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arXiv 2022年

作者： Ali Al-Radhawi, M. Tripathi, Shubham Zhang, Yun Sontag, Eduardo D. Levine, Herbert Department of Electrical and Computer Engineering Northeastern University BostonMA02115 United States Center for Theoretical Biological Physics Northeastern University BostonMA02115 United States PhD Program in Systems Synthetic and Physical Biology Rice University HoustonTX77005 United States Whitehead Institute for Biomedical Research CambridgeMA02142 United States Department of Bioengineering Northeastern University BostonMA02115 United States Department of Physics Northeastern University BostonMA02115 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States State Key Laboratory of Molecular Oncology National Cancer Center National Clinical Research Center for Cancer Cancer Hospital Chinese Academy of Medical Sciences Peking Union Medical College Beijing100021 China

The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as Gene Regulatory Networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. In this paper, we propose a conceptual and mathematical modeling framework that incorporates both local and global competition effects between antagonistic epigenetic regulators in addition to local transcription factors, and show the counter-intuitive consequences of such interactions. We apply our approach to recent experimental findings on the Epithelial-Mesenchymal Transition (EMT). We show that it can explain the puzzling experimental data as well provide new verifiable predictions. © 2022, CC BY-NC-ND.

关键词： Transcription factors

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The transit timing and atmosphere of hot jupiter HAT-P-37b

arXiv

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arXiv 2021年

作者： A-Thano, Napaporn Jiang, Ing-Guey Awiphan, Supachai Rattanamala, Ronnakrit Su, Li-Hsin Hengpiya, Torik Sariya, Devesh P. Yeh, Li-Chin Shlyapnikov, A.A. Gorbachev, Mark A. Rublevski, Alexey N. Mannaday, Vineet Kumar Thakur, Parijat Sahu, D.K. Mkrtichian, David Griv, Evgeny Department of Physics and Institute of Astronomy National Tsing-Hua University Hsinchu30013 Taiwan National Astronomical Research Institute of Thailand 260 Moo 4 Donkaew Mae Rim Chiang Mai50180 Thailand PhD Program in Astronomy Department of Physics and Materials Science Faculty of Science Chiang Mai University Chiang Mai50200 Thailand Department of Physics and General Science Faculty of Science and Technology Nakhon Ratchasima Rajabhat University Nakhon Ratchasima30000 Thailand Regional Observatory for the Public Songkhla 79/4 Moo 4 Khao Roop Chang Muang District Songkhla90000 Thailand Institute of Computational and Modeling Science National Tsing-Hua University Hsinchu30013 Taiwan Crimean Astrophysical Observatory 298409 Nauchny Crimea 495009 India Indian Institute of Astrophysics Bangalore560034 India Department of Physics Ben-Gurion University Beer-Sheva84105 Israel

The transit timing variation (TTV) and transmission spectroscopy analyses of the planet HAT-P-37b, which is a hot Jupiter orbiting an G-type star, were performed. Nine new transit light curves are obtained and analysed together with 21 published light curves from the literature. The updated physical parameters of HAT-P-37b are presented. The TTV analyses show a possibility that the system has an additional planet which induced the TTVs amplitude signal of 1.74 ± 0.17 minutes. If the body is located near the 1:2 mean motion resonance orbit, the sinusoidal TTV signal could be caused by the gravitational interaction of a sub-Earth mass planet with mass of 0.06 MO. From the analysis of an upper mass limit for the second planet, the Saturn mass planet with orbital period less than 6 days is excluded. The broad-band transmission spectra of HAT-P-37b favours a cloudy atmospheric model with an outlier spectrum in B-filter. Copyright © 2021, The Authors. All rights reserved.

关键词： Planets

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Strengthening the Link Between Fullerenes and a Subset of Diffuse Interstellar Bands

arXiv

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arXiv 2025年

作者： Majaess, Daniel Harriott, Tina A. Seuret, Halis Morera-Boado, Cercis Massa, Lou Matta, Chérif F. Department of Chemistry and Physics Mount Saint Vincent University HalifaxNSB3M2J6 Canada Department of Mathematics and Statistics Mount Saint Vincent University HalifaxNSB3M2J6 Canada Centro de Investigaciones Químicas IICBA Universidad Autónoma del Estado de Morelos Morelos Cuernavaca62209 Mexico IXM-Cátedra Conahcyt-Centro de Investigaciones Químicas IICBA Universidad Autónoma del Estado de Morelos Morelos Cuernavaca62209 Mexico Hunter College The PhD Program of the Graduate Center City University of New York New York United States Department of Chemistry Saint Mary’s University HalifaxNSB3H3C3 Canada Département de Chimie Université Laval QuébecG1V0A6 Canada Department of Chemistry Dalhousie University HalifaxNSB3H4J3 Canada

A debate persists regarding the correlation between the DIBs 9577 and 9632 Å, and whether they share a common molecular carrier (i.e., C+60). A robust high correlation determination emerges after bridging the baseline across an order of magnitude ( 50 − 700 mÅ, r = 0.93 ± 0.02), and nearly doubling the important higher equivalent width domain by adding new Mg II-corrected sightlines. Moreover, additional evidence is presented of possible DIB linkages to fullerenes, whereby attention is drawn to DIBs at 7470.38, 7558.44, and 7581.47 Å, which match the Campbell experimental results for C+70 within 1 Å, and the same is true of 6926.48 and 7030.26 Å for C2+70 . Yet their current correlation uncertainties are unsatisfactory and exacerbated by expectedly low EWs (e.g., EW = 4 mÅ for 6926.48 Å), and thus further observations are required to assess whether they represent a bona fide connection or numerical coincidence. © 2025, CC BY.

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Potential Vibrational Modes Tied to Diffuse Interstellar Bands

arXiv

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arXiv 2025年

作者： Majaess, Daniel Seuret, Halis Harriott, Tina A. Morera-Boado, Cercis Sullivan, Ailish Massa, Lou Matta, Chérif F. Department of Chemistry and Physics Mount Saint Vincent University HalifaxNSB3M2J6 Canada Centro de Investigaciones Químicas IICBA Universidad Autónoma del Estado de Morelos Morelos Cuernavaca62209 Mexico Department of Mathematics and Statistics Mount Saint Vincent University HalifaxNSB3M2J6 Canada IXM-Cátedra Conahcyt Centro de Investigaciones Químicas IICBA Universidad Autónoma del Estado de Morelos Morelos Cuernavaca62209 Mexico Hunter College PhD Program of the Graduate Center City University of New York New York United States Department of Chemistry Saint Mary’s University HalifaxNSB3H3C3 Canada Département de Chimie Université Laval QuébecG1V0A6 Canada Department of Chemistry Dalhousie University HalifaxNSB3H4J3 Canada

Potential vibrational modes associated with diffuse interstellar bands (DIBs) could be discerned by examining energy differences between correlated DIBs. Consequently, ≈ 103 higher correlated DIB pairs (r − σr ≥ 0.8, ≥ 12 sightlines) were extracted from the Apache Point Observatory DIB catalog, and their energy spacings computed. In this first macro exploratory step, a histogram possibly reveals chemical bond signatures of C≡C, C≡N, S−H, C−O, C=O, Si−H, N−H, C−H (aliphatic), C...C (in-ring), and aromatics (C−H stretch, C...C in-ring, oop C−H bending, and overtones). Continued research is required to (in)validate the histogram approach, mitigate noise, scrutinize maxima, break degeneracies, and converge upon an optimal framework. © 2025, CC BY.

关键词： Bond strength (chemical)

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BPS2025 - Structure and inhibition of SARS-CoV-2 spike refolding in membranes

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Biophysical Journal 2025年第3期124卷 580a-580a页

作者： Walther Mothes Mikey W. Grunst Zhuan Qin Esteban Dodero-Rojas Shilei Ding Jeremie Prevost Yaozong Chen Yanping Hu Marzena Pazgier Shenping Wu Xuping Xie Andrés Finzi José N. Onuchic Paul C. Whitford Wenwei Li Department of Microbial Pathogenesis Yale University New Haven CT USA Systems Synthetic and Physical Biology PhD Program Rice University Houston TX USA Centre de Recherche du CHUM Montréal QC Canada Département de Microbiologi Université de Montréal Montréal QC Canada School of Medicine Uniformed Services University of the Health Sciences Bethesda MD USA Department of Biochemistry and Molecular Biology University of Texas Medical Branch Galveston TX USA Department of Pharmacology Yale University West Haven CT USA Center for Theoretical Biological Physics Rice University Houston TX USA Department of Physics Northeastern University Boston MA USA

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Metal ratio and bimetal nanoarchitectonics of ammonia-based fluoride complex induced nickel hydroxide and manganese oxide composites as active materials of an energy storage device

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Journal of Energy Storage 2024年 80卷

作者： Hsu, Chuan-Chih Yu, You Zher Wu, Chung-Hsien Lee, Pin-Yan Chen, Hung-Ming Husain, Sadang Kongvarhodom, Chutima Hsiao, Yu-Cheng Lin, Lu-Yin Division of Cardiovascular Surgery Department of Surgery School of Medicine College of Medicine Taipei Medical University Taiwan Division of Cardiovascular Surgery Department of Surgery Taipei Medical University Hospital Taiwan Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taipei Taiwan Gingen Technology Co. LTD. Rm. 7 10F. No.189 Sec. 2 Keelung Rd. Xinyi Dist. Taipei11054 Taiwan Department of Physics Faculty of Mathematics and Natural Science Lambung Mangkurat University Banjarmasin70124 Indonesia Department of Chemical Engineering King Mongkut's University of Technology Thonburi 126 Pracha-u-thit Toong-kru Bangkok10140 Thailand Department of Chemical Engineering Ming Chi University of Technology New Taipei City24301 Taiwan Cell Physiology and Molecular Image Research Center Wan Fang Hospital Taipei Medical University Taipei11696 Taiwan International PhD Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Stanford Byers Center for Biodesign Stanford University CA94305-5428 United States Graduate Institute of Biomedical Optomechatronics College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan

Nickel and manganese compounds are widely applied as efficient battery-type active materials for energy storage devices, due to high theoretical capacities and abundant redox states for generating redox reactions to store charges. Morphology plays significant roles on energy storage ability. Structure directing agent (SDA) is widely reported to have ability for modulating configurations of active materials and to achieve excellent surface properties. In this work, it is the first time to use NH4BF4 and NH4HF2 as structure directing agents for synthesizing nickel manganese compounds derived from ZIF67 as active materials of energy storage devices. Bimetallic compounds are composed of nickel hydroxide and manganese oxide, which presents the favorable two-dimensional flower-like structure with high surface area and abundant redox states. The largest specific capacitance (CF) of 1358.2 F/g corresponding to the capacity of 226.4 mAh/g are achieved for the bimetallic compound synthesized using the Ni to Mn precursor ratio of 1 to 1 (NiMn11). The energy storage device assembled using NiMn11 and reduced graphene oxide on Ni foams presents a maximum energy density of 11.45 Wh/kg at the power density of 0.35 kW/kg, and excellent long-term stability with the CF retention of 85.6% and Coulombic efficiency of 87.5% after 10,000 cycles. © 2023

关键词： Fluorine compounds

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Transparent, low-autofluorescence microECoG device for simultaneous Ca2+ imaging and cortical electrophysiology in vivo

Transparent, low-autofluorescence microECoG device for simul...

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作者： Zátonyi, A. Madarász, M. Szabó, O. Lőrincz, T. Hodován, R. Rózsa, B. Fekete, Z. Research Group for Implantable Microsystems Faculty of Information Technology and Bionics Pázmány Péter Catholic University Budapest Hungary Microsystems Laboratory Institute for Technical Physics and Material Sciences Centre for Energy Research HAS Budapest Hungary Doctoral School of Chemical Engineering and Material Sciences University of Pannonia Veszprém Hungary Laboratory of 3D Functional Network and Dendritic Imaging Institute of Experimental Medicine HAS Budapest Hungary János Szentágothai PhD Program Semmelweis University Budapest Hungary Roska Tamás Doctoral School of Sciences and Technology Pázmány Péter Catholic University Budapest Hungary

Objective. Multimodal neuroimaging approaches are beneficial to discover brain functionalities at high spatial and temporal resolution. In our work, a novel material composition of a microECoG device relying on Parylene HT and indium-tin-oxide (ITO) is presented, which facilitates two-photon imaging of Ca2+ signals and concurrent recording of cortical EEG. Approach. Long-term stability of the interfaces of the transparent microdevice is confirmed in vitro by electrochemical and mechanical tests. The outstanding optical properties, like high transmittance and low auto-fluorescent are proven by fluorimetric measurements. Spatial resolution of fluorescent two-photon imaging through the microECoG device is presented in transgenic hippocampal slices, while concurrent recording of Ca2+ signals and cortical EEG is demonstrated in vivo. Photoartefacts and photodegradation of the materials are also investigated in detail to provide safety guidelines for further use in two-photon in vivo imaging schemes. Main results. Two-photon imaging of Ca signals can be safely performed through the proposed transparent ECoG device, without significant distortion in the dimensions of detected neuronal structures or in the temporal signaling. In chronic use, we demonstrated that fluorescent Ca signals of individual neurons can be clearly recorded even after 51 d. Significance. Our results give a firm indication that highly transparent microECoG electrode arrays made of Parylene HT/ITO/Parylene HT multilayer are excellent candidates for synergetic recording of optical signals and EEG from intact brains with high resolution and are free of electrical and optical artefacts. © 2020 IOP Publishing Ltd.

关键词： Electrophysiology

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Effect of a small loss or gain in the periodic nonlinear Schrödinger anomalous wave dynamics

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Physical Review E 2020年第3期101卷 032204-032204页

作者： F. Coppini P. G. Grinevich P. M. Santini PhD Program in Physics Dipartimento di Fisica Università di Roma “La Sapienza” and Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Roma Piazzale Aldo Moro 2 I-00185 Roma Italy Steklov Mathematical Institute of Russian Academy of Sciences 8 Gubkina Street Moscow 199911 Russia and L. D. Landau Institute for Theoretical Physics Prospekt Akademika Semenova 1a Chernogolovka 142432 Russia Dipartimento di Fisica Università di Roma “La Sapienza” and Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Roma Piazzale Aldo Moro 2 I-00185 Roma Italy

The focusing nonlinear Schrödinger (NLS) equation is the simplest universal model describing the modulation instability of quasimonochromatic waves in weakly nonlinear media, the main physical mechanism for the appearance of anomalous (rogue) waves (AWs) in nature. In this paper, concentrating on the simplest case of a single unstable mode, we study the special Cauchy problem for the NLS equation perturbed by a linear loss or gain term, corresponding to periodic initial perturbations of the unstable background solution of the NLS. Using the finite gap method and the theory of perturbations of soliton partial differential equations, we construct the proper analytic model describing quantitatively how the solution evolves after a suitable transient into slowly varying lower dimensional patterns (attractors) on the (x,t) plane, characterized by ΔX=L/2 in the case of loss and by ΔX=0 in the case of gain, where ΔX is the x shift of the position of the AW during the recurrence, and L is the period. This process is described, to leading order, in terms of elementary functions of the initial data. Since dissipation can hardly be avoided in all natural phenomena involving AWs, and since a small dissipation induces O(1) effects on the periodic AW dynamics, generating the slowly varying loss or gain attractors analytically described in this paper, we expect that these attractors together with their generalizations corresponding to more unstable modes will play a basic role in the theory of periodic AWs in nature.

关键词： Nonlinear waves Solitons

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Application of artificial intelligence in endoscopic image analysis for the diagnosis of a gastric cancer pathogen-Helicobacter pylori infection

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Scientific Reports 2023年第1期13卷 1-12页

作者： Lin, Chih-Hsueh Hsu, Ping-I Tseng, Chin-Dar Chao, Pei-Ju Wu, I-Ting Ghose, Supratip Shih, Chih-An Lee, Shen-Hao Ren, Jia-Hong Shie, Chang-Bih Lee, Tsair-Fwu Department of Electronic Engineering National Kaohsiung University of Science and Technology Kaohsiung 80778 Taiwan Medical Physics and Informatics Laboratory of Electronic Engineering National Kaohsiung University of Science and Technology Kaohsiung 80778 Taiwan Division of Gastroenterology Department of Medicine An Nan Hospital China Medical University Tainan Taiwan Department of Education and Research An Nan Hospital China Medical University Tainan Taiwan Division of Gastroenterology and Hepatology Department of Internal Medicine Antai Medical Care Corporation Antai Tian-Sheng Memorial Hospital Pingtung County Donggan Taiwan Department of Nursing Meiho University Pingtung County Neipu Taiwan Department of Radiation Oncology Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine Linkou Taiwan Department of Medical Imaging and Radiological Sciences Kaohsiung Medical University Kaohsiung 80708 Taiwan PhD Program in Biomedical Engineering Kaohsiung Medical University Kaohsiung 80708 Taiwan School of Dentistry College of Dental Medicine Kaohsiung Medical University Kaohsiung 80708 Taiwan

Helicobacter pylori (H. pylori) infection is the principal cause of chronic gastritis, gastric ulcers, duodenal ulcers, and gastric cancer. In clinical practice, diagnosis of H. pylori infection by a gastroenterologists’ impression of endoscopic images is inaccurate and cannot be used for the management of gastrointestinal diseases. The aim of this study was to develop an artificial intelligence classification system for the diagnosis of H. pylori infection by pre-processing endoscopic images and machine learning methods. Endoscopic images of the gastric body and antrum from 302 patients receiving endoscopy with confirmation of H. pylori status by a rapid urease test at An Nan Hospital were obtained for the derivation and validation of an artificial intelligence classification system. The H. pylori status was interpreted as positive or negative by Convolutional Neural Network (CNN) and Concurrent Spatial and Channel Squeeze and Excitation (scSE) network, combined with different classification models for deep learning of gastric images. The comprehensive assessment for H. pylori status by scSE-CatBoost classification models for both body and antrum images from same patients achieved an accuracy of 0.90, sensitivity of 1.00, specificity of 0.81, positive predictive value of 0.82, negative predicted value of 1.00, and area under the curve of 0.88. The data suggest that an artificial intelligence classification model using scSE-CatBoost deep learning for gastric endoscopic images can distinguish H. pylori status with good performance and is useful for the survey or diagnosis of H. pylori infection in clinical practice. © 2023, Springer Nature Limited.

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Biological regulatory networks are minimally frustrated

arXiv

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arXiv 2019年

作者： Tripathi, Shubham Kessler, David A. Levine, Herbert PhD Program in Systems Synthetic and Physical Biology Rice University HoustonTX77005 United States Center for Theoretical Biological Physics Rice Univeristy HoustonTX77005 United States Department of Physics Northeastern Univeristy BostonMA02115 United States Department of Physics Bar-Ilan Univeristy Ramat-Gan52900 Israel

Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous studies, focusing on identifying topological features that are present in biological networks but not in random networks, have, however, provided few functional insights. We use a Boolean modeling framework and ideas from spin glass literature to identify functional differences between five real biological networks and random networks with similar topo-logical features. We show that minimal frustration is a fundamental property that allows biological networks to robustly establish cell types and regulate cell fate choice, and this property can emerge in complex networks via Darwinian evolution. The study also provides clues regarding how the regulation of cell fate choice can go awry in a disease like cancer and lead to the emergence of aberrant cell types. Copyright © 2019, The Authors. All rights reserved.

关键词： Spin glass

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