We wish to thank the New England Aquarium (Protocol 2022-14 to JHC) for generously providing Aurelia aurita medusae for laboratory work.
\n[ { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/nkste-7tj29", "doi": "10.1038/s41556-024-01367-1", "_Key": "nkste-7tj29", "date": "2024-03-05", "issn": "1465-7392", "note": "
© The Author(s) 2024. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
\n\nThe authors thank patients at CARE, Herts & Essex, Bourn Hall Fertility and King’s Fertility Clinics for their generous donations, as well as the embryologists and members of each clinic for facilitating donations. We thank G. Serapio-García for advice on Bayesian statistical analysis and the bioinformaticians and data scientists who made their code, packages and vignettes available. This work is supported by Wellcome Trust (207415/Z/17/Z) and Open Atlas and NOMIS awards to M.Z.-G. B.A.T.W. was supported by the Gates Cambridge Trust. C.W.G. was supported by a Leverhulme Trust Early Career Fellowship. L.K.I.-S. was supported by the Rosetrees Trust.
\nThese authors contributed equally: Bailey A. T. Weatherbee, Antonia Weberling, Carlos W. Gantner.
\nB.A.T.W., A.W., C.W.G. and L.K.I.-S. thawed and cultured human embryos for research. B.A.T.W. performed single-cell sequencing analyses. Z.B., A.B., A.C., P.C., C.D., P.E., S.F., S.G.V., M.L., R.O., C.P., N.C., L.R., A.M., L.W., L.C., K.E. and P.S. interfaced with patients, prepared informed consent documentation and prepared embryos for transfer from clinical to research setting. A.W. dissected and cultured mouse embryos. B.A.T.W. and C.W.G. cultured and differentiated human and mouse stem cells. B.A.T.W. and C.W.G. performed quantitative image analyses. B.A.T.W., C.W.G., A.W. and M.Z.-G. wrote the manuscript and conceived the study. B.A.T.W., A.W. and C.W.G. contributed equally.
\n\nAll raw data used here are previously published and publicly available. For aligning sequencing data, GRCh38 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/), Genome assembly Macaca_fascicularis_5.0 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000364345.1/) and GRCm39 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.27/) were used. For human data: Molè et al.10, ArrayExpress E-MTAB-8060; Xiang et al.26, Gene Expression Omnibus GSE136447; Zhou et al.27, Gene Expression Omnibus GSE109555; Petropoulos et al.45, ArrayExpress E-MTAB-3929; Blakely et al.36, Gene Expression Omnibus GSE66507. For cynomolgus monkey data: Yang et al.35, Gene Expression Omnibus GSE148683; Ma et al.28, Gene Expression Omnibus GSE130114; Nakamura et al.21, Gene Expression Omnibus GSE74767. For mouse data: Pijuan-Sala et al.71, ArrayExpress E-MTAB-6967; Mohammed et al.70, Gene Expression Omnibus GSE100597; Cheng et al.68, Gene Expression Omnibus GSE109071; Deng et al.69, Gene Expression Omnibus GSE45719. Scripts used for analysis are available at ref. 79. The integrated Seurat objects for each species are available on Zenodo100 (https://doi.org/10.5281/zenodo.7689580). All other data supporting the findings of this study are available from the corresponding author on reasonable request. Source data are provided with this paper.
\nThe authors declare no competing interests.
\nDevelopment requires coordinated interactions between the epiblast, which generates the embryo proper; the trophectoderm, which generates the placenta; and the hypoblast, which forms both the anterior signalling centre and the yolk sac. These interactions remain poorly understood in human embryogenesis because mechanistic studies have only recently become possible. Here we examine signalling interactions post-implantation using human embryos and stem cell models of the epiblast and hypoblast. We find anterior hypoblast specification is NODAL dependent, as in the mouse. However, while BMP inhibits anterior signalling centre specification in the mouse, it is essential for its maintenance in human. We also find contrasting requirements for BMP in the naive pre-implantation epiblast of mouse and human embryos. Finally, we show that NOTCH signalling is important for human epiblast survival. Our findings of conserved and species-specific factors that drive these early stages of embryonic development highlight the strengths of comparative species studies.
\n© 2024 American Chemical Society.
\n\nWe acknowledge Dr. Erica Sutcliffe and Nathanael P. Kazmierczak for helpful discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 883987 (D.B.). K.M.L. and D.A.C. acknowledge support from the National Science Foundation Graduate Research Fellowship (NSF GRFP) under grant no. DGE-1745301. Support has been provided by the National Institutes of Health (National Institute of General Medical Sciences, R35-GM142595). The computations presented here were in part conducted in the Resnick High Performance Computing Center, a facility supported by Resnick Sustainability Institute at the California Institute of Technology and in part by the IT4Innovations National Supercomputing Center under the programme of the Ministry of Education, Youth and Sports of the Czech Republic through the e-INFRA CZ (ID:90254).
\nD.B.: conceptualization; methodology; investigation; formal analysis; writing─original draft; writing─review and editing. K.M.L.: methodology; investigation; formal analysis; writing─original draft; writing─review and editing. D.A.C.: methodology; writing─review and editing. R.G.H.: conceptualization; methodology; writing─original draft; writing─review and editing; supervision; project administration; funding acquisition.
\n\nThe authors declare no competing financial interest.
\n\nExperimental and computational methods, synthetic details, UV–vis/photochemical data, kinetic modeling, transient absorption spectra analysis, NMR spectra, calculated properties, XYZ of the optimized structures, and additional comments (PDF)
\nTransition-metal photoredox catalysis has transformed organic synthesis by harnessing light to construct complex molecules. Nickel(II)–bipyridine (bpy) aryl halide complexes are a significant class of cross-coupling catalysts that can be activated via direct light excitation. This study investigates the effects of molecular structure on the photophysics of these catalysts by considering an underexplored, structurally constrained Ni(II)–bpy aryl halide complex in which the aryl and bpy ligands are covalently tethered alongside traditional unconstrained complexes. Intriguingly, the tethered complex is photochemically stable but features a reversible Ni(II)–C(aryl) ⇄ [Ni(I)···C(aryl)•] equilibrium upon direct photoexcitation. When an electrophile is introduced during photoirradiation, we demonstrate a preference for photodissociation over recombination, rendering the parent Ni(II) complex a stable source of a reactive Ni(I) intermediate. Here, we characterize the reversible photochemical behavior of the tethered complex by kinetic analyses, quantum chemical calculations, and ultrafast transient absorption spectroscopy. Comparison to the previously characterized Ni(II)–bpy aryl halide complex indicates that the structural constraints considered here dramatically influence the excited state relaxation pathway and provide insight into the characteristics of excited-state Ni(II)–C bond homolysis and aryl radical reassociation dynamics. This study enriches the understanding of molecular structure effects in photoredox catalysis and offers new possibilities for designing customized photoactive catalysts for precise organic synthesis.
\n© The Author(s), under exclusive licence to Springer Nature Limited 2024.
\n\nWe are grateful to K. Vahala and L. Wu for lending equipment useful to this work. We thank D. Nelson and N. Hatano for their comments on this work. The authors acknowledge support from NSF Grants No. 1846273 and 1918549 and AFOSR Award No. FA9550-20-1-0040. F.N. is supported in part by the Office of Naval Research (ONR), Japan Science and Technology Agency (JST) (via the Quantum Leap Flagship Program (Q-LEAP) and the Moonshot R&D Grant No. JPMJMS2061) and the Asian Office of Aerospace Research and Development (AOARD) (via Grant No. FA2386-20-1-4069). We wish to thank NTT Research for their financial and technical support.
\nThe data used to generate the plots and results in this paper are available on figshare (https://doi.org/10.6084/m9.figshare.25050494). Source data are provided with this paper. All other data that support the findings of this study are available from the corresponding author upon reasonable request.
\n\nThe code used to generate the plots and simulation results in this paper is available from the corresponding author upon reasonable request.
\nA.M. has a financial interest in PINC Technologies Inc., which is developing photonic integrated nonlinear circuits. The other authors declare no competing interests.
", "type": "article", "title": "Topological temporally mode-locked laser", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Science Foundation", "grant_number": "ECCS-1846273" }, { "agency": "National Science Foundation", "grant_number": "CCF-1918549" }, { "agency": "United States Air Force Office of Scientific Research", "grant_number": "FA9550-20-1-0040" }, { "agency": "Office of Naval Research" }, { "agency": "Japan Science and Technology Agency", "grant_number": "JPMJMS2061" }, { "agency": "United States Air Force Office of Scientific Research", "grant_number": "FA2386-20-1-4069" }, { "agency": "NTT (United States)" } ] }, "lastmod": "2024-03-05 19:37:32", "abstract": "Mode-locked lasers play a crucial role in modern science and technology. They are essential to the study of ultrafast and nonlinear optics, and they have applications in metrology, telecommunications and imaging. Recently, there has been interest in studying topological phenomena in mode-locked lasers. From a fundamental perspective, such study promises to reveal nonlinear topological physics, and from a practical perspective it may lead to the development of topologically protected short-pulse sources. Despite this promising outlook, the interplay between topological photonic lattices and laser mode-locking has not been studied experimentally. In this work, we theoretically propose and experimentally realize a topological temporally mode-locked laser. We demonstrate a nonlinearity-driven non-Hermitian skin effect in a laser cavity and observe the robustness of the laser against disorder-induced localization. Our experiments demonstrate fundamental point-gap topological physics that was previously inaccessible to photonics experiments, and they suggest potential applications of our mode-locked laser to sensing, optical computing and robust topological frequency combs. The experimental architecture employed in this work also provides a template for studying topology in other mode-locked photonic sources, including dissipative cavity solitons and synchronously pumped optical parametric oscillators.
\n© 2024 IOP Publishing Ltd.
\n\nWe wish to thank the New England Aquarium (Protocol 2022-14 to JHC) for generously providing Aurelia aurita medusae for laboratory work.
\nWe gratefully acknowledge the US NSF (CBET-2100705, IOS-2114171 to JHC, CBET-2100156, IOS-2114169 to SPC, CBET-2100703 to BJG, CBET-210020, RAISE IOS-2034043 to EK) and the US ONR (N00014-23-1-2754 to JHC, N00014-22-1-2655, N00014-19-1-2035, N00014-19-1-2035 to EK).
\nAll data that support the findings of this study are included within the article (and any supplementary files). Data will be available from 01 January 2026.
\nThe authors declare no competing interests.
\nScyphomedusae are widespread in the oceans and their swimming has provided valuable insights into the hydrodynamics of animal propulsion. Most of this research has focused on symmetrical, linear swimming. However, in nature, medusae typically swim circuitous, nonlinear paths involving frequent turns. Here we describe swimming turns by the scyphomedusa Aurelia aurita during which asymmetric bell margin motions produce rotation around a linearly translating body center. These jellyfish 'skid' through turns and the degree of asynchrony between opposite bell margins is an approximate predictor of turn magnitude during a pulsation cycle. The underlying neuromechanical organization of bell contraction contributes substantially to asynchronous bell motions and inserts a stochastic rotational component into the directionality of scyphomedusan swimming. These mechanics are important for natural populations because asynchronous bell contraction patterns are common in situ and result in frequent turns by naturally swimming medusae.
\n© 2024 American Physical Society.
\n\n ", "type": "article", "title": "Characterization of the low electric field and zero-temperature two-level-system loss in hydrogenated amorphous silicon", "number": "3", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "volume": "8", "funders": { "items": [ { "agency": "Jet Propulsion Laboratory", "grant_number": "JPL Research and Technology Development Fund" }, { "agency": "National Aeronautics and Space Administration", "grant_number": "80NSSC18K0385" }, { "agency": "National Aeronautics and Space Administration", "grant_number": "80NSSC22K1556" }, { "agency": "United States Department of Energy", "grant_number": "DE-SC0018126" }, { "agency": "National Aeronautics and Space Administration", "grant_number": "80NM0018D0004" } ] }, "lastmod": "2024-03-06 19:17:20", "abstract": "Two-level systems (TLS) are an important, if not dominant, source of loss and noise for superconducting resonators such as those used in kinetic inductance detectors and some quantum information science platforms. They are similarly important for loss in photolithographically fabricated superconducting mm-wave/THz transmission lines. For both lumped-element and transmission-line structures, native amorphous surface oxide films are typically the sites of such TLS in nonmicrostripline geometries, while loss in the (usually amorphous) dielectric film itself usually dominates in microstriplines. We report here on the demonstration of low TLS loss at GHz frequencies in hydrogenated amorphous silicon (a-Si:H) films deposited by plasma-enhanced chemical vapor deposition in superconducting lumped-element resonators using parallel-plate capacitors (PPCs). The values we obtain from two recipes in different deposition machines, 7 × 10⁻⁶ and 12 × 10⁻⁶, improve on the best achieved in the literature by a factor of 2–4 for a-Si:H and are comparable to recent measurements of amorphous germanium. Moreover, we have taken care to extract the true zero-temperature, low-field loss tangent of these films, accounting for temperature and field saturation effects that can yield misleading results. Such robustly fabricated and characterized films render the use of PPCs with deposited amorphous films a viable architecture for superconducting resonators and they also promise extremely low loss and high quality factor for photolithographically fabricated superconducting mm-wave/THz transmission lines used in planar antennas and resonant filters.
", "creators": { "items": [ { "name": { "given": "Fabien", "family": "Defrance" }, "orcid": "0000-0002-3746-5296" }, { "name": { "given": "Andrew D.", "family": "Beyer" }, "orcid": "0000-0002-1045-1652" }, { "name": { "given": "Shibo", "family": "Shu" } }, { "name": { "given": "Jack", "family": "Sayers" } }, { "id": "Golwala-S-R", "name": { "given": "Sunil R.", "family": "Golwala" }, "orcid": "0000-0002-1098-7174" } ] }, "date_type": "published", "datestamp": "2024-03-06 19:17:20", "pagerange": "035602", "publisher": "American Physical Society", "collection": "CaltechAUTHORS", "ispublished": "pub", "publication": "Physical Review Materials", "official_url": "https://authors.library.caltech.edu/records/hkz48-qrd45", "eprint_status": "archive", "full_text_status": "public", "metadata_visibility": "show" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/vvn3r-m7g89", "doi": "10.1038/s41598-024-55073-x", "_Key": "vvn3r-m7g89", "date": "2024-02-25", "issn": "2045-2322", "note": "© The Author(s) 2024. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
\n\nJASV, CIH, SM, MM, MS and DH acknowledge support through the project “CoCi: Co-Evolving City Life”, which has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 833168. The authors would like to express their gratitude to several individuals who provided valuable assistance and support during this study. We thank Stefan Wehrli and Manuel Widmer from the Decision Science Laboratory (DeSciL) at ETH Zürich for their expert feedback on experimental methods, as well as for their invaluable assistance in carrying out the experiments. We are also grateful to Michal Gath Morad for providing insightful comments during a productive Zoom call. Additionally, we extend our thanks to Fabian Schläfli for his thoughtful feedback on the project during a helpful Zoom call. Their contributions were instrumental in the successful completion of this research, and we deeply appreciate their time, effort, and expertise contributed.
\n\nOpen access funding provided by Swiss Federal Institute of Technology Zurich.
\nJ.A.S.V. proposed and designed the three scenarios and co-designed the virtual traffic situations. He supervised the students, performed the data processing and statistical analysis, and contributed to drafting, writing and reviewing the manuscript, and the figures. C.I.H. worked out the details of the treatment variations and supervised the students. She co-developed ideas for scenarios and situations, drafted the hypotheses, and introduced the idea of using sensors to monitor physiological data. Furthermore, she specified procedural details with the Decision Science Laboratory (DeSciL) and acquired ethics approval. She also contributed to writing the manuscript, the statistical analysis, and particularly the stability point analysis. S.M. contributed technical details on responsive street technology and searched for appropriate sensors as well as papers describing a connection between sensor data and behaviour. He performed heart rate data analysis and also contributed to writing the manuscript. M.S. and M.M. developed the virtual reality (VR) setting and contributed to preprocessing the data and writing the manuscript. D.H. proposed to study adaptive infrastructures and flexible uses of streets, acquired funding, engaged the VR developers, provided feedback and ideas, and contributed to the manuscript. M.E. read the paper and provided feedback on experimental details. He also contributed a section on pedestrian–vehicle interaction. All authors critically reviewed and edited the manuscript and approved the final version for submission.
\n\nTo ensure the transparency and reproducibility of our research, we will make raw and processed data, analysis scripts and code publicly available after acceptance via an open-access GitHub repository. The working repository, https://github.com/ethz-coss/VR_future_streets, can be accessed upon invitation.
\n\nThe authors declare no competing interests.
\nThe current allocation of street space is based on expected vehicular peak-hour flows. Flexible and adaptive use of this space can respond to changing needs. To evaluate the acceptability of flexible street layouts, several urban environments were designed and implemented in virtual reality. Participants explored these designs in immersive virtual reality in a 2 × 3 mixed factorial experiment, in which we analysed self-reported, behavioural and physiological responses from participants. Distinct communication strategies were varied between subjects. Participants' responses reveal a preference for familiar solutions. Unconventional street layouts are less preferred, perceived as unsafe and cause a measurably greater stress response. Furthermore, information provision focusing on comparisons lead participants to focus primarily on the drawbacks, instead of the advantages of novel scenarios. When being able to freely express thoughts and opinions, participants are focused more on the impact of space design on behaviour rather than the objective physical features themselves. Especially, this last finding suggests that it is vital to develop new street scenarios in an inclusive and democratic way: the success of innovating urban spaces depends on how well the vast diversity of citizens' needs is considered and met.
", "creators": { "items": [ { "name": { "given": "Javier", "family": "Argota Sánchez-Vaquerizo" }, "orcid": "0000-0001-9389-6616" }, { "name": { "given": "Carina I.", "family": "Hausladen" } }, { "name": { "given": "Sachit", "family": "Mahajan" }, "orcid": "0000-0001-9558-8895" }, { "name": { "given": "Marc", "family": "Matter" } }, { "name": { "given": "Michael", "family": "Siebenmann" } }, { "name": { "given": "Michael A. B.", "family": "van Eggermond" } }, { "name": { "given": "Dirk", "family": "Helbing" } } ] }, "date_type": "published", "datestamp": "2024-02-26 20:45:56", "pagerange": "4571", "publisher": "Nature", "ispublished": "pub", "publication": "Scientific Reports", "official_url": "https://authors.library.caltech.edu/records/vvn3r-m7g89", "eprint_status": "archive", "full_text_status": "public", "metadata_visibility": "show" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/xt1r5-e1z39", "doi": "10.1016/j.cels.2024.01.011", "_Key": "xt1r5-e1z39", "date": "2024-02-23", "issn": "2405-4712", "note": "© 2024 Elsevier.
\n\nWe thank the members of the Shaffer Lab for input on the experiments and figures of the manuscript. We thank the Arjun Raj Lab at the University of Pennsylvania for the barcoding plasmid library and Nimbus Image software. A.J.F., P.E.W., and S.M.S. recognize support from Grants for Faculty Mentoring Undergraduate Research (A.J.F. and S.M.S., 2021; P.E.W. and S.M.S., 2022). S.M.S. recognizes support from the Wistar/Penn SPORE (P50 CA261608) and NIH Director’s Early Independence Award (DP5OD028144).
\n\nConceptualization, D.L.S., A.J.F., and S.M.S.; methodology, D.L.S., A.J.F., and S.M.S.; software, D.L.S., A.J.F., and R.J.V.V.; formal analysis, D.L.S., A.J.F., and R.J.V.V.; investigation, D.L.S., A.J.F., and P.E.W.; data curation, D.L.S., A.J.F., P.E.W., and R.J.V.V.; writing – original draft, D.L.S., A.J.F., P.E.W., R.J.V.V., and S.M.S.; writing – review & editing, D.L.S., A.J.F., P.E.W., R.J.V.V., and S.M.S.; visualization, D.L.S., A.J.F., P.E.W., R.J.V.V., and S.M.S.; funding acquisition, S.M.S., A.J.F., and P.E.W.; supervision, S.M.S.
\n\nThe authors declare no competing interests.
\n\nDuring the preparation of this work the author(s) used ChatGPT in order to help in paraphrasing and avoiding redundancy in our STAR Methods section. After using this tool/service, the author(s) reviewed and edited the content as needed and take(s) full responsibility for the content of the publication.
\n\n\nCancer cells exhibit dramatic differences in gene expression at the single-cell level, which can predict whether they become resistant to treatment. Treatment perpetuates this heterogeneity, resulting in a diversity of cell states among resistant clones. However, it remains unclear whether these differences lead to distinct responses when another treatment is applied or the same treatment is continued. In this study, we combined single-cell RNA sequencing with barcoding to track resistant clones through prolonged and sequential treatments. We found that cells within the same clone have similar gene expression states after multiple rounds of treatment. Moreover, we demonstrated that individual clones have distinct and differing fates, including growth, survival, or death, when subjected to a second treatment or when the first treatment is continued. By identifying gene expression states that predict clone survival, this work provides a foundation for selecting optimal therapies that target the most aggressive resistant clones within a tumor. A record of this paper’s transparent peer review process is included in the supplemental information.
\n© The Author(s), under exclusive licence to Springer Nature Limited 2024.
\n\nWe thank M. Mirhosseini, M. Kalaee, A. Sipahigil and J. Banker for contributions in the early stages of this work, E. Kim, A. Butler, G. Kim, S. Sonar, U. Hatipoglu and J. Rochman for helpful discussions and B. Baker and M. McCoy for experimental support. We thank MIT Lincoln Laboratories for providing the travelling-wave parametric amplifier used in the microwave readout chain in our experimental set-up. NbN deposition during the fabrication process was performed at the Jet Propulsion Laboratory. This work was supported by the ARO/LPS Cross Quantum Technology Systems program (grant W911NF-18-1-0103), the US Department of Energy Office of Science National Quantum Information Science Research Centers (Q-NEXT, award DE-AC02-06CH11357), the Institute for Quantum Information and Matter (IQIM) and the NSF Physics Frontiers Center (grant PHY-1125565) with support from the Gordon and Betty Moore Foundation, the Kavli Nanoscience Institute at Caltech and the AWS Center for Quantum Computing. L.J. acknowledges support from the AFRL (FA8649-21-P-0781), NSF (ERC-1941583, OMA-2137642) and the Packard Foundation (2020-71479). S.M. acknowledges support from the IQIM Postdoctoral Fellowship.
\n\nThese authors contributed equally: Srujan Meesala, Steven Wood, David Lake.
\nS.M., S.W., D.L. and O.P. came up with the concept, S.M., S.W. and D.L. planned the experiment. S.M., S.W., D.L. and P.C. designed the device. S.M. and S.W. performed device fabrication with help from A.D.B. and M.D.S. for NbN deposition. M.D.S. provided the single photon detector used in the experiments. S.M., S.W. and D.L. performed the measurements and analysed the data. S.M., D.L., C.Z. and L.J. developed the theoretical model. O.P. supervised the project. All authors contributed to the writing of the manuscript.
\n\nData shown in the main text and Supplementary Information are available on Zenodo50. Source data are provided with this paper.
\n\nO.P. is currently employed by Amazon Web Services (AWS) as Director of their quantum hardware program. AWS provided partial funding support for this work through a sponsored research grant.
\nModern computing and communication technologies such as supercomputers and the Internet are based on optically connected networks of microwave-frequency information processors. An analogous architecture has been proposed for quantum networks, using optical photons to distribute entanglement between remote superconducting quantum processors. Here we report a step towards such a network by observing non-classical correlations between photons in an optical link and a superconducting quantum device. We generate these states of light through a spontaneous parametric down-conversion process in a chip-scale piezo-optomechanical transducer, and we measure a microwave–optical cross-correlation exceeding the Cauchy–Schwarz classical bound for thermal states. As further evidence of the non-classical character of the microwave–optical photon pairs, we observe antibunching in the microwave state conditioned on detection of an optical photon. Such a transducer can be readily connected to an independent superconducting qubit module and serve as a key building block for optical quantum networks of microwave-frequency qubits.
\n© 2024 The Authors. Published by American Chemical Society. This publication is licensed under CC-BY 4.0.
\n\nThis research was supported by funding from Hong Kong Quantum AI Lab, AIR@InnoHK of the Hong Kong Government. The authors thank Prof. Lisa Hall and Dr. Kuan-Hsuan Shen for providing the LAMMPS solvation potential source code.
\nThe authors declare no competing financial interest.
\n\nSimulation details, determination of the glass transition, ion–polymer coordination, Rouse-mode analysis and friction coefficient, specific conductivity at infinite dilution, and VFT analysis (PDF)
\nWe construct a coarse-grained molecular dynamics model based on poly(ethylene oxide) and lithium bis(trifluoromethane)sulfonimide salt to examine the combined effects of temperature and salt concentration on the transport properties. Salt doping notably slows the dynamics of polymer chains and reduces ion diffusivity, resulting in a glass transition temperature increase proportional to the salt concentration. The polymer diffusion is shown to be well represented by a modified Vogel–Fulcher–Tamman (M-VFT) equation that accounts for both the temperature and salt concentration dependence. Furthermore, we find that, at any temperature, the concentration dependence of the conductivity is well described by the product of its infinite dilution value and a correction factor accounting for the reduced segmental mobility with increasing salt concentration. These results highlight the important role of polymer segmental mobility in the salt concentration dependence of ion conductivity for temperatures near and above the glass transition.
\n© 2024 Zhang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
\n\nWe thank Dr. Xin Sun (Carnegie Institution for Science) and Dr. Bess B. Ward, Dr. Amal Jayakumar, and Dr. Samantha G. Fortin (Princeton University) for sample collection, DNA extractions, and providing the resulting metagenomics data we used to assemble MAGs for this study. We are also grateful for the generosity of Dr. Bruce Heflinger in supporting the Bablab, including this work.
\n\nFunding for this project came from the Simons Foundation award 622065 and the National Science Foundation award OCE-2142998 to A.R.B. I.H.Z. was supported in part by an MIT School of Science MathWorks Science Fellowship, and B.B. was supported in part by a Swiss National Science Foundation fellowship (P500PN_202842). Grants to S.W. (from the National Science Foundation Graduate Fellowship Program) and to D.K.N. (from the NIH, R01 HL152190-03) also contributed.
\n\nI.H.Z. and A.R.B. conceptualized this study. I.H.Z. assembled metagenomes and MAGs, conducted bioinformatics analyses, and drafted the paper. B.B. and A.R.B. conceived and carried out analyses regarding the N2O uptake model. R.Z. provided bioinformatics and overall guidance. D.K.N. and S.W. conceived the heterologous complementation test for the nosZ homologs and provided all strains used in this study, and S.W. performed genetic engineering within the Pseudomonas model system.
", "type": "article", "title": "Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential", "funders": { "items": [ { "agency": "Simons Foundation", "grant_number": "622065" }, { "agency": "National Science Foundation", "grant_number": "OCE-2142998" }, {}, { "grant_number": "P500PN_202842" }, { "grant_number": "NSF Graduate Research Fellowship" }, { "grant_number": "R01 HL152190-03" } ] }, "lastmod": "2024-02-22 19:34:06", "abstract": "© 2024 American Chemical Society.
\n\nThis work was supported by the NSF Center for Synthetic Organic Electrochemistry, CHE-2002158 (the discovery and optimization effort). NIGMS (GM-118176) supported the scope and application study. A.C.H. was supported by an NSF Ascend fellowship (award number: 2138035). The authors are grateful to Dr. Laura Pasternack (Scripps Research) for assistance with nuclear magnetic resonance (NMR) spectroscopy, to Dr. Jason Chen, Brittany Sanchez, and Quynh Nguyen Wong (Scripps Automated Synthesis Facility) for assistance with HRMS and chiral SFC analysis. Elemental analysis data were obtained from the CENTC Elemental Analysis Facility at the University of Rochester, funded by NSF CHE-0650456. Mass spectral data were acquired by field desorption ionization mass spectrometry using an JMS-T2000 AccuTOF GC-Alpha (JEOL, Inc). The purchase of the instrument was enabled by funds from DOW Next Generation Instrumentation (CCEC.DOWINSTR-1-GRANT.DOWINSTR). The authors would like to thank Jay Winkler for assistance with CV experiments and Mona Shahgoli for assistance with HRMS experiments, as well as the Caltech CCE NMR facility and Multiuser Mass Spectrometry Laboratory, which is also supported by the NSF CRIF program (CHE-0541745).
\nThe authors declare no competing financial interest.
\n\nAll experimental procedures, analysis, and compound characterization data (PDF)
\nThe first general enantioselective alkyl-Nozaki–Hiyama–Kishi (NHK) coupling reactions are disclosed herein by employing a Cr-electrocatalytic decarboxylative approach. Using easily accessible aliphatic carboxylic acids (via redox-active esters) as alkyl nucleophile synthons, in combination with aldehydes and enabling additives, chiral secondary alcohols are produced in a good yield with high enantioselectivity under mild reductive electrolysis. This reaction, which cannot be mimicked using stoichiometric metal or organic reductants, tolerates a broad range of functional groups and is successfully applied to dramatically simplify the synthesis of multiple medicinally relevant structures and natural products. Mechanistic studies revealed that this asymmetric alkyl e-NHK reaction was enabled by using catalytic tetrakis(dimethylamino)ethylene, which acts as a key reductive mediator to mediate the electroreduction of the CrIII/chiral ligand complex.
\n© 2024 American Chemical Society.
\n\nSupport from the Office of Naval Research (Chad Stoltz, program manager) under award N00014-22-1-2060 to M.J.Z., ONR N00014-22-WX0-0310 to J.P.H., and ONR N00014-23-1-2105 to W.A.G. is gratefully acknowledged.
\nONR- N00014–22–1–2060 – MJZ ONR N00014–22-WX0–0310 – JPH ONR N00014–23–1–2105– WAG
\n\nJ.E.A. and S.V.Z. contributed equally to this work. The manuscript was written through contributions of all authors.
\n\nThe authors declare no competing financial interest.
\n\n2183424 contains the supplementary crystallographic data for this paper.
", "type": "article", "title": "High-Energy-Density Material with Magnetically Modulated Ignition", "number": "7", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "volume": "146", "funders": { "items": [ { "agency": "Office of Naval Research", "grant_number": "N00014-22-1-2060" }, { "agency": "Office of Naval Research", "grant_number": "N00014-22-WX0-0310" }, { "agency": "Office of Naval Research", "grant_number": "N00014-23-1-2105" } ] }, "lastmod": "2024-03-06 22:29:38", "abstract": " CCDCPreparation of a redox-frustrated high-energy-density energetic material is achieved by gentle protolysis of Mn[N(SiMe3)2]2 with the perchlorate salt of the tetrazolamide [H2NtBuMeTz]ClO4 (Tz = tetrazole), yielding the Mn6N6 hexagonal prismatic cluster, Mn6(μ3-NTztBuMe)6(ClO4)6. Quantum mechanics-based molecular dynamics simulations of the decomposition of this molecule predict that magnetic ordering of the d5 Mn2+ ions influences the pathway and rates of decomposition, suggesting that the initiation of decomposition of the bulk material might be significantly retarded by an applied magnetic field. We report here experimental tests of the prediction showing that the presence of a 0.5 T magnetic field modulates the ignition onset temperature by +10.4 ± 3.9 °C (from 414 ± 4 °C), demonstrating the first example of a magnetically modulated explosive.
\n© 2024 The Authors. Published by American Chemical Society. This publication is licensed under CC-BY-NC-ND 4.0.
\n\nThis manuscript is dedicated to Professor Larry E. Overman of the University of California, Irvine, on the occasion of his 80th birthday. The NIH-NIGMS (R35GM145239), Heritage Medical Research Investigators Program, and Caltech are thanked for the support of our research program. We thank Dr. David VanderVelde (Caltech) for NMR expertise; Dr. Mona Shagholi (Caltech) for mass spectrometry assistance; Dr. Michael Takase (Caltech) for assistance with X-ray crystallography; and Dr. Scott C. Virgil (Caltech) for instrumentation, HPLC, and SFC assistance. Additional thanks to Kevin Gonzalez, Ben Gross, Samir Rezgui, and Hao Yu for many helpful discussions. E.F.H. would like to thank the NSF GRFP for funding.
\nThe Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.3c13590.
\nExperimental procedures, spectroscopic data (1H NMR, 13C NMR, IR, and HRMS), and crystallographic data
\nCCDC 2308829–2308831 contain the supplementary crystallographic data for this paper.
", "type": "article", "title": "Enantioselective Total Synthesis of (−)-Hunterine A Enabled by a Desymmetrization/Rearrangement Strategy", "number": "7", "volume": "146", "funders": { "items": [ { "grant_number": "R35GM145239" }, { "grant_number": "Heritage Medical Research Institute" }, { "grant_number": "NSF Graduate Research Fellowship" } ] }, "lastmod": "2024-02-27 19:19:33", "abstract": "The first enantioselective total synthesis of (−)-hunterine A is disclosed. Our strategy employs a catalytic asymmetric desymmetrization of a symmetrical diketone and subsequent Beckmann rearrangement to construct a 5,6-α-aminoketone. A convergent 1,2-addition joins a vinyl dianion nucleophile and the enantioenriched ketone. The endgame of the synthesis features an aza-Cope/Mannich reaction and azide-olefin dipolar cycloaddition to complete the pentacyclic ring system. The synthesis is completed through a regioselective aziridine ring opening.
", "creators": { "items": [ { "id": "Hicks-Elliot-F", "name": { "given": "Elliot F.", "family": "Hicks" } }, { "id": "Inoue-Kengo", "name": { "given": "Kengo", "family": "Inoue" } }, { "id": "Stoltz-B-M", "name": { "given": "Brian M.", "family": "Stoltz" }, "orcid": "0000-0001-9837-1528" } ] }, "date_type": "published", "datestamp": "2024-02-27 19:19:33", "pagerange": "4340-4345", "publisher": "American Chemical Society", "ispublished": "pub", "publication": "Journal of the American Chemical Society", "official_url": "https://authors.library.caltech.edu/records/dhwpw-c6z37", "eprint_status": "archive", "full_text_status": "public", "metadata_visibility": "show" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hyrbw-ve413", "_Key": "hyrbw-ve413", "date": "2024-02-21", "issn": "0077-2933", "type": "article", "title": "Felix Hans Boehm (June 9, 1924–May 25, 2021): A Biographical Memoir", "volume": "2024", "lastmod": "2024-02-21 17:15:09", "abstract": "An outstanding nuclear experimentalist, Felix Hans Boehm made vital and lasting contributions to many branches of nuclear physics, particularly the application of nuclear techniques to the study of fundamental particle physics problems. His scientific career, lasting more than four decades, spans the evolution of nuclear experiments from brief measurements carried out by a small group of physicists to the present-day endeavors involving large groups of people with varying responsibilities, large and expensive apparatus, long measurements, and complicated efforts to obtain the necessary funding. His career and his achievements illustrate this remarkable transition.
", "creators": { "items": [ { "id": "Vogel-P", "name": { "given": "Petr", "family": "Vogel" }, "orcid": "0000-0003-0587-5466" }, { "id": "Vuilleumier-Jean-Luc", "name": { "given": "Jean-Luc", "family": "Vuilleumier" } } ] }, "date_type": "published", "datestamp": "2024-02-21 17:15:09", "pagerange": "1-5", "publisher": "National Academy of Sciences", "ispublished": "pub", "publication": "Biographical Memoirs", "official_url": "https://authors.library.caltech.edu/records/hyrbw-ve413", "eprint_status": "archive", "full_text_status": "restricted", "metadata_visibility": "show" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/m8yt9-taq64", "doi": "10.1038/s41524-024-01220-x", "_Key": "m8yt9-taq64", "date": "2024-02-20", "issn": "2057-3960", "note": "© The Author(s) 2024. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
\n\nWe thank J. Cano, B.-J. Yang, T. Suzuki, G. Tritsaris, D. Tabor, and A. Aspuru-Guzik for useful discussions. This research is funded in part by the Gordon and Betty Moore Foundation EPiQS Initiative, through Grant GBMF9070 to J.G.C. (computation), NSF grant DMR-2104964 (statistical analysis), and AFOSR grant FA9550-22-1-0432 (crystallographic analysis). H.N. and L.Y. acknowledge support by the STC Center for Integrated Quantum Materials, NSF grant number DMR-1231319. This work was performed in part at the Aspen Center for Physics, which is supported by National Science Foundation grant PHY-1607611.
\nP.M.N. wrote the code with input from J.P.W. and S.F., P.M.N., J.P.W., and S.F. interpreted the search results with input from L.Y. H.N., J.P.W., and L.Y. performed preliminary geometry-based searches. J.G.C. supervised the project. All authors analyzed the results and contributed to writing the manuscript.
\n\nThe search results and curated list are available as a supplementary data sheet. See Supplementary Note 3 for more information.
\nCode used to generate tight-binding models and identify/classify flat bands is available at https://github.com/pmneves7/Crystal-Net-Flat-Bands/tree/main.
\nThe authors declare no competing interests.
\nFlat band systems are currently under intense investigation in quantum materials, optical lattices, and metamaterials. These efforts are motivated by potential realization of strongly correlated phenomena enabled by frustration-induced flat band dispersions; identification of candidate platforms plays an important role in these efforts. Here, we develop a high-throughput materials search for bulk crystalline flat bands by automated construction of uniform-hopping near-neighbor tight-binding models. We show that this approach captures many of the essential features relevant to identifying flat band lattice motifs in candidate materials in a computationally inexpensive manner, and is of use to identify systems for further detailed investigation as well as theoretical and metamaterials studies of model systems. We apply this algorithm to 139,367 materials in the Materials Project database and identify 63,076 materials that host at least one flat band elemental sublattice. We further categorize these candidate systems into at least 31,635 unique flat band crystal nets and identify candidates of interest from both lattice and band structure perspectives. This work expands the number of known flat band lattices that exist in physically realizable crystal structures and classifies the majority of these systems by the underlying lattice, providing additional insights for familiar (e.g., kagome, pyrochlore, Lieb, and dice) as well as previously unknown motifs.
\n© 2024 the Author(s). Published by PNAS. This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).
\n\nA.T., P.B., and V.C. designed research; performed research; and wrote the paper.
\n\nAll study data are included in the article. The code for implementing our methods is available at https://github.com/armeentaeb/model-selection-over-posets (30).
\n\nThe authors declare no competing interest.
", "type": "article", "title": "Model selection over partially ordered sets", "number": "8", "volume": "121", "funders": { "items": [ {}, { "grant_number": "786461" }, { "grant_number": "FA9550-22-1-0225" }, { "grant_number": "FA9550-23-1-0204" }, { "grant_number": "DMS-2113724" } ] }, "lastmod": "2024-02-21 00:17:41", "abstract": "In problems such as variable selection and graph estimation, models are characterized by Boolean logical structure such as the presence or absence of a variable or an edge. Consequently, false-positive error or false-negative error can be specified as the number of variables/edges that are incorrectly included or excluded in an estimated model. However, there are several other problems such as ranking, clustering, and causal inference in which the associated model classes do not admit transparent notions of false-positive and false-negative errors due to the lack of an underlying Boolean logical structure. In this paper, we present a generic approach to endow a collection of models with partial order structure, which leads to a hierarchical organization of model classes as well as natural analogs of false-positive and false-negative errors. We describe model selection procedures that provide false-positive error control in our general setting, and we illustrate their utility with numerical experiments.", "creators": { "items": [ { "id": "Taeb-Armeen", "name": { "given": "Armeen", "family": "Taeb" }, "orcid": "0000-0002-5647-3160" }, { "id": "Bühlmann-Peter", "name": { "given": "Peter", "family": "Bühlmann" }, "orcid": "0000-0002-1782-6015" }, { "id": "Chandrasekaran-V", "name": { "given": "Venkat", "family": "Chandrasekaran" } } ] }, "date_type": "published", "datestamp": "2024-02-21 00:17:41", "pagerange": "e2314228121", "publisher": "National Academy of Sciences", "ispublished": "pub", "publication": "Proceedings of the National Academy of Sciences", "official_url": "https://authors.library.caltech.edu/records/bq29r-5a373", "eprint_status": "archive", "full_text_status": "public", "metadata_visibility": "show" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/spg9t-yra67", "doi": "10.1016/j.jmst.2023.07.027", "_Key": "spg9t-yra67", "date": "2024-02-20", "issn": "1005-0302", "note": "© 2024 Published by Elsevier Ltd on behalf of The editorial office of Journal of Materials Science & Technology Under a Creative Commons license.
\n\nThis work was financially supported by the Research Council of Norway under the M-HEAT project (No. 294689) and the HyLINE Project (No. 294739). All simulation resources are provided by the Norwegian Metacenter for Computational Science (Nos. NN9110K and NN9391K).
\n\nThe project was planned and supervised by Z.Z. The simulation design and data analysis were performed by Y.D. All authors participated in the discussion and co-wrote the paper.
Yu Ding: Visualization, Formal analysis, Writing – original draft. Haiyang Yu: Writing – original draft. Meichao Lin: Writing – original draft. Michael Ortiz: Writing – original draft. Senbo Xiao: Writing – original draft. Jianying He: Writing – original draft. Zhiliang Zhang: Project administration, Supervision, Writing – original draft.
\n\nThe data that support the findings of this study are available from the corresponding authors upon request.
\n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
", "type": "article", "title": "Hydrogen trapping and diffusion in polycrystalline nickel: The spectrum of grain boundary segregation", "volume": "173", "funders": { "items": [ { "grant_number": "294689" }, { "grant_number": "294739" } ] }, "lastmod": "2023-12-18 22:05:05", "abstract": "Hydrogen as an interstitial solute at grain boundaries (GBs) can have a catastrophic impact on the mechanical properties of many metals. Despite the global research effort, the underlying hydrogen-GB interactions in polycrystals remain inadequately understood. In this study, using Voronoi tessellations and atomistic simulations, we elucidate the hydrogen segregation energy spectrum at the GBs of polycrystalline nickel by exploring all the topologically favorable segregation sites. Three distinct peaks in the energy spectrum are identified, corresponding to different structural fingerprints. The first peak (−0.205 eV) represents the most favorable segregation sites at GB core, while the second and third peaks account for the sites at GB surface. By incorporating a thermodynamic model, the spectrum enables the determination of the equilibrium hydrogen concentrations at GBs, unveiling a remarkable two to three orders of magnitude increase compared to the bulk hydrogen concentration reported in experimental studies. The identified structures from the GB spectrum exhibit vastly different behaviors in hydrogen segregation and diffusion, with the low-barrier channels inside GB core contributing to short-circuit diffusion, while the high energy gaps between GB and neighboring lattice serving as on-plane diffusion barriers. Mean square displacement analysis further confirms the findings, and shows that the calculated GB diffusion coefficient is three orders of magnitude greater than that of lattice. The present study has a significant implication for practical applications since it offers a tool to bridge the gap between atomic-scale interactions and macroscopic behaviors in engineering materials.
", "creators": { "items": [ { "id": "Ding-Yu", "name": { "given": "Yu", "family": "Ding" } }, { "id": "Yu-Haiyang", "name": { "given": "Haiyang", "family": "Yu" }, "orcid": "0000-0002-2419-6736" }, { "id": "Lin-Meichao", "name": { "given": "Meichao", "family": "Lin" }, "orcid": "0000-0003-1234-5957" }, { "id": "Ortiz-M", "name": { "given": "Michael", "family": "Ortiz" }, "orcid": "0000-0001-5877-4824" }, { "id": "Xiao-Senbo", "name": { "given": "Senbo", "family": "Xiao" }, "orcid": "0000-0001-7021-9591" }, { "id": "He-Jianying", "name": { "given": "Jianying", "family": "He" }, "orcid": "0000-0001-8485-7893" }, { "id": "Zhang-Zhiliang", "name": { "given": "Zhiliang", "family": "Zhang" }, "orcid": "0000-0002-9557-3455" } ] }, "date_type": "published", "datestamp": "2023-12-18 22:05:05", "pagerange": "225-236", "publisher": "Elsevier", "ispublished": "pub", "publication": "Journal of Materials Science & Technology", "official_url": "https://authors.library.caltech.edu/records/spg9t-yra67", "eprint_status": "archive", "full_text_status": "public", "metadata_visibility": "show" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/2s161-n2a31", "doi": "10.1021/acs.est.3c09250", "_Key": "2s161-n2a31", "date": "2024-02-20", "issn": "0013-936X", "note": "This work was supported by the National Aeronautics and Space Administration under Grant No. 80NSSC21K1005. Part of this work was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (NASA).
\nWetCHARTs model results can be downloaded from https://daac.ornl.gov/cgi-bin/dsviewer.pl?ds_id=1502 (version 1.3.1). The CYGNSS data are publicly available from NASA JPL: https://podaac.jpl.nasa.gov/dataset/CYGNSS_L1_V2.1 (version 2.1). TROPOMI data are publicly available from NASA Earth Data: https://www.earthdata.nasa.gov/ (last access: August 2022). X-STILT with TROPOMI modification is accessed from https://github.com/uataq/X-STILT. Python 3.9 was used for data analysis and plotting.
\nThe Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.est.3c09250.
\nThe authors declare no competing financial interest.
", "type": "article", "title": "Underestimated Dry Season Methane Emissions from Wetlands in the Pantanal", "number": "7", "volume": "58", "funders": { "items": [ { "grant_number": "80NSSC21K1005" } ] }, "lastmod": "2024-02-27 19:10:17", "abstract": "Tropical wetlands contribute ∼30% of the global methane (CH4) budget. Limited observational constraints on tropical wetland CH4 emissions lead to large uncertainties and disparities in representing emissions. In this work, we combine remote sensing observations with atmospheric and wetland models to investigate dry season wetland CH4 emissions from the Pantanal region of South America. We incorporate inundation maps generated from the Cyclone Global Navigation Satellite System (CYGNSS) satellite constellation together with traditional inundation maps to generate an ensemble of wetland CH4 emission realizations. We challenge these realizations with daily satellite observations for May–July when wetland CH4 emission predictions diverge. We find that the CYGNSS inundation products predict larger emissions in May, in better agreement with observations. We use the model ensemble to generate an empirical observational constraint on CH4 emissions independent of choice of inundation map, finding large dry season wetland CH4 emissions (31.7 ± 13.6 and 32.0 ± 20.2 mg CH4/m2/day in May and June/July during 2018/2019, respectively). These May/June/July emissions are 2–3 times higher than current models, suggesting that annual wetland emissions may be higher than traditionally simulated. Observed trends in the early dry season indicate that dynamics during this period are of importance in representing tropical wetland CH4 behaviors.
\n© Te Author(s) 2024. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
\n\nWe would like to express our deepest gratitude to the patients who volunteered to participate in this study. We thank the clinical team at Cedars-Sinai Medical Center for patient management, Michael Kyzar for advice on NWB usage, and Nand Chandravadia, and April Carlson for assistance with data processing. We thank Rhodri Cusack for sharing the edited version of the Hitchcock movie with us. This study was supported by the NIMH Caltech Conte Center (P50MH094258 to R.A. and U.R.), the BRAIN initiative through the National Institute of Neurological Disorders and Stroke (U01NS117839 to U.R.), the Simons Collaboration on the Global Brain (542941 to R.A. and U.R.), and the National Science Foundation (BCS-2219800).
\n\nJ.D. and U.R. conceived the original study and designed the experiment. J.D., U.R. and J.M.T. performed experiments. U.K., J.D., K.J.M.L., J.M.T. and D.A.K. organized the data. U.K. analyzed the data. A.N.M. performed surgery and supervised clinical care. J.M.C. and C.M.R. enrolled patients, provided clinical care, and supervised MRI scanning. U.R. and R.A. provided supervision and acquired funding. U.K., K.J.M.L., J.M.T., R.A. and U.R. wrote the manuscript. All the authors reviewed and approved the manuscript for submission.
\n\nAll code is available in the GitHub repository (https://github.com/rutishauserlab/bmovie-release-NWB-BIDS). The python code includes scripts to read and plot the data from the NWB files and perform the analyses presented in this data descriptor. The code relies heavily on open-source Python packages such as numpy61, scipy62, pynwb18, mne-python63, nilearn48, and pycortex64. The movie annotation files are also provided in the GitHub repository under ‘assets/annotations’ folder. The scripts related to the estimation of tSNR and ISC were adapted from the code provided in the GitHub repository associated with the budapest-fmri-data study49,50 (see: https://github.com/mvdoc/budapest-fmri-data).
\n\nThe authors declare no competing interests.
\nWe present a multimodal dataset of intracranial recordings, fMRI, and eye tracking in 20 participants during movie watching. Recordings consist of single neurons, local field potential, and intracranial EEG activity acquired from depth electrodes targeting the amygdala, hippocampus, and medial frontal cortex implanted for monitoring of epileptic seizures. Participants watched an 8-min long excerpt from the video “Bang! You’re Dead” and performed a recognition memory test for movie content. 3 T fMRI activity was recorded prior to surgery in 11 of these participants while performing the same task. This NWB- and BIDS-formatted dataset includes spike times, field potential activity, behavior, eye tracking, electrode locations, demographics, and functional and structural MRI scans. For technical validation, we provide signal quality metrics, assess eye tracking quality, behavior, the tuning of cells and high-frequency broadband power field potentials to familiarity and event boundaries, and show brain-wide inter-subject correlations for fMRI. This dataset will facilitate the investigation of brain activity during movie watching, recognition memory, and the neural basis of the fMRI-BOLD signal.
\n© The Author(s) 2024. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
\n\nWe thank Dr. Pinghui Feng (University of Southern California) for cell lines and the support in mass spectrometry analysis. We are also grateful to Dr. Jae U Jung (Cleveland Clinic), Dr. Michael Lagunoff (University of Washington), Dr. Ren Sun (University of California Los Angeles) and Dr. Young-Kwon Hong (University of Southern California) for cell lines and KSHV reagents. We also thank Cleveland Clinic Lerner Research Institute Proteomics and Metabolomics Core, as well as Florida Research and Innovation Flow Cytometry Core for services and analyses. J.Z. is supported by a grant from NIDCR (R00DE028973), startup funds from the Cleveland Clinic Florida Research and Innovation Center, and a Cleveland Clinic Global Center for Pathogen and Human Health Research Fast Track Research Award. Z.H. is supported by a grant from NIAID (R01AI173277).
\nQ.W. and J.Z. designed the experiments. Q.W., L.T., T.Y.W., A.J.T., R.Z., and J.Z. performed the experiments. Q.L., S.F. and D.C. contributed to key biological resources. Q.W., L.T., T.Y.W., A.J.T., R.Z., Z.H., M.U.G. and J.Z. contributed to the interpretation of the data. J.Z. conceived the study. Q.W., M.U.G. and J.Z. wrote the manuscript, with input from all the authors.
\n\nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange80 Consortium via the PRIDE81 partner repository with the dataset identifier PXD043435. All data needed to evaluate the conclusions for the study are present in the paper. Unique expression vectors and reagents generated for this study are available upon request. Source data are provided with this paper.
\nThe authors declare no competing interests.
", "type": "article", "title": "Hijacking of nucleotide biosynthesis and deamidation-mediated glycolysis by an oncogenic herpesvirus", "volume": "15", "funders": { "items": [ { "grant_number": "R00DE028973" }, {}, { "grant_number": "R01AI173277" } ] }, "lastmod": "2024-02-21 19:48:03", "abstract": "Kaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi’s sarcoma (KS) and multiple types of B cell malignancies. Emerging evidence demonstrates that KSHV reprograms host-cell central carbon metabolic pathways, which contributes to viral persistence and tumorigenesis. However, the mechanisms underlying KSHV-mediated metabolic reprogramming remain poorly understood. Carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase (CAD) is a key enzyme of the de novo pyrimidine synthesis, and was recently identified to deamidate the NF-κB subunit RelA to promote aerobic glycolysis and cell proliferation. Here we report that KSHV infection exploits CAD for nucleotide synthesis and glycolysis. Mechanistically, KSHV vCyclin binds to and hijacks cyclin-dependent kinase CDK6 to phosphorylate Ser-1900 on CAD, thereby activating CAD-mediated pyrimidine synthesis and RelA-deamidation-mediated glycolytic reprogramming. Correspondingly, genetic depletion or pharmacological inhibition of CDK6 and CAD potently impeded KSHV lytic replication and thwarted tumorigenesis of primary effusion lymphoma (PEL) cells in vitro and in vivo. Altogether, our work defines a viral metabolic reprogramming mechanism underpinning KSHV oncogenesis, which may spur the development of new strategies to treat KSHV-associated malignancies and other diseases.
\n© 2024 American Chemical Society.
\n\nWith thanks to M. Prator for performing the Bradford assays of the lysates, to Z. Jurado for purifying the mNeonGreen fluorescence standard, to Prof. Dianne Newman for the Pseudomonas strains and R. Alcalde for the Pa10403-mNeonGreen plasmid and the P. synxantha strain, to Dr. R. Sidney Cox III for assistance with data visualization, to Dr. A. Pandey for assistance with data processing, and to Dr. Dmitri Mavrodi for assistance with the genomic integration protocol for P. synxantha. This research is supported by the Institute for Collaborative Biotechnologies through contract W911NF-19-D-0001, cooperative agreement W911NF-19-2-0026, and grant W911NF-09-0001 from the U.S. Army Research Office, the National Science Foundation through grant CBET-1903477, and the International Human Frontiers Science Program. The content of this paper does not necessarily reflect the position or the policy of the U.S. Government, and no official endorsement should be inferred.
\nJ.T.M. and E.M.L. equally contributed. J.T.M., E.M.L., and R.M.M. conceptualized the project. J.T.M. and E.M.L. designed the experiments and analyzed the data. J.T.M. performed TX–TL experiments. E.M.L. performed in vivo experiments, with the exception of the syringaldehyde experiment which was performed by J.T.M. E.M.L. did the plasmid construction and integration. J.T.M. and E.M.L. wrote the manuscript with input from R.M.M.
\n\nThe authors declare no competing financial interest.
\n\n(ZIP)
\nPhylogenetic relationships and genome-to-genome distances for species in this study; growth rates of the three Pseudomonads and E. coli; details of the growth inhibition and dose–response to tested growth inhibitors; protein concentrations of clarified lysates; negative controls for selected reaction conditions; time course data for in vitro TX–TL promoter panel reactions; time course data for in vitro promoter panel measurements; schematic representation of plasmids used in this study; and illustration of the lysate production protocol (PDF)
\nSequences of primers, promoters, and Addgene deposition information for strains used in this study (XLSX)
\nIn vitro transcription–translation (TX–TL) can enable faster engineering of biological systems. This speed-up can be significant, especially in difficult-to-transform chassis. This work shows the successful development of TX–TL systems using three soil-derived wild-type Pseudomonads known to promote plant growth: Pseudomonas synxantha, Pseudomonas chlororaphis, and Pseudomonas aureofaciens. All three species demonstrated multiple sonication, runoff, and salt conditions producing detectable protein synthesis. One of these new TX–TL systems, P. synxantha, demonstrated a maximum protein yield of 2.5 μM at 125 proteins per DNA template, a maximum protein synthesis rate of 20 nM/min, and a range of DNA concentrations with a linear correspondence with the resulting protein synthesis. A set of different constitutive promoters driving mNeonGreen expression were tested in TX–TL and integrated into the genome, showing similar normalized strengths for in vivo and in vitro fluorescence. This correspondence between the TX–TL-derived promoter strength and the in vivo promoter strength indicates that these lysate-based cell-free systems can be used to characterize and engineer biological parts without genomic integration, enabling a faster design–build–test cycle.
\n© 2024 The Authors. Published by American Chemical Society. This publication is licensed under CC-BY 4.0.
\n\nWe thank M. E. Bronner for reading a draft of the manuscript and G. Shin of the Molecular Technologies resource within the Beckman Institute at Caltech for providing HCR reagents. This work was funded by the National Institutes of Health (NIBIB R01EB006192 and NIGMS training grant GM008042 to S.J.S.) and by the Beckman Institute at Caltech (Programmable Molecular Technology Center, PMTC). The Leica Stellaris 8 confocal microscope in the Biological Imaging Facility within the Beckman Institute at Caltech was purchased with support from Caltech and the following Caltech entities: the Beckman Institute, the Resnick Sustainability Institute, the Division of Biology and Biological Engineering, and the Merkin Institute for Translational Research.
\nThe authors declare the following competing financial interest(s): Patents, pending patent applications, and the startup company Molecular Instruments.
", "type": "article", "title": "Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction", "number": "2", "volume": "19", "funders": { "items": [ { "grant_number": "R01EB006192" }, { "grant_number": "GM008042" }, { "agency": "Beckman Institute, California Institute of Technology" } ] }, "lastmod": "2024-02-22 17:02:35", "abstract": "Signal amplification based on the mechanism of hybridization chain reaction (HCR) facilitates spatial exploration of gene regulatory networks by enabling multiplex, quantitative, high-resolution imaging of RNA and protein targets. Here, we extend these capabilities to the imaging of protein:protein complexes, using proximity-dependent cooperative probes to conditionally generate a single amplified signal if and only if two target proteins are colocalized within the sample. HCR probes and amplifiers combine to provide automatic background suppression throughout the protocol, ensuring that even if reagents bind nonspecifically in the sample, they will not generate amplified background. We demonstrate protein:protein imaging with a high signal-to-background ratio in human cells, mouse proT cells, and highly autofluorescent formalin-fixed paraffin-embedded (FFPE) human breast tissue sections. Further, we demonstrate multiplex imaging of three different protein:protein complexes simultaneously and validate that HCR enables accurate and precise relative quantitation of protein:protein complexes with subcellular resolution in an anatomical context. Moreover, we establish a unified framework for simultaneous multiplex, quantitative, high-resolution imaging of RNA, protein, and protein:protein targets, with one-step, isothermal, enzyme-free HCR signal amplification performed for all target classes simultaneously.
\n© 2024 The Authors. Advanced Materials published by Wiley-VCH GmbH. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
\n\nF.C.-G. and M.L. contributed equally to this work. Veronika Biegler (TU Wien) is acknowledged for her support the preparation of UV-casted samples. Till Jarnot and Pablo Vazquez Conde (both UpNano GmbH) are acknowledged for their help with CAD design of the testing specimens. Peter Gruber and Josef Thalhammer (both UpNano GmbH) are gratefully acknowledged for fruitful discussions. This work was supported by the Vienna Business Agency (Grant No. 2864518). The authors acknowledge TU Wien Bibliothek for financial support through its Open Access Funding Programme.
\n\nA.O. is a co-founder and CSO of UpNano GmbH, a TU Wien spin-off and the manufacturer of the NanoOne device used in parts of this study. A.O. is a co-inventor of a patent on a two-photon polymerization apparatus, which UpNano GmbH is licensing from TU Wien. M.L. is an employee of UpNano GmbH. The authors declare no other conflict of interest.
\n\nThe data that support the findings of this study are available from the corresponding author upon reasonable request.
", "type": "article", "title": "Approaching Standardization: Mechanical Material Testing of Macroscopic Two‐Photon Polymerized Specimens", "rights": "The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited.", "funders": { "items": [ { "agency": "Wirtschaftsagentur Wien", "grant_number": "2864518" }, { "agency": "TU Wien" } ] }, "lastmod": "2024-03-06 00:31:55", "abstract": "Two-photon polymerization (2PP) is becoming increasingly established as additive manufacturing technology for microfabrication due to its high-resolution and the feasibility of generating complex parts. Until now, the high resolution of 2PP is also its bottleneck, as it limited throughput and therefore restricted the application to the production of microparts. Thus, mechanical properties of 2PP materials can only be characterized using nonstandardized specialized microtesting methods. Due to recent advances in 2PP technology, it is now possible to produce parts in the size of several millimeters to even centimeters, finally permitting the fabrication of macrosized testing specimens. Besides suitable hardware systems, 2PP materials exhibiting favorable mechanical properties that allow printing of up-scaled parts are strongly demanded. In this work, the up-scalability of three different photopolymers is investigated using a high-throughput 2PP system and low numerical aperture optics. Testing specimens in the cm-range are produced and tested with common or even standardized material testing methods available in conventionally equipped polymer testing labs. Examples of the characterization of mechanical, thermo-mechanical, and fracture properties of 2PP processed materials are shown. Additionally, aspects such as postprocessing and aging are investigated. This lays a foundation for future expansion of the 2PP technology to broader industrial application.
\nPublished by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article’s title, journal citation, and DOI.
\n\nFunded by SCOAP3.
\n\nWe show via explicit construction that for six or more parties, there exist extreme rays of the subadditivity cone that can be realized by quantum states, but not by holographic states. This is a counterexample to a conjecture first formulated in Hernández-Cuenca et al. [The holographic entropy cone from marginal independence, J. High Energy Phys. 09 (2022) 190.], and implies the existence of deep holographic constraints that restrict the allowed patterns of independence among various subsystems beyond the universal quantum mechanical restrictions.
", "creators": { "items": [ { "id": "He-Temple", "name": { "given": "Temple", "family": "He" }, "orcid": "0000-0002-2873-3746" }, { "id": "Hubeny-Veronika-E", "name": { "given": "Veronika E.", "family": "Hubeny" }, "orcid": "0000-0003-0268-5587" }, { "id": "Rota-Massimiliano", "name": { "given": "Massimiliano", "family": "Rota" }, "orcid": "0000-0001-5097-8259" } ] }, "date_type": "published", "datestamp": "2024-02-21 00:21:46", "pagerange": "L041901", "publisher": "American Physical Society", "ispublished": "pub", "publication": "Physical Review D", "official_url": "https://authors.library.caltech.edu/records/a9b3f-r2r87", "eprint_status": "archive", "full_text_status": "public", "metadata_visibility": "show" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/cm70w-08d37", "doi": "10.1103/physrevd.109.044032", "_Key": "cm70w-08d37", "date": "2024-02-15", "issn": "2470-0010", "note": "Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article’s title, journal citation, and DOI.
\n\n ", "type": "article", "title": "Catalog of precessing black-hole-binary numerical-relativity simulations", "number": "4", "volume": "109", "funders": { "items": [ { "grant_number": "ST/V00154X/1" }, { "grant_number": "647839" }, { "grant_number": "IZCOZ0-189876" }, { "grant_number": "PHY-1707549" }, { "grant_number": "UIDB/00099/2020" }, { "grant_number": "ST/P002293/1" }, { "grant_number": "ST/R002371/1" }, { "grant_number": "ST/S002502/1" }, {}, {}, { "grant_number": "ST/R000832/1" }, { "grant_number": "European Regional Development Fund" } ] }, "lastmod": "2024-02-21 00:47:45", "abstract": "We present a public catalog of numerical-relativity binary-black-hole simulations. The catalog contains datasets from 80 distinct configurations of precessing binary-black-hole systems, with mass ratios up to m₂/m₁ = 8, dimensionless spin magnitudes on the larger black hole up to |^→S₂|/m₂² = 0.8 (the small black hole is nonspinning), and a range of five values of spin misalignment for each mass-ratio/spin combination. We discuss the physical properties of the configurations in our catalog, and assess the accuracy of the initial configuration of each simulation and of the gravitational waveforms. We perform a careful analysis of the errors due to the finite resolution of our simulations and the finite distance from the source at which we extract the waveform data and provide a conservative estimate of the mismatch accuracy. We find that the upper limit on the mismatch uncertainty of our waveforms (including multipoles ℓ ≤ 5) is 0.4%. In doing this we present a consistent approach to combining mismatch uncertainties from multiple error sources. We compare this release to previous catalogs and discuss how these new simulations complement the existing public datasets. In particular, this is the first catalog to uniformly cover this parameter space of single-spin binaries and there was previously only sparse coverage of the precessing-binary parameter space for mass ratios ≳5. We discuss applications of these new data, and the most urgent directions for future simulation work.
", "creators": { "items": [ { "id": "Hamilton-Eleanor", "name": { "given": "Eleanor", "family": "Hamilton" }, "orcid": "0000-0003-0098-9114" }, { "id": "Fauchon-Jones-Edward", "name": { "given": "Edward", "family": "Fauchon-Jones" }, "orcid": "0000-0002-4200-892X" }, { "id": "Hannam-Mark", "name": { "given": "Mark", "family": "Hannam" }, "orcid": "0000-0001-5571-325X" }, { "id": "Hoy-Charlie", "name": { "given": "Charlie", "family": "Hoy" }, "orcid": "0000-0002-8843-6719" }, { "id": "Kalaghatgi-Chinmay", "name": { "given": "Chinmay", "family": "Kalaghatgi" }, "orcid": "0000-0002-4688-867X" }, { "id": "London-Lionel", "name": { "given": "Lionel", "family": "London" }, "orcid": "0000-0001-8239-4370" }, { "id": "Thompson-Jonathan-E", "name": { "given": "Jonathan E.", "family": "Thompson" }, "orcid": "0000-0002-0419-5517" }, { "id": "Yeeles-Dave", "name": { "given": "Dave", "family": "Yeeles" }, "orcid": "0000-0002-8571-543X" }, { "id": "Ghosh-Shrobana", "name": { "given": "Shrobana", "family": "Ghosh" }, "orcid": "0000-0002-7654-478X" }, { "id": "Khan-Sebastian", "name": { "given": "Sebastian", "family": "Khan" }, "orcid": "0000-0003-4953-5754" }, { "id": "Kolitsidou-Panagiota", "name": { "given": "Panagiota", "family": "Kolitsidou" }, "orcid": "0000-0002-6719-8686" }, { "id": "Vano-Vinuales-Alex", "name": { "given": "Alex", "family": "Vano-Vinuales" }, "orcid": "0000-0002-8589-006X" } ] }, "date_type": "published", "datestamp": "2024-02-21 00:47:45", "pagerange": "044032", "publisher": "American Physical Society", "ispublished": "pub", "publication": "Physical Review D", "official_url": "https://authors.library.caltech.edu/records/cm70w-08d37", "eprint_status": "archive", "full_text_status": "public", "metadata_visibility": "show" } ]