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scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs

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Cell systems 2023年第4期14卷 302-311.e4页

作者： Yongjian Yang Guanxun Li Yan Zhong Qian Xu Yu-Te Lin Cristhian Roman-Vicharra Robert S Chapkin James J Cai Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA. Department of Statistics Texas A&M University College Station TX 77843 USA. Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of Statistics East China Normal University 3663 North Zhongshan Road Shanghai 200062 China. Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA. Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan. Department of Nutrition and the Program in Integrative Nutrition & Complex Diseases Texas A&M University College Station TX 77843 USA. Electronic address: r-chapkin@tamu.edu. Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA Interdisciplinary Program of Genetics Texas A&M University College Station TX 77843 USA. Electronic address: jcai@tamu.edu.

We present scTenifoldXct, a semi-supervised computational tool for detecting ligand-receptor (LR)-mediated cell-cell interactions and mapping cellular communication graphs. Our method is based on manifold alignment, using LR pairs as inter-data correspondences to embed ligand and receptor genes expressed in interacting cells into a unified latent space. Neural networks are employed to minimize the distance between corresponding genes while preserving the structure of gene regression networks. We apply scTenifoldXct to real datasets for testing and demonstrate that our method detects interactions with high consistency compared with other methods. More importantly, scTenifoldXct uncovers weak but biologically relevant interactions overlooked by other methods. We also demonstrate how scTenifoldXct can be used to compare different samples, such as healthy vs. diseased and wild type vs. knockout, to identify differential interactions, thereby revealing functional implications associated with changes in cellular communication status.

关键词： cell-cell interaction cellular communication gene regression network machine learning manifold alignment neural networks scRNA-seq single-cell RNA sequencing

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A phase vocoder without requiring phase unwrapping

IEEJ Transactions on Electronics, Information and Systems

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IEEJ Transactions on electronics, Information and Systems 2018年第4期138卷 352-359页

作者： Yoneguchi, Ryoichi Murakami, Takahiro Electrical Engineering Program Graduate School of Science and Technology Meiji University 1-1-1 Higashi-mita Tama-ku Kawasaki Kanagawa214-8571 Japan Department of Electronics and Bioinformatics School of Science and Technology Meiji University 1-1-1 Higashi-mita Tama-ku Kawasaki Kanagawa214-8571 Japan

In recent years, a number of algorithms for controlling parameters of an acoustic signal have been realized according as hardware technologies have been developed. A phase vocoder is one of the widely known methods for time scale modification (TSM) and pitch scale modification (PSM). The phase vocoder converts the length and the pitch of the acoustic signal by increasing or decreasing an instantaneous angular frequency. However, due to the phase unwrapping problem that occurs when the instantaneous angular frequency is estimated, the phase vocoder distorts the waveform of the modified signal. In order to alleviate this problem, we present a new algorithm for the phase vocoder. Our method does not encounter the phase unwrapping problem since we directly use the difference of phases between adjacent analysis frames to avoid estimating the instantaneous angular frequency. Moreover, our approach is effective even when the characteristics of the acoustic signal, e.g., a frequency and amplitude, change rapidly. © 2018 The Institute of electrical Engineers of Japan.

关键词： Acoustic waves

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Bi-directional Sub-60mV/dec, Hysteresis-Free, Reducing Onset Voltage and High Speed Response of Ferroelectric-AntiFerroelectric Hf0.25Zr0.75O2 Negative Capacitance FETs

Bi-directional Sub-60mV/dec, Hysteresis-Free, Reducing Onset...

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International Electron Devices Meeting (IEDM)

作者： M. H. Lee K.-T. Chen C.-Y. Liao G.-Y. Siang C. Lo H.-Y. Chen Y.-J. Tseng C.-Y. Chueh C. Chang Y.-Y. Lin Y.-J. Yang F.-C. Hsieh S. T. Chang M.-H. Liao K.-S. Li C. W. Liu Institute and Undergraduate Program of Electro-Optical Engineering National Taiwan Normal University Taipei Taiwan Department of Electrical Engineering National Chung Hsing University Taichung Taiwan Department of Mechanical Engineering National Taiwan University Taipei Taiwan Taiwan Semiconductor Research Institute Hsinchu Taiwan Graduate Institute of Electronics Engineering National Taiwan University Taipei Taiwan

Being the first demonstration of quasi-antiferroelertic Hf 1-x Zr x O 2 (QAFE-HZO, Zr=75%) negative-capacitance (NC) FET with non-hysteretic bi-directional sub-60mV/dec (SS for =51mV/dec, SS rev =53mV/dec, ΔV T FE o...

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Phase-change metal ink with pH-controlled chemical sintering for versatile and scalable fabrication of variable stiffness electronics

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Science advances 2025年第22期11卷 eadv4921页

作者： Simok Lee Gun-Hee Lee Inho Kang Woojin Jeon Semin Kim Yejin Ahn Choong Yeon Kim Do A Kwon Michael D Dickey Steve Park Seongjun Park Jae-Woong Jeong School of Electrical Engineering Korea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea. Medical Research Center Seoul National University Seoul 03080 Republic of Korea. Departments of Cogno-Mechatronics Engineering and Optics and Mechatronics Engineering Pusan National University Busan 46241 Republic of Korea. Graduate School of Semiconductor Technology Korea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea. KAIST Information and Electronics Research Institute Daejeon 34141 Republic of Korea. Research Laboratory of Electronics Massachusetts Institute of Technology (MIT) Cambridge MA 02139 USA. Department of Mechanical Engineering Massachusetts Institute of Technology (MIT) Cambridge MA 02139 USA. Department of Chemical and Biomolecular Engineering North Carolina State University (NCSU) Raleigh NC 27606 USA. Department of Materials Science and Engineering Korea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea. KAIST Institute for NanoCentury Daejeon 34141 Republic of Korea. Department of Biomedical Sciences College of Medicine Seoul National University Seoul 03080 Republic of Korea. School of Transdisciplinary Innovations Seoul National University Seoul 03080 Republic of Korea. Interdisciplinary Program in Bioengineering College of Engineering Seoul National University Seoul 08826 Republic of Korea. Department of Transdisciplinary Medicine Seoul National University Hospital Seoul 03080 Republic of Korea. KAIST Institute for Health Science and Technology Daejeon 34141 Republic of Korea.

Variable stiffness electronics represent the forefront of adaptive technology, integrating rigid and soft electronics in a single system through dynamic mechanical modulation. While gallium's high modulus tuning ratio and rapid phase transitions make it ideal for transformative electronic systems (TES), its liquid-state instability, high surface tension, and unintended phase transitions during processing pose substantial challenges. Here, we introduce STiffness-Adjustable temperature-Responsive ink (STAR ink), a chemically sinterable gallium composite electronic ink designed to overcome these obstacles. STAR ink enables high-resolution (~50 micrometers) circuit patterning, large-scale batch fabrication, and three-dimensional structure coating at room temperature. Through pH-controlled chemical sintering, STAR ink-based TES exhibits exceptional mechanical tunability (tuning ratio: 1465) and electrical conductivity (2.27 × 10 siemens per meter). Demonstrated applications-from multilayered variable stiffness printed circuit boards (PCBs) matching standard PCBs' complexity to body-temperature responsive neural probe-underscore STAR ink's potential for reconfigurable electronics across consumer electronics and biomedical devices.

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Active ISFET sensor readout circuit 2

Active ISFET sensor readout circuit

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2nd International Symposium on Instrumentation Systems, Circuits and Transducers, INSCIT 2017

作者： Furtado Da Silva, Luciano Lourenco Silveira, Felipe De Moraes Cruz, Carlos Augusto Daniel De Oliveira Moura, Thiago Graduate Program in Electrical Engineering Department of Electronics and Computation Federal University of Amazonas Manaus AM Brazil Federal Institute of Amazonas Manaus AM Brazil Graduate Program in Electrical Engineering Department of Electrical Engineering Federal University of Minas Gerais Belo Horizonte MG Brazil

ISBN: (纸本)9781538620212

An improved readout circuit interface for ion-sensitive field-effect transistor (ISFET) is proposed in this work. When compared with conventional topologies found on the literature, the proposed ISFET readout circuit presents at least two advantages. The first concerns the simplicity of the new circuity topology, and the second is the additional gain conferred to the sensor output signal. The performance of the proposed readout circuit integrated with the electrical ISFET model was investigated through BSIM3v3 simulations. The conventional ISFET readout topologies are found not to confer gain to the electrical ISFET output signal, and the sensor output signal has its limit predicted by the Nernst s model. Simulation results shows that the proposed ISFET readout circuit topology grants additional gain to the sensor output signal increasing its sensitivity up to three times the Nernst limit. © 2017 IEEE.

关键词： Topology

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GO synthesis of offset dual reflector antennas using local axis-displaced confocal quadrics

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Journal of Microwaves, Optoelectronics and Electromagnetic Applications 2020年第2期19卷 177-190页

作者： Assis, Aline R. Moreira, Fernando J. S. Bergmann, José R. Graduate Program in Electrical Engineering Federal University of Minas Gerais Av. Pres. Antonio Carlos 6627 Belo Horizonte MG31270-901 Brazil Department of Electronics Engineering Federal University of Minas Gerais Av. Pres. Antonio Carlos 6627 Belo Horizonte MG31270-901 Brazil Rua Marquês de São Vicente 225 Rio de Janeiro RJ22451-900 Brazil Departamento de Engenharia Elétrica Universidade Federal de Ouro Preto Rua Trinta e Seis 115 João Monlevade MG35931-008 Brazil

This work investigates an alternative numerical scheme for the solution of an exact formulation based on Geometrical Optics (GO) principles to synthesize offset dual reflector antennas. The technique is suited to solve a second-order nonlinear partial differential equation of the Monge-Ampère type as a boundary value problem. An iterative algorithm based on Newton's method was developed, using axis-displaced confocal quadrics to locally represent the subreflector surface, thus enabling an analytical description of the partial derivatives within the formulation. Such approach reduces discretization errors, as exact expressions for the mapping function and its derivatives are analytically determined. To check the robustness of the methodology, an offset dual-reflector Gregorian antenna was shaped to provide a Gaussian aperture field distribution with uniform phase within a superelliptical contour. The shaped surfaces were further interpolated by quintic pseudo-splines and analyzed by Physical Optics (PO) with equivalent edge currents to validate the synthesis procedure at 11,725 GHz. © 2020 SBMO/SBMag.

关键词： Geometrical optics

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Influence of Magnetic Fields on Electrochemical Reactions of Redox Cofactor Solutions

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Angewandte Chemie 2021年第33期133卷

作者： Jimin Park Florian Koehler Georgios Varnavides Marc-Joseph Antonini Prof. Dr. Polina Anikeeva Department of Materials Science and Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA Research Laboratory of Electronics and McGovern Institute for Brain Research Massachusetts Institute of Technology Cambridge MA 02139 USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA 02139 USA Harvard/MIT Health Science & Technology Graduate Program Cambridge MA 02139 USA Department of Brain and Cognitive Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA

Redox cofactors mediate many enzymatic processes and are increasingly employed in biomedical and energy applications. Exploring the influence of external magnetic fields on redox cofactor chemistry can enhance our understanding of magnetic-field-sensitive biological processes and allow the application of magnetic fields to modulate redox reactions involving cofactors. Through a combination of experiments and modeling, we investigate the influence of magnetic fields on electrochemical reactions in redox cofactor solutions. By employing flavin mononucleotide (FMN) cofactor as a model system, we characterize magnetically induced changes in Faradaic currents. We find that radical pair intermediates have negligible influence on current increases in FMN solution upon application of a magnetic field. The dominant mechanism underlying the observed current increases is the magneto-hydrodynamic effect. We extend our analyses to other diffusion-limited electrochemical reactions of redox cofactor solutions and arrive at similar conclusions, highlighting the opportunity to use this framework in redox cofactor chemistry.

关键词： electrochemistry magnetic field effects magneto-hydrodynamic effect radicals redox cofactors

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Regularization of Extreme Learning Machines with information of spatial relations of the projected data

Regularization of Extreme Learning Machines with information...

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International Conference on Control, Decision and Information Technologies (CoDIT)

作者： Lourenço R. G. Araújo Luiz C. B. Torres Leonardo J. Silvestre Carla Takahashi Antônio P. Braga Graduate Program in Electrical Engineering Universidade Federal de Minas Gerais Belo Horizonte MG Brazil Department of Computing and Systems Federal University of Ouro Preto Jo??o Monlevade Brazil Department of Computing and Electronics Federal University of Esp??rito Santo S??o Mateus ES Brazil Loggi Tecnologia Alameda Santos S??o Paulo SP Brazil Department of Electronics Engineering Federal University of Minas Gerais Belo Horizonte MG Brazil

The following work presents a new approach to automatic selection of Tikhonov's regularization parameter, responsible for controlling the weight value of an ELM neural network. A strategy based on measurements obtained from data projection (Fisher-Score) is introduced. Seven datasets are tested and results are compared to those obtained when the regularization parameter is selected through cross-validation. The strategy shows satisfactory classification performance (in terms of p-value), while presenting significant training time reduction.

关键词： Neurons Training Cybernetics Minimization Testing Biological neural networks Aerospace electronics

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Mitigating Intentional Electromagnetic Interferences over the GSM-R System with Adaptive Filters

Mitigating Intentional Electromagnetic Interferences over th...

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International Conference on Applied Electromagnetics and Communications (ICECom)

作者： Artur N. de São José Virginie Deniau Úrsula do C. Resende Ricardo Adriano Graduate Program in Electrical Engineering Federal University of Minas Gerais French Institute of Science and Technology for Transport France Laboratory on Electronics Waves and Signal Processing for Transport French Institute of Science and Technology for Transport Development and Networks Villeneuve d’Ascq France Eletrical Engineering Department Federal Center for Technological Education of Minas Gerais Belo Horizonte Brazil Eletrical Engineering Department Federal University of Minas Gerais Belo Horizonte Brazil

ISBN: (数字)9781728155142

ISBN: (纸本)9781728155159

Intentional electromagnetic interference is a potential issue for railway networks based on ground-to-train communications. Reported mitigation techniques usually rely on electromagnetic compatibility classical procedures, which are not always the best option for such an unpredictable event. In this work, offline adaptive filtering is used to recover global system for mobile communications - railway damaged data.

关键词： Jamming Rail transportation Base stations Time-frequency analysis Downlink Noise measurement Convergence

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PID Tuning for Time-Varying Delay Systems Based on Modified Smith Predictor

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IFAC-PapersOnLine 2017年第1期50卷 1269-1274页

作者： de Oliveira F.S.S. Souza F.O. Palhares R.M. Graduate Program in Electrical Engineering United States Department of Electronics Engineering Federal University of Minas Gerais Belo Horizonte MG Brazil

This paper presents a new linear matrix inequality (LMI) based control strategy for second-order systems with time-varying delay based on a modified Smith predictor with a proportional-integral-derivative (PID) controller. The main idea consists in representing the predictor model as a closed-loop observer, which takes into account only the estimated average value of the time-delay such that no real time measurement of the delay is required. A numerical example is introduced to illustrate the effectiveness of the proposed method. © 2017

关键词： linear matrix inequalities PID controller Process time-delay Smith predictor

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