Simple connectome inference from partial correlation statistics in calcium imaging

In this work, we propose a simple yet effective solution to the problem of connectome inference in calcium imaging data. The proposed algorithm consists of two steps. First, processing the raw signals to detect neural peak activities. Second, inferring the degree of association between neurons from partial correlation statistics. This paper summarises the methodology that led us to win the Connectomics Challenge, proposes a simplified version of our method, and finally compares our results with respect to other inference methods

Diffusion in grid turbulence of isotropic macro-particles using a Lagrangian stochastic method: theory and validation.

The prediction of solid bodies transport (such as algae, debris, sediment grains, or corrosion deposits) is a necessary requirement in many industrial or environmental processes. The physical processes involved cover a wide range of processes, from tidal flow to turbulent eddies and particle drag. A stochastic model was therefore developed to link the different scales of the physical processes where it was assumed that the particles are dilute enough that they do not affect the flow or the motion of other particles while being large enough that each particle does not follow exactly the fluid motions (i.e., macro-particles). The stochastic model is built in such a way that it uses Reynolds-averaged fluid properties to predict trajectories of individual particles. This model was then tested using experimental measurements obtained for isotropic particles released in semi-homogeneous turbulence. The turbulent flow was generated using a pair of oscillating grids and was characterized using particle image velocimetry measurements. The trajectories of the particles were measured using a pair of high resolution cameras. The comparison between the experimental data and different numerical models gives satisfactory results

Population Estimate for the Bluenose-East Caribou Herd Using Post-calving Photography

Genetic and spatial analyses suggest that what was previously described as the Bluenose herd of barren-ground caribou (Rangifer tarandus groenlandicus) comprises three separate populations. Of these, the Bluenose-East caribou herd (BECH) has received little coverage in past surveys. Existing estimates of abundance suggested that current harvest rates of Bluenose-East caribou (~5000 animals/year) might be excessive. We used post-calving photography in June-July 2000 to estimate the size of the BECH. A maximum of 33 radio-collared caribou were available for location in June 2000. We located 30 of these caribou and photographed distinct groups containing 23 collared individuals. Excluding caribou assumed to belong to the neighboring Bluenose-West herd, we photographed a minimum of 84 412 adult and 4193 calf caribou. Using a simple mark-recapture model to account for caribou associated with collared individuals not photographed, we calculated an estimate of 104 000 ± 22 100 (95% CI 84 412 - 126 100) non-calf caribou. A recently published stochastic model produced a considerably higher and more variable estimate of 208 700 (95% CI 112 600 - 474 700). In March 2001, we deployed seven more radio collars in anticipation of repeating the census in 2001, but poor weather conditions precluded the formation of large aggregations. Present densities of Bluenose-East caribou seem high, and we recommend regular monitoring of body condition to assess the potential for a forage-induced population crash.Des analyses génétiques et spatiales suggèrent que ce que l'on a décrit précédemment comme le troupeau de caribous des toundras Bluenose (Rangifer tarandus groenlandicus) est en fait composé de trois populations distinctes. De ces trois hardes, le troupeau de caribous Bluenose de l'Est (TCBE) n'a pas reçu beaucoup d'attention au cours des relevés antérieurs. Les estimations d'abondance qui existent ont suggéré que le taux de prélèvement actuel de ce caribou (~ 5000 animaux/an) pourrait être excessif. On a eu recours à des clichés pris immédiatement après la mise bas en juin-juillet 2000 pour évaluer la taille du TCBE. En juin 2000, un maximum de 33 caribous munis de colliers émetteurs étaient disponibles pour la localisation. On en a repéré 30 et on a photographié des groupes distincts contenant 23 individus équipés de colliers émetteurs. Si l'on exclut les caribous qui feraient partie de la harde voisine Bluenose de l'Ouest, on a photographié un minimum de 84 412 adultes et 4193 veaux. En utilisant un simple modèle de marquage-recapture pour tenir compte des caribous reliés aux individus munis de colliers émetteurs non photographiés, on en arrive à une estimation du nombre de caribous excluant les veaux de 104 000 ± 22 100 (intervalle de confiance de 95 %: 84 412 - 126 000). Un modèle probabiliste publié récemment a donné une estimation nettement plus élevée et plus variable de 208 700 (intervalle de confiance de 95 %: 112 600 - 474 700). En mars 2001, on a eu recours à sept colliers émetteurs supplémentaires en prévision d'une reprise du recensement en 2001, mais le mauvais temps a empêché la formation de grands regroupements. Les densités actuelles du caribou Bluenose de l'Est semblent élevées, et on recommande une surveillance continue de l'état corporel afin d'évaluer le potentiel d'un effondrement de la population dû à un manque de fourrage

Estimating the potential impact of canine distemper virus on the Amur tiger population (Panthera tigris altaica) in Russia

Lethal infections with canine distemper virus (CDV) have recently been diagnosed in Amur tigers (Panthera tigris altaica), but long-term implications for the population are unknown. This study evaluates the potential impact of CDV on a key tiger population in Sikhote-Alin Biosphere Zapovednik (SABZ), and assesses how CDV might influence the extinction potential of other tiger populations of varying sizes. An individual-based stochastic, SIRD (susceptible-infected-recovered/dead) model was used to simulate infection through predation of infected domestic dogs, and/or wild carnivores, and direct tiger-to-tiger transmission. CDV prevalence and effective contact based on published and observed data was used to define plausible low- and high-risk infection scenarios. CDV infection increased the 50-year extinction probability of tigers in SABZ by 6.3% to 55.8% compared to a control population, depending on risk scenario. The most significant factors influencing model outcome were virus prevalence in the reservoir population(s) and its effective contact rate with tigers. Adjustment of the mortality rate had a proportional impact, while inclusion of epizootic infection waves had negligible additional impact. Small populations were found to be disproportionately vulnerable to extinction through CDV infection. The 50-year extinction risk in populations consisting of 25 individuals was 1.65 times greater when CDV was present than that of control populations. The effects of density dependence do not protect an endangered population from the impacts of a multi-host pathogen, such as CDV, where they coexist with an abundant reservoir presenting a persistent threat. Awareness of CDV is a critical component of a successful tiger conservation management policy

Digital Surveillance: A Novel Approach to Monitoring the Illegal Wildlife Trade

A dearth of information obscures the true scale of the global illegal trade in wildlife. Herein, we introduce an automated web crawling surveillance system developed to monitor reports on illegally traded wildlife. A resource for enforcement officials as well as the general public, the freely available website, http://www.healthmap.org/wildlifetrade, provides a customizable visualization of worldwide reports on interceptions of illegally traded wildlife and wildlife products. From August 1, 2010 to July 31, 2011, publicly available English language illegal wildlife trade reports from official and unofficial sources were collected and categorized by location and species involved. During this interval, 858 illegal wildlife trade reports were collected from 89 countries. Countries with the highest number of reports included India (n = 146, 15.6%), the United States (n = 143, 15.3%), South Africa (n = 75, 8.0%), China (n = 41, 4.4%), and Vietnam (n = 37, 4.0%). Species reported as traded or poached included elephants (n = 107, 12.5%), rhinoceros (n = 103, 12.0%), tigers (n = 68, 7.9%), leopards (n = 54, 6.3%), and pangolins (n = 45, 5.2%). The use of unofficial data sources, such as online news sites and social networks, to collect information on international wildlife trade augments traditional approaches drawing on official reporting and presents a novel source of intelligence with which to monitor and collect news in support of enforcement against this threat to wildlife conservation worldwide

Transport of isotropic particles in a partially obstructed channel flow

The transport of particles in turbulent flows is a common problem in hydraulic engineering. In this paper, the focus is set on a numerical model used to simulate the transport of small bodies (debris, algae, etc.) along a coastline. In this problem, the particles are larger than the small turbulent eddies, but smaller than the large turbulent eddies, and sufficiently diluted within the flow so that each particle does not affect the flow or the motion of other particles. A mixed Eulerian-Lagrangian approach was chosen in order to model a large flow area with sufficient information for the turbulent diffusion. This model is validated through an experiment on particles released into a partially obstructed channel flow. The measurements are then compared with simulations using two Eulerian industrial codes, Telemac-2D and OpenFoam. Finally, an application to algae bloom transport in a harbour is presented