Two distinct feedback codes in V1 for ‘real’ and ‘imaginary’ internal experiences, bioRxiv, 2019-06-14
AbstractVisual illusions and visual imagery are conscious sensory events that lack a corresponding physical input. But while everyday mental imagery feels distinct from incoming stimulus input, visual illusions, like hallucinations, are under limited volitional control and appear indistinguishable from physical reality. Illusions are thought to arise from lower-level processes within sensory cortices. In contrast, imagery involves a wide network of brain areas that recruit early visual cortices for the sensory representation of the imagined stimulus. Here, we combine laminar fMRI brain imaging with psychophysical methods and multivariate pattern analysis to investigate in human participants how seemingly ‘real’ and imaginary non-physical experiences are processed in primary visual cortex (V1). We find that the content of mental imagery is only decodable in deep layers, whereas illusory content is only decodable at superficial depths. This suggests that feedback to the different layers may serve distinct functions low-level feedback to superficial layers might be responsible for shaping perception-like experiences, while deep-layer feedback might serve the formation of a more malleable ‘inner’ world, separate from ongoing perception.
biorxiv neuroscience 0-100-users 2019Independent population coding of the present and the past in prefrontal cortex during learning, bioRxiv, 2019-06-13
AbstractMedial prefrontal cortex (mPfC) plays a role in both immediate behaviour and short-term memory. Unknown is whether the present and past are represented simultaneously or separately in mPfC populations. To address this, we analysed mPfC population activity of rats learning rules in a Y-maze, with self-initiated choice trials followed by a self-paced return during the inter-trial interval. Joint mPfC population activity encoded solely present events and actions during the trial, with decoding of the past at chance; conversely, population encoding of the same features in the immediately following inter-trial interval was solely of the past. Despite being contiguous in time, each population orthogonally encoded the present and past of the same events and actions. Consequently, only the population code of the present during the trials, and not the past coding of the inter-trials intervals, was re-activated in subsequent sleep. Our results suggest that representations of the past and present in the mPfC independently contribute to the learning of a new rule.
biorxiv neuroscience 0-100-users 2019Teaching R in the undergraduate ecology classroom approaches, lessons learned, and recommendations, bioRxiv, 2019-06-11
AbstractEcology requires training in data management and analysis. In this paper, we present data from the last 10 years demonstrating the increase in the use of R, an open-source programming environment, in ecology and its prevalence as a required skill in job descriptions. Because of its transparent and flexible nature, R is increasingly used for data management and analysis in the field of ecology. Consequently, job postings targeting candidates with a bachelor’s degree and a required knowledge of R have increased over the past ten years. We discuss our experiences teaching undergraduates R in two advanced ecology classes using different approaches. One approach, in a course with a field lab, focused on collecting, cleaning, and preparing data for analysis. The other approach, in a course without a field lab, focused on analyzing existing data sets and applying the results to content discussed in the lecture portion of the course. Our experiences determined that each approach had strengths and weaknesses. We recommend that above all, instructors of ecology and related subjects should be encouraged to include R in their coursework. Furthermore, instructors should be aware of the following learning R is a separate skill from learning statistics; writing R assignments is a significant time sink for course preparation; and, there is a tradeoff between teaching R and teaching content. Determining how one’s course fits into the curriculum and identifying resources outside of the classroom for students’ continued practice will ensure that R training is successful and will extend beyond a one-semester course.
biorxiv scientific-communication-and-education 0-100-users 2019Wild pollinator activities negatively related to honey bee colony densities in urban context, bioRxiv, 2019-06-11
AbstractAs pollinator decline is increasingly reported in natural and agricultural environments, cities are perceived as shelters for pollinators because of low pesticide exposure and high floral diversity throughout the year. This has led to the development of environmental policies supporting pollinators in urban areas. However, policies are often restricted to the promotion of honey bee colony installations, which resulted in a strong increase in apiary numbers in cities. Recently, competition for floral resources between wild pollinators and honey bees has been highlighted in semi-natural contexts, but whether urban beekeeping could impact wild pollinators remains unknown. Here, we show that in the city of Paris (France), wild pollinator visitation rates is negatively correlated to honey bee colony densities present in the surrounding (500m – slope = −0.614; p = 0.001 – and 1000m – slope = −0.489; p = 0.005). More particularly, large solitary bees and beetles were significantly affected at 500m (respectively slope = −0.425, p = 0.007 and slope = - 0.671, p = 0.002) and bumblebees were significantly affected at 1000m (slope = - 0.451, p = 0.012). Further, lower interaction evenness in plant-pollinator networks was observed with honey bee colony densities within 1000 meter buffers (slope = −0.487, p = 0.008). Finally, honey bees tended to focus their foraging activity on managed rather than spontaneous plant species (student t-test, p = 0.001) whereas wild pollinators equally visited managed and spontaneous species. We advocate responsible practices mitigating the introduction of high density of hives in urban environments. Future studies are needed to deepen our knowledge about the potential negative interactions between wild and domesticated pollinators.
biorxiv ecology 0-100-users 2019Optogenetic control of Wnt signaling for modeling early embryogenic patterning with human pluripotent stem cells, bioRxiv, 2019-06-10
ABSTRACTThe processes of cell proliferation, differentiation, migration, and self-organization during early embryonic development are governed by dynamic, spatially and temporally varying morphogen signals. Analogous tissue patterns emerge spontaneously in embryonic stem cell (ESC) models for gastrulation, but mechanistic insight into this self-organization is limited by a lack of molecular methods to precisely control morphogen signal dynamics. Here we combine optogenetic stimulation and single-cell imaging approaches to study self-organization of human pluripotent stem cells. Precise control of morphogen signal dynamics, achieved through activation of canonical Wntβ-catenin signaling over a broad high dynamic range (>500-fold) using an optoWnt optogenetic system, drove broad transcriptional changes and mesendoderm differentiation of human ESCs at high efficiency (>95% cells). Furthermore, activating Wnt signaling in subpopulations of ESCs in 2D and 3D cultures induced cell self-organization and morphogenesis reminiscent of human gastrulation, including changes in cell migration and epithelial to mesenchymal transition. Our findings thus reveal an instructive role for Wnt in directing cell patterning in this ESC model for gastrulation.
biorxiv bioengineering 0-100-users 2019Multiparametric phenotyping of compound effects on patient derived organoids, bioRxiv, 2019-06-07
AbstractPatient derived organoids (PDOs) closely resemble individual tumor biology and allow testing of small molecules ex vivo. To systematically dissect compound effects on 3D organoids, we developed a high-throughput imaging and quantitative analysis approach. We generated PDOs from colorectal cancer patients, treated them with >500 small molecules and captured >3 million images by confocal microscopy. We developed the software framework SCOPE to measure compound induced re-organization of PDOs. We found diverse, but re-occurring phenotypes that clustered by compound mode-of-action. Complex phenotypes were not congruent with PDO viability and many were specific to subsets of PDO lines or were influenced by recurrent mutations. We further analyzed specific phenotypes induced by compound classes and found GSK3 inhibitors to disassemble PDOs via focal adhesion signaling or that MEK inhibition led to bloating of PDOs by enhancing of stemness. Finally, by viability classification, we show heterogeneous susceptibilities of PDOs to clinical anticancer drugs.
biorxiv genomics 0-100-users 2019