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Proteomic clustering reveals the kinetics of disease biomarkers in bovine and human models of post-traumatic osteoarthritis

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Osteoarthritis and Cartilage Open 2021年第4期3卷 100191-100191页

作者： Black, Rebecca Mae Wang, Yang Struglics, André Lorenzo, Pilar Chubinskaya, Susan Grodzinsky, Alan J. Önnerfjord, Patrik Departments of Biological Engineering Massachusetts Institute of Technology Cambridge MA United States Orthopaedics Department of Clinical Sciences Lund Faculty of Medicine Lund University Lund Sweden Rheumatology and Molecular Skeletal Biology Department of Clinical Sciences Lund Faculty of Medicine Lund University Lund Sweden Departments of Pediatrics Orthopedic Surgery and Medicine (Section of Rheumatology) Rush University Medical Center Chicago IL United States Mechanical Engineering Massachusetts Institute of Technology Cambridge MA United States Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA United States

Objectives: In this study, we apply a clustering method to proteomic data sets from bovine and human models of post-traumatic osteoarthritis (PTOA) to distinguish clusters of proteins based on their kinetics of release from cartilage and examined these groups for PTOA biomarker candidates. We then quantified the effects of dexamethasone (Dex) on the kinetics of release of the cartilage media proteome. Design: Mass spectrometry was performed on sample medium collected from two separate experiments using juvenile bovine and human cartilage explants (3 samples/treatment condition) during 20- or 21-day treatment with inflammatory cytokines (TNF-α, IL-6, sIL-6R) with or without a single compressive mechanical injury. All samples were incubated with or without 100 nM Dex. Clustering was performed on the correlation between normalized averaged release vectors for each protein. Results: Our proteomic method identified the presence of distinct clusters of proteins based on the kinetics of their release over three weeks of culture. Clusters of proteins with peak release after one to two weeks had biomarker candidates with increased release compared to control. Dex rescued some of the changes in protein release kinetics the level of control, and in all conditions except control, there was late release of immune-related proteins. Conclusions: We demonstrate a clustering method applied to proteomic data sets to identify and validate biomarkers of early PTOA progression and explore the relationships between the release of spatially related matrix components. Dex restored the kinetics of release to many matrix components, but not all factors that contribute to cartilage homeostasis. © 2021 The Author(s)

关键词： Cartilage matrix Cytokines Dexamethasone Mass spectrometry Post-traumatic osteoarthritis Proteomics

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A New Heuristic Reinforcement Learning for Container Relocation Problem

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Journal of Physics: Conference Series 2021年第1期1873卷

作者： Tiecheng Jiang Bo Zeng Yong Wang Wei Yan College of Information Science and Engineering Ocean University of China Qingdao Shandong 266100 China Department of Industrial Engineering and Department of Electrical and Computer Engineering University of Pittsburgh Pittsburgh PA 15101 USA

Many research efforts on reinforcement learning (RL) is dedicated to solving challenging combinatorial optimization problems, including the container relocation problem (CRP) arising from maritime industry. In CRP, large and heavy containers are stacked on top of each other, those above the target container should be relocated elsewhere before retrieving it. This problem, which minimizes the number of relocations in the retrieval process, is NP-hard, while existing RL studies do not provide satisfactory results yet. We study the structure of CRP problem and design a new heuristic RL framework. On a set of commonly used examples, our RL demonstrates a performance almost equivalent to the most famous results.

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Analysis of 3D Collagen Organization in Non-pregnant Rat Cervix Tissue

Analysis of 3D Collagen Organization in Non-pregnant Rat Cer...

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Frontiers in Optics, FiO_2019

作者： Lee, Woowon Moghaddam, Amir Ostadi McFarlin, Barbara L. Wagoner Johnson, Amy J. Toussaint, Kimani C. University of Illinois at Urbana-Champaign Department of Mechanical Science and Engineering UrbanaIL United States University of Illinois at Chicago Department of Women Children and Family Health Science ChicagoIL United States University of Illinois at Urbana-Champaign Departments of Electrical and Computer Engineering and Bioengineering UrbanaIL United States

We quantitatively analyze non-pregnant rat cervix on three distinct regions using second-harmonic generation imaging. 3D structural parameters related to collagen organization are obtained on each region respectively.... 详细信息

ISBN: (纸本)9781943580675

关键词： Rats

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Embedded Index Coding

Embedded Index Coding

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IEEE (first ITW conference of the year) Information Theory Workshop (ITW)

作者： Alexandra Porter Mary Wootters Department of Computer Science Stanford University Stanford CA Departments of Computer Science and Electrical Engineering Stanford University Stanford CA

Motivated by applications in distributed storage and distributed computation, we introduce embedded index coding (EIC). EIC is a type of distributed index coding in which nodes in a distributed system act as both senders and receivers of information. We show how embedded index coding is related to index coding in general, and give characterizations and bounds on the communication costs of optimal embedded index codes. We also define task-based EIC, in which each sending node encodes and sends data blocks independently of the other nodes. Task-based EIC is more computationally tractable and has advantages in applications such as distributed storage, in which senders may complete their broadcasts at different times. Finally, we give heuristic algorithms for approximating optimal embedded index codes, and demonstrate empirically that these algorithms perform well.

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Lifted multiplicity codes and the disjoint repair group property

arXiv

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arXiv 2019年

作者： Li, Ray Wootters, Mary Department of Computer Science Stanford University United States Departments of Computer Science and Electrical Engineering Stanford University United States

Lifted Reed Solomon Codes (Guo, Kopparty, Sudan 2013) were introduced in the context of locally correctable and testable codes. They are multivariate polynomials whose restriction to any line is a codeword of a Reed-Solomon code. We consider a generalization of their construction, which we call lifted multiplicity codes. These are multivariate polynomial codes whose restriction to any line is a codeword of a multiplicity code (Kopparty, Saraf, Yekhanin 2014). We show that lifted multiplicity codes have a better trade-off between redundancy and a notion of locality called the t-disjoint-repair-group property than previously known constructions. More precisely, we show that lifted multiplicity codes with length N and redundancy O(t0585√N) have the property that any symbol of a codeword can be reconstructed in t different ways, each using a disjoint subset of the other coordinates. This gives the best known trade-off for this problem for any super-constant t Copyright © 2019, The Authors. All rights reserved.

关键词： Reed-Solomon codes

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Interactive Protocols for Classically-Verifiable Quantum Advantage

arXiv

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arXiv 2021年

作者： Zhu, Daiwei Kahanamoku-Meyer, Gregory D. Lewis, Laura Noel, Crystal Katz, Or Harraz, Bahaa Wang, Qingfeng Risinger, Andrew Feng, Lei Biswas, Debopriyo Egan, Laird Gheorghiu, Alexandru Nam, Yunseong Vidick, Thomas Vazirani, Umesh Yao, Norman Y. Cetina, Marko Monroe, Christopher Joint Quantum Institute Departments of Physics and Electrical and Computer Engineering University of Maryland College ParkMD20742 United States Joint Center for Quantum Information and Computer Science NIST University of Maryland College ParkMD20742 United States Department of Physics University of California BerkeleyCA94720 United States Materials Sciences Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Department of Computing and Mathematical Sciences California Institute of Technology CA91125 United States Division of Physics Mathematics and Astronomy California Institute of Technology CA91125-0001 United States Duke Quantum Center Department of Physics Duke University DurhamNC27708 United States Department of Electrical and Computer Engineering Duke University DurhamNC27708 United States IonQ Inc. College ParkMD20740 United States Institute for Theoretical Studies ETH Zürich CH 8001 Switzerland Chemical Physics Program Institute for Physical Science and Technology University of Maryland College ParkMD20742 United States Departments of Electrical and Computer Engineering University of Maryland College ParkMD20742 United States

Interaction is a powerful resource for quantum computation. It can be utilized in applications ranging from the verification of quantum algorithms all the way to verifying quantum mechanics itself. Here, we present the first implementation of interactive protocols for proofs of quantumness — which when suitably scaled promise the efficient verification of quantum computational advantage. The key feature that distinguishes these protocols from existing demonstrations of quantum advantage is that the classical verification is efficient and scales polynomially rather than exponentially with the number of qubits. The experimental implementation of such interactive protocols requires the ability to independently measure subsets of qubits in the middle of a quantum circuit and to continue coherent evolution afterwards. This is achieved by spatially isolating target qubits via shuttling, and opens the door to a range of quantum interactive protocols as well as new information processing architectures. Copyright © 2021, The Authors. All rights reserved.

关键词： Qubits

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Glassy carbon microelectrode arrays enable voltage-peak separated simultaneous detection of dopamine and serotonin using fast scan cyclic voltammetry

arXiv

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arXiv 2020年

作者： Castagnola, Elisa Thongpang, Sanitta Hirabayashi, Mieko Nava, Giorgio Nimbalkar, Surabhi Nguyen, Tri Lara, Sandra Oyawalea, Alexis Bunnella, James Moritz, Chet Kassegne, Sam NanoFAB. SDSU Lab Department of Mechanical Engineering San Diego State University San DiegoCA United States University of Washington Departments of Electrical & Computer Engineering Rehabilitation Medicine and Physiology & Biophysics SeattleWA United States Department of Biomedical Engineering Faculty of Engineering Mahidol University Nakorn Pathom Thailand Department of Mechanical Engineering University of California Riverside RiversideCA United States Bill & Melinda Gates Center for Computer Science & Engineering SeattleWA98195 United States

Progress in real-time, simultaneous in vivo detection of multiple neurotransmitters will help accelerate advances in neuroscience research. The need for development of probes capable of stable electrochemical detection of rapid neurotransmitter fluctuations with high sensitivity and selectivity and sub-second temporal resolution has, therefore, become compelling. Additionally, a higher spatial resolution multi-channel capability is required to capture the complex neurotransmission dynamics across different brain regions. These research needs have inspired the introduction of glassy carbon (GC) microelectrode arrays on flexible polymer substrates through carbon MEMS (C-MEMS) microfabrication process followed by a novel pattern transfer technique. These implantable GC microelectrodes offer unique advantages in electrochemical detection of electroactive neurotransmitters through the presence of active carboxyl, carbonyl, and hydroxyl functional groups. In addition, they offer fast electron transfer kinetics, capacitive electrochemical behavior, and wide electrochemical window. Here, we combine the use of these GC microelectrodes with the fast scan cyclic voltammetry (FSCV) technique to optimize the co-detection of dopamine and serotonin in vitro and in vivo. We demonstrate that using optimized FSCV triangular waveform at scan rates ≤ 700 V/s and holding and switching at potentials of 0.4 and 1V respectively, it is possible to discriminate voltage reduction and oxidation peaks of serotonin and dopamine, with serotonin contributing distinct multiple oxidation peaks. Taken together, our results present a compelling case for a carbon-based MEA platform rich with active functional groups that allows for repeatable and stable detection of electroactive multiple neurotransmitters at concentrations as low as 10 nM. © 2020, CC-BY.

关键词： Carbon

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Triggering phase-coherent spin packets by pulsed electrical spin injection across an Fe/GaAs Schottky barrier

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Physical Review B 2021年第19期104卷 195202-195202页

作者： L. R. Schreiber C. Schwark G. Güntherodt M. Lepsa C. Adelmann C. J. Palmstrøm X. Lou P. A. Crowell B. Beschoten 2nd Institute of Physics and JARA-FIT RWTH Aachen University 52074 Aachen Germany JARA-FIT Institute for Quantum Information Forschungszentrum Jülich GmbH and RWTH Aachen University 52074 Aachen Germany Peter Grünberg Institute (PGI-10) Forschungszentrum Jülich GmbH 52425 Jülich Germany Department of Chemical Engineering and Material Science University of Minnesota Minneapolis Minnesota 55455 USA IMEC 3001 Leuven Belgium Departments of Electrical and Computer Engineering and Materials University of California Santa Barbara California 93106 USA School of Physics and Astronomy University of Minnesota Minneapolis Minnesota 55455 USA

The precise control of spins in semiconductor spintronic devices requires electrical means to generate spin packets with a well-defined initial phase. We demonstrate a pulsed electrical scheme that triggers the spin ensemble phase in a similar way as circularly polarized optical pulses generate phase coherent spin packets. Here, we use fast current pulses to initialize phase coherent spin packets, which are injected across an Fe/GaAs Schottky barrier into n-GaAs. By means of time-resolved Faraday rotation, we demonstrate phase coherence by the observation of multiple Larmor precession cycles for current pulse widths down to 500 ps at 17 K. We show that the current pulses are broadened by the charging and discharging time of the Schottky barrier. At high frequencies, the observable spin coherence is limited only by the finite bandwidth of the current pulses, which is of the order of 2 GHz. These results therefore demonstrate that all-electrical injection and phase control of electron spin packets at microwave frequencies is possible in metallic-ferromagnet–semiconductor heterostructures.

关键词： Faraday effect Spin injection Spintronics III-V semiconductors Schottky barriers

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Inverse identification of dynamically important regions in turbulent flows using 3D Convolutional Neural Networks

arXiv

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arXiv 2020年

作者： Jagodinski, Eric Zhu, Xingquan Verma, Siddhartha Department of Ocean and Mechanical Engineering Florida Atlantic University Boca RatonFL33431 United States Department of Computer & Electrical Engineering and Computer Science Florida Atlantic University Boca RatonFL33431 United States Harbor Branch Oceanographic Institute Florida Atlantic University Fort PierceFL34946 United States

Near-wall regions in wall-bounded turbulent flows experience intermittent ejection of slow-moving fluid packets away from the wall and sweeps of faster moving fluid towards the wall. These extreme events play a central role in regulating the energy budget of the boundary layer, and are analyzed here with the help of a three-dimensional (3D) Convolutional Neural Network (CNN). A CNN is trained on Direct Numerical Simulation data from a periodic channel flow to deduce the intensity of such extreme events, and more importantly, to reveal contiguous three-dimensional salient structures in the flow that are determined autonomously by the network to be critical to the formation and evolution of ejection events. These salient regions, reconstructed using a multilayer Gradient-weighted Class Activation Mapping (GradCAM) technique proposed here, correlate well with bursting streaks and coherent fluid packets being ejected away from the wall. The focus on explainable interpretation of the network’s learned associations also reveals that ejections are not associated with regions where turbulent kinetic energy (TKE) production reaches a maximum, but instead with regions that entail extremely low dissipation and a significantly higher tendency for positive TKE production than negative production. This is a key finding of the study, and indicates that CNNs can help reveal dynamically important three-dimensional salient regions using a single scalar-valued metric provided as the quantity of interest, which in the present case is the ejection intensity. While the current work presents an alternate means of analyzing nonlinear spatial correlations associated with near-wall bursts, the framework presented is sufficiently general so as to be extendable to other scenarios where the underlying spatial dynamics are not known a-priori. Copyright © 2020, The Authors. All rights reserved.

关键词： Turbulent flow

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Direct mapping FBMC based underwater transmission scheme for audio signals

Direct mapping FBMC based underwater transmission scheme for...

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International Conference on Physics, Mechanics of New Materials and Their Applications, PHENMA 2018

作者： Lin, Chin-Feng Li, Chun-Kang Chang, Shun-Hsyung Parinov, Ivan A. Shevtsov, Sergey Department of Electrical Engineering National Taiwan Ocean University Keelung Taiwan Department of Microelectronic Engineering National Kaohsuing University of Science and Technology Kaohsiung Taiwan I. I. Vorovich Mathematics Mechanics and Computer Science Institute Southern Federal University Rostov-on-Don Russia South Center of Russian Academy of Science Rostov-on-Don Russia

ISBN: (纸本)9783030198930

This paper proposes a direct mapping (DM) filter bank multicarrier (FBMC) based underwater transmission scheme for audio signals. Figure 50.1 schematically shows the proposed FBMC scheme, and DM transmission technology, low-density parity-check (LDPC) channel coding, adaptive binary phase shift keying (BPSK) modulation or offset quadrature amplitude modulation (OQAM), FBMC transmission technology, and a power assignment mechanism are integrated into an underwater audio transmission system. The BER performances of the proposed scheme in an underwater channel were explored through simulations, and the power saving ratios for the underwater transmissions of audio signals were discussed. © 2019, Springer Nature Switzerland AG.

关键词： Transmissions

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