scholarly journals Motion prediction enables simulated MR-imaging of freely moving model organisms

2019 ◽  
Author(s):  
Markus Reischl ◽  
Mazin Jouda ◽  
Neil MacKinnon ◽  
Erwin Fuhrer ◽  
Natalia Bakhtina ◽  
...  
Keyword(s):  
High Resolution ◽  
Region Of Interest ◽  
Magnetic Resonance Tomography ◽  
Reconstruction Algorithm ◽  
Model Organisms ◽  
Body Parts ◽  
C Elegans ◽  
Phase Errors ◽  
Freely Moving ◽  
The Impact

AbstractMagnetic resonance tomography typically applies the Fourier transform tok-space signals repeatedly acquired from a frequency encoded spatial region of interest, therefore requiring a stationary object during scanning. Any movement of the object results in phase errors in the recorded signal, leading to deformed images, phantoms, and artifacts, since the encoded information does not originate from the intended region of the object. However, if the type and magnitude of movement is known instantaneously, the scanner or the reconstruction algorithm could be adjusted to compensate for the movement, directly allowing high quality imaging with non-stationary objects. This would be an enormous boon to studies that tie cell metabolomics to spontaneous organism behaviour, eliminating the stress otherwise necessitated by restraining measures such as anesthesia or clamping.In the present theoretical study, we use a phantom of the animal modelC. elegansto examine the feasibility to automatically predict its movement and position, and to evaluate the impact of movement prediction, within a sufficiently long time horizon, on image reconstruction. For this purpose, we use automated image processing to annotate body parts in freely movingC. elegans, and predict their path of movement. We further introduce an MRI simulation platform based on brightfield-videos of the moving worm, combined with a stack of high resolution transmission electron microscope (TEM) slice images as virtual high resolution phantoms. A phantom provides an indication of the spatial distribution of signal-generating nuclei on a particular imaging slice. We show that adjustment of the scanning to the predicted movements strongly reduces distortions in the resulting image, opening the door for implementation in a high-resolution NMR scanner.

scholarly journals Azimuth Multichannel Reconstruction Based on Advanced Hyperbolic Range Equation

2021 ◽  
Vol 13 (22) ◽  
pp. 4705
Author(s):  
Wei Xu ◽  
Ruibo Li ◽  
Chonghua Fang ◽  
Pingping Huang ◽  
Weixian Tan ◽  
...  
Keyword(s):  
High Resolution ◽  
Phase Error ◽  
Reconstruction Algorithm ◽  
Doppler Spectrum ◽  
Time Varying ◽  
Reconstruction Algorithms ◽  
Additional Time ◽  
Frequency Dependent ◽  
Phase Errors ◽  
Range Equation

To acquire high-resolution wide-swath (HRWS) imaging capacity, the displaced phase center multichannel azimuth beam (DPCMAB) technology is usually adopted in spaceborne synthetic aperture radar (SAR), while multichannel reconstruction must be carried out before imaging process due to azimuth nonuniform sampling. Up to now, almost all azimuth multichannel reconstruction algorithms have been mainly based on conventional hyperbolic range equation (CHRE), but the accuracy of the CHRE model is usually not suitable for the HRWS mode, especially for high resolution and large squint observation cases. In this study, the azimuth multichannel signal model based on the advanced hyperbolic range equation (AHRE) is established and analyzed. The major difference between multichannel signal models based on CHRE and AHRE is the additional time-varying phase error between azimuth channels. The time-varying phase error is small and can be ignored in the monostatic DPCMAB SAR system, but it must be considered and compensated in the distributed DPCMAB SAR system. In addition to the time-varying phase error, additional Doppler spectrum shift and extended Doppler bandwidth should be considered in the squint case during azimuth multichannel reconstruction. The azimuth multichannel reconstruction algorithm based on AHRE is proposed in this paper. Before multichannel reconstruction and combination, time-varying phase errors between azimuth channels were first compensated, and the range-frequency-dependent de-skewing function was derived to remove the two-dimension (2D) spectrum tilt to avoid azimuth under-sampling. Then, azimuth multichannel data were reconstructed according to the azimuth multichannel impulse response based on AHRE. Finally, the range-frequency dependent re-skewing function was introduced to recover the tilted 2D spectrum. Simulation results on both point and distributed targets validated the proposed azimuth multichannel reconstruction approach.

scholarly journals AVATAR: AI Vision Analysis for Three-dimensional Action in Real-time

2022 ◽  
Author(s):  
Daesoo Kim ◽  
Dae-Gun Kim ◽  
Anna Shin ◽  
Yong-Cheol Jeong ◽  
Seahyung Park
Keyword(s):  
Artificial Intelligence ◽  
High Resolution ◽  
Real Time ◽  
Closed Loop ◽  
Three Dimensional ◽  
Body Parts ◽  
Behavioural Analysis ◽  
Action Sequences ◽  
Freely Moving ◽  
Behavioural Experiments

Artificial intelligence (AI) is an emerging tool for high-resolution behavioural analysis and conduction of human-free behavioural experiments. Here, we applied an AI-based system, AVATAR, which automatically virtualises 3D motions from the detection of 9 body parts. This allows quantification, classification and detection of specific action sequences in real-time and facilitates closed-loop manipulation, triggered by the onset of specific behaviours, in freely moving mice.

scholarly journals FreiPose: A Deep Learning Framework for Precise Animal Motion Capture in 3D Spaces

2020 ◽  
Author(s):  
Christian Zimmermann ◽  
Artur Schneider ◽  
Mansour Alyahyay ◽  
Thomas Brox ◽  
Ilka Diester
Keyword(s):  
Motor Cortex ◽  
Body Length ◽  
High Reliability ◽  
Body Parts ◽  
Learning Framework ◽  
Spontaneous Movements ◽  
Electrophysiological Recordings ◽  
Median Error ◽  
Freely Moving ◽  
The Impact

AbstractThe increasing awareness of the impact of spontaneous movements on neuronal activity has raised the need to track behavior. We present FreiPose, a versatile learning-based framework to directly capture 3D motion of freely definable points with high precision (median error < 3.5% body length, 41.9% improvement compared to state-of-the-art) and high reliability (82.8% keypoints within < 5% body length error boundary, 72.0% improvement). The versatility of FreiPose is demonstrated in two experiments: (1) By tracking freely moving rats with simultaneous electrophysiological recordings in motor cortex, we identified neuronal tuning to behavioral states and individual paw trajectories. (2) We inferred time points of optogenetic stimulation in rat motor cortex from the measured pose across individuals and attributed the stimulation effect automatically to body parts. The versatility and accuracy of FreiPose open up new possibilities for quantifying behavior of freely moving animals and may lead to new ways of setting up experiments.

scholarly journals Impact of Using a New High-Resolution Solar Reference Spectrum on OMI Ozone Profile Retrievals

2021 ◽  
Vol 14 (1) ◽  
pp. 37
Author(s):  
Juseon Bak ◽  
Odele Coddington ◽  
Xiong Liu ◽  
Kelly Chance ◽  
Hyo-Jung Lee ◽  
...  
Keyword(s):  
High Resolution ◽  
Stratospheric Ozone ◽  
Region Of Interest ◽  
Spectral Irradiance ◽  
Reference Spectrum ◽  
Radiometric Calibration ◽  
Ozone Monitoring Instrument ◽  
Ozone Profile ◽  
Relative Differences ◽  
The Impact

We evaluated a new high-resolution solar reference spectrum for characterizing space-borne Ozone Monitoring Instrument (OMI) measurements as well as for retrieving ozone profile retrievals over the ultraviolet (UV) wavelength range from 270 to 330 nm. The SAO2010 solar reference has been a standard for use in atmospheric trace gas retrievals, which is a composite of ground-based and balloon-based solar measurements from the Kitt Peak National Observatory (KPNO) and Air Force Geophysics Laboratory (AFGL), respectively. The new reference spectrum, called the TSIS-1 Hybrid Solar Reference Spectrum (HSRS), spans 202–2730 nm at a 0.01 to ~0.001 nm spectral resolution. The TSIS-1 HSRS in the UV region of interest in this study is a composite of AFGL and ground-based solar measurements from the Quality Assurance of Spectral Ultraviolet Measurements In Europe (QASUME) campaign, with a radiometric calibration that used the lower resolution Spectral Irradiance Monitor (SIM) instrument on the space-based Total and Spectral Solar Irradiance Sensor-1 (TSIS-1) mission. The TSIS-1 HSRS radiometric uncertainties were below 1% whereas those of SAO2010 ranged from 5% in the longer UV part to 15% in the shorter UV part. In deriving slit functions and wavelength shifts from OMI solar irradiances, the resulting fitting residuals showed significant improvements of 0.5–0.7% (relatively, 20–50%) due to switching from the SAO2010 to the TSIS-1 HSRS. Correspondingly, in performing ozone profile retrievals from OMI radiances, the fitting residuals showed relative improvements of up to ~5% in 312–330 nm with relative differences of 5–7% in the tropospheric layer column ozone; the impact on stratospheric ozone retrievals was negligible.

Atomic resolution characterisation of interface structures by Electron Energy Loss Spectroscopy

1993 ◽  
Vol 51 ◽  
pp. 576-577
Author(s):  
N. D. Browning ◽  
M. M. McGibbon ◽  
M. F. Chisholm ◽  
S. J. Pennycook
Keyword(s):  
High Resolution ◽  
Energy Loss ◽  
Electron Energy ◽  
Electron Energy Loss Spectroscopy ◽  
Imaging Technique ◽  
Atomic Scale ◽  
Atomic Resolution ◽  
Reference Image ◽  
The Impact ◽  
Electron Energy Loss

The recent development of the Z-contrast imaging technique for the VG HB501 UX dedicated STEM, has added a high-resolution imaging facility to a microscope used mainly for microanalysis. This imaging technique not only provides a high-resolution reference image, but as it can be performed simultaneously with electron energy loss spectroscopy (EELS), can be used to position the electron probe at the atomic scale. The spatial resolution of both the image and the energy loss spectrum can be identical, and in principle limited only by the 2.2 Å probe size of the microscope. There now exists, therefore, the possibility to perform chemical analysis of materials on the scale of single atomic columns or planes.In order to achieve atomic resolution energy loss spectroscopy, the range over which a fast electron can cause a particular excitation event, must be less than the interatomic spacing. This range is described classically by the impact parameter, b, which ranges from ~10 Å for the low loss region of the spectrum to <1Å for the core losses.

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.

Quantitative accuracy of serotonergic neurotrans-mission imaging with high-resolution 123I SPECT

2004 ◽  
Vol 43 (06) ◽  
pp. 185-189 ◽  
Author(s):  
J. T. Kuikka
Keyword(s):  
High Resolution ◽  
Scatter Correction ◽  
Region Of Interest ◽  
Binding Potential ◽  
Partial Volume ◽  
Therapeutic Drugs ◽  
Quantitative Accuracy ◽  
Critical Error ◽  
Statistical Noise

Summary Aim: Serotonin transporter (SERT) imaging can be used to study the role of regional abnormalities of neurotransmitter release in various mental disorders and to study the mechanism of action of therapeutic drugs or drugs’ abuse. We examine the quantitative accuracy and reproducibility that can be achieved with high-resolution SPECT of serotonergic neurotransmission. Method: Binding potential (BP) of 123I labeled tracer specific for midbrain SERT was assessed in 20 healthy persons. The effects of scatter, attenuation, partial volume, mis-registration and statistical noise were estimated using phantom and human studies. Results: Without any correction, BP was underestimated by 73%. The partial volume error was the major component in this underestimation whereas the most critical error for the reproducibility was misplacement of region of interest (ROI). Conclusion: The proper ROI registration, the use of the multiple head gamma camera with transmission based scatter correction introduce more relevant results. However, due to the small dimensions of the midbrain SERT structures and poor spatial resolution of SPECT, the improvement without the partial volume correction is not great enough to restore the estimate of BP to that of the true one.

High-Resolution Climate Change Impact Analysis on Expected Future Water Availability in the Upper Jordan Catchment and the Middle East

2014 ◽  
Vol 15 (4) ◽  
pp. 1517-1531 ◽  
Author(s):  
Gerhard Smiatek ◽  
Harald Kunstmann ◽  
Andreas Heckl
Keyword(s):  
Climate Change ◽  
High Resolution ◽  
Water Availability ◽  
Impact Analysis ◽  
River Flow ◽  
Climate Model ◽  
Mesoscale Model ◽  
Global Climate Model ◽  
Full Range ◽  
The Impact

Abstract The impact of climate change on the future water availability of the upper Jordan River (UJR) and its tributaries Dan, Snir, and Hermon located in the eastern Mediterranean is evaluated by a highly resolved distributed approach with the fifth-generation Pennsylvania State University–NCAR Mesoscale Model (MM5) run at 18.6- and 6.2-km resolution offline coupled with the Water Flow and Balance Simulation Model (WaSiM). The MM5 was driven with NCEP reanalysis for 1971–2000 and with Hadley Centre Coupled Model, version 3 (HadCM3), GCM forcings for 1971–2099. Because only one regional–global climate model combination was applied, the results may not give the full range of possible future projections. To describe the Dan spring behavior, the hydrological model was extended by a bypass approach to allow the fast discharge components of the Snir to enter the Dan catchment. Simulation results for the period 1976–2000 reveal that the coupled system was able to reproduce the observed discharge rates in the partially karstic complex terrain to a reasonable extent with the high-resolution 6.2-km meteorological input only. The performed future climate simulations show steadily rising temperatures with 2.2 K above the 1976–2000 mean for the period 2031–60 and 3.5 K for the period 2070–99. Precipitation trends are insignificant until the middle of the century, although a decrease of approximately 12% is simulated. For the end of the century, a reduction in rainfall ranging between 10% and 35% can be expected. Discharge in the UJR is simulated to decrease by 12% until 2060 and by 26% until 2099, both related to the 1976–2000 mean. The discharge decrease is associated with a lower number of high river flow years.

scholarly journals Myosinome: A Database of Myosins from Select Eukaryotic Genomes to Facilitate Analysis of Sequence-Structure-Function Relationships

2012 ◽  
Vol 6 ◽  
pp. BBI.S9902 ◽  
Author(s):  
Divya P. Syamaladevi ◽  
Margaret S Sunitha ◽  
S. Kalaimathy ◽  
Chandrashekar C. Reddy ◽  
Mohammed Iftekhar ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Atp Hydrolysis ◽  
Homo Sapiens ◽  
Relevant Literature ◽  
Myosin Ii ◽  
Coiled Coil ◽  
Structural Features ◽  
Model Organisms ◽  
Congenital Diseases ◽  
C Elegans

Myosins are one of the largest protein superfamilies with 24 classes. They have conserved structural features and catalytic domains yet show huge variation at different domains resulting in a variety of functions. Myosins are molecules driving various kinds of cellular processes and motility until the level of organisms. These are ATPases that utilize the chemical energy released by ATP hydrolysis to bring about conformational changes leading to a motor function. Myosins are important as they are involved in almost all cellular activities ranging from cell division to transcriptional regulation. They are crucial due to their involvement in many congenital diseases symptomatized by muscular malfunctions, cardiac diseases, deafness, neural and immunological dysfunction, and so on, many of which lead to death at an early age. We present Myosinome, a database of selected myosin classes (myosin II, V, and VI) from five model organisms. This knowledge base provides the sequences, phylogenetic clustering, domain architectures of myosins and molecular models, structural analyses, and relevant literature of their coiled-coil domains. In the current version of Myosinome, information about 71 myosin sequences belonging to three myosin classes (myosin II, V, and VI) in five model organisms ( Homo Sapiens, Mus musculus, D. melanogaster, C. elegans and S. cereviseae) identified using bioinformatics surveys are presented, and several of them are yet to be functionally characterized. As these proteins are involved in congenital diseases, such a database would be useful in short-listing candidates for gene therapy and drug development. The database can be accessed from http://caps.ncbs.res.in/myosinome .

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