Trainable, vision-based automated home cage behavioral phenotyping

We describe a fully trainable computer vision system enabling the automated analysis of complex mouse behaviors. Our system computes a sequence of feature descriptors for each video sequence and a classifier is used to learn a mapping from these features to behaviors of interest. We collected a very large manually annotated video database of mouse behaviors for training and testing the system. Our system performs on par with human scoring, as measured from the ground-truth manual annotations of thousands of clips of freely behaving mice. As a validation of the system, we characterized the home cage behaviors of two standard inbred and two nonstandard mouse strains. From this data, we were able to predict the strain identity of individual mice with high accuracy.California Institute of Technology. Broad Fellows Program in Brain CircuitryNational Science Council of Taiwan (TMS-094-1-A032

Towards understanding action recognition

International audienceAlthough action recognition in videos is widely studied, current methods often fail on real-world datasets. Many recent approaches improve accuracy and robustness to cope with challenging video sequences, but it is often unclear what affects the results most. This paper attempts to provide insights based on a systematic performance evaluation using thoroughly-annotated data of human actions. We annotate human Joints for the HMDB dataset (J-HMDB). This annotation can be used to derive ground truth optical flow and segmentation. We evaluate current methods using this dataset and systematically replace the output of various algorithms with ground truth. This enables us to discover what is important - for example, should we work on improving flow algorithms, estimating human bounding boxes, or enabling pose estimation? In summary, we find that highlevel pose features greatly outperform low/mid level features; in particular, pose over time is critical, but current pose estimation algorithms are not yet reliable enough to provide this information. We also find that the accuracy of a top-performing action recognition framework can be greatly increased by refining the underlying low/mid level features; this suggests it is important to improve optical flow and human detection algorithms. Our analysis and JHMDB dataset should facilitate a deeper understanding of action recognition algorithms

Algorithms in nature: the convergence of systems biology and computational thinking

Biologists rely on computational methods to analyze and integrate large data sets, while several computational methods were inspired by the high-level design principles of biological systems. This Perspectives discusses the recent convergence of these two ways of thinking

Automated Home-Cage Behavioural Phenotyping of Mice

Neurobehavioral analysis of mouse phenotypes requires the monitoring of mouse behavior over long periods of time. Here, we describe a trainable computer vision system enabling the automated analysis of complex mouse behaviors. We provide software and an extensive manually annotated video database used for training and testing the system. Our system performs on par with human scoring, as measured from ground-truth manual annotations of thousands of clips of freely behaving mice. As a validation of the system, we characterized the home-cage behaviors of two standard inbred and two non-standard mouse strains. From this data we were able to predict in a blind test the strain identity of individual animals with high accuracy. Our video-based software will complement existing sensor based automated approaches and enable an adaptable, comprehensive, high-throughput, fine-grained, automated analysis of mouse behavior.McGovern Institute for Brain ResearchCalifornia Institute of Technology. Broad Fellows Program in Brain CircuitryNational Science Council (China) (TMS-094-1-A032

Functional Characterization of a Lipoprotein-Encoding Operon in Campylobacter jejuni

Background: Bacterial lipoproteins have important functions in bacterial pathogenesis and physiology. In Campylobacter jejuni, a major foodborne pathogen causing gastroenteritis in humans, the majority of lipoproteins have not been functionally characterized. Previously, we showed by DNA microarray that CmeR, a transcriptional regulator repressing the expression of the multidrug efflux pump CmeABC, modulates the expression of a three-gene operon (cj0089, cj0090, and cj0091) encoding a cluster of lipoproteins in C. jejuni. Methodology/Principal Findings: In this work, we characterized the function and regulation of the cj0089-cj0090-cj0091 operon. In contrast to the repression of cmeABC, CmeR activates the expression of the lipoprotein genes and the regulation is confirmed by immunoblotting using anti-Cj0089 and anti-Cj0091 antibodies. Gel mobility shift assay showed that CmeR directly binds to the promoter of the lipoprotein operon, but the binding is much weaker compared with the promoter of cmeABC. Analysis of different cellular fractions indicated that Cj0089 was associated with the inner membrane, while Cj0091 was located on the outer membrane. Inactivation of cj0091, but not cj0089, significantly reduced the adherence of C. jejuni to INT 407 cells in vitro, indicating that Cj0091 has a function in adherence. When inoculated into chickens, the Cj0091 mutant also showed a defect in early colonization of the intestinal tract, suggesting that Cj0091 contributes to Campylobacter colonization in vivo. It was also shown that Cj0091 was produced and immunogenic in chickens that wer

Chitosan Modification of Adenovirus to Modify Transfection Efficiency in Bovine Corneal Epithelial Cells

BACKGROUND: The purpose of this study is to modulate the transfection efficiency of adenovirus (Ad) on the cornea by the covalent attachment of chitosan on adenoviral capsids via a thioether linkage between chitosan modified with 2-iminothiolane and Ad cross-linked with N-[gamma-maleimidobutyryloxy]succinimide ester (GMBS). METHODOLOGY/PRINCIPAL FINDINGS: Modified Ad was obtained by reaction with the heterobifunctional crosslinking reagent, GMBS, producing maleimide-modified Ad (Ad-GMBS). Then, the chitosan-SH was conjugated to Ad-GMBS via a thioether bond at different ratios of Ad to GMBS to chitosan-SH. The sizes and zeta potentials of unmodified Ad and chitosan-modified Ads were measured, and the morphologies of the virus particles were observed under transmission electron microscope. Primary cultures of bovine corneal epithelial cells were transfected with Ads and chitosan-modified Ads in the absence or presence of anti-adenovirus antibodies. Chitosan modification did not significantly change the particle size of Ad, but the surface charge of Ad increased significantly from -24.3 mV to nearly neutral. Furthermore, primary cultures of bovine corneal epithelial cells were transfected with Ad or chitosan-modified Ad in the absence or presence of anti-Ad antibodies. The transfection efficiency was attenuated gradually with increasing amounts of GMBS. However, incorporation of chitosan partly restored transfection activity and rendered the modified antibody resistant to antibody neutralization. CONCLUSIONS/SIGNIFICANCE: Chitosan can provide a platform for chemical modification of Ad, which offers potential for further in vivo applications

The midlatitude electron density enhancement observed by DEMETER

International audienceNighttime enhancements of the ionospheric F2 region electron density have been observed by ionosonde, incoherent scatter radar (ISR), GPS total electron content, and tomograpgic techniques. The French micro satellite DEMETER was launched on 29 June 2004. DEMETER is a sun-synchronized orbital satellite at 710 km altitude, and named after the Greek goddess of agriculture. The scientific mission is mainly designed to investigate the Earth ionosphere disturbances due to seismic and volcanic activities but also survey the electro-magnetic disturbances of planet linked with anthropogenic activity. Several scientific payloads are embedded in DEMETER, such as IMSC, IDP, ISL, ICE. In this paper, we study the electron density and electron temperature variations observed by ISL onboard DEMETER. ISL is the Langmuir probe produced by the European Space Technology and Research Centre to measure the density and temperature of thermal plasma. Based on long-term observations, the midlatitude enhancements of the electron density are also observed by DEMETER ISL data. We investigate 5 years data during 2005-2009 and find that the midlatitude enhancement mainly appear in nighttime from September to April. The detail results will be presented and discussed

The midlatitude electron density enhancement observed by DEMETER

International audienceNighttime enhancements of the ionospheric F2 region electron density have been observed by ionosonde, incoherent scatter radar (ISR), GPS total electron content, and tomograpgic techniques. The French micro satellite DEMETER was launched on 29 June 2004. DEMETER is a sun-synchronized orbital satellite at 710 km altitude, and named after the Greek goddess of agriculture. The scientific mission is mainly designed to investigate the Earth ionosphere disturbances due to seismic and volcanic activities but also survey the electro-magnetic disturbances of planet linked with anthropogenic activity. Several scientific payloads are embedded in DEMETER, such as IMSC, IDP, ISL, ICE. In this paper, we study the electron density and electron temperature variations observed by ISL onboard DEMETER. ISL is the Langmuir probe produced by the European Space Technology and Research Centre to measure the density and temperature of thermal plasma. Based on long-term observations, the midlatitude enhancements of the electron density are also observed by DEMETER ISL data. We investigate 5 years data during 2005-2009 and find that the midlatitude enhancement mainly appear in nighttime from September to April. The detail results will be presented and discussed

Multidisciplinary Approach for Earthquake Atmospheric Precursors Validation by Joint Satellite and Ground Based Observations

International audiencePrevious studies have shown that there were electromagnetic (EM) effects in the atmosphere/ionosphere caused by some strong earthquakes. Several major earthquakes are accompanied by an intensification of the vertical transport of charged aerosols in the lower atmosphere. These processes lead to the generation of external electric currents in specific regions of the atmosphere and the modifications, by DC electric fields, in the ionosphere-atmosphere electric circuit. Our methodology of integrated satellite terrestrial framework (ISTF) is based on the use of multi-sensor data and a cross-correlation between ground and satellite observations to record any atmospheric thermal anomalies and ionospheric perturbations associated with these activities. We record thermal infrared data from the Aqua, GOES, POES satellites and DEMETER provides space plasma variations related to the growth of the DC electric field. Simultaneously we continuously monitor ground-based multi-parameter GPS/TEC, ion concentration, radon, and magnetic field array data. We integrate these joint observations into the Lithosphere-Atmosphere-Ionosphere Coupling (LAIC) model. The significance of this combined satellite and ground-based analysis is that it permits us to generate hindcasts of historical seismicity in Japan, Taiwan (2003-2009) and recent catastrophic events in Italy (M6.3, 2009), Haiti (M7.0, 2010) and Chile (M8.8, 2010). This joint analysis of ground and satellite data during the time of major earthquakes has shown the presence of persistent anomalies in the atmosphere over regions of maximum stress (along plate boundaries), and are not of meteorological origin, since they are stationary over the same region. Our approach provides the framework for a multidisciplinary validation of earthquake precursors and we are looking forward to validating this approach over high seismicity regions