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arXiv 2024年

作者： Roberts, Miles D. Davis, Olivia Josephs, Emily B. Williamson, Robert J. Genetics and Genome Sciences Program Michigan State University East LansingMI48824 United States Department of Computer Science and Software Engineering Rose-Hulman Institute of Technology Terre HauteIN47803 United States Department of Biology and Biomedical Engineering Rose-Hulman Institute of Technology Terre HauteIN47803 United States Department of Plant Biology Michigan State University East LansingMI48824 United States Ecology Evolution and Behavior Program Michigan State University East LansingMI48824 United States Plant Resilience Institute Michigan State University East LansingMI48824 United States

Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously missed by approaches that map short reads to a single reference. However, many species still lack multiple reference genomes and correctly aligning references to build pangenomes is challenging, limiting our ability to study this missing genomic variation in population genetics. Here, we argue that k-mers are a crucial stepping stone to bridging the reference-focused paradigms of population genetics with the reference-free paradigms of pangenomics. We review current literature on the uses of k-mers for performing three core components of most population genetics analyses: identifying, measuring, and explaining patterns of genetic variation. We also demonstrate how different k-mer-based measures of genetic variation behave in population genetic simulations according to the choice of k, depth of sequencing coverage, and degree of data compression. Overall, we find that k-mer-based measures of genetic diversity scale consistently with pairwise nucleotide diversity (π) up to values of about π = 0.025 (R2 = 0.97) for neutrally evolving populations. For populations with even more variation, using shorter k-mers will maintain the scalability up to at least π = 0.1. Furthermore, in our simulated populations, k-mer dissimilarity values can be reliably approximated from counting bloom filters, highlighting a potential avenue to decreasing the memory burden of k-mer based genomic dissimilarity analyses. For future studies, there is a great opportunity to further develop methods to identifying selected loci using k-mers. © 2024, CC BY.

关键词： Genome

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Multifunctional Metasurface Architecture for Amplitude, Polarization and Wave-Front Control

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Physical Review Applied 2022年第6期17卷 064060-064060页

作者： A. Pitilakis M. Seckel A.C. Tasolamprou F. Liu A. Deltsidis D. Manessis A. Ostmann N.V. Kantartzis C. Liaskos C.M. Soukoulis S.A. Tretyakov M. Kafesaki O. Tsilipakos School of Electrical and Computer Engineering Aristotle University of Thessaloniki Thessaloniki GR-54124 Greece System Integration and Interconnection Technologies Fraunhofer IZM Berlin 13355 Germany Institute of Electronic Structure and Laser Foundation for Research and Technology Hellas Crete Heraklion GR-70013 Greece Xi’an Jiaotong University School of Electronic Science and Engineering Xi’an 710049 China Department of Electronics and Nanoengineering Aalto University Aalto FI-00076 Finland Department of Computer Science Engineering University of Ioannina Ioannina Greece Ames Laboratory U.S. Department of Energy and Department of Physics and Astronomy Iowa State University Ames Iowa 50011 USA Department of Materials Science and Technology University of Crete Crete Heraklion GR-70013 Greece

Metasurfaces (MSs) have been utilized to manipulate different properties of electromagnetic waves. By combining local control over the wave amplitude, phase, and polarization into a single tunable structure, a multifunctional and reconfigurable metasurface can be realized, capable of full control over incident radiation. Here, we experimentally validate a multifunctional metasurface architecture for the microwave regime, where variable loads are connected behind the back plane to reconfigurably shape the complex surface impedance. As a proof-of-concept step, we fabricate several metasurface instances with static loads in different configurations (surface mount capacitors and resistors of different values in different connection topologies) to validate the approach and showcase the different achievable functionalities. Specifically, we show perfect absorption for oblique incidence (both polarizations), broadband linear-polarization conversion, and beam splitting, demonstrating control over the amplitude, polarization state, and wave front, respectively. Measurements are performed in the 4–18-GHz range inside an anechoic chamber and show good agreement with theoretically anticipated results. Our results clearly demonstrate the practical potential of the proposed architecture for reconfigurable electromagnetic wave manipulation.

关键词： Electromagnetism Light-matter interaction Optical & microwave phenomena Optoelectronics Polarization of light Metasurfaces Electromagnetic wave theory Finite-element method

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No-boundary thinking: a viable solution to ethical data-driven AI in precision medicine

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AI and ethics 2022年第4期2卷 635-643页

作者： Tayo Obafemi-Ajayi Andy Perkins Bindu Nanduri Donald C Wunsch Ii James A Foster Joan Peckham Engineering Program Missouri State University Springfield MO USA. Department of Computer Science and Engineering Mississippi State University Starkville MS USA. Department of Comparative Biomedical Sciences College of Veterinary Medicine Mississippi State University Starkville MS USA. Electrical & Computer Engineering Department Missouri University of Science and Technology Rolla MO USA. Biological Sciences Department University of Idaho Moscow ID USA. Computer Science & Statistics Department University of Rhode Island Kingston RI USA.

Today Artificial Intelligence (AI) supports difficult decisions about policy, health, and our personal lives. The AI algorithms we develop and deploy to make sense of information, are informed by data, and based on models that capture and use pertinent details of the population or phenomenon being analyzed. For any application area, more importantly in precision medicine which directly impacts human lives, the data upon which algorithms are run must be procured, cleaned, and organized well to assure reliable and interpretable results, and to assure that they do not perpetrate or amplify human prejudices. This must be done without violating basic assumptions of the algorithms in use. Algorithmic results need to be clearly communicated to stakeholders and domain experts to enable sound conclusions. Our position is that AI holds great promise for supporting precision medicine, but we need to move forward with great care, with consideration for possible ethical implications. We make the case that a no-boundary or convergent approach is essential to support sound and ethical decisions. No-boundary thinking supports problem definition and solving with teams of experts possessing diverse perspectives. When dealing with AI and the data needed to use AI, there is a spectrum of activities that needs the attention of a no-boundary team. This is necessary if we are to draw viable conclusions and develop actions and policies based on the AI, the data, and the scientific foundations of the domain in question.

关键词： Artificial intelligence Data science Ethics Precision medicine

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Characterizing biomolecular structure features through an innovative elliptical dichroism spectrometry for cancer detection

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Heliyon 2024年第19期10卷 e38399页

作者： Asad, Yusuf Jangili, Keerthi Priya Arshad, Amara Elma, Maliha Rasuleva, Komila Akinlalu, Alfred Gao, Tommy Tida, Umamaheswara Rao Xia, Wenjie Sun, Dali Biomedical Engineering Program North Dakota State University 1401 Centennial Blvd Engineering Administration Room 203 Fargo 58102 ND United States Materials and Nanotechnology North Dakota State University Fargo 58108 ND United States Department of Aerospace Engineering Iowa State University Ames 50011 IA United States Department of Electrical and Computer Engineering North Dakota State University 1411 Centennial Blvd. 101S Fargo 58102 ND United States Department of Electrical & Computer Engineering University of Denver 2155 E. Wesley Ave. Denver 80210 CO United States Knoebel Institute for Healthy Aging University of Denver United States

This research introduces a novel method for evaluating the structural features of biomolecules, utilizing our innovative Elliptical Dichroism (ED) spectrometer specifically designed for stereochemical analysis. By integrating ED spectrometry with autocorrelation (AC) analysis, we investigate the conformational characteristics of biological molecules such as amino acids, proteins, and extracellular vesicles (EVs) induced by elliptically polarized UV absorption. Our streamlined approach offers a cost-effective and portable solution with minimal sample consumption and supports multiple working modes to efficiently characterize biomolecular structures. The insight from this new approach demonstrates potential applications in using biomolecular characterization for cancer detection. © 2024

关键词： Autocorrelation function Density-functional theory Elliptical dichroism Molecular dynamics simulation Spectrometer Stereochemical analysis Tumor differentiation

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AI-powered multimodal modeling of personalized hemodynamics in aortic stenosis

arXiv

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arXiv 2024年

作者： Ozturk, Caglar Pak, Daniel H. Rosalia, Luca Goswami, Debkalpa Robakowski, Mary E. McKay, Raymond Nguyen, Christopher T. Duncan, James S. Roche, Ellen T. Institute for Medical Engineering and Science Massachusetts Institute of Technology CambridgeMA United States Bioengineering Science Research Group School of Engineering University of Southampton Southampton United Kingdom Department of Biomedical Engineering Yale University New HavenCT United States Health Sciences and Technology Program Harvard–Massachusetts Institute of Technology CambridgeMA United States Cardiovascular Innovation Research Center Heart Vascular & Thoracic Institute Cleveland Clinic ClevelandOH United States Department of Cardiovascular Medicine Heart Vascular & Thoracic Institute Cleveland Clinic ClevelandOH United States Department of Chemical and Biomedical Engineering Cleveland State University ClevelandOH United States Interventional Cardiology Hartford Hospital HartfordCT United States Department of Mechanical Engineering Massachusetts Institute of Technology CambridgeMA United States

Aortic stenosis (AS) is the most common valvular heart disease in developed countries. High-fidelity preclinical models can improve AS management by enabling therapeutic innovation, early diagnosis, and tailored treatment planning. However, their use is currently limited by complex workflows necessitating lengthy expert-driven manual operations. Here, we propose an AI-powered computational framework for accelerated and democratized patient-specific modeling of AS hemodynamics from computed tomography. First, we demonstrate that our automated meshing algorithms can generate task-ready geometries for both computational and benchtop simulations with higher accuracy and 100 times faster than existing approaches. Then, we show that our approach can be integrated with fluid-structure interaction and soft robotics models to accurately recapitulate a broad spectrum of clinical hemodynamic measurements of diverse AS patients. The efficiency and reliability of these algorithms make them an ideal complementary tool for personalized high-fidelity modeling of AS biomechanics, hemodynamics, and treatment planning. Copyright © 2024, The Authors. All rights reserved.

关键词： Computational fluid dynamics

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Stacking up electron-rich and electron-deficient monolayers to achieve extraordinary mid- to far-infrared excitonic absorption: Interlayer excitons in the C3B/C3N bilayer

arXiv

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arXiv 2022年

作者： Tang, Zhao Cruz, Greis J. Jia, Fanhao Wu, Yabei Xia, Weiyi Zhang, Peihong Department of Physics University at Buffalo State University of New York BuffaloNY14260 United States School of Materials Science and Engineering International Centre of Quantum and Molecular Structures Shanghai University Shanghai200444 China Department of Materials Science and Engineering Guangdong Provincial Key Lab for Computational Science and Materials Design Southern University of Science and Technology Guangdong Shenzhen518055 China Ames Laboratory U.S. Department of Energy Iowa State University AmesIA50011 United States

Our ability to efficiently detect and generate far-infrared (i.e., terahertz) radiation is vital in areas spanning from biomedical imaging to interstellar spectroscopy. Despite decades of intense research, bridging the terahertz gap between electronics and optics remains a major challenge due to the lack of robust materials that can efficiently operate in this frequency range, and two-dimensional (2D) type-II heterostructures may be ideal candidates to fill this gap. Herein, using highly accurate many-body perturbation theory within the GW plus Bethe-Salpeter equation approach, we predict that a type-II heterostructure consisting of an electron rich C3N and an electron deficient C3B monolayers can give rise to extraordinary optical activities in the mid- to far-infrared range. C3N and C3B are two graphene-derived 2D materials that have attracted increasing research attention. Although both C3N and C3B monolayers are moderate gap 2D materials, and they only couple through the rather weak van der Waals interactions, the bilayer heterostructure surprisingly supports extremely bright, low-energy interlayer excitons with large binding energies of 0.2 ~ 0.4 eV, offering an ideal material with interlayer excitonic states for mid-to far-infrared applications at room temperature. We also investigate in detail the properties and formation mechanism of the inter- and intra-layer excitons. Copyright © 2022, The Authors. All rights reserved.

关键词： Excitons

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Multi-Aptamer Targeting of Listeria Monocytogenes in Agricultural Waters Using Platinum-Coated Laser Inscribed Graphene Biosensors

SSRN

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SSRN 2023年

作者： Cavallaro, Nicholas Xiang, Dong Datta, Shoumen P.A. Gomes, Carmen McLamore, Eric S. Agricultural and Biological Engineering Institute of Food and Agricultural Sciences University of Florida United States School of Chemistry Chemical Engineering and Biotechnology Nanyang Technological University Singapore MIT Auto-ID Labs Department of Mechanical Engineering Massachusetts Institute of Technology United States MDPnP Labs Biomedical Engineering Program Department of Anesthesiology Massachusetts General Hospital Harvard Medical School United States Department of Mechanical Engineering Iowa State University United States Agricultural Sciences Clemson University United States

Fresh produce is often associate with foodborne illnesses. Listeria monocytogenes is a source of fresh produce contamination. L. monocytogenes is among the leading causes of severe foodborne illnesses in the United states, with a 16% mortality rate. The organism can survive in a wide range of conditions and is known to form biofilms on different surfaces, which poses challenges in monitoring and prevention. Tools for rapid monitoring are needed for transient pathogens such as L. monocytogenes to prevent outbreaks. In this manuscript, we demonstrated the feasibility of the multi-aptamer approach for development of label-free aptasensors targeting Listeria monocytogenes in irrigation water for lettuce production. We use in silico modeling and experimental validation studies with surface plasmon resonance to rationally develop mixtures of relevant aptamers (including scrambled aptamers as negative control). Based on this screening, multiple aptamers targeting extracellular structures on intact L. monocytogenes were tethered to platinum-modified laser inscribed graphene electrodes. We show that mixing multiple aptamers with varying affinity improves the diagnostic performance in complex sample matrices (lettuce hydroponic water). In a challenge study, multi-aptamer biosensors showed enhanced sensitivity, higher accuracy (>85%), improved limit of detection (10 CFU/mL), and improved selectivity over single aptamer biosensors. Rapid screening of pathogens in agricultural water is a global need to meet food safety and water quality regulatory needs. Given the diversity of extracellular targets on intact bacteria, this strategy could be further extended by including additional aptamers (both positive and negative control), as well as other mechanisms for account for non-specific binding. © 2023, The Authors. All rights reserved.

关键词： Lettuce

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Quadrupole dynamics of carbon isotopes and Be10

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Physical Review C 2024年第6期110卷 064325-064325页

作者： H. Li D. Fang H. J. Ong A. M. Shirokov J. P. Vary P. Yin X. Zhao Institute of Modern Physics Chinese Academy of Sciences Lanzhou 730000 China School of Nuclear Science and Technology Lanzhou University Lanzhou 730000 China School of Nuclear Physics University of Chinese Academy of Sciences Beijing 100049 China CAS Key Laboratory of High Precision Nuclear Spectroscopy Institute of Modern Physics Chinese Academy of Sciences Lanzhou 730000 China Joint Department for Nuclear Physics Lanzhou University and Institute of Modern Physics Chinese Academy of Sciences Lanzhou 730000 China Research Center for Nuclear Physics Osaka University Ibaraki Osaka 5670047 Japan RIKEN Nishina Center Wako Saitama 3510198 Japan Skobeltsyn Institute of Nuclear Physics Lomonosov Moscow State University Moscow 119991 Russia Department of Physics and Astronomy Iowa State University Ames Iowa 50011 USA College of Physics and Engineering Henan University of Science and Technology Luoyang 471023 China

Electric quadrupole (E2) moments and transitions provide measures of nuclear deformation and related collective structure. However, matrix elements of the E2 operator are sensitive to the nuclear wave function at large distances and are poorly convergent within the ab initio no-core shell model approach. We perform for the first time a systematic study of the ratio of neutron to proton quadrupole transition matrix elements, Mn/Mp, with the no-core shell model. We find this observable is well-converged and provides a new and robust tool for comparing with experimental results. Our parameter-free results for Mn/Mp for the carbon isotopes and Be10 compare well with experiment, where available, and provide additional support for the emerging picture that ab initio results align well with collective enhancements in light nuclei.

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The Pull of Tissue engineering: A STEM Outreach program with a Modular Cyclic Stretch Device to Engage High School Students

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biomedical engineering Education 2021年第1期2卷 31-39页

作者： Ozdemir, Tugba Senocak, Erdal Gerber, Gene Tayhan, Secil Erden Brown, Justin L. Biomedical Engineering Program Chemical and Biological Engineering Department South Dakota School of Mines and Technology Rapid City USA Department of Science Education Tokat Gaziosmanpasa University Tokat Turkey Department of Biomedical Engineering The Pennsylvania State University State College USA Department of Genetics and Bioengineering Tokat Gaziosmanpasa University Tokat Turkey

In this paper we designed a STEM outreach program with a modular tissue engineering education tool (we refer to as “modular cyclic-stretch device”) to engage high school students in STEM hands-on activities. Using simple machines such as gears and rotating cams, students were able to build a custom device to apply cyclic stretch to biomaterials. With the help of this hands-on activity, our outreach program helped students grasp tendon tissue biomechanics and understand the importance of applying biomechanical force to regenerate tendon tissue in a laboratory setting. The two-day outreach program comprised: 1. pre- and post-tests; 2. lectures; 3. laboratory sessions, including the microscopic examination of stained tissue sections and a hands-on group activity employing the modular cyclic-stretch device; and 4. homework. Assessment results suggest that our program supports improved student awareness and interest in tissue engineering as a future profession. The program elevated students’ confidence in their ability to apply engineering principles to tasks such as building a modular cyclic-stretch device and measuring the mechanical properties of biological tissues. Building an educational bioreactor improved students’ understanding of the dynamic nature of the human body and the importance of tissue engineering as an emerging discipline towards replacing or regenerating damaged organs. We propose that our modular device has great outreach potential to introduce tissue engineering concepts to high school and potentially college freshmen engineering students.

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Challenges for and Pathways toward Li-MetalBased All-Solid-state Batteries

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ACS ENERGY LETTERS 2021年第4期6卷 1399-1404页

作者： Albertus, Paul Anandan, Venkataramani Ban, Chunmei Balsara, Nitash Belharouak, Ilias Buettner-Garrett, Josh Chen, Zonghai Daniel, Claus Doeff, Marca Dudney, Nancy J. Dunn, Bruce Harris, Stephen J. Herle, Subramanya Herbert, Eric Kalnaus, Sergiy Libera, Joesph A. Lu, Dongping Martin, Steve McCloskey, Bryan D. McDowell, Matthew T. Meng, Y. Shirley Nanda, Jagjit Sakamoto, Jeff Self, Ethan C. Tepavcevic, Sanja Wachsman, Eric Wang, Chunsheng Westover, Andrew S. Xiao, Jie Yersak, Thomas Department of Chemical and Biomolecular Engineering University of Maryland College Park Maryland 20742 United States Ford Motor Company Dearborn Michigan 48121 United States Mechanical Engineering Department University of Colorado Boulder Colorado 80309 United States Department of Chemical and Biomolecular Engineering and Lawrence Berkeley National Laboratory Materials Sciences Division University of California Berkeley California 94720 United States Energy and Transportation Science Division Oak Ridge National Laboratory Oak Ridge Tennessee 37831 United States Solid Power Inc. Louisville Colorado 80027 United States Chemical Sciences and Engineering Division Argonne National Laboratory 9700 South Cass Avenue Argonne Illinois 60439 United States Lawrence Berkeley National Laboratory Energy Storage and Distributed Resources Division University of California Berkeley California 94720 United States Department of Materials Science and Engineering University of California Los Angeles California 90095 United States Applied Materials Inc. 3225 Oakmead Village Drive B12_2F6 Santa Clara California 95054 United States Department of Materials Science and Engineering Michigan Technological University Houghton Michigan 49931 United States Energy and Environmental Directorate Pacific Northwest National Laboratory Richland Washington 99352 United States Department of Materials Science & Engineering Iowa State University of Science & Technology Ames Iowa 50011 United States Woodruff School of Mechanical Engineering and School of Materials Science and Engineering Georgia Institute of Technology Atlanta Georgia 30332 United States Department of NanoEngineering and Materials Science and Engineering Program University of California San Diego La Jolla California 92093 United States Department of Materials Science and Engineering and Department of Mechanical Engineering University of Michigan Ann Arbor Michigan 48109 United States Chemical and Materials Systems Laborat

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