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1. Photosynthetic responses to temperature across the tropics: a meta-analytic approach

Author

Carter, Kelsey R, Cavaleri, Molly A, Atkin, Owen K, Bahar, Nur HA, Cheesman, Alex W, Choury, Zineb, Crous, Kristine Y, Doughty, Christopher E, Dusenge, Mirindi E, Ely, Kim S, Evans, John R, da Silva, Jéssica Fonseca, Mau, Alida C, Medlyn, Belinda E, Meir, Patrick, Norby, Richard J, Read, Jennifer, Reed, Sasha C, Reich, Peter B, Rogers, Alistair, Serbin, Shawn P, Slot, Martijn, Schwartz, Elsa C, Tribuzy, Edgard S, Uddling, Johan, Vårhammar, Angelica, Walker, Anthony P, Winter, Klaus, Wood, Tana E, and Wu, Jin

Subjects
Plant Biology, Biological Sciences, Ecology, Climate Action, A-Ci curves, Maximum rate of Rubisco carboxylation, Maximum rate of photosynthetic electron transport, Meta-analysis, Photosynthesis, Temperature Response, Tropics, Forestry Sciences, Plant Biology & Botany, Plant biology
Abstract

Background and aimsTropical forests exchange more carbon dioxide (CO2) with the atmosphere than any other terrestrial biome. Yet, uncertainty in the projected carbon balance over the next century is roughly three-times greater for the tropics than other ecosystems. Our limited knowledge of tropical plant physiological responses, including photosynthetic, to climate change is a substantial source of uncertainty in our ability to forecast the global terrestrial carbon sink.MethodsWe used a meta-analytic approach, focusing on tropical photosynthetic temperature responses, to address this knowledge gap. Our dataset, gleaned from 18 independent studies, included leaf-level light saturated photosynthetic (Asat) temperature responses from 108 woody species, with additional temperature parameters (35 species) and rates (250 species) of both maximum rates of electron transport (Jmax) and Rubisco carboxylation (Vcmax). We investigated how these parameters responded to mean annual temperature (MAT), temperature variability, aridity, and elevation, as well as also how responses differed among successional strategy, leaf habit, and light environment.Key resultsOptimum temperatures for Asat (ToptA) and Jmax (ToptJ) increased with MAT but not for Vcmax (ToptV). Although photosynthetic rates were higher for "light" than "shaded" leaves, light conditions did not generate differences in temperature response parameters. ToptA did not differ with successional strategy, but early successional species had ~4 °C wider thermal niches than mid/late species. Semi-deciduous species had ~1 °C higher ToptA than broadleaf evergreen. Most global modeling efforts consider all tropical forests as a single "broadleaf evergreen" functional type, but our data show that tropical species with different leaf habits display distinct temperature responses that should be included in modeling efforts.ConclusionsThis novel research will inform modeling efforts to quantify tropical ecosystem carbon cycling and provide more accurate representations of how these key ecosystems will respond to altered temperature patterns in the face of climate warming.

Published
2024

2. A Gamma-ray Stacking Survey of Fermi-LAT Undetected Globular Clusters

Author

Henry, Owen K., Paglione, Timothy A. D., Song, Yuzhe, Tan, Joshua, Zurek, David, and Pinto, Vanessa

Subjects
Astrophysics - High Energy Astrophysical Phenomena
Abstract

We present evidence for $\gamma$-ray emission from a stacked population of 39 high-latitude globular clusters (GCs) not detected in the Fermi Point Source Catalog, likely attributable to populations of millisecond pulsars within them. In this work, we use 13 years of data collected by the Large Area Telescope aboard the Fermi Gamma-Ray Space Telescope to search for a cumulative signal from undetected GCs and compared them to control fields (CFs), selected to match the celestial distribution of the target clusters so as to distinguish the $\gamma$-ray signal from background emission. The joint likelihood distribution of the GCs has a significant separation ($\sim4\sigma$) from that of the CFs. We also investigate correlations between detected cluster luminosities and other cluster properties such as distance, the number of millisecond pulsars associated with each cluster, and stellar encounter rate but find no significant relationships., Comment: 9 pages, 9 figures

Published
2024

3. Linking leaf dark respiration to leaf traits and reflectance spectroscopy across diverse forest types

Author

Wu, Fengqi, Liu, Shuwen, Lamour, Julien, Atkin, Owen K, Yang, Nan, Dong, Tingting, Xu, Weiying, Smith, Nicholas G, Wang, Zhihui, Wang, Han, Su, Yanjun, Liu, Xiaojuan, Shi, Yue, Xing, Aijun, Dai, Guanhua, Dong, Jinlong, Swenson, Nathan G, Kattge, Jens, Reich, Peter B, Serbin, Shawn P, Rogers, Alistair, Wu, Jin, and Yan, Zhengbing

Subjects
Environmental Sciences, Biological Sciences, Ecology, Life on Land, carbon cycling, gas exchange, leaf mitochondrial respiration, leaf spectroscopy, partial least squares regression, plant functional traits, transferability, Agricultural and Veterinary Sciences, Plant Biology & Botany, Plant biology, Climate change impacts and adaptation, Ecological applications
Abstract

Leaf dark respiration (Rdark), an important yet rarely quantified component of carbon cycling in forest ecosystems, is often simulated from leaf traits such as the maximum carboxylation capacity (Vcmax), leaf mass per area (LMA), nitrogen (N) and phosphorus (P) concentrations, in terrestrial biosphere models. However, the validity of these relationships across forest types remains to be thoroughly assessed. Here, we analyzed Rdark variability and its associations with Vcmax and other leaf traits across three temperate, subtropical and tropical forests in China, evaluating the effectiveness of leaf spectroscopy as a superior monitoring alternative. We found that leaf magnesium and calcium concentrations were more significant in explaining cross-site Rdark than commonly used traits like LMA, N and P concentrations, but univariate trait-Rdark relationships were always weak (r2 ≤ 0.15) and forest-specific. Although multivariate relationships of leaf traits improved the model performance, leaf spectroscopy outperformed trait-Rdark relationships, accurately predicted cross-site Rdark (r2 = 0.65) and pinpointed the factors contributing to Rdark variability. Our findings reveal a few novel traits with greater cross-site scalability regarding Rdark, challenging the use of empirical trait-Rdark relationships in process models and emphasize the potential of leaf spectroscopy as a promising alternative for estimating Rdark, which could ultimately improve process modeling of terrestrial plant respiration.

Published
2024

5. Temperature responses of ecosystem respiration

Author

Niu, Shuli, Chen, Weinan, Liáng, Lìyǐn L., Sierra, Carlos A., Xia, Jianyang, Wang, Song, Heskel, Mary, Patel, Kaizad F., Bond-Lamberty, Ben, Wang, Jinsong, Yvon-Durocher, Gabriel, Kirschbaum, Miko U. F., Atkin, Owen K., Huang, Yuanyuan, Yu, Guirui, and Luo, Yiqi

Published
2024
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6. Protease shaving of Mycobacterium tuberculosis facilitates vaccine antigen discovery and delivery of novel cargoes to the Mtb surface

Author

Bianca A. Lepe, Christine R. Zheng, Owen K. Leddy, Benjamin L. Allsup, Sydney L. Solomon, and Bryan D. Bryson

Subjects
tuberculosis, cell surface, proteomics, surface antigens, Microbiology, QR1-502
Abstract

ABSTRACT Tuberculosis (TB) is the leading cause of infectious disease death and lacks a vaccine capable of protecting adults from pulmonary TB. The bacterial surface is a critical interface that shapes host-pathogen interactions. Several knowledge gaps persist in our understanding of Mycobacterium tuberculosis (Mtb)-host interactions that may be addressed by an improved understanding of the Mtb surface proteome, including the identification of novel vaccine targets as well as developing new approaches to interrogate host-pathogen interactions. Here, we sought to expand our understanding of the Mtb surface proteome in service of these knowledge gaps by adapting protease shaving protocols for multiplexed quantitative mass spectrometry. Pairing quantitative mass spectrometry with the construction of validation strains, we revealed several novel Mtb proteins on the Mtb surface largely derived from the PE/PPE class of Mtb proteins, including PPE18, a component of a leading Mtb vaccine candidate. We next exploited the localization of PPE18 to decorate the Mtb surface with heterologous proteins. Together, these studies reveal potential novel targets for new Mtb vaccines as well as facilitate new approaches to study difficult-to-study cellular compartments during bacterial growth and infection.IMPORTANCEThe surface of a bacterial pathogen is a critical interface between the bacterium and the immune system. A better understanding of this interface would facilitate the discovery of new vaccine targets, new virulence proteins, and enable new technologies that modify the bacterial surface. In this study, we established a multiplexed and quantitative biochemical strategy to study the surface of Mycobacterium tuberculosis (Mtb) and identified new vaccine targets. We furthermore established design rules for new technologies aimed at modifying the composition of the bacterial surface. Specifically, we achieved a biological milestone that has not been rigorously reported previously, which is the successful modification of the Mtb surface with a non-native protein.

Published
2025
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7. The fully coupled regionally refined model of E3SM version 2: overview of the atmosphere, land, and river results

Author

Tang, Qi, Golaz, Jean-Christophe, Van Roekel, Luke P, Taylor, Mark A, Lin, Wuyin, Hillman, Benjamin R, Ullrich, Paul A, Bradley, Andrew M, Guba, Oksana, Wolfe, Jonathan D, Zhou, Tian, Zhang, Kai, Zheng, Xue, Zhang, Yunyan, Zhang, Meng, Wu, Mingxuan, Wang, Hailong, Tao, Cheng, Singh, Balwinder, Rhoades, Alan M, Qin, Yi, Li, Hong-Yi, Feng, Yan, Zhang, Yuying, Zhang, Chengzhu, Zender, Charles S, Xie, Shaocheng, Roesler, Erika L, Roberts, Andrew F, Mametjanov, Azamat, Maltrud, Mathew E, Keen, Noel D, Jacob, Robert L, Jablonowski, Christiane, Hughes, Owen K, Forsyth, Ryan M, Di Vittorio, Alan V, Caldwell, Peter M, Bisht, Gautam, McCoy, Renata B, Leung, L Ruby, and Bader, David C

Subjects
Earth Sciences, Oceanography, Atmospheric Sciences, Climate Action, Earth sciences
Abstract

This paper provides an overview of the United States (US) Department of Energy's (DOE's) Energy Exascale Earth System Model version 2 (E3SMv2) fully coupled regionally refined model (RRM) and documents the overall atmosphere, land, and river results from the Coupled Model Intercomparison Project 6 (CMIP6) DECK (Diagnosis, Evaluation, and Characterization of Klima) and historical simulations - a first-of-its-kind set of climate production simulations using RRM. The North American (NA) RRM (NARRM) is developed as the high-resolution configuration of E3SMv2 with the primary goal of more explicitly addressing DOE's mission needs regarding impacts to the US energy sector facing Earth system changes. The NARRM features finer horizontal resolution grids centered over NA, consisting of 25→100¯km atmosphere and land, a 0.125 river-routing model, and 14→60¯km ocean and sea ice. By design, the computational cost of NARRM is 1/43× of the uniform low-resolution (LR) model at 100¯km but only 1/4¯10¯%-20¯% of a globally uniform high-resolution model at 25¯km. A novel hybrid time step strategy for the atmosphere is key for NARRM to achieve improved climate simulation fidelity within the high-resolution patch without sacrificing the overall global performance. The global climate, including climatology, time series, sensitivity, and feedback, is confirmed to be largely identical between NARRM and LR as quantified with typical climate metrics. Over the refined NA area, NARRM is generally superior to LR, including for precipitation and clouds over the contiguous US (CONUS), summertime marine stratocumulus clouds off the coast of California, liquid and ice phase clouds near the North Pole region, extratropical cyclones, and spatial variability in land hydrological processes. The improvements over land are related to the better-resolved topography in NARRM, whereas those over ocean are attributable to the improved air-sea interactions with finer grids for both atmosphere and ocean and sea ice. Some features appear insensitive to the resolution change analyzed here, for instance the diurnal propagation of organized mesoscale convective systems over CONUS and the warm-season land-atmosphere coupling at the southern Great Plains. In summary, our study presents a realistically efficient approach to leverage the fully coupled RRM framework for a standard Earth system model release and high-resolution climate production simulations.

Published
2023

8. The global spectrum of plant form and function: enhanced species-level trait dataset.

Author

Díaz, Sandra, Kattge, Jens, Cornelissen, Johannes HC, Wright, Ian J, Lavorel, Sandra, Dray, Stéphane, Reu, Björn, Kleyer, Michael, Wirth, Christian, Prentice, I Colin, Garnier, Eric, Bönisch, Gerhard, Westoby, Mark, Poorter, Hendrik, Reich, Peter B, Moles, Angela T, Dickie, John, Zanne, Amy E, Chave, Jérôme, Wright, S Joseph, Sheremetiev, Serge N, Jactel, Hervé, Baraloto, Christopher, Cerabolini, Bruno EL, Pierce, Simon, Shipley, Bill, Casanoves, Fernando, Joswig, Julia S, Günther, Angela, Falczuk, Valeria, Rüger, Nadja, Mahecha, Miguel D, Gorné, Lucas D, Amiaud, Bernard, Atkin, Owen K, Bahn, Michael, Baldocchi, Dennis, Beckmann, Michael, Blonder, Benjamin, Bond, William, Bond-Lamberty, Ben, Brown, Kerry, Burrascano, Sabina, Byun, Chaeho, Campetella, Giandiego, Cavender-Bares, Jeannine, Chapin, F Stuart, Choat, Brendan, Coomes, David Anthony, Cornwell, William K, Craine, Joseph, Craven, Dylan, Dainese, Matteo, de Araujo, Alessandro Carioca, de Vries, Franciska T, Domingues, Tomas Ferreira, Enquist, Brian J, Fagúndez, Jaime, Fang, Jingyun, Fernández-Méndez, Fernando, Fernandez-Piedade, Maria T, Ford, Henry, Forey, Estelle, Freschet, Gregoire T, Gachet, Sophie, Gallagher, Rachael, Green, Walton, Guerin, Greg R, Gutiérrez, Alvaro G, Harrison, Sandy P, Hattingh, Wesley Neil, He, Tianhua, Hickler, Thomas, Higgins, Steven I, Higuchi, Pedro, Ilic, Jugo, Jackson, Robert B, Jalili, Adel, Jansen, Steven, Koike, Fumito, König, Christian, Kraft, Nathan, Kramer, Koen, Kreft, Holger, Kühn, Ingolf, Kurokawa, Hiroko, Lamb, Eric G, Laughlin, Daniel C, Leishman, Michelle, Lewis, Simon, Louault, Frédérique, Malhado, Ana CM, Manning, Peter, Meir, Patrick, Mencuccini, Maurizio, Messier, Julie, Miller, Regis, Minden, Vanessa, Molofsky, Jane, and Montgomery, Rebecca

Abstract

Here we provide the 'Global Spectrum of Plant Form and Function Dataset', containing species mean values for six vascular plant traits. Together, these traits -plant height, stem specific density, leaf area, leaf mass per area, leaf nitrogen content per dry mass, and diaspore (seed or spore) mass - define the primary axes of variation in plant form and function. The dataset is based on ca. 1 million trait records received via the TRY database (representing ca. 2,500 original publications) and additional unpublished data. It provides 92,159 species mean values for the six traits, covering 46,047 species. The data are complemented by higher-level taxonomic classification and six categorical traits (woodiness, growth form, succulence, adaptation to terrestrial or aquatic habitats, nutrition type and leaf type). Data quality management is based on a probabilistic approach combined with comprehensive validation against expert knowledge and external information. Intense data acquisition and thorough quality control produced the largest and, to our knowledge, most accurate compilation of empirically observed vascular plant species mean traits to date.

Published
2022

10. Molecular conflicts disrupting centromere maintenance contribute to Xenopus hybrid inviability

Author

Kitaoka, Maiko, Smith, Owen K, Straight, Aaron F, and Heald, Rebecca

Subjects
Biological Sciences, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Centromere, Centromere Protein A, Chromatin, Chromosomal Proteins, Non-Histone, DNA, Ribosomal, Histones, Male, RNA Polymerase I, Semen, Xenopus laevis, CENP-A, Xenopus, centromere, chromosome segregation, hybrid incompatibility, speciation, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Psychology
Abstract

Although central to evolution, the causes of hybrid inviability that drive reproductive isolation are poorly understood. Embryonic lethality occurs when the eggs of the frog X. tropicalis are fertilized with either X. laevis or X. borealis sperm. We observed that distinct subsets of paternal chromosomes failed to assemble functional centromeres, causing their mis-segregation during embryonic cell divisions. Core centromere DNA sequence analysis revealed little conservation among the three species, indicating that epigenetic mechanisms that normally operate to maintain centromere integrity are disrupted on specific paternal chromosomes in hybrids. In vitro reactions combining X. tropicalis egg extract with either X. laevis or X. borealis sperm chromosomes revealed that paternally matched or overexpressed centromeric histone CENP-A and its chaperone HJURP could rescue centromere assembly on affected chromosomes in interphase nuclei. However, although the X. laevis chromosomes maintained centromeric CENP-A in metaphase, X. borealis chromosomes did not and also displayed ultra-thin regions containing ribosomal DNA. Both centromere assembly and morphology of X. borealis mitotic chromosomes could be rescued by inhibiting RNA polymerase I or preventing the collapse of stalled DNA replication forks. These results indicate that specific paternal centromeres are inactivated in hybrids due to the disruption of associated chromatin regions that interfere with CENP-A incorporation, at least in some cases due to conflicts between replication and transcription machineries. Thus, our findings highlight the dynamic nature of centromere maintenance and its susceptibility to disruption in vertebrate interspecies hybrids.

Published
2022

11. DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide

Author

Altemose, Nicolas, Maslan, Annie, Smith, Owen K, Sundararajan, Kousik, Brown, Rachel R, Mishra, Reet, Detweiler, Angela M, Neff, Norma, Miga, Karen H, Straight, Aaron F, and Streets, Aaron

Subjects
Biotechnology, Human Genome, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Centromere Protein A, Chromatin, DNA, DNA Methylation, Genome, Human, High-Throughput Nucleotide Sequencing, Humans, Sequence Analysis, DNA, Biological Sciences, Technology, Medical and Health Sciences, Developmental Biology
Abstract

Studies of genome regulation routinely use high-throughput DNA sequencing approaches to determine where specific proteins interact with DNA, and they rely on DNA amplification and short-read sequencing, limiting their quantitative application in complex genomic regions. To address these limitations, we developed directed methylation with long-read sequencing (DiMeLo-seq), which uses antibody-tethered enzymes to methylate DNA near a target protein's binding sites in situ. These exogenous methylation marks are then detected simultaneously with endogenous CpG methylation on unamplified DNA using long-read, single-molecule sequencing technologies. We optimized and benchmarked DiMeLo-seq by mapping chromatin-binding proteins and histone modifications across the human genome. Furthermore, we identified where centromere protein A localizes within highly repetitive regions that were unmappable with short sequencing reads, and we estimated the density of centromere protein A molecules along single chromatin fibers. DiMeLo-seq is a versatile method that provides multimodal, genome-wide information for investigating protein-DNA interactions.

Published
2022

14. Identification and characterization of centromeric sequences in Xenopus laevis

Author

Smith, Owen K, Limouse, Charles, Fryer, Kelsey A, Teran, Nicole A, Sundararajan, Kousik, Heald, Rebecca, and Straight, Aaron F

Subjects
Biological Sciences, Genetics, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Animals, Centromere, Centromere Protein A, Chromatin, Nucleosomes, Repetitive Sequences, Nucleic Acid, Xenopus laevis, Medical and Health Sciences, Bioinformatics
Abstract

Centromeres play an essential function in cell division by specifying the site of kinetochore formation on each chromosome for mitotic spindle attachment. Centromeres are defined epigenetically by the histone H3 variant Centromere Protein A (Cenpa). Cenpa nucleosomes maintain the centromere by designating the site for new Cenpa assembly after dilution by replication. Vertebrate centromeres assemble on tandem arrays of repetitive sequences, but the function of repeat DNA in centromere formation has been challenging to dissect due to the difficulty in manipulating centromeres in cells. Xenopus laevis egg extracts assemble centromeres in vitro, providing a system for studying centromeric DNA functions. However, centromeric sequences in Xenopus laevis have not been extensively characterized. In this study, we combine Cenpa ChIP-seq with a k-mer based analysis approach to identify the Xenopus laevis centromere repeat sequences. By in situ hybridization, we show that Xenopus laevis centromeres contain diverse repeat sequences, and we map the centromere position on each Xenopus laevis chromosome using the distribution of centromere-enriched k-mers. Our identification of Xenopus laevis centromere sequences enables previously unapproachable centromere genomic studies. Our approach should be broadly applicable for the analysis of centromere and other repetitive sequences in any organism.

Published
2021

15. AusTraits, a curated plant trait database for the Australian flora

Author

Falster, Daniel, Gallagher, Rachael, Wenk, Elizabeth H, Wright, Ian J, Indiarto, Dony, Andrew, Samuel C, Baxter, Caitlan, Lawson, James, Allen, Stuart, Fuchs, Anne, Monro, Anna, Kar, Fonti, Adams, Mark A, Ahrens, Collin W, Alfonzetti, Matthew, Angevin, Tara, Apgaua, Deborah MG, Arndt, Stefan, Atkin, Owen K, Atkinson, Joe, Auld, Tony, Baker, Andrew, von Balthazar, Maria, Bean, Anthony, Blackman, Chris J, Bloomfield, Keith, Bowman, David MJS, Bragg, Jason, Brodribb, Timothy J, Buckton, Genevieve, Burrows, Geoff, Caldwell, Elizabeth, Camac, James, Carpenter, Raymond, Catford, Jane A, Cawthray, Gregory R, Cernusak, Lucas A, Chandler, Gregory, Chapman, Alex R, Cheal, David, Cheesman, Alexander W, Chen, Si-Chong, Choat, Brendan, Clinton, Brook, Clode, Peta L, Coleman, Helen, Cornwell, William K, Cosgrove, Meredith, Crisp, Michael, Cross, Erika, Crous, Kristine Y, Cunningham, Saul, Curran, Timothy, Curtis, Ellen, Daws, Matthew I, DeGabriel, Jane L, Denton, Matthew D, Dong, Ning, Du, Pengzhen, Duan, Honglang, Duncan, David H, Duncan, Richard P, Duretto, Marco, Dwyer, John M, Edwards, Cheryl, Esperon-Rodriguez, Manuel, Evans, John R, Everingham, Susan E, Farrell, Claire, Firn, Jennifer, Fonseca, Carlos Roberto, French, Ben J, Frood, Doug, Funk, Jennifer L, Geange, Sonya R, Ghannoum, Oula, Gleason, Sean M, Gosper, Carl R, Gray, Emma, Groom, Philip K, Grootemaat, Saskia, Gross, Caroline, Guerin, Greg, Guja, Lydia, Hahs, Amy K, Harrison, Matthew Tom, Hayes, Patrick E, Henery, Martin, Hochuli, Dieter, Howell, Jocelyn, Huang, Guomin, Hughes, Lesley, Huisman, John, Ilic, Jugoslav, Jagdish, Ashika, Jin, Daniel, Jordan, Gregory, Jurado, Enrique, Kanowski, John, and Kasel, Sabine

Subjects
Plant Biology, Biological Sciences, Ecology, Australia, Databases, Factual, Phenotype, Plant Physiological Phenomena, Plants
Abstract

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.

Published
2021

17. The global spectrum of plant form and function: enhanced species-level trait dataset

Author

Sandra Díaz, Jens Kattge, Johannes H. C. Cornelissen, Ian J. Wright, Sandra Lavorel, Stéphane Dray, Björn Reu, Michael Kleyer, Christian Wirth, I. Colin Prentice, Eric Garnier, Gerhard Bönisch, Mark Westoby, Hendrik Poorter, Peter B. Reich, Angela T. Moles, John Dickie, Amy E. Zanne, Jérôme Chave, S. Joseph Wright, Serge N. Sheremetiev, Hervé Jactel, Christopher Baraloto, Bruno E. L. Cerabolini, Simon Pierce, Bill Shipley, Fernando Casanoves, Julia S. Joswig, Angela Günther, Valeria Falczuk, Nadja Rüger, Miguel D. Mahecha, Lucas D. Gorné, Bernard Amiaud, Owen K. Atkin, Michael Bahn, Dennis Baldocchi, Michael Beckmann, Benjamin Blonder, William Bond, Ben Bond-Lamberty, Kerry Brown, Sabina Burrascano, Chaeho Byun, Giandiego Campetella, Jeannine Cavender-Bares, F. Stuart Chapin, Brendan Choat, David Anthony Coomes, William K. Cornwell, Joseph Craine, Dylan Craven, Matteo Dainese, Alessandro Carioca de Araujo, Franciska T. de Vries, Tomas Ferreira Domingues, Brian J. Enquist, Jaime Fagúndez, Jingyun Fang, Fernando Fernández-Méndez, Maria T. Fernandez-Piedade, Henry Ford, Estelle Forey, Gregoire T. Freschet, Sophie Gachet, Rachael Gallagher, Walton Green, Greg R. Guerin, Alvaro G. Gutiérrez, Sandy P. Harrison, Wesley Neil Hattingh, Tianhua He, Thomas Hickler, Steven I. Higgins, Pedro Higuchi, Jugo Ilic, Robert B. Jackson, Adel Jalili, Steven Jansen, Fumito Koike, Christian König, Nathan Kraft, Koen Kramer, Holger Kreft, Ingolf Kühn, Hiroko Kurokawa, Eric G. Lamb, Daniel C. Laughlin, Michelle Leishman, Simon Lewis, Frédérique Louault, Ana C. M. Malhado, Peter Manning, Patrick Meir, Maurizio Mencuccini, Julie Messier, Regis Miller, Vanessa Minden, Jane Molofsky, Rebecca Montgomery, Gabriel Montserrat-Martí, Marco Moretti, Sandra Müller, Ülo Niinemets, Romà Ogaya, Kinga Öllerer, Vladimir Onipchenko, Yusuke Onoda, Wim A. Ozinga, Juli G. Pausas, Begoña Peco, Josep Penuelas, Valério D. Pillar, Clara Pladevall, Christine Römermann, Lawren Sack, Norma Salinas, Brody Sandel, Jordi Sardans, Brandon Schamp, Michael Scherer-Lorenzen, Ernst-Detlef Schulze, Fritz Schweingruber, Satomi Shiodera, Ênio Sosinski, Nadejda Soudzilovskaia, Marko J. Spasojevic, Emily Swaine, Nathan Swenson, Susanne Tautenhahn, Ken Thompson, Alexia Totte, Rocío Urrutia-Jalabert, Fernando Valladares, Peter van Bodegom, François Vasseur, Kris Verheyen, Denis Vile, Cyrille Violle, Betsy von Holle, Patrick Weigelt, Evan Weiher, Michael C. Wiemann, Mathew Williams, Justin Wright, and Gerhard Zotz

Subjects
Science
Abstract

Measurement(s) plant trait Technology Type(s) various Factor Type(s) none Sample Characteristic - Organism Tracheophyta Sample Characteristic - Environment natural environment Sample Characteristic - Location global

Published
2022
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19. Technical Report for Real-Time Certified Probabilistic Pedestrian Forecasting

Author

Jacobs, Henry O., Hughes, Owen K., Johnson-Roberson, Matthew, and Vasudevan, Ram

Subjects
Computer Science - Robotics, Mathematics - Optimization and Control
Abstract

The success of autonomous systems will depend upon their ability to safely navigate human-centric environments. This motivates the need for a real-time, probabilistic forecasting algorithm for pedestrians, cyclists, and other agents since these predictions will form a necessary step in assessing the risk of any action. This paper presents a novel approach to probabilistic forecasting for pedestrians based on weighted sums of ordinary differential equations that are learned from historical trajectory information within a fixed scene. The resulting algorithm is embarrassingly parallel and is able to work at real-time speeds using a naive Python implementation. The quality of predicted locations of agents generated by the proposed algorithm is validated on a variety of examples and considerably higher than existing state of the art approaches over long time horizons., Comment: This is an augmented version of our paper published in RA-L containing additional material that was cut from the paper

Published
2017

25. Leaf trait variation is similar among genotypes of Eucalyptus camaldulensis from differing climates and arises in plastic responses to the seasons rather than water availability

Author

Asao, Shinichi, Hayes, Lucy, Aspinwall, Michael J., Rymer, Paul D., Blackman, Chris, Bryant, Callum J., Cullerne, Darren, Egerton, John J. G., Fan, Yuzhen, Innes, Peter, Millar, A. Harvey, Tucker, Josephine, Shah, Shahen, Wright, Ian J., Yvon-Durocher, Gabriel, Tissue, David, and Atkin, Owen K.

Published
2020

26. AusTraits, a curated plant trait database for the Australian flora

Author

Daniel Falster, Rachael Gallagher, Elizabeth H. Wenk, Ian J. Wright, Dony Indiarto, Samuel C. Andrew, Caitlan Baxter, James Lawson, Stuart Allen, Anne Fuchs, Anna Monro, Fonti Kar, Mark A. Adams, Collin W. Ahrens, Matthew Alfonzetti, Tara Angevin, Deborah M. G. Apgaua, Stefan Arndt, Owen K. Atkin, Joe Atkinson, Tony Auld, Andrew Baker, Maria von Balthazar, Anthony Bean, Chris J. Blackman, Keith Bloomfield, David M. J. S. Bowman, Jason Bragg, Timothy J. Brodribb, Genevieve Buckton, Geoff Burrows, Elizabeth Caldwell, James Camac, Raymond Carpenter, Jane A. Catford, Gregory R. Cawthray, Lucas A. Cernusak, Gregory Chandler, Alex R. Chapman, David Cheal, Alexander W. Cheesman, Si-Chong Chen, Brendan Choat, Brook Clinton, Peta L. Clode, Helen Coleman, William K. Cornwell, Meredith Cosgrove, Michael Crisp, Erika Cross, Kristine Y. Crous, Saul Cunningham, Timothy Curran, Ellen Curtis, Matthew I. Daws, Jane L. DeGabriel, Matthew D. Denton, Ning Dong, Pengzhen Du, Honglang Duan, David H. Duncan, Richard P. Duncan, Marco Duretto, John M. Dwyer, Cheryl Edwards, Manuel Esperon-Rodriguez, John R. Evans, Susan E. Everingham, Claire Farrell, Jennifer Firn, Carlos Roberto Fonseca, Ben J. French, Doug Frood, Jennifer L. Funk, Sonya R. Geange, Oula Ghannoum, Sean M. Gleason, Carl R. Gosper, Emma Gray, Philip K. Groom, Saskia Grootemaat, Caroline Gross, Greg Guerin, Lydia Guja, Amy K. Hahs, Matthew Tom Harrison, Patrick E. Hayes, Martin Henery, Dieter Hochuli, Jocelyn Howell, Guomin Huang, Lesley Hughes, John Huisman, Jugoslav Ilic, Ashika Jagdish, Daniel Jin, Gregory Jordan, Enrique Jurado, John Kanowski, Sabine Kasel, Jürgen Kellermann, Belinda Kenny, Michele Kohout, Robert M. Kooyman, Martyna M. Kotowska, Hao Ran Lai, Etienne Laliberté, Hans Lambers, Byron B. Lamont, Robert Lanfear, Frank van Langevelde, Daniel C. Laughlin, Bree-Anne Laugier-Kitchener, Susan Laurance, Caroline E. R. Lehmann, Andrea Leigh, Michelle R. Leishman, Tanja Lenz, Brendan Lepschi, James D. Lewis, Felix Lim, Udayangani Liu, Janice Lord, Christopher H. Lusk, Cate Macinnis-Ng, Hannah McPherson, Susana Magallón, Anthony Manea, Andrea López-Martinez, Margaret Mayfield, James K. McCarthy, Trevor Meers, Marlien van der Merwe, Daniel J. Metcalfe, Per Milberg, Karel Mokany, Angela T. Moles, Ben D. Moore, Nicholas Moore, John W. Morgan, William Morris, Annette Muir, Samantha Munroe, Áine Nicholson, Dean Nicolle, Adrienne B. Nicotra, Ülo Niinemets, Tom North, Andrew O’Reilly-Nugent, Odhran S. O’Sullivan, Brad Oberle, Yusuke Onoda, Mark K. J. Ooi, Colin P. Osborne, Grazyna Paczkowska, Burak Pekin, Caio Guilherme Pereira, Catherine Pickering, Melinda Pickup, Laura J. Pollock, Pieter Poot, Jeff R. Powell, Sally A. Power, Iain Colin Prentice, Lynda Prior, Suzanne M. Prober, Jennifer Read, Victoria Reynolds, Anna E. Richards, Ben Richardson, Michael L. Roderick, Julieta A. Rosell, Maurizio Rossetto, Barbara Rye, Paul D. Rymer, Michael A. Sams, Gordon Sanson, Hervé Sauquet, Susanne Schmidt, Jürg Schönenberger, Ernst-Detlef Schulze, Kerrie Sendall, Steve Sinclair, Benjamin Smith, Renee Smith, Fiona Soper, Ben Sparrow, Rachel J. Standish, Timothy L. Staples, Ruby Stephens, Christopher Szota, Guy Taseski, Elizabeth Tasker, Freya Thomas, David T. Tissue, Mark G. Tjoelker, David Yue Phin Tng, Félix de Tombeur, Kyle Tomlinson, Neil C. Turner, Erik J. Veneklaas, Susanna Venn, Peter Vesk, Carolyn Vlasveld, Maria S. Vorontsova, Charles A. Warren, Nigel Warwick, Lasantha K. Weerasinghe, Jessie Wells, Mark Westoby, Matthew White, Nicholas S. G. Williams, Jarrah Wills, Peter G. Wilson, Colin Yates, Amy E. Zanne, Graham Zemunik, and Kasia Ziemińska

Subjects
Science
Abstract

Measurement(s) plant trait Technology Type(s) digital curation Sample Characteristic - Organism Viridiplantae Sample Characteristic - Location Australia Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.14545755

Published
2021
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28. Addressing Research Bottlenecks to Crop Productivity

Author

Reynolds, Matthew, Atkin, Owen K., Bennett, Malcolm, Cooper, Mark, Dodd, Ian C., Foulkes, M. John, Frohberg, Claus, Hammer, Graeme, Henderson, Ian R., Huang, Bingru, Korzun, Viktor, McCouch, Susan R., Messina, Carlos D., Pogson, Barry J., Slafer, Gustavo A., Taylor, Nicolas L., and Wittich, Peter E.

Published
2021
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29. Mapping local and global variability in plant trait distributions

Author

Butler, Ethan E, Datta, Abhirup, Flores-Moreno, Habacuc, Chen, Ming, Wythers, Kirk R, Fazayeli, Farideh, Banerjee, Arindam, Atkin, Owen K, Kattge, Jens, Amiaud, Bernard, Blonder, Benjamin, Boenisch, Gerhard, Bond-Lamberty, Ben, Brown, Kerry A, Byun, Chaeho, Campetella, Giandiego, Cerabolini, Bruno EL, Cornelissen, Johannes HC, Craine, Joseph M, Craven, Dylan, de Vries, Franciska T, Díaz, Sandra, Domingues, Tomas F, Forey, Estelle, González-Melo, Andrés, Gross, Nicolas, Han, Wenxuan, Hattingh, Wesley N, Hickler, Thomas, Jansen, Steven, Kramer, Koen, Kraft, Nathan JB, Kurokawa, Hiroko, Laughlin, Daniel C, Meir, Patrick, Minden, Vanessa, Niinemets, Ülo, Onoda, Yusuke, Peñuelas, Josep, Read, Quentin, Sack, Lawren, Schamp, Brandon, Soudzilovskaia, Nadejda A, Spasojevic, Marko J, Sosinski, Enio, Thornton, Peter E, Valladares, Fernando, van Bodegom, Peter M, Williams, Mathew, Wirth, Christian, and Reich, Peter B

Subjects
Ecosystem, Environment, Geography, Models, Statistical, Plant Dispersal, Plants, Quantitative Trait, Heritable, Spatial Analysis, plant traits, Bayesian modeling, spatial statistics, global, climate
Abstract

Our ability to understand and predict the response of ecosystems to a changing environment depends on quantifying vegetation functional diversity. However, representing this diversity at the global scale is challenging. Typically, in Earth system models, characterization of plant diversity has been limited to grouping related species into plant functional types (PFTs), with all trait variation in a PFT collapsed into a single mean value that is applied globally. Using the largest global plant trait database and state of the art Bayesian modeling, we created fine-grained global maps of plant trait distributions that can be applied to Earth system models. Focusing on a set of plant traits closely coupled to photosynthesis and foliar respiration-specific leaf area (SLA) and dry mass-based concentrations of leaf nitrogen ([Formula: see text]) and phosphorus ([Formula: see text]), we characterize how traits vary within and among over 50,000 [Formula: see text]-km cells across the entire vegetated land surface. We do this in several ways-without defining the PFT of each grid cell and using 4 or 14 PFTs; each model's predictions are evaluated against out-of-sample data. This endeavor advances prior trait mapping by generating global maps that preserve variability across scales by using modern Bayesian spatial statistical modeling in combination with a database over three times larger than that in previous analyses. Our maps reveal that the most diverse grid cells possess trait variability close to the range of global PFT means.

Published
2017

31. A gamma-ray stacking survey of Fermi-LAT undetected globular clusters.

Author

Henry, Owen K, Paglione, Timothy A D, (宋宇哲), Yuzhe Song, Tan, Joshua, Zurek, David, and Pinto, Vanessa

Subjects
*FERMI Gamma-ray Space Telescope (Spacecraft), *PULSARS, *ACQUISITION of data, *LUMINOSITY
Abstract

We present evidence for |$\gamma$| -ray emission from a stacked population of 39 high-latitude globular clusters (GCs) not detected in the Fermi Point Source Catalogue, likely attributable to populations of millisecond pulsars within them. In this work, we use 13 yr of data collected by the Large Area Telescope aboard the Fermi Gamma-Ray Space Telescope to search for a cumulative signal from undetected GCs and compared them to control fields (CFs), selected to match the celestial distribution of the target clusters so as to distinguish the |$\gamma$| -ray signal from background emission. The joint likelihood distribution of the GCs has a significant separation (⁠|$\sim 4\sigma$|⁠) from that of the CFs. We also investigate correlations between detected cluster luminosities and other cluster properties such as distance, the number of millisecond pulsars associated with each cluster, and stellar encounter rate but find no significant relationships. [ABSTRACT FROM AUTHOR]

Published
2024
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36. Robustness of trait connections across environmental gradients and growth forms

Author

Flores-Moreno, Habacuc, Fazayeli, Farideh, Banerjee, Arindam, Datta, Abhirup, Kattge, Jens, Butler, Ethan E., Atkin, Owen K., Wythers, Kirk, Chen, Ming, Anand, Madhur, Bahn, Michael, Byun, Chaeho, Cornelissen, J. Hans C., Craine, Joseph, Gonzalez-Melo, Andres, Hattingh, Wesley N., Jansen, Steven, Kraft, Nathan J. B., Kramer, Koen, Laughlin, Daniel C., Minden, Vanessa, Niinemets, Ülo, Onipchenko, Vladimir, Peñuelas, Josep, Soudzilovskaia, Nadejda A., Dalrymple, Rhiannon L., and Reich, Peter B.

Published
2019

42. Gradient of Developmental and Injury Response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity

Author

Richards, Laura M., Whitley, Owen K. N., MacLeod, Graham, Cavalli, Florence M. G., Coutinho, Fiona J., Jaramillo, Julia E., Svergun, Nataliia, Riverin, Mazdak, Croucher, Danielle C., Kushida, Michelle, Yu, Kenny, Guilhamon, Paul, Rastegar, Naghmeh, Ahmadi, Moloud, Bhatti, Jasmine K., Bozek, Danielle A., Li, Naijin, Lee, Lilian, Che, Clare, Luis, Erika, Park, Nicole I., Xu, Zhiyu, Ketela, Troy, Moore, Richard A., Marra, Marco A., Spears, Julian, Cusimano, Michael D., Das, Sunit, Bernstein, Mark, Haibe-Kains, Benjamin, Lupien, Mathieu, Luchman, H. Artee, Weiss, Samuel, Angers, Stephane, Dirks, Peter B., Bader, Gary D., and Pugh, Trevor J.

Published
2021
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45. Lipid biomarkers and compound specific δ13C analysis indicate early development of a dual-economic system for the Arctic Small Tool tradition in northern Alaska

Author

Buonasera, Tammy Y, Tremayne, Andrew H, Darwent, Christyann M, Eerkens, Jelmer W, and Mason, Owen K

Subjects
Lipid analysis, Marine biomarkers, Stable isotopes, Arctic Small Tool tradition, Maritime adaptation, Alaska archaeology, Cemented organic residue, Geochemistry, Geology, Archaeology
Abstract

Analysis of preserved lipids from archaeological sites in northwest Alaska indicates hunters exploited marine animal resources as early as 4500 years ago. Bone preservation at early prehistoric sites in northern Alaska is generally poor, contributing to uncertainty about the economic orientation of the earliest Arctic Small Tool tradition (ASTt) hunters. We used lipid analysis and compound specific stable isotope analysis (CSIA) of burned, cemented sand and organic residue features to detect the use of marine versus terrestrial animals at several coastal sites in northwest Alaska. Though the sample size for this initial study was small (n=5), comparisons among samples from early ASTt, and later Norton and Thule sites indicate all three groups made use of marine animals for food and/or fuel. Recently obtained radiocarbon dates suggest ASTt hunters settled coastal regions of Alaska prior to moving inland to exploit terrestrial habitats. Our results provide empirical evidence that suggests the economy of the early ASTt population included a maritime component. In Arctic settings where bone preservation is poor, lipid analysis of cemented sand and organic residue features can provide an effective alternative for detecting the use and processing of marine versus terrestrial animals.

Published
2015

46. Anaesthetic depth and complications after major surgery: an international, randomised controlled trial

Author

Shulman, M, Wallace, S, Farrington, C, Gallagher, W, Ditoro, A, Peyton, P, Baulch, S, Dalyell, A, Sidiropoulos, S, Reynolds, J, Rowley, J, Tan, N, McCallum, D, O'Loughlin, E, Wong, S, Owen, K, Sim, I-K, Glazov, L, Coutts, P, Pushpanathan, M, Findlay, V, Paech, M, Cavill, D, Chuan, A, Pope, L, Lucas, J, Robinson, B, Millard, A, Allen, S, Allen, M, McKeown, S, Sivalingam, P, Wilkes, T, Jowett, C, Kearney, A, Bennett, M, Favero, J-P, Sawhney, S, Drummond, K, Osborn, S, Wing, A, Taylor, J, Edwards, M, Reynolds, H, Town, C, Terblanche, N, Challis, M, Seale, R, Button, K, Cotter, R, Stewart, M, Zingerle, N, Hannon, S, Middleton, D, Edgley, C, March, S, McCulloch, T, Wong, G, Jeong, S, Connell, K, Kramer, K, Henderson, G, Ward, V, Buller, Y, Hird, N, Scott, D, Evered, L, Snyder, G, Silbert, B, Corcoran, P, Fitzgerald, E, Said, S, Watson, A, Baby, D, Bolsin, S, Marriott, A, Ives, K, Wakefeld, B-J, Jeffreys, A, Bates, S, Halliwell, R, Elliott, D, Cope, L, Paranthoiene, R, Peng, P, Liu, X, Zhou, X, Jin, X, Liu, H, An, L, Cui, W, Zhang, L, Jia, B, Fang, J, Koo, E, Lo, E, Fung, B, Tsang, M, Lam, L, Pang, E, Lau, V, Choi, G, Kwok, R, Yau, K, Cheng, B, Lam, C, Lee, E, Buggy, D, Keane, H, Byrne, K, Connolly, C, Ali, M, Cervantes, A, Kumar, K, Dandy, S, Ritchie, L, Kennedy, R, McKellow, M, Read, C, France, D, Truong, H, Chapman, C, Walker, S, Olliff, S, Houston, H, Scott, M, Minchin, I, Moniwa, A, McAlpine, J, Chaddock, M, Gray, L, Czepanski, C, Vinish, S, Buehner, U, Williams, E, Zhou, C, Goodman, L, Bermaat, J, Mans, G, Garden, A, Franks, R, Deiterle, J, Barrett, J, Roubos, S, van Lier, F, Verbrugge, S, Kalkman, C, Dieleman, J, Verdam-Veldkamp, J, van Kampen, A, Pai, A, Sevillano, A, Yeung, J, Melody, T, Atterbury, K, Hough, M, Dukes, S, Williams, S, Milan, Z, Kunst, G, Bhatia, K, MacNab, W, Weaver, E, Moulding, R, Doble, P, Klepsch, P, Self, J, Howes, T, Rees, B, Faulkner, B, Blackburn, J, Crombie, N, Cooper, L, Nair, A, Bell, G, Longfellow, R, Nicholas, C, Garratt, T, Pollard, M, Brown, G, Morrison, G, Lang, A, Dawson, H, MacDonald, M, Martin, T, Niebrzegowska, E, Dias, P, Rao Baikady, R, Jhanji, S, Siddaiah, N, Bird, L, Mittal, R, Nalawaya, P, Sonksen, J, Gidda, R, Wrench, I, Craw, N, Pippard, L, Davies, S, Wright, M, Turan, M, Maheshwari, K, Cohen, B, Saasouh, W, Singh, P, Govindarajan, S, Cuko, E, Marcano, F, Babazade, R, Leung, S, Raza, S, Reville, E, Hanline, C, Ayad, S, Buttar, M, Akhtar, Z, Niazi, A, Saha, P, Morris, A, Lokhande, C, Hassan, M, Honar, H, Bairacharya, G, Saxon, J, Chelnick, D, Carlson, R, Ruiz, J, Wilks, J, Williams, W, Dangler, L, Ifeanyi-Pillette, I, Suarez, J, Erfe, R, Perez, A, Veselis, R, Yang, G, Mehta, M, Pryor, K, Rubin, L, Malhotra, J, Steinkamp, M, Cooke, F, Friedlander, R, Short, Timothy G, Campbell, Douglas, Frampton, Christopher, Chan, Matthew T V, Myles, Paul S, Corcoran, Tomás B, Sessler, Daniel I, Mills, Gary H, Cata, Juan P, Painter, Thomas, Byrne, Kelly, Han, Ruquan, Chu, Mandy H M, McAllister, Davina J, and Leslie, Kate

Published
2019
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