Coarse--graining, fixed points, and scaling in a large population of neurons

We develop a phenomenological coarse--graining procedure for activity in a large network of neurons, and apply this to recordings from a population of 1000+ cells in the hippocampus. Distributions of coarse--grained variables seem to approach a fixed non--Gaussian form, and we see evidence of scaling in both static and dynamic quantities. These results suggest that the collective behavior of the network is described by a non--trivial fixed point

Automatic Neuron Detection in Calcium Imaging Data Using Convolutional Networks

Calcium imaging is an important technique for monitoring the activity of thousands of neurons simultaneously. As calcium imaging datasets grow in size, automated detection of individual neurons is becoming important. Here we apply a supervised learning approach to this problem and show that convolutional networks can achieve near-human accuracy and superhuman speed. Accuracy is superior to the popular PCA/ICA method based on precision and recall relative to ground truth annotation by a human expert. These results suggest that convolutional networks are an efficient and flexible tool for the analysis of large-scale calcium imaging data.Comment: 9 pages, 5 figures, 2 ancillary files; minor changes for camera-ready version. appears in Advances in Neural Information Processing Systems 29 (NIPS 2016

Sources of noise during accumulation of evidence in unrestrained and voluntarily head-restrained rats

Abstract Decision-making behavior is often characterized by substantial variability, but its source remains unclear. We developed a visual accumulation of evidence task designed to quantify sources of noise and to be performed during voluntary head restraint, enabling cellular resolution imaging in future studies. Rats accumulated discrete numbers of flashes presented to the left and right visual hemifields and indicated the side that had the greater number of flashes. Using a signaldetection theory-based model, we found that the standard deviation in their internal estimate of flash number scaled linearly with the number of flashes. This indicates a major source of noise that, surprisingly, is not consistent with the widely used 'drift-diffusion modeling' (DDM) approach but is instead closely related to proposed models of numerical cognition and counting. We speculate that this form of noise could be important in accumulation of evidence tasks generally

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111924/1/nph13491-sup-0001-FigS1-TableS1-S2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111924/2/nph13491.pd

Watershed Classification Predicts Streamflow Regime and Organic Carbon Dynamics in the Northeast Pacific Coastal Temperate Rainforest

Watershed classification has long been a key tool in the hydrological sciences, but few studies have been extended to biogeochemistry. We developed a combined hydro-biogeochemical classification for watersheds draining to the coastal margin of the Northeast Pacific coastal temperate rainforest (1,443,062 km2), including 2,695 small coastal rivers (SCR) and 10 large continental watersheds. We used cluster analysis to group SCR watersheds into 12 types, based on watershed properties. The most important variables for distinguishing SCR watershed types were evapotranspiration, slope, snowfall, and total precipitation. We used both streamflow and dissolved organic carbon (DOC) measurements from rivers (n = 104 and 90 watersheds respectively) to validate the classification. Watershed types corresponded with broad differences in streamflow regime, mean annual runoff, DOC seasonality, and mean DOC concentration. These links between watershed type and river conditions enabled the first region-wide empirical characterization of river hydrobiogeochemistry at the land-sea margin, spanning extensive ungauged and unsampled areas. We found very high annual runoff (mean > 3,000 mm, n = 10) in three watershed types totaling 59,024 km2 and ranging from heavily glacierized mountain watersheds with high flow in summer to a rain-fed mountain watershed type with high flow in fall-winter. DOC hotspots (mean > 4 mg L−1, n = 14) were found in three other watershed types (48,557 km2) with perhumid rainforest climates and less-mountainous topography. We described four patterns of DOC seasonality linked to watershed hydrology, with fall-flushing being widespread. Hydro-biogeochemical watershed classification may be useful for other complex regions with sparse observation networks.Author Contributions: Conceptualization: Ian J. W. Giesbrecht, Suzanne E. Tank, Gordon W. Frazer, Eran Hood, David E. Butman, David V. D’Amore, Allison Bidlack, Ken P. Lertzman Data curation: Ian J. W. Giesbrecht, Santiago G. Gonzalez Arriola, David Hutchinson Formal analysis: Ian J. W. Giesbrecht, Gordon W. Frazer, Santiago G. Gonzalez ArriolaYe

Imaging cortical dynamics in GCaMP transgenic rats with a head-mounted widefield macroscope

Widefield imaging of calcium dynamics is an emerging method for mapping regional neural activity but is currently limited to restrained animals. Here we describe cScope, a head- mounted widefield macroscope developed to image large-scale cortical dynamics in rats during natural behavior. cScope provides a 7.8 by 4 mm field of view, dual illumination paths for both fluorescence and hemodynamic correction, and can be fabricated at low cost using readily attainable components. We also report the development of Thy-1 transgenic rat strains with widespread neuronal expression of the calcium indicator GCaMP6f. We combined these two technologies to image large-scale calcium dynamics in the dorsal neocortex during a visual evidence accumulation task. Quantitative analysis of task-related dynamics revealed multiple regions having neural signals that encode behavioral choice and sensory evidence. Our results provide a new transgenic resource for calcium imaging in rats and extend the domain of headmounted microscopes to larger-scale cortical dynamics.Accepted manuscrip

The BRAIN Initiative: developing technology to catalyse neuroscience discovery

The evolution of the field of neuroscience has been propelled by the advent of novel technological capabilities, and the pace at which these capabilities are being developed has accelerated dramatically in the past decade. Capitalizing on this momentum, the United States launched the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative to develop and apply new tools and technologies for revolutionizing our understanding of the brain. In this article, we review the scientific vision for this initiative set forth by the National Institutes of Health and discuss its implications for the future of neuroscience research. Particular emphasis is given to its potential impact on the mapping and study of neural circuits, and how this knowledge will transform our understanding of the complexity of the human brain and its diverse array of behaviours, perceptions, thoughts and emotions

“Candidatus Thermonerobacter thiotrophicus,” A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities

In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named “Candidatus Thermonerobacter thiotrophicus,” which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade (“Ca. Kapabacteria”) within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism

Functional distinctiveness of major plant lineages

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106060/1/jec12208.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/106060/2/jec12208-sup-0001-Supp_Info.pd

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes