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4,376 results on '"Harris, P. J."'

1. Modelling floral and arthropod electrostatics using a two-domain AAA-least squares algorithm

Author

Harris, Samuel J., Palmer, Ryan A., and McDonald, N. R.

Subjects
Physics - Biological Physics, Condensed Matter - Soft Condensed Matter
Abstract

Relationships between plants and insects vitally underpin the health of global ecosystems and food production. Through co-evolution, insects have acquired a variety of senses in response to the emergence of floral cues such as scent, colour and shape. Therefore, the recent discovery of electroreception among terrestrial arthropods motivates the investigation of floral electrics as part of their wider sensory ecology. We examine how a flower's morphology and material properties produce and propagate detectable, ecologically relevant electrical signals in several biologically inspired scenarios. As the electrical field both interior and exterior to the flower must be solved for, we develop an extension of the two-dimensional AAA-least squares algorithm for solving such two-domain electrostatics problems. It is found that the electrical signals produced by the plant can reveal information to the insect about the flower shape, available pollen and the presence of other nearby arthropods. These results show good qualitative agreement with an equivalent three-dimensional scenario, computed using finite element methods. The extension of the AAA-least squares algorithm to two-domain problems provides a fast and accurate method for modelling electrostatic problems, with possible further application in fluid dynamics and magnetostatics. Biologically, our results highlight the significant role floral electrics may play in plant-pollinator and predator-prey relationships, unveiling previously unstudied facets of these key relationships., Comment: Submitted to the SIAM Journal on Applied Mathematics

Published
2024

2. Hidden in Plain Sight: Searching for Dark Companions to Bright Stars with the Large Binocular Telescope and SHARK-VIS

Author

Rowan, D. M., Thompson, Todd A., Kochanek, C. S., Causi, G. Li, Roth, J., Vaccari, P., Pedichini, F., Piazzesi, R., Antoniucci, S., Testa, V., Johnson, M. C., Crass, J., Crepp, J. R., Bechter, A., Bechter, E. B., Sands, B. L., and Harris, R. J.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

We report the results from a pilot study to search for black holes and other dark companions in binary systems using direct imaging with SHARK-VIS and the iLocater pathfinder "Lili" on the Large Binocular Telescope. Starting from known single-lined spectroscopic binaries, we select systems with high mass functions that could host dark companions and whose spectroscopic orbits indicate a projected orbital separation $\geq 30$ mas. For this first exploration, we selected four systems (HD 137909, HD 104438, HD 117044, and HD 176695). In each case, we identify a luminous companion and measure the flux ratio and angular separation. However, two of the systems (HD 104438 and HD 176695) are not consistent with simple binary systems and are most likely hierarchical triples. The observed companions rule out a massive compact object for HD 137909, HD 117044, and HD 176695. HD 104438 requires further study because the identified star cannot be responsible for the RV orbit and is likely a dwarf tertiary companion. The SHARK-VIS observation was taken near pericenter, and a second image near apocenter is needed to discriminate between a closely separated luminous secondary and a compact object. We show how the combination of RVs and direct imaging can be used to constrain the orbital inclination and companion mass, and discuss the potential of high resolution direct imaging surveys to identify and confirm non-interacting compact object candidates., Comment: 23 pages, 11 figures. Submitted to ApJ

Published
2024

3. Kinetic magnetism and stripe order in the doped AFM bosonic ${t-J}$ model

Author

Harris, Timothy J., Schollwöck, Ulrich, Bohrdt, Annabelle, and Grusdt, Fabian

Subjects
Condensed Matter - Quantum Gases, Condensed Matter - Strongly Correlated Electrons, Quantum Physics
Abstract

Unraveling the microscopic mechanisms governing the physics of doped quantum magnets is a central challenge in strongly correlated many-body physics. Quantum simulation platforms, e.g. ultracold atoms trapped in optical lattices or tweezer arrays, offer an exciting pathway to investigate the interplay between spin and charge motion, thereby providing an avenue to addressing longstanding questions such as the nature of charge pairing in high-temperature superconductors. Here, in a new twist, we seek to disentangle the role of particle statistics in the physics of strongly correlated systems by exploring the strong coupling limit of doped bosonic quantum magnets, specifically the antiferromagnetic (AFM) bosonic $t-J$ model. We perform large-scale density matrix renormalization group (DMRG) calculations to map out the phase diagram of the AFM bosonic $t-J$ model on the 2D square lattice at finite doping. We find that in the low doping regime, bosonic holes tend to form partially-filled stripes, akin to those observed in high-$T_c$ cuprates. As doping increases beyond a critical value $\delta \gtrsim \delta^*_\mathrm{PP} (\delta^*_\mathrm{FM})$, a transition occurs between AFM and ferromagnetic (FM) ground states, driven by the competition between Heisenberg-type AFM and Nagaoka-type FM mediated by the motion of mobile bosonic holes. In the high doping or large $t/J$ limit, the system evolves into a fully-polarized SU(2) ferromagnet, consistent with a phase transition linked to Nagaoka polarons. Our findings shed light on the role of particle statistics in strongly correlated quantum matter and connect to phases in the 2D Fermi-Hubbard and $t-J$ models. Our results may be realized in state-of-the-art quantum simulation experiments with bosonic quantum gas microscopes, paving the way for further exploration of doped bosonic quantum magnets., Comment: 5+1 pages, 3 figures

Published
2024

4. Current fluctuations for the boundary-driven zero-range process on graphs: microscopic versus macroscopic approach and a theory of non-reversible resistor-like networks

Author

Gabrielli, Davide and Harris, Rosemary J.

Subjects
Condensed Matter - Statistical Mechanics, Mathematical Physics, Mathematics - Probability
Abstract

We compute the joint large deviation rate functional in the limit of large time for the current flowing through the edges of a finite graph for a boundary-driven zero-range dynamics. This generalizes one-dimensional results previously obtained with different approaches \cite{BDGJL1,HRS}; our alternative techniques illuminate various connections and complementary perspectives. In particular, we here use a variational approach to derive the rate functional by contraction from a level 2.5 large deviation rate functional. We perform an exact minimization and finally obtain the rate functional as a variational problem involving a superposition of cost functions for each edge. The contributions from different edges are not independent since they are related by the values of a potential function on the nodes of the graph. The rate functional on the graph is a microscopic version of the continuous rate functional predicted by the macroscopic fluctuation theory \cite{MFT}, and we indeed show a convergence in the scaling limit. If we split the graph into two connected regions by a cutset and are interested just in the current flowing through the cutset, we find that the result is the same as that of an effective system composed of only one effective edge (as happens at macroscopic level and is expected also for other models \cite{Cap}). The characteristics of this effective edge are related to the ``capacities'' of the graph and can be obtained by a reduction using elementary transformations as in electrical networks; specifically, we treat components in parallel, in series, and in $N$-star configurations (reduced to effective complete $N$-graphs). Our reduction procedure is directly related to the reduction to the trace process \cite{L} and, since the dynamics is in general not reversible, it is also closely connected to the theory of non-reversible electrical networks in \cite{B}., Comment: 35 pages, 6 figures

Published
2024

5. The global distribution and drivers of wood density and their impact on forest carbon stocks.

Author

Mo, Lidong, Crowther, Thomas W, Maynard, Daniel S, van den Hoogen, Johan, Ma, Haozhi, Bialic-Murphy, Lalasia, Liang, Jingjing, de-Miguel, Sergio, Nabuurs, Gert-Jan, Reich, Peter B, Phillips, Oliver L, Abegg, Meinrad, Adou Yao, Yves C, Alberti, Giorgio, Almeyda Zambrano, Angelica M, Alvarado, Braulio Vilchez, Alvarez-Dávila, Esteban, Alvarez-Loayza, Patricia, Alves, Luciana F, Amaral, Iêda, Ammer, Christian, Antón-Fernández, Clara, Araujo-Murakami, Alejandro, Arroyo, Luzmila, Avitabile, Valerio, Aymard, Gerardo A, Baker, Timothy R, Bałazy, Radomir, Banki, Olaf, Barroso, Jorcely G, Bastian, Meredith L, Bastin, Jean-Francois, Birigazzi, Luca, Birnbaum, Philippe, Bitariho, Robert, Boeckx, Pascal, Bongers, Frans, Boonman, Coline CF, Bouriaud, Olivier, Brancalion, Pedro HS, Brandl, Susanne, Brearley, Francis Q, Brienen, Roel, Broadbent, Eben N, Bruelheide, Helge, Bussotti, Filippo, Gatti, Roberto Cazzolla, César, Ricardo G, Cesljar, Goran, Chazdon, Robin, Chen, Han YH, Chisholm, Chelsea, Cho, Hyunkook, Cienciala, Emil, Clark, Connie, Clark, David, Colletta, Gabriel D, Coomes, David A, Valverde, Fernando Cornejo, Corral-Rivas, José J, Crim, Philip M, Cumming, Jonathan R, Dayanandan, Selvadurai, de Gasper, André L, Decuyper, Mathieu, Derroire, Géraldine, DeVries, Ben, Djordjevic, Ilija, Dolezal, Jiri, Dourdain, Aurélie, Engone Obiang, Nestor Laurier, Enquist, Brian J, Eyre, Teresa J, Fandohan, Adandé Belarmain, Fayle, Tom M, Feldpausch, Ted R, Ferreira, Leandro V, Finér, Leena, Fischer, Markus, Fletcher, Christine, Frizzera, Lorenzo, Gamarra, Javier GP, Gianelle, Damiano, Glick, Henry B, Harris, David J, Hector, Andrew, Hemp, Andreas, Hengeveld, Geerten, Hérault, Bruno, Herbohn, John L, Herold, Martin, Hietz, Peter, Hillers, Annika, Honorio Coronado, Eurídice N, Hui, Cang, Ibanez, Thomas, Imai, Nobuo, Jagodziński, Andrzej M, Jaroszewicz, Bogdan, and Johannsen, Vivian Kvist

Subjects
Ecology, Evolutionary biology, Environmental management
Abstract

The density of wood is a key indicator of the carbon investment strategies of trees, impacting productivity and carbon storage. Despite its importance, the global variation in wood density and its environmental controls remain poorly understood, preventing accurate predictions of global forest carbon stocks. Here we analyse information from 1.1 million forest inventory plots alongside wood density data from 10,703 tree species to create a spatially explicit understanding of the global wood density distribution and its drivers. Our findings reveal a pronounced latitudinal gradient, with wood in tropical forests being up to 30% denser than that in boreal forests. In both angiosperms and gymnosperms, hydrothermal conditions represented by annual mean temperature and soil moisture emerged as the primary factors influencing the variation in wood density globally. This indicates similar environmental filters and evolutionary adaptations among distinct plant groups, underscoring the essential role of abiotic factors in determining wood density in forest ecosystems. Additionally, our study highlights the prominent role of disturbance, such as human modification and fire risk, in influencing wood density at more local scales. Factoring in the spatial variation of wood density notably changes the estimates of forest carbon stocks, leading to differences of up to 21% within biomes. Therefore, our research contributes to a deeper understanding of terrestrial biomass distribution and how environmental changes and disturbances impact forest ecosystems.

Published
2024

6. Atomistic mechanisms of the regulation of small-conductance Ca2+-activated K+ channel (SK2) by PIP2

Author

Woltz, Ryan L, Zheng, Yang, Choi, Woori, Ngo, Khoa, Trinh, Pauline, Ren, Lu, Thai, Phung N, Harris, Brandon J, Han, Yanxiao, Rouen, Kyle C, Mateos, Diego Lopez, Jian, Zhong, Chen-Izu, Ye, Dickson, Eamonn J, Yamoah, Ebenezer N, Yarov-Yarovoy, Vladimir, Vorobyov, Igor, Zhang, Xiao-Dong, and Chiamvimonvat, Nipavan

Subjects
Medical Physiology, Biomedical and Clinical Sciences, Cardiovascular, 1.1 Normal biological development and functioning, 5.1 Pharmaceuticals, Phosphatidylinositol 4, 5-Diphosphate, Small-Conductance Calcium-Activated Potassium Channels, Molecular Dynamics Simulation, Animals, Calmodulin, Humans, Ion Channel Gating, Calcium, Protein Binding, Myocytes, Cardiac, atrial arrhythmias, calmodulin, optogenetics, phosphatidylinositol 4, 5-bisphosphate, small conductance Ca2+-activated K+ channel
Abstract

Small-conductance Ca2+-activated K+ channels (SK, KCa2) are gated solely by intracellular microdomain Ca2+. The channel has emerged as a therapeutic target for cardiac arrhythmias. Calmodulin (CaM) interacts with the CaM binding domain (CaMBD) of the SK channels, serving as the obligatory Ca2+ sensor to gate the channels. In heterologous expression systems, phosphatidylinositol 4,5-bisphosphate (PIP2) coordinates with CaM in regulating SK channels. However, the roles and mechanisms of PIP2 in regulating SK channels in cardiomyocytes remain unknown. Here, optogenetics, magnetic nanoparticles, combined with Rosetta structural modeling, and molecular dynamics (MD) simulations revealed the atomistic mechanisms of how PIP2 works in concert with Ca2+-CaM in the SK channel activation. Our computational study affords evidence for the critical role of the amino acid residue R395 in the S6 transmembrane segment, which is localized in propinquity to the intracellular hydrophobic gate. This residue forms a salt bridge with residue E398 in the S6 transmembrane segment from the adjacent subunit. Both R395 and E398 are conserved in all known isoforms of SK channels. Our findings suggest that the binding of PIP2 to R395 residue disrupts the R395:E398 salt bridge, increasing the flexibility of the transmembrane segment S6 and the activation of the channel. Importantly, our findings serve as a platform for testing of structural-based drug designs for therapeutic inhibitors and activators of the SK channel family. The study is timely since inhibitors of SK channels are currently in clinical trials to treat atrial arrhythmias.

Published
2024

7. A Multiscale Model to Understand the Interface Chemistry, Contacts, and Dynamics During Lithium Stripping

Author

Feng, Min, Liu, Xing, Harris, Stephen J, Sheldon, Brian W, and Qi, Yue

Subjects
Engineering, Materials Engineering, Mathematical Sciences, Physical Sciences, Mechanical Engineering & Transports, Mathematical sciences, Physical sciences
Abstract

A reversible Li-metal electrode, paired with a solid electrolyte, is critical for attaining higher energy density and safer batteries beyond the current lithium-ion cells. A stable stripping process may be even harder to attain as the stripping process will remove Li-atoms from the surface, and naturally reduce surface contact area, if not self-corrected by other mechanisms, such as diffusion and plastic deformation under an applied external stack pressure. Here, we capture these mechanisms occurring at multiple length- and time- scales, i.e., interface interactions, vacancy hopping, and plastic deformation, by integrating density functional theory (DFT) simulations, kinetic Monte Carlo (KMC), and continuum finite element method (FEM). By assuming the self-affine nature of multiscale contacts, we predict the steady-state contact area as a function of stripping current density, interface wettability, and stack pressure. We further estimate the exponential increase of overpotential due to contact area loss to maintain the same stripping current density. We demonstrate that a lithiophilic interface requires less stack pressure to reach the same steady-state contact area fraction than a lithiophobic interface. A “tolerable steady-state” contact area loss for maintaining stable stripping is estimated at 20 %, corresponding to a 10 % increase in overpotential. To constrain contact loss within the tolerance, the required stack pressure is 0.1, 0.5, and 2 times the yield strength of lithium metal for three distinct interfaces, lithiophilic Li/lithium oxide(Li2O), Li/lithium lanthanum zirconium oxide(LLZO), and lithiophoblic Li/lithium fluoride(LiF), respectively. The modeling results agree with experiments on the impact of the stack pressure quantitatively, while the discrepancy in stripping rate sensitivity is attributed to the simplifying interface interaction in our simulations. Overall, this multiscale simulation framework demonstrates the importance of electrochemical-mechanical coupling in understanding the dynamics of the Li/SE interface during stripping.

Published
2024

8. Modelling wildfire spread and spotfire merger using conformal mapping and AAA-least squares methods

Author

Harris, Samuel J. and McDonald, N. R.

Subjects
Physics - Computational Physics, Physics - Fluid Dynamics, 65E10
Abstract

A two-dimensional model of wildfire spread and merger is presented. Three features affect the fire propagation: (i) a constant basic rate of spread term accounting for radiative and convective heat transfer, (ii) the unidirectional, constant ambient wind, and (iii) a fire-induced pyrogenic wind. Two numerical methods are proposed to solve for the harmonic pyrogenic potential. The first utilizes the conformal invariance of the Laplace equation, reducing the wildfire system to a single Polubarinova-Galin type equation. The second method uses a AAA-least squares method to find a rational approximation of the potential. Various wildfire scenarios are presented and the effects of the pyrogenic wind and the radiative/convective basic rate of spread terms investigated. Firebreaks such as roads and lakes are also included and solutions are found to match well with existing numerical and experimental results. The methods proposed in this work are suitably fast and accurate to be considered for operational use., Comment: 22 pages, 12 figures. Submitted to Elsevier Environmental Modelling and Software

Published
2024

9. Extra Throughput versus Days Lost in load-shifting V2G services: Influence of dominant degradation mechanism

Author

Movahedi, Hamidreza, Pannala, Sravan, Siegel, Jason, Harris, Stephen J., Howey, David, and Stefanopoulou, Anna

Subjects
Electrical Engineering and Systems Science - Systems and Control
Abstract

Electric vehicle (EV) batteries are often underutilized. Vehicle-to-grid (V2G) services can tap into this unused potential, but increased battery usage may lead to more degradation and shorter battery life. This paper substantiates the advantages of providing load-shifting V2G services when the battery is aging, primarily due to calendar aging mechanisms (active degradation mechanisms while the battery is not used). After parameterizing a physics-based digital-twin for three different dominant degradation patterns within the same chemistry (NMC), we introduce a novel metric for evaluating the benefit and associated harm of V2G services: \textit{throughput gained versus days lost (TvD)} and show its strong relationship to the ratio of loss of lithium inventory (LLI) due to calendar aging to the total LLI ($\text{LLI}_\text{Cal}/\text{LLI}$). Our results that focus systematically on degradation mechanisms via lifetime simulation of digital-twins significantly expand prior work that was primarily concentrating on quantifying and reducing the degradation of specific cells by probing their usage and charging patterns. Examining various cell chemistries and conditions enables us to take a broader view and determine whether a particular battery pack is appropriate for load-shifting (V2G) services. Our research demonstrates that the decision "to V2G or not to V2G" can be made by merely estimating the portion of capacity deterioration caused by calendar aging. Specifically, TvD is primarily influenced by the chemistry of cells and the environmental temperature where the car is parked, while the usage intensity and charging patterns of EVs play a lesser role.

Published
2024

10. Far from Perfect: Quantum Error Correction with (Hyperinvariant) Evenbly Codes

Author

Steinberg, Matthew, Fan, Junyu, Harris, Robert J., Elkouss, David, Feld, Sebastian, and Jahn, Alexander

Subjects
Quantum Physics, High Energy Physics - Theory
Abstract

We introduce a new class of qubit codes that we call Evenbly codes, building on a previous proposal of hyperinvariant tensor networks. Its tensor network description consists of local, non-perfect tensors describing CSS codes interspersed with Hadamard gates, placed on a hyperbolic $\{p,q\}$ geometry with even $q\geq 4$, yielding an infinitely large class of subsystem codes. We construct an example for a $\{5,4\}$ manifold and describe strategies of logical gauge fixing that lead to different rates $k/n$ and distances $d$, which we calculate analytically, finding distances which range from $d=2$ to $d \sim n^{2/3}$ in the ungauged case. Investigating threshold performance under erasure, depolarizing, and pure Pauli noise channels, we find that the code exhibits a depolarizing noise threshold of about $19.1\%$ in the code-capacity model and $50\%$ for pure Pauli and erasure channels under suitable gauges. We also test a constant-rate version with $k/n = 0.125$, finding excellent error resilience (about $40\%$) under the erasure channel. Recovery rates for these and other settings are studied both under an optimal decoder as well as a more efficient but non-optimal greedy decoder. We also consider generalizations beyond the CSS tensor construction, compute error rates and thresholds for other hyperbolic geometries, and discuss the relationship to holographic bulk/boundary dualities. Our work indicates that Evenbly codes may show promise for practical quantum computing applications., Comment: 22 pages, 13 figures

Published
2024

11. Classroom-Based STEM Assessment: Contemporary Issues and Perspectives

Author

Community for Advancing Discovery Research in Education (CADRE), Education Development Center, Inc. (EDC), Harris, Christopher J., Wiebe, Eric, Grover, Shuchi, and Pellegrino, James W.

Abstract

This report is focused on what research and practice indicate about how assessment impacts the teaching and learning of STEM subject matter in K-12 classrooms. The intent is to take stock of what is currently known as well as what needs to be known to make classroom assessment in STEM maximally beneficial for the instructional practices of teachers and the learning outcomes of students. The volume draws inspiration from the cumulative body of research on STEM education that has accrued over the last two decades. The major sections in this report, individually and collectively, focus on critical issues regarding assessment integration and use at the classroom level. [For the executive summary, see ED631657. For the recommendations, see ED631658.]

Published
2023

12. Particle elasticity influences polymeric artificial antigen presenting cell effectiveness in vivo via CD8+ T cell activation, macrophage uptake, and the protein corona

Author

Est-Witte, Savannah E., Shannon, Sydney R., Gong, Dennis H., Calabresi, Kaitlyn G., Harris, Jawaun J., Storm, Kaitlyn, Yoo, Edwin J., Isser, Ariel, Jani, Vivek P., Livingston, Natalie K., Omotoso, Mary O., Rhodes, Kelly, Ben-Akiva, Elana, Meyer, Randall A., Hsieh, Zoe T., Sidoli, Simone, Tzeng, Stephany Y., Schneck, Jonathan P., and Green, Jordan J.

Published
2024
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17. 2023 Astrophotonics Roadmap: pathways to realizing multi-functional integrated astrophotonic instruments

Author

Jovanovic, Nemanja, Gatkine, Pradip, Anugu, Narsireddy, Amezcua-Correa, Rodrigo, Thakur, Ritoban Basu, Beichman, Charles, Bender, Chad, Berger, Jean-Philippe, Bigioli, Azzurra, Bland-Hawthorn, Joss, Bourdarot, Guillaume, Bradford, Charles M., Broeke, Ronald, Bryant, Julia, Bundy, Kevin, Cheriton, Ross, Cvetojevic, Nick, Diab, Momen, Diddams, Scott A., Dinkelaker, Aline N., Duis, Jeroen, Eikenberry, Stephen, Ellis, Simon, Endo, Akira, Figer, Donald F., Fitzgerald, Michael, Gris-Sanchez, Itandehui, Gross, Simon, Grossard, Ludovic, Guyon, Olivier, Haffert, Sebastiaan Y., Halverson, Samuel, Harris, Robert J., He, Jinping, Herr, Tobias, Hottinger, Philipp, Huby, Elsa, Ireland, Michael, Jenson-Clem, Rebecca, Jewell, Jeffrey, Jocou, Laurent, Kraus, Stefan, Labadie, Lucas, Lacour, Sylvestre, Laugier, Romain, Ławniczuk, Katarzyna, Lin, Jonathan, Leifer, Stephanie, Leon-Sava, Sergio, Martin, Guillermo, Martinache, Frantz, Martinod, Marc-Antoine, Mazin, Benjamin A., Minardi, Stefano, Monnier, John D., Moreira, Reinan, Mourard, Denis, Nayak, Abani Shankar, Norris, Barnaby, Obrzud, Ewelina, Perraut, Karine, Reynaud, François, Sallum, Steph, Schiminovich, David, Schwab, Christian, Serbayn, Eugene, Soliman, Sherif, Stoll, Andreas, Tang, Liang, Tuthill, Peter, Vahala, Kerry, Vasisht, Gautam, Veilleux, Sylvain, Walter, Alexander B., Wollack, Edward J., Xin, Yinzi, Yang, Zongyin, Yerolatsitis, Stephanos, Zhang, Yang, and Zou, Chang-Ling

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Physics - Instrumentation and Detectors
Abstract

Photonics offer numerous functionalities that can be used to realize astrophotonic instruments. The most spectacular example to date is the ESO Gravity instrument at the Very Large Telescope in Chile. Integrated astrophotonic devices stand to offer critical advantages for instrument development, including extreme miniaturization, as well as integration, superior thermal and mechanical stabilization owing to the small footprint, and high replicability offering cost savings. Numerous astrophotonic technologies have been developed to address shortcomings of conventional instruments to date, including for example the development of photonic lanterns, complex aperiodic fiber Bragg gratings, complex beam combiners to enable long baseline interferometry, and laser frequency combs for high precision spectral calibration of spectrometers. Despite these successes, the facility implementation of photonic solutions in astronomical instrumentation is currently limited because of (1) low throughputs from coupling to fibers, coupling fibers to chips, propagation and bend losses, device losses, etc, (2) difficulties with scaling to large channel count devices needed for large bandwidths and high resolutions, and (3) efficient integration of photonics with detectors, to name a few. In this roadmap, we identify 24 areas that need further development. We outline the challenges and advances needed across those areas covering design tools, simulation capabilities, fabrication processes, the need for entirely new components, integration and hybridization and the characterization of devices. To realize these advances the astrophotonics community will have to work cooperatively with industrial partners who have more advanced manufacturing capabilities. With the advances described herein, multi-functional instruments will be realized leading to novel observing capabilities for both ground and space platforms., Comment: 191 pages, 47 figures. This is the version of the article before peer review or editing, as submitted by an author to J. Phys. Photonics. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at https://iopscience.iop.org/article/10.1088/2515-7647/ace869/meta

Published
2023
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18. Toward high-resolution modeling of small molecule–ion channel interactions

Author

Harris, Brandon J, Nguyen, Phuong T, Zhou, Guangfeng, Wulff, Heike, DiMaio, Frank, and Yarov-Yarovoy, Vladimir

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Bioengineering, Cardiovascular, Chronic Pain, Pain Research, Neurosciences, 5.1 Pharmaceuticals, 1.1 Normal biological development and functioning, Rosetta, ligand docking, ion channel, computational modeling, ligand-protein interactions, computer-aided drug discovery, ligand–protein interactions, Pharmacology and pharmaceutical sciences
Abstract

Ion channels are critical drug targets for a range of pathologies, such as epilepsy, pain, itch, autoimmunity, and cardiac arrhythmias. To develop effective and safe therapeutics, it is necessary to design small molecules with high potency and selectivity for specific ion channel subtypes. There has been increasing implementation of structure-guided drug design for the development of small molecules targeting ion channels. We evaluated the performance of two RosettaLigand docking methods, RosettaLigand and GALigandDock, on the structures of known ligand-cation channel complexes. Ligands were docked to voltage-gated sodium (NaV), voltage-gated calcium (CaV), and transient receptor potential vanilloid (TRPV) channel families. For each test case, RosettaLigand and GALigandDock methods frequently sampled a ligand-binding pose within a root mean square deviation (RMSD) of 1-2 Å relative to the experimental ligand coordinates. However, RosettaLigand and GALigandDock scoring functions cannot consistently identify experimental ligand coordinates as top-scoring models. Our study reveals that the proper scoring criteria for RosettaLigand and GALigandDock modeling of ligand-ion channel complexes should be assessed on a case-by-case basis using sufficient ligand and receptor interface sampling, knowledge about state-specific interactions of the ion channel, and inherent receptor site flexibility that could influence ligand binding.

Published
2024

19. Integrated global assessment of the natural forest carbon potential

Author

Mo, Lidong, Zohner, Constantin M, Reich, Peter B, Liang, Jingjing, de Miguel, Sergio, Nabuurs, Gert-Jan, Renner, Susanne S, van den Hoogen, Johan, Araza, Arnan, Herold, Martin, Mirzagholi, Leila, Ma, Haozhi, Averill, Colin, Phillips, Oliver L, Gamarra, Javier GP, Hordijk, Iris, Routh, Devin, Abegg, Meinrad, Adou Yao, Yves C, Alberti, Giorgio, Almeyda Zambrano, Angelica M, Alvarado, Braulio Vilchez, Alvarez-Dávila, Esteban, Alvarez-Loayza, Patricia, Alves, Luciana F, Amaral, Iêda, Ammer, Christian, Antón-Fernández, Clara, Araujo-Murakami, Alejandro, Arroyo, Luzmila, Avitabile, Valerio, Aymard, Gerardo A, Baker, Timothy R, Bałazy, Radomir, Banki, Olaf, Barroso, Jorcely G, Bastian, Meredith L, Bastin, Jean-Francois, Birigazzi, Luca, Birnbaum, Philippe, Bitariho, Robert, Boeckx, Pascal, Bongers, Frans, Bouriaud, Olivier, Brancalion, Pedro HS, Brandl, Susanne, Brearley, Francis Q, Brienen, Roel, Broadbent, Eben N, Bruelheide, Helge, Bussotti, Filippo, Cazzolla Gatti, Roberto, César, Ricardo G, Cesljar, Goran, Chazdon, Robin L, Chen, Han YH, Chisholm, Chelsea, Cho, Hyunkook, Cienciala, Emil, Clark, Connie, Clark, David, Colletta, Gabriel D, Coomes, David A, Cornejo Valverde, Fernando, Corral-Rivas, José J, Crim, Philip M, Cumming, Jonathan R, Dayanandan, Selvadurai, de Gasper, André L, Decuyper, Mathieu, Derroire, Géraldine, DeVries, Ben, Djordjevic, Ilija, Dolezal, Jiri, Dourdain, Aurélie, Engone Obiang, Nestor Laurier, Enquist, Brian J, Eyre, Teresa J, Fandohan, Adandé Belarmain, Fayle, Tom M, Feldpausch, Ted R, Ferreira, Leandro V, Finér, Leena, Fischer, Markus, Fletcher, Christine, Frizzera, Lorenzo, Gianelle, Damiano, Glick, Henry B, Harris, David J, Hector, Andrew, Hemp, Andreas, Hengeveld, Geerten, Hérault, Bruno, Herbohn, John L, Hillers, Annika, Honorio Coronado, Eurídice N, Hui, Cang, Ibanez, Thomas, Imai, Nobuo, and Jagodziński, Andrzej M

Subjects
Agricultural, Veterinary and Food Sciences, Ecological Applications, Environmental Sciences, Forestry Sciences, Life on Land, Biodiversity, Carbon, Carbon Sequestration, Conservation of Natural Resources, Forests, Human Activities, Environmental Restoration and Remediation, Sustainable Development, Global Warming, Agricultural, Ecosystem, General Science & Technology, Humans, Veterinary and Food Sciences
Abstract

Forests are a substantial terrestrial carbon sink, but anthropogenic changes in land use and climate have considerably reduced the scale of this system1. Remote-sensing estimates to quantify carbon losses from global forests2-5 are characterized by considerable uncertainty and we lack a comprehensive ground-sourced evaluation to benchmark these estimates. Here we combine several ground-sourced6 and satellite-derived approaches2,7,8 to evaluate the scale of the global forest carbon potential outside agricultural and urban lands. Despite regional variation, the predictions demonstrated remarkable consistency at a global scale, with only a 12% difference between the ground-sourced and satellite-derived estimates. At present, global forest carbon storage is markedly under the natural potential, with a total deficit of 226 Gt (model range = 151-363 Gt) in areas with low human footprint. Most (61%, 139 Gt C) of this potential is in areas with existing forests, in which ecosystem protection can allow forests to recover to maturity. The remaining 39% (87 Gt C) of potential lies in regions in which forests have been removed or fragmented. Although forests cannot be a substitute for emissions reductions, our results support the idea2,3,9 that the conservation, restoration and sustainable management of diverse forests offer valuable contributions to meeting global climate and biodiversity targets.

Published
2023

20. Bulgarian Solitaire: A new representation for depth generating functions

Author

Harris, A. J. and Nguyen, Son

Subjects
Mathematics - Combinatorics
Abstract

Bulgarian Solitaire is an interesting self-map on the set of integer partitions of a fixed number $n$. As a finite dynamical system, its long-term behavior is well-understood, having recurrent orbits parametrized by necklaces of beads with two colors black $B$ and white $W$. However, the behavior of the transient elements within each orbit is much less understood. Recent work of Pham considered the orbits corresponding to a family of necklaces $P^\ell$ that are concatenations of $\ell$ copies of a fixed primitive necklace $P$. She proved striking limiting behavior as $\ell$ goes to infinity: the level statistic for the orbit, counting how many steps it takes a partition to reach the recurrent cycle, has a limiting distribution, whose generating function $H_p(x)$ is rational. Pham also conjectured that $H_P(x), H_{P^*}(x)$ share the same denominator whenever $P^*$ is obtained from $P$ by reading it backwards and swapping $B$ for $W$. Here we introduce a new representation of Bulgarian Solitaire that is convenient for the study of these generating functions. We then use it to prove two instances of Pham's conjecture, showing that $$H_{BWBWB \cdots WB}(x)=H_{WBWBW \cdots BW}(x)$$ and that $H_{BWWW\cdots W}(x),H_{WBBB\cdots B}(x)$ share the same denominator.

Published
2023

21. The global biogeography of tree leaf form and habit

Author

Ma, Haozhi, Crowther, Thomas W, Mo, Lidong, Maynard, Daniel S, Renner, Susanne S, van den Hoogen, Johan, Zou, Yibiao, Liang, Jingjing, de-Miguel, Sergio, Nabuurs, Gert-Jan, Reich, Peter B, Niinemets, Ülo, Abegg, Meinrad, Adou Yao, Yves C, Alberti, Giorgio, Almeyda Zambrano, Angelica M, Alvarado, Braulio Vilchez, Alvarez-Dávila, Esteban, Alvarez-Loayza, Patricia, Alves, Luciana F, Ammer, Christian, Antón-Fernández, Clara, Araujo-Murakami, Alejandro, Arroyo, Luzmila, Avitabile, Valerio, Aymard, Gerardo A, Baker, Timothy R, Bałazy, Radomir, Banki, Olaf, Barroso, Jorcely G, Bastian, Meredith L, Bastin, Jean-Francois, Birigazzi, Luca, Birnbaum, Philippe, Bitariho, Robert, Boeckx, Pascal, Bongers, Frans, Bouriaud, Olivier, Brancalion, Pedro HS, Brandl, Susanne, Brearley, Francis Q, Brienen, Roel, Broadbent, Eben N, Bruelheide, Helge, Bussotti, Filippo, Cazzolla Gatti, Roberto, César, Ricardo G, Cesljar, Goran, Chazdon, Robin, Chen, Han YH, Chisholm, Chelsea, Cho, Hyunkook, Cienciala, Emil, Clark, Connie, Clark, David, Colletta, Gabriel D, Coomes, David A, Valverde, Fernando Cornejo, Corral-Rivas, José J, Crim, Philip M, Cumming, Jonathan R, Dayanandan, Selvadurai, de Gasper, André L, Decuyper, Mathieu, Derroire, Géraldine, DeVries, Ben, Djordjevic, Ilija, Dolezal, Jiri, Dourdain, Aurélie, Engone Obiang, Nestor Laurier, Enquist, Brian J, Eyre, Teresa J, Fandohan, Adandé Belarmain, Fayle, Tom M, Feldpausch, Ted R, Ferreira, Leandro V, Finér, Leena, Fischer, Markus, Fletcher, Christine, Fridman, Jonas, Frizzera, Lorenzo, Gamarra, Javier GP, Gianelle, Damiano, Glick, Henry B, Harris, David J, Hector, Andrew, Hemp, Andreas, Hengeveld, Geerten, Hérault, Bruno, Herbohn, John L, Herold, Martin, Hillers, Annika, Honorio Coronado, Eurídice N, Hui, Cang, Ibanez, Thomas T, Amaral, Iêda, Imai, Nobuo, Jagodziński, Andrzej M, Jaroszewicz, Bogdan, and Johannsen, Vivian Kvist

Subjects
Biological Sciences, Ecology, Climate Action, Plant Biology, Crop and Pasture Production, Plant biology
Abstract

Understanding what controls global leaf type variation in trees is crucial for comprehending their role in terrestrial ecosystems, including carbon, water and nutrient dynamics. Yet our understanding of the factors influencing forest leaf types remains incomplete, leaving us uncertain about the global proportions of needle-leaved, broadleaved, evergreen and deciduous trees. To address these gaps, we conducted a global, ground-sourced assessment of forest leaf-type variation by integrating forest inventory data with comprehensive leaf form (broadleaf vs needle-leaf) and habit (evergreen vs deciduous) records. We found that global variation in leaf habit is primarily driven by isothermality and soil characteristics, while leaf form is predominantly driven by temperature. Given these relationships, we estimate that 38% of global tree individuals are needle-leaved evergreen, 29% are broadleaved evergreen, 27% are broadleaved deciduous and 5% are needle-leaved deciduous. The aboveground biomass distribution among these tree types is approximately 21% (126.4 Gt), 54% (335.7 Gt), 22% (136.2 Gt) and 3% (18.7 Gt), respectively. We further project that, depending on future emissions pathways, 17-34% of forested areas will experience climate conditions by the end of the century that currently support a different forest type, highlighting the intensification of climatic stress on existing forests. By quantifying the distribution of tree leaf types and their corresponding biomass, and identifying regions where climate change will exert greatest pressure on current leaf types, our results can help improve predictions of future terrestrial ecosystem functioning and carbon cycling.

Published
2023

22. Author Correction: Native diversity buffers against severity of non-native tree invasions

Author

Delavaux, Camille S, Crowther, Thomas W, Zohner, Constantin M, Robmann, Niamh M, Lauber, Thomas, van den Hoogen, Johan, Kuebbing, Sara, Liang, Jingjing, de-Miguel, Sergio, Nabuurs, Gert-Jan, Reich, Peter B, Abegg, Meinrad, Adou Yao, Yves C, Alberti, Giorgio, Almeyda Zambrano, Angelica M, Alvarado, Braulio Vilchez, Alvarez-Dávila, Esteban, Alvarez-Loayza, Patricia, Alves, Luciana F, Ammer, Christian, Antón-Fernández, Clara, Araujo-Murakami, Alejandro, Arroyo, Luzmila, Avitabile, Valerio, Aymard, Gerardo A, Baker, Timothy R, Bałazy, Radomir, Banki, Olaf, Barroso, Jorcely G, Bastian, Meredith L, Bastin, Jean-Francois, Birigazzi, Luca, Birnbaum, Philippe, Bitariho, Robert, Boeckx, Pascal, Bongers, Frans, Bouriaud, Olivier, Brancalion, Pedro HS, Brandl, Susanne, Brienen, Roel, Broadbent, Eben N, Bruelheide, Helge, Bussotti, Filippo, Gatti, Roberto Cazzolla, César, Ricardo G, Cesljar, Goran, Chazdon, Robin, Chen, Han YH, Chisholm, Chelsea, Cho, Hyunkook, Cienciala, Emil, Clark, Connie, Clark, David, Colletta, Gabriel D, Coomes, David A, Cornejo Valverde, Fernando, Corral-Rivas, José J, Crim, Philip M, Cumming, Jonathan R, Dayanandan, Selvadurai, de Gasper, André L, Decuyper, Mathieu, Derroire, Géraldine, DeVries, Ben, Djordjevic, Ilija, Dolezal, Jiri, Dourdain, Aurélie, Engone Obiang, Nestor Laurier, Enquist, Brian J, Eyre, Teresa J, Fandohan, Adandé Belarmain, Fayle, Tom M, Feldpausch, Ted R, Ferreira, Leandro V, Fischer, Markus, Fletcher, Christine, Frizzera, Lorenzo, Gamarra, Javier GP, Gianelle, Damiano, Glick, Henry B, Harris, David J, Hector, Andrew, Hemp, Andreas, Hengeveld, Geerten, Hérault, Bruno, Herbohn, John L, Herold, Martin, Hillers, Annika, Honorio Coronado, Eurídice N, Hui, Cang, Ibanez, Thomas T, Amaral, Iêda, Imai, Nobuo, Jagodziński, Andrzej M, Jaroszewicz, Bogdan, Johannsen, Vivian Kvist, Joly, Carlos A, Jucker, Tommaso, Jung, Ilbin, and Karminov, Viktor

Subjects
General Science & Technology
Published
2023

29. BECLIN1 is essential for intestinal homeostasis involving autophagy-independent mechanisms through its function in endocytic trafficking

Author

Tran, Sharon, Juliani, Juliani, Harris, Tiffany J., Evangelista, Marco, Ratcliffe, Julian, Ellis, Sarah L., Baloyan, David, Reehorst, Camilla M., Nightingale, Rebecca, Luk, Ian Y., Jenkins, Laura J., Ghilas, Sonia, Yakou, Marina H., Inguanti, Chantelle, Johnson, Chad, Buchert, Michael, Lee, James C., De Cruz, Peter, Duszyc, Kinga, Gleeson, Paul A., Kile, Benjamin T., Mielke, Lisa A., Yap, Alpha S., Mariadason, John M., Douglas Fairlie, W., and Lee, Erinna F.

Published
2024
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30. Universality of graph homomorphism games and the quantum coloring problem

Author

Harris, Samuel J.

Subjects
Quantum Physics, Mathematics - Operator Algebras
Abstract

We show that quantum graph parameters for finite, simple, undirected graphs encode winning strategies for all possible synchronous non-local games. Given a synchronous game $\mathcal{G}=(I,O,\lambda)$ with $|I|=n$ and $|O|=k$, we demonstrate what we call a weak $*$-equivalence between $\mathcal{G}$ and a $3$-coloring game on a graph with at most $3+n+9n(k-2)+6|\lambda^{-1}(\{0\})|$ vertices, strengthening and simplifying work implied by Z. Ji (arXiv:1310.3794) for winning quantum strategies for synchronous non-local games. As an application, we obtain a quantum version of L. Lov\'{a}sz's reduction (Proc. 4th SE Conf. on Comb., Graph Theory & Computing, 1973) of the $k$-coloring problem for a graph $G$ with $n$ vertices and $m$ edges to the $3$-coloring problem for a graph with $3+n+9n(k-2)+6mk$ vertices. Moreover, winning strategies for a synchronous game $\mathcal{G}$ can be transformed into winning strategies for an associated graph coloring game, where the strategies exhibit perfect zero knowledge for an honest verifier. We also show that, for ``graph of the game" $X(\mathcal{G})$ associated to $\mathcal{G}$ from A. Atserias et al (J. Comb. Theory Series B, Vol. 136, 2019), the independence number game $\text{Hom}(K_{|I|},\overline{X(\mathcal{G})})$ is hereditarily $*$-equivalent to $\mathcal{G}$, so that the possibility of winning strategies is the same in both games for all models, except the game algebra. Thus, the quantum versions of the chromatic number, independence number and clique number encode winning strategies for all synchronous games in all quantum models., Comment: 30 pages; 2 figures. v2 adds an application of graph coloring games to perfect zero knowledge

Published
2023

31. Penguin huddling: a continuum model

Author

Harris, Samuel J. and McDonald, N. R.

Subjects
Physics - Fluid Dynamics
Abstract

Penguins huddling in a cold wind are represented by a two-dimensional, continuum model. The huddle boundary evolves due to heat loss to the huddle exterior and through the reorganisation of penguins as they seek to regulate their heat production within the huddle. These two heat transfer mechanisms, along with area, or penguin number, conservation, gives a free boundary problem whose dynamics depend on both the dynamics interior and exterior to the huddle. Assuming the huddle shape evolves slowly compared to the advective timescale of the exterior wind, the interior temperature is governed by a Poisson equation and the exterior temperature by the steady advection-diffusion equation. The exterior, advective wind velocity is the gradient of a harmonic, scalar field. The conformal invariance of the exterior governing equations is used to convert the system to a Polubarinova-Galin type equation, with forcing depending on both the interior and exterior temperature gradients at the huddle boundary. The interior Poisson equation is not conformally invariant, so the interior temperature gradient is found numerically using a combined adaptive Antoulas-Anderson and least squares algorithm. The results show that, irrespective of the starting shape, penguin huddles evolve into an egg-like steady shape. This shape is dependent on the wind strength, parameterised by the P\'eclet number Pe, and a parameter \b{eta} which effectively measures the strength of the interior self-generation of heat by the penguins. The numerical method developed is applicable to a further five free boundary problems., Comment: 16 pages, 8 figures, submitted to Acta Applicandae Mathematicae

Published
2023
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32. Antiferromagnetic bosonic $t$-$J$ models and their quantum simulation in tweezer arrays

Author

Homeier, Lukas, Harris, Timothy J., Blatz, Tizian, Geier, Sebastian, Hollerith, Simon, Schollwöck, Ulrich, Grusdt, Fabian, and Bohrdt, Annabelle

Subjects
Condensed Matter - Quantum Gases, Condensed Matter - Strongly Correlated Electrons, Quantum Physics
Abstract

The combination of optical tweezer arrays with strong interactions -- via dipole-exchange of molecules and van-der-Waals interactions of Rydberg atoms -- has opened the door for the exploration of a wide variety of quantum spin models. A next significant step will be the combination of such settings with mobile dopants: This will enable to simulate the physics believed to underlie many strongly correlated quantum materials. Here we propose an experimental scheme to realize bosonic t-J models via encoding the local Hilbert space in a set of three internal atomic or molecular states. By engineering antiferromagnetic (AFM) couplings between spins, competition between charge motion and magnetic order similar to that in high-$T_c$ cuprates can be realized. Since the ground states of the 2D bosonic AFM t-J model we propose to realize have not been studied extensively before, we start by analyzing the case of two dopants -- the simplest instance in which their bosonic statistics plays a role, and contrast our results to the fermionic case. We perform large-scale density matrix renormalization group (DMRG) calculations on six-legged cylinders, and find a strong tendency for bosonic holes to form stripes. This demonstrates that bosonic, AFM t-J models may contain similar physics as the collective phases in strongly correlated electrons.

Published
2023
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35. Native diversity buffers against severity of non-native tree invasions.

Author

Delavaux, Camille S, Crowther, Thomas W, Zohner, Constantin M, Robmann, Niamh M, Lauber, Thomas, van den Hoogen, Johan, Kuebbing, Sara, Liang, Jingjing, de-Miguel, Sergio, Nabuurs, Gert-Jan, Reich, Peter B, Abegg, Meinrad, Adou Yao, Yves C, Alberti, Giorgio, Almeyda Zambrano, Angelica M, Alvarado, Braulio Vilchez, Alvarez-Dávila, Esteban, Alvarez-Loayza, Patricia, Alves, Luciana F, Ammer, Christian, Antón-Fernández, Clara, Araujo-Murakami, Alejandro, Arroyo, Luzmila, Avitabile, Valerio, Aymard, Gerardo A, Baker, Timothy R, Bałazy, Radomir, Banki, Olaf, Barroso, Jorcely G, Bastian, Meredith L, Bastin, Jean-Francois, Birigazzi, Luca, Birnbaum, Philippe, Bitariho, Robert, Boeckx, Pascal, Bongers, Frans, Bouriaud, Olivier, Brancalion, Pedro HS, Brandl, Susanne, Brienen, Roel, Broadbent, Eben N, Bruelheide, Helge, Bussotti, Filippo, Gatti, Roberto Cazzolla, César, Ricardo G, Cesljar, Goran, Chazdon, Robin, Chen, Han YH, Chisholm, Chelsea, Cho, Hyunkook, Cienciala, Emil, Clark, Connie, Clark, David, Colletta, Gabriel D, Coomes, David A, Cornejo Valverde, Fernando, Corral-Rivas, José J, Crim, Philip M, Cumming, Jonathan R, Dayanandan, Selvadurai, de Gasper, André L, Decuyper, Mathieu, Derroire, Géraldine, DeVries, Ben, Djordjevic, Ilija, Dolezal, Jiri, Dourdain, Aurélie, Engone Obiang, Nestor Laurier, Enquist, Brian J, Eyre, Teresa J, Fandohan, Adandé Belarmain, Fayle, Tom M, Feldpausch, Ted R, Ferreira, Leandro V, Fischer, Markus, Fletcher, Christine, Frizzera, Lorenzo, Gamarra, Javier GP, Gianelle, Damiano, Glick, Henry B, Harris, David J, Hector, Andrew, Hemp, Andreas, Hengeveld, Geerten, Hérault, Bruno, Herbohn, John L, Herold, Martin, Hillers, Annika, Honorio Coronado, Eurídice N, Hui, Cang, Ibanez, Thomas T, Amaral, Iêda, Imai, Nobuo, Jagodziński, Andrzej M, Jaroszewicz, Bogdan, Johannsen, Vivian Kvist, Joly, Carlos A, Jucker, Tommaso, Jung, Ilbin, and Karminov, Viktor

Subjects
General Science & Technology
Abstract

Determining the drivers of non-native plant invasions is critical for managing native ecosystems and limiting the spread of invasive species1,2. Tree invasions in particular have been relatively overlooked, even though they have the potential to transform ecosystems and economies3,4. Here, leveraging global tree databases5-7, we explore how the phylogenetic and functional diversity of native tree communities, human pressure and the environment influence the establishment of non-native tree species and the subsequent invasion severity. We find that anthropogenic factors are key to predicting whether a location is invaded, but that invasion severity is underpinned by native diversity, with higher diversity predicting lower invasion severity. Temperature and precipitation emerge as strong predictors of invasion strategy, with non-native species invading successfully when they are similar to the native community in cold or dry extremes. Yet, despite the influence of these ecological forces in determining invasion strategy, we find evidence that these patterns can be obscured by human activity, with lower ecological signal in areas with higher proximity to shipping ports. Our global perspective of non-native tree invasion highlights that human drivers influence non-native tree presence, and that native phylogenetic and functional diversity have a critical role in the establishment and spread of subsequent invasions.

Published
2023

36. Energetic landscape of polycystin channel gating

Author

Ng, Leo CT, Harris, Brandon J, Larmore, Megan, Ta, My C, Vien, Thuy N, Tokars, Valerie L, Yarov‐Yarovoy, Vladimir, and DeCaen, Paul G

Subjects
Biochemistry and Cell Biology, Biological Sciences, Congenital Structural Anomalies, Polycystic Kidney Disease, Kidney Disease, Pediatric, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Humans, Mice, Animals, TRPP Cation Channels, Signal Transduction, Ion Transport, Transient Receptor Potential Channels, Mutation, Receptors, Cell Surface, Calcium Channels, calcium, polycystic kidney disease, polycystins, structural biology, TRP channels, Developmental Biology, Biochemistry and cell biology
Abstract

Members of the polycystin family (PKD2 and PKD2L1) of transient receptor potential (TRP) channels conduct Ca2+ and depolarizing monovalent cations. Variants in PKD2 cause autosomal dominant polycystic kidney disease (ADPKD) in humans, whereas loss of PKD2L1 expression causes seizure susceptibility in mice. Understanding structural and functional regulation of these channels will provide the basis for interpreting their molecular dysregulation in disease states. However, the complete structures of polycystins are unresolved, as are the conformational changes regulating their conductive states. To provide a holistic understanding of the polycystin gating cycle, we use computational prediction tools to model missing PKD2L1 structural motifs and evaluate more than 150 mutations in an unbiased mutagenic functional screen of the entire pore module. Our results provide an energetic landscape of the polycystin pore, which enumerates gating sensitive sites and interactions required for opening, inactivation, and subsequent desensitization. These findings identify the external pore helices and specific cross-domain interactions as critical structural regulators controlling the polycystin ion channel conductive and nonconductive states.

Published
2023

37. Morphodynamics of dendrite growth in alumina based all solid-state sodium metal batteries

Author

Geng, Lin, Xue, Dingchuan, Yao, Jingming, Dai, Qiushi, Sun, Haiming, Zhu, Dingding, Rong, Zhaoyu, Fang, Ruyue, Zhang, Xuedong, Su, Yong, Yan, Jitong, Harris, Stephen J, Ichikawa, Satoshi, Zhang, Liqiang, Tang, Yongfu, Zhang, Sulin, and Huang, Jianyu

Subjects
Engineering, Materials Engineering, Chemical Sciences, Physical Chemistry, Affordable and Clean Energy, Energy
Abstract

All solid-state batteries (ASSBs) with ceramic electrolytes and alkali metal anodes are a potential future energy storage technology for vehicle electrification and smart grids. However, uncontrollable dendrite growth toward ultimate short circuiting in solid electrolytes (SEs) has become a serious concern in the design of long-cycle, safe ASSBs, and the underlying mechanism has remained unclear. Here through multiscale imaging and morphodynamic tracking we show that Na dendrites grow in β′′-Al2O3 SEs through an alternating sequence of Na deposition and crack propagation. Atomic-scale imaging evidenced that electrochemical cycling causes massive delamination cracking along the Na+ conduction planes, accompanied by the closure of neighboring conduction channels. In situ SEM observations revealed a dynamic interplay between Na deposition and crack propagation: Na deposition accumulates mechanical stress that induces cracking; cracking releases the local stress, which promotes further Na deposition. Thus, Na deposition and cracking alternatingly proceed until short circuits take place. A multiscale phase-field model is developed to recapitulate the morphodynamics of Na dendrite growth, predicting the tree-like fractal morphology of the growing dendrites. Our findings suggest that decoupling between Na deposition and cracking represents an important route to mitigate uncontrollable dendrite growth in ASSBs.

Published
2023

38. Curriculum Materials Designed for the Next Generation Science Standards Show Promise: Initial Results from a Randomized Controlled Trial in Middle Schools

Author

WestEd, SRI International, University of California, Berkeley, Harris, Christopher J., Feng, Mingyu, Murphy, Robert, and Rutstein, Daisy W.

Abstract

This report describes initial findings from a study of middle school science curriculum materials that were designed to promote learning as called for by the Next Generation Science Standards (NGSS). WestEd led an independent randomized controlled trial to evaluate the efficacy of the NGSS-designed Amplify Science Middle School (ASMS) curriculum. This study examined the impact of the materials in 7th grade classrooms across three school districts. Schools were randomly assigned to one of two groups: an intervention group in which teachers implemented ASMS and a comparison group in which teachers implemented their regular curricular units. Science teachers in both groups implemented instruction that aimed for the same NGSS performance expectations. Hierarchical linear regression modeling was used to analyze the impact of the curriculum on student learning outcomes in physical science, as measured by an assessment aligned to NGSS performance expectations. Initial findings show promise that the ASMS curriculum can be used to support next generation science learning. The main result was that students in intervention classrooms significantly outperformed students in comparison classrooms. This study is among the first rigorous studies of widely available curriculum materials for the NGSS.

Published
2022

39. Quantum no-signalling bicorrelations

Author

Brannan, Michael, Harris, Samuel J., Todorov, Ivan G., and Turowska, Lyudmila

Subjects
Mathematics - Operator Algebras
Abstract

We introduce classical and quantum no-signalling bicorrelations and characterise the different types thereof in terms of states on operator system tensor products, exhibiting connections with bistochastic operator matrices and with dilations of quantum magic squares. We define concurrent bicorrelations as a quantum input-output generalisation of bisynchronous correlations. We show that concurrent bicorrelations of quantum commuting type correspond to tracial states on the universal C*-algebra of the projective free unitary quantum group, showing that in the quantum input-output setup, quantum permutations of finite sets must be replaced by quantum automorphisms of matrix algebras. We apply our results to study the quantum graph isomorphism game, describing the game C*-algebra in this case, and make precise connections with the algebraic notions of quantum graph isomorphism, existing presently in the literature., Comment: 76 pages

Published
2023

40. Statistical and machine learning-based durability-testing strategies for energy storage

Author

Harris, Stephen J and Noack, Marcus M

Subjects
Engineering, Materials Engineering, Bioengineering, Affordable and Clean Energy, Chemical sciences
Abstract

There is considerable interest in developing new energy storage technologies for the electric grid, but economic viability will require that manufacturers provide warranties guaranteeing 15+ years of life. Although there are extensive efforts to make early predictions for the expected life of new storage technologies, we argue here that for the purposes of pricing warranties and valuing second-life potential—considerations that are crucial to whether the technologies can be commercialized—the full failure probability distribution, not just the expected life, is required. We use published battery cycle-life data to suggest efficient statistical and machine learning-based testing and analysis strategies that can rapidly estimate and also take advantage of the failure probability distribution. One approach is a Weibull analysis, which can (1) reduce the number of testing machine hours required for setting a warranty, (2) quickly determine whether a new technology is better than a baseline technology, and (3) estimate the maximum intensity of testing acceleration that does not change the failure mode. A second approach is driven by the idea that all measured data—such as capacity or energy as a function of time or cycle number—are valuable and generated by an underlying latent function. This analysis employs a Gaussian process to find the underlying latent function, together with its uncertainties, which can be used to calculate the failure distribution.

Published
2023

41. A genomic timescale for placental mammal evolution

Author

Foley, Nicole M, Mason, Victor C, Harris, Andrew J, Bredemeyer, Kevin R, Damas, Joana, Lewin, Harris A, Eizirik, Eduardo, Gatesy, John, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Springer, Mark S, Murphy, William J, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Fan, Kaili, Fanter, Cornelia, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, Sullivan, Patrick F, and Sundström, Elisabeth

Subjects
Genetics, Human Genome, Biotechnology, Animals, Female, Biological Evolution, Eutheria, Evolution, Molecular, Fossils, Genomics, Phylogeny, Genetic Variation, Time Factors, Zoonomia Consortium‡, General Science & Technology
Abstract

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.

Published
2023

42. Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs

Author

Moon, Katherine L, Huson, Heather J, Morrill, Kathleen, Wang, Ming-Shan, Li, Xue, Srikanth, Krishnamoorthy, Lindblad-Toh, Kerstin, Svenson, Gavin J, Karlsson, Elinor K, Shapiro, Beth, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, Sullivan, Patrick F, Sundström, Elisabeth, Supple, Megan A, and Swofford, Ross

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Animals, Dogs, Male, Genome, Genomics, Genotype, Phenotype, Wolves, Biodiversity, Genetic Variation, Zoonomia Consortium, General Science & Technology
Abstract

We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto's genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto's population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.

Published
2023

43. The contribution of historical processes to contemporary extinction risk in placental mammals

Author

Wilder, Aryn P, Supple, Megan A, Subramanian, Ayshwarya, Mudide, Anish, Swofford, Ross, Serres-Armero, Aitor, Steiner, Cynthia, Koepfli, Klaus-Peter, Genereux, Diane P, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Marques-Bonet, Tomas, Munoz Fuentes, Violeta, Foley, Kathleen, Meyer, Wynn K, Ryder, Oliver A, Shapiro, Beth, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Mason, Victor C, Meadows, Jennifer RS, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Smit, Arian FA, Springer, Mark, and Srinivasan, Chaitanya

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Behavioral and Social Science, Human Genome, Basic Behavioral and Social Science, Life on Land, Animals, Female, Pregnancy, Eutheria, Extinction, Biological, Genetic Variation, Genome, Population Density, Risk, Zoonomia Consortium‡, General Science & Technology
Abstract

Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.

Published
2023

44. The functional and evolutionary impacts of human-specific deletions in conserved elements

Author

Xue, James R, Mackay-Smith, Ava, Mouri, Kousuke, Garcia, Meilin Fernandez, Dong, Michael X, Akers, Jared F, Noble, Mark, Li, Xue, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Noonan, James P, Capellini, Terence D, Brennand, Kristen J, Tewhey, Ryan, Sabeti, Pardis C, Reilly, Steven K, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Lind, Abigail, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, and Steiner, Cynthia

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Neurosciences, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Neurological, Humans, Conserved Sequence, Evolution, Molecular, Genome, Genomics, RNA-Binding Proteins, Sequence Deletion, Brain, Gene Expression Regulation, Developmental, Zoonomia Consortium†, General Science & Technology
Abstract

Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.

Published
2023

45. Integrating gene annotation with orthology inference at scale

Author

Kirilenko, Bogdan M, Munegowda, Chetan, Osipova, Ekaterina, Jebb, David, Sharma, Virag, Blumer, Moritz, Morales, Ariadna E, Ahmed, Alexis-Walid, Kontopoulos, Dimitrios-Georgios, Hilgers, Leon, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Hiller, Michael, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, and Sullivan, Patrick F

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Animals, Female, Mice, Eutheria, Genome, Genomics, Molecular Sequence Annotation, Birds, Zoonomia Consortium‡, General Science & Technology
Abstract

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.

Published
2023

46. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

Author

Kaplow, Irene M, Lawler, Alyssa J, Schäffer, Daniel E, Srinivasan, Chaitanya, Sestili, Heather H, Wirthlin, Morgan E, Phan, BaDoi N, Prasad, Kavya, Brown, Ashley R, Zhang, Xiaomeng, Foley, Kathleen, Genereux, Diane P, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Meyer, Wynn K, Pfenning, Andreas R, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, and Steiner, Cynthia

Subjects
Biological Sciences, Genetics, Pediatric, Human Genome, Rare Diseases, Congenital Structural Anomalies, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Mental health, Animals, Enhancer Elements, Genetic, Genetic Variation, Machine Learning, Mammals, Phenotype, Zoonomia Consortium**, General Science & Technology
Abstract

Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.

Published
2023

47. Three-dimensional genome rewiring in loci with human accelerated regions

Author

Keough, Kathleen C, Whalen, Sean, Inoue, Fumitaka, Przytycki, Pawel F, Fair, Tyler, Deng, Chengyu, Steyert, Marilyn, Ryu, Hane, Lindblad-Toh, Kerstin, Karlsson, Elinor, Nowakowski, Tomasz, Ahituv, Nadav, Pollen, Alex, Pollard, Katherine S, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Karlsson, Elinor K, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, and Sullivan, Kevin AM

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Stem Cell Research, Human Genome, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Animals, Humans, Chromatin, Genome, Human, Genomics, Pan troglodytes, Genetic Loci, Neurogenesis, Deep Learning, Zoonomia Consortium§, General Science & Technology
Abstract

Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.

Published
2023

48. Leveraging base-pair mammalian constraint to understand genetic variation and human disease

Author

Sullivan, Patrick F, Meadows, Jennifer RS, Gazal, Steven, Phan, BaDoi N, Li, Xue, Genereux, Diane P, Dong, Michael X, Bianchi, Matteo, Andrews, Gregory, Sakthikumar, Sharadha, Nordin, Jessika, Roy, Ananya, Christmas, Matthew J, Marinescu, Voichita D, Wang, Chao, Wallerman, Ola, Xue, James, Yao, Shuyang, Sun, Quan, Szatkiewicz, Jin, Wen, Jia, Huckins, Laura M, Lawler, Alyssa, Keough, Kathleen C, Zheng, Zhili, Zeng, Jian, Wray, Naomi R, Li, Yun, Johnson, Jessica, Chen, Jiawen, Paten, Benedict, Reilly, Steven K, Hughes, Graham M, Weng, Zhiping, Pollard, Katherine S, Pfenning, Andreas R, Forsberg-Nilsson, Karin, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Armstrong, Joel C, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Garcia, Carlos J, Gatesy, John, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Lind, Abigail, Mackay-Smith, Ava, Marques-Bonet, Tomas, Mason, Victor C, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, and Navarro, Arcadi

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Clinical Research, Human Genome, Brain Disorders, Generic health relevance, Animals, Humans, Biological Evolution, Genetic Variation, Genome, Human, Genome-Wide Association Study, Genomics, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Disease, Zoonomia Consortium§, General Science & Technology
Abstract

Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.

Published
2023

50. Consistent patterns of common species across tropical tree communities

Author

Cooper, Declan L. M., Lewis, Simon L., Sullivan, Martin J. P., Prado, Paulo I., ter Steege, Hans, Barbier, Nicolas, Slik, Ferry, Sonké, Bonaventure, Ewango, Corneille E. N., Adu-Bredu, Stephen, Affum-Baffoe, Kofi, de Aguiar, Daniel P. P., Ahuite Reategui, Manuel Augusto, Aiba, Shin-Ichiro, Albuquerque, Bianca Weiss, de Almeida Matos, Francisca Dionízia, Alonso, Alfonso, Amani, Christian A., do Amaral, Dário Dantas, do Amaral, Iêda Leão, Andrade, Ana, de Andrade Miranda, Ires Paula, Angoboy, Ilondea B., Araujo-Murakami, Alejandro, Arboleda, Nicolás Castaño, Arroyo, Luzmila, Ashton, Peter, Aymard C, Gerardo A., Baider, Cláudia, Baker, Timothy R., Balinga, Michael Philippe Bessike, Balslev, Henrik, Banin, Lindsay F., Bánki, Olaf S., Baraloto, Chris, Barbosa, Edelcilio Marques, Barbosa, Flávia Rodrigues, Barlow, Jos, Bastin, Jean-Francois, Beeckman, Hans, Begne, Serge, Bengone, Natacha Nssi, Berenguer, Erika, Berry, Nicholas, Bitariho, Robert, Boeckx, Pascal, Bogaert, Jan, Bonyoma, Bernard, Boundja, Patrick, Bourland, Nils, Boyemba Bosela, Faustin, Brambach, Fabian, Brienen, Roel, Burslem, David F. R. P., Camargo, José Luís, Campelo, Wegliane, Cano, Angela, Cárdenas, Sasha, Cárdenas López, Dairon, de Sá Carpanedo, Rainiellen, Carrero Márquez, Yrma Andreina, Carvalho, Fernanda Antunes, Casas, Luisa Fernanda, Castellanos, Hernán, Castilho, Carolina V., Cerón, Carlos, Chapman, Colin A., Chave, Jerome, Chhang, Phourin, Chutipong, Wanlop, Chuyong, George B., Cintra, Bruno Barçante Ladvocat, Clark, Connie J., Coelho de Souza, Fernanda, Comiskey, James A., Coomes, David A., Cornejo Valverde, Fernando, Correa, Diego F., Costa, Flávia R. C., Costa, Janaina Barbosa Pedrosa, Couteron, Pierre, Culmsee, Heike, Cuni-Sanchez, Aida, Dallmeier, Francisco, Damasco, Gabriel, Dauby, Gilles, Dávila, Nállarett, Dávila Doza, Hilda Paulette, De Alban, Jose Don T., de Assis, Rafael L., De Canniere, Charles, De Haulleville, Thales, de Jesus Veiga Carim, Marcelo, Demarchi, Layon O., Dexter, Kyle G., Di Fiore, Anthony, Din, Hazimah Haji Mohammad, Disney, Mathias I., Djiofack, Brice Yannick, Djuikouo, Marie-Noël K., Do, Tran Van, Doucet, Jean-Louis, Draper, Freddie C., Droissart, Vincent, Duivenvoorden, Joost F., Engel, Julien, Estienne, Vittoria, Farfan-Rios, William, Fauset, Sophie, Feeley, Kenneth J., Feitosa, Yuri Oliveira, Feldpausch, Ted R., Ferreira, Cid, Ferreira, Joice, Ferreira, Leandro Valle, Fletcher, Christine D., Flores, Bernardo Monteiro, Fofanah, Alusine, Foli, Ernest G., Fonty, Émile, Fredriksson, Gabriella M., Fuentes, Alfredo, Galbraith, David, Gallardo Gonzales, George Pepe, Garcia-Cabrera, Karina, García-Villacorta, Roosevelt, Gomes, Vitor H. F., Gómez, Ricardo Zárate, Gonzales, Therany, Gribel, Rogerio, Guedes, Marcelino Carneiro, Guevara, Juan Ernesto, Hakeem, Khalid Rehman, Hall, Jefferson S., Hamer, Keith C., Hamilton, Alan C., Harris, David J., Harrison, Rhett D., Hart, Terese B., Hector, Andy, Henkel, Terry W., Herbohn, John, Hockemba, Mireille B. N., Hoffman, Bruce, Holmgren, Milena, Honorio Coronado, Euridice N., Huamantupa-Chuquimaco, Isau, Hubau, Wannes, Imai, Nobuo, Irume, Mariana Victória, Jansen, Patrick A., Jeffery, Kathryn J., Jimenez, Eliana M., Jucker, Tommaso, Junqueira, André Braga, Kalamandeen, Michelle, Kamdem, Narcisse G., Kartawinata, Kuswata, Kasongo Yakusu, Emmanuel, Katembo, John M., Kearsley, Elizabeth, Kenfack, David, Kessler, Michael, Khaing, Thiri Toe, Killeen, Timothy J., Kitayama, Kanehiro, Klitgaard, Bente, Labrière, Nicolas, Laumonier, Yves, Laurance, Susan G. W., Laurance, William F., Laurent, Félix, Le, Tinh Cong, Le, Trai Trong, Leal, Miguel E., Leão de Moraes Novo, Evlyn Márcia, Levesley, Aurora, Libalah, Moses B., Licona, Juan Carlos, Lima Filho, Diógenes de Andrade, Lindsell, Jeremy A., Lopes, Aline, Lopes, Maria Aparecida, Lovett, Jon C., Lowe, Richard, Lozada, José Rafael, Lu, Xinghui, Luambua, Nestor K., Luize, Bruno Garcia, Maas, Paul, Magalhães, José Leonardo Lima, Magnusson, William E., Mahayani, Ni Putu Diana, Makana, Jean-Remy, Malhi, Yadvinder, Maniguaje Rincón, Lorena, Mansor, Asyraf, Manzatto, Angelo Gilberto, Marimon, Beatriz S., Marimon-Junior, Ben Hur, Marshall, Andrew R, Martins, Maria Pires, Mbayu, Faustin M., de Medeiros, Marcelo Brilhante, Mesones, Italo, Metali, Faizah, Mihindou, Vianet, Millet, Jerome, Milliken, William, Mogollón, Hugo F., Molino, Jean-François, Mohd. Said, Mohd. Nizam, Monteagudo Mendoza, Abel, Montero, Juan Carlos, Moore, Sam, Mostacedo, Bonifacio, Mozombite Pinto, Linder Felipe, Mukul, Sharif Ahmed, Munishi, Pantaleo K. T., Nagamasu, Hidetoshi, Nascimento, Henrique Eduardo Mendonça, Nascimento, Marcelo Trindade, Neill, David, Nilus, Reuben, Noronha, Janaína Costa, Nsenga, Laurent, Núñez Vargas, Percy, Ojo, Lucas, Oliveira, Alexandre A., de Oliveira, Edmar Almeida, Ondo, Fidèle Evouna, Palacios Cuenca, Walter, Pansini, Susamar, Pansonato, Marcelo Petratti, Paredes, Marcos Ríos, Paudel, Ekananda, Pauletto, Daniela, Pearson, Richard G., Pena, José Luis Marcelo, Pennington, R. Toby, Peres, Carlos A., Permana, Andrea, Petronelli, Pascal, Peñuela Mora, Maria Cristina, Phillips, Juan Fernando, Phillips, Oliver L., Pickavance, Georgia, Piedade, Maria Teresa Fernandez, Pitman, Nigel C. A., Ploton, Pierre, Popelier, Andreas, Poulsen, John R., Prieto, Adriana, Primack, Richard B., Priyadi, Hari, Qie, Lan, Quaresma, Adriano Costa, de Queiroz, Helder Lima, Ramirez-Angulo, Hirma, Ramos, José Ferreira, Reis, Neidiane Farias Costa, Reitsma, Jan, Revilla, Juan David Cardenas, Riutta, Terhi, Rivas-Torres, Gonzalo, Robiansyah, Iyan, Rocha, Maira, Rodrigues, Domingos de Jesus, Rodriguez-Ronderos, M. Elizabeth, Rovero, Francesco, Rozak, Andes H., Rudas, Agustín, Rutishauser, Ervan, Sabatier, Daniel, Sagang, Le Bienfaiteur, Sampaio, Adeilza Felipe, Samsoedin, Ismayadi, Satdichanh, Manichanh, Schietti, Juliana, Schöngart, Jochen, Scudeller, Veridiana Vizoni, Seuaturien, Naret, Sheil, Douglas, Sierra, Rodrigo, Silman, Miles R., Silva, Thiago Sanna Freire, da Silva Guimarães, José Renan, Simo-Droissart, Murielle, Simon, Marcelo Fragomeni, Sist, Plinio, Sousa, Thaiane R., de Sousa Farias, Emanuelle, de Souza Coelho, Luiz, Spracklen, Dominick V., Stas, Suzanne M., Steinmetz, Robert, Stevenson, Pablo R., Stropp, Juliana, Sukri, Rahayu S., Sunderland, Terry C. H., Suzuki, Eizi, Swaine, Michael D., Tang, Jianwei, Taplin, James, Taylor, David M., Tello, J. 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2024
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