Human VMPFC encodes early signatures of confidence in perceptual decisions, bioRxiv, 2017-11-26

AbstractChoice confidence, an individual’s internal estimate of judgment accuracy, plays a critical role in adaptive behaviour. Despite its importance, the early (decisional) stages of confidence processing remain underexplored. Here, we recorded simultaneous EEGfMRI while participants performed a direction discrimination task and rated their confidence on each trial. Using multivariate single-trial discriminant analysis of the EEG, we identified a stimulus- and accuracy-independent component encoding confidence, appearing prior to subjects’ choice and explicit confidence report. The trial-to-trial variability in this EEG-derived confidence signal was uniquely associated with fMRI responses in the ventromedial prefrontal cortex (VMPFC), a region not typically associated with confidence for perceptual decisions. Furthermore, we showed that the VMPFC was functionally coupled with regions of the prefrontal cortex that support neural representations of confidence during explicit metacognitive report. Our results suggest that the VMPFC encodes an early confidence readout, preceding and potentially informing metacognitive evaluation and learning, by acting as an implicit valuereward signal.

biorxiv neuroscience 0-100-users 2017

Nonequilibrium entropic bounds for Darwinian replicators, bioRxiv, 2017-11-26

Life evolved on our planet by means of a combination of Darwinian selection and innovations leading to higher levels of complexity. The emergence and selection of replicating entities is a central problem in prebiotic evolution. Theoretical models have shown how populations of different types of replicating entities exclude or coexist with other classes of replicators. Models are typically kinetic, based on standard replicator equations. On the other hand, the presence of thermodynamical constrains for these systems remain an open question. This is largely due to the lack of a general theory of out of statistical methods for systems far from equilibrium. Nonetheless, a first approach to this problem has been put forward in a series of novel developements in non-equilibrium physics, under the rubric of the extended second law of thermodynamics. The work presented here is twofold firstly, we review this theoretical framework and provide a brief description of the three fundamental replicator types in prebiotic evolution parabolic, malthusian and hyperbolic. Finally, we employ these previously mentioned techinques to explore how replicators are constrained by thermodynamics.

biorxiv biophysics 0-100-users 2017

5-Formylcytosine controls nucleosome positioning through covalent histone-DNA interaction, bioRxiv, 2017-11-25

Nucleosomes are the basic unit of chromatin that ensure genome integrity and control access to the genetic information. The organization of nucleosomes is influenced by the underlying DNA sequence itself, transcription factors or other transcriptional machinery associated proteins and chromatin remodeling complexes (1–4). Herein, we show that the naturally occurring DNA modification, 5-formylcytosine (5fC) contributes to the positioning of nucleosomes. We show that the ability of 5fC to position nucleosomes in vitro is associated with the formation of covalent interactions between histone residues and 5fC in the form of Schiff bases. We demonstrate that similar interactions can occur in a cellular environment and define their specific genomic loci in mouse embryonic stem cells. Collectively, our findings identify 5fC as a determinant of nucleosomal organization in which 5fC plays a role in establishing distinct regulatory regions that are linked to gene expression Our study provides a previously unknown molecular mechanism, involving the formation of reversible-covalent bonds between chromatin and DNA that supports a molecular linkage between DNA sequence, DNA base modification and chromatin structure.

biorxiv genomics 0-100-users 2017

Experimental evidence that female rhesus macaques (Macaca mulatta) perceive variation in male facial masculinity, bioRxiv, 2017-11-25

AbstractAmong many primate species, face shape is sexually dimorphic, and male facial masculinity has been proposed to influence female mate choice and male-male competition by signalling competitive ability. However, whether conspecifics pay attention to facial masculinity has only been assessed in humans. In a study of free-ranging rhesus macaques, Macaca mulatta, we used a two-alternative look-time experiment to test whether females perceive male facial masculinity. We presented 107 females with pairs of images of male faces – one with a more masculine shape and one more feminine – and recorded their looking behaviour. Females looked at the masculine face longer than at the feminine face in more trials than predicted by chance. Although there was no overall difference in average look-time between masculine and feminine faces across all trials, females looked significantly longer at masculine faces in a subset of trials for which the within-pair difference in masculinity was most pronounced. Additionally, the proportion of time subjects looked toward the masculine face increased as the within-pair difference in masculinity increased. This study provides evidence that female macaques perceive variation in male facial shape, a necessary condition for intersexual selection to operate on such a trait. It also highlights the potential impact of perceptual thresholds on look-time experiments.

biorxiv animal-behavior-and-cognition 0-100-users 2017

Sensory cortex is optimised for prediction of future input, bioRxiv, 2017-11-25

Neurons in sensory cortex are tuned to diverse features in natural scenes. But what determines which features neurons become selective to? Here we explore the idea that neuronal selectivity is optimised to represent features in the recent past of sensory input that best predict immediate future inputs. We tested this hypothesis using simple feedforward neural networks, which were trained to predict the next few video or audio frames in clips of natural scenes. The networks developed receptive fields that closely matched those of real cortical neurons, including the oriented spatial tuning of primary visual cortex, the frequency selectivity of primary auditory cortex and, most notably, in their temporal tuning properties. Furthermore, the better a network predicted future inputs the more closely its receptive fields tended to resemble those in the brain. This suggests that sensory processing is optimised to extract those features with the most capacity to predict future input.Impact statementPrediction of future input explains diverse neural tuning properties in sensory cortex.

biorxiv neuroscience 0-100-users 2017

Expressed Exome Capture Sequencing (EecSeq) a method for cost-effective exome sequencing for all organisms with or without genomic resources, bioRxiv, 2017-11-24

AbstractExome capture is an effective tool for surveying the genome for loci under selection. However, traditional methods require annotated genomic resources. Here, we present a method for creating cDNA probes from expressed mRNA, which are then used to enrich and capture genomic DNA for exon regions. This approach, called “EecSeq”, eliminates the need for costly probe design and synthesis. We tested EecSeq in the eastern oyster, Crassostrea virginica, using a controlled exposure experiment. Four adult oysters were heat shocked at 36° C for 1 hour along with four control oysters kept at 14° C. Stranded mRNA libraries were prepared for two individuals from each treatment and pooled. Half of the combined library was used for probe synthesis and half was sequenced to evaluate capture efficiency. Genomic DNA was extracted from all individuals, enriched via captured probes, and sequenced directly. We found that EecSeq had an average capture sensitivity of 86.8% across all known exons and had over 99.4% sensitivity for exons with detectable levels of expression in the mRNA library. For all mapped reads, over 47.9% mapped to exons and 37.0% mapped to expressed targets, which is similar to previously published exon capture studies. EecSeq displayed relatively even coverage within exons (i.e. minor “edge effects”) and even coverage across exon GC content. We discovered 5,951 SNPs with a minimum average coverage of 80X, with 3,508 SNPs appearing in exonic regions. We show that EecSeq provides comparable, if not superior, specificity and capture efficiency compared to costly, traditional methods.

biorxiv genomics 0-100-users 2017