151
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Wu S, Zeng L, Zhai Y, Shin C, Eedugurala N, Azoulay JD, Ng TN. Retinomorphic Motion Detector Fabricated with Organic Infrared Semiconductors. Adv Sci (Weinh) 2023; 10:e2304688. [PMID: 37672884 PMCID: PMC10625071 DOI: 10.1002/advs.202304688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Indexed: 09/08/2023]
Abstract
Organic retinomorphic sensors offer the advantage of in-sensor processing to filter out redundant static backgrounds and are well suited for motion detection. To improve this promising structure, here, the key role of interfacial energetics in promoting charge accumulation to raise the inherent photoresponse of the light-sensitive capacitor is studied. Specifically, incorporating appropriate interfacial layers around the photoactive layer is crucial to extend the carrier lifetime, as confirmed by intensity-modulated photovoltage spectroscopy. Compared to its photodiode counterpart, the retinomorphic sensor shows better detectivity and response speed due to the additional insulating layer, which reduces the dark current and the RC time constant. Lastly, three retinomorphic sensors are integrated into a line array to demonstrate the detection of movement speed and direction, showing the potential of retinomorphic designs for efficient motion tracking.
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Affiliation(s)
- Shuo‐En Wu
- Materials Science and Engineering ProgramUniversity of California San DiegoLa JollaCA92093USA
| | - Longhui Zeng
- Department of Electrical and Computer EngineeringUniversity of California San DiegoLa JollaCA92093USA
| | - Yichen Zhai
- Department of Mechanical EngineeringUniversity of California San DiegoLa JollaCA92093USA
| | - Chanho Shin
- Materials Science and Engineering ProgramUniversity of California San DiegoLa JollaCA92093USA
| | - Naresh Eedugurala
- School of Chemistry and Biochemistry and School of Materials Science and EngineeringGeorgia Institute of TechnologyAtlantaGA30332USA
| | - Jason D. Azoulay
- School of Chemistry and Biochemistry and School of Materials Science and EngineeringGeorgia Institute of TechnologyAtlantaGA30332USA
| | - Tse Nga Ng
- Materials Science and Engineering ProgramUniversity of California San DiegoLa JollaCA92093USA
- Department of Electrical and Computer EngineeringUniversity of California San DiegoLa JollaCA92093USA
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152
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Illarionov A, Sakipov S, Pereyaslavets L, Kurnikov IV, Kamath G, Butin O, Voronina E, Ivahnenko I, Leontyev I, Nawrocki G, Darkhovskiy M, Olevanov M, Cherniavskyi YK, Lock C, Greenslade S, Sankaranarayanan SKRS, Kurnikova MG, Potoff J, Kornberg RD, Levitt M, Fain B. Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions. J Am Chem Soc 2023; 145:23620-23629. [PMID: 37856313 PMCID: PMC10623557 DOI: 10.1021/jacs.3c07628] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Indexed: 10/21/2023]
Abstract
A key goal of molecular modeling is the accurate reproduction of the true quantum mechanical potential energy of arbitrary molecular ensembles with a tractable classical approximation. The challenges are that analytical expressions found in general purpose force fields struggle to faithfully represent the intermolecular quantum potential energy surface at close distances and in strong interaction regimes; that the more accurate neural network approximations do not capture crucial physics concepts, e.g., nonadditive inductive contributions and application of electric fields; and that the ultra-accurate narrowly targeted models have difficulty generalizing to the entire chemical space. We therefore designed a hybrid wide-coverage intermolecular interaction model consisting of an analytically polarizable force field combined with a short-range neural network correction for the total intermolecular interaction energy. Here, we describe the methodology and apply the model to accurately determine the properties of water, the free energy of solvation of neutral and charged molecules, and the binding free energy of ligands to proteins. The correction is subtyped for distinct chemical species to match the underlying force field, to segment and reduce the amount of quantum training data, and to increase accuracy and computational speed. For the systems considered, the hybrid ab initio parametrized Hamiltonian reproduces the two-body dimer quantum mechanics (QM) energies to within 0.03 kcal/mol and the nonadditive many-molecule contributions to within 2%. Simulations of molecular systems using this interaction model run at speeds of several nanoseconds per day.
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Affiliation(s)
- Alexey Illarionov
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Serzhan Sakipov
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Leonid Pereyaslavets
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Igor V. Kurnikov
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Ganesh Kamath
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Oleg Butin
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Ekaterina Voronina
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
- Lomonosov
MSU, Skobeltsyn Institute of Nuclear Physics, Moscow, 119991, Russia
| | - Ilya Ivahnenko
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Igor Leontyev
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Grzegorz Nawrocki
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Mikhail Darkhovskiy
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Michael Olevanov
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
- Lomonosov
MSU, Dept. of Physics, Moscow, 119991, Russia
| | - Yevhen K. Cherniavskyi
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Christopher Lock
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
- Department
of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, California 94304, United States
| | - Sean Greenslade
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Subramanian KRS Sankaranarayanan
- Center
for Nanoscale Materials, Argonne National
Lab, Argonne, Illinois 604391, United States
- Department
of Mechanical and Industrial Engineering, University of Illinois, Chicago, Illinois 60607, United States
| | - Maria G. Kurnikova
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jeffrey Potoff
- Department
of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Roger D. Kornberg
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94304, United States
| | - Michael Levitt
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94304, United States
| | - Boris Fain
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
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153
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Ricker B, Mitra S, Castellanos EA, Grady CJ, Woldring D, Pelled G, Gilad AA. Proposed three-phenylalanine motif involved in magnetoreception signalling of an Actinopterygii protein expressed in mammalian cells. Open Biol 2023; 13:230019. [PMID: 37989224 PMCID: PMC10688439 DOI: 10.1098/rsob.230019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 10/17/2023] [Indexed: 11/23/2023] Open
Abstract
Studies at the cellular and molecular level of magnetoreception-sensing and responding to magnetic fields-are a relatively new research area. It appears that different mechanisms of magnetoreception in animals evolved from different origins, and, therefore, many questions about its mechanisms remain left open. Here we present new information regarding the Electromagnetic Perceptive Gene (EPG) from Kryptopterus vitreolus that may serve as part of the foundation to understanding and applying magnetoreception. Using HaloTag coupled with fluorescent ligands and phosphatidylinositol specific phospholipase C we show that EPG is associated with the membrane via glycosylphosphatidylinositol anchor. EPG's function of increasing intracellular calcium was also used to generate an assay using GCaMP6m to observe the function of EPG and to compare its function with that of homologous proteins. It was also revealed that EPG relies on a motif of three phenylalanine residues to function-stably swapping these residues using site directed mutagenesis resulted in a loss of function in EPG. This information not only expands upon our current understanding of magnetoreception but may provide a foundation and template to continue characterizing and discovering more within the emerging field.
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Affiliation(s)
- Brianna Ricker
- Department of Chemical Engineering and Materials Sciences, Michigan State University, East Lansing, MI, USA
| | - Sunayana Mitra
- Department of Chemical Engineering and Materials Sciences, Michigan State University, East Lansing, MI, USA
| | | | - Connor J. Grady
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
| | - Daniel Woldring
- Department of Chemical Engineering and Materials Sciences, Michigan State University, East Lansing, MI, USA
| | - Galit Pelled
- Department of Radiology, Michigan State University, East Lansing, MI, USA
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI, USA
| | - Assaf A. Gilad
- Department of Chemical Engineering and Materials Sciences, Michigan State University, East Lansing, MI, USA
- Department of Radiology, Michigan State University, East Lansing, MI, USA
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154
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Flores-Arguedas H, Antolin-Camarena O, Saavedra S, Angulo MT. Assembly archetypes in ecological communities. J R Soc Interface 2023; 20:20230349. [PMID: 38016640 PMCID: PMC10684342 DOI: 10.1098/rsif.2023.0349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023] Open
Abstract
An instrumental discovery in comparative and developmental biology is the existence of assembly archetypes that synthesize the vast diversity of organisms' body plans-from legs and wings to human arms-into simple, interpretable and general design principles. Here, we combine a novel mathematical formalism based on category theory with experimental data to show that similar 'assembly archetypes' exist at the larger organization scale of ecological communities when assembling a species pool across diverse environmental contexts, particularly when species interactions are highly structured. We applied our formalism to clinical data discovering two assembly archetypes that differentiate between healthy and unhealthy human gut microbiota. The concept of assembly archetypes and the methods to synthesize them can pave the way to discovering the general assembly principles of the ecological communities we observe in nature.
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Affiliation(s)
- Hugo Flores-Arguedas
- Institute of Mathematics, Universidad Nacional Autónoma de México, Juriquilla, Queretaro, Mexico
| | - Omar Antolin-Camarena
- Institute of Mathematics, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Serguei Saavedra
- Department of Civil and Environmental Engineering, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Marco Tulio Angulo
- Institute of Mathematics, Universidad Nacional Autónoma de México, Juriquilla, Queretaro, Mexico
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155
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Weber N, Nagy M, Markotter W, Schaer J, Puechmaille SJ, Sutton J, Dávalos LM, Dusabe MC, Ejotre I, Fenton MB, Knörnschild M, López-Baucells A, Medellin RA, Metz M, Mubareka S, Nsengimana O, O'Mara MT, Racey PA, Tuttle M, Twizeyimana I, Vicente-Santos A, Tschapka M, Voigt CC, Wikelski M, Dechmann DK, Reeder DM. Robust evidence for bats as reservoir hosts is lacking in most African virus studies: a review and call to optimize sampling and conserve bats. Biol Lett 2023; 19:20230358. [PMID: 37964576 PMCID: PMC10646460 DOI: 10.1098/rsbl.2023.0358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
Africa experiences frequent emerging disease outbreaks among humans, with bats often proposed as zoonotic pathogen hosts. We comprehensively reviewed virus-bat findings from papers published between 1978 and 2020 to evaluate the evidence that African bats are reservoir and/or bridging hosts for viruses that cause human disease. We present data from 162 papers (of 1322) with original findings on (1) numbers and species of bats sampled across bat families and the continent, (2) how bats were selected for study inclusion, (3) if bats were terminally sampled, (4) what types of ecological data, if any, were recorded and (5) which viruses were detected and with what methodology. We propose a scheme for evaluating presumed virus-host relationships by evidence type and quality, using the contrasting available evidence for Orthoebolavirus versus Orthomarburgvirus as an example. We review the wording in abstracts and discussions of all 162 papers, identifying key framing terms, how these refer to findings, and how they might contribute to people's beliefs about bats. We discuss the impact of scientific research communication on public perception and emphasize the need for strategies that minimize human-bat conflict and support bat conservation. Finally, we make recommendations for best practices that will improve virological study metadata.
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Affiliation(s)
- Natalie Weber
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
| | - Martina Nagy
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juliane Schaer
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
- Institute of Biology, Humboldt University, Berlin, Germany
| | - Sébastien J. Puechmaille
- ISEM, University of Montpellier, Montpellier, France
- Institut Universitaire de France, Paris, France
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | | | - Liliana M. Dávalos
- Department of Ecology and Evolution and Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, USA
| | | | - Imran Ejotre
- Institute of Biology, Humboldt University, Berlin, Germany
- Muni University, Arua, Uganda
| | - M. Brock Fenton
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Mirjam Knörnschild
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
- Evolutionary Ethology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | | | - Rodrigo A. Medellin
- Institute of Ecology, National Autonomous University of Mexico, Mexico City, Mexico
| | | | - Samira Mubareka
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | | | - M. Teague O'Mara
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Bat Conservation International Austin, TX, USA
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, USA
| | - Paul A. Racey
- Centre for Ecology and Conservation, University of Exeter, Exeter, UK
| | - Merlin Tuttle
- Merlin Tuttle's Bat Conservation, Austin, TX USA
- Department of Integrative Biology, University of Texas, Austin, USA
| | | | - Amanda Vicente-Santos
- Graduate Program in Population Biology, Ecology and Emory University, Atlanta, GA, USA
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Marco Tschapka
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | | | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dina K.N. Dechmann
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Department of Biology, University of Konstanz, Konstanz, Germany
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156
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Warkentin CL, Frontiera RR. Quantifying the ultrafast and steady-state molecular reduction potential of a plasmonic photocatalyst. Proc Natl Acad Sci U S A 2023; 120:e2305932120. [PMID: 37874859 PMCID: PMC10623017 DOI: 10.1073/pnas.2305932120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/15/2023] [Indexed: 10/26/2023] Open
Abstract
Plasmonic materials are promising photocatalysts as they are well suited to convert light into hot carriers and heat. Hot electron transfer is suggested as the driving force in many plasmon-driven reactions. However, to date, there are no direct molecular measures of the rate and yield of plasmon-to-molecule electron transfer or energy of these electrons on the timescale of plasmon decay. Here, we use ultrafast and spectroelectrochemical surface-enhanced Raman spectroscopy to quantify electron transfer from a plasmonic substrate to adsorbed methyl viologen molecules. We observe a reduction yield of 2.4 to 3.5% on the picosecond timescale, with plasmon-induced potentials ranging from [Formula: see text]3.1 to [Formula: see text]4.5 mV. Excitingly, some of these reduced species are stabilized and persist for tens of minutes. This work provides concrete metrics toward optimizing material-molecule interactions for efficient plasmon-driven photocatalysis.
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157
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Roth AM, Calalo JA, Lokesh R, Sullivan SR, Grill S, Jeka JJ, van der Kooij K, Carter MJ, Cashaback JGA. Reinforcement-based processes actively regulate motor exploration along redundant solution manifolds. Proc Biol Sci 2023; 290:20231475. [PMID: 37848061 PMCID: PMC10581769 DOI: 10.1098/rspb.2023.1475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/06/2023] [Indexed: 10/19/2023] Open
Abstract
From a baby's babbling to a songbird practising a new tune, exploration is critical to motor learning. A hallmark of exploration is the emergence of random walk behaviour along solution manifolds, where successive motor actions are not independent but rather become serially dependent. Such exploratory random walk behaviour is ubiquitous across species' neural firing, gait patterns and reaching behaviour. The past work has suggested that exploratory random walk behaviour arises from an accumulation of movement variability and a lack of error-based corrections. Here, we test a fundamentally different idea-that reinforcement-based processes regulate random walk behaviour to promote continual motor exploration to maximize success. Across three human reaching experiments, we manipulated the size of both the visually displayed target and an unseen reward zone, as well as the probability of reinforcement feedback. Our empirical and modelling results parsimoniously support the notion that exploratory random walk behaviour emerges by utilizing knowledge of movement variability to update intended reach aim towards recently reinforced motor actions. This mechanism leads to active and continuous exploration of the solution manifold, currently thought by prominent theories to arise passively. The ability to continually explore muscle, joint and task redundant solution manifolds is beneficial while acting in uncertain environments, during motor development or when recovering from a neurological disorder to discover and learn new motor actions.
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Affiliation(s)
- Adam M. Roth
- Department of Mechanical Engineering, University of Delaware, Newark, DE 19716, USA
| | - Jan A. Calalo
- Department of Mechanical Engineering, University of Delaware, Newark, DE 19716, USA
| | - Rakshith Lokesh
- Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA
| | - Seth R. Sullivan
- Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA
| | - Stephen Grill
- Kinesiology and Applied Physiology, University of Delaware, Newark, DE 19716, USA
| | - John J. Jeka
- Kinesiology and Applied Physiology, University of Delaware, Newark, DE 19716, USA
- Interdisciplinary Neuroscience Graduate Program, University of Delaware, Newark, DE 19716, USA
- Biomechanics and Movement Science Program, University of Delaware, Newark, DE 19716, USA
| | - Katinka van der Kooij
- Faculty of Behavioural and Movement Science, Vrije University Amsterdam, Amsterdam, 1081HV, The Netherlands
| | - Michael J. Carter
- Department of Kinesiology, McMaster University, Room 203, Ivor Wynne Centre, Hamilton, L8S 4L8, Ontario, Canada
| | - Joshua G. A. Cashaback
- Department of Mechanical Engineering, University of Delaware, Newark, DE 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA
- Kinesiology and Applied Physiology, University of Delaware, Newark, DE 19716, USA
- Interdisciplinary Neuroscience Graduate Program, University of Delaware, Newark, DE 19716, USA
- Biomechanics and Movement Science Program, University of Delaware, Newark, DE 19716, USA
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158
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Ray AM, Gordon EC, Seeley TD, Rasgon JL, Grozinger CM. Signatures of adaptive decreased virulence of deformed wing virus in an isolated population of wild honeybees ( Apis mellifera). Proc Biol Sci 2023; 290:20231965. [PMID: 37876196 PMCID: PMC10598435 DOI: 10.1098/rspb.2023.1965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 09/28/2023] [Indexed: 10/26/2023] Open
Abstract
Understanding the ecological and evolutionary processes that drive host-pathogen interactions is critical for combating epidemics and conserving species. The Varroa destructor mite and deformed wing virus (DWV) are two synergistic threats to Western honeybee (Apis mellifera) populations across the globe. Distinct honeybee populations have been found to self-sustain despite Varroa infestations, including colonies within the Arnot Forest outside Ithaca, NY, USA. We hypothesized that in these bee populations, DWV has been selected to produce an avirulent infection phenotype, allowing for the persistence of both host and disease-causing agents. To investigate this, we assessed the titre of viruses in bees from the Arnot Forest and managed apiaries, and assessed genomic variation and virulence differences between DWV isolates. Across groups, we found viral abundance was similar, but DWV genotypes were distinct. We also found that infections with isolates from the Arnot Forest resulted in higher survival and lower rates of symptomatic deformed wings, compared to analogous isolates from managed colonies, providing preliminary evidence to support the hypothesis of adaptive decreased viral virulence. Overall, this multi-level investigation of virus genotype and phenotype indicates that host ecological context can be a significant driver of viral evolution and host-pathogen interactions in honeybees.
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Affiliation(s)
- Allyson M. Ray
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802-1503, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37240-0002, USA
| | - Emma C. Gordon
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802-1503, USA
| | - Thomas D. Seeley
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14850, USA
| | - Jason L. Rasgon
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802-1503, USA
| | - Christina M. Grozinger
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802-1503, USA
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159
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Al Musawi AF, Roy S, Ghosh P. Examining indicators of complex network vulnerability across diverse attack scenarios. Sci Rep 2023; 13:18208. [PMID: 37875564 PMCID: PMC10598276 DOI: 10.1038/s41598-023-45218-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/17/2023] [Indexed: 10/26/2023] Open
Abstract
Complex networks capture the structure, dynamics, and relationships among entities in real-world networked systems, encompassing domains like communications, society, chemistry, biology, ecology, politics, etc. Analysis of complex networks lends insight into the critical nodes, key pathways, and potential points of failure that may impact the connectivity and operational integrity of the underlying system. In this work, we investigate the topological properties or indicators, such as shortest path length, modularity, efficiency, graph density, diameter, assortativity, and clustering coefficient, that determine the vulnerability to (or robustness against) diverse attack scenarios. Specifically, we examine how node- and link-based network growth or depletion based on specific attack criteria affect their robustness gauged in terms of the largest connected component (LCC) size and diameter. We employ partial least squares discriminant analysis to quantify the individual contribution of the indicators on LCC preservation while accounting for the collinearity stemming from the possible correlation between indicators. Our analysis of 14 complex network datasets and 5 attack models invariably reveals high modularity and disassortativity to be prime indicators of vulnerability, corroborating prior works that report disassortative modular networks to be particularly susceptible to targeted attacks. We conclude with a discussion as well as an illustrative example of the application of this work in fending off strategic attacks on critical infrastructures through models that adaptively and distributively achieve network robustness.
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Affiliation(s)
- Ahmad F Al Musawi
- Department of Information Technology, University of Thi Qar, Thi Qar, Iraq.
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA.
| | - Satyaki Roy
- Department of Mathematical Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
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160
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Grady C, Wolfe R, Dawop D, Inks L. How contact can promote societal change amid conflict: An intergroup contact field experiment in Nigeria. Proc Natl Acad Sci U S A 2023; 120:e2304882120. [PMID: 37856543 PMCID: PMC10614933 DOI: 10.1073/pnas.2304882120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Intergroup contact, originally designed as a tool for prejudice reduction, offers a promising means to resolve intergroup conflict. Evidence for contact-based interventions to improve intergroup relations is sparse, however, with most studies focusing only on the individuals who directly engage in contact. We test the ability of a contact-based intervention to promote peace between conflicting groups with a field experiment in Nigeria, where farmer and pastoralist communities are embroiled in a deadly conflict over land use. We examine the effectiveness of the contact intervention on the wider population-not just those directly engaged in contact-using surveys, direct observation of behavior in markets and social events, and a behavioral game. We find those who lived in the communities that received the intervention had more positive intergroup attitudes and feelings of physical security, as well as were more likely to engage in voluntary intergroup contact measured through self-reports and observed behavior in markets. Exploratory analyses show that those who directly participated in the program and those who were exposed to it by living in the communities where activities were taking place changed similarly with regard to attitudes and perceptions of security, but not with regard to behaviors, indicating the spread to the wider community was likely due to norm change. These results suggest that contact interventions can have wider societal change and reduce the barriers to peace between conflicting groups.
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Affiliation(s)
- Christopher Grady
- Department of Political Science, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Rebecca Wolfe
- Harris School for Public Policy, University of Chicago, Chicago, IL60637
| | | | - Lisa Inks
- Peace and Conflict Team, Mercy Corps, Washington, DC20036
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161
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Korenaga J, Marchi S. Vestiges of impact-driven three-phase mixing in the chemistry and structure of Earth's mantle. Proc Natl Acad Sci U S A 2023; 120:e2309181120. [PMID: 37812730 PMCID: PMC10614616 DOI: 10.1073/pnas.2309181120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/22/2023] [Indexed: 10/11/2023] Open
Abstract
Highly siderophile elements (HSEs; namely Ru, Rh, Pd, Re, Os, Ir, Pt, and Au) in Earth's mantle require the addition of metals after the formation of Earth's core. Early, large collisions have the potential to deliver metals, but the details of their mixing with Earth's mantle remain unresolved. As a large projectile disrupts and penetrates Earth's mantle, a fraction of its metallic core may directly merge with Earth's core. Ensuing gravitational instabilities remove the remaining projectile's core stranded in Earth's mantle, leaving the latter deprived of HSEs. Here, we propose a framework that can efficiently retain the metallic components during large impacts. The mechanism is based on the ubiquitous presence of a partially molten region in the mantle beneath an impact-generated magma ocean, and it involves rapid three-phase flow with solid silicate, molten silicate, and liquid metal as well as long-term mixing by mantle convection. In addition, large low-shear-velocity provinces in the lower mantle may originate from compositional heterogeneities resulting from the proposed three-phase flow during high-energy collisions.
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Affiliation(s)
- Jun Korenaga
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT06520
| | - Simone Marchi
- Department of Space Studies, Southwest Research Institute, Boulder, CO80302
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162
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Tatsuoka C, Chen W, Lu X. Bayesian group testing with dilution effects. Biostatistics 2023; 24:885-900. [PMID: 35403204 PMCID: PMC10583721 DOI: 10.1093/biostatistics/kxac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/18/2022] [Accepted: 01/26/2022] [Indexed: 10/19/2023] Open
Abstract
A Bayesian framework for group testing under dilution effects has been developed, using lattice-based models. This work has particular relevance given the pressing public health need to enhance testing capacity for coronavirus disease 2019 and future pandemics, and the need for wide-scale and repeated testing for surveillance under constantly varying conditions. The proposed Bayesian approach allows for dilution effects in group testing and for general test response distributions beyond just binary outcomes. It is shown that even under strong dilution effects, an intuitive group testing selection rule that relies on the model order structure, referred to as the Bayesian halving algorithm, has attractive optimal convergence properties. Analogous look-ahead rules that can reduce the number of stages in classification by selecting several pooled tests at a time are proposed and evaluated as well. Group testing is demonstrated to provide great savings over individual testing in the number of tests needed, even for moderately high prevalence levels. However, there is a trade-off with higher number of testing stages, and increased variability. A web-based calculator is introduced to assist in weighing these factors and to guide decisions on when and how to pool under various conditions. High-performance distributed computing methods have also been implemented for considering larger pool sizes, when savings from group testing can be even more dramatic.
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Affiliation(s)
- Curtis Tatsuoka
- Department of Population and Quantitative Health Sciences, CaseWestern Reserve University, Cleveland, OH, 44106, USA
| | - Weicong Chen
- Department of Computer and Data Science, CaseWestern Reserve University, Cleveland, OH, USA
| | - Xiaoyi Lu
- Department of Computer Science and Engineering, University of California Merced, Merced, CA, 95343, USA
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163
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Zhao W, Xu F, Liu L, Liu M, Weng B. Strain-Induced Electronic Structure Modulation on MnO 2 Nanosheet by Ir Incorporation for Efficient Water Oxidation in Acid. Adv Mater 2023:e2308060. [PMID: 37845788 DOI: 10.1002/adma.202308060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/14/2023] [Indexed: 10/18/2023]
Abstract
Oxygen electrochemistry plays a key role in renewable energy technologies, such as fuel cells and electrolyzers, but its slow kinetics limits the performance and the commercialization of such devices. Here, a strained MnO2 nanosheet induced by Ir incorporation is developed with optimized electronic structure by a simple hydrothermal method. With the incorporation of Ir, the strain induces elongated Mn─O bond length, and thereby tuning the electronic structure to favor the oxygen evolution reaction (OER) performance. The obtained catalyst exhibits an excellent mass activity of 5681 A g-1 at an overpotential of 300 mV in 0.5 m H2 SO4 , and reaches 50 and 100 mA cm-2 at overpotentials of only 240 and 277 mV, respectively. The catalyst is also stable even at 300 mA cm-2 in 0.5 m H2 SO4 . Using the nanosheet as the OER catalyst and the Pt/C as the hydrogen evolution reaction catalyst, a two-electrode electrolyzer achieves 10 mA cm-2 with only a cell voltage of 1.453 V for overall water splitting in 0.5 m H2 SO4 . This strategy enables the material with high feasibility for practical applications on hydrogen production.
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Affiliation(s)
- Wenli Zhao
- Department of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan Province, 410083, China
| | - Fenghua Xu
- Department of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan Province, 410083, China
| | - Luqiong Liu
- Department of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan Province, 410083, China
| | - Min Liu
- Hunan Joint International Research Center for Carbon Dioxide Resource Utilization, School of Physics and Electronics, Central South University, Changsha, Hunan Province, 410083, China
| | - Baicheng Weng
- Department of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan Province, 410083, China
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164
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Rucker G, Qin H, Zhang L. Structure, dynamics and free energy studies on the effect of point mutations on SARS-CoV-2 spike protein binding with ACE2 receptor. PLoS One 2023; 18:e0289432. [PMID: 37796794 PMCID: PMC10553274 DOI: 10.1371/journal.pone.0289432] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023] Open
Abstract
The ongoing COVID-19 pandemic continues to infect people worldwide, and the virus continues to evolve in significant ways which can pose challenges to the efficiency of available vaccines and therapeutic drugs and cause future pandemic. Therefore, it is important to investigate the binding and interaction of ACE2 with different RBD variants. A comparative study using all-atom MD simulations was conducted on ACE2 binding with 8 different RBD variants, including N501Y, E484K, P479S, T478I, S477N, N439K, K417N and N501Y-E484K-K417N on RBD. Based on the RMSD, RMSF, and DSSP results, overall the binding of RBD variants with ACE2 is stable, and the secondary structure of RBD and ACE2 are consistent after the point mutation. Besides that, a similar buried surface area, a consistent binding interface and a similar amount of hydrogen bonds formed between RBD and ACE2 although the exact residue pairs on the binding interface were modified. The change of binding free energy from point mutation was predicted using the free energy perturbation (FEP) method. It is found that N501Y, N439K, and K417N can strengthen the binding of RBD with ACE2, while E484K and P479S weaken the binding, and S477N and T478I have negligible effect on the binding. Point mutations modified the dynamic correlation of residues in RBD based on the dihedral angle covariance matrix calculation. Doing dynamic network analysis, a common intrinsic network community extending from the tail of RBD to central, then to the binding interface region was found, which could communicate the dynamics in the binding interface region to the tail thus to the other sections of S protein. The result can supply unique methodology and molecular insight on studying the molecular structure and dynamics of possible future pandemics and design novel drugs.
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Affiliation(s)
- George Rucker
- Chemical Engineering Department, Tennessee Technological University, Cookeville, TN, United States of America
| | - Hong Qin
- Computer Science Department, University of Tennessee Chattanooga, Chattanooga, TN, United States of America
| | - Liqun Zhang
- Chemical Engineering Department, University of Rhode Island, Kingston, RI, United States of America
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165
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Elsler LG, Oostdijk M, Gephart JA, Free CM, Zhao J, Tekwa E, Bochniewicz EM, Giron-Nava A, Johnson AF. Global trade network patterns are coupled to fisheries sustainability. PNAS Nexus 2023; 2:pgad301. [PMID: 37817775 PMCID: PMC10560747 DOI: 10.1093/pnasnexus/pgad301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/12/2023] [Accepted: 08/31/2023] [Indexed: 10/12/2023]
Abstract
The rapid development of seafood trade networks alongside the decline in biomass of many marine populations raises important questions about the role of global trade in fisheries sustainability. Mounting empirical and theoretical evidence shows the importance of trade development on commercially exploited species. However, there is limited understanding of how the development of trade networks, such as differences in connectivity and duration, affects fisheries sustainability. In a global analysis of over 400,000 bilateral trade flows and stock status estimates for 876 exploited fish and marine invertebrates from 223 territories, we reveal patterns between seafood trade network indicators and fisheries sustainability using a dynamic panel regression analysis. We found that fragmented networks with strong connectivity within a group of countries and weaker links between those groups (modularity) are associated with higher relative biomass. From 1995 to 2015, modularity fluctuated, and the number of trade connections (degree) increased. Unlike previous studies, we found no relationship between the number or duration of trade connections and fisheries sustainability. Our results highlight the need to jointly investigate fisheries and trade. Improved coordination and partnerships between fisheries authorities and trade organizations present opportunities to foster more sustainable fisheries.
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Affiliation(s)
- Laura G Elsler
- Stockholm Resilience Centre, Stockholm University, 11419 Stockholm, Sweden
| | - Maartje Oostdijk
- School of Environment and Natural Resources, University of Iceland, 101 Reykjavik, Iceland
| | - Jessica A Gephart
- Department of Environmental Science, American University, Washington, DC 20016, USA
| | - Christopher M Free
- Bren School of Environmental Science and Management, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Junfu Zhao
- Institute of Marxism, Fudan University, Shanghai 200433, China
| | - Eden Tekwa
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | | | - Alfredo Giron-Nava
- Stanford Center for Ocean Solutions, Stanford University, Palo Alto, CA 94305, USA
| | - Andrew F Johnson
- Marine SPACE group, The Lyell Centre, Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh, Currie, Scotland EH14 4AS, UK
- MarFishEco Fisheries Consultants Ltd., Edinburgh, Scotland EH7 5HT, UK
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166
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Han L, Yu H, Xiang Z. Asymmetric Active Sites for Boosting Oxygen Evolution Reaction. Small 2023; 19:e2304108. [PMID: 37317013 DOI: 10.1002/smll.202304108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/06/2023] [Indexed: 06/16/2023]
Abstract
Transition metal-nitrogen-carbon materials with atomically dispersed active sites are promising catalysts for oxygen evolution reaction (OER) since they combine the strengths of both homogeneous and heterogeneous catalysts. However, the canonically symmetric active site usually exhibits poor OER intrinsic activity due to its excessively strong or weak oxygen species adsorption. Here, a catalyst with asymmetric MN4 sites based on the 3-s-triazine of g-C3 N4 (termed as a-MN4 @NC) is proposed. Compared to symmetric, the asymmetric active sites directly modulate the oxygen species adsorption via unifying planar and axial orbitals (dx2 -y2 , dz2 ), thus enabling higher OER intrinsic activity. In Silico screening suggested that cobalt has the best OER activity among familiar nonprecious transition metal. These experimental results suggest that the intrinsic activity of asymmetric active sites (179 mV overpotential at onset potential) is enhanced by 48.4% compared to symmetric under similar conditions. Remarkably, a-CoN4 @NC showed excellent activity in alkaline water electrolyzer (AWE) device as OER catalyst, the electrolyzer only required 1.7 V and 2.1 V respectively to reach the current density of 150 mA cm-2 and 500 mA cm-2 . This work opens an avenue for modulating the active sites to obtain high intrinsic electrocatalytic performance including, but not limited to, OER.
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Affiliation(s)
- Linkai Han
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Haifeng Yu
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Zhonghua Xiang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, PR China
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167
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Uddin LQ, Betzel RF, Cohen JR, Damoiseaux JS, De Brigard F, Eickhoff SB, Fornito A, Gratton C, Gordon EM, Laird AR, Larson-Prior L, McIntosh AR, Nickerson LD, Pessoa L, Pinho AL, Poldrack RA, Razi A, Sadaghiani S, Shine JM, Yendiki A, Yeo BTT, Spreng RN. Controversies and progress on standardization of large-scale brain network nomenclature. Netw Neurosci 2023; 7:864-905. [PMID: 37781138 PMCID: PMC10473266 DOI: 10.1162/netn_a_00323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/10/2023] [Indexed: 10/03/2023] Open
Abstract
Progress in scientific disciplines is accompanied by standardization of terminology. Network neuroscience, at the level of macroscale organization of the brain, is beginning to confront the challenges associated with developing a taxonomy of its fundamental explanatory constructs. The Workgroup for HArmonized Taxonomy of NETworks (WHATNET) was formed in 2020 as an Organization for Human Brain Mapping (OHBM)-endorsed best practices committee to provide recommendations on points of consensus, identify open questions, and highlight areas of ongoing debate in the service of moving the field toward standardized reporting of network neuroscience results. The committee conducted a survey to catalog current practices in large-scale brain network nomenclature. A few well-known network names (e.g., default mode network) dominated responses to the survey, and a number of illuminating points of disagreement emerged. We summarize survey results and provide initial considerations and recommendations from the workgroup. This perspective piece includes a selective review of challenges to this enterprise, including (1) network scale, resolution, and hierarchies; (2) interindividual variability of networks; (3) dynamics and nonstationarity of networks; (4) consideration of network affiliations of subcortical structures; and (5) consideration of multimodal information. We close with minimal reporting guidelines for the cognitive and network neuroscience communities to adopt.
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Affiliation(s)
- Lucina Q. Uddin
- Department of Psychiatry and Biobehavioral Sciences and Department of Psychology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Richard F. Betzel
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Jessica R. Cohen
- Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill, NC, USA
| | - Jessica S. Damoiseaux
- Institute of Gerontology and Department of Psychology, Wayne State University, Detroit, MI, USA
| | | | - Simon B. Eickhoff
- Institute of Systems Neuroscience, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alex Fornito
- Turner Institute for Brain and Mental Health, Monash University, Melbourne, Australia
| | - Caterina Gratton
- Department of Psychology, Northwestern University, Evanston, IL, USA
| | - Evan M. Gordon
- Mallinckrodt Institute of Radiology, Washington University, St. Louis, MO, USA
| | - Angela R. Laird
- Department of Physics, Florida International University, Miami, FL, USA
| | - Linda Larson-Prior
- Deptartment of Psychiatry and Department of Neurobiology and Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - A. Randal McIntosh
- Institute for Neuroscience and Neurotechnology, Simon Fraser University, Vancouver, BC, Canada
| | | | - Luiz Pessoa
- Department of Psychology, University of Maryland, College Park, MD, USA
| | - Ana Luísa Pinho
- Brain and Mind Institute, Western University, London, Ontario, Canada
| | | | - Adeel Razi
- Turner Institute for Brain and Mental Health, Monash University, Melbourne, Australia
| | - Sepideh Sadaghiani
- Department of Psychology, University of Illinois, Urbana Champaign, IL, USA
| | - James M. Shine
- Brain and Mind Center, University of Sydney, Sydney, Australia
| | - Anastasia Yendiki
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - B. T. Thomas Yeo
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore
| | - R. Nathan Spreng
- Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
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168
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Rosin SP, Shook-Sa BE, Cole SR, Hudgens MG. Estimating SARS-CoV-2 seroprevalence. J R Stat Soc Ser A Stat Soc 2023; 186:834-851. [PMID: 38145241 PMCID: PMC10746549 DOI: 10.1093/jrsssa/qnad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 11/08/2022] [Accepted: 04/25/2023] [Indexed: 12/26/2023]
Abstract
Governments and public health authorities use seroprevalence studies to guide responses to the COVID-19 pandemic. Seroprevalence surveys estimate the proportion of individuals who have detectable SARS-CoV-2 antibodies. However, serologic assays are prone to misclassification error, and non-probability sampling may induce selection bias. In this paper, non-parametric and parametric seroprevalence estimators are considered that address both challenges by leveraging validation data and assuming equal probabilities of sample inclusion within covariate-defined strata. Both estimators are shown to be consistent and asymptotically normal, and consistent variance estimators are derived. Simulation studies are presented comparing the estimators over a range of scenarios. The methods are used to estimate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence in New York City, Belgium, and North Carolina.
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Affiliation(s)
- Samuel P Rosin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Bonnie E Shook-Sa
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Stephen R Cole
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Michael G Hudgens
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
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169
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Cao R, Zhang N, Yu H, Webster PJ, Paul LK, Li X, Lin C, Wang S. Comprehensive Social Trait Judgments From Faces in Autism Spectrum Disorder. Psychol Sci 2023; 34:1121-1145. [PMID: 37671893 PMCID: PMC10626626 DOI: 10.1177/09567976231192236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/13/2023] [Indexed: 09/07/2023] Open
Abstract
Processing social information from faces is difficult for individuals with autism spectrum disorder (ASD). However, it remains unclear whether individuals with ASD make high-level social trait judgments from faces in the same way as neurotypical individuals. Here, we comprehensively addressed this question using naturalistic face images and representatively sampled traits. Despite similar underlying dimensional structures across traits, online adult participants with self-reported ASD showed different judgments and reduced specificity within each trait compared with neurotypical individuals. Deep neural networks revealed that these group differences were driven by specific types of faces and differential utilization of features within a face. Our results were replicated in well-characterized in-lab participants and partially generalized to more controlled face images (a preregistered study). By investigating social trait judgments in a broader population, including individuals with neurodevelopmental variations, we found important theoretical implications for the fundamental dimensions, variations, and potential behavioral consequences of social cognition.
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Affiliation(s)
- Runnan Cao
- Department of Radiology, Washington University in St. Louis
- Lane Department of Computer Science and Electrical Engineering, West Virginia University
| | - Na Zhang
- Lane Department of Computer Science and Electrical Engineering, West Virginia University
| | - Hongbo Yu
- Department of Psychological & Brain Sciences, University of California, Santa Barbara
| | - Paula J. Webster
- Department of Chemical and Biomedical Engineering, West Virginia University
| | - Lynn K. Paul
- Division of the Humanities and Social Sciences, California Institute of Technology
| | - Xin Li
- Lane Department of Computer Science and Electrical Engineering, West Virginia University
| | - Chujun Lin
- Department of Psychology, University of California, San Diego
| | - Shuo Wang
- Department of Radiology, Washington University in St. Louis
- Lane Department of Computer Science and Electrical Engineering, West Virginia University
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170
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Chill HH, Martin LC, Abramowitch SD, Rostaminia G. Quantifying the effect of an endo-vaginal probe on position of the pelvic floor viscera and muscles. Int Urogynecol J 2023; 34:2399-2406. [PMID: 37145123 DOI: 10.1007/s00192-023-05557-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023]
Abstract
INTRODUCTION AND HYPOTHESIS Endovaginal ultrasound has long been hypothesized to have a significant effect on locations of what it visualizes. However, little work has directly quantified its effect. This study aimed to quantify it. METHODS This cross-sectional study consisted of 20 healthy asymptomatic volunteers who underwent both endovaginal ultrasound and MRI. The urethra, vagina, rectum, pelvic floor, and pubic bone were segmented in both ultrasound and MRI using 3DSlicer. Then, using 3DSlicer's transform tool the volumes were rigidly aligned based on the posterior curvature of the pubic bone. The organs were then split into thirds along their long axis to compare their distal, middle, and proximal sections. Using Houdini, we compared the location of the centroid of each of the urethra, vagina, and rectum and the surface-to-surface difference of the urethra and rectum. The anterior curvature of the pelvic floor was also compared. Normality of all variables was assessed by Shapiro-Wilk test. RESULTS The largest amount of surface-to-surface distance was observed in the proximal region for the urethra and rectum. Across all three organs, the majority of the deviation was in the anterior direction for geometries obtained from ultrasound versus those from MRI. For each subject, the trace defining the midline of the levator plate was more anterior for ultrasound compared to MRI. CONCLUSIONS While it has often been assumed that placing a probe in the vagina probably distorts the anatomy, this study quantified the distortion and displacement of the pelvic viscera. This allows for better interpretation of clinical and research findings based on this modality.
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Affiliation(s)
- Henry H Chill
- Female Pelvic Medicine and Reconstructive Surgery (FPMRS) Division, University of Chicago Pritzker School of Medicine, Northshore University HealthSystem, Skokie, IL, USA
| | - Liam C Martin
- Translational Biomechanics Laboratory, Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steven D Abramowitch
- Translational Biomechanics Laboratory, Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ghazaleh Rostaminia
- Female Pelvic Medicine and Reconstructive Surgery (FPMRS) Division, University of Chicago Pritzker School of Medicine, Northshore University HealthSystem, Skokie, IL, USA.
- Division of Urogynecology, NorthShore University HealthSystem, 9650 Gross Point Road, Suite 3900, Skokie, IL, 60076, USA.
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171
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Quiroga-Carmona M, Storz JF, D’Elía G. Elevational range extension of the Puna Mouse, Punomys (Cricetidae), with the first record of the genus from Chile. J Mammal 2023; 104:1144-1151. [PMID: 37800100 PMCID: PMC10550245 DOI: 10.1093/jmammal/gyad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/22/2023] [Indexed: 10/07/2023] Open
Abstract
We report an elevational record for the Andean sigmodontine Puna Mouse Punomys, which is also the first record of the genus in Chile. The record is based on a mummified specimen that we discovered at an elevation of 5,461 m (17,917 feet) in the caldera of Volcán Acamarachi, Región de Antofagasta, Chile. Results of a morphological assessment suggest that the specimen can be provisionally referred to the species P. lemminus. This new record also extends the known geographic distribution of the genus by 700 km to the south and brings the known Chilean mammal richness to a total of 170 living species and 88 genera. This finding highlights the need for increased survey efforts in more remote, high-elevation regions and demonstrates that there is still much to be learned about the mammal fauna of the Andean Altiplano.
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Affiliation(s)
- Marcial Quiroga-Carmona
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
- Colección de Mamíferos, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
| | - Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
- Colección de Mamíferos, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
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172
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Fu N, Hu J, Feng Y, Morrison G, zur Loye H, Hu J. Composition Based Oxidation State Prediction of Materials Using Deep Learning Language Models. Adv Sci (Weinh) 2023; 10:e2301011. [PMID: 37551059 PMCID: PMC10558692 DOI: 10.1002/advs.202301011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/05/2023] [Indexed: 08/09/2023]
Abstract
Oxidation states (OS) are the charges on atoms due to electrons gained or lost upon applying an ionic approximation to their bonds. As a fundamental property, OS has been widely used in charge-neutrality verification, crystal structure determination, and reaction estimation. Currently, only heuristic rules exist for guessing the oxidation states of a given compound with many exceptions. Recent work has developed machine learning models based on heuristic structural features for predicting the oxidation states of metal ions. However, composition-based oxidation state prediction still remains elusive so far, which has significant implications for the discovery of new materials for which the structures have not been determined. This work proposes a novel deep learning-based BERT transformer language model BERTOS for predicting the oxidation states for all elements of inorganic compounds given only their chemical composition. This model achieves 96.82% accuracy for all-element oxidation states prediction benchmarked on the cleaned ICSD dataset and achieves 97.61% accuracy for oxide materials. It is also demonstrated how it can be used to conduct large-scale screening of hypothetical material compositions for materials discovery.
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Affiliation(s)
- Nihang Fu
- Department of Computer Science and EngineeringUniversity of South CarolinaColumbiaSC29201USA
| | - Jeffrey Hu
- Department of Computer Science and EngineeringUniversity of South CarolinaColumbiaSC29201USA
- Dutch Fork High SchoolIrmoSC29063USA
| | - Ying Feng
- Hangzhou University of Electronic Science and TechnologyHangzhou311305China
| | - Gregory Morrison
- Department of Chemistry and BiochemistryUniversity of South CarolinaColumbiaSC29201USA
| | - Hans‐Conrad zur Loye
- Department of Chemistry and BiochemistryUniversity of South CarolinaColumbiaSC29201USA
| | - Jianjun Hu
- Department of Computer Science and EngineeringUniversity of South CarolinaColumbiaSC29201USA
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173
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Keeley RE, Nierenberg AM, Gilman D, Birrer S, Benson A, Treu T. Pushing the limits of detectability: mixed dark matter from strong gravitational lenses. Mon Not R Astron Soc 2023; 524:6159-6166. [PMID: 37559879 PMCID: PMC10408735 DOI: 10.1093/mnras/stad2251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023]
Abstract
One of the frontiers for advancing what is known about dark matter lies in using strong gravitational lenses to characterize the population of the smallest dark matter haloes. There is a large volume of information in strong gravitational lens images - the question we seek to answer is to what extent we can refine this information. To this end, we forecast the detectability of a mixed warm and cold dark matter scenario using the anomalous flux ratio method from strong gravitational lensed images. The halo mass function of the mixed dark matter scenario is suppressed relative to cold dark matter but still predicts numerous low-mass dark matter haloes relative to warm dark matter. Since the strong lensing signal receives a contribution from a range of dark matter halo masses and since the signal is sensitive to the specific configuration of dark matter haloes, not just the halo mass function, degeneracies between different forms of suppression in the halo mass function, relative to cold dark matter, can arise. We find that, with a set of lenses with different configurations of the main deflector and hence different sensitivities to different mass ranges of the halo mass function, the different forms of suppression of the halo mass function between the warm dark matter model and the mixed dark matter model can be distinguished with 40 lenses with Bayesian odds of 30:1.
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Affiliation(s)
- Ryan E Keeley
- Department of Physics, University of California Merced, 5200 North Lake Road, Merced, CA 95343, USA
| | - Anna M Nierenberg
- Department of Physics, University of California Merced, 5200 North Lake Road, Merced, CA 95343, USA
| | - Daniel Gilman
- Department of Astronomy and Astrophysics, University of Toronto, Toronto, ON M5S 3H4, Canada
| | - Simon Birrer
- Department of Physics, Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, Stanford, CA 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Andrew Benson
- Carnegie Institution for Science, 813 Santa Barbara Street, Pasadena, CA 91101, USA
| | - Tommaso Treu
- Department of Physics and Astronomy, University of California, Los Angeles, CA 90095, USA
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174
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Schwenkert S, Lo WT, Szulc B, Yip CK, Pratt AI, Cusack SA, Brandt B, Leister D, Kunz HH. Probing the physiological role of the plastid outer-envelope membrane using the oemiR plasmid collection. G3 (Bethesda) 2023; 13:jkad187. [PMID: 37572358 PMCID: PMC10542568 DOI: 10.1093/g3journal/jkad187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 08/14/2023]
Abstract
Plastids are the site of complex biochemical pathways, most prominently photosynthesis. The organelle evolved through endosymbiosis with a cyanobacterium, which is exemplified by the outer envelope membrane that harbors more than 40 proteins in Arabidopsis. Their evolutionary conservation indicates high significance for plant cell function. While a few proteins are well-studied as part of the protein translocon complex the majority of outer envelope protein functions is unclear. Gaining a deeper functional understanding has been complicated by the lack of observable loss-of-function mutant phenotypes, which is often rooted in functional genetic redundancy. Therefore, we designed outer envelope-specific artificial micro RNAs (oemiRs) capable of downregulating transcripts from several loci simultaneously. We successfully tested oemiR function by performing a proof-of-concept screen for pale and cold-sensitive mutants. An in-depth analysis of pale mutant alleles deficient in the translocon component TOC75 using proteomics provided new insights into putative compensatory import pathways. The cold stress screen not only recapitulated 3 previously known phenotypes of cold-sensitive mutants but also identified 4 mutants of additional oemiR outer envelope loci. Altogether our study revealed a role of the outer envelope to tolerate cold conditions and showcasts the power of the oemiR collection to research the significance of outer envelope proteins.
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Affiliation(s)
- Serena Schwenkert
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Wing Tung Lo
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Beata Szulc
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Chun Kwan Yip
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Anna I Pratt
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
| | | | - Benjamin Brandt
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Hans-Henning Kunz
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
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175
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Holtz MA, Racicot R, Preininger D, Stuckert AMM, Mangiamele LA. Genome assembly of the foot-flagging frog, Staurois parvus: a resource for understanding mechanisms of behavior. G3 (Bethesda) 2023; 13:jkad193. [PMID: 37625789 PMCID: PMC10542557 DOI: 10.1093/g3journal/jkad193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 03/22/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023]
Abstract
Elaborate and skilled movements of the body have been selected in a variety of species as courtship and rivalry signals. One roadblock in studying these behaviors has been a lack of resources for understanding how they evolved at the genetic level. The Bornean rock frog (Staurois parvus) is an ideal species in which to address this issue. Males wave their hindlimbs in a "foot-flagging" display when competing for mates. The evolution of foot flagging in S. parvus and other species is accompanied by increases in the expression of the androgen receptor gene within its neuromuscular system, but it remains unclear what genetic or transcriptional changes are associated with this behavioral phenotype. We have now assembled the genome of S. parvus, resulting in 3.98 Gbp of 22,402 contigs with an N50 of 611,229 bp. The genome will be a resource for finding genes related to the physiology underlying foot flagging and to adaptations of the neuromuscular system. As a first application of the genome, we also began work in comparative genomics and differential gene expression analysis. We show that the androgen receptor is diverged from other anuran species, and we identify unique expression patterns of genes in the spinal cord and leg muscle that are important for axial patterning, cell specification and morphology, or muscle contraction. This genome will continue to be an important tool for future -omics studies to understand the evolution of elaborate signaling behaviors in this and potentially related species.
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Affiliation(s)
- Mika A Holtz
- Department of Biological Sciences, Smith College, Northampton, MA 01053, USA
| | - Riccardo Racicot
- Department of Biological Sciences, Smith College, Northampton, MA 01053, USA
| | - Doris Preininger
- Vienna Zoo, 1130 Vienna, Austria
- Department of Evolutionary Biology, University of Vienna, 1030 Vienna, Austria
| | - Adam M M Stuckert
- Department of Biology & Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Lisa A Mangiamele
- Department of Biological Sciences, Smith College, Northampton, MA 01053, USA
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176
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Leung W, Torosin N, Cao W, Reed LK, Arrigo C, Elgin SCR, Ellison CE. Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai, Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae. G3 (Bethesda) 2023; 13:jkad191. [PMID: 37611223 PMCID: PMC10542312 DOI: 10.1093/g3journal/jkad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/25/2023]
Abstract
Flow cytometry estimates of genome sizes among species of Drosophila show a 3-fold variation, ranging from ∼127 Mb in Drosophila mercatorum to ∼400 Mb in Drosophila cyrtoloma. However, the assembled portion of the Muller F element (orthologous to the fourth chromosome in Drosophila melanogaster) shows a nearly 14-fold variation in size, ranging from ∼1.3 Mb to >18 Mb. Here, we present chromosome-level long-read genome assemblies for 4 Drosophila species with expanded F elements ranging in size from 2.3 to 20.5 Mb. Each Muller element is present as a single scaffold in each assembly. These assemblies will enable new insights into the evolutionary causes and consequences of chromosome size expansion.
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Affiliation(s)
- Wilson Leung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicole Torosin
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Weihuan Cao
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Laura K Reed
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Cindy Arrigo
- Department of Biology, New Jersey City University, Jersey City, NJ 07305, USA
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Christopher E Ellison
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
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177
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Pérez-Garza J, Parrish-Mulliken E, Deane Z, Ostroff LE. Rehydration of Freeze Substituted Brain Tissue for Pre-embedding Immunoelectron Microscopy. Microsc Microanal 2023; 29:1694-1704. [PMID: 37584524 PMCID: PMC10541149 DOI: 10.1093/micmic/ozad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/27/2023] [Accepted: 07/16/2023] [Indexed: 08/17/2023]
Abstract
Electron microscopy (EM) volume reconstruction is a powerful tool for investigating the fundamental structure of brain circuits, but the full potential of this technique is limited by the difficulty of integrating molecular information. High quality ultrastructural preservation is necessary for EM reconstruction, and intact, highly contrasted cell membranes are essential for following small neuronal processes through serial sections. Unfortunately, the antibody labeling methods used to identify most endogenous molecules result in compromised morphology, especially of membranes. Cryofixation can produce superior morphological preservation and has the additional advantage of allowing indefinite storage of valuable samples. We have developed a method based on cryofixation that allows sensitive immunolabeling of endogenous molecules, preserves excellent ultrastructure, and is compatible with high-contrast staining for serial EM reconstruction.
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Affiliation(s)
- Janeth Pérez-Garza
- Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Rd. Unit 3156, Storrs, CT 06269-3156, USA
| | - Emily Parrish-Mulliken
- Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Rd. Unit 3156, Storrs, CT 06269-3156, USA
| | - Zachary Deane
- Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Rd. Unit 3156, Storrs, CT 06269-3156, USA
| | - Linnaea E Ostroff
- Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Rd. Unit 3156, Storrs, CT 06269-3156, USA
- Connecticut Institute for the Brain and Cognitive Sciences, University of Connecticut, 337 Mansfield Rd. Unit 1272, Storrs, CT 06269-1272, USA
- Institute of Materials Science, University of Connecticut, 25 King Hill Rd. Unit 3136, Storrs, CT 06269-3136, USA
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178
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Zhang AC, Maguire SM, Ford JT, Composto RJ. Using Focused Ion Beam Time-of-Flight Secondary Ion Mass Spectrometry to Depth Profile Nanoparticles in Polymer Nanocomposites. Microsc Microanal 2023; 29:1557-1565. [PMID: 37639375 DOI: 10.1093/micmic/ozad085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/10/2023] [Accepted: 07/30/2023] [Indexed: 08/31/2023]
Abstract
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a versatile surface-sensitive technique for characterizing both hard and soft matter. Its chemical and molecular specificity, high spatial resolution, and superior sensitivity make it an ideal method for depth profiling polymeric systems, including those comprised of both inorganic and organic constituents (i.e., polymer nanocomposites, PNCs). To best utilize ToF-SIMS for characterizing PNCs, experimental conditions must be optimized to minimize challenges such as the matrix effect and charge accumulation. Toward that end, we have successfully used ToF-SIMS with a Xe+ focused ion beam to depth profile silica nanoparticles grafted with poly(methyl methacrylate) (PMMA-NP) in a poly(styrene-ran-acrylonitrile) matrix film by selecting conditions that address charge compensation and the primary incident beam angles. By tracking the sputtered Si+ species and fitting the resultant concentration profile, the diffusion coefficient of PMMA-NP was determined to be D = 2.4 × 10-14 cm2/s. This value of D lies between that measured using Rutherford backscattering spectrometry (6.4 × 10-14 cm2/s) and the value predicted by the Stokes-Einstein model (2.5 × 10-15 cm2/s). With carefully tuned experimental parameters, ToF-SIMS holds great potential for quantitatively characterizing the nanoparticles at the surfaces and interfaces within PNC materials as well as soft matter in general.
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Affiliation(s)
- Aria C Zhang
- Materials Science and Engineering, University of Pennsylvania, 3231 Walnut Street, Philadelphia, Pennsylvania 19104, USA
- Materials Research Science & Engineering Center (MRSEC), University of Pennsylvania, 3231 Walnut Street, Philadelphia 19104, USA
| | - Shawn M Maguire
- Materials Science and Engineering, University of Pennsylvania, 3231 Walnut Street, Philadelphia, Pennsylvania 19104, USA
| | - Jamie T Ford
- Nanoscale Characterization Facility, University of Pennsylvania, 3205 Walnut Street, Philadelphia, Pennsylvania 19104, USA
| | - Russell J Composto
- Materials Science and Engineering, University of Pennsylvania, 3231 Walnut Street, Philadelphia, Pennsylvania 19104, USA
- Materials Research Science & Engineering Center (MRSEC), University of Pennsylvania, 3231 Walnut Street, Philadelphia 19104, USA
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179
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Sotoudeh Bagha P, Kolanthai E, Wei F, Neal CJ, Kumar U, Braun G, Coathup M, Seal S, Razavi M. Ultrasound-Responsive Nanobubbles for Combined siRNA-Cerium Oxide Nanoparticle Delivery to Bone Cells. Pharmaceutics 2023; 15:2393. [PMID: 37896153 PMCID: PMC10609961 DOI: 10.3390/pharmaceutics15102393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
This study aims to present an ultrasound-mediated nanobubble (NB)-based gene delivery system that could potentially be applied in the future to treat bone disorders such as osteoporosis. NBs are sensitive to ultrasound (US) and serve as a controlled-released carrier to deliver a mixture of Cathepsin K (CTSK) siRNA and cerium oxide nanoparticles (CeNPs). This platform aimed to reduce bone resorption via downregulating CTSK expression in osteoclasts and enhance bone formation via the antioxidant and osteogenic properties of CeNPs. CeNPs were synthesized and characterized using transmission electron microscopy and X-ray photoelectron spectroscopy. The mixture of CTSK siRNA and CeNPs was adsorbed to the surface of NBs using a sonication method. The release profiles of CTSK siRNA and CeNPs labeled with a fluorescent tag molecule were measured after low-intensity pulsed ultrasound (LIPUS) stimulation using fluorescent spectroscopy. The maximum release of CTSK siRNA and the CeNPs for 1 mg/mL of NB-(CTSK siRNA + CeNPs) was obtained at 2.5 nM and 1 µg/mL, respectively, 3 days after LIPUS stimulation. Then, Alizarin Red Staining (ARS) was applied to human bone marrow-derived mesenchymal stem cells (hMSC) and tartrate-resistant acid phosphatase (TRAP) staining was applied to human osteoclast precursors (OCP) to evaluate osteogenic promotion and osteoclastogenic inhibition effects. A higher mineralization and a lower number of osteoclasts were quantified for NB-(CTSK siRNA + CeNPs) versus control +RANKL with ARS (p < 0.001) and TRAP-positive staining (p < 0.01). This study provides a method for the delivery of gene silencing siRNA and CeNPs using a US-sensitive NB system that could potentially be used in vivo and in the treatment of bone fractures and disorders such as osteoporosis.
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Affiliation(s)
- Pedram Sotoudeh Bagha
- BiionixTM (Bionic Materials, Implants & Interfaces) Cluster, Department of Medicine, University of Central Florida College of Medicine, Orlando, FL 32827, USA; (P.S.B.); (F.W.); (M.C.)
| | - Elayaraja Kolanthai
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32826, USA; (E.K.); (C.J.N.); (U.K.); (S.S.)
| | - Fei Wei
- BiionixTM (Bionic Materials, Implants & Interfaces) Cluster, Department of Medicine, University of Central Florida College of Medicine, Orlando, FL 32827, USA; (P.S.B.); (F.W.); (M.C.)
| | - Craig J. Neal
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32826, USA; (E.K.); (C.J.N.); (U.K.); (S.S.)
| | - Udit Kumar
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32826, USA; (E.K.); (C.J.N.); (U.K.); (S.S.)
| | - Gillian Braun
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA 01075, USA;
| | - Melanie Coathup
- BiionixTM (Bionic Materials, Implants & Interfaces) Cluster, Department of Medicine, University of Central Florida College of Medicine, Orlando, FL 32827, USA; (P.S.B.); (F.W.); (M.C.)
| | - Sudipta Seal
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32826, USA; (E.K.); (C.J.N.); (U.K.); (S.S.)
| | - Mehdi Razavi
- BiionixTM (Bionic Materials, Implants & Interfaces) Cluster, Department of Medicine, University of Central Florida College of Medicine, Orlando, FL 32827, USA; (P.S.B.); (F.W.); (M.C.)
- Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
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180
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Fan Y, Zhang Z, Yu Q, Lai Y, Su K, Wang Y, Pan S, Latecki LJ. Iterated Clique Reductions in Vertex Weighted Coloring for Large Sparse Graphs. Entropy (Basel) 2023; 25:1376. [PMID: 37895498 PMCID: PMC10606255 DOI: 10.3390/e25101376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023]
Abstract
The Minimum Vertex Weighted Coloring (MinVWC) problem is an important generalization of the classic Minimum Vertex Coloring (MinVC) problem which is NP-hard. Given a simple undirected graph G=(V,E), the MinVC problem is to find a coloring s.t. any pair of adjacent vertices are assigned different colors and the number of colors used is minimized. The MinVWC problem associates each vertex with a positive weight and defines the weight of a color to be the weight of its heaviest vertices, then the goal is the find a coloring that minimizes the sum of weights over all colors. Among various approaches, reduction is an effective one. It tries to obtain a subgraph whose optimal solutions can conveniently be extended into optimal ones for the whole graph, without costly branching. In this paper, we propose a reduction algorithm based on maximal clique enumeration. More specifically our algorithm utilizes a certain proportion of maximal cliques and obtains lower bounds in order to perform reductions. It alternates between clique sampling and graph reductions and consists of three successive procedures: promising clique reductions, better bound reductions and post reductions. Experimental results show that our algorithm returns considerably smaller subgraphs for numerous large benchmark graphs, compared to the most recent method named RedLS. Also, we evaluate individual impacts and some practical properties of our algorithm. Furthermore, we have a theorem which indicates that the reduction effects of our algorithm are equivalent to that of a counterpart which enumerates all maximal cliques in the whole graph if the run time is sufficiently long.
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Affiliation(s)
- Yi Fan
- School of Mathematics and Statistic, Qiannan Normal University for Nationalities, Duyun 558000, China; (Y.F.); (Q.Y.)
| | - Zaijun Zhang
- School of Mathematics and Statistic, Qiannan Normal University for Nationalities, Duyun 558000, China; (Y.F.); (Q.Y.)
- Key Laboratory of Complex Systems and Intelligent Optimization of Guizhou Province, Duyun 558000, China
| | - Quan Yu
- School of Mathematics and Statistic, Qiannan Normal University for Nationalities, Duyun 558000, China; (Y.F.); (Q.Y.)
| | - Yongxuan Lai
- School of Mathematics and Information Engineering, Longyan University, Longyan 364000, China;
| | - Kaile Su
- Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, QLD 4111, Australia;
| | - Yiyuan Wang
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130024, China; (Y.W.); (S.P.)
| | - Shiwei Pan
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130024, China; (Y.W.); (S.P.)
| | - Longin Jan Latecki
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA;
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181
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Vijjamarri AK, Gupta N, Onu C, Niu X, Zhang F, Kumar R, Lin Z, Greenberg M, Hinnebusch AG. mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability. Nucleic Acids Res 2023; 51:9314-9336. [PMID: 37439347 PMCID: PMC10516646 DOI: 10.1093/nar/gkad584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/17/2023] [Accepted: 07/10/2023] [Indexed: 07/14/2023] Open
Abstract
We have examined the roles of yeast mRNA decapping-activators Pat1 and Dhh1 in repressing the translation and abundance of specific mRNAs in nutrient-replete cells using ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs, RNA Polymerase II ChIP-Seq, and TMT-mass spectrometry of mutants lacking one or both factors. Although the Environmental Stress Response (ESR) is activated in dhh1Δ and pat1Δ mutants, hundreds of non-ESR transcripts are elevated in a manner indicating cumulative repression by Pat1 and Dhh1 in wild-type cells. These mRNAs show both reduced decapping and diminished transcription in the mutants, indicating that impaired mRNA turnover drives transcript derepression in cells lacking Dhh1 or Pat1. mRNA degradation stimulated by Dhh1/Pat1 is not dictated by poor translation nor enrichment for suboptimal codons. Pat1 and Dhh1 also collaborate to reduce translation and protein production from many mRNAs. Transcripts showing concerted translational repression by Pat1/Dhh1 include mRNAs involved in cell adhesion or utilization of the poor nitrogen source allantoin. Pat1/Dhh1 also repress numerous transcripts involved in respiration, catabolism of non-preferred carbon or nitrogen sources, or autophagy; and we obtained evidence for elevated respiration and autophagy in the mutants. Thus, Pat1 and Dhh1 function as post-transcriptional repressors of multiple pathways normally activated only during nutrient limitation.
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Affiliation(s)
- Anil Kumar Vijjamarri
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neha Gupta
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chisom Onu
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Xiao Niu
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Fan Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rakesh Kumar
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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182
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Sullivan J, Cramer-Benjamin S, Alvarez J, Barner D. Everything is Infinite: Children's Beliefs About Endless Space, Time, and Number. Open Mind (Camb) 2023; 7:715-731. [PMID: 37840760 PMCID: PMC10575555 DOI: 10.1162/opmi_a_00104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/05/2023] [Indexed: 10/17/2023] Open
Abstract
How do children form beliefs about the infinity of space, time, and number? We asked whether children held similar beliefs about infinity across domains, and whether beliefs in infinity for domains like space and time might be scaffolded upon numerical knowledge (e.g., knowledge successors within the count list). To test these questions, 112 U.S. children (aged 4;0-7;11) completed an interview regarding their beliefs about infinite space, time, and number. We also measured their knowledge of counting, and other factors that might impact performance on linguistic assessments of infinity belief (e.g., working memory, ability to respond to hypothetical questions). We found that beliefs about infinity were very high across all three domains, suggesting that infinity beliefs may arise early in development for space, time, and number. Second, we found that-across all three domains-children were more likely to believe that it is always possible to add a unit than to believe that the domain is endless. Finally, we found that understanding the rules underlying counting predicted children's belief that it is always possible to add 1 to any number, but did not predict any of the other elements of infinity belief.
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Affiliation(s)
| | - Sophie Cramer-Benjamin
- Skidmore College, Department of Psychology
- Yale Child Study Center, Yale School of Medicine
| | | | - David Barner
- University of California, San Diego, Department of Psychology
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183
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Nusser BD, Accardo JV, Zhu L. Luminescence and Stability of 1,4,5-Triaryl-1,2,3-Triazoles. Chemphyschem 2023; 24:e202300209. [PMID: 37395382 DOI: 10.1002/cphc.202300209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/04/2023]
Abstract
The fluorescence, phosphorescence, and photochemical properties of di- and triaryl-substituted-1,2,3-triazoles are reported in this work. The ease of synthesis of regioisomers of substituted triazoles enables a systematic study on the correlation between regiochemistry and excited state properties, which include the solvent dependence of fluorescence, energy gap between singlet and triplet emitters, and propensity to photon-triggered transformations. The triazoles that carry electron (e)-donor and e-acceptor aryl substituents show high fluorescence quantum yields in weakly polar solvents and exhibit solvent-dependent fluorescence. The luminescence properties of these compounds in glass matrices at 77 K are characterized. The thermal and photo-stability, two parameters that are crucial to their potential utilities in optical devices, of these compounds are determined. The position of the e-donor substituent has a significant impact on the fluorescence emission energy and solvent sensitivity, singlet-triplet energy gap, and photochemical reactivity and stability. The experimental observations on the structural correlation with the photophysical and photochemical properties are explained by quantum chemical calculations. This study provides a rationale on the placement of substituent on a donor-acceptor type fluorophore to maneuver a range of photo-related properties.
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Affiliation(s)
- Brandon D Nusser
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA
| | - Joseph V Accardo
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA
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184
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Branch CL, Welklin JF, Sonnenberg BR, Benedict LM, Heinen VK, Pitera AM, Bridge ES, Pravosudov VV. What's in a mate? Social pairing decisions and spatial cognitive ability in food-caching mountain chickadees. Proc Biol Sci 2023; 290:20231073. [PMID: 37700643 PMCID: PMC10498033 DOI: 10.1098/rspb.2023.1073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
While researchers have investigated mating decisions for decades, gaps remain in our understanding of how behaviour influences social mate choice. We compared spatial cognitive performance and food caching propensity within social pairs of mountain chickadees inhabiting differentially harsh winter climates to understand how these measures contribute to social mate choice. Chickadees rely on specialized spatial cognitive abilities to recover food stores and survive harsh winters, and females can discriminate among males with varying spatial cognition. Because spatial cognition and caching propensity are critical for survival and likely heritable, pairing with a mate with such enhanced traits may provide indirect benefits to offspring. Comparing the behaviour of social mates, we found that spatial cognitive performance approached a significant correlation within pairs at low, but not at high elevation. We found no correlation within pairs in spatial reversal cognitive performance at either elevation; however, females at high elevation tended to perform better than their social mates. Finally, we found that caching propensity correlated within pairs at low, while males cached significantly more food than their social mates at high elevations. These results suggest that cognition and caching propensity may influence social mating decisions, but only in certain environments and for some aspects of cognition.
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Affiliation(s)
- Carrie L. Branch
- Department of Psychology, The University of Western Ontario, London, Ontario, Canada
| | | | - Benjamin R. Sonnenberg
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Ecology, Evolution, and Conservation Biology Graduate Program, University of Nevada, Reno, Reno, NV, USA
| | - Lauren M. Benedict
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Ecology, Evolution, and Conservation Biology Graduate Program, University of Nevada, Reno, Reno, NV, USA
| | | | - Angela M. Pitera
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Ecology, Evolution, and Conservation Biology Graduate Program, University of Nevada, Reno, Reno, NV, USA
| | - Eli S. Bridge
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Vladimir V. Pravosudov
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Ecology, Evolution, and Conservation Biology Graduate Program, University of Nevada, Reno, Reno, NV, USA
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185
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McClintock H, Xiong Z, Rergis B, Lipson H. Design and fabrication of carbon fiber lattices using 3D weaving. Sci Rep 2023; 13:14919. [PMID: 37691024 PMCID: PMC10493227 DOI: 10.1038/s41598-023-40962-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/19/2023] [Indexed: 09/12/2023] Open
Abstract
We present a method of designing and fabricating 3D carbon fiber lattices. The lattice design and fabrication is based on crocheting and sewing techniques, where carbon fiber tow is woven through two parallel carbon fiber grids and reinforced with vertical carbon fiber tubes. Compression testing is then performed on three different designs, and these results are compared to other similar lattice structures, finding that the lattices perform similarly to comparable lattices. Finite element analysis is also performed to validate the experimental findings, and provides some insight into the experimental results. The process presented here allows for more design flexibility than other current methods. For example, within a single lattice, different density weave patterns can be used to address specific load requirements. Though fabricated manually here, this process can also be automated for large scale production. With this design flexibility, simplified fabrication, and high strength, the lattices proposed here offer an advantage as compared to similar existing structures.
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Affiliation(s)
- Hayley McClintock
- Fu Foundation School of Engineering and Applied Science, Columbia University, New York, NY, 10027, USA.
| | - Zechen Xiong
- Fu Foundation School of Engineering and Applied Science, Columbia University, New York, NY, 10027, USA
| | - Bruno Rergis
- Fu Foundation School of Engineering and Applied Science, Columbia University, New York, NY, 10027, USA
| | - Hod Lipson
- Fu Foundation School of Engineering and Applied Science, Columbia University, New York, NY, 10027, USA
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186
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Lewis JA, Zhang B, Harza R, Palmer N, Sarath G, Sattler SE, Twigg P, Vermerris W, Kang C. Structural Similarities and Overlapping Activities among Dihydroflavonol 4-Reductase, Flavanone 4-Reductase, and Anthocyanidin Reductase Offer Metabolic Flexibility in the Flavonoid Pathway. Int J Mol Sci 2023; 24:13901. [PMID: 37762209 PMCID: PMC10531346 DOI: 10.3390/ijms241813901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Flavonoids are potent antioxidants that play a role in defense against pathogens, UV-radiation, and the detoxification of reactive oxygen species. Dihydroflavonol 4-reductase (DFR) and flavanone 4-reductase (FNR) reduce dihydroflavonols and flavanones, respectively, using NAD(P)H to produce flavan-(3)-4-(di)ols in flavonoid biosynthesis. Anthocyanidin reductase (ANR) reduces anthocyanidins to flavan-3-ols. In addition to their sequences, the 3D structures of recombinant DFR, FNR and ANR from sorghum and switchgrass showed a high level of similarity. The catalytic mechanism, substrate-specificity and key residues of three reductases were deduced from crystal structures, site-directed mutagenesis, molecular docking, kinetics, and thermodynamic ana-lyses. Although DFR displayed its highest activity against dihydroflavonols, it also showed activity against flavanones and anthocyanidins. It was inhibited by the flavonol quercetin and high concentrations of dihydroflavonols/flavonones. SbFNR1 and SbFNR2 did not show any activity against dihydroflavonols. However, SbFNR1 displayed activity against flavanones and ANR activity against two anthocyanidins, cyanidin and pelargonidin. Therefore, SbFNR1 and SbFNR2 could be specific ANR isozymes without delphinidin activity. Sorghum has high concentrations of 3-deoxyanthocyanidins in vivo, supporting the observed high activity of SbDFR against flavonols. Mining of expression data indicated substantial induction of these three reductase genes in both switchgrass and sorghum in response to biotic stress. Key signature sequences for proper DFR/ANR classification are proposed and could form the basis for future metabolic engineering of flavonoid metabolism.
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Affiliation(s)
- Jacob A. Lewis
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (B.Z.)
| | - Bixia Zhang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (B.Z.)
| | - Rishi Harza
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (B.Z.)
| | - Nathan Palmer
- Wheat, Sorghum, Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA; (N.P.); (G.S.); (S.E.S.)
| | - Gautam Sarath
- Wheat, Sorghum, Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA; (N.P.); (G.S.); (S.E.S.)
| | - Scott E. Sattler
- Wheat, Sorghum, Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA; (N.P.); (G.S.); (S.E.S.)
| | - Paul Twigg
- Biology Department, University of Nebraska at Kearney, Kearney, NE 68849, USA;
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science and UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA;
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (B.Z.)
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187
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Xue Z, Ren K, Wu R, Sun Z, Zheng R, Tian Q, Ali A, Mi L, You M. Targeted RNA condensation in living cells via genetically encodable triplet repeat tags. Nucleic Acids Res 2023; 51:8337-8347. [PMID: 37486784 PMCID: PMC10484661 DOI: 10.1093/nar/gkad621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023] Open
Abstract
Living systems contain various membraneless organelles that segregate proteins and RNAs via liquid-liquid phase separation. Inspired by nature, many protein-based synthetic compartments have been engineered in vitro and in living cells. Here, we introduce a genetically encoded CAG-repeat RNA tag to reprogram cellular condensate formation and recruit various non-phase-transition RNAs for cellular modulation. With the help of fluorogenic RNA aptamers, we have systematically studied the formation dynamics, spatial distributions, sizes and densities of these cellular RNA condensates. The cis- and trans-regulation functions of these CAG-repeat tags in cellular RNA localization, life time, RNA-protein interactions and gene expression have also been investigated. Considering the importance of RNA condensation in health and disease, we expect that these genetically encodable modular and self-assembled tags can be widely used for chemical biology and synthetic biology studies.
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Affiliation(s)
- Zhaolin Xue
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Zhining Sun
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Ru Zheng
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Qian Tian
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Ahsan Ausaf Ali
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Lan Mi
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, USA
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188
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Aziz MF, Mughal F, Caetano-Anollés G. Tracing the birth of structural domains from loops during protein evolution. Sci Rep 2023; 13:14688. [PMID: 37673948 PMCID: PMC10482863 DOI: 10.1038/s41598-023-41556-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
The structures and functions of proteins are embedded into the loop scaffolds of structural domains. Their origin and evolution remain mysterious. Here, we use a novel graph-theoretical approach to describe how modular and non-modular loop prototypes combine to form folded structures in protein domain evolution. Phylogenomic data-driven chronologies reoriented a bipartite network of loops and domains (and its projections) into 'waterfalls' depicting an evolving 'elementary functionome' (EF). Two primordial waves of functional innovation involving founder 'p-loop' and 'winged-helix' domains were accompanied by an ongoing emergence and reuse of structural and functional novelty. Metabolic pathways expanded before translation functionalities. A dual hourglass recruitment pattern transferred scale-free properties from loop to domain components of the EF network in generative cycles of hierarchical modularity. Modeling the evolutionary emergence of the oldest P-loop and winged-helix domains with AlphFold2 uncovered rapid convergence towards folded structure, suggesting that a folding vocabulary exists in loops for protein fold repurposing and design.
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Affiliation(s)
- M Fayez Aziz
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
- C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.
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189
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An SY, Wu X, Zhao Y, Liu T, Yin R, Ahn JH, Walker LM, Whitacre JF, Matyjaszewski K. Highly Conductive Polyoxanorbornene-Based Polymer Electrolyte for Lithium-Metal Batteries. Adv Sci (Weinh) 2023; 10:e2302932. [PMID: 37455678 PMCID: PMC10520635 DOI: 10.1002/advs.202302932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/14/2023] [Indexed: 07/18/2023]
Abstract
This present study illustrates the synthesis and preparation of polyoxanorbornene-based bottlebrush polymers with poly(ethylene oxide) (PEO) side chains by ring-opening metathesis polymerization for solid polymer electrolytes (SPE). In addition to the conductive PEO side chains, the polyoxanorbornene backbones may act as another ion conductor to further promote Li-ion movement within the SPE matrix. These results suggest that these bottlebrush polymer electrolytes provide impressively high ionic conductivity of 7.12 × 10-4 S cm-1 at room temperature and excellent electrochemical performance, including high-rate capabilities and cycling stability when paired with a Li metal anode and a LiFePO4 cathode. The new design paradigm, which has dual ionic conductive pathways, provides an unexplored avenue for inventing new SPEs and emphasizes the importance of molecular engineering to develop highly stable and conductive polymer electrolytes for lithium-metal batteries (LMB).
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Affiliation(s)
- So Young An
- Department of ChemistryCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Xinsheng Wu
- Department of Materials Science and EngineeringCarnegie Mellon University5000 Forbes AvenuePittsburghPA15213USA
| | - Yuqi Zhao
- Department of Materials Science and EngineeringCarnegie Mellon University5000 Forbes AvenuePittsburghPA15213USA
| | - Tong Liu
- Department of ChemistryCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Rongguan Yin
- Department of ChemistryCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Jung Hyun Ahn
- Department of Chemical EngineeringCarnegie Mellon University5000 Forbes AvenuePittsburghPA15213USA
| | - Lynn M. Walker
- Department of Chemical EngineeringCarnegie Mellon University5000 Forbes AvenuePittsburghPA15213USA
| | - Jay F. Whitacre
- Department of Materials Science and EngineeringCarnegie Mellon University5000 Forbes AvenuePittsburghPA15213USA
- Scott Institute for Energy InnovationCarnegie Mellon University5000 Forbes AvenuePittsburghPA15213USA
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190
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Zhou Y, Shi C, Li L, Yao Q. Testing for the Markov property in time series via deep conditional generative learning. J R Stat Soc Series B Stat Methodol 2023; 85:1204-1222. [PMID: 37780936 PMCID: PMC10541293 DOI: 10.1093/jrsssb/qkad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/27/2023] [Indexed: 10/03/2023]
Abstract
The Markov property is widely imposed in analysis of time series data. Correspondingly, testing the Markov property, and relatedly, inferring the order of a Markov model, are of paramount importance. In this article, we propose a nonparametric test for the Markov property in high-dimensional time series via deep conditional generative learning. We also apply the test sequentially to determine the order of the Markov model. We show that the test controls the type-I error asymptotically, and has the power approaching one. Our proposal makes novel contributions in several ways. We utilise and extend state-of-the-art deep generative learning to estimate the conditional density functions, and establish a sharp upper bound on the approximation error of the estimators. We derive a doubly robust test statistic, which employs a nonparametric estimation but achieves a parametric convergence rate. We further adopt sample splitting and cross-fitting to minimise the conditions required to ensure the consistency of the test. We demonstrate the efficacy of the test through both simulations and the three data applications.
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Affiliation(s)
- Yunzhe Zhou
- Division of Biostatistics, University of California at Berkeley, Berkeley, CA, USA
| | - Chengchun Shi
- London School of Economics and Political Science, London, UK
| | - Lexin Li
- Division of Biostatistics, University of California at Berkeley, Berkeley, CA, USA
| | - Qiwei Yao
- London School of Economics and Political Science, London, UK
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191
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Park TJ, Deng S, Manna S, Islam ANMN, Yu H, Yuan Y, Fong DD, Chubykin AA, Sengupta A, Sankaranarayanan SKRS, Ramanathan S. Complex Oxides for Brain-Inspired Computing: A Review. Adv Mater 2023; 35:e2203352. [PMID: 35723973 DOI: 10.1002/adma.202203352] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
The fields of brain-inspired computing, robotics, and, more broadly, artificial intelligence (AI) seek to implement knowledge gleaned from the natural world into human-designed electronics and machines. In this review, the opportunities presented by complex oxides, a class of electronic ceramic materials whose properties can be elegantly tuned by doping, electron interactions, and a variety of external stimuli near room temperature, are discussed. The review begins with a discussion of natural intelligence at the elementary level in the nervous system, followed by collective intelligence and learning at the animal colony level mediated by social interactions. An important aspect highlighted is the vast spatial and temporal scales involved in learning and memory. The focus then turns to collective phenomena, such as metal-to-insulator transitions (MITs), ferroelectricity, and related examples, to highlight recent demonstrations of artificial neurons, synapses, and circuits and their learning. First-principles theoretical treatments of the electronic structure, and in situ synchrotron spectroscopy of operating devices are then discussed. The implementation of the experimental characteristics into neural networks and algorithm design is then revewed. Finally, outstanding materials challenges that require a microscopic understanding of the physical mechanisms, which will be essential for advancing the frontiers of neuromorphic computing, are highlighted.
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Affiliation(s)
- Tae Joon Park
- School of Materials Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Sunbin Deng
- School of Materials Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Sukriti Manna
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - A N M Nafiul Islam
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Haoming Yu
- School of Materials Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Yifan Yuan
- School of Materials Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Dillon D Fong
- Materials Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Alexander A Chubykin
- Department of Biological Sciences, Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, 47907, USA
| | - Abhronil Sengupta
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Subramanian K R S Sankaranarayanan
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL, 60439, USA
- Department of Mechanical and Industrial Engineering, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Shriram Ramanathan
- School of Materials Engineering, Purdue University, West Lafayette, IN, 47907, USA
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192
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Yang Y, Xu T, Conant G, Kishino H, Thorne JL, Ji X. Interlocus Gene Conversion, Natural Selection, and Paralog Homogenization. Mol Biol Evol 2023; 40:msad198. [PMID: 37675606 PMCID: PMC10503786 DOI: 10.1093/molbev/msad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/07/2023] [Accepted: 09/05/2023] [Indexed: 09/08/2023] Open
Abstract
Following a duplication, the resulting paralogs tend to diverge. While mutation and natural selection can accelerate this process, they can also slow it. Here, we quantify the paralog homogenization that is caused by point mutations and interlocus gene conversion (IGC). Among 164 duplicated teleost genes, the median percentage of postduplication codon substitutions that arise from IGC rather than point mutation is estimated to be between 7% and 8%. By differentiating between the nonsynonymous codon substitutions that homogenize the protein sequences of paralogs and the nonhomogenizing nonsynonymous substitutions, we estimate the homogenizing nonsynonymous rates to be higher for 163 of the 164 teleost data sets as well as for all 14 data sets of duplicated yeast ribosomal protein-coding genes that we consider. For all 14 yeast data sets, the estimated homogenizing nonsynonymous rates exceed the synonymous rates.
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Affiliation(s)
- Yixuan Yang
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Tanchumin Xu
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Gavin Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Hirohisa Kishino
- AI/Data Science Social Implementation Laboratory, Chuo University, Tokyo, Japan
| | - Jeffrey L Thorne
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Xiang Ji
- Department of Mathematics, Tulane University, New Orleans, LA, USA
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193
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Vinken K, Prince JS, Konkle T, Livingstone MS. The neural code for "face cells" is not face-specific. Sci Adv 2023; 9:eadg1736. [PMID: 37647400 PMCID: PMC10468123 DOI: 10.1126/sciadv.adg1736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 07/27/2023] [Indexed: 09/01/2023]
Abstract
Face cells are neurons that respond more to faces than to non-face objects. They are found in clusters in the inferotemporal cortex, thought to process faces specifically, and, hence, studied using faces almost exclusively. Analyzing neural responses in and around macaque face patches to hundreds of objects, we found graded response profiles for non-face objects that predicted the degree of face selectivity and provided information on face-cell tuning beyond that from actual faces. This relationship between non-face and face responses was not predicted by color and simple shape properties but by information encoded in deep neural networks trained on general objects rather than face classification. These findings contradict the long-standing assumption that face versus non-face selectivity emerges from face-specific features and challenge the practice of focusing on only the most effective stimulus. They provide evidence instead that category-selective neurons are best understood by their tuning directions in a domain-general object space.
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Affiliation(s)
- Kasper Vinken
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jacob S. Prince
- Department of Psychology, Harvard University, Cambridge, MA 02478, USA
| | - Talia Konkle
- Department of Psychology, Harvard University, Cambridge, MA 02478, USA
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194
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Sim J, Wu S, Dai J, Zhao RR. Magneto-Mechanical Bilayer Metamaterial with Global Area-Preserving Density Tunability for Acoustic Wave Regulation. Adv Mater 2023; 35:e2303541. [PMID: 37335806 DOI: 10.1002/adma.202303541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/05/2023] [Indexed: 06/21/2023]
Abstract
2D metamaterials have immense potential in acoustics, optics, and electromagnetic applications due to their unique properties and ability to conform to curved substrates. Active metamaterials have attracted significant research attention because of their on-demand tunable properties and performances through shape reconfigurations. 2D active metamaterials often achieve active properties through internal structural deformations, which lead to changes in overall dimensions. This demands corresponding alterations of the conforming substrate, or the metamaterial fails to provide complete area coverage, which can be a significant limitation for their practical applications. To date, achieving area-preserving active 2D metamaterials with distinct shape reconfigurations remains a prominent challenge. In this paper, magneto-mechanical bilayer metamaterials are presented that demonstrate area density tunability with area-preserving capability. The bilayer metamaterials consist of two arrays of magnetic soft materials with distinct magnetization distributions. Under a magnetic field, each layer behaves differently, which allows the metamaterial to reconfigure its shape into multiple modes and to significantly tune its area density without changing its overall dimensions. The area-preserving multimodal shape reconfigurations are further exploited as active acoustic wave regulators to tune bandgaps and wave propagations. The bilayer approach thus provides a new concept for the design of area-preserving active metamaterials for broader applications.
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Affiliation(s)
- Jay Sim
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Shuai Wu
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Jize Dai
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ruike Renee Zhao
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
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195
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Liao W, Aranson IS. Viscoelasticity enhances collective motion of bacteria. PNAS Nexus 2023; 2:pgad291. [PMID: 37719751 PMCID: PMC10503537 DOI: 10.1093/pnasnexus/pgad291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/28/2023] [Indexed: 09/19/2023]
Abstract
Bacteria form human and animal microbiota. They are the leading causes of many infections and constitute an important class of active matter. Concentrated bacterial suspensions exhibit large-scale turbulent-like locomotion and swarming. While the collective behavior of bacteria in Newtonian fluids is relatively well understood, many fundamental questions remain open for complex fluids. Here, we report on the collective bacterial motion in a representative biological non-Newtonian viscoelastic environment exemplified by mucus. Experiments are performed with synthetic porcine gastric mucus, natural cow cervical mucus, and a Newtonian-like polymer solution. We have found that an increase in mucin concentration and, correspondingly, an increase in the suspension's elasticity monotonously increases the length scale of collective bacterial locomotion. On the contrary, this length remains practically unchanged in Newtonian polymer solution in a wide range of concentrations. The experimental observations are supported by computational modeling. Our results provide insight into how viscoelasticity affects the spatiotemporal organization of bacterial active matter. They also expand our understanding of bacterial colonization of mucosal surfaces and the onset of antibiotic resistance due to swarming.
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Affiliation(s)
- Wentian Liao
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Igor S Aranson
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
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196
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Metzner C, Stringham A, Hislop B, Bonham J, Chatterton L, DeFigueiredo R, Charles SK. Brief Submotor-Threshold Electrical Stimulation Applied Synchronously Over Wrist Flexor and Extensor Muscles does Not Suppress Essential Tremor, Independent of Stimulation Frequency. Tremor Other Hyperkinet Mov (N Y) 2023; 13:30. [PMID: 37663530 PMCID: PMC10473161 DOI: 10.5334/tohm.740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 08/05/2023] [Indexed: 09/05/2023] Open
Abstract
Background Electrical stimulation of muscles below motoneuron threshold has shown potential as a low-cost and minimally invasive treatment for Essential Tremor (ET). Prior studies have stimulated wrist flexor and extensor muscles synchronously with diverging results, calling for further investigation. Also, prior studies have only used a narrow range of stimulation parameters, so stimulation parameters have not been optimized. Our purpose was to further investigate synchronous submotor stimulation and identify the effect of stimulation frequency on tremor suppression. Methods We quantified the effect of brief, synchronous stimulation at 15 different frequencies from 10-150 Hz applied over wrist flexors and extensors on both tremor power and frequency in 20 ET patients. We compared tremor power and frequency from hand acceleration and sEMG between pre-, per-, and post-stimulation phases. Results Our stimulation paradigm did not result in significant tremor suppression or tremor frequency changes at any tested stimulation frequency, showing no significant interaction between phase and stimulation frequency for tremor power measured by either hand acceleration (p = 0.69) or sEMG (p = 0.07). Additionally, the effect of phase interacting with stimulation frequency on tremor frequency was statistically insignificant for acceleration (p = 0.64) and sEMG (p = 0.37). Discussion We conclude that brief synchronous submotor-threshold stimulation does not reduce tremor in ET patients, independent of stimulation frequency (from 10 to 150 Hz). Our results are consistent with the hypothesis that brief submotor-threshold stimulation suppresses tremor via reciprocal inhibition, which requires asynchronous stimulation. In contrast, it is hypothesized that synchronous stimulation might require longer stimulation durations to affect supraspinal tremor networks. Highlights We studied the effects of synchronous submotor electrical stimulation over wrist flexor and extensor muscles on Essential Tremor. Our results indicate that suppressing tremor with brief synchronous stimulation is ineffective. Based on recently hypothesized mechanisms of peripheral tremor suppression, we hypothesize that asynchronous stimulation or long-duration synchronous stimulation are more effective approaches to peripheral tremor suppression.
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Affiliation(s)
| | - Adam Stringham
- Mechanical Engineering, Brigham Young University, Provo, UT, USA
| | - Brenna Hislop
- Mechanical Engineering, Brigham Young University, Provo, UT, USA
| | - Joseph Bonham
- Mechanical Engineering, Brigham Young University, Provo, UT, USA
| | | | | | - Steven K. Charles
- Neuroscience, Brigham Young University, Provo, UT, USA
- Mechanical Engineering, Brigham Young University, Provo, UT, USA
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197
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Huang H, Ning S, Xie Y, He Z, Teng J, Chen Z, Fan Y, Shi JY, Barboiu M, Wang D, Su CY. Synergistic Modulation of Electronic Interaction to Enhance Intrinsic Activity and Conductivity of Fe-Co-Ni Hydroxide Nanotube for Highly Efficient Oxygen Evolution Electrocatalyst. Small 2023; 19:e2302272. [PMID: 37127855 DOI: 10.1002/smll.202302272] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/14/2023] [Indexed: 05/03/2023]
Abstract
The large-scale hydrogen production and application through electrocatalytic water splitting depends crucially on the development of highly efficient, cost-effective electrocatalysts for oxygen evolution reaction (OER), which, however, remains challenging. Here, a new electrocatalyst of trimetallic Fe-Co-Ni hydroxide (denoted as FeCoNiOx Hy ) with a nanotubular structure is developed through an enhanced Kirkendall process under applied potential. The FeCoNiOx Hy features synergistic electronic interaction between Fe, Co, and Ni, which not only notably increases the intrinsic OER activity of FeCoNiOx Hy by facilitating the formation of *OOH intermediate, but also substantially improves the intrinsic conductivity of FeCoNiOx Hy to facilitate charge transfer and activate catalytic sites through electrocatalyst by promoting the formation of abundant Co3+ . Therefore, FeCoNiOx Hy delivers remarkably accelerated OER kinetics and superior apparent activity, indicated by an ultra-low overpotential potential of 257 mV at a high current density of 200 mA cm-2 . This work is of fundamental and practical significance for synergistic catalysis related to advanced energy conversion materials and technologies.
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Affiliation(s)
- Huanfeng Huang
- Lehn Institute of Functional Materials, School of Chemistry, MOE Laboratory of Bioinorganic and Synthetic Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shunlian Ning
- Lehn Institute of Functional Materials, School of Chemistry, MOE Laboratory of Bioinorganic and Synthetic Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yanyu Xie
- Lehn Institute of Functional Materials, School of Chemistry, MOE Laboratory of Bioinorganic and Synthetic Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhujie He
- Lehn Institute of Functional Materials, School of Chemistry, MOE Laboratory of Bioinorganic and Synthetic Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jun Teng
- Lehn Institute of Functional Materials, School of Chemistry, MOE Laboratory of Bioinorganic and Synthetic Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhuodi Chen
- Lehn Institute of Functional Materials, School of Chemistry, MOE Laboratory of Bioinorganic and Synthetic Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yanan Fan
- Lehn Institute of Functional Materials, School of Chemistry, MOE Laboratory of Bioinorganic and Synthetic Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jian-Ying Shi
- Lehn Institute of Functional Materials, School of Chemistry, MOE Laboratory of Bioinorganic and Synthetic Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Mihail Barboiu
- Lehn Institute of Functional Materials, School of Chemistry, MOE Laboratory of Bioinorganic and Synthetic Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
- Adaptive Supramolecular Nanosystems Group, Institut Europeen des Membranes, University of Montpellier, ENSCM-CNRS, Place E. Bataillon CC047, Montpellier, 34095, France
| | - Dawei Wang
- Lehn Institute of Functional Materials, School of Chemistry, MOE Laboratory of Bioinorganic and Synthetic Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Cheng-Yong Su
- Lehn Institute of Functional Materials, School of Chemistry, MOE Laboratory of Bioinorganic and Synthetic Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
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198
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Aguilar-Calvo P, Malik A, Sandoval DR, Barback C, Orrù CD, Standke HG, Thomas OR, Dwyer CA, Pizzo DP, Bapat J, Soldau K, Ogawa R, Riley MB, Nilsson KPR, Kraus A, Caughey B, Iliff JJ, Vera DR, Esko JD, Sigurdson CJ. Neuronal Ndst1 depletion accelerates prion protein clearance and slows neurodegeneration in prion infection. PLoS Pathog 2023; 19:e1011487. [PMID: 37747931 PMCID: PMC10586673 DOI: 10.1371/journal.ppat.1011487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/19/2023] [Accepted: 08/11/2023] [Indexed: 09/27/2023] Open
Abstract
Select prion diseases are characterized by widespread cerebral plaque-like deposits of amyloid fibrils enriched in heparan sulfate (HS), a abundant extracellular matrix component. HS facilitates fibril formation in vitro, yet how HS impacts fibrillar plaque growth within the brain is unclear. Here we found that prion-bound HS chains are highly sulfated, and that the sulfation is essential for accelerating prion conversion in vitro. Using conditional knockout mice to deplete the HS sulfation enzyme, Ndst1 (N-deacetylase / N-sulfotransferase) from neurons or astrocytes, we investigated how reducing HS sulfation impacts survival and prion aggregate distribution during a prion infection. Neuronal Ndst1-depleted mice survived longer and showed fewer and smaller parenchymal plaques, shorter fibrils, and increased vascular amyloid, consistent with enhanced aggregate transit toward perivascular drainage channels. The prolonged survival was strain-dependent, affecting mice infected with extracellular, plaque-forming, but not membrane bound, prions. Live PET imaging revealed rapid clearance of recombinant prion protein monomers into the CSF of neuronal Ndst1- deficient mice, neuronal, further suggesting that HS sulfate groups hinder transit of extracellular prion protein monomers. Our results directly show how a host cofactor slows the spread of prion protein through the extracellular space and identify an enzyme to target to facilitate aggregate clearance.
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Affiliation(s)
| | - Adela Malik
- Department of Pathology, UC San Diego, La Jolla, California, United States of America
| | - Daniel R. Sandoval
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, California, United States of America
| | - Christopher Barback
- Department of Radiology, UC San Diego, La Jolla, California, United States of America
| | - Christina D. Orrù
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America
| | - Heidi G. Standke
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Olivia R. Thomas
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Chrissa A. Dwyer
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, California, United States of America
| | - Donald P. Pizzo
- Department of Pathology, UC San Diego, La Jolla, California, United States of America
| | - Jaidev Bapat
- Department of Pathology, UC San Diego, La Jolla, California, United States of America
| | - Katrin Soldau
- Department of Pathology, UC San Diego, La Jolla, California, United States of America
| | - Ryotaro Ogawa
- Department of Radiology, UC San Diego, La Jolla, California, United States of America
| | - Mckenzie B. Riley
- Department of Neurology, University of Alabama, Birmingham, Alabama, United States of America
| | - K. Peter R. Nilsson
- Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden
| | - Allison Kraus
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Byron Caughey
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America
| | - Jeffrey J. Iliff
- VISN 20 NW Mental Illness Research, Education and Clinical Center, VA Puget Sound Health Care System, Seattle, Washington, United States of America
- Department of Psychiatry and Behavioral Science, Department of Neurology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - David R. Vera
- Department of Radiology, UC San Diego, La Jolla, California, United States of America
| | - Jeffrey D. Esko
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, California, United States of America
| | - Christina J. Sigurdson
- Department of Pathology, UC San Diego, La Jolla, California, United States of America
- Department of Medicine, UC San Diego, La Jolla, California, United States of America
- Department of Pathology, Microbiology, and Immunology, UC Davis, Davis, California, United States of America
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199
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Kim BQ, Füredi M, Venkatesh RB, Guldin S, Lee D. Water-Induced Separation of Polymers from High Nanoparticle-Content Nanocomposite Films. Small 2023; 19:e2302676. [PMID: 37263985 DOI: 10.1002/smll.202302676] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Polymer nanocomposites with high loadings of nanoparticles (NPs) exhibit exceptional mechanical and transport properties. Separation of polymers and NPs from such nanocomposites is a critical step in enabling the recycling of these components and reducing the potential environmental hazards that can be caused by the accumulation of nanocomposite wastes in landfills. However, the separation typically requires the use of organic solvents or energy-intensive processes. Using polydimethylsiloxane (PDMS)-infiltrated SiO2 NP films, we demonstrate that the polymers can be separated from the SiO2 NP packings when these nanocomposites are exposed to high humidity and water. The findings indicate that the charge state of the NPs plays a significant role in the propensity of water to undergo capillary condensation within the PDMS-filled interstitial pores. We also show that the size of NPs has a crucial impact on the kinetics and extent of PDMS expulsion, illustrating the importance of capillary forces in inducing PDMS expulsion. We demonstrate that the separated polymer can be collected and reused to produce a new nanocomposite film. The work provides insightful guidelines on how to design and fabricate end-of-life recyclable high-performance nanocomposites.
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Affiliation(s)
- Baekmin Q Kim
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Máté Füredi
- Department of Chemical Engineering, University College London, London, WC1E 7JE, UK
| | - R Bharath Venkatesh
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stefan Guldin
- Department of Chemical Engineering, University College London, London, WC1E 7JE, UK
| | - Daeyeon Lee
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
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200
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Le VN, Bombile JH, Rupasinghe GS, Baustert KN, Li R, Maria IP, Shahi M, Alarcon Espejo P, McCulloch I, Graham KR, Risko C, Paterson AF. New Chemical Dopant and Counterion Mechanism for Organic Electrochemical Transistors and Organic Mixed Ionic-Electronic Conductors. Adv Sci (Weinh) 2023; 10:e2207694. [PMID: 37466175 PMCID: PMC10520668 DOI: 10.1002/advs.202207694] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/07/2023] [Indexed: 07/20/2023]
Abstract
Organic mixed ionic-electronic conductors (OMIECs) have varied performance requirements across a diverse application space. Chemically doping the OMIEC can be a simple, low-cost approach for adapting performance metrics. However, complex challenges, such as identifying new dopant materials and elucidating design rules, inhibit its realization. Here, these challenges are approached by introducing a new n-dopant, tetrabutylammonium hydroxide (TBA-OH), and identifying a new design consideration underpinning its success. TBA-OH behaves as both a chemical n-dopant and morphology additive in donor acceptor co-polymer naphthodithiophene diimide-based polymer, which serves as an electron transporting material in organic electrochemical transistors (OECTs). The combined effects enhance OECT transconductance, charge carrier mobility, and volumetric capacitance, representative of the key metrics underpinning all OMIEC applications. Additionally, when the TBA+ counterion adopts an "edge-on" location relative to the polymer backbone, Coulombic interaction between the counterion and polaron is reduced, and polaron delocalization increases. This is the first time such mechanisms are identified in doped-OECTs and doped-OMIECs. The work herein therefore takes the first steps toward developing the design guidelines needed to realize chemical doping as a generic strategy for tailoring performance metrics in OECTs and OMIECs.
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Affiliation(s)
- Vianna N. Le
- Department of Chemical and Materials EngineeringDepartment of Electrical EngineeringCentre for Applied Energy ResearchUniversity of KentuckyLexingtonKY40506USA
| | - Joel H. Bombile
- Department of Chemistryand Centre for Applied Energy ResearchUniversity of KentuckyLexingtonKY40506USA
| | - Gehan S. Rupasinghe
- Department of Chemical and Materials EngineeringDepartment of Electrical EngineeringCentre for Applied Energy ResearchUniversity of KentuckyLexingtonKY40506USA
| | - Kyle N. Baustert
- Department of ChemistryUniversity of KentuckyLexingtonKY40506USA
| | | | - Iuliana P. Maria
- Department of ChemistryChemistry Research LaboratoryUniversity of OxfordOxfordOX1 3TAUK
| | - Maryam Shahi
- Department of Chemical and Materials EngineeringDepartment of Electrical EngineeringCentre for Applied Energy ResearchUniversity of KentuckyLexingtonKY40506USA
| | - Paula Alarcon Espejo
- Department of Chemical and Materials EngineeringDepartment of Electrical EngineeringCentre for Applied Energy ResearchUniversity of KentuckyLexingtonKY40506USA
| | - Iain McCulloch
- Department of ChemistryChemistry Research LaboratoryUniversity of OxfordOxfordOX1 3TAUK
- King Abdullah University of Science and TechnologyKAUST Solar CentreThuwal23955‐6900Saudi Arabia
| | | | - Chad Risko
- Department of Chemistryand Centre for Applied Energy ResearchUniversity of KentuckyLexingtonKY40506USA
| | - Alexandra F. Paterson
- Department of Chemical and Materials EngineeringDepartment of Electrical EngineeringCentre for Applied Energy ResearchUniversity of KentuckyLexingtonKY40506USA
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