Towards the bridging of molecular genetics data across Xenopus species

Indexación: ScopusBackground: The clawed African frog Xenopus laevis has been one of the main vertebrate models for studies in developmental biology. However, for genetic studies, Xenopus tropicalis has been the experimental model of choice because it shorter life cycle and due to a more tractable genome that does not result from genome duplication as in the case of X. laevis. Today, although still organized in a large number of scaffolds, nearly 85 % of X. tropicalis and 89 % of X. laevis genomes have been sequenced. There is expectation for a comparative physical map that can be used as a Rosetta Stone between X. laevis genetic studies and X. tropicalis genomic research. Results: In this work, we have mapped using coarse-grained alignment the 18 chromosomes of X. laevis, release 9.1, on the 10 reference scaffolds representing the haploid genome of X. tropicalis, release 9.0. After validating the mapping with theoretical data, and estimating reference averages of genome sequence identity, 37 to 44 % between the two species, we have carried out a synteny analysis for 2,112 orthologous genes. We found that 99.6 % of genes are in the same organization. Conclusions: Taken together, our results make possible to establish the correspondence between 62 and 65.5 % of both genomes, percentage of identity, synteny and automatic annotation of transcripts of both species, providing a new and more comprehensive tool for comparative analysis of these two species, by allowing to bridge molecular genetics data among them.https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2440-

Error Control and Loss Functions for the Deep Learning Inversion of Borehole Resistivity Measurements

Deep learning (DL) is a numerical method that approximates functions. Recently, its use has become attractive for the simulation and inversion of multiple problems in computational mechanics, including the inversion of borehole logging measurements for oil and gas applications. In this context, DL methods exhibit two key attractive features: a) once trained, they enable to solve an inverse problem in a fraction of a second, which is convenient for borehole geosteering operations as well as in other real-time inversion applications. b) DL methods exhibit a superior capability for approximating highly-complex functions across different areas of knowledge. Nevertheless, as it occurs with most numerical methods, DL also relies on expert design decisions that are problem specific to achieve reliable and robust results. Herein, we investigate two key aspects of deep neural networks (DNNs) when applied to the inversion of borehole resistivity measurements: error control and adequate selection of the loss function. As we illustrate via theoretical considerations and extensive numerical experiments, these interrelated aspects are critical to recover accurate inversion results

Irrelevant tactile stimulation biases visual exploration in external coordinates

Ossandón JP, König P, Heed T. Irrelevant tactile stimulation biases visual exploration in external coordinates. Scientific Reports. 2015;5(1): 10664

The contributions of image content and behavioral relevancy to overt attention

During free-viewing of natural scenes, eye movements are guided by bottom-up factors inherent to the stimulus, as well as top-down factors inherent to the observer. The question of how these two different sources of information interact and contribute to fixation behavior has recently received a lot of attention. Here, a battery of 15 visual stimulus features was used to quantify the contribution of stimulus properties during free-viewing of 4 different categories of images (Natural, Urban, Fractal and Pink Noise). Behaviorally relevant information was estimated in the form of topographical interestingness maps by asking an independent set of subjects to click at image regions that they subjectively found most interesting. Using a Bayesian scheme, we computed saliency functions that described the probability of a given feature to be fixated. In the case of stimulus features, the precise shape of the saliency functions was strongly dependent upon image category and overall the saliency associated with these features was generally weak. When testing multiple features jointly, a linear additive integration model of individual saliencies performed satisfactorily. We found that the saliency associated with interesting locations was much higher than any low-level image feature and any pair-wise combination thereof. Furthermore, the low-level image features were found to be maximally salient at those locations that had already high interestingness ratings. Temporal analysis showed that regions with high interestingness ratings were fixated as early as the third fixation following stimulus onset. Paralleling these findings, fixation durations were found to be dependent mainly on interestingness ratings and to a lesser extent on the low-level image features. Our results suggest that both low- and high-level sources of information play a significant role during exploration of complex scenes with behaviorally relevant information being more effective compared to stimulus features.publisher versio

Universal and non-universal features of musical pitch perception revealed by singing

Musical pitch perception is argued to result from nonmusical biological constraints and thus to have similar characteristics across cultures, but its universality remains unclear. We probed pitch representations in residents of the Bolivian Amazon—the Tsimane', who live in relative isolation from Western culture—as well as US musicians and non-musicians. Participants sang back tone sequences presented in different frequency ranges. Sung responses of Amazonian and US participants approximately replicated heard intervals on a logarithmic scale, even for tones outside the singing range. Moreover, Amazonian and US reproductions both deteriorated for high-frequency tones even though they were fully audible. But whereas US participants tended to reproduce notes an integer number of octaves above or below the heard tones, Amazonians did not, ignoring the note “chroma” (C, D, etc.). Chroma matching in US participants was more pronounced in US musicians than non-musicians, was not affected by feedback, and was correlated with similarity-based measures of octave equivalence as well as the ability to match the absolute f0 of a stimulus in the singing range. The results suggest the cross-cultural presence of logarithmic scales for pitch, and biological constraints on the limits of pitch, but indicate that octave equivalence may be culturally contingent, plausibly dependent on pitch representations that develop from experience with particular musical systems

Unmasking the contribution of low-level features to the guidance of attention.

The role of low-level stimulus-driven control in the guidance of overt visual attention has been difficult to establish because low- and high-level visual content are spatially correlated within natural visual stimuli. Here we show that impairment of parietal cortical areas, either permanently by a lesion or reversibly by repetitive transcranial magnetic stimulation (rTMS), leads to fixation of locations with higher values of low-level features as compared to control subjects or in a no-rTMS condition. Moreover, this unmasking of stimulus-driven control crucially depends on the intrahemispheric balance between top-down and bottom-up cortical areas. This result suggests that although in normal behavior high-level features might exert a strong influence, low-level features do contribute to guide visual selection during the exploration of complex natural stimuli