scholarly journals Hierarchical dinucleotide distribution in genome along evolution and its effect on chromatin packing

2021 ◽  
Vol 4 (8) ◽  
pp. e202101028
Author(s):  
Zhicheng Cai ◽  
Yueying He ◽  
Sirui Liu ◽  
Yue Xue ◽  
Hui Quan ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Chromatin Structure ◽  
Distribution Patterns ◽  
Length Scales ◽  
Multi Scale ◽  
Topologically Associating Domain ◽  
Domain Boundaries ◽  
Chromatin Packing ◽  
The Difference ◽  
Genomic Length

Dinucleotide densities and their distribution patterns vary significantly among species. Previous studies revealed that CpG is susceptible to methylation, enriched at topologically associating domain boundaries and its distribution along the genome correlates with chromatin compartmentalization. However, the multi-scale organizations of CpG in the linear genome, their role in chromatin organization, and how they change along the evolution are only partially understood. By comparing the CpG distribution at different genomic length scales, we quantify the difference between the CpG distributions of different species and evaluate how the hierarchical uneven CpG distribution appears in evolution. The clustering of species based on the CpG distribution is consistent with the phylogenetic tree. Interestingly, we found the CpG distribution and chromatin structure to be correlated in many different length scales, especially for mammals and avians, consistent with the mosaic CpG distribution in the genomes of these species.

Antiphase Boundaries in Ordered Ni3FE Crystals

1969 ◽  
Vol 27 ◽  
pp. 62-63
Author(s):  
Y. H. Liu
Keyword(s):  
Domain Size ◽  
Antiphase Domain ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hardening Mechanism ◽  
Superlattice Structure ◽  
Disordered Phase ◽  
Domain Boundaries ◽  
Atomic Scattering ◽  
The Difference

Ordered Ni3Fe crystals possess a LI2 type superlattice similar to the Cu3Au structure. The difference in slip behavior of the superlattice as compared with that of a disordered phase has been well established. Cottrell first postulated that the increase in resistance for slip in the superlattice structure is attributed to the presence of antiphase domain boundaries. Following Cottrell's domain hardening mechanism, numerous workers have proposed other refined models also involving the presence of domain boundaries. Using the anomalous X-ray diffraction technique, Davies and Stoloff have shown that the hardness of the Ni3Fe superlattice varies with the domain size. So far, no direct observation of antiphase domain boundaries in Ni3Fe has been reported. Because the atomic scattering factors of the elements in NijFe are so close, the superlattice reflections are not easily detected. Furthermore, the domain configurations in NioFe are thought to be independent of the crystallographic orientations.

scholarly journals SAR Image Change Detection Based on Multi-scale Feature Extraction

2021 ◽  
Vol 10 (4) ◽  
pp. 077-081
Author(s):  
Xiaoqian Yuan ◽  
Chao Chen ◽  
Shan Tian ◽  
Jiandan Zhong
Keyword(s):  
Feature Extraction ◽  
Change Detection ◽  
Speckle Noise ◽  
Kernel Matrix ◽  
Sar Image ◽  
Scale Feature ◽  
Difference Image ◽  
Multi Scale ◽  
Image Change Detection ◽  
The Difference

In order to improve the contrast of the difference image and reduce the interference of the speckle noise in the synthetic aperture radar (SAR) image, this paper proposes a SAR image change detection algorithm based on multi-scale feature extraction. In this paper, a kernel matrix with weights is used to extract features of two original images, and then the logarithmic ratio method is used to obtain the difference images of two images, and the change area of the images are extracted. Then, the different sizes of kernel matrix are used to extract the abstract features of different scales of the difference image. This operation can make the difference image have a higher contrast. Finally, the cumulative weighted average is obtained to obtain the final difference image, which can further suppress the speckle noise in the image.

scholarly journals Nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform bridges 4-D chromatin organization with molecular function

2020 ◽  
Author(s):  
Yue Li ◽  
Adam Eshein ◽  
Ranya K.A. Virk ◽  
Aya Eid ◽  
Wenli Wu ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Electron Tomography ◽  
Population Level ◽  
Average Diameter ◽  
Chromatin Organization ◽  
Live Cells ◽  
Molecular Function ◽  
Label Free ◽  
A Cell ◽  
Chromatin Packing

AbstractIn eukaryotic cells, chromatin structure is linked to transcription processes through the regulation of genome organization. Extending across multiple length-scales - from the nucleosome to higher-order three-dimensional structures - chromatin is a dynamic system which evolves throughout the lifetime of a cell. However, no individual technique can fully elucidate the behavior of chromatin organization and its relation to molecular function at all length- and timescales at both a single-cell and a cell population level. Herein, we present a multi-technique nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform that bridges electron tomography and optical superresolution imaging of chromatin conformation and transcriptional processes, with resolution down to the level of individual nucleosomes, with high-throughput, label-free analysis of chromatin packing and its dynamics in live cells. Utilizing nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nm, sub-Mb genomic size, and an internal fractal structure. The chromatin packing behavior of these domains is directly influenced by active gene transcription. Furthermore, we demonstrated that the chromatin packing domain structure is correlated among progenitor cells and all their progeny, indicating that the organization of chromatin into fractal packing domains is heritable across cell division. Further studies employing the nano-ChIA platform have the potential to provide a more coherent picture of chromatin structure and its relation to molecular function.

scholarly journals Pendugaan Kejadian Pemutihan Karang Berdasarkan Analisis Suhu Permukaan Laut (SPL) Tahun 2015-2016 di Perairan Bali

2017 ◽  
Vol 4 (2) ◽  
pp. 286
Author(s):  
Jajang Nuryana ◽  
I Gede Hendrawan ◽  
Widiastuti Karim
Keyword(s):  
Coral Bleaching ◽  
Hot Spot ◽  
Satellite Image ◽  
Distribution Patterns ◽  
Triangle Center ◽  
Moderate Resolution ◽  
Resolution Imaging ◽  
Moderate Resolution Imaging Spectroradiometer ◽  
The Difference ◽  
Level 2

National Ocean Atmospheric Administrations (NOAA) by the program coral reef Watch (CRW) has developed a method to estimate the potential of coral bleaching using Sea Surface Temperature (SST). The products are hot spot (HS) and degree heating week (DHW). HS is the SST 1°C (SSTL?1) above normal and DHW is the length of HS inhabits a place. The CRW product do not provided detail informations because it has a lower resolution. It is need a satellite image with a higher resolution to provide better informations. One of the satellite images that can be used is Moderate Resolution Imaging Spectroradiometer (MODIS) with a spatial resolution of 1 km. The purpose of this study was to know HS and DHW distribution patterns and status of coral bleaching in Bali waters seen from the analysis of HS and DHW. MODIS data is used daily, then do mosaicing process to get a weekly SPL (8 daily) and the monthly SST. Monthly SPL normally used to get maximum montly mean (MMM). HS obtained from the difference between 8 daily weekly SST and SST normal (MMM).).Location bleaching based on data Coral Triangle Center (CTC) and coralwatch.org.  SST results revealed difference of SPL in 2015 and 2016 amounted to 1.48°C. Highest DHW in Bali Hai, Nusa Penida is 10 465° C-weeks in April 2016. Based on the value HS and DHW coral reefs in Bali waters threatened bleaching level Alert 1 and Alert level 2.

Passive Multi-Scale Alignment

2011 ◽  
Author(s):  
David O. Kazmer ◽  
Stephen P. Johnston ◽  
Mary E. Moriarty ◽  
Christopher Santeufemio
Keyword(s):  
Numerical Modeling ◽  
Ion Beam ◽  
Systematic Errors ◽  
Imprint Lithography ◽  
Physical Realization ◽  
Length Scales ◽  
Ion Beam Etching ◽  
Multi Scale ◽  
Kinematic Coupling ◽  
Multiple Length Scales

Methods are presented for self-alignment and assembly of objects with micron and nanometer-level features. The approach is a combination of kinematic coupling and elastic averaging in which mating alignment features spanning multiple length scales are successively brought into contact. When the objects are pressed together, the larger alignment features cause necessary deformation to ensure adequate alignment at the smaller length scales. Analytical and numerical modeling indicate that the largest alignment features can be designed to generally resolve global systematic errors while the smaller alignment features can correct local errors to achieve sub-micron alignment. Physical realization with ion beam etching, deposition, and thermal imprint lithography are also discussed.

scholarly journals TADBD: a sensitive and fast method for detection of typologically associated domain boundaries

BioTechniques ◽  
2020 ◽  
Vol 69 (1) ◽  
pp. 18-25
Author(s):  
Hongqiang Lyu ◽  
Lin Li ◽  
Zhifang Wu ◽  
Tian Wang ◽  
Jiguang Zheng ◽  
...  
Keyword(s):  
R Package ◽  
Computational Method ◽  
Genome Architecture ◽  
Fast Method ◽  
3D Genome ◽  
Multi Scale ◽  
Comparison Results ◽  
Contact Matrix ◽  
Domain Boundaries ◽  
Template Size

A topologically associated domain (TAD) is a self-interacting genomic block. Detection of TAD boundaries on Hi-C contact matrix is one of the most important issues in the analysis of 3D genome architecture at TAD level. Here, we present TAD boundary detection (TADBD), a sensitive and fast computational method for detection of TAD boundaries on Hi-C contact matrix. This method implements a Haar-based algorithm by considering Haar diagonal template, acceleration via a compact integrogram, multi-scale aggregation at template size and statistical filtering. In most cases, comparison results from simulated and experimental data show that TADBD outperforms the other five methods. In addition, a new R package for TADBD is freely available online.

scholarly journals Differences between the sensory organs of phytal and bottom-dwelling <i>Loxoconcha</i> (Ostracoda, Crustacea)

1989 ◽  
Vol 8 (1) ◽  
pp. 37-47 ◽  
Author(s):  
Takahiro Kamiya
Keyword(s):  
Distribution Pattern ◽  
Distribution Patterns ◽  
Morphological Features ◽  
Basal Part ◽  
Sieve Plate ◽  
Sensory Organs ◽  
Special Morphology ◽  
Mode Of Life ◽  
The Difference ◽  
Ventral Area

Abstract. The morphology and distribution patterns of pores with a bristle were studied on two Loxoconcha species living in adjacent but different habitats: the phytal species L. japonica and the bottom-dwelling species L. uranouchiensis. Both species have only one kind of pore – sieve-pore – from which either of two kinds of bristles emerges. The two types of bristles are here called the “smooth”– and the “twisted”–type according to their morphological features. The sieve-pore orifice of the phytal Loxoconcha remains completely open, whereas that of the bottom-dwelling species has a special morphology both in the sieve-plate and the basal part of the bristle to cope with the adhesion of dirt. The number and distribution pattern of “twisted”-type bristles (chemo-receptors?) are the same in both species. The “smooth”-type bristles (mechano-receptors?), however, are distributed more densely in the ventral area of the bottom-dwelling species compared with those of the phytal species. This difference seems to be related to the mode of life, specifically the difference in the manner of ventral contact with substrata. Some adaptive characters of ostracod pores are clarified and their significance to ostracod taxonomy and palaeocology is discussed.

scholarly journals Cluster formation in complex multi-scale systems

2005 ◽  
Vol 461 (2062) ◽  
pp. 3089-3097 ◽  
Author(s):  
J.D Gibbon ◽  
E.S Titi
Keyword(s):  
Spin Glasses ◽  
Cluster Formation ◽  
Generic Property ◽  
Swiss Cheese ◽  
Scaling Exponents ◽  
Length Scales ◽  
Fluid Turbulence ◽  
Multi Scale

Based on the competition between members of a hierarchy of length scales in complex multi-scale systems, it is shown how clustering of active quantities into concentrated sets, like bubbles in a Swiss cheese, is a generic property that dominates the intermittent structure. The halo-like surfaces of these clusters have scaling exponents lower than that of their kernels, which can be as high as the domain dimension. Possible examples include spots in fluid turbulence and droplets in spin-glasses.

scholarly journals The dynamics of chromatin condensation: redistribution of topoisomerase II in the 87A7 heat shock locus during induction and recovery.

1993 ◽  
Vol 13 (12) ◽  
pp. 7522-7530 ◽  
Author(s):  
A Udvardy ◽  
P Schedl
Keyword(s):  
Heat Shock ◽  
Chromatin Structure ◽  
Topoisomerase Ii ◽  
Chromatin Condensation ◽  
Intergenic Spacer ◽  
Domain Boundaries ◽  
Shock Locus ◽  
Sites Of Action ◽  
Putative Domain

We have examined the in vivo sites of action for topoisomerases II in the 87A7 heat shock locus as a function of gene activity. When the hsp70 genes are induced, there is a dramatic redistribution of topoisomerase II in the locus which parallels many of the observed alterations in chromatin structure. In addition to changes in the topoisomerase II distribution within the locus, we find topoisomerase II localized around the putative domain boundaries scs and scs'. During recovery, when the chromatin fiber of the locus recondenses, the major sites of action for topoisomerase II appear to be located within the two hsp70 genes and in the intergenic spacer separating the two genes.

scholarly journals POTENTIAL OF MULTI-TEMPORAL UAV-BORNE LIDAR IN ASSESSING EFFECTIVENESS OF SILVICULTURAL TREATMENTS

2017 ◽  
Vol XLII-2/W6 ◽  
pp. 393-397 ◽  
Author(s):  
U. Vepakomma ◽  
D. Cormier
Keyword(s):  
Resource Competition ◽  
Distribution Patterns ◽  
Forest Stand ◽  
Partial Cutting ◽  
Silvicultural Treatments ◽  
Short Period ◽  
The Difference ◽  
Silvicultural System ◽  
Individual Trees ◽  
Almost All

Silvicultural treatments are practiced to control resource competition and direct forest stand development to meet management objectives. Effective tracking of thinning and partial cutting treatments help in timely mitigation and ensuring future stand productivity. Based on a study conducted in autumn 2015, our findings in a white pine dominant forest stand in Petawawa (Ontario, Canada) showed that almost all individual trees were detectable, structure of individual trees and undergrowth was well pronounced and underlying terrain below dense undisturbed canopy was well captured with UAS based Riegl Vux-1 lidar even at a range of 150&amp;thinsp;m. Thereafter, the site was re-scanned the following summer with the same system. Besides understanding the difference in distribution patterns due to foliage conditions, co-registering the two datasets, in the current study, we tested the potential of quantifying effectiveness of a partial cutting silvicultural system especially in terms of filling of 3D spaces through vertical or lateral growth and mortality in a very short period of time.

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