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  1. Article ; Online: AdaCS: Adaptive Compressive Sensing with Restricted Isometry Property-Based Error-clamping.

    Qiu, Chenxi / Hu, Xuemei

    IEEE transactions on pattern analysis and machine intelligence

    2024  Volume PP

    Abstract: Scene-dependent adaptive compressive sensing (CS) has been a long pursuing goal that has huge potential to significantly improve the performance of CS. However, with no access to the ground truth, how to design the scene-dependent adaptive strategy is ... ...

    Abstract Scene-dependent adaptive compressive sensing (CS) has been a long pursuing goal that has huge potential to significantly improve the performance of CS. However, with no access to the ground truth, how to design the scene-dependent adaptive strategy is still an open problem. In this paper, a restricted isometry property (RIP) condition-based error-clamping is proposed, which could directly predict the reconstruction error, i.e., the difference between the current-stage reconstructed image and the ground truth image, and adaptively allocate more samples to regions with larger reconstruction error at the next sampling stage. Furthermore, we propose a CS reconstruction network composed of Progressively inverse transform and Alternating Bi-directional Multi-grid Network, named PiABM-Net, that could efficiently utilize the multi-scale information for reconstructing the target image. The effectiveness of the proposed adaptive and cascaded CS method is demonstrated with extensive quantitative and qualitative experiments, compared with the state-of-the-art CS algorithms.
    Language English
    Publishing date 2024-01-23
    Publishing country United States
    Document type Journal Article
    ISSN 1939-3539
    ISSN (online) 1939-3539
    DOI 10.1109/TPAMI.2024.3357704
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Higher-order epistasis within Pol II trigger loop haplotypes.

    Duan, Bingbing / Qiu, Chenxi / Lockless, Steve W / Sze, Sing-Hoi / Kaplan, Craig D

    bioRxiv : the preprint server for biology

    2024  

    Abstract: RNA polymerase II (Pol II) has a highly conserved domain, the trigger loop (TL), that controls transcription fidelity and speed. We previously probed pairwise genetic interactions between residues within and surrounding the TL and identified widespread ... ...

    Abstract RNA polymerase II (Pol II) has a highly conserved domain, the trigger loop (TL), that controls transcription fidelity and speed. We previously probed pairwise genetic interactions between residues within and surrounding the TL and identified widespread incompatibility between TLs of different species when placed in the
    Language English
    Publishing date 2024-01-21
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.20.576280
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  3. Article: Widespread epistasis shapes RNA Polymerase II active site function and evolution.

    Duan, Bingbing / Qiu, Chenxi / Sze, Sing-Hoi / Kaplan, Craig

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Multi-subunit RNA Polymerases (msRNAPs) are responsible for transcription in all kingdoms of life. At the heart of these msRNAPs is an ultra-conserved active site domain, the trigger loop (TL), coordinating transcription speed and fidelity by critical ... ...

    Abstract Multi-subunit RNA Polymerases (msRNAPs) are responsible for transcription in all kingdoms of life. At the heart of these msRNAPs is an ultra-conserved active site domain, the trigger loop (TL), coordinating transcription speed and fidelity by critical conformational changes impacting multiple steps in substrate selection, catalysis, and translocation. Previous studies have observed several different types of genetic interactions between eukaryotic RNA polymerase II (Pol II) TL residues, suggesting that the TL's function is shaped by functional interactions of residues within and around the TL. The extent of these interaction networks and how they control msRNAP function and evolution remain to be determined. Here we have dissected the Pol II TL interaction landscape by deep mutational scanning in
    Language English
    Publishing date 2023-04-04
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.27.530048
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  4. Article ; Online: Wideband Anti-Jamming Based on Free Space Optical Communication and Photonic Signal Processing.

    Wu, Ben / Qi, Yang / Qiu, Chenxi / Tang, Ying

    Sensors (Basel, Switzerland)

    2021  Volume 21, Issue 4

    Abstract: We propose and demonstrate an anti-jamming system to defend against wideband jamming attack. Free space optical communication is deployed to provide a reference for jamming cancellation. The mixed signal is processed and separated with photonic signal ... ...

    Abstract We propose and demonstrate an anti-jamming system to defend against wideband jamming attack. Free space optical communication is deployed to provide a reference for jamming cancellation. The mixed signal is processed and separated with photonic signal processing method to achieve large bandwidth. As an analog signal processing method, the cancellation system introduces zero latency. The radio frequency signals are modulated on optical carriers to achieve wideband and unanimous frequency response. With wideband and zero latency, the system meets the key requirements of high speed and real-time communications in transportation systems.
    Language English
    Publishing date 2021-02-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s21041136
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  5. Article ; Online: Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning.

    Dutagaci, Bercem / Duan, Bingbing / Qiu, Chenxi / Kaplan, Craig D / Feig, Michael

    PLoS computational biology

    2023  Volume 19, Issue 3, Page(s) e1010999

    Abstract: Catalysis and fidelity of multisubunit RNA polymerases rely on a highly conserved active site domain called the trigger loop (TL), which achieves roles in transcription through conformational changes and interaction with NTP substrates. The mutations of ... ...

    Abstract Catalysis and fidelity of multisubunit RNA polymerases rely on a highly conserved active site domain called the trigger loop (TL), which achieves roles in transcription through conformational changes and interaction with NTP substrates. The mutations of TL residues cause distinct effects on catalysis including hypo- and hyperactivity and altered fidelity. We applied molecular dynamics simulation (MD) and machine learning (ML) techniques to characterize TL mutations in the Saccharomyces cerevisiae RNA Polymerase II (Pol II) system. We did so to determine relationships between individual mutations and phenotypes and to associate phenotypes with MD simulated structural alterations. Using fitness values of mutants under various stress conditions, we modeled phenotypes along a spectrum of continual values. We found that ML could predict the phenotypes with 0.68 R2 correlation from amino acid sequences alone. It was more difficult to incorporate MD data to improve predictions from machine learning, presumably because MD data is too noisy and possibly incomplete to directly infer functional phenotypes. However, a variational auto-encoder model based on the MD data allowed the clustering of mutants with different phenotypes based on structural details. Overall, we found that a subset of loss-of-function (LOF) and lethal mutations tended to increase distances of TL residues to the NTP substrate, while another subset of LOF and lethal substitutions tended to confer an increase in distances between TL and bridge helix (BH). In contrast, some of the gain-of-function (GOF) mutants appear to cause disruption of hydrophobic contacts among TL and nearby helices.
    MeSH term(s) RNA Polymerase II/metabolism ; Transcription, Genetic ; Molecular Dynamics Simulation ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Mutation ; DNA-Directed RNA Polymerases/metabolism
    Chemical Substances RNA Polymerase II (EC 2.7.7.-) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2023-03-22
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1010999
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  6. Article ; Online: On-Chip Compressive Sensing with a Single-Photon Avalanche Diode Array.

    Qiu, Chenxi / Wang, Peng / Kong, Xiangshun / Yan, Feng / Mao, Cheng / Yue, Tao / Hu, Xuemei

    Sensors (Basel, Switzerland)

    2023  Volume 23, Issue 9

    Abstract: Single-photon avalanche diodes (SPADs) are novel image sensors that record photons at extremely high sensitivity. To reduce both the required sensor area for readout circuits and the data throughput for SPAD array, in this paper, we propose a snapshot ... ...

    Abstract Single-photon avalanche diodes (SPADs) are novel image sensors that record photons at extremely high sensitivity. To reduce both the required sensor area for readout circuits and the data throughput for SPAD array, in this paper, we propose a snapshot compressive sensing single-photon avalanche diode (CS-SPAD) sensor which can realize on-chip snapshot-type spatial compressive imaging in a compact form. Taking advantage of the digital counting nature of SPAD sensing, we propose to design the circuit connection between the sensing unit and the readout electronics for compressive sensing. To process the compressively sensed data, we propose a convolution neural-network-based algorithm dubbed CSSPAD-Net which could realize both high-fidelity scene reconstruction and classification. To demonstrate our method, we design and fabricate a CS-SPAD sensor chip, build a prototype imaging system, and demonstrate the proposed on-chip snapshot compressive sensing method on the MINIST dataset and real handwritten digital images, with both qualitative and quantitative results.
    Language English
    Publishing date 2023-04-30
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s23094417
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  7. Article: An Unprecedented CeO

    Qiu, Chenxi / Zhou, Qiang / Gao, Rui / Guo, Yizheng / Qin, Jiaqi / Wang, Dongqi / Song, Yujiang

    Nanomaterials (Basel, Switzerland)

    2023  Volume 13, Issue 19

    Abstract: Direct ascorbic acid fuel cells (DAAFCs) employ biocompatible ascorbic acid (AA) as fuel, allowing convenient storage, transportation, and fueling as well as avoiding fuel crossover. The AA oxidation reaction (AAOR) largely governs the performance of ... ...

    Abstract Direct ascorbic acid fuel cells (DAAFCs) employ biocompatible ascorbic acid (AA) as fuel, allowing convenient storage, transportation, and fueling as well as avoiding fuel crossover. The AA oxidation reaction (AAOR) largely governs the performance of DAAFCs. However, AAOR electrocatalysts currently have low activity, and state-of-the-art ones are limited to carbon black. Herein, we report the synthesis of an unprecedented AAOR electrocatalyst comprising 3.9 ± 1.1 nm CeO
    Language English
    Publishing date 2023-09-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662255-5
    ISSN 2079-4991
    ISSN 2079-4991
    DOI 10.3390/nano13192669
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  8. Article ; Online: Functional assays for transcription mechanisms in high-throughput.

    Qiu, Chenxi / Kaplan, Craig D

    Methods (San Diego, Calif.)

    2019  Volume 159-160, Page(s) 115–123

    Abstract: Dramatic increases in the scale of programmed synthesis of nucleic acid libraries coupled with deep sequencing have powered advances in understanding nucleic acid and protein biology. Biological systems centering on nucleic acids or encoded proteins ... ...

    Abstract Dramatic increases in the scale of programmed synthesis of nucleic acid libraries coupled with deep sequencing have powered advances in understanding nucleic acid and protein biology. Biological systems centering on nucleic acids or encoded proteins greatly benefit from such high-throughput studies, given that large DNA variant pools can be synthesized and DNA, or RNA products of transcription, can be easily analyzed by deep sequencing. Here we review the scope of various high-throughput functional assays for studies of nucleic acids and proteins in general, followed by discussion of how these types of study have yielded insights into the RNA Polymerase II (Pol II) active site as an example. We discuss methodological considerations in the design and execution of these experiments that should be valuable to studies in any system.
    MeSH term(s) Eukaryota/genetics ; Eukaryota/metabolism ; High-Throughput Nucleotide Sequencing/methods ; RNA Polymerase II/metabolism ; Transcription, Genetic
    Chemical Substances RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2019-02-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2019.02.017
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    Zs.A 3239: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  9. Article: Five-week music therapy improves overall symptoms in schizophrenia by modulating theta and gamma oscillations.

    Wang, Lujie / Wang, Liju / Chen, Jiaxian / Qiu, Chenxi / Liu, Ting / Wu, Yulin / Li, Yan / Zou, Pengyu / Guo, Sijia / Lu, Jing

    Frontiers in psychiatry

    2024  Volume 15, Page(s) 1358726

    Abstract: Introduction: Some clinical studies have shown that music therapy as an adjunctive therapy can improve overall symptoms in patients with schizophrenia. However, the neural mechanisms of this improvement remain unclear due to insufficient neuroimaging ... ...

    Abstract Introduction: Some clinical studies have shown that music therapy as an adjunctive therapy can improve overall symptoms in patients with schizophrenia. However, the neural mechanisms of this improvement remain unclear due to insufficient neuroimaging evidence.
    Methods: In this work, 17 patients with schizophrenia accepted a five-week music therapy (music group) that integrated listening, singing, and composing, and required patients to cooperate in a group to complete music therapy tasks. Meanwhile, 15 patients with schizophrenia received a five-week visual art intervention as the control group including handicraft and painting activities. We collected the Manchester Scale (MS) and Positive and Negative Symptom Scale (PANSS) scores and electroencephalography (EEG) data before and after intervention in two groups.
    Results: Behavioral results showed that both interventions mentioned above can effectively help patients with schizophrenia relieve their overall symptoms, while a trend-level effect was observed in favor of music therapy. The EEG results indicated that music therapy can improve abnormal neural oscillations in schizophrenia which is reflected by a decrease in theta oscillation in the parietal lobe and an increase in gamma oscillation in the prefrontal lobe. In addition, correlation analysis showed that in the music group, both reductions in theta oscillations in the parietal lobe and increases in gamma oscillations in the prefrontal lobe were positively correlated with the improvement of overall symptoms.
    Discussion: These findings help us to better understand the neural mechanisms by which music therapy improves overall symptoms in schizophrenia and provide more evidence for the application of music therapy in other psychiatric disorders.
    Language English
    Publishing date 2024-03-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2564218-2
    ISSN 1664-0640
    ISSN 1664-0640
    DOI 10.3389/fpsyt.2024.1358726
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  10. Article ; Online: Thiolutin has complex effects in vivo but is a direct inhibitor of RNA polymerase II in vitro.

    Qiu, Chenxi / Arora, Payal / Malik, Indranil / Laperuta, Amber J / Pavlovic, Emily M / Ugochukwu, Scott / Naik, Mandar / Kaplan, Craig D

    Nucleic acids research

    2024  Volume 52, Issue 5, Page(s) 2546–2564

    Abstract: Thiolutin is a natural product transcription inhibitor with an unresolved mode of action. Thiolutin and the related dithiolopyrrolone holomycin chelate Zn2+ and previous studies have concluded that RNA Polymerase II (Pol II) inhibition in vivo is ... ...

    Abstract Thiolutin is a natural product transcription inhibitor with an unresolved mode of action. Thiolutin and the related dithiolopyrrolone holomycin chelate Zn2+ and previous studies have concluded that RNA Polymerase II (Pol II) inhibition in vivo is indirect. Here, we present chemicogenetic and biochemical approaches to investigate thiolutin's mode of action in Saccharomyces cerevisiae. We identify mutants that alter sensitivity to thiolutin. We provide genetic evidence that thiolutin causes oxidation of thioredoxins in vivo and that thiolutin both induces oxidative stress and interacts functionally with multiple metals including Mn2+ and Cu2+, and not just Zn2+. Finally, we show direct inhibition of RNA polymerase II (Pol II) transcription initiation by thiolutin in vitro in support of classical studies that thiolutin can directly inhibit transcription in vitro. Inhibition requires both Mn2+ and appropriate reduction of thiolutin as excess DTT abrogates its effects. Pause prone, defective elongation can be observed in vitro if inhibition is bypassed. Thiolutin effects on Pol II occupancy in vivo are widespread but major effects are consistent with prior observations for Tor pathway inhibition and stress induction, suggesting that thiolutin use in vivo should be restricted to studies on its modes of action and not as an experimental tool.
    MeSH term(s) Pyrrolidinones/pharmacology ; RNA Polymerase II/antagonists & inhibitors ; Saccharomyces cerevisiae/drug effects ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae Proteins/genetics ; Transcription, Genetic ; Zinc
    Chemical Substances acetopyrrothine (02C005Q20B) ; Pyrrolidinones ; RNA Polymerase II (EC 2.7.7.-) ; Saccharomyces cerevisiae Proteins ; Zinc (J41CSQ7QDS)
    Language English
    Publishing date 2024-01-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad1258
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
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