1
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Wu DT, Zhu WX, Dong Y, Daboczi M, Ham G, Hsieh HJ, Huang CJ, Xu W, Henderson C, Kim JS, Eslava S, Cha H, Macdonald TJ, Lin CT. Enhancing the Efficiency and Stability of Tin-Lead Perovskite Solar Cells via Sodium Hydroxide Dedoping of PEDOT:PSS. Small Methods 2024:e2400302. [PMID: 38634222 DOI: 10.1002/smtd.202400302] [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: 04/01/2024] [Revised: 04/09/2024] [Indexed: 04/19/2024]
Abstract
Tin-lead (Sn-Pb) perovskite solar cells (PSCs) have gained interest as candidates for the bottom cell of all-perovskite tandem solar cells due to their broad absorption of the solar spectrum. A notable challenge arises from the prevalent use of the hole transport layer, PEDOT:PSS, known for its inherently high doping level. This high doping level can lead to interfacial recombination, imposing a significant limitation on efficiency. Herein, NaOH is used to dedope PEDOT:PSS, with the aim of enhancing the efficiency of Sn-Pb PSCs. Secondary ion mass spectrometer profiles indicate that sodium ions diffuse into the perovskite layer, improving its crystallinity and enlarging its grains. Comprehensive evaluations, including photoluminescence and nanosecond transient absorption spectroscopy, confirm that dedoping significantly reduces interfacial recombination, resulting in an open-circuit voltage as high as 0.90 V. Additionally, dedoping PEDOT:PSS leads to increased shunt resistance and high fill factor up to 0.81. As a result of these improvements, the power conversion efficiency is enhanced from 19.7% to 22.6%. Utilizing NaOH to dedope PEDOT:PSS also transitions its nature from acidic to basic, enhancing stability and exhibiting less than a 7% power conversion efficiency loss after 1176 h of storage in N2 atmosphere.
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Affiliation(s)
- Dong-Tai Wu
- Department of Chemical Engineering, National Chung Hsing University, 145 Xingda Road, Taichung, 402-27, Taiwan
| | - Wen-Xian Zhu
- Department of Chemical Engineering, National Chung Hsing University, 145 Xingda Road, Taichung, 402-27, Taiwan
| | - Yueyao Dong
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Matyas Daboczi
- Department of Chemical Engineering and Centre for Processable Electronics, Imperial College London, London, SW7 2AZ, UK
| | - Gayoung Ham
- Department of Energy Convergence and Climate Change, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hsing-Jung Hsieh
- Department of Chemical Engineering, National Chung Hsing University, 145 Xingda Road, Taichung, 402-27, Taiwan
| | - Chi-Jing Huang
- Department of Chemical Engineering, National Chung Hsing University, 145 Xingda Road, Taichung, 402-27, Taiwan
| | - Weidong Xu
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Charlie Henderson
- Department of Physics and Centre for Processable Electronics, Imperial College London, London, SW7 2AZ, UK
| | - Ji-Seon Kim
- Department of Physics and Centre for Processable Electronics, Imperial College London, London, SW7 2AZ, UK
| | - Salvador Eslava
- Department of Chemical Engineering and Centre for Processable Electronics, Imperial College London, London, SW7 2AZ, UK
| | - Hyojung Cha
- Department of Energy Convergence and Climate Change, Kyungpook National University, Daegu, 41566, Republic of Korea
- Department of Hydrogen and Renewable Energy, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Thomas J Macdonald
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Chieh-Ting Lin
- Department of Chemical Engineering, National Chung Hsing University, 145 Xingda Road, Taichung, 402-27, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung City, 402, Taiwan
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2
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Lomax DR, de la Salle P, Perillo M, Reynolds J, Reynolds R, Waldron JF. The last giants: New evidence for giant Late Triassic (Rhaetian) ichthyosaurs from the UK. PLoS One 2024; 19:e0300289. [PMID: 38630678 PMCID: PMC11023487 DOI: 10.1371/journal.pone.0300289] [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: 11/19/2023] [Accepted: 02/24/2024] [Indexed: 04/19/2024] Open
Abstract
Giant ichthyosaurs with body length estimates exceeding 20 m were present in the latest Triassic of the UK. Here we report on the discovery of a second surangular from the lower jaw of a giant ichthyosaur from Somerset, UK. The new find is comparable in size and morphology to a specimen from Lilstock, Somerset, described in 2018, but it is more complete and better preserved. Both finds are from the uppermost Triassic Westbury Mudstone Formation (Rhaetian), but the new specimen comes from Blue Anchor, approximately 10 km west along the coast from Lilstock. The more complete surangular would have been >2 m long, from an individual with a body length estimated at ~25 m. The identification of two specimens with the same unique morphology and from the same geologic age and geographic location warrants the erection of a new genus and species, Ichthyotitan severnensis gen. et sp. nov. Thin sections of the new specimen revealed the same histological features already observed in similar giant ichthyosaurian specimens. Our data also supports the previous suggestion of an atypical osteogenesis in the lower jaws of giant ichthyosaurs. The geological age and giant size of the specimens suggest shastasaurid affinities, but the material is too incomplete for a definitive referral. Ichthyotitan severnensis gen. et sp. nov., is the first-named giant ichthyosaur from the Rhaetian and probably represents the largest marine reptile formally described.
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Affiliation(s)
- Dean R. Lomax
- Palaeobiology Research Group, School of Earth Sciences, University of Bristol, Bristol, United Kingdom
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
| | - Paul de la Salle
- The Etches Collection – Museum of Jurassic Marine Life, Dorset, United Kingdom
| | - Marcello Perillo
- Paleontology division, Institute of Geosciences, University of Bonn, Bonn, Germany
| | | | | | - James F. Waldron
- Dinosaurs Will Always Be Awesome, DWABA Museum, Orlando, Florida, United States of America
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3
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Lee JR, Shaw JD, Ropert-Coudert Y, Terauds A, Chown SL. Conservation features of the terrestrial Antarctic Peninsula. Ambio 2024:10.1007/s13280-024-02009-4. [PMID: 38589654 DOI: 10.1007/s13280-024-02009-4] [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] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/02/2024] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
Conserving landscapes used by multiple stakeholder groups requires understanding of what each stakeholder values. Here we employed a semi-structured, participatory approach to identify features of value in the terrestrial Antarctic Peninsula related to biodiversity, science and tourism. Stakeholders identified 115 features, ranging from Adélie penguin colonies to sites suitable for snowshoeing tourists. We split the features into seven broad categories: science, tourism, historic, biodiversity, geographic, habitat, and intrinsic features, finding that the biodiversity category contained the most features of any one category, while science stakeholders identified the most features of any stakeholder group. Stakeholders have overlapping interests in some features, particularly for seals and seabirds, indicating that thoughtful consideration of their inclusion in future management is required. Acknowledging the importance of tourism and other social features in Antarctica and ensuring their integration into conservation planning and assessment will increase the likelihood of implementing successful environmental management strategies into the future.
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Affiliation(s)
- Jasmine R Lee
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia.
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
- Securing Antarctica's Environmental Future, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia.
| | - Justine D Shaw
- Securing Antarctica's Environmental Future, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - Yan Ropert-Coudert
- Centre d'Etudes Biologiques de Chizé, UMR 7372, La Rochelle Université - CNRS, 79360, Villiers en Bois, France
| | - Aleks Terauds
- Securing Antarctica's Environmental Future, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia
- Integrated Digital East Antarctic Program, Australian Antarctic Division, Department of Climate Change, the Environment, Energy and Water, Kingston, TAS, 7050, Australia
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
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4
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Foffa D, Nesbitt SJ, Butler RJ, Brusatte SL, Walsh S, Fraser NC, Barrett PM. The osteology of the Late Triassic reptile Scleromochlus taylori from μCT data. Anat Rec (Hoboken) 2024; 307:1113-1146. [PMID: 37846180 DOI: 10.1002/ar.25335] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/10/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023]
Abstract
Scleromochlus taylori is one of the most enigmatic members of the herpetofauna from the Lossiemouth Sandstone Formation (Upper Triassic) of Elgin (Moray, Scotland). For many years it was thought to be closely related to pterosaurs and dinosaurs, but the anatomy of this animal is difficult to interpret because of the notoriously poor preservation of the six available specimens, which comprise void space in the sandstone after the bones were destroyed by diagenesis. Historically, these fossils have been studied using physical molds, which provide only incomplete, and potentially distorted, information. Due to these uncertainties, interpretations of the anatomy, phylogenetic relationships, and paleobiology of Scleromochlus taylori have remained contentious. Here, we use microcomputed tomographic (μCT) techniques to redescribe and illustrate the osteology of Scleromochlus in detail, building upon a short redescription of keystone features of the anatomy that we recently published. We digitally visualize, describe, and figure previously inaccessible-and thus unaltered-portions of its skeleton, as well as providing new observations on the exposed parts of each specimen. This work reveals many novel features of the skull, mandible, trunk, tail, girdles, forelimb, and hindlimb (particularly of the manus, femur, and pes), demonstrating that historic molding techniques failed, in some cases, to accurately capture the anatomy of Scleromochlus. Our review sheds light on some of the most controversial aspects of Scleromochlus morphology showing that this taxon retains plesiomorphic features of Avemetatarsalia in the postcranial skeleton, alongside a suite of synapomorphies diagnostic of pterosauromorphs (the broad clade of pterosaurs and taxa more closely related to them than dinosaurs), particularly one subgroup, the lagerpetids. Consistent with recent work, our updated phylogenetic analyses (Maximum Parsimony and Bayesian Inference) demonstrate that Scleromochlus taylori is an avemetatarsalian archosaur that is recovered firmly in an early diverging position within Pterosauromorpha, as a member of Lagerpetidae, thus shedding important information on the origin of pterosaurs, the first group of vertebrates to evolve powered flight.
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Affiliation(s)
- Davide Foffa
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
- Department of Geosciences, Virginia Tech, Blacksburg, Virginia, USA
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | | | - Richard J Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Stephen L Brusatte
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
- School of GeoSciences, University of Edinburgh, Grant Institute, Edinburgh, UK
| | - Stig Walsh
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
- School of GeoSciences, University of Edinburgh, Grant Institute, Edinburgh, UK
| | - Nicholas C Fraser
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
- School of GeoSciences, University of Edinburgh, Grant Institute, Edinburgh, UK
| | - Paul M Barrett
- Fossil Reptiles, Amphibians and Birds Section, Natural History Museum, London, UK
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5
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Manentzos AN, Pahl AMC, Melloh P, Martin EA, Leybourne DJ. Low prevalence of secondary endosymbionts in aphids sampled from rapeseed crops in Germany. Bull Entomol Res 2024:1-6. [PMID: 38444236 DOI: 10.1017/s0007485324000063] [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] [Indexed: 03/07/2024]
Abstract
Peach-potato aphids, Myzus persicae Sulzer (Hemiptera:Aphididae), and cabbage aphids, Brevicoryne brassicae Linnaeus (Hemiptera:Aphididae), are herbivorous insects of significant agricultural importance. Aphids can harbour a range of non-essential (facultative) endosymbiotic bacteria that confer multiple costs and benefits to the host aphid. A key endosymbiont-derived phenotype is protection against parasitoid wasps, and this protective phenotype has been associated with several defensive enodsymbionts. In recent years greater emphasis has been placed on developing alternative pest management strategies, including the increased use of natural enemies such as parasitoids wasps. For the success of aphid control strategies to be estimated the presence of defensive endosymbionts that can potentially disrupt the success of biocontrol agents needs to be determined in natural aphid populations. Here, we sampled aphids and mummies (parasitised aphids) from an important rapeseed production region in Germany and used multiplex PCR assays to characterise the endosymbiont communities. We found that aphids rarely harboured facultative endosymbionts, with 3.6% of M. persicae and 0% of B. brassicae populations forming facultative endosymbiont associations. This is comparable with endosymbiont prevalence described for M. persicae populations surveyed in Australia, Europe, Chile, and USA where endosymbiont infection frequencies range form 0-2%, but is in contrast with observations from China where M. persicae populations have more abundant and diverse endosymbiotic communities (endosymbionts present in over 50% of aphid populations).
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Affiliation(s)
- A N Manentzos
- Zoological Biodiversity, Institute of Geobotany, Gottfried Wilhelm Leibniz University Hannover, Hannover, Germany
| | - A M C Pahl
- Zoological Biodiversity, Institute of Geobotany, Gottfried Wilhelm Leibniz University Hannover, Hannover, Germany
| | - P Melloh
- Zoological Biodiversity, Institute of Geobotany, Gottfried Wilhelm Leibniz University Hannover, Hannover, Germany
| | - E A Martin
- Animal Ecology, Institute of Animal Ecology and Systematics, Justus Liebig University of Gießen, Gießen, Germany
| | - D J Leybourne
- Department of Evolution, Ecology, and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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Oldroyd P, Oldroyd S, Meng M, Makwana R, Sanger G, Bulmer D, Malliaras GG, Owens RM. Stretchable Device for Simultaneous Measurements of Contractility and Electrophysiology of Neuromuscular Tissue in the Gastrointestinal Tract. Adv Mater 2024:e2312735. [PMID: 38290128 DOI: 10.1002/adma.202312735] [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: 11/26/2023] [Revised: 01/15/2024] [Indexed: 02/01/2024]
Abstract
Devices interfacing with biological tissues can provide valuable insights into function, disease, and metabolism through electrical and mechanical signals. However, certain neuromuscular tissues, like those in the gastrointestinal tract, undergo significant strains of up to 40%. Conventional inextensible devices cannot capture the dynamic responses in these tissues. This study introduces electrodes made from poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) and polydimethylsiloxane (PDMS) that enable simultaneous monitoring of electrical and mechanical responses of gut tissue. The soft PDMS layers conform to tissue surfaces during gastrointestinal movement. Dopants, including Capstone FS-30 and polyethylene glycol, are explored to enhance the conductivity, electrical sensitivity to strain, and stability of the PEDOT:PSS. The devices are fabricated using shadow masks and solution-processing techniques, providing a faster and simpler process than traditional clean-room-based lithography. Tested on ex vivo mouse colon and human stomach, the device recorded voltage changes of up to 300 µV during contraction and distension consistent with muscle activity, while simultaneously recording resistance changes of up to 150% due to mechanical strain. These devices detect and respond to chemical stimulants and blockers, and can induce contractions through electrical stimulation. They hold great potential for studying and treating complex disorders like irritable bowel syndrome and gastroparesis.
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Affiliation(s)
- Poppy Oldroyd
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Sophie Oldroyd
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Michelle Meng
- Department of Pharmacology, Tennis Ct Rd, University of Cambridge, Cambridge, CB2 1PD, UK
| | - Rajesh Makwana
- Blizard Institute, Queen Mary University of London, Cambridge, E1 2AT, UK
| | - Gareth Sanger
- Blizard Institute, Queen Mary University of London, Cambridge, E1 2AT, UK
| | - David Bulmer
- Department of Pharmacology, Tennis Ct Rd, University of Cambridge, Cambridge, CB2 1PD, UK
| | - George G Malliaras
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Róisín M Owens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
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7
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Krause AL, Gaffney EA, Jewell TJ, Klika V, Walker BJ. Turing Instabilities are Not Enough to Ensure Pattern Formation. Bull Math Biol 2024; 86:21. [PMID: 38253936 PMCID: PMC10803432 DOI: 10.1007/s11538-023-01250-4] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024]
Abstract
Symmetry-breaking instabilities play an important role in understanding the mechanisms underlying the diversity of patterns observed in nature, such as in Turing's reaction-diffusion theory, which connects cellular signalling and transport with the development of growth and form. Extensive literature focuses on the linear stability analysis of homogeneous equilibria in these systems, culminating in a set of conditions for transport-driven instabilities that are commonly presumed to initiate self-organisation. We demonstrate that a selection of simple, canonical transport models with only mild multistable non-linearities can satisfy the Turing instability conditions while also robustly exhibiting only transient patterns. Hence, a Turing-like instability is insufficient for the existence of a patterned state. While it is known that linear theory can fail to predict the formation of patterns, we demonstrate that such failures can appear robustly in systems with multiple stable homogeneous equilibria. Given that biological systems such as gene regulatory networks and spatially distributed ecosystems often exhibit a high degree of multistability and nonlinearity, this raises important questions of how to analyse prospective mechanisms for self-organisation.
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Affiliation(s)
- Andrew L Krause
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, UK.
| | - Eamonn A Gaffney
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, OX2 6GG, UK
| | - Thomas Jun Jewell
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, OX2 6GG, UK
| | - Václav Klika
- Department of Mathematics, FNSPE, Czech Technical University in Prague, Trojanova 13, 120 00, Prague, Czech Republic
| | - Benjamin J Walker
- Department of Mathematical Sciences, University of Bath, Bath, BA2 7AY, UK
- Department of Mathematics, University College London, London, WC1E 6BT, UK
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8
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Lyons A, Zickus V, Álvarez-Mendoza R, Triggiani D, Tamma V, Westerberg N, Tassieri M, Faccio D. Fluorescence lifetime Hong-Ou-Mandel sensing. Nat Commun 2023; 14:8005. [PMID: 38049423 PMCID: PMC10696080 DOI: 10.1038/s41467-023-43868-x] [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: 05/24/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
Fluorescence Lifetime Imaging Microscopy in the time domain is typically performed by recording the arrival time of photons either by using electronic time tagging or a gated detector. As such the temporal resolution is limited by the performance of the electronics to 100's of picoseconds. Here, we demonstrate a fluorescence lifetime measurement technique based on photon-bunching statistics with a resolution that is only dependent on the duration of the reference photon or laser pulse, which can readily reach the 1-0.1 picosecond timescale. A range of fluorescent dyes having lifetimes spanning from 1.6 to 7 picoseconds have been here measured with only ~1 s measurement duration. We corroborate the effectiveness of the technique by measuring the Newtonian viscosity of glycerol/water mixtures by means of a molecular rotor having over an order of magnitude variability in lifetime, thus introducing a new method for contact-free nanorheology. Accessing fluorescence lifetime information at such high temporal resolution opens a doorway for a wide range of fluorescent markers to be adopted for studying yet unexplored fast biological processes, as well as fundamental interactions such as lifetime shortening in resonant plasmonic devices.
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Affiliation(s)
- Ashley Lyons
- School of Physics and Astronomy, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Vytautas Zickus
- School of Physics and Astronomy, University of Glasgow, Glasgow, G12 8QQ, UK
- Department of Laser Technologies, Center for Physical Sciences and Technology, LT-10257, Vilnius, Lithuania
| | | | - Danilo Triggiani
- School of Mathematics and Physics, University of Portsmouth, Portsmouth, PO1 3QL, UK
| | - Vincenzo Tamma
- School of Mathematics and Physics, University of Portsmouth, Portsmouth, PO1 3QL, UK
- Institute of Cosmology and Gravitation, University of Portsmouth, Portsmouth, PO1 3FX, UK
| | - Niclas Westerberg
- School of Physics and Astronomy, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Manlio Tassieri
- James Watt School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Daniele Faccio
- School of Physics and Astronomy, University of Glasgow, Glasgow, G12 8QQ, UK.
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9
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Corner TP, Teo RZR, Wu Y, Salah E, Nakashima Y, Fiorini G, Tumber A, Brasnett A, Holt-Martyn JP, Figg WD, Zhang X, Brewitz L, Schofield CJ. Structure-guided optimisation of N-hydroxythiazole-derived inhibitors of factor inhibiting hypoxia-inducible factor-α. Chem Sci 2023; 14:12098-12120. [PMID: 37969593 PMCID: PMC10631261 DOI: 10.1039/d3sc04253g] [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: 08/14/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023] Open
Abstract
The human 2-oxoglutarate (2OG)- and Fe(ii)-dependent oxygenases factor inhibiting hypoxia-inducible factor-α (FIH) and HIF-α prolyl residue hydroxylases 1-3 (PHD1-3) regulate the response to hypoxia in humans via catalysing hydroxylation of the α-subunits of the hypoxia-inducible factors (HIFs). Small-molecule PHD inhibitors are used for anaemia treatment; by contrast, few selective inhibitors of FIH have been reported, despite their potential to regulate the hypoxic response, either alone or in combination with PHD inhibition. We report molecular, biophysical, and cellular evidence that the N-hydroxythiazole scaffold, reported to inhibit PHD2, is a useful broad spectrum 2OG oxygenase inhibitor scaffold, the inhibition potential of which can be tuned to achieve selective FIH inhibition. Structure-guided optimisation resulted in the discovery of N-hydroxythiazole derivatives that manifest substantially improved selectivity for FIH inhibition over PHD2 and other 2OG oxygenases, including Jumonji-C domain-containing protein 5 (∼25-fold), aspartate/asparagine-β-hydroxylase (>100-fold) and histone Nε-lysine demethylase 4A (>300-fold). The optimised N-hydroxythiazole-based FIH inhibitors modulate the expression of FIH-dependent HIF target genes and, consistent with reports that FIH regulates cellular metabolism, suppressed lipid accumulation in adipocytes. Crystallographic studies reveal that the N-hydroxythiazole derivatives compete with both 2OG and the substrate for binding to the FIH active site. Derivatisation of the N-hydroxythiazole scaffold has the potential to afford selective inhibitors for 2OG oxygenases other than FIH.
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Affiliation(s)
- Thomas P Corner
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Ryan Z R Teo
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Yue Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization and Department of Chemistry, China Pharmaceutical University Nanjing 211198 China
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Yu Nakashima
- Institute of Natural Medicine, University of Toyama 2630-Sugitani 930-0194 Toyama Japan
| | - Giorgia Fiorini
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Amelia Brasnett
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - James P Holt-Martyn
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - William D Figg
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Xiaojin Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization and Department of Chemistry, China Pharmaceutical University Nanjing 211198 China
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
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10
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Walker BJ, Townsend AK, Chudasama AK, Krause AL. VisualPDE: Rapid Interactive Simulations of Partial Differential Equations. Bull Math Biol 2023; 85:113. [PMID: 37823924 PMCID: PMC10570185 DOI: 10.1007/s11538-023-01218-4] [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: 08/02/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Computing has revolutionised the study of complex nonlinear systems, both by allowing us to solve previously intractable models and through the ability to visualise solutions in different ways. Using ubiquitous computing infrastructure, we provide a means to go one step further in using computers to understand complex models through instantaneous and interactive exploration. This ubiquitous infrastructure has enormous potential in education, outreach and research. Here, we present VisualPDE, an online, interactive solver for a broad class of 1D and 2D partial differential equation (PDE) systems. Abstract dynamical systems concepts such as symmetry-breaking instabilities, subcritical bifurcations and the role of initial data in multistable nonlinear models become much more intuitive when you can play with these models yourself, and immediately answer questions about how the system responds to changes in parameters, initial conditions, boundary conditions or even spatiotemporal forcing. Importantly, VisualPDE is freely available, open source and highly customisable. We give several examples in teaching, research and knowledge exchange, providing high-level discussions of how it may be employed in different settings. This includes designing web-based course materials structured around interactive simulations, or easily crafting specific simulations that can be shared with students or collaborators via a simple URL. We envisage VisualPDE becoming an invaluable resource for teaching and research in mathematical biology and beyond. We also hope that it inspires other efforts to make mathematics more interactive and accessible.
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Affiliation(s)
- Benjamin J Walker
- Department of Mathematical Sciences, University of Bath, Bath, BA2 7AY, UK
- Department of Mathematics, University College London, London, WC1E 6BT, UK
| | - Adam K Townsend
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, UK
| | - Alexander K Chudasama
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, UK
| | - Andrew L Krause
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, UK.
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11
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Liu HY, Hill MS, Mahon MF, McMullin CL, Schwamm RJ. Seven-Membered Cyclic Diamidoalumanyls of Heavier Alkali Metals: Structures and C-H Activation of Arenes. Organometallics 2023; 42:2881-2892. [PMID: 37829511 PMCID: PMC10565898 DOI: 10.1021/acs.organomet.3c00323] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Indexed: 10/14/2023]
Abstract
Like the previously reported potassium-based system, rubidium and cesium reduction of [{SiNDipp}AlI] ({SiNDipp} = {CH2SiMe2NDipp}2) with the heavier alkali metals [M = Rb and Cs] provides dimeric group 1 alumanyl derivatives, [{SiNDipp}AlM]2. In contrast, similar treatment with sodium results in over-reduction and incorporation of a formal equivalent of [{SiNDipp}Na2] into the resultant sodium alumanyl species. The dimeric K, Rb, and Cs compounds display a variable efficacy toward the C-H oxidative addition of arene C-H bonds at elevated temperatures (Cs > Rb > K, 110 °C) to yield (hydrido)(organo)aluminate species. Consistent with the synthetic experimental observations, computational (DFT) assessment of the benzene C-H activation indicates that rate-determining attack of the Al(I) nucleophile within the dimeric species is facilitated by π-engagement of the arene with the electrophilic M+ cation, which becomes increasingly favorable as group 1 is descended.
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Affiliation(s)
- Han-Ying Liu
- Department of Chemistry, University
of Bath, Claverton
Down, Bath BA2 7AY, U.K.
| | - Michael S. Hill
- Department of Chemistry, University
of Bath, Claverton
Down, Bath BA2 7AY, U.K.
| | - Mary F. Mahon
- Department of Chemistry, University
of Bath, Claverton
Down, Bath BA2 7AY, U.K.
| | - Claire L. McMullin
- Department of Chemistry, University
of Bath, Claverton
Down, Bath BA2 7AY, U.K.
| | - Ryan J. Schwamm
- Department of Chemistry, University
of Bath, Claverton
Down, Bath BA2 7AY, U.K.
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12
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Kerr R, Macdonald TJ, Tanner AJ, Yu J, Davies JA, Fielding HH, Thornton G. Zero Threshold for Water Adsorption on MAPbBr 3. Small 2023; 19:e2301014. [PMID: 37267942 DOI: 10.1002/smll.202301014] [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: 02/04/2023] [Revised: 04/19/2023] [Indexed: 06/04/2023]
Abstract
Hybrid organic-inorganic perovskites (HOIPs) have shown great promise in a wide range of optoelectronic applications. However, this performance is inhibited by the sensitivity of HOIPs to various environmental factors, particularly high levels of relative humidity. This study uses X-ray photoelectron spectroscopy (XPS) to determine that there is essentially no threshold to water adsorption on the in situ cleaved MAPbBr3 (001) single crystal surface. Using scanning tunneling microscopy (STM), it shows that the initial surface restructuring upon exposure to water vapor occurs in isolated regions, which grow in area with increasing exposure, providing insight into the initial degradation mechanism of HOIPs. The electronic structure evolution of the surface was also monitored via ultraviolet photoemission spectroscopy (UPS), evidencing an increased bandgap state density following water vapor exposure, which is attributed to surface defect formation due to lattice swelling. This study will help to inform the surface engineering and designs of future perovskite-based optoelectronic devices.
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Affiliation(s)
- Robin Kerr
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
| | - Thomas J Macdonald
- Department of Chemistry & Centre for Processable Electronics, Imperial College London, London, W12 0BZ, UK
- School of Engineering & Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Alex J Tanner
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
| | - Jiangdong Yu
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
| | - Julia A Davies
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
| | - Helen H Fielding
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
| | - Geoff Thornton
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
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13
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Naritsuka M, Benedičič I, Rhodes LC, Marques CA, Trainer C, Li Z, Komarek AC, Wahl P. Compass-like manipulation of electronic nematicity in Sr 3Ru 2O 7. Proc Natl Acad Sci U S A 2023; 120:e2308972120. [PMID: 37639583 PMCID: PMC10483601 DOI: 10.1073/pnas.2308972120] [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: 05/28/2023] [Accepted: 07/26/2023] [Indexed: 08/31/2023] Open
Abstract
Electronic nematicity has been found in a wide range of strongly correlated electron materials, resulting in the electronic states having-4.5pc]Please note that the spelling of the following author name(s) in the manuscript differs from the spelling provided in the article metadata: Izidor Benedičič. The spelling provided in the manuscript has been retained; please confirm. a symmetry that is lower than that of the crystal that hosts them. One of the most astonishing examples is [Formula: see text], in which a small in-plane component of a magnetic field induces significant resistivity anisotropy. The direction of this anisotropy follows the direction of the in-plane field. The microscopic origin of this field-induced nematicity has been a long-standing puzzle, with recent experiments suggesting a field-induced spin density wave driving the anisotropy. Here, we report spectroscopic imaging of a field-controlled anisotropy of the electronic structure at the surface of [Formula: see text]. We track the electronic structure as a function of the direction of the field, revealing a continuous change with the angle. This continuous evolution suggests a mechanism based on spin-orbit coupling resulting in compass-like control of the electronic bands. The anisotropy of the electronic structure persists to temperatures about an order of magnitude higher compared to the bulk, demonstrating novel routes to stabilize such phases over a wider temperature range.
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Affiliation(s)
- Masahiro Naritsuka
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS, United Kingdom
| | - Izidor Benedičič
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS, United Kingdom
| | - Luke C. Rhodes
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS, United Kingdom
| | - Carolina A. Marques
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS, United Kingdom
| | - Christopher Trainer
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS, United Kingdom
| | - Zhiwei Li
- Max Planck Institute for Chemical Physics of Solids, Dresden01187, Germany
| | | | - Peter Wahl
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS, United Kingdom
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14
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Keene ST, Laulainen JEM, Pandya R, Moser M, Schnedermann C, Midgley PA, McCulloch I, Rao A, Malliaras GG. Hole-limited electrochemical doping in conjugated polymers. Nat Mater 2023; 22:1121-1127. [PMID: 37414944 PMCID: PMC10465356 DOI: 10.1038/s41563-023-01601-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
Simultaneous transport and coupling of ionic and electronic charges is fundamental to electrochemical devices used in energy storage and conversion, neuromorphic computing and bioelectronics. While the mixed conductors enabling these technologies are widely used, the dynamic relationship between ionic and electronic transport is generally poorly understood, hindering the rational design of new materials. In semiconducting electrodes, electrochemical doping is assumed to be limited by motion of ions due to their large mass compared to electrons and/or holes. Here, we show that this basic assumption does not hold for conjugated polymer electrodes. Using operando optical microscopy, we reveal that electrochemical doping speeds in a state-of-the-art polythiophene can be limited by poor hole transport at low doping levels, leading to substantially slower switching speeds than expected. We show that the timescale of hole-limited doping can be controlled by the degree of microstructural heterogeneity, enabling the design of conjugated polymers with improved electrochemical performance.
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Affiliation(s)
- Scott T Keene
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | | | - Raj Pandya
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Laboratoire Kastler Brossel, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Collège de France, Paris, France
| | | | | | - Paul A Midgley
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, UK
| | - Iain McCulloch
- Department of Chemistry, University of Oxford, Oxford, UK
- KAUST Solar Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Akshay Rao
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - George G Malliaras
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge, UK.
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15
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Zhang FF, Aw E, Eaton AG, Shutt RRC, Lim J, Kim JH, Macdonald TJ, Reyes CIIIDL, Ashoka A, Pandya R, Payton OD, Picco L, Knapp CE, Corà F, Rao A, Howard CA, Clancy AJ. Production of Magnetic Arsenic-Phosphorus Alloy Nanoribbons with Small Band Gaps and High Hole Conductivities. J Am Chem Soc 2023; 145:18286-18295. [PMID: 37551934 PMCID: PMC10450688 DOI: 10.1021/jacs.3c03230] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Indexed: 08/09/2023]
Abstract
Quasi-1D nanoribbons provide a unique route to diversifying the properties of their parent 2D nanomaterial, introducing lateral quantum confinement and an abundance of edge sites. Here, a new family of nanomaterials is opened with the creation of arsenic-phosphorus alloy nanoribbons (AsPNRs). By ionically etching the layered crystal black arsenic-phosphorus using lithium electride followed by dissolution in amidic solvents, solutions of AsPNRs are formed. The ribbons are typically few-layered, several micrometers long with widths tens of nanometers across, and both highly flexible and crystalline. The AsPNRs are highly electrically conducting above 130 K due to their small band gap (ca. 0.035 eV), paramagnetic in nature, and have high hole mobilities, as measured with the first generation of AsP devices, directly highlighting their properties and utility in electronic devices such as near-infrared detectors, quantum computing, and charge carrier layers in solar cells.
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Affiliation(s)
- Feng Fei Zhang
- Department
of Chemistry, University College London, London WC1E 6BT, U.K.
- Department
of Physics and Astronomy, University College
London, London WC1E 6BT, U.K.
| | - Eva Aw
- Department
of Physics and Astronomy, University College
London, London WC1E 6BT, U.K.
| | - Alexander G. Eaton
- Cavendish
Laboratory, Department of Physics University
of Cambridge, Cambridge CB3 0HE, U.K.
| | - Rebecca R. C. Shutt
- Department
of Physics and Astronomy, University College
London, London WC1E 6BT, U.K.
| | - Juhwan Lim
- Cavendish
Laboratory, Department of Physics University
of Cambridge, Cambridge CB3 0HE, U.K.
| | - Jung Ho Kim
- Department
of Materials Science and Metallurgy, University
of Cambridge, Cambridge CB3 0FS, U.K.
| | - Thomas J. Macdonald
- School
of Engineering and Materials Science, Queen
Mary University of London, London E1 4NS, U.K.
| | | | - Arjun Ashoka
- Cavendish
Laboratory, Department of Physics University
of Cambridge, Cambridge CB3 0HE, U.K.
| | - Raj Pandya
- Cavendish
Laboratory, Department of Physics University
of Cambridge, Cambridge CB3 0HE, U.K.
- Laboratoire
Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 rue Lhomond, 75005 Paris, France
| | - Oliver D. Payton
- Interface
Analysis Centre, H. H. Wills Physics Laboratory, University of Bristol, Bristol, BS8 1TL, U.K.
| | - Loren Picco
- Interface
Analysis Centre, H. H. Wills Physics Laboratory, University of Bristol, Bristol, BS8 1TL, U.K.
| | - Caroline E. Knapp
- Department
of Chemistry, University College London, London WC1E 6BT, U.K.
| | - Furio Corà
- Department
of Chemistry, University College London, London WC1E 6BT, U.K.
| | - Akshay Rao
- Cavendish
Laboratory, Department of Physics University
of Cambridge, Cambridge CB3 0HE, U.K.
| | - Christopher A. Howard
- Department
of Physics and Astronomy, University College
London, London WC1E 6BT, U.K.
| | - Adam J. Clancy
- Department
of Chemistry, University College London, London WC1E 6BT, U.K.
- Cavendish
Laboratory, Department of Physics University
of Cambridge, Cambridge CB3 0HE, U.K.
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16
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Brewitz L, Nakashima Y, Piasecka SK, Salah E, Fletcher SC, Tumber A, Corner TP, Kennedy TJ, Fiorini G, Thalhammer A, Christensen KE, Coleman ML, Schofield CJ. 5-Substituted Pyridine-2,4-dicarboxylate Derivatives Have Potential for Selective Inhibition of Human Jumonji-C Domain-Containing Protein 5. J Med Chem 2023; 66:10849-10865. [PMID: 37527664 PMCID: PMC10424186 DOI: 10.1021/acs.jmedchem.3c01114] [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: 06/20/2023] [Indexed: 08/03/2023]
Abstract
Jumonji-C domain-containing protein 5 (JMJD5) is a 2-oxoglutarate (2OG)-dependent oxygenase that plays important roles in development, circadian rhythm, and cancer through unclear mechanisms. JMJD5 has been reported to have activity as a histone protease, as an Nε-methyl lysine demethylase, and as an arginine residue hydroxylase. Small-molecule JMJD5-selective inhibitors will be useful for investigating its (patho)physiological roles. Following the observation that the broad-spectrum 2OG oxygenase inhibitor pyridine-2,4-dicarboxylic acid (2,4-PDCA) is a 2OG-competing JMJD5 inhibitor, we report that 5-aminoalkyl-substituted 2,4-PDCA derivatives are potent JMJD5 inhibitors manifesting selectivity for JMJD5 over other human 2OG oxygenases. Crystallographic analyses with five inhibitors imply induced fit binding and reveal that the 2,4-PDCA C5 substituent orients into the JMJD5 substrate-binding pocket. Cellular studies indicate that the lead compounds display similar phenotypes as reported for clinically observed JMJD5 variants, which have a reduced catalytic activity compared to wild-type JMJD5.
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Affiliation(s)
- Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Yu Nakashima
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Sonia K. Piasecka
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, B15 2TT Birmingham, U.K.
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Sally C. Fletcher
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, B15 2TT Birmingham, U.K.
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Thomas P. Corner
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Tristan J. Kennedy
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, B15 2TT Birmingham, U.K.
| | - Giorgia Fiorini
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Armin Thalhammer
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Kirsten E. Christensen
- Chemical
Crystallography, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
| | - Mathew L. Coleman
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, B15 2TT Birmingham, U.K.
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.
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17
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Couto A, Young FJ, Atzeni D, Marty S, Melo-Flórez L, Hebberecht L, Monllor M, Neal C, Cicconardi F, McMillan WO, Montgomery SH. Rapid expansion and visual specialisation of learning and memory centres in the brains of Heliconiini butterflies. Nat Commun 2023; 14:4024. [PMID: 37419890 PMCID: PMC10328955 DOI: 10.1038/s41467-023-39618-8] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 06/15/2023] [Indexed: 07/09/2023] Open
Abstract
Changes in the abundance and diversity of neural cell types, and their connectivity, shape brain composition and provide the substrate for behavioral evolution. Although investment in sensory brain regions is understood to be largely driven by the relative ecological importance of particular sensory modalities, how selective pressures impact the elaboration of integrative brain centers has been more difficult to pinpoint. Here, we provide evidence of extensive, mosaic expansion of an integration brain center among closely related species, which is not explained by changes in sites of primary sensory input. By building new datasets of neural traits among a tribe of diverse Neotropical butterflies, the Heliconiini, we detected several major evolutionary expansions of the mushroom bodies, central brain structures pivotal for insect learning and memory. The genus Heliconius, which exhibits a unique dietary innovation, pollen-feeding, and derived foraging behaviors reliant on spatial memory, shows the most extreme enlargement. This expansion is primarily associated with increased visual processing areas and coincides with increased precision of visual processing, and enhanced long term memory. These results demonstrate that selection for behavioral innovation and enhanced cognitive ability occurred through expansion and localized specialization in integrative brain centers.
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Affiliation(s)
- Antoine Couto
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Fletcher J Young
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Daniele Atzeni
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Life Science, University of Trieste, Trieste, Italy
| | - Simon Marty
- Department of Zoology, University of Cambridge, Cambridge, UK
- École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | | | - Laura Hebberecht
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | | | - Chris Neal
- Wolfson Bioimaging Facility, University of Bristol, Bristol, UK
| | | | | | - Stephen H Montgomery
- School of Biological Sciences, University of Bristol, Bristol, UK.
- Smithsonian Tropical Research Institute, Gamboa, Panama.
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18
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Young TR, Deery E, Foster AW, Martini MA, Osman D, Warren MJ, Robinson NJ. Two Distinct Thermodynamic Gradients for Cellular Metalation of Vitamin B 12. JACS Au 2023; 3:1472-1483. [PMID: 37234125 PMCID: PMC10206600 DOI: 10.1021/jacsau.3c00119] [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: 03/14/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
The acquisition of CoII by the corrin component of vitamin B12 follows one of two distinct pathways, referred to as early or late CoII insertion. The late insertion pathway exploits a CoII metallochaperone (CobW) from the COG0523 family of G3E GTPases, while the early insertion pathway does not. This provides an opportunity to contrast the thermodynamics of metalation in a metallochaperone-requiring and a metallochaperone-independent pathway. In the metallochaperone-independent route, sirohydrochlorin (SHC) associates with the CbiK chelatase to form CoII-SHC. CoII-buffered enzymatic assays indicate that SHC binding enhances the thermodynamic gradient for CoII transfer from the cytosol to CbiK. In the metallochaperone-dependent pathway, hydrogenobyrinic acid a,c-diamide (HBAD) associates with the CobNST chelatase to form CoII-HBAD. Here, CoII-buffered enzymatic assays indicate that CoII transfer from the cytosol to HBAD-CobNST must somehow traverse a highly unfavorable thermodynamic gradient for CoII binding. Notably, there is a favorable gradient for CoII transfer from the cytosol to the MgIIGTP-CobW metallochaperone, but further transfer of CoII from the GTP-bound metallochaperone to the HBAD-CobNST chelatase complex is thermodynamically unfavorable. However, after nucleotide hydrolysis, CoII transfer from the chaperone to the chelatase complex is calculated to become favorable. These data reveal that the CobW metallochaperone can overcome an unfavorable thermodynamic gradient for CoII transfer from the cytosol to the chelatase by coupling this process to GTP hydrolysis.
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Affiliation(s)
- Tessa R. Young
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Evelyne Deery
- School
of Biosciences, University of Kent, Canterbury CT2 7NJ, U.K.
| | - Andrew W. Foster
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Maria Alessandra Martini
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Inorganic Spectroscopy, Max Planck Institute
for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Deenah Osman
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Martin J. Warren
- School
of Biosciences, University of Kent, Canterbury CT2 7NJ, U.K.
- Quadram
Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, U.K.
| | - Nigel J. Robinson
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
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19
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Aynetdinova D, Jacques R, Christensen KE, Donohoe TJ. Alcohols as Efficient Intermolecular Initiators for a Highly Stereoselective Polyene Cyclisation Cascade. Chemistry 2023; 29:e202203732. [PMID: 36478469 PMCID: PMC10946764 DOI: 10.1002/chem.202203732] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
The use of benzylic and allylic alcohols in HFIP solvent together with Ti(Oi Pr)4 has been shown to trigger a highly stereoselective polyene cyclisation cascade. Three new carbon-carbon bonds are made during the process and complete stereocontrol of up to five new stereogenic centers is observed. The reaction is efficient, has high functional group tolerance and is atom-economic generating water as a stoichiometric by-product. A new polyene substrate-class is employed, and subsequent mechanistic studies indicate a stereoconvergent mechanism. The products of this reaction can be used to synthesize steroid-analogues in a single step.
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Affiliation(s)
- Daniya Aynetdinova
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryOxfordOX1 3TAUK
| | - Reece Jacques
- Early Chemical Development, Medicinal Chemistry R&DVertex PharmaceuticalsAbingtonOX14 4RWUK
| | | | - Timothy J. Donohoe
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryOxfordOX1 3TAUK
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20
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Andrews KG, Christensen KE. Access to Amide-Linked Organic Cages by in situ Trapping of Metastable Imine Assemblies: Solution Phase Bisamine Recognition. Chemistry 2023; 29:e202300063. [PMID: 36638051 DOI: 10.1002/chem.202300063] [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: 01/09/2023] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/14/2023]
Abstract
Molecular cages are sought after as receptors and catalysts. However, typical dynamic covalent chemistry approaches restrict the shape-persistence, solubility and stability of self-assembled organic cages. As a result, organic cages occupy a narrow chemical and functional space, and solution-phase applications and studies remain rare. We report an in situ trapping protocol, using Pinnick oxidation conditions, to convert soluble metastable imine assemblies to robust amide cages, and exemplify the method to access previously inaccessible organic cages. The new cages are internally functionalised with two constrained and diametrically opposed carboxylic acid groups that can distinguish between functionalised piperazines in THF. We anticipate our approach will broaden access to robust, soluble, self-assembled organic cages of an unsymmetrical or semi-flexible nature, which in turn will drive advances in solution-phase applications of molecular cages.
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Affiliation(s)
- Keith G Andrews
- Department of Chemistry, University of Oxford, 12 Mansfield Rd, Oxford, OX1 3TA, UK
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21
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Krause AL, Gaffney EA, Walker BJ. Concentration-Dependent Domain Evolution in Reaction-Diffusion Systems. Bull Math Biol 2023; 85:14. [PMID: 36637542 PMCID: PMC9839823 DOI: 10.1007/s11538-022-01115-2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/24/2022] [Indexed: 01/14/2023]
Abstract
Pattern formation has been extensively studied in the context of evolving (time-dependent) domains in recent years, with domain growth implicated in ameliorating problems of pattern robustness and selection, in addition to more realistic modelling in developmental biology. Most work to date has considered prescribed domains evolving as given functions of time, but not the scenario of concentration-dependent dynamics, which is also highly relevant in a developmental setting. Here, we study such concentration-dependent domain evolution for reaction-diffusion systems to elucidate fundamental aspects of these more complex models. We pose a general form of one-dimensional domain evolution and extend this to N-dimensional manifolds under mild constitutive assumptions in lieu of developing a full tissue-mechanical model. In the 1D case, we are able to extend linear stability analysis around homogeneous equilibria, though this is of limited utility in understanding complex pattern dynamics in fast growth regimes. We numerically demonstrate a variety of dynamical behaviours in 1D and 2D planar geometries, giving rise to several new phenomena, especially near regimes of critical bifurcation boundaries such as peak-splitting instabilities. For sufficiently fast growth and contraction, concentration-dependence can have an enormous impact on the nonlinear dynamics of the system both qualitatively and quantitatively. We highlight crucial differences between 1D evolution and higher-dimensional models, explaining obstructions for linear analysis and underscoring the importance of careful constitutive choices in defining domain evolution in higher dimensions. We raise important questions in the modelling and analysis of biological systems, in addition to numerous mathematical questions that appear tractable in the one-dimensional setting, but are vastly more difficult for higher-dimensional models.
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Affiliation(s)
- Andrew L Krause
- Mathematical Sciences Department, Durham University, Upper Mountjoy Campus, Stockton Rd, Durham, DH1 3LE, UK.
| | - Eamonn A Gaffney
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Benjamin J Walker
- Department of Mathematics, University College London, London, WC1H 0AY, UK
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22
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Lee JR, Terauds A, Carwardine J, Shaw JD, Fuller RA, Possingham HP, Chown SL, Convey P, Gilbert N, Hughes KA, McIvor E, Robinson SA, Ropert-Coudert Y, Bergstrom DM, Biersma EM, Christian C, Cowan DA, Frenot Y, Jenouvrier S, Kelley L, Lee MJ, Lynch HJ, Njåstad B, Quesada A, Roura RM, Shaw EA, Stanwell-Smith D, Tsujimoto M, Wall DH, Wilmotte A, Chadès I. Threat management priorities for conserving Antarctic biodiversity. PLoS Biol 2022; 20:e3001921. [PMID: 36548240 PMCID: PMC9778584 DOI: 10.1371/journal.pbio.3001921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/16/2022] [Indexed: 12/24/2022] Open
Abstract
Antarctic terrestrial biodiversity faces multiple threats, from invasive species to climate change. Yet no large-scale assessments of threat management strategies exist. Applying a structured participatory approach, we demonstrate that existing conservation efforts are insufficient in a changing world, estimating that 65% (at best 37%, at worst 97%) of native terrestrial taxa and land-associated seabirds are likely to decline by 2100 under current trajectories. Emperor penguins are identified as the most vulnerable taxon, followed by other seabirds and dry soil nematodes. We find that implementing 10 key threat management strategies in parallel, at an estimated present-day equivalent annual cost of US$23 million, could benefit up to 84% of Antarctic taxa. Climate change is identified as the most pervasive threat to Antarctic biodiversity and influencing global policy to effectively limit climate change is the most beneficial conservation strategy. However, minimising impacts of human activities and improved planning and management of new infrastructure projects are cost-effective and will help to minimise regional threats. Simultaneous global and regional efforts are critical to secure Antarctic biodiversity for future generations.
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Affiliation(s)
- Jasmine R. Lee
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
- CSIRO, Dutton Park, Queensland, Australia
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
- British Antarctic Survey, NERC, High Cross, Cambridge, United Kingdom
- * E-mail:
| | - Aleks Terauds
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia
| | | | - Justine D. Shaw
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia
| | - Richard A. Fuller
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Hugh P. Possingham
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
- The Nature Conservancy, Arlington, Virginia, United States of America
| | - Steven L. Chown
- Securing Antarctica’s Environmental Future, School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Cambridge, United Kingdom
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Neil Gilbert
- Constantia Consulting, Christchurch, New Zealand
| | - Kevin A. Hughes
- British Antarctic Survey, NERC, High Cross, Cambridge, United Kingdom
| | - Ewan McIvor
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia
| | - Sharon A. Robinson
- Centre for Sustainable Ecosystem Solutions, School of Earth, Atmosphere and Life Sciences and Global Challenges Program, University of Wollongong, Wollongong, New South Wales, Australia
- Securing Antarctica’s Environmental Future, University of Wollongong, Wollongong, New South Wales, Australia
| | - Yan Ropert-Coudert
- Centre d’Etudes Biologiques de Chizé, La Rochelle Université − CNRS, UMR 7372, Villiers en Bois, France
| | - Dana M. Bergstrom
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa
- Centre for Sustainable Ecosystem Solutions, School of Earth, Atmosphere and Life Sciences and Global Challenges Program, University of Wollongong, Wollongong, New South Wales, Australia
| | - Elisabeth M. Biersma
- British Antarctic Survey, NERC, High Cross, Cambridge, United Kingdom
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Claire Christian
- Antarctic and Southern Ocean Coalition, Washington DC, United States of America
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Yves Frenot
- University of Rennes 1, CNRS, EcoBio (Ecosystèmes, biodiversité, évolution)—UMR 6553, Rennes, France
| | - Stéphanie Jenouvrier
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Lisa Kelley
- International Association of Antarctica Tour Operators (IAATO), South Kingstown, Rhode Island, United States of America
| | | | - Heather J. Lynch
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | | | - Antonio Quesada
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ricardo M. Roura
- Antarctic and Southern Ocean Coalition, Washington DC, United States of America
| | - E. Ashley Shaw
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Damon Stanwell-Smith
- International Association of Antarctica Tour Operators (IAATO), South Kingstown, Rhode Island, United States of America
- Viking Expeditions, Basel, Switzerland
| | - Megumu Tsujimoto
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa Japan
- National Institute of Polar Research, Tachikawa, Tokyo, Japan
| | - Diana H. Wall
- Department of Biology and School of Global Environmental Sustainability, Colorado State University, Fort Collins, Colorado, United States of America
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23
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Wijesinghe P, Corsetti S, Chow DJX, Sakata S, Dunning KR, Dholakia K. Experimentally unsupervised deconvolution for light-sheet microscopy with propagation-invariant beams. Light Sci Appl 2022; 11:319. [PMID: 36319636 PMCID: PMC9626625 DOI: 10.1038/s41377-022-00975-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 05/25/2023]
Abstract
Deconvolution is a challenging inverse problem, particularly in techniques that employ complex engineered point-spread functions, such as microscopy with propagation-invariant beams. Here, we present a deep-learning method for deconvolution that, in lieu of end-to-end training with ground truths, is trained using known physics of the imaging system. Specifically, we train a generative adversarial network with images generated with the known point-spread function of the system, and combine this with unpaired experimental data that preserve perceptual content. Our method rapidly and robustly deconvolves and super-resolves microscopy images, demonstrating a two-fold improvement in image contrast to conventional deconvolution methods. In contrast to common end-to-end networks that often require 1000-10,000s paired images, our method is experimentally unsupervised and can be trained solely on a few hundred regions of interest. We demonstrate its performance on light-sheet microscopy with propagation-invariant Airy beams in oocytes, preimplantation embryos and excised brain tissue, as well as illustrate its utility for Bessel-beam LSM. This method aims to democratise learned methods for deconvolution, as it does not require data acquisition outwith the conventional imaging protocol.
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Affiliation(s)
- Philip Wijesinghe
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9SS, UK.
| | - Stella Corsetti
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9SS, UK
| | - Darren J X Chow
- Robinson Research Institute, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, SA, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, SA, Australia
| | - Shuzo Sakata
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Kylie R Dunning
- Robinson Research Institute, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, SA, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, SA, Australia
| | - Kishan Dholakia
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9SS, UK.
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
- Department of Physics, College of Science, Yonsei University, Seoul, 03722, South Korea.
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24
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Marques CA, Rhodes LC, Benedičič I, Naritsuka M, Naden AB, Li Z, Komarek AC, Mackenzie AP, Wahl P. Atomic-scale imaging of emergent order at a magnetic field-induced Lifshitz transition. Sci Adv 2022; 8:eabo7757. [PMID: 36179031 PMCID: PMC9524824 DOI: 10.1126/sciadv.abo7757] [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] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
The phenomenology and radical changes seen in material properties traversing a quantum phase transition have captivated condensed matter research over the past decades. Strong electronic correlations lead to exotic electronic ground states, including magnetic order, nematicity, and unconventional superconductivity. Providing a microscopic model for these requires detailed knowledge of the electronic structure in the vicinity of the Fermi energy, promising a complete understanding of the physics of the quantum critical point. Here, we demonstrate such a measurement at the surface of Sr3Ru2O7. Our results show that, even in zero field, the electronic structure is strongly C2 symmetric and that a magnetic field drives a Lifshitz transition and induces a charge-stripe order. We track the changes of the electronic structure as a function of field via quasiparticle interference imaging at ultralow temperatures. Our results provide a complete microscopic picture of the field-induced changes of the electronic structure across the Lifshitz transition.
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Affiliation(s)
- Carolina A. Marques
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, UK
| | - Luke C. Rhodes
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, UK
| | - Izidor Benedičič
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, UK
| | - Masahiro Naritsuka
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, UK
| | - Aaron B. Naden
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Zhiwei Li
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Straße 40, 01187 Dresden, Germany
| | - Alexander C. Komarek
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Straße 40, 01187 Dresden, Germany
| | - Andrew P. Mackenzie
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, UK
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Straße 40, 01187 Dresden, Germany
| | - Peter Wahl
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, UK
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25
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Song C, Simmons BI, Fortin MJ, Gonzalez A. Generalism drives abundance: A computational causal discovery approach. PLoS Comput Biol 2022; 18:e1010302. [PMID: 36173959 PMCID: PMC9521805 DOI: 10.1371/journal.pcbi.1010302] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022] Open
Abstract
A ubiquitous pattern in ecological systems is that more abundant species tend to be more generalist; that is, they interact with more species or can occur in wider range of habitats. However, there is no consensus on whether generalism drives abundance (a selection process) or abundance drives generalism (a drift process). As it is difficult to conduct direct experiments to solve this chicken-and-egg dilemma, previous studies have used a causal discovery method based on formal logic and have found that abundance drives generalism. Here, we refine this method by correcting its bias regarding skewed distributions, and employ two other independent causal discovery methods based on nonparametric regression and on information theory, respectively. Contrary to previous work, all three independent methods strongly indicate that generalism drives abundance when applied to datasets on plant-hummingbird communities and reef fishes. Furthermore, we find that selection processes are more important than drift processes in structuring multispecies systems when the environment is variable. Our results showcase the power of the computational causal discovery approach to aid ecological research. Ever since Aristotle, the chicken-or-egg causality dilemma has baffled researchers. Such causality dilemmas are abundant in ecological research, where causal directions are often assumed but not tested. An archetypal example is whether being a generalist causes a species to be more abundant, or whether being more abundant causes a species to be generalists. Without doubt, the gold standard to establish causal directions is controlled experiments. However, controlled experiments that can disentangle the direction of causality in this case are challenging because it involves controlling biotic or abiotic niche breadth. These challenges create an opportunity for computational tools to detect the most likely causal direction. Here, by adapting a set of recently developed computational methods, we provide strong evidence that generalism drives abundance, overturning the previously established direction. We hope our work raises awareness of the potential for computational discovery methods to address long-standing questions in ecology, especially increasingly large datasets become available.
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Affiliation(s)
- Chuliang Song
- Department of Biology, Quebec Centre for Biodiversity Science, McGill University, Montreal, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
- * E-mail:
| | - Benno I. Simmons
- Department of Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Andrew Gonzalez
- Department of Biology, Quebec Centre for Biodiversity Science, McGill University, Montreal, Canada
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26
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Cole JM, Gosztola DJ, Velazquez-Garcia JDJ. Structural Capture of η 1-OSO to η 2-(OS)O Coordination Isomerism in a New Ruthenium-Based SO 2-Linkage Photoisomer That Exhibits Single-Crystal Optical Actuation. J Phys Chem C Nanomater Interfaces 2022; 126:6047-6059. [PMID: 35573119 PMCID: PMC9098168 DOI: 10.1021/acs.jpcc.2c00170] [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] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/11/2022] [Indexed: 06/15/2023]
Abstract
Recent discoveries of a range of single-crystal optical actuators are feeding a new form of materials chemistry, given their broad range of potential applications, from light-induced molecular motors to light sensors and optical-memory media. A series of ruthenium-based coordination complexes that exhibit sulfur dioxide linkage photoisomerization is of particular interest because they exhibit single-crystal optical actuation via either optical switching or nano-optomechanical transduction processes. We report the discovery of a new complex in this series of chemicals, [Ru(SO2)(NH3)4(3-fluoropyridine)]tosylate2 (1), which forms an η1-OSO photoisomer with 70% photoconversion upon the application of 505 nm light. The uncoordinated oxygen atom in this η1-OSO photoisomer impinges on one of the arene rings in a neighboring tosylate counter ion of 1 just enough that incipient nano-optomechanical transduction is observed. The structure and optical properties of this actuator are characterized via in situ light-induced single-crystal X-ray diffraction (photocrystallography), single-crystal optical absorption spectroscopy and microscopy, as well as single-crystal Raman spectroscopy. These materials-characterization methods were also used to track thermally induced reverse isomerization processes in 1. One of these processes involves an η1-OSO to η2-(OS)O transition, which was found to proceed sufficiently slowly at 110 K that its structural mechanism could be determined via a time sequence of photocrystallography experiments. The resulting data allowed us to structurally capture the transition, which was shown to occur via a form of coordination isomerism. Our newfound knowledge about this structural mechanism will aid the molecular design of new [RuSO2] complexes with functional applications.
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Affiliation(s)
- Jacqueline M. Cole
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K.
- ISIS
Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, U.K.
- Center
for Nanoscale Materials, Argonne National
Laboratory, 9700 S Cass Avenue, Lemont, Illinois 60439, United
States
| | - David J. Gosztola
- Center
for Nanoscale Materials, Argonne National
Laboratory, 9700 S Cass Avenue, Lemont, Illinois 60439, United
States
| | - Jose de J. Velazquez-Garcia
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K.
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27
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Hornsby AN, Love BC. Sequential consumer choice as multi-cued retrieval. Sci Adv 2022; 8:eabl9754. [PMID: 35213230 PMCID: PMC8880769 DOI: 10.1126/sciadv.abl9754] [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] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Whether adding songs to a playlist or groceries during an online shop, how do we decide what to choose next? We develop a model that predicts such open-ended, sequential choices using a process of cued retrieval from long-term memory. Using the past choice to cue subsequent retrievals, this model predicts the sequential purchases and response times of nearly 5 million grocery purchases made by more than 100,000 online shoppers. Products can be associated in different ways, such as by their episodic association or semantic overlap, and we find that consumers query multiple forms of associative knowledge when retrieving options. Attending to certain knowledge sources, as estimated by our model, predicts important retrieval errors, such as the propensity to forget or add unwanted products. Our results demonstrate how basic memory retrieval mechanisms shape choices in real-world, goal-directed tasks.
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Affiliation(s)
- Adam N. Hornsby
- Dunnhumby, 184 Shepherds Bush Road, London W6 7NL, UK
- Department of Experimental Psychology, University College London, London WC1H 0AP, UK
| | - Bradley C. Love
- Department of Experimental Psychology, University College London, London WC1H 0AP, UK
- The Alan Turing Institute, London UK
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28
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Pallaseni A, Peets E, Koeppel J, Weller J, Vanderstichele T, Ho U, Crepaldi L, van Leeuwen J, Allen F, Parts L. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3551-3564. [PMID: 35286377 PMCID: PMC8989541 DOI: 10.1093/nar/gkac161] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/19/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas base editors promise nucleotide-level control over DNA sequences, but the determinants of their activity remain incompletely understood. We measured base editing frequencies in two human cell lines for two cytosine and two adenine base editors at ∼14 000 target sequences and find that base editing activity is sequence-biased, with largest effects from nucleotides flanking the target base. Whether a base is edited depends strongly on the combination of its position in the target and the preceding base, acting to widen or narrow the effective editing window. The impact of features on editing rate depends on the position, with sequence bias efficacy mainly influencing bases away from the center of the window. We use these observations to train a machine learning model to predict editing activity per position, with accuracy ranging from 0.49 to 0.72 between editors, and with better generalization across datasets than existing tools. We demonstrate the usefulness of our model by predicting the efficacy of disease mutation correcting guides, and find that most of them suffer from more unwanted editing than pure outcomes. This work unravels the position-specificity of base editing biases and allows more efficient planning of editing campaigns in experimental and therapeutic contexts.
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Affiliation(s)
| | | | | | | | | | - Uyen Linh Ho
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Jolanda van Leeuwen
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Leopold Parts
- To whom correspondence should be addressed. Tel: +44 1223 834 244;
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29
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Abstract
Sodium reduction of [{SiNDipp}Mg] [{SiNDipp} = {CH2SiMe2N(Dipp)}2; Dipp = 2,6-i-Pr2C6H3] provides the Mg(I) species, [{SiNDipp}MgNa]2, in which the long Mg-Mg bond (>3.2 Å) is augmented by persistent Na-aryl interactions. Computational assessment indicates that this molecule is best considered to comprise a contiguous tetrametallic core, a viewpoint borne out by its reaction with CO, which results in ethynediolate formation mediated by the dissimilar metal centers.
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Affiliation(s)
- Han-Ying Liu
- Department
of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K.
| | - Ryan J. Schwamm
- Department
of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K.
| | - Samuel E. Neale
- Department
of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K.
| | - Michael S. Hill
- Department
of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K.
| | - Claire L. McMullin
- Department
of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K.
| | - Mary F. Mahon
- Department
of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K.
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30
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Tanoh AOA, Alexander-Webber J, Fan Y, Gauriot N, Xiao J, Pandya R, Li Z, Hofmann S, Rao A. Giant photoluminescence enhancement in MoSe 2 monolayers treated with oleic acid ligands. Nanoscale Adv 2021; 3:4216-4225. [PMID: 34355119 PMCID: PMC8276785 DOI: 10.1039/d0na01014f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/09/2021] [Indexed: 05/28/2023]
Abstract
The inherently low photoluminescence (PL) yields in the as prepared transition metal dichalcogenide (TMD) monolayers are broadly accepted to be the result of atomic vacancies (i.e., defects) and uncontrolled doping, which give rise to non-radiative exciton decay pathways. To date, a number of chemical passivation schemes have been successfully developed to improve PL in sulphur based TMDs i.e., molybdenum disulphide (MoS2) and tungsten disulphide (WS2) monolayers. Studies on solution based chemical passivation schemes for improving PL yields in selenium (Se) based TMDs are however lacking in comparison. Here, we demonstrate that treatment with oleic acid (OA) provides a simple wet chemical passivation method for monolayer MoSe2, enhancing PL yields by an average of 58-fold, while also improving spectral uniformity across the material and reducing the emission linewidth. Excitation intensity dependent PL reveals trap-free PL dynamics dominated by neutral exciton recombination. Time-resolved PL (TRPL) studies reveal significantly increased PL lifetimes, with pump intensity dependent TRPL measurements also confirming trap free PL dynamics in OA treated MoSe2. Field effect transistors show reduced charge trap density and improved on-off ratios after treatment with OA. These results indicate defect passivation by OA, which we hypothesise as ligands passivating chalcogen defects through oleate coordination to Mo dangling bonds. Importantly, this work combined with our previous study on OA treated WS2, verifies OA treatment as a simple solution-based chemical passivation protocol for improving PL yields and electronic characteristics in both selenide and sulphide TMDs - a property that has not been reported previously for other solution-based passivation schemes.
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Affiliation(s)
- Arelo O A Tanoh
- Cavendish Laboratory, Cambridge JJ Thomson Avenue CB3 0HE Cambridge UK
- Cambridge Graphene Centre, University of Cambridge 9 JJ Thomson Avenue CB3 0FA Cambridge UK
| | - Jack Alexander-Webber
- Department of Engineering, University of Cambridge JJ Thomson Avenue CB3 0FA Cambridge UK
| | - Ye Fan
- Department of Engineering, University of Cambridge JJ Thomson Avenue CB3 0FA Cambridge UK
| | - Nicholas Gauriot
- Cavendish Laboratory, Cambridge JJ Thomson Avenue CB3 0HE Cambridge UK
| | - James Xiao
- Cavendish Laboratory, Cambridge JJ Thomson Avenue CB3 0HE Cambridge UK
| | - Raj Pandya
- Cavendish Laboratory, Cambridge JJ Thomson Avenue CB3 0HE Cambridge UK
| | - Zhaojun Li
- Cavendish Laboratory, Cambridge JJ Thomson Avenue CB3 0HE Cambridge UK
| | - Stephan Hofmann
- Department of Engineering, University of Cambridge JJ Thomson Avenue CB3 0FA Cambridge UK
| | - Akshay Rao
- Cavendish Laboratory, Cambridge JJ Thomson Avenue CB3 0HE Cambridge UK
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31
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Dunn FS, Liu AG, Grazhdankin DV, Vixseboxse P, Flannery-Sutherland J, Green E, Harris S, Wilby PR, Donoghue PCJ. The developmental biology of Charnia and the eumetazoan affinity of the Ediacaran rangeomorphs. Sci Adv 2021; 7:eabe0291. [PMID: 34301594 PMCID: PMC8302126 DOI: 10.1126/sciadv.abe0291] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
Molecular timescales estimate that early animal lineages diverged tens of millions of years before their earliest unequivocal fossil evidence. The Ediacaran macrobiota (~574 to 538 million years ago) are largely eschewed from this debate, primarily due to their extreme phylogenetic uncertainty, but remain germane. We characterize the development of Charnia masoni and establish the affinity of rangeomorphs, among the oldest and most enigmatic components of the Ediacaran macrobiota. We provide the first direct evidence for the internal interconnected nature of rangeomorphs and show that Charnia was constructed of repeated branches that derived successively from pre-existing branches. We find homology and rationalize morphogenesis between disparate rangeomorph taxa, before producing a phylogenetic analysis, resolving Charnia as a stem-eumetazoan and expanding the anatomical disparity of that group to include a long-extinct bodyplan. These data bring competing records of early animal evolution into closer agreement, reformulating our understanding of the evolutionary emergence of animal bodyplans.
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Affiliation(s)
- Frances S Dunn
- Oxford University Museum of Natural History, University of Oxford, Parks Road, Oxford OX1 3PW, UK.
- British Geological Survey, Nicker Hill, Keyworth, Nottingham NG12 5GG, UK
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Alexander G Liu
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
| | - Dmitriy V Grazhdankin
- Trofimuk Institute of Petroleum Geology and Geophysics, Prospekt Akademika Koptyuga 3, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova Street 1, Novosibirsk 630090, Russia
| | - Philip Vixseboxse
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Joseph Flannery-Sutherland
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Emily Green
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Simon Harris
- British Geological Survey, Nicker Hill, Keyworth, Nottingham NG12 5GG, UK
| | - Philip R Wilby
- British Geological Survey, Nicker Hill, Keyworth, Nottingham NG12 5GG, UK
- School of Geography, Geology and the Environment, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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32
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Reinwald M, Moseley B, Szenicer A, Nissen-Meyer T, Oduor S, Vollrath F, Markham A, Mortimer B. Seismic localization of elephant rumbles as a monitoring approach. J R Soc Interface 2021; 18:20210264. [PMID: 34255988 PMCID: PMC8277467 DOI: 10.1098/rsif.2021.0264] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/23/2021] [Indexed: 11/12/2022] Open
Abstract
African elephants (Loxodonta africana) are sentient and intelligent animals that use a variety of vocalizations to greet, warn or communicate with each other. Their low-frequency rumbles propagate through the air as well as through the ground and the physical properties of both media cause differences in frequency filtering and propagation distances of the respective wave. However, it is not well understood how each mode contributes to the animals' abilities to detect these rumbles and extract behavioural or spatial information. In this study, we recorded seismic and co-generated acoustic rumbles in Kenya and compared their potential use to localize the vocalizing animal using the same multi-lateration algorithms. For our experimental set-up, seismic localization has higher accuracy than acoustic, and bimodal localization does not improve results. We conclude that seismic rumbles can be used to remotely monitor and even decipher elephant social interactions, presenting us with a tool for far-reaching, non-intrusive and surprisingly informative wildlife monitoring.
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Affiliation(s)
| | - Ben Moseley
- Department of Computer Science, University of Oxford, Oxford, UK
| | | | | | | | - Fritz Vollrath
- Department of Zoology, University of Oxford, Oxford, UK
- Save the Elephants, Marula Manor, Karen, Nairobi, Kenya
| | - Andrew Markham
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Beth Mortimer
- Department of Zoology, University of Oxford, Oxford, UK
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33
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Bretscher H, Li Z, Xiao J, Qiu DY, Refaely-Abramson S, Alexander-Webber JA, Tanoh A, Fan Y, Delport G, Williams CA, Stranks SD, Hofmann S, Neaton JB, Louie SG, Rao A. Rational Passivation of Sulfur Vacancy Defects in Two-Dimensional Transition Metal Dichalcogenides. ACS Nano 2021; 15:8780-8789. [PMID: 33983711 PMCID: PMC8158852 DOI: 10.1021/acsnano.1c01220] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/07/2021] [Indexed: 06/01/2023]
Abstract
Structural defects vary the optoelectronic properties of monolayer transition metal dichalcogenides, leading to concerted efforts to control defect type and density via materials growth or postgrowth passivation. Here, we explore a simple chemical treatment that allows on-off switching of low-lying, defect-localized exciton states, leading to tunable emission properties. Using steady-state and ultrafast optical spectroscopy, supported by ab initio calculations, we show that passivation of sulfur vacancy defects, which act as exciton traps in monolayer MoS2 and WS2, allows for controllable and improved mobilities and an increase in photoluminescence up to 275-fold, more than twice the value achieved by other chemical treatments. Our findings suggest a route for simple and rational defect engineering strategies for tunable and switchable electronic and excitonic properties through passivation.
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Affiliation(s)
| | - Zhaojun Li
- University
of Cambridge, Cambridge, CB2 1TN, U.K.
- Uppsala
University, Uppsala, 751 20, Sweden
| | - James Xiao
- University
of Cambridge, Cambridge, CB2 1TN, U.K.
| | - Diana Yuan Qiu
- Yale
University, New Haven, Connecticut 06520, United States
| | | | | | - Arelo Tanoh
- University
of Cambridge, Cambridge, CB2 1TN, U.K.
| | - Ye Fan
- University
of Cambridge, Cambridge, CB2 1TN, U.K.
| | | | | | | | | | - Jeffrey B. Neaton
- University
of California Berkeley, Berkeley, California 94720, United States
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Steven G. Louie
- University
of California Berkeley, Berkeley, California 94720, United States
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Akshay Rao
- University
of Cambridge, Cambridge, CB2 1TN, U.K.
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Cole JM, Gosztola DJ, Velazquez-Garcia JDJ. Nanooptomechanical Transduction in a Single Crystal with 100% Photoconversion. J Phys Chem C Nanomater Interfaces 2021; 125:8907-8915. [PMID: 34084264 PMCID: PMC8162413 DOI: 10.1021/acs.jpcc.1c02457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Materials that exhibit nanooptomechanical transduction in their single-crystal form have prospective use in light-driven molecular machinery, nanotechnology, and quantum computing. Linkage photoisomerization is typically the source of such transduction in coordination complexes, although the isomers tend to undergo only partial photoconversion. We present a nanooptomechanical transducer, trans-[Ru(SO2)(NH3)4(3-bromopyridine)]tosylate2, whose S-bound η1-SO2 isomer fully converts into an O-bound η1-OSO photoisomer that is metastable while kept at 100 K. Its 100% photoconversion is confirmed structurally via photocrystallography, while single-crystal optical absorption and Raman spectroscopies reveal its metal-to-ligand charge-transfer and temperature-dependent characteristics. This perfect optical switching affords the material good prospects for nanooptomechanical transduction with single-photon control.
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Affiliation(s)
- Jacqueline M. Cole
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, U.K.
- ISIS
Neutron and Muon Source, STFC Rutherford
Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, U.K.
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
- Argonne
National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United
States
| | - David J. Gosztola
- Argonne
National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United
States
| | - Jose de J. Velazquez-Garcia
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, U.K.
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35
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Pandya R, Alvertis AM, Gu Q, Sung J, Legrand L, Kréher D, Barisien T, Chin AW, Schnedermann C, Rao A. Exciton Diffusion in Highly-Ordered One Dimensional Conjugated Polymers: Effects of Back-Bone Torsion, Electronic Symmetry, Phonons and Annihilation. J Phys Chem Lett 2021; 12:3669-3678. [PMID: 33829788 PMCID: PMC8154834 DOI: 10.1021/acs.jpclett.1c00193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/19/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Many optoelectronic devices based on organic materials require rapid and long-range singlet exciton transport. Key factors controlling exciton transport include material structure, exciton-phonon coupling and electronic state symmetry. Here, we employ femtosecond transient absorption microscopy to study the influence of these parameters on exciton transport in one-dimensional conjugated polymers. We find that excitons with 21Ag- symmetry and a planar backbone exhibit a significantly higher diffusion coefficient (34 ± 10 cm2 s-1) compared to excitons with 11Bu+ symmetry (7 ± 6 cm2 s-1) with a twisted backbone. We also find that exciton transport in the 21Ag- state occurs without exciton-exciton annihilation. Both 21Ag- and 11Bu+ states are found to exhibit subdiffusive behavior. Ab initio GW-BSE calculations reveal that this is due to the comparable strengths of the exciton-phonon interaction and exciton coupling. Our results demonstrate the link between electronic state symmetry, backbone torsion and phonons in exciton transport in π-conjugated polymers.
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Affiliation(s)
- Raj Pandya
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CB3 0HE, Cambridge, United Kingdom
| | - Antonios M. Alvertis
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CB3 0HE, Cambridge, United Kingdom
| | - Qifei Gu
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CB3 0HE, Cambridge, United Kingdom
| | - Jooyoung Sung
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CB3 0HE, Cambridge, United Kingdom
| | - Laurent Legrand
- Sorbonne
Université, CNRS, Institut
des NanoSciences de Paris, INSP, 4 place Jussieu, F-75005 Paris, France
| | - David Kréher
- Sorbonne
Université, CNRS, Institut
Parisien de Chimie Moléculaire (IPCM) UMR 8232, Chimie des
Polymères, 4 Place
Jussieu, 75005 Paris, France
| | - Thierry Barisien
- Sorbonne
Université, CNRS, Institut
des NanoSciences de Paris, INSP, 4 place Jussieu, F-75005 Paris, France
| | - Alex W. Chin
- Sorbonne
Université, CNRS, Institut
des NanoSciences de Paris, INSP, 4 place Jussieu, F-75005 Paris, France
| | - Christoph Schnedermann
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CB3 0HE, Cambridge, United Kingdom
| | - Akshay Rao
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CB3 0HE, Cambridge, United Kingdom
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Navidtehrani Y, Betegón C, Martínez-Pañeda E. A Unified Abaqus Implementation of the Phase Field Fracture Method Using Only a User Material Subroutine. Materials (Basel) 2021; 14:1913. [PMID: 33920471 PMCID: PMC8070186 DOI: 10.3390/ma14081913] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 03/14/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 12/04/2022]
Abstract
We present a simple and robust implementation of the phase field fracture method in Abaqus. Unlike previous works, only a user material (UMAT) subroutine is used. This is achieved by exploiting the analogy between the phase field balance equation and heat transfer, which avoids the need for a user element mesh and enables taking advantage of Abaqus' in-built features. A unified theoretical framework and its implementation are presented, suitable for any arbitrary choice of crack density function and fracture driving force. Specifically, the framework is exemplified with the so-called AT1, AT2 and phase field-cohesive zone models (PF-CZM). Both staggered and monolithic solution schemes are handled. We demonstrate the potential and robustness of this new implementation by addressing several paradigmatic 2D and 3D boundary value problems. The numerical examples show how the current implementation can be used to reproduce numerical and experimental results from the literature, and efficiently capture advanced features such as complex crack trajectories, crack nucleation from arbitrary sites and contact problems. The code developed is made freely available.
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Affiliation(s)
- Yousef Navidtehrani
- Department of Construction and Manufacturing Engineering, University of Oviedo, 33203 Gijón, Spain; (Y.N.); (C.B.)
| | - Covadonga Betegón
- Department of Construction and Manufacturing Engineering, University of Oviedo, 33203 Gijón, Spain; (Y.N.); (C.B.)
| | - Emilio Martínez-Pañeda
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, UK
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37
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Yim CM, Chakraborti D, Rhodes LC, Khim S, Mackenzie AP, Wahl P. Quasiparticle interference and quantum confinement in a correlated Rashba spin-split 2D electron liquid. Sci Adv 2021; 7:7/15/eabd7361. [PMID: 33837075 PMCID: PMC8034857 DOI: 10.1126/sciadv.abd7361] [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] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Exploiting inversion symmetry breaking (ISB) in systems with strong spin-orbit coupling promises control of spin through electric fields-crucial to achieve miniaturization in spintronic devices. Delivering on this promise requires a two-dimensional electron gas with a spin precession length shorter than the spin coherence length and a large spin splitting so that spin manipulation can be achieved over length scales of nanometers. Recently, the transition metal oxide terminations of delafossite oxides were found to exhibit a large Rashba spin splitting dominated by ISB. In this limit, the Fermi surface exhibits the same spin texture as for weak ISB, but the orbital texture is completely different, raising questions about the effect on quasiparticle scattering. We demonstrate that the spin-orbital selection rules relevant for conventional Rashba system are obeyed as true spin selection rules in this correlated electron liquid and determine its spin coherence length from quasiparticle interference imaging.
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Affiliation(s)
- Chi Ming Yim
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, UK.
- Tsung Dao Lee Institute and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dibyashree Chakraborti
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, UK
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Straße 40, 01187 Dresden, Germany
| | - Luke C Rhodes
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, UK
| | - Seunghyun Khim
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Straße 40, 01187 Dresden, Germany
| | - Andrew P Mackenzie
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, UK
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Straße 40, 01187 Dresden, Germany
| | - Peter Wahl
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SS, UK.
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Abstract
In this work, self-assembled amino-acid appended perylene bisimides (PBIs) have been studied that when processed into thin films change their resistivity in response to being bent. The PBIs assemble into structures in water and form thin films upon drying. These normally delicate thin films can be tolerant to bending, depending on the aggregates they form. Furthermore, the films then reversibly change their resistivity in response to this mechanical stimulus. This change is proportional to the degree of bending of the film giving them the potential to be used quantitatively to measure mechanical movement, such as in wearable devices.
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Affiliation(s)
- Victoria Adams
- School of ChemistryUniversity of GlasgowGlasgowG12 8QQUK
| | - Joseph Cameron
- School of ChemistryUniversity of GlasgowGlasgowG12 8QQUK
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Kovaltsuk A, Raybould MIJ, Wong WK, Marks C, Kelm S, Snowden J, Trück J, Deane CM. Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice. PLoS Comput Biol 2020; 16:e1007636. [PMID: 32069281 PMCID: PMC7048297 DOI: 10.1371/journal.pcbi.1007636] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/28/2020] [Accepted: 01/07/2020] [Indexed: 01/18/2023] Open
Abstract
Most current analysis tools for antibody next-generation sequencing data work with primary sequence descriptors, leaving accompanying structural information unharnessed. We have used novel rapid methods to structurally characterize the complementary-determining regions (CDRs) of more than 180 million human and mouse B-cell receptor (BCR) repertoire sequences. These structurally annotated CDRs provide unprecedented insights into both the structural predetermination and dynamics of the adaptive immune response. We show that B-cell types can be distinguished based solely on these structural properties. Antigen-unexperienced BCR repertoires use the highest number and diversity of CDR structures and these patterns of naïve repertoire paratope usage are highly conserved across subjects. In contrast, more differentiated B-cells are more personalized in terms of CDR structure usage. Our results establish the CDR structure differences in BCR repertoires and have applications for many fields including immunodiagnostics, phage display library generation, and “humanness” assessment of BCR repertoires from transgenic animals. The software tool for structural annotation of BCR repertoires, SAAB+, is available at https://github.com/oxpig/saab_plus. B-cell receptors (BCR) are the major components of the adaptive immune system. These are immunoglobulin molecules that bind to foreign substances known as antigens. Each individual has a huge BCR repertoire, where each individual BCR has a specific binding site composed of the complementary-determining regions (CDRs) capable of recognising a specific antigen. Drug discovery and immunodiagnostics inspired by the adaptive immune system rely on our ability to accurately interrogate the structural diversity of the binding sites of the BCR repertoire. Here we report our novel rapid pipeline, SAAB+, which has enabled us to interrogate how the structure of the CDR changes in BCR repertoires along the B-cell differentiation axis. By analysing human and mouse BCR repertoires at an unprecedented scale, we observed species-specific structural predetermination and detected CDR dynamics across multiple stages of B-cell differentiation. We showed that naïve repertoires share the highest number and diversity of CDR structures, a pattern which was highly conserved in all B-cell donors. Our results suggest that increased B-cell differentiation is associated with a personalization of CDR structure usages. Finally, we established the differences in CDR usages between humans and mice, analysis with immediate relevance for BCR repertoire “humanness” assessment and rational immunotherapeutic engineering.
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Affiliation(s)
| | | | - Wing Ki Wong
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Claire Marks
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | | | | | - Johannes Trück
- Division of Immunology, University Children's Hospital, University of Zurich, Zurich, Switzerland
| | - Charlotte M. Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- * E-mail:
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40
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Abstract
Computational models using text corpora have proved useful in understanding the nature of language and human concepts. One appeal of this work is that text, such as from newspaper articles, should reflect human behaviour and conceptual organization outside the laboratory. However, texts do not directly reflect human activity, but instead serve a communicative function and are highly curated or edited to suit an audience. Here, we apply methods devised for text to a data source that directly reflects thousands of individuals’ activity patterns. Using product co-occurrence data from nearly 1.3-m supermarket shopping baskets, we trained a topic model to learn 25 high-level concepts (or topics). These topics were found to be comprehensible and coherent by both retail experts and consumers. The topics indicated that human concepts are primarily organized around goals and interactions (e.g. tomatoes go well with vegetables in a salad), rather than their intrinsic features (e.g. defining a tomato by the fact that it has seeds and is fleshy). These results are consistent with the notion that human conceptual knowledge is tailored to support action. Individual differences in the topics sampled predicted basic demographic characteristics. Our findings suggest that human activity patterns can reveal conceptual organization and may give rise to it.
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Affiliation(s)
- Adam N. Hornsby
- University College London, London, UK
- dunnhumby, 184 Shepherds Bush Road, London, W6 7NL UK
| | - Thomas Evans
- dunnhumby, 184 Shepherds Bush Road, London, W6 7NL UK
| | | | - Rosie Prior
- dunnhumby, 184 Shepherds Bush Road, London, W6 7NL UK
| | - Bradley C. Love
- University College London, London, UK
- The Alan Turing Institute, 96 Euston Rd, Kings Cross, London, NW1 2DB UK
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41
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Davranoglou LR, Cicirello A, Taylor GK, Mortimer B. Planthopper bugs use a fast, cyclic elastic recoil mechanism for effective vibrational communication at small body size. PLoS Biol 2019; 17:e3000155. [PMID: 30860993 PMCID: PMC6413918 DOI: 10.1371/journal.pbio.3000155] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/05/2019] [Indexed: 11/18/2022] Open
Abstract
Vibrations through substrates are an important source of information for diverse organisms, from nematodes to elephants. The fundamental challenge for small animals using vibrational communication is to move their limited mass fast enough to provide sufficient kinetic energy for effective information transfer through the substrate whilst optimising energy efficiency over repeated cycles. Here, we describe a vibratory organ found across a commercially important group of plant-feeding insects, the planthoppers (Hemiptera: Fulgoromorpha). This elastic recoil snapping organ generates substrate-borne broadband vibrations using fast, cyclical abdominal motion that transfers kinetic energy to the substrate through the legs. Elastic potential energy is stored and released twice using two different latched energy-storage mechanisms, each utilising a different form of elastic recoil to increase the speed of motion. Comparison to the acoustic tymbal organ of cicadas (Hemiptera: Cicadomorpha) reveals functional convergence in their use of elastic mechanisms to increase the efficacy of mechanical communication. Planthopper insects produce fast abdominal twerks for vibrational communication through the substrate, employing a novel vibratory organ that uses two reciprocal elastic recoil mechanisms to generate fast cyclical motion. Animals use substrate-borne vibrations for eavesdropping and communication over an immense range of body size—from elephants to nematodes. Vibrational communication is especially challenging for small animals because of the high mechanical power that is needed to transmit information effectively over extended distances through a substrate. Here, we show that planthoppers, a commercially important group of insects, produce vibrations for communication using a reciprocal elastic recoil mechanism that proves remarkably effective at small body size. By combining morphological and biomechanical analyses of a previously overlooked vibratory organ on the abdomen, we show that planthoppers use fast, cyclical abdominal motions to generate substrate-borne vibrations. This novel, to our knowledge, mechanism, which we term the snapping organ, makes use of slow energy storage and fast elastic recoil twice during each cycle of motion, involving two distinct elastic elements. This cyclical mechanism allows planthoppers to transmit signal pulses containing a broad range of frequencies to the substrate. The mechanism is efficient, achieving fast cyclical motion without relying on high muscle power and mass, both of which are limited for animals of small size. The snapping organ is ubiquitous across planthoppers and presents an interesting example of how elastic mechanisms can be used to enable nonacoustic vibrational communication between animals.
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Affiliation(s)
| | - Alice Cicirello
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Graham K. Taylor
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Beth Mortimer
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
- * E-mail:
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42
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Abstract
In a recent work we introduced a measure of importance for groups of vertices in a complex network. This centrality for groups is always between 0 and 1 and induces the eigenvector centrality over vertices. Furthermore, its value over any group is the fraction of all network flows intercepted by this group. Here we provide the rigorous mathematical constructions underpinning these results via a semi-commutative extension of a number theoretic sieve. We then established further relations between the eigenvector centrality and the centrality proposed here, showing that the latter is a proper extension of the former to groups of nodes. We finish by comparing the centrality proposed here with the notion of group-centrality introduced by Everett and Borgatti on two real-world networks: the Wolfe's dataset and the protein-protein interaction network of the yeast Saccharomyces cerevisiae. In this latter case, we demonstrate that the centrality is able to distinguish protein complexes.
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Affiliation(s)
- Pierre-Louis Giscard
- Department of Computer Science, University of York, Deramore Lane, Heslington, York, YO10 5GH UK
| | - Richard C. Wilson
- Department of Computer Science, University of York, Deramore Lane, Heslington, York, YO10 5GH UK
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Lyons A, Knee GC, Bolduc E, Roger T, Leach J, Gauger EM, Faccio D. Attosecond-resolution Hong-Ou-Mandel interferometry. Sci Adv 2018; 4:eaap9416. [PMID: 29736414 PMCID: PMC5935478 DOI: 10.1126/sciadv.aap9416] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 03/13/2018] [Indexed: 05/24/2023]
Abstract
When two indistinguishable photons are each incident on separate input ports of a beamsplitter, they "bunch" deterministically, exiting via the same port as a direct consequence of their bosonic nature. This two-photon interference effect has long-held the potential for application in precision measurement of time delays, such as those induced by transparent specimens with unknown thickness profiles. However, the technique has never achieved resolutions significantly better than the few-femtosecond (micrometer) scale other than in a common-path geometry that severely limits applications. We develop the precision of Hong-Ou-Mandel interferometry toward the ultimate limits dictated by statistical estimation theory, achieving few-attosecond (or nanometer path length) scale resolutions in a dual-arm geometry, thus providing access to length scales pertinent to cell biology and monoatomic layer two-dimensional materials.
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Affiliation(s)
- Ashley Lyons
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
- School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
| | - George C. Knee
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Eliot Bolduc
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Thomas Roger
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Jonathan Leach
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Erik M. Gauger
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Daniele Faccio
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
- School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
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Chamberlain BP, Levy-Kramer J, Humby C, Deisenroth MP. Real-time community detection in full social networks on a laptop. PLoS One 2018; 13:e0188702. [PMID: 29342158 PMCID: PMC5771570 DOI: 10.1371/journal.pone.0188702] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/20/2017] [Indexed: 11/19/2022] Open
Abstract
For a broad range of research and practical applications it is important to understand the allegiances, communities and structure of key players in society. One promising direction towards extracting this information is to exploit the rich relational data in digital social networks (the social graph). As global social networks (e.g., Facebook and Twitter) are very large, most approaches make use of distributed computing systems for this purpose. Distributing graph processing requires solving many difficult engineering problems, which has lead some researchers to look at single-machine solutions that are faster and easier to maintain. In this article, we present an approach for analyzing full social networks on a standard laptop, allowing for interactive exploration of the communities in the locality of a set of user specified query vertices. The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates the edge weights between vertices in a derived graph. Local communities can be constructed by selecting vertices that are connected to the query vertices with high edge weights in the derived graph. This compression is robust to noise and allows for interactive queries of local communities in real-time, which we define to be less than the average human reaction time of 0.25s. We achieve single-machine real-time performance by compressing the neighborhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing. These techniques reduce query times from hours using industrial desktop machines operating on the full graph to milliseconds on standard laptops. Our method allows exploration of strongly associated regions (i.e., communities) of large graphs in real-time on a laptop. It has been deployed in software that is actively used by social network analysts and offers another channel for media owners to monetize their data, helping them to continue to provide free services that are valued by billions of people globally.
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Rollinson AN. Engineering and technology of industrial water power at Castleford Mills from the seventeenth century to the twentieth century. Notes Rec R Soc Lond 2016; 70:45-63. [PMID: 31390388 PMCID: PMC4759717 DOI: 10.1098/rsnr.2015.0044] [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] [Indexed: 06/10/2023]
Abstract
This article tells the story of engineering and technology at Castleford Water Mills from the seventeenth century to the twentieth century through the presentation of recently discovered design plans and deeds, supplemented by other historical research. One of Castleford's mills was operated by Dr Thomas Allinson's Natural Food Company and therefore retained stoneground milling when fashions for white flour prompted other mills to switch to roller systems. The millstones were powered by a high-efficiency breastshot wheel, believed to be the last of its type taken out of industrial service in Britain. Many of its features, and its subsequent longevity, can be attributed to the influential works of William Fairbairn and John Smeaton. Detailed colour designs show the construction specifications of this water-wheel and its civil housing, along with other engineering plans such as a previously unrecorded Henry Simon horizontal turbine. Links with John Smeaton and the entry in his catalogue of designs for Castleford Oil Mill are also explored, and a former flood mill is identified at the site.
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