The local method applied to the robust detection of changes in the poles of a pole-zero system

AbstractTopologically associating domains (TADs) are the organizational units of chromosome structures. TADs can contain TADs, thus forming a hierarchy. TAD hierarchies can be inferred from Hi-C data through coding trees. However, the current method for computing coding trees is not optimal. In this paper, we propose optimal algorithms for this computation. In comparison with seven state-of-art methods using two public datasets, from GM12878 and IMR90 cells, SuperTAD shows a significant enrichment of structural proteins around detected boundaries and histone modifications within TADs and displays a high consistency between various resolutions of identical Hi-C matrices.

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Structure-guided engineering of adenine base editor with minimized RNA off-targeting activity

Nature Communications ◽

10.1038/s41467-021-22519-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Jianan Li ◽

Wenxia Yu ◽

Shisheng Huang ◽

Susu Wu ◽

Liping Li ◽

...

Keyword(s):

Rna Editing ◽

Potential Interaction ◽

Reporter System ◽

Independent Manner ◽

Robust Detection ◽

Guide Rna ◽

Highly Efficient ◽

Adenine Base

AbstractBoth adenine base editors (ABEs) and cytosine base editors (CBEs) have been recently revealed to induce transcriptome-wide RNA off-target editing in a guide RNA-independent manner. Here we construct a reporter system containing E.coli Hokb gene with a tRNA-like motif for robust detection of RNA editing activities as the optimized ABE, ABEmax, induces highly efficient A-to-I (inosine) editing within an E.coli tRNA-like structure. Then, we design mutations to disrupt the potential interaction between TadA and tRNAs in structure-guided principles and find that Arginine 153 (R153) within TadA is essential for deaminating RNAs with core tRNA-like structures. Two ABEmax or mini ABEmax variants (TadA* fused with Cas9n) with deletion of R153 within TadA and/or TadA* (named as del153/del153* and mini del153) are successfully engineered, showing minimized RNA off-targeting, but comparable DNA on-targeting activities. Moreover, R153 deletion in recently reported ABE8e or ABE8s can also largely reduce their RNA off-targeting activities. Taken together, we develop a strategy to generate engineered ABEs (eABEs) with minimized RNA off-targeting activities.

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Clutter Cancellation and Long Time Integration for GNSS-Based Passive Bistatic Radar

Remote Sensing ◽

10.3390/rs13040701 ◽

2021 ◽

Vol 13 (4) ◽

pp. 701 ◽

Cited By ~ 1

Author(s):

Binbin Wang ◽

Hao Cha ◽

Zibo Zhou ◽

Bin Tian

Keyword(s):

Fourier Transform ◽

Target Detection ◽

Time Integration ◽

Detection Performance ◽

Bistatic Radar ◽

Detection Range ◽

Robust Detection ◽

Coherent Integration ◽

Long Time ◽

Long Time Integration

Clutter cancellation and long time integration are two vital steps for global navigation satellite system (GNSS)-based bistatic radar target detection. The former eliminates the influence of direct and multipath signals on the target detection performance, and the latter improves the radar detection range. In this paper, the extensive cancellation algorithm (ECA), which projects the surveillance channel signal in the subspace orthogonal to the clutter subspace, is first applied in GNSS-based bistatic radar. As a result, the clutter has been removed from the surveillance channel effectively. For long time integration, a modified version of the Fourier transform (FT), called long-time integration Fourier transform (LIFT), is proposed to obtain a high coherent processing gain. Relative acceleration (RA) is defined to describe the Doppler variation results from the motion of the target and long integration time. With the estimated RA, the Doppler frequency shift compensation is carried out in the LIFT. This method achieves a better and robust detection performance when comparing with the traditional coherent integration method. The simulation results demonstrate the effectiveness and advantages of the proposed processing method.

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Probe-Based Real-Time qPCR Assays for a Reliable Differentiation of Capripox Virus Species

Microorganisms ◽

10.3390/microorganisms9040765 ◽

2021 ◽

Vol 9 (4) ◽

pp. 765

Author(s):

Janika Wolff ◽

Martin Beer ◽

Bernd Hoffmann

Keyword(s):

Real Time ◽

Animal Health ◽

Diagnostic Methods ◽

Virus Species ◽

Time Saving ◽

Robust Detection ◽

Highly Sensitive ◽

Reliable Differentiation ◽

World Organization ◽

Real Time Qpcr

Outbreaks of the three capripox virus species, namely lumpy skin disease virus, sheeppox virus, and goatpox virus, severely affect animal health and both national and international economies. Therefore, the World Organization for Animal Health (OIE) classified them as notifiable diseases. Until now, discrimination of capripox virus species was possible by using different conventional PCR protocols. However, more sophisticated probe-based real-time qPCR systems addressing this issue are, to our knowledge, still missing. In the present study, we developed several duplex qPCR assays consisting of different types of fluorescence-labelled probes that are highly sensitive and show a high analytical specificity. Finally, our assays were combined with already published diagnostic methods to a diagnostic workflow that enables time-saving, reliable, and robust detection, differentiation, and characterization of capripox virus isolates.

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Pt Nanoparticles Anchored on NH2-MIL-101 with Efficient Peroxidase-Like Activity for Colorimetric Detection of Dopamine

Chemosensors ◽

10.3390/chemosensors9060140 ◽

2021 ◽

Vol 9 (6) ◽

pp. 140

Author(s):

Jing Li ◽

Keying Xu ◽

Yang Chen ◽

Jie Zhao ◽

Peiyao Du ◽

...

Keyword(s):

Active Sites ◽

Clinical Medicine ◽

Colorimetric Assay ◽

Colorimetric Detection ◽

Pt Nanoparticles ◽

Robust Detection ◽

Color Changes ◽

Relevant Role ◽

Metal Organic ◽

The Central Nervous System

Dopamine (DA) is an important catecholamine neurotransmitter that plays a highly relevant role in regulating the central nervous system, and abnormal DA content can cause many immune-related diseases. Hence, it is of significance to sensitively and specifically identify DA for clinical medicine. In this work, Pt/NH2-MIL-101 hybrid nanozymes with bimetallic catalytic centers were fabricated by forming coordinate bonds between Pt nanoparticles (Pt NPs) and –NH2 on metal–organic frameworks (MOF). The catalytic activity of Pt/NH2-MIL-101 was increased by 1.5 times via enlarging the exposure of more active sites and improving the activity of the active sites through the strategy of forming bimetallic catalytic centers. In the presence of DA, competing with 3, 3′, 5, 5′-tetramethylbenzidine (TMB) for the generated hydroxyl radicals (•OH), the blue oxidation state TMB (Ox-TMB) is reduced to colorless TMB, showing dramatic color changes. The Pt/NH2-MIL-101-based colorimetric assay enables the sensitive and robust detection of DA molecules with a detection limit of only 0.42 μM and has an observable potential in clinical applications.

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