scholarly journals WormPose: Image synthesis and convolutional networks for pose estimation in C. elegans

2021 ◽  
Vol 17 (4) ◽  
pp. e1008914
Author(s):  
Laetitia Hebert ◽  
Tosif Ahamed ◽  
Antonio C. Costa ◽  
Liam O’Shaughnessy ◽  
Greg J. Stephens
Keyword(s):  
Pose Estimation ◽  
Synthetic Data ◽  
Image Synthesis ◽  
Video Data ◽  
C Elegans ◽  
Convolutional Networks ◽  
Food Conditions ◽  
And Behavior ◽  
Nematode Worm ◽  
Imaging Conditions

An important model system for understanding genes, neurons and behavior, the nematode worm C. elegans naturally moves through a variety of complex postures, for which estimation from video data is challenging. We introduce an open-source Python package, WormPose, for 2D pose estimation in C. elegans, including self-occluded, coiled shapes. We leverage advances in machine vision afforded from convolutional neural networks and introduce a synthetic yet realistic generative model for images of worm posture, thus avoiding the need for human-labeled training. WormPose is effective and adaptable for imaging conditions across worm tracking efforts. We quantify pose estimation using synthetic data as well as N2 and mutant worms in on-food conditions. We further demonstrate WormPose by analyzing long (∼ 8 hour), fast-sampled (∼ 30 Hz) recordings of on-food N2 worms to provide a posture-scale analysis of roaming/dwelling behaviors.

scholarly journals WormPose: Image synthesis and convolutional networks for pose estimation in C. elegans

2020 ◽  
Author(s):  
Laetitia Hebert ◽  
Tosif Ahamed ◽  
Antonio C. Costa ◽  
Liam O’Shaugnessy ◽  
Greg J. Stephens
Keyword(s):  
Pose Estimation ◽  
Synthetic Data ◽  
Image Synthesis ◽  
Video Data ◽  
C Elegans ◽  
Convolutional Networks ◽  
Food Conditions ◽  
And Behavior ◽  
Nematode Worm ◽  
Imaging Conditions

An important model system for understanding genes, neurons and behavior, the nematode worm C. elegans naturally moves through a variety of complex postures, for which estimation from video data is challenging. We introduce an open-source Python package, WormPose, for 2D pose estimation in C. elegans, including self-occluded, coiled shapes. We leverage advances in machine vision afforded from convolutional neural networks and introduce a synthetic yet realistic generative model for images of worm posture, thus avoiding the need for human-labeled training. WormPose is effective and adaptable for imaging conditions across worm tracking efforts. We quantify pose estimation using synthetic data as well as N2 and mutant worms in on-food conditions. We further demonstrate WormPose by analyzing long (∼ 10 hour), fast-sampled (∼ 30 Hz) recordings of on-food N2 worms to provide a posture-scale analysis of roaming/dwelling behaviors.

The glycomes of Caenorhabditis elegans and other model organisms

2002 ◽  
Vol 69 ◽  
pp. 117-134 ◽  
Author(s):  
Stuart M. Haslam ◽  
David Gems ◽  
Howard R. Morris ◽  
Anne Dell
Keyword(s):  
Caenorhabditis Elegans ◽  
Current Knowledge ◽  
Structural Data ◽  
Model Organisms ◽  
Entire Genome ◽  
C Elegans ◽  
The Face ◽  
Area Of Concern ◽  
Nematode Worm

There is no doubt that the immense amount of information that is being generated by the initial sequencing and secondary interrogation of various genomes will change the face of glycobiological research. However, a major area of concern is that detailed structural knowledge of the ultimate products of genes that are identified as being involved in glycoconjugate biosynthesis is still limited. This is illustrated clearly by the nematode worm Caenorhabditis elegans, which was the first multicellular organism to have its entire genome sequenced. To date, only limited structural data on the glycosylated molecules of this organism have been reported. Our laboratory is addressing this problem by performing detailed MS structural characterization of the N-linked glycans of C. elegans; high-mannose structures dominate, with only minor amounts of complex-type structures. Novel, highly fucosylated truncated structures are also present which are difucosylated on the proximal N-acetylglucosamine of the chitobiose core as well as containing unusual Fucα1–2Gal1–2Man as peripheral structures. The implications of these results in terms of the identification of ligands for genomically predicted lectins and potential glycosyltransferases are discussed in this chapter. Current knowledge on the glycomes of other model organisms such as Dictyostelium discoideum, Saccharomyces cerevisiae and Drosophila melanogaster is also discussed briefly.

scholarly journals Hydrogen Sulfide Increases Hypoxia-inducible Factor-1 Activity Independently of von Hippel–Lindau Tumor Suppressor-1 inC. elegans

2010 ◽  
Vol 21 (1) ◽  
pp. 212-217 ◽  
Author(s):  
Mark W. Budde ◽  
Mark B. Roth
Keyword(s):  
Hydrogen Sulfide ◽  
Tumor Suppressor ◽  
Environmental Changes ◽  
Hypoxia Inducible Factor ◽  
Low Oxygen ◽  
Animal Cells ◽  
Von Hippel Lindau ◽  
C Elegans ◽  
Reporter Activity ◽  
And Behavior

Rapid alteration of gene expression in response to environmental changes is essential for normal development and behavior. The transcription factor hypoxia-inducible factor (HIF)-1 is well known to respond to alterations in oxygen availability. In nature, low oxygen environments are often found to contain high levels of hydrogen sulfide (H2S). Here, we show that Caenorhabditis elegans can have mutually exclusive responses to H2S and hypoxia, both involving HIF-1. Specifically, H2S results in HIF-1 activity throughout the hypodermis, whereas hypoxia causes HIF-1 activity in the gut as judged by a reporter for HIF-1 activity. C. elegans require hif-1 to survive in room air containing trace amounts of H2S. Exposure to H2S results in HIF-1 nuclear localization and transcription of HIF-1 targets. The effects of H2S on HIF-1 reporter activity are independent of von Hippel–Lindau tumor suppressor (VHL)-1, whereas VHL-1 is required for hypoxic regulation of HIF-1 reporter activity. Because H2S is naturally produced by animal cells, our results suggest that endogenous H2S may influence HIF-1 activity.

In-Cabin vehicle synthetic data to test Deep Learning based human pose estimation models

2021 ◽  
Author(s):  
Luis Gustavo Tomal Ribas ◽  
Marta Pereira Cocron ◽  
Joed Lopes Da Silva ◽  
Alessandro Zimmer ◽  
Thomas Brandmeier
Keyword(s):  
Deep Learning ◽  
Pose Estimation ◽  
Synthetic Data ◽  
Human Pose Estimation ◽  
Human Pose ◽  
Estimation Models

6DoF Pose Estimation for Industrial Manipulation Based on Synthetic Data

2020 ◽  
pp. 675-684
Author(s):  
Manuel Brucker ◽  
Maximilian Durner ◽  
Zoltán-Csaba Márton ◽  
Ferenc Bálint-Benczédi ◽  
Martin Sundermeyer ◽  
...  
Keyword(s):  
Pose Estimation ◽  
Synthetic Data

scholarly journals Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans

2016 ◽  
Vol 113 (36) ◽  
pp. 10055-10060 ◽  
Author(s):  
Xinxing Zhang ◽  
Kunhua Li ◽  
Rachel A. Jones ◽  
Steven D. Bruner ◽  
Rebecca A. Butcher
Keyword(s):  
Caenorhabditis Elegans ◽  
Nematode Species ◽  
Binding Pocket ◽  
Pheromone Biosynthesis ◽  
Atp Binding ◽  
Metabolic State ◽  
C Elegans ◽  
Acyl Coa Oxidase ◽  
Key Residues ◽  
And Behavior

Caenorhabditis elegans secretes ascarosides as pheromones to communicate with other worms and to coordinate the development and behavior of the population. Peroxisomal β-oxidation cycles shorten the side chains of ascaroside precursors to produce the short-chain ascaroside pheromones. Acyl-CoA oxidases, which catalyze the first step in these β-oxidation cycles, have different side chain-length specificities and enable C. elegans to regulate the production of specific ascaroside pheromones. Here, we determine the crystal structure of the acyl-CoA oxidase 1 (ACOX-1) homodimer and the ACOX-2 homodimer bound to its substrate. Our results provide a molecular basis for the substrate specificities of the acyl-CoA oxidases and reveal why some of these enzymes have a very broad substrate range, whereas others are quite specific. Our results also enable predictions to be made for the roles of uncharacterized acyl-CoA oxidases in C. elegans and in other nematode species. Remarkably, we show that most of the C. elegans acyl-CoA oxidases that participate in ascaroside biosynthesis contain a conserved ATP-binding pocket that lies at the dimer interface, and we identify key residues in this binding pocket. ATP binding induces a structural change that is associated with tighter binding of the FAD cofactor. Mutations that disrupt ATP binding reduce FAD binding and reduce enzyme activity. Thus, ATP may serve as a regulator of acyl-CoA oxidase activity, thereby directly linking ascaroside biosynthesis to ATP concentration and metabolic state.

Spatiotemporal multi-graph convolutional networks with synthetic data for traffic volume forecasting

2021 ◽  
pp. 115992
Author(s):  
Kun Zhu ◽  
Shuai Zhang ◽  
Jiusheng Li ◽  
Di Zhou ◽  
Hua Dai ◽  
...  
Keyword(s):  
Synthetic Data ◽  
Traffic Volume ◽  
Convolutional Networks

Structure-aware human pose estimation with graph convolutional networks

2020 ◽  
Vol 106 ◽  
pp. 107410 ◽  
Author(s):  
Yanrui Bin ◽  
Zhao-Min Chen ◽  
Xiu-Shen Wei ◽  
Xinya Chen ◽  
Changxin Gao ◽  
...  
Keyword(s):  
Pose Estimation ◽  
Human Pose Estimation ◽  
Convolutional Networks ◽  
Human Pose
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