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An Open-Source Knowledge Graph Ecosystem for the Life sciences

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arXiv 2023年

作者： Callahan, Tiffany J. Tripodi, Ignacio J. Stefanski, Adrianne L. Cappelletti, Luca Taneja, Sanya B. Wyrwa, Jordan M. Casiraghi, Elena Matentzoglu, Nicolas A. Reese, Justin Silverstein, Jonathan C. Hoyt, Charles Tapley Boyce, Richard D. Malec, Scott A. Unni, Deepak R. Joachimiak, Marcin P. Robinson, Peter N. Mungall, Christopher J. Cavalleri, Emanuele Fontana, Tommaso Valentini, Giorgio Mesiti, Marco Gillenwater, Lucas A. Santangelo, Brook Vasilevsky, Nicole A. Hoehndorf, Robert Bennett, Tellen D. Ryan, Patrick B. Hripcsak, George Kahn, Michael G. Bada, Michael Baumgartner, William A. Hunter, Lawrence E. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Computer Science Department Interdisciplinary Quantitative Biology University of Colorado Boulder BoulderCO80301 United States AnacletoLab Computer Science Department University of Milan 20122 Italy Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Semanticly Ltd Athens Greece Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15206 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States Division of Translational Informatics University of New Mexico School of Medicine AlbuquerqueNM87131 United States SIB Swiss Institute of Bioinformatics Basel Switzerland Berlin Institute of Health at Charité-Universitatsmedizin Berlin10117 Germany ELLIS European Laboratory for Learning and Intelligent Systems Germany Department of Biomedical Informatics University of Colorado School of Medicine AuroraCO80045 United States Data Collaboration Center Critical Path Institute 1840 E River Rd. Suite 100 TucsonAZ85718 United States Computer Electrical and Mathematical Sciences & Engineering Division Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Janssen Research and Development RaritanNJ08869 United States Division of General Internal Medicine University of Colorado School of Medicine A

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability. © 2023, CC BY.

关键词： Ecosystems

Yogurt-inspired hybrid membrane vesicles for the prevention and treatment of Helicobacter pylori infection

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Cell Biomaterials 2025年第4期1卷

作者： Lujie Liu Yiming Guo Baikui Wang Yuanwei Pan Chenchen Zhao Zhiping Xiao Yu Liu Guocan Yu Xiaoyuan Chen Lang Rao Institute of Chemical Biology Shenzhen Bay Laboratory Shenzhen 518132 China Department of Diagnostic Radiology Yong Loo Lin School of Medicine and Faculty of Engineering National University of Singapore Singapore 119074 Singapore College of Animal Science Zhejiang University Hangzhou 310058 China Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China Clinical Imaging Research Centre Centre for Translational Medicine Yong Loo Lin School of Medicine National University of Singapore Singapore 117599 Singapore Nanomedicine Translational Research Program Yong Loo Lin School of Medicine National University of Singapore Singapore 117597 Singapore Theranostics Center of Excellence (TCE) Yong Loo Lin School of Medicine National University of Singapore Singapore 138667 Singapore Institute of Molecular and Cell Biology Agency for Science Technology and Research (A∗STAR) Singapore 138673 Singapore Department of Chemical and Biomolecular Engineering College of Design and Engineering National University of Singapore Singapore 117575 Singapore Department of Biomedical Engineering College of Design and Engineering National University of Singapore Singapore 117575 Singapore Department of Pharmacy and Pharmaceutical Sciences Faculty of Science National University of Singapore Singapore 117544 Singapore

Helicobacter pylori ( H. pylori ) infection is a critical initiating factor in numerous gastrointestinal diseases. Here, we present yogurt-inspired hybrid membrane vesicles (hMVs) engineered by fusing bacterial outer membrane vesicles (OMVs) with modified milk fat globule membrane vesicles (MMVs) to prevent and treat H. pylori infection. The hMVs function as binding site competitors, reducing bacterial adhesion while regulating epithelial integrity and immune responses. This dual mechanism synergistically inhibits H. pylori infection and promotes gastric epithelial repair. In vitro , hMVs demonstrated remarkable efficacy in accelerating scratch-wound healing, enhancing lipid raft formation, increasing tight junction protein ZO-1 expression, and promoting macrophage phagocytosis of apoptotic epithelial cells. In mouse models for both H. pylori prevention and treatment, oral administration of hMVs effectively reduced H. pylori loads by 86% and 66%, respectively. Additionally, this treatment mitigated inflammatory factor secretion, decreased neutrophil recruitment, and preserved the abundance of beneficial probiotics in the stomach.

关键词： Helicobacter pylori infection drug delivery nanomedicine extracellular vesicles nanobiotechnology

Triboelectro-responsive DNA hydrogels for accelerated healing of bacterium-infected diabetic wounds

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Nano Energy 2025年 142卷

作者： Jiarong Guo Yihan Wei Zhenzhen Guo Tingting Wang Ying Ma Hongyang Li Xuan Qin Yina Liu Zhen Wen Peng Miao University of Science and Technology of China Hefei 230026 China Suzhou Institute of Biomedical Engineering and Technology Chinese Academy of Sciences Suzhou 215163 China Institute of Functional Nano and Soft Materials (FUNSOM) Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices Soochow University Suzhou 215123 China Jiangsu Key Laboratory for Molecular and Medical Biotechnology College of Life Sciences Nanjing Normal University Nanjing 210023 China Department of Applied Mathematics School of Mathematics and Physics Xi’an Jiaotong-Liverpool University Suzhou 215123 China

Disturbances in endogenous electric fields always impede the wound healing process, particularly in the presence of bacterium infections. Remodeling the electric field within anti-bacterial dressings remains challenging. DNA hydrogels comprising networks of DNA strands emerge as a new class of polymeric biomaterials. In this study, we report the first triboelectro-responsive DNA hydrogels. Conductive polymers are incorporated to remodel the bioelectrical behavior with pulsed triboelectric stimulation, which activate the electrotaxis of tissues and accelerate wound healing. The specific sequences inside DNA hydrogels also assist drug delivering in response to acute events at the wound site. The integration of functional DNA materials with a triboelectric nanogenerator system exhibits excellent anti-bacterial and anti-inflammatory properties. Collagen deposition, angiogenesis, and hair follicle regeneration are promoted. A striking closure of bacterium-infected diabetic wounds is achieved within 14 days (99.8 %). The prepared triboelectro-responsive DNA hydrogels are expected to constitute the next generation of smart dressings for electro-coherent therapy of chronic diabetic wounds.

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Flash nanocomplexation as a scalable production method for therapeutic pdna/lpei nanoparticles 42

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Flash nanocomplexation as a scalable production method for t...

42nd Society for Biomaterials Annual Meeting and Exposition 2019: The Pinnacle of Biomaterials Innovation and Excellence

作者： Liu, Heng-Wen Hu, Yizong Minn, Il Pomper, Martin Mao, Hai-Quan Department of Materials Science and Engineering Johns Hopkins University BaltimoreMD21218 United States Institute for NanoBioTechnology Johns Hopkins University BaltimoreMD21218 United States Department of Biomedical Engineering Johns Hopkins School of Medicine MD21205 United States Russell H. Morgan Department of Radiology and Radiological Science Johns Hopkins School of Medicine MD21205 United States Translational Tissue Engineering Center Johns Hopkins School of Medicine MD21205 United States

ISBN: (纸本)9781510883901

Statement of Purpose: Plasmid DNA (pDNA) nanoparticles synthesized by linear polyethylenimine (lPEI) have shown to be effective gene delivery vehicles for therapeutic applications in animal models. However, a critical barrier to clinical translation lies with producing nanoparticles with optimized physicochemical properties in a scalable and reproducible manner. The method should be validated by reliable characterization standards, with a good level of quality control. We have developed a scalable and controllable manufacturing method for production of shelf-stable pDNA/lPEI nanoparticles. Specifically, we have turned a batch mode (pipet mixing) method into a continuous process using the flash nanocomplexation (FNC) method [1]. We have demonstrated excellent reproducibility for this FNC process under quality assurance and quality control standards at different production batch sizes. The sizes of the FNC pDNA/lPEI nanoparticles were tunable with a PDI lower than 0.2. In addition, the FNC nanoparticles could be reliably lyophilized. The lyophilized formulation preserved the composition, physicochemical properties, and bioactivity of the nanoparticles;and, to date, a stability for at least 9 months in-20°C has been achieved. Furthermore, systemically delivered FNC nanoparticles were well tolerated in mice and a large animal model, and biodistribution, determined by bioluminescence and QPCR respectively, showed the efficacy to deliver into many organs/tissues. In vitro and in vivo toxicity assessment of pDNA/lPEI nanoparticles were studied and demonstrated the safety in the translation. These results confirmed that FNC production could overcome many manufacturing limitations of pDNA/lPEI nanoparticles and open up new opportunities for clinical translation of DNA nanomedicine products. © 2019 Omnipress - All rights reserved.

关键词： Nanoparticles

Acoustic Ghost Imaging in the Time Domain

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Physical Review Applied 2020年第6期13卷 064044-064044页

作者： Yuan Tian Hao Ge Xiu-Juan Zhang Xiang-Yuan Xu Ming-Hui Lu Yun Jing Yan-Feng Chen National Laboratory of Solid State Microstructures and Department of Materials Science and Engineering Nanjing University Nanjing 210093 Jiangsu China The Institute of Acoustics of the Chinese Academy of Sciences 100190 Beijing China Collaborative Innovation Center of Advanced Microstructures Nanjing 210093 Jiangsu China Department of Mechanical and Aerospace Engineering North Caroline State University Raleigh North Carolina 27695 USA Graduate Program in Acoustics The Pennsylvania State University University Park Pennsylvania 16802 USA

Ghost imaging (GI) enables reconstruction of the image of an object by measuring the intensity correlation of two beams, neither of which independently carries the spatial characteristics of the object. By exploiting the space-time duality, GI has been extended from the spatial domain to the time domain, and has been successfully demonstrated in the optical regime. This article reports on the experimental demonstration of acoustic GI in the time domain. Using ultrasound instead of photons, we created high-quality ghost images of a temporal object, even in the presence of strong ambient noise. Our work offers a fresh approach for imaging disturbance-sensitive acoustic signals, and could open the gateway to identifying new approaches in acoustic sensing, dynamic imaging, and communications.

关键词： Acoustic measurements Acoustic signal processing & noise Ghost imaging Ultrasonics Ultrasound techniques

Project 1000 x 1000: Centrifugal melt spinning for distributed manufacturing of N95 filtering facepiece respirators

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arXiv 2020年

作者： Molina, Anton Vyas, Pranav Khlystov, Nikita Kumar, Shailabh Kothari, Anesta Deriso, Dave Liu, Zhiru Banavar, Samhita Flaum, Eliott Prakash, Manu Department of Materials Science and Engineering Stanford University StanfordCA94305 United States Department of Bioengineering Stanford University StanfordCA94305 United States Department of Chemical Engineering Stanford University StanfordCA94305 United States Department of Electrical Engineering Stanford University StanfordCA94305 United States Department of Applied Physics Stanford University StanfordCA94305 United States Program in Biophysics Stanford University StanfordCA94305 United States

The COVID-19 pandemic has caused a global shortage of personal protective equipment. While existing supply chains are struggling to meet the surge in demand, the limited supply of N95 filtering facepiece respirators (FFRs) has placed healthcare workers at risk. This paper presents a method for scalable and distributed manufacturing of FFR filter material based on a combination of centrifugal melt spinning utilizing readily available cotton candy machines as an example. The proposed method produces nonwoven polypropylene fabric material with filtering efficiency of up to 96% for particles 0.30-0.49 µm in diameter. We additionally demonstrate a scalable means to test for filtration efficiency and pressure drop to ensure a standardized degree of quality in the output material. We perform preliminary optimization of relevant parameters for scale-up and propose that this is a viable method to rapidly produce up to one million N95 FFRs per day in distributed manner with just six machines per site operating across 200 locations. We share this work as a starting point for others to rapidly construct, replicate and develop their own affordable modular processes aimed at producing high quality filtration material to address the current FFR shortage globally. Copyright © 2020, The Authors. All rights reserved.

关键词： Melt spinning

Molecular Mechanism of Vitronectin Structural Evolution on Distinct Surface Chemistries: The Mediation for Cell Adhesion

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SSRN

SSRN 2019年

作者： Li, Tianjie Hao, Lijing Li, Jiangyu Du, Chang Wang, Yingjun Department of Biomedical Engineering School of Materials Science and Engineering South China University of Technology Guangzhou510641 China Department of Mechanical Engineering University of Washington SeattleWA98195 United States

Surface chemistry of biomaterials plays a fundamental role in the adsorption of vitronectin (Vn), a crucial mediator for cell adhesion. However, the detailed structural information and dynamics mechanism of Vn adsorption to distinct surface chemistries relevant to its biological effect remains elusive. Herein, the conformation and orientation evolution during Vn adsorption to self-assembled monolayers terminating with -COOH, -NH2, -CH3 and -OH were investigated. To unravel the interplay between cell binding and surface charge and wettability, the N-terminal somatomedin-B domain housing the cell-binding motif of Vn was recruited in molecular dynamics simulations optimized with orientation initialization by Monte Carlo method. Experimental evidences including protein adsorption, cell adhesion and integrin gene expressions were thoroughly investigated. The adsorption of Vn on different surface chemistries showed very complex profiles. Cell adhesion was enabled on all the Vn-adsorbed surfaces but with distinct mechanisms relating to the adsorption quantity and orientation of Vn. The negatively charged surface (COOH) and the hydrophobic surface (CH3) adsorbed Vn with higher quantity and density. However, advantageous orientations with unrestrained and active cell-binding RGD loops were only obtained on the charged surfaces (COOH and NH2) instead of the non-charged (CH3 and OH). Specifically, the negatively charged surface stretched and stood up the Vn into a higher density, whereas the hydrophobic surface squashed the Vn into higher density multilayer by tracking adsorption but with the RGD loops restrained. These findings may have a broad implication on the understanding of Vn functionality as well as the designing of advanced biomaterials. © 2019, The Authors. All rights reserved.

关键词： Molecular dynamics

Kramers Nodal Lines and Weyl Fermions in SmAlSi

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arXiv 2022年

作者： Zhang, Yichen Gao, Yuxiang Gao, Xue-Jian Lei, Shiming Ni, Zhuoliang Oh, Ji Seop Huang, Jianwei Yue, Ziqin Zonno, Marta Gorovikov, Sergey Hashimoto, Makoto Lu, Donghui Denlinger, Jonathan D. Birgeneau, Robert J. Kono, Junichiro Wu, Liang Law, Kam Tuen Morosan, Emilia Yi, Ming Department of Physics and Astronomy Rice University HoustonTX77005 United States Department of Physics Hong Kong University of Science and Technology Clear Water Bay Hong Kong Department of Physics and Astronomy University of Pennsylvania PhiladelphiaPA19104 United States Department of Physics University of California BerkeleyCA94720 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Canadian Light Source Inc. 44 Innovation Boulevard SaskatoonSKS7N 2V3 Canada Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo ParkCA94025 United States Advanced Light Source Lawrence Berekeley National Laboratory BerkeleyCA94720 United States Materials Science Division Lawrence Berekeley National Laboratory BerkeleyCA94720 United States Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Department of Materials Science and Nanoengineering Rice University HoustonTX77005 United States

Kramers nodal lines (KNLs) have recently been proposed theoretically as a special type of Weyl line degeneracy connecting time-reversal invariant momenta. KNLs are robust to spin orbit coupling and are inherent to all non-centrosymmetric achiral crystal structures, leading to unusual spin, magneto-electric, and optical properties. However, their existence in in real quantum materials has not been experimentally established. Here we gather the experimental evidence pointing at the presence of KNLs in SmAlSi, a non-centrosymmetric metal that develops incommensurate spin density wave order at low temperature. Using angle-resolved photoemission spectroscopy, density functional theory calculations, and magneto-transport methods, we provide evidence suggesting the presence of KNLs, together with observing Weyl fermions under the broken inversion symmetry in the paramagnetic phase of SmAlSi. We discuss the nesting possibilities regarding the emergent magnetic orders in SmAlSi. Our results provide a solid basis of experimental observations for exploring correlated topology in SmAlSi. © 2022, CC BY-NC-SA.

关键词： Temperature

The bulk van der Waals layered magnet CrSBr is a quasi-1D material

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arXiv 2022年

作者： Klein, Julian Pingault, Benjamin Florian, Matthias Heißenbüttel, Marie-Christin Steinhoff, Alexander Song, Zhigang Torres, Kierstin Dirnberger, Florian Curtis, Jonathan B. Weile, Mads Penn, Aubrey Deilmann, Thorsten Dana, Rami Bushati, Rezlind Quan, Jiamin Luxa, Jan Sofer, Zdenek Alù, Andrea Menon, Vinod M. Wurstbauer, Ursula Rohlfing, Michael Narang, Prineha Lončar, Marko Ross, Frances M. Department of Materials Science and Engineering Massachusetts Institute of Technology CambridgeMA02139 United States John A. Paulson School of Engineering and Applied Sciences Harvard University CambridgeMA02138 United States QuTech Delft University of Technology Delft2600 GA Netherlands Department of Electrical and Computer Engineering Department of Physics University of Michigan Ann ArborMI48109 United States Institut für Festkörpertheorie Westfälische Wilhelms-Universität Münster Münster48149 Germany Institut für Theoretische Physik Universität Bremen P.O. Box 330 440 Bremen28334 Germany Bremen Center for Computational Materials Science University of Bremen Bremen28359 Germany Department of Physics City College of New York New YorkNY10031 United States College of Letters and Science UCLA Los AngelesCA90095 United States Department of Physics Technical University of Denmark Kgs. LyngbyDK-2800 Denmark MIT.nano Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics The Graduate Center City University of New York New YorkNY10016 United States Photonics Initiative CUNY Advanced Science Research Center New YorkNY10031 United States Physics Program Graduate Center City University of New York New YorkNY10026 United States Department of Inorganic Chemistry University of Chemistry and Technology Prague Technická 5 Prague 6166 28 Czech Republic Institute of Physics Center for Nanotechnology University of Münster Münster48149 Germany

Correlated quantum phenomena in one-dimensional (1D) systems that exhibit competing electronic and magnetic order are of strong interest for studying fundamental interactions and excitations, such as Tomonaga-Luttinger liquids and topological orders and defects with properties completely different from the quasiparticles expected in their higher-dimensional counterparts. However, clean 1D electronic systems are difficult to realize experimentally, particularly magnetically ordered systems. Here, we show that the van der Waals layered magnetic semiconductor CrSBr behaves like a quasi-1D material embedded in a magnetically ordered environment. The strong 1D electronic character originates from the Cr-S chains and the combination of weak interlayer hybridization and anisotropy in effective mass and dielectric screening with an effective electron mass ratio of meX/meY ∼ 50. This extreme anisotropy experimentally manifests in strong electron-phonon and exciton-phonon interactions, a Peierls-like structural instability and a Fano resonance from a van Hove singularity of similar strength of metallic carbon nanotubes. Moreover, due to the reduced dimensionality and interlayer coupling, CrSBr hosts spectrally narrow (1 meV) excitons of high binding energy and oscillator strength that inherit the 1D character. Overall, CrSBr is best understood as a stack of weakly hybridized monolayers and appears to be an experimentally attractive candidate for the study of exotic exciton and 1D correlated many-body physics in the presence of magnetic order. Copyright © 2022, The Authors. All rights reserved.

关键词： Excitons