Diffusive Nested Sampling

We introduce a general Monte Carlo method based on Nested Sampling (NS), for sampling complex probability distributions and estimating the normalising constant. The method uses one or more particles, which explore a mixture of nested probability distributions, each successive distribution occupying ~e^-1 times the enclosed prior mass of the previous distribution. While NS technically requires independent generation of particles, Markov Chain Monte Carlo (MCMC) exploration fits naturally into this technique. We illustrate the new method on a test problem and find that it can achieve four times the accuracy of classic MCMC-based Nested Sampling, for the same computational effort; equivalent to a factor of 16 speedup. An additional benefit is that more samples and a more accurate evidence value can be obtained simply by continuing the run for longer, as in standard MCMC.Comment: Accepted for publication in Statistics and Computing. C++ code available at http://lindor.physics.ucsb.edu/DNes

Feed-Forward Propagation of Temporal and Rate Information between Cortical Populations during Coherent Activation in Engineered In Vitro Networks.

Transient propagation of information across neuronal assembles is thought to underlie many cognitive processes. However, the nature of the neural code that is embedded within these transmissions remains uncertain. Much of our understanding of how information is transmitted among these assemblies has been derived from computational models. While these models have been instrumental in understanding these processes they often make simplifying assumptions about the biophysical properties of neurons that may influence the nature and properties expressed. To address this issue we created an in vitro analog of a feed-forward network composed of two small populations (also referred to as assemblies or layers) of living dissociated rat cortical neurons. The populations were separated by, and communicated through, a microelectromechanical systems (MEMS) device containing a strip of microscale tunnels. Delayed culturing of one population in the first layer followed by the second a few days later induced the unidirectional growth of axons through the microtunnels resulting in a primarily feed-forward communication between these two small neural populations. In this study we systematically manipulated the number of tunnels that connected each layer and hence, the number of axons providing communication between those populations. We then assess the effect of reducing the number of tunnels has upon the properties of between-layer communication capacity and fidelity of neural transmission among spike trains transmitted across and within layers. We show evidence based on Victor-Purpura's and van Rossum's spike train similarity metrics supporting the presence of both rate and temporal information embedded within these transmissions whose fidelity increased during communication both between and within layers when the number of tunnels are increased. We also provide evidence reinforcing the role of synchronized activity upon transmission fidelity during the spontaneous synchronized network burst events that propagated between layers and highlight the potential applications of these MEMs devices as a tool for further investigation of structure and functional dynamics among neural populations

Repeating Spatial-Temporal Motifs of CA3 Activity Dependent on Engineered Inputs from Dentate Gyrus Neurons in Live Hippocampal Networks.

Anatomical and behavioral studies, and in vivo and slice electrophysiology of the hippocampus suggest specific functions of the dentate gyrus (DG) and the CA3 subregions, but the underlying activity dynamics and repeatability of information processing remains poorly understood. To approach this problem, we engineered separate living networks of the DG and CA3 neurons that develop connections through 51 tunnels for axonal communication. Growing these networks on top of an electrode array enabled us to determine whether the subregion dynamics were separable and repeatable. We found spontaneous development of polarized propagation of 80% of the activity in the native direction from DG to CA3 and different spike and burst dynamics for these subregions. Spatial-temporal differences emerged when the relationships of target CA3 activity were categorized with to the number and timing of inputs from the apposing network. Compared to times of CA3 activity when there was no recorded tunnel input, DG input led to CA3 activity bursts that were 7× more frequent, increased in amplitude and extended in temporal envelope. Logistic regression indicated that a high number of tunnel inputs predict CA3 activity with 90% sensitivity and 70% specificity. Compared to no tunnel input, patterns of >80% tunnel inputs from DG specified different patterns of first-to-fire neurons in the CA3 target well. Clustering dendrograms revealed repeating motifs of three or more patterns at up to 17 sites in CA3 that were importantly associated with specific spatial-temporal patterns of tunnel activity. The number of these motifs recorded in 3 min was significantly higher than shuffled spike activity and not seen above chance in control networks in which CA3 was apposed to CA3 or DG to DG. Together, these results demonstrate spontaneous input-dependent repeatable coding of distributed activity in CA3 networks driven by engineered inputs from DG networks. These functional configurations at measured times of activation (motifs) emerge from anatomically accurate feed-forward connections from DG through tunnels to CA3

The Einstein Ring 0047-2808 Revisited: A Bayesian Inversion

In a previous paper, we outlined a new Bayesian method for inferring the properties of extended gravitational lenses, given data in the form of resolved images. This method holds the most promise for optimally extracting information from the observed image, whilst providing reliable uncertainties in all parameters. Here, we apply the method to the well studied optical Einstein ring 0047-2808. Our results are in broad agreement with previous studies, showing that the density profile of the lensing galaxy is aligned within a few degrees of the light profile, and suggesting that the source galaxy (at redshift 3.6) is a binary system, although its size is only of order 1-2 kpc. We also find that the mass of the elliptical lensing galaxy enclosed by the image is (2.91$\pm$0.01)$\times10^{11}$ M_{\sun}. Our method is able to achieve improved resolution for the source reconstructions, although we also find that some of the uncertainties are greater than has been found in previous analyses, due to the inclusion of extra pixels and a more general lens model.Comment: Accepted for publication in Ap

Student Days : March Two-Step

https://digitalcommons.library.umaine.edu/mmb-vp/2532/thumbnail.jp

Meteorological profiling in the fire environment using UAS

With the increase in commercially available small unmanned aircraft systems (UAS), new observations in extreme environments are becoming more obtainable. One such application is the fire environment, wherein measuring both fire and atmospheric properties are challenging. The Fire and Smoke Model Evaluation Experiment offered the unique opportunity of a large controlled wildfire, which allowed measurements that cannot generally be taken during an active wildfire. Fire–atmosphere interactions have typically been measured from stationary instrumented towers and by remote sensing systems such as lidar. Advances in UAS and compact meteorological instrumentation have allowed for small moving weather stations that can move with the fire front while sampling. This study highlights the use of DJI Matrice 200, which was equipped with a TriSonica Mini Wind and Weather station sonic anemometer weather station in order to sample the fire environment in an experimental and controlled setting. The weather station was mounted on to a carbon fiber pole extending off the side of the platform. The system was tested against an RM-Young 81,000 sonic anemometer, mounted at 6 and 2 m above ground levelto assess any bias in the UAS platform. Preliminary data show that this system can be useful for taking vertical profiles of atmospheric variables, in addition to being used in place of meteorological tower measurements when suitable

The 2018 Camp Fire: Meteorological analysis using in situ observations and numerical simulations

The November 2018 Camp Fire quickly became the deadliest and most destructive wildfire in California history. In this case study, we investigate the contribution of meteorological conditions and, in particular, a downslope windstorm that occurred during the 2018 Camp Fire. Dry seasonal conditions prior to ignition led to 100-h fuel moisture contents in the region to reach record low levels. Meteorological observations were primarily made from a number of remote automatic weather stations and a mobile scanning Doppler lidar deployed to the fire on 8 November 2018. Additionally, gridded operational forecast models and high-resolution meteorological simulations were synthesized in the analysis to provide context for the meteorological observations and structure of the downslope windstorm. Results show that this event was associated with mid-level anti-cyclonic Rossby wave breaking likely caused by cold air advection aloft. An inverted surface trough over central California created a pressure gradient which likely enhanced the downslope winds. Sustained surface winds between 3-6 m s1 were observed with gusts of over 25 m s-1 while winds above the surface were associated with an intermittent low-level jet. The meteorological conditions of the event were well forecasted, and the severity of the fire was not surprising given the fire danger potential for that day. However, use of surface networks alone do not provide adequate observations for understanding downslope windstorm events and their impact on fire spread. Fire management operations may benefit from the use of operational wind profilers to better understand the evolution of downslope windstorms and other fire weather phenomena that are poorly understood and observed

Antigen depot is not required for alum adjuvanticity

Alum adjuvants have been in continuous clinical use for more than 80 yr. While the prevailing theory has been that depot formation and the associated slow release of antigen and/or inflammation are responsible for alum enhancement of antigen presentation and subsequent T- and B-cell responses, this has never been formally proven. To examine antigen persistence, we used the chimeric fluorescent protein EαGFP, which allows assessment of antigen presentation in situ, using the Y-Ae antibody. We demonstrate that alum and/or CpG adjuvants induced similar uptake of antigen, and in all cases, GFP signal did not persist beyond 24 h in draining lymph node antigen-presenting cells. Antigen presentation was first detectable on B cells within 6–12 h of antigen administration, followed by conventional dendritic cells (DCs) at 12–24 h, then finally plasmacytoid DCs at 48 h or later. Again, alum and/or CpG adjuvants did not have an effect on the magnitude or sequence of this response; furthermore, they induced similar antigen-specific T-cell activation in vivo. Notably, removal of the injection site and associated alum depot, as early as 2 h after administration, had no appreciable effect on antigen-specific T- and B-cell responses. This study clearly rules out a role for depot formation in alum adjuvant activity