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Select item 83107061.

Novel Strategies to Address the Challenges in Top-Down Proteomics

Jake A. Melby, David S. Roberts, Eli J. Larson, Kyle A. Brown, Elizabeth F. Bayne, Song Jin, Ying Ge

J Am Soc Mass Spectrom. Author manuscript; available in PMC 2021 Jul 25.

Published in final edited form as: J Am Soc Mass Spectrom. 2021 Jun 2; 32(6): 1278–1294. Published online 2021 May 13. doi: 10.1021/jasms.1c00099

PMCID:: PMC8310706

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Relative precision of top-down attentional modulations is lower in early visual cortex compared to mid- and high-level visual areas

Sunyoung Park, John T. Serences

J Neurophysiol. 2022 Feb 1; 127(2): 504–518. Published online 2022 Jan 12. doi: 10.1152/jn.00300.2021

PMCID:: PMC8836715

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Select item 78648893.

Top-down Proteomics: Challenges, Innovations, and Applications in Basic and Clinical Research

Kyle A. Brown, Jake A. Melby, David S. Roberts, Ying Ge

Expert Rev Proteomics. Author manuscript; available in PMC 2021 Dec 17.

Published in final edited form as: Expert Rev Proteomics. 2020 Oct; 17(10): 719–733. Published online 2020 Dec 17. doi: 10.1080/14789450.2020.1855982

PMCID:: PMC7864889

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Effects of top-down influence suppression on behavioral and V1 neuronal contrast sensitivity functions in cats

Jian Ding, Zheng Ye, Fei Xu, Xiangmei Hu, Hao Yu, Shen Zhang, Yanni Tu, Qiuyu Zhang, Qingyan Sun, Tianmiao Hua, Zhong-Lin Lu

iScience. 2022 Jan 21; 25(1): 103683. Published online 2021 Dec 24. doi: 10.1016/j.isci.2021.103683

PMCID:: PMC8760559

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Select item 101218215.

Development of Top-Down Cortical Propagations in Youth

Adam Pines, Arielle S. Keller, Bart Larsen, Maxwell Bertolero, Arian Ashourvan, Dani S. Bassett, Matthew Cieslak, Sydney Covitz, Yong Fan, Eric Feczko, Audrey Houghton, Amanda R. Rueter, Manish Saggar, Golia Shafiei, Tinashe M. Tapera, Jacob Vogel, Sarah M. Weinstein, Russell T. Shinohara, Leanne M. Williams, Damien A. Fair, Theodore D. Satterthwaite

Neuron. Author manuscript; available in PMC 2024 Apr 19.

Published in final edited form as: Neuron. 2023 Apr 19; 111(8): 1316–1330.e5. Published online 2023 Feb 17. doi: 10.1016/j.neuron.2023.01.014

PMCID:: PMC10121821

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Object segmentation controls image reconstruction from natural scenes

Peter Neri

PLoS Biol. 2017 Aug; 15(8): e1002611. Published online 2017 Aug 21. doi: 10.1371/journal.pbio.1002611

PMCID:: PMC5565198

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Progress in Top-Down Proteomics and the Analysis of Proteoforms

Timothy K. Toby, Luca Fornelli, Neil L. Kelleher

Annu Rev Anal Chem (Palo Alto Calif) Author manuscript; available in PMC 2017 Jun 12.

Published in final edited form as: Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12; 9(1): 499–519. doi: 10.1146/annurev-anchem-071015-041550

PMCID:: PMC5373801

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Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database

Yunxiang Dai, Katherine E. Buxton, Leah V. Schaffer, Rachel M. Miller, Robert J. Millikin, Mark Scalf, Brian L. Frey, Michael R. Shortreed, Lloyd M. Smith

J Proteome Res. Author manuscript; available in PMC 2020 Oct 4.

Published in final edited form as: J Proteome Res. 2019 Oct 4; 18(10): 3671–3680. Published online 2019 Sep 18. doi: 10.1021/acs.jproteome.9b00339

PMCID:: PMC6890418

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Top-down beta oscillatory signaling conveys behavioral context in early visual cortex

Craig G. Richter, Richard Coppola, Steven L. Bressler

Sci Rep. 2018; 8: 6991. Published online 2018 May 3. doi: 10.1038/s41598-018-25267-1

PMCID:: PMC5934398

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Signature Patterns for Top-Down and Bottom-Up Information Processing via Cross-Frequency Coupling in Macaque Auditory Cortex

Christian D. Márton, Makoto Fukushima, Corrie R. Camalier, Simon R. Schultz, Bruno B. Averbeck

eNeuro. 2019 Mar-Apr; 6(2): ENEURO.0467-18.2019. Prepublished online 2019 Mar 28. Published online 2019 Apr 30. doi: 10.1523/ENEURO.0467-18.2019

PMCID:: PMC6520641

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Top-Down Control of Inhibitory Granule Cells in the Main Olfactory Bulb Reshapes Neural Dynamics Giving Rise to a Diversity of Computations

Zhen Chen, Krishnan Padmanabhan

Front Comput Neurosci. 2020; 14: 59. Published online 2020 Jul 13. doi: 10.3389/fncom.2020.00059

PMCID:: PMC7381246

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Trade-Offs between Competitive Ability and Resistance to Top-Down Control in Marine Microbes

Jinny Wu Yang, Feng-Hsun Chang, Yi-Chun Yeh, An-Yi Tsai, Kuo-Ping Chiang, Fuh-Kwo Shiah, Gwo-Ching Gong, Chih-hao Hsieh

mSystems. 2023 Mar-Apr; 8(2): e01017-22. Published online 2023 Mar 14. doi: 10.1128/msystems.01017-22

PMCID:: PMC10134844

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Characterization of Proteoform Post-Translational Modifications by Top-Down and Bottom-Up Mass Spectrometry in Conjunction with Annotations

Wenrong Chen, Zhengming Ding, Yong Zang, Xiaowen Liu

J Proteome Res. 2023 Oct 6; 22(10): 3178–3189. Published online 2023 Sep 20. doi: 10.1021/acs.jproteome.3c00207

PMCID:: PMC10563160

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Top-Down Beta Enhances Bottom-Up Gamma

Craig G. Richter, William H. Thompson, Conrado A. Bosman, Pascal Fries

J Neurosci. 2017 Jul 12; 37(28): 6698–6711. doi: 10.1523/JNEUROSCI.3771-16.2017

PMCID:: PMC5508256

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Suppression of top-down influence decreases both behavioral and V1 neuronal response sensitivity to stimulus orientations in cats

Zheng Ye, Jian Ding, Yanni Tu, Qiuyu Zhang, Shunshun Chen, Hao Yu, Qingyan Sun, Tianmiao Hua

Front Behav Neurosci. 2023; 17: 1061980. Published online 2023 Feb 8. doi: 10.3389/fnbeh.2023.1061980

PMCID:: PMC9944033

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Capillary zone electrophoresis-mass spectrometry for top-down proteomics

Xiaojing Shen, Zhichang Yang, Elijah N. McCool, Rachele A. Lubeckyj, Daoyang Chen, Liangliang Sun

Trends Analyt Chem. Author manuscript; available in PMC 2020 Nov 1.

Published in final edited form as: Trends Analyt Chem. 2019 Nov; 120: 115644. Published online 2019 Aug 28. doi: 10.1016/j.trac.2019.115644

PMCID:: PMC6752746

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Adolescent frontal top-down neurons receive heightened local drive to establish adult attentional behavior in mice

Elisa M. Nabel, Yury Garkun, Hiroyuki Koike, Masato Sadahiro, Ana Liang, Kevin J. Norman, Giulia Taccheri, Michael P. Demars, Susanna Im, Keaven Caro, Sarah Lopez, Julia Bateh, Patrick R. Hof, Roger L. Clem, Hirofumi Morishita

Nat Commun. 2020; 11: 3983. Published online 2020 Aug 7. doi: 10.1038/s41467-020-17787-0

PMCID:: PMC7414856

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Select item 777587818.

Construction of Human Proteoform Families from 21 Tesla FT-ICR Mass Spectrometry Top-Down Proteomic Data

Leah V. Schaffer, Lissa C. Anderson, David S. Butcher, Michael R. Shortreed, Rachel M. Miller, Caitlin Pavelec, Lloyd M. Smith

J Proteome Res. Author manuscript; available in PMC 2022 Jan 1.

Published in final edited form as: J Proteome Res. 2021 Jan 1; 20(1): 317–325. Published online 2020 Oct 19. doi: 10.1021/acs.jproteome.0c00403

PMCID:: PMC7775878

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Select item 1017572819.

High sensitivity top–down proteomics captures single muscle cell heterogeneity in large proteoforms

Jake A. Melby, Kyle A. Brown, Zachery R. Gregorich, David S. Roberts, Emily A. Chapman, Lauren E. Ehlers, Zhan Gao, Eli J. Larson, Yutong Jin, Justin R. Lopez, Jared Hartung, Yanlong Zhu, Sean J. McIlwain, Daojing Wang, Wei Guo, Gary M. Diffee, Ying Ge

Proc Natl Acad Sci U S A. 2023 May 9; 120(19): e2222081120. Published online 2023 May 1. doi: 10.1073/pnas.2222081120

PMCID:: PMC10175728

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Select item 502663820.

Top-down Proteomics: Technology Advancements and Applications to Heart Diseases

Wenxuan Cai, Trisha M. Tucholski, Zachery R. Gregorich, Ying Ge

Expert Rev Proteomics. Author manuscript; available in PMC 2017 Aug 1.

Published in final edited form as: Expert Rev Proteomics. 2016 Aug; 13(8): 717–730. Published online 2016 Jul 26. doi: 10.1080/14789450.2016.1209414

PMCID:: PMC5026638

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PMC Images search for top-down analysis procedure

Fig. 1

Top-down bottom-up procedure for data collection and cost efficiency analysis

“Top-down bottom-up” estimation of per capita cost of new-born care interventions in four regions of Ghana: beyond implementation to scalability and sustainability

Health Econ Rev. 2021;11:8.
Figure 2

General procedure for synthesis of QDs by top-down techniques.

Ternary Quantum Dots in Chemical Analysis. Synthesis and Detection Mechanisms

Molecules. 2021 May;26(9):2764.
Figure 2

Event-related potentials (ERPs) procedure. (A) The continuous auditory stimulus comprised both rarely presented target sounds and frequently presented standard sounds in two tasks. (B) The 2-tone auditory oddball task (P300, for top-down analyses). The participants were required to discriminate the target stimulus from the standard tone by pressing a button. (C) The passive listening task (MMN, for bottom-up analysis). The participants were instructed to watch the silent movie without responding to the presented auditory stimulus.

Bottom-Up and Top-Down Attention Impairment Induced by Long-Term Exposure to Noise in the Absence of Threshold Shifts

Front Neurol. 2022;13:836683.
Figure 5.

Early visual areas are under top-down control by FEF as reflected by modulations of alpha-band activity. A, Sources of the alpha power modulation (t = −1 to 0 s; f = 8–13 Hz) with respect to left versus right cues were found in V1 (thresholded at p < 0.05 after permutation approach). Signals from these locations were used as seeds in the GC analysis. B, GC spectra (left and right plots) separately for the top-down (black traces) and bottom-up (red traces) control. GC spectra were calculated from the left and rFEF, respectively. Whole-brain analysis contrasting “All to V1” vs “V1 to All” confirmed a significant top-down drive of V1 by the rFEF. p < 0.05, cluster-based random permutation procedure.

FEF-Controlled Alpha Delay Activity Precedes Stimulus-Induced Gamma-Band Activity in Visual Cortex

J Neurosci. 2017 Apr 12;37(15):4117-4127.