance is analyzed in fourreal data sets that belong to a neuroeducational problem and a neuropathologicalproblem.Funding for open access charge: CRUE-Universitat Jaume

A neuroimaging data set on problem solving in the case of the reversal error: Putamen data

Structural Magnetic Resonance Images (sMRI) for a sample of university students were recorded. Out of magnetic resonance, students performed a test of algebra problem solving. As we are interested in reversal errors, the test was prepared to detect this kind of error. Depending on the number of mistakes made, students were divided into two groups: one group contains 15 students that responded erroneously to more than 60% of the 16 questions, and the other group contains 18 students that did not make any mistake. We are interested in the more relevant brain structures for this neuroeducation problem. The analysis of these data can be found in Ferrando et al. (2020) [1]. The results of the volumetric analysis showed differences between groups in the right and left putamen. Therefore, both putamens were pre-processed and segmented to use them in the shape analysis. The dataset contains the slices of the left and right putamen and the left putamen of each of 33 subjects, 20 females. It also contains a vector that indicates the group to each subject belongs to

The underlying neural bases of the reversal error while solving algebraic word problems

Problem solving is a core element in mathematical learning. The reversal error in problem solving occurs when students are able to recognize the information in the statement of comparison word problems, but they reverse the relationship between two variables when building the equations. Functional magnetic resonance images were acquired to identify for the first time the neural bases associated with the reversal error. The neuronal bases linked to this error have been used as inputs in 13 classifiers to discriminate between reversal error and non-reversal error groups. We found brain activation in bilateral fronto-parietal areas in the participants who committed reversal errors, and only left fronto-parietal activation in those who did not, suggesting that the reversal error group needed a greater cognitive demand. Instead, the non-reversal error group seems to show that they have developed solid algebraic knowledge. Additionally, the results showed brain activation in the right middle temporal gyrus when comparing the reversal error vs non-reversal error groups. This activation would be associated with the semantic processing which is required to understand the statement and build the equation. Finally, the classifier results show that the brain areas activated could be considered good biomarkers to help us identify competent solvers

Microbenthic Net Metabolism Along Intertidal Gradients (Cadiz Bay, SW Spain): Spatio-Temporal Patterns and Environmental Factors

Microphytobenthos (MPB), the photosynthetic primary producing component of microbenthos, shows variable patterns in its biomass distribution along the intertidal gradient as a result of the interactions of factors such as light, tides, temperature, and grazing pressure. These patterns have been studied more extensively in northern European estuaries than southern European coastal systems. Even less information is available regarding temporal changes in MPB primary production rates in these systems. For this reason, we followed the seasonal changes in net production in light and dark respiration rates (determined by oxygen microelectrodes) and MPB biomass (estimated by sediment chlorophyll a) along the intertidal gradient of the inner Cadiz Bay during a year. Sediment cores were collected along two transects (five sampling stations per transect) with distinct sediment granulometry: one muddy [Puerto Real (PR)] and one muddy-sandy transect [San Fernando (SF)]. Our results show that MPB biomass and net production increased seawards reaching their maxima in winter. In contrast to what is observed in northern European systems, the higher solar irradiance and temperatures occurring in summer in southern Spain likely inhibit MPB production. In Cadiz Bay, spatial patterns of MPB biomass and net production depended on season and location due to the environmental heterogeneity observed. Environmental variables, analyzed by principal component analysis (PCA), were used to explain the variability of MPB metabolism by multiple regression. Selected principal component (PC) axes explained 60% of the net production in light and 41% of the dark respiration rates variability in PR, while they only accounted for 25% of the same rates in SF. The differences observed between transects and the variability in the environmental variables explaining them highlight the importance of considering the spatial heterogeneity of our system to estimate the contribution of MPB to the inner Cadiz Bay productivity. In our case, this contribution is significant accounting for up to 49% of the total benthic production of the inner Cadiz Bay intertidal sediments, confirming previous global estimates

Los españoles: ¿así somos o así nos ven? LARA

In this task we will work Spanish stereotypes from a communicative point of view. Here, the use of ICTs is very important because we are going to use them at communicative competence as much as production of texts. In addition, real resources as personal experiences from foreign people living in Spain are integrated together in this task with jokes and humor. To manage the information, we will use mind maps, a resource which not only develop creativity but it is also very attractive for learners. With these activities we pretend not only develop communicative competence of learners, but also sociocultural and intercultural competence, as well as we will approach the learners to the Spanish cultural reality through stereotypes that will be refuted

Distilling a visual network of Retinitis Pigmentosa gene-protein interactions to uncover new disease candidates

BACKGROUND: Retinitis pigmentosa (RP) is a highly heterogeneous genetic visual disorder with more than 70 known causative genes, some of them shared with other non-syndromic retinal dystrophies (e.g. Leber congenital amaurosis, LCA). The identification of RP genes has increased steadily during the last decade, and the 30% of the cases that still remain unassigned will soon decrease after the advent of exome/genome sequencing. A considerable amount of genetic and functional data on single RD genes and mutations has been gathered, but a comprehensive view of the RP genes and their interacting partners is still very fragmentary. This is the main gap that needs to be filled in order to understand how mutations relate to progressive blinding disorders and devise effective therapies. METHODOLOGY: We have built an RP-specific network (RPGeNet) by merging data from different sources: high-throughput data from BioGRID and STRING databases, manually curated data for interactions retrieved from iHOP, as well as interactions filtered out by syntactical parsing from up-to-date abstracts and full-text papers related to the RP research field. The paths emerging when known RP genes were used as baits over the whole interactome have been analysed, and the minimal number of connections among the RP genes and their close neighbors were distilled in order to simplify the search space. CONCLUSIONS: In contrast to the analysis of single isolated genes, finding the networks linking disease genes renders powerful etiopathological insights. We here provide an interactive interface, RPGeNet, for the molecular biologist to explore the network centered on the non-syndromic and syndromic RP and LCA causative genes. By integrating tissue-specific expression levels and phenotypic data on top of that network, a more comprehensive biological view will highlight key molecular players of retinal degeneration and unveil new RP disease candidates

Diel patterns of microphytobenthic primary production in intertidal sediments: the role of photoperiod on the vertical migration circadian rhythm

Diel primary production patterns of intertidal microphytobenthos (MPB) have been attributed to short-term physiological changes in the photosynthetic apparatus or to diel changes in the photoautotrophic biomass in the sediment photic layer due to vertical migration. Diel changes in primary production and vertical migration are entrained by external factors like photoperiod and tides. However, the role of photoperiod and tides has not been experimentally separated to date. Here, we performed laboratory experiments with sediment cores kept in immersion, in the absence of tides, with photoperiod or under continuous light. Measurements of net production, made with O-2 microsensors, and of spectral reflectance at the sediment surface showed that, in intertidal sediments, the photoperiod signal was the major driver of the diel patterns of net primary production and sediment oxygen availability through the vertical migration of the MPB photoautotrophic biomass. Vertical migration was controlled by an endogenous circadian rhythm entrained by photoperiod in the absence of tides. The pattern progressively disappeared after 3 days in continuous light but was immediately reset by photoperiod. Even though a potential contribution of a subjective in situ tidal signal cannot be completely discarded, Fourier and cross spectral analysis of temporal patterns indicated that the photosynthetic circadian rhythm was mainly characterized by light/dark migratory cycles

¿Conocemos todas las interacciones farmacológicas?: el transportador OATP1B1

En ancianos es frecuente la polimedicación. Esto incrementa el riesgo de sufrir reac­ciones adversas a los medicamentos, y también el riesgo de sufrir interacciones que pueden ser relevantes.Las interacciones más frecuentes son las que afectan a la farmacocinética de los medicamentos y, especialmente, al metabolismo de estos. Aquí el citocromo P450 tiene mucha relevancia, pero desde hace poco más de una década se conoce otro mecanismo implicado, las proteínas transportadoras de membrana. Dentro de estas tienen especial relevancia las OATP (Organic anion transporting polypeptide) de las que existen diferentes tipos y ubicaciones. La competición de diferentes substratos por estas proteínas puede generar interacciones que acaban repercutiendo en el tratamiento farmacoterapeutico del paciente

RPGeNet v2 .0: expanding the universe of retinal disease gene interactions network

RPGeNet offers researchers a user-friendly queriable tool to visualize the interactome network of visual disorder genes, thus enabling the identification of new potential causative genes and the assignment of novel candidates to specific retinal or cellular pathways. This can be highly relevant for clinical applications as retinal dystrophies affect 1:3000 people worldwide, and the causative genes are still unknown for 30% of the patients. RPGeNet is a refined interaction network interface that limits its skeleton network to the shortest paths between each and every known causative gene of inherited syndromic and non-syndromic retinal dystrophies. RPGeNet integrates interaction information from STRING, BioGRID and PPaxe, along with retina-specific expression data and associated genetic variants, over a Cytoscape.js web interface. For the new version, RPGeNet v2.0, the database engine was migrated to Neo4j graph database manager, which speeds up the initial queries and can handle whole interactome data for new ways to query the network. Further, user facilities have been introduced as the capability of saving and restoring a researcher customized network layout or as novel features to facilitate navigation and data projection on the network explorer interface. Responsiveness has been further improved by transferring some functionality to the client side