scholarly journals Single-cell absolute contact probability detection reveals that chromosomes are organized by multiple, low-frequency yet specific interactions

2017 ◽  
Author(s):  
Diego I. Cattoni ◽  
Andrés M. Cardozo Gizzi ◽  
Mariya Georgieva ◽  
Marco Di Stefano ◽  
Alessandro Valeri ◽  
...  
Keyword(s):  
Single Cell ◽  
Low Frequency ◽  
Super Resolution ◽  
Specific Interactions ◽  
Chromosome Architecture ◽  
Dna Labeling ◽  
Topologically Associated Domains ◽  
Large Heterogeneity ◽  
Transcriptional State ◽  
Eukaryotic Genomes

AbstractAt the kilo- to mega-base pair scales, eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that associate to form nuclear compartments. Here, we combined high-content super-resolution microscopies with state-of-the-art DNA labeling methods to reveal the variability in the multiscale organization of the Drosophila genome. We found that association frequencies within TADs and between TAD borders are below ~10%, independently of TAD size, epigenetic state, or cell type. Critically, despite this large heterogeneity, we were able to visualize nanometer-sized epigenetic domains at the single-cell level. In addition, absolute contact frequencies within and between TADs were to a large extent defined by genomic distance, higher-order chromosome architecture, and epigenetic identity. We propose that TADs and compartments are organized by multiple, small frequency, yet specific interactions that are regulated by epigenetics and transcriptional state.

scholarly journals Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Diego I. Cattoni ◽  
Andrés M. Cardozo Gizzi ◽  
Mariya Georgieva ◽  
Marco Di Stefano ◽  
Alessandro Valeri ◽  
...  
Keyword(s):  
Single Cell ◽  
Low Frequency ◽  
Specific Interactions ◽  
Contact Probability

Single-cell approaches to understand genome organisation throughout the cell cycle

2019 ◽  
Vol 63 (2) ◽  
pp. 209-216
Author(s):  
Sarah E. McClelland
Keyword(s):  
Cell Cycle ◽  
Single Cell ◽  
Biological Data ◽  
Genome Architecture ◽  
Chromosome Architecture ◽  
Current State ◽  
Topologically Associated Domains ◽  
Mammalian Genomes ◽  
A Cell ◽  
Cell Variation

Abstract Mammalian genomes are ordered at several scales, ranging from nucleosomes (beads on a string), to topologically associated domains (TADs), laminar associated domains (LADs), and chromosome territories. These are described briefly below and we refer the reader to some recent comprehensive reviews on genome architecture summarising the current state of knowledge of the organisational principles of the nucleus [1,2]. Biological observations from populations of millions of individual cells can reveal consensus behaviour. New methods to study and interpret biological data at the single-cell level have recently been instrumental in revealing new understanding of cell-to-cell variation and novel biology. Here we will summarise the recent advances in single-cell technology that have provided insights into the behaviour of the mammalian genome during a cell cycle. We will focus on the interphase domain structure of chromosomes, including TADs and LADs, and how chromosome architecture changes during the cell cycle. The role of genome architecture relating to gene expression has been reviewed elsewhere [3].

scholarly journals Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joris J. B. Messelink ◽  
Muriel C. F. van Teeseling ◽  
Jacqueline Janssen ◽  
Martin Thanbichler ◽  
Chase P. Broedersz
Keyword(s):  
Single Cell ◽  
Caulobacter Crescentus ◽  
Model Organism ◽  
Super Resolution ◽  
Chromosome Organization ◽  
General Strategy ◽  
Cell Axis ◽  
Cellular Processes ◽  
Emergent Order ◽  
Genomic Clusters

AbstractThe order and variability of bacterial chromosome organization, contained within the distribution of chromosome conformations, are unclear. Here, we develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi–C experiments on the model organism Caulobacter crescentus. The predictive power of our model is validated by independent experiments. We find that on large genomic scales, organizational features are predominantly present along the long cell axis: chromosomal loci exhibit striking long-ranged two-point axial correlations, indicating emergent order. This organization is associated with large genomic clusters we term Super Domains (SuDs), whose existence we support with super-resolution microscopy. On smaller genomic scales, our model reveals chromosome extensions that correlate with transcriptional and loop extrusion activity. Finally, we quantify the information contained in chromosome organization that may guide cellular processes. Our approach can be extended to other species, providing a general strategy to resolve variability in single-cell chromosomal organization.

The enhanced deep Plug-and-play super-resolution algorithm with residual channel attention networks

2021 ◽  
pp. 1-10
Author(s):  
Hongguang Pan ◽  
Fan Wen ◽  
Xiangdong Huang ◽  
Xinyu Lei ◽  
Xiaoling Yang
Keyword(s):  
Signal To Noise Ratio ◽  
Low Frequency ◽  
Super Resolution ◽  
Structural Similarity ◽  
Plug And Play ◽  
Attention Networks ◽  
Frequency Information ◽  
Blind Deblurring ◽  
Adaptive Adjustment ◽  
Deep Feature Extraction

In the field of super-resolution image reconstruction, as a learning-based method, deep plug-and-play super-resolution (DPSR) algorithm can be used to find the blur kernel by using the existing blind deblurring methods. However, DPSR is not flexible enough in processing images with high- and low-frequency information. Considering a channel attention mechanism can distinguish low-frequency information and features in low-resolution images, in this paper, we firstly introduce this mechanism and design a new residual channel attention networks (RCAN); then the RCAN is adopted to replace deep feature extraction part in DPSR to achieve the adaptive adjustment of channel characteristics. Through four test experiments based on Set5, Set14, Urban100 and BSD100 datasets, we find that, under different blur kernels and different scale factors, the average peak signal to noise ratio (PSNR) and structural similarity (SSIM) values of our proposed method increase by 0.31dB and 0.55%, respectively; under different noise levels, the average PSNR and SSIM values increase by 0.26dB and 0.51%, respectively.

scholarly journals TADs or no TADS: Lessons From Single-cell Imaging of Chromosome Architecture

2020 ◽  
Vol 432 (3) ◽  
pp. 682-693 ◽  
Author(s):  
Andrés M. Cardozo Gizzi ◽  
Diego I. Cattoni ◽  
Marcelo Nollmann
Keyword(s):  
Single Cell ◽  
Cell Imaging ◽  
Chromosome Architecture ◽  
Single Cell Imaging

scholarly journals Super-resolution imaging of a low frequency levitated oscillator

2019 ◽  
Vol 90 (9) ◽  
pp. 093201 ◽  
Author(s):  
N. P. Bullier ◽  
A. Pontin ◽  
P. F. Barker
Keyword(s):  
Low Frequency ◽  
Super Resolution ◽  
Resolution Imaging

SiC BJT's for High Power Switching and RF Applications

2002 ◽  
Vol 742 ◽  
Author(s):  
Anant Agarwal ◽  
Sei-Hyung Ryu ◽  
Craig Capell ◽  
James Richmond ◽  
John W. Palmour ◽  
...  
Keyword(s):  
Single Cell ◽  
Temperature Coefficient ◽  
Supply Voltage ◽  
Maximum Output Power ◽  
Low Frequency ◽  
Current Gain ◽  
Maximum Output ◽  
Positive Temperature ◽  
Power Gain ◽  
Power Switching

ABSTRACTIn this paper, high performance, high voltage NPN bipolar junction transistors in 4H-SiC are presented for applications in low frequency (< 5 MHz) power conversion systems as well as in RF (425 MHz) power amplifiers. The power BJTs for low frequency switching applications were designed to block 1300 V and showed a specific on-resistance of 8.0 mohm-cm2, which outperforms all SiC power switching devices ever reported. Moreover, these transistors show a positive temperature coefficient in the on-resistance and a negative temperature coefficient in the current gain, which enable easy paralleling of the devices. In addition, RF BJTs were designed, fabricated and tested for operation at UHF frequencies. The common emitter breakdown voltage was in excess of 500 V consistent with the 5 micron collector thickness. For VCC = 20 V, fT peaked at about 1.5 GHz. A single cell was measured in common emitter mode with a collector supply voltage of 80 V in class AB at 425 MHz. A 100 μs pulse width with 10% duty cycle was used. A maximum output power of 50 W for a single cell was achieved. The peak large signal power gain was 9.6 dB. The collector efficiency at the power output of 50 W was 51% with a power gain of 9.3 dB. This represents the first demonstration of a SiC RF BJT.

scholarly journals EXPOSURE TO EXTREMELY LOW-FREQUENCY MAGNETIC FIELDS IN LOW- AND MIDDLE-INCOME COUNTRIES: AN OVERVIEW

2020 ◽  
Vol 191 (4) ◽  
pp. 487-500
Author(s):  
Dan Baaken ◽  
Daniel Wollschläger ◽  
Theodoros Samaras ◽  
Joachim Schüz ◽  
Isabelle Deltour
Keyword(s):  
Literature Search ◽  
Low Frequency ◽  
Limited Data ◽  
Qualitative Synthesis ◽  
Middle Income ◽  
Extremely Low Frequency ◽  
Middle Income Countries ◽  
Frequency Magnetic Field ◽  
Large Heterogeneity ◽  
Low And Middle Income

Abstract To compare extremely low-frequency magnetic field (ELF-MF) exposure in the general population in low- and middle-income countries (LMICs) with high-income countries (HIC), we carried out a systematic literature search resulting in 1483 potentially eligible articles; however, only 25 studies could be included in the qualitative synthesis. Studies showed large heterogeneity in design, exposure environment and exposure assessment. Exposure assessed by outdoor spot measurements ranged from 0.03 to 4μT. Average exposure by indoor spot measurements in homes ranged from 0.02 to 0.4μT. Proportions of homes exposed to a threshold of ≥0.3μT were many times higher in LMICs compared to HIC. Based on the limited data available, exposure to ELF-MF in LMICs appeared higher than in HIC, but a direct comparison is hampered by a lack of representative and systematic monitoring studies. Representative measurement studies on residential exposure to ELF-MF are needed in LMICs together with better standardisation in the reporting.

ac Impedance Study of a Proton Exchange Membrane Fuel Cell Stack Under Various Loading Conditions

2010 ◽  
Vol 7 (3) ◽  
Author(s):  
N. V. Dale ◽  
M. D. Mann ◽  
H. Salehfar ◽  
A. M. Dhirde ◽  
T. Han
Keyword(s):  
Fuel Cell ◽  
Single Cell ◽  
Proton Exchange Membrane ◽  
Low Frequency ◽  
Impedance Analysis ◽  
Pem Fuel Cell ◽  
Ac Impedance ◽  
Proton Exchange ◽  
Fuel Cell Stack ◽  
Exchange Membrane

This paper presents the ac impedance study and analysis of a proton exchange membrane (PEM) fuel cell operated under various loading conditions. Ballard’s 1.2 kW Nexa™ fuel cell used for this study is integrated with a control system. The PEM fuel cell stack was operated using room air and pure hydrogen (99.995%) as input. Impedance data were collected for the fuel cell to study the behavior of the stack and groups of cells under various loads. Single cell impedance analysis was also performed for individual cells placed at different locations in the stack. The ac impedance analysis, also known as electrochemical impedance analysis, showed low frequency inductive effects and mass transport losses due to liquid water accumulation at high current densities. Results show that the stack run time to achieve steady state for impedance measurements is important. Using impedance plots, the average Ohmic resistance for the whole stack was estimated to be 41 mΩ, the same value obtained when summing the resistance value of all individual cells. Impedance analysis for groups of cells at different locations in the stack shows changes in both polarization resistance and capacitive component only in the low frequency region. At high frequencies, single cell inductive and capacitive behavior varied as a function of location in the stack. The effects of artifacts on the high frequency loop and on the high and low frequency intercept loops are also discussed.

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