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1. xTern: Energy-Efficient Ternary Neural Network Inference on RISC-V-Based Edge Systems

Author

Rutishauser, Georg, Mihali, Joan, Scherer, Moritz, and Benini, Luca

Subjects
Computer Science - Hardware Architecture, Computer Science - Machine Learning
Abstract

Ternary neural networks (TNNs) offer a superior accuracy-energy trade-off compared to binary neural networks. However, until now, they have required specialized accelerators to realize their efficiency potential, which has hindered widespread adoption. To address this, we present xTern, a lightweight extension of the RISC-V instruction set architecture (ISA) targeted at accelerating TNN inference on general-purpose cores. To complement the ISA extension, we developed a set of optimized kernels leveraging xTern, achieving 67% higher throughput than their 2-bit equivalents. Power consumption is only marginally increased by 5.2%, resulting in an energy efficiency improvement by 57.1%. We demonstrate that the proposed xTern extension, integrated into an octa-core compute cluster, incurs a minimal silicon area overhead of 0.9% with no impact on timing. In end-to-end benchmarks, we demonstrate that xTern enables the deployment of TNNs achieving up to 1.6 percentage points higher CIFAR-10 classification accuracy than 2-bit networks at equal inference latency. Our results show that xTern enables RISC-V-based ultra-low-power edge AI platforms to benefit from the efficiency potential of TNNs., Comment: Accepted for publication at IEEE ASAP 2024

Published
2024

2. A unified kinematic wave theory for melt infiltration into firn

Author

Shadab, Mohammad Afzal, Rutishauser, Anja, Grima, Cyril, and Hesse, Marc Andre

Subjects
Physics - Fluid Dynamics, Mathematics - Analysis of PDEs, Physics - Geophysics
Abstract

Motivated by the refreezing of melt water in firn we revisit the one-dimensional percolation of liquid water and non-reactive gas in porous ice. We analyze the dynamics of infiltration in the absence of capillary forces and heat conduction to understand the coupling between advective heat and mass transport in firn. In this limit, we formulate a kinematic wave theory that results in a 2X2-system of hyperbolic partial differential equations (PDEs) corresponding to the conservation of composition and enthalpy. For simple initial conditions (Riemann problems) this system admits self-similar solutions that illuminate the structure of melting/refreezing fronts and analytical solutions are provided for 12 basic cases of physical relevance encountered in the literature. Further we develop an extended kinematic theory that encompasses the cases when the firn saturates completely to form a perched water table governed by elliptic PDE so that the model is no longer fully hyperbolic (local). These solutions provide benchmarks for numerical models of melt infiltration into firn. They also provide insight into important physical processes such as the formation of frozen fringes, the perching of meltwater on pre-existing low porosity layers and the conditions required for impermeable ice lens formation. Lastly, these analytic solutions can be utilized to improve and compare the performance of the firn hydrology, ice-sheet and Earth system models. Our analysis provides a theoretical framework to understand these important processes in firn which affect the partitioning between meltwater infiltration and surface runoff and therefore determine the surface mass loss from ice sheets and its contribution to sea level rise., Comment: 36 pages, 13 figures

Published
2024

3. Combining Local and Global Perception for Autonomous Navigation on Nano-UAVs

Author

Lamberti, Lorenzo, Rutishauser, Georg, Conti, Francesco, and Benini, Luca

Subjects
Computer Science - Robotics, Electrical Engineering and Systems Science - Systems and Control
Abstract

A critical challenge in deploying unmanned aerial vehicles (UAVs) for autonomous tasks is their ability to navigate in an unknown environment. This paper introduces a novel vision-depth fusion approach for autonomous navigation on nano-UAVs. We combine the visual-based PULP-Dronet convolutional neural network for semantic information extraction, i.e., serving as the global perception, with 8x8px depth maps for close-proximity maneuvers, i.e., the local perception. When tested in-field, our integration strategy highlights the complementary strengths of both visual and depth sensory information. We achieve a 100% success rate over 15 flights in a complex navigation scenario, encompassing straight pathways, static obstacle avoidance, and 90{\deg} turns., Comment: 5 pages, 2 figures, 1 table, 1 video

Published
2024

5. Exploring synergies between B- and T-cell vaccine approaches to optimize immune responses against HIV-workshop report.

Author

Maciel, Milton, Amara, Rama, Bar, Katharine, Crotty, Shane, Deeks, Steven, Duplessis, Christopher, Gaiha, Gaurav, McElrath, M, McMichael, Andrew, Palin, Amy, Rutishauser, Rachel, Shapiro, Stuart, Smiley, Stephen, and DSouza, M

Abstract

The US National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institute of Health (NIH), convened a virtual workshop on August 8-9th, 2023 to explore potential synergies between HIV vaccine approaches that are designed to induce cellular or humoral immune responses. The goal of this workshop was to review data on leading vaccine candidates and to discuss the best strategies for combining these approaches to optimize immunity against HIV. Here, we summarize the findings reviewed at the workshop and discuss the knowledge gaps and priorities for future studies that will help accelerate the development of a preventive HIV vaccine.

Published
2024

7. Phylogenomics and the rise of the angiosperms

Author

Zuntini, Alexandre R., Carruthers, Tom, Maurin, Olivier, Bailey, Paul C., Leempoel, Kevin, Brewer, Grace E., Epitawalage, Niroshini, Françoso, Elaine, Gallego-Paramo, Berta, McGinnie, Catherine, Negrão, Raquel, Roy, Shyamali R., Simpson, Lalita, Toledo Romero, Eduardo, Barber, Vanessa M. A., Botigué, Laura, Clarkson, James J., Cowan, Robyn S., Dodsworth, Steven, Johnson, Matthew G., Kim, Jan T., Pokorny, Lisa, Wickett, Norman J., Antar, Guilherme M., DeBolt, Lucinda, Gutierrez, Karime, Hendriks, Kasper P., Hoewener, Alina, Hu, Ai-Qun, Joyce, Elizabeth M., Kikuchi, Izai A. B. S., Larridon, Isabel, Larson, Drew A., de Lírio, Elton John, Liu, Jing-Xia, Malakasi, Panagiota, Przelomska, Natalia A. S., Shah, Toral, Viruel, Juan, Allnutt, Theodore R., Ameka, Gabriel K., Andrew, Rose L., Appelhans, Marc S., Arista, Montserrat, Ariza, María Jesús, Arroyo, Juan, Arthan, Watchara, Bachelier, Julien B., Bailey, C. Donovan, Barnes, Helen F., Barrett, Matthew D., Barrett, Russell L., Bayer, Randall J., Bayly, Michael J., Biffin, Ed, Biggs, Nicky, Birch, Joanne L., Bogarín, Diego, Borosova, Renata, Bowles, Alexander M. C., Boyce, Peter C., Bramley, Gemma L. C., Briggs, Marie, Broadhurst, Linda, Brown, Gillian K., Bruhl, Jeremy J., Bruneau, Anne, Buerki, Sven, Burns, Edie, Byrne, Margaret, Cable, Stuart, Calladine, Ainsley, Callmander, Martin W., Cano, Ángela, Cantrill, David J., Cardinal-McTeague, Warren M., Carlsen, Mónica M., Carruthers, Abigail J. A., de Castro Mateo, Alejandra, Chase, Mark W., Chatrou, Lars W., Cheek, Martin, Chen, Shilin, Christenhusz, Maarten J. M., Christin, Pascal-Antoine, Clements, Mark A., Coffey, Skye C., Conran, John G., Cornejo, Xavier, Couvreur, Thomas L. P., Cowie, Ian D., Csiba, Laszlo, Darbyshire, Iain, Davidse, Gerrit, Davies, Nina M. J., Davis, Aaron P., van Dijk, Kor-jent, Downie, Stephen R., Duretto, Marco F., Duvall, Melvin R., Edwards, Sara L., Eggli, Urs, Erkens, Roy H. J., Escudero, Marcial, de la Estrella, Manuel, Fabriani, Federico, Fay, Michael F., Ferreira, Paola de L., Ficinski, Sarah Z., Fowler, Rachael M., Frisby, Sue, Fu, Lin, Fulcher, Tim, Galbany-Casals, Mercè, Gardner, Elliot M., German, Dmitry A., Giaretta, Augusto, Gibernau, Marc, Gillespie, Lynn J., González, Cynthia C., Goyder, David J., Graham, Sean W., Grall, Aurélie, Green, Laura, Gunn, Bee F., Gutiérrez, Diego G., Hackel, Jan, Haevermans, Thomas, Haigh, Anna, Hall, Jocelyn C., Hall, Tony, Harrison, Melissa J., Hatt, Sebastian A., Hidalgo, Oriane, Hodkinson, Trevor R., Holmes, Gareth D., Hopkins, Helen C. F., Jackson, Christopher J., James, Shelley A., Jobson, Richard W., Kadereit, Gudrun, Kahandawala, Imalka M., Kainulainen, Kent, Kato, Masahiro, Kellogg, Elizabeth A., King, Graham J., Klejevskaja, Beata, Klitgaard, Bente B., Klopper, Ronell R., Knapp, Sandra, Koch, Marcus A., Leebens-Mack, James H., Lens, Frederic, Leon, Christine J., Léveillé-Bourret, Étienne, Lewis, Gwilym P., Li, De-Zhu, Li, Lan, Liede-Schumann, Sigrid, Livshultz, Tatyana, Lorence, David, Lu, Meng, Lu-Irving, Patricia, Luber, Jaquelini, Lucas, Eve J., Luján, Manuel, Lum, Mabel, Macfarlane, Terry D., Magdalena, Carlos, Mansano, Vidal F., Masters, Lizo E., Mayo, Simon J., McColl, Kristina, McDonnell, Angela J., McDougall, Andrew E., McLay, Todd G. B., McPherson, Hannah, Meneses, Rosa I., Merckx, Vincent S. F. T., Michelangeli, Fabián A., Mitchell, John D., Monro, Alexandre K., Moore, Michael J., Mueller, Taryn L., Mummenhoff, Klaus, Munzinger, Jérôme, Muriel, Priscilla, Murphy, Daniel J., Nargar, Katharina, Nauheimer, Lars, Nge, Francis J., Nyffeler, Reto, Orejuela, Andrés, Ortiz, Edgardo M., Palazzesi, Luis, Peixoto, Ariane Luna, Pell, Susan K., Pellicer, Jaume, Penneys, Darin S., Perez-Escobar, Oscar A., Persson, Claes, Pignal, Marc, Pillon, Yohan, Pirani, José R., Plunkett, Gregory M., Powell, Robyn F., Prance, Ghillean T., Puglisi, Carmen, Qin, Ming, Rabeler, Richard K., Rees, Paul E. J., Renner, Matthew, Roalson, Eric H., Rodda, Michele, Rogers, Zachary S., Rokni, Saba, Rutishauser, Rolf, de Salas, Miguel F., Schaefer, Hanno, Schley, Rowan J., Schmidt-Lebuhn, Alexander, Shapcott, Alison, Al-Shehbaz, Ihsan, Shepherd, Kelly A., Simmons, Mark P., Simões, André O., Simões, Ana Rita G., Siros, Michelle, Smidt, Eric C., Smith, James F., Snow, Neil, Soltis, Douglas E., Soltis, Pamela S., Soreng, Robert J., Sothers, Cynthia A., Starr, Julian R., Stevens, Peter F., Straub, Shannon C. K., Struwe, Lena, Taylor, Jennifer M., Telford, Ian R. H., Thornhill, Andrew H., Tooth, Ifeanna, Trias-Blasi, Anna, Udovicic, Frank, Utteridge, Timothy M. A., Del Valle, Jose C., Verboom, G. Anthony, Vonow, Helen P., Vorontsova, Maria S., de Vos, Jurriaan M., Al-Wattar, Noor, Waycott, Michelle, Welker, Cassiano A. D., White, Adam J., Wieringa, Jan J., Williamson, Luis T., Wilson, Trevor C., Wong, Sin Yeng, Woods, Lisa A., Woods, Roseina, Worboys, Stuart, Xanthos, Martin, Yang, Ya, Zhang, Yu-Xiao, Zhou, Meng-Yuan, Zmarzty, Sue, Zuloaga, Fernando O., Antonelli, Alexandre, Bellot, Sidonie, Crayn, Darren M., Grace, Olwen M., Kersey, Paul J., Leitch, Ilia J., Sauquet, Hervé, Smith, Stephen A., Eiserhardt, Wolf L., Forest, Félix, and Baker, William J.

Published
2024
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9. Flexible and Fully Quantized Ultra-Lightweight TinyissimoYOLO for Ultra-Low-Power Edge Systems

Author

Moosmann, Julian, Mueller, Hanna, Zimmerman, Nicky, Rutishauser, Georg, Benini, Luca, and Magno, Michele

Subjects
Computer Science - Computer Vision and Pattern Recognition, Electrical Engineering and Systems Science - Image and Video Processing
Abstract

This paper deploys and explores variants of TinyissimoYOLO, a highly flexible and fully quantized ultra-lightweight object detection network designed for edge systems with a power envelope of a few milliwatts. With experimental measurements, we present a comprehensive characterization of the network's detection performance, exploring the impact of various parameters, including input resolution, number of object classes, and hidden layer adjustments. We deploy variants of TinyissimoYOLO on state-of-the-art ultra-low-power extreme edge platforms, presenting an in-depth a comparison on latency, energy efficiency, and their ability to efficiently parallelize the workload. In particular, the paper presents a comparison between a novel parallel RISC-V processor (GAP9 from Greenwaves) with and without use of its on-chip hardware accelerator, an ARM Cortex-M7 core (STM32H7 from ST Microelectronics), two ARM Cortex-M4 cores (STM32L4 from STM and Apollo4b from Ambiq), and a multi-core platform with a CNN hardware accelerator (Analog Devices MAX78000). Experimental results show that the GAP9's hardware accelerator achieves the lowest inference latency and energy at 2.12ms and 150uJ respectively, which is around 2x faster and 20% more efficient than the next best platform, the MAX78000. The hardware accelerator of GAP9 can even run an increased resolution version of TinyissimoYOLO with 112x112 pixels and 10 detection classes within 3.2ms, consuming 245uJ. To showcase the competitiveness of a versatile general-purpose system we also deployed and profiled a multi-core implementation on GAP9 at different operating points, achieving 11.3ms with the lowest-latency and 490uJ with the most energy-efficient configuration. With this paper, we demonstrate the suitability and flexibility of TinyissimoYOLO on state-of-the-art detection datasets for real-time ultra-low-power edge inference., Comment: * The first three authors contributed equally to this research

Published
2023
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10. Free Bits: Latency Optimization of Mixed-Precision Quantized Neural Networks on the Edge

Author

Rutishauser, Georg, Conti, Francesco, and Benini, Luca

Subjects
Computer Science - Machine Learning
Abstract

Mixed-precision quantization, where a deep neural network's layers are quantized to different precisions, offers the opportunity to optimize the trade-offs between model size, latency, and statistical accuracy beyond what can be achieved with homogeneous-bit-width quantization. To navigate the intractable search space of mixed-precision configurations for a given network, this paper proposes a hybrid search methodology. It consists of a hardware-agnostic differentiable search algorithm followed by a hardware-aware heuristic optimization to find mixed-precision configurations latency-optimized for a specific hardware target. We evaluate our algorithm on MobileNetV1 and MobileNetV2 and deploy the resulting networks on a family of multi-core RISC-V microcontroller platforms with different hardware characteristics. We achieve up to 28.6% reduction of end-to-end latency compared to an 8-bit model at a negligible accuracy drop from a full-precision baseline on the 1000-class ImageNet dataset. We demonstrate speedups relative to an 8-bit baseline, even on systems with no hardware support for sub-byte arithmetic at negligible accuracy drop. Furthermore, we show the superiority of our approach with respect to differentiable search targeting reduced binary operation counts as a proxy for latency., Comment: Accepted for publication at the 2023 IEEE International Conference of Artificial Intelligence Circuits and Systems (AICAS '23)

Published
2023

11. A 3 TOPS/W RISC-V Parallel Cluster for Inference of Fine-Grain Mixed-Precision Quantized Neural Networks

Author

Nadalini, Alessandro, Rutishauser, Georg, Burrello, Alessio, Bruschi, Nazareno, Garofalo, Angelo, Benini, Luca, Conti, Francesco, and Rossi, Davide

Subjects
Computer Science - Hardware Architecture
Abstract

The emerging trend of deploying complex algorithms, such as Deep Neural Networks (DNNs), increasingly poses strict memory and energy efficiency requirements on Internet-of-Things (IoT) end-nodes. Mixed-precision quantization has been proposed as a technique to minimize a DNN's memory footprint and maximize its execution efficiency, with negligible end-to-end precision degradation. In this work, we present a novel hardware and software stack for energy-efficient inference of mixed-precision Quantized Neural Networks (QNNs). We introduce Flex-V, a processor based on the RISC-V Instruction Set Architecture (ISA) that features fused Mac&Load mixed-precision dot product instructions; to avoid the exponential growth of the encoding space due to mixed-precision variants, we encode formats into the Control-Status Registers (CSRs). Flex-V core is integrated into a tightly-coupled cluster of eight processors; in addition, we provide a full framework for the end-to-end deployment of DNNs including a compiler, optimized libraries, and a memory-aware deployment flow. Our results show up to 91.5 MAC/cycle and 3.26 TOPS/W on the cluster, implemented in a commercial 22nm FDX technology, with up to 8.5x speed-up, and an area overhead of only 5.6% with respect to the baseline. To demonstrate the capabilities of the architecture, we benchmark it with end-to-end real-life QNNs, improving performance by 2x - 2.5x with respect to existing solutions using fully flexible programmable processors.

Published
2023

12. Benefits of sharing neurophysiology data from the BRAIN Initiative Research Opportunities in Humans Consortium.

Author

Rahimzadeh, Vasiliki, Jones, Kathryn, Majumder, Mary, Kahana, Michael, Rutishauser, Ueli, Williams, Ziv, Cash, Sydney, Paulk, Angelique, Zheng, Jie, Beauchamp, Michael, Collinger, Jennifer, Pouratian, Nader, McGuire, Amy, and Sheth, Sameer

Subjects
BRAIN Initiative, FAIR principles, data sharing, electrocorticography, implanted human neurophysiology, intracortical human physiology, intracranial EEG, invasive human neurophysiology, Humans, Neurophysiology, Brain, Information Dissemination
Abstract

Sharing human brain data can yield scientific benefits, but because of various disincentives, only a fraction of these data is currently shared. We profile three successful data-sharing experiences from the NIH BRAIN Initiative Research Opportunities in Humans (ROH) Consortium and demonstrate benefits to data producers and to users.

Published
2023

13. Generating and measuring effective vaccine-elicited HIV-specific CD8+ T cell responses

Author

Borgo, Gina M and Rutishauser, Rachel L

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Immunization, Infectious Diseases, Biotechnology, Vaccine Related (AIDS), Clinical Trials and Supportive Activities, HIV/AIDS, Vaccine Related, Prevention, Clinical Research, 3.4 Vaccines, Prevention of disease and conditions, and promotion of well-being, Infection, Good Health and Well Being, Humans, AIDS Vaccines, HIV Infections, CD8-Positive T-Lymphocytes, Genetic Vectors, Epitopes, Public Health and Health Services, Virology, Clinical sciences, Medical microbiology, Epidemiology
Abstract

Purpose of reviewThere is growing consensus that eliciting CD8 + T cells in addition to antibodies may be required for an effective HIV vaccine for both prevention and cure. Here, we review key qualities of vaccine-elicited CD8 + T cells as well as major CD8 + T cell-based delivery platforms used in recent HIV vaccine clinical trials.Recent findingsMuch progress has been made in improving HIV immunogen design and delivery platforms to optimize CD8 + T cell responses. With regards to viral vectors, recent trials have tested newer chimp and human adenovirus vectors as well as a CMV vector. DNA vaccine immunogenicity has been increased by delivering the vaccines by electroporation and together with adjuvants as well as administering them as part of a heterologous regimen. In preclinical models, self-amplifying RNA vaccines can generate durable tissue-based CD8 + T cells. While it may be beneficial for HIV vaccines to recapitulate the functional and phenotypic features of HIV-specific CD8 + T cells isolated from elite controllers, most of these features are not routinely measured in HIV vaccine clinical trials.SummaryIdentifying a vaccine capable of generating durable T cell responses that target mutationally vulnerable epitopes and that can rapidly intercept infecting or rebounding virus remains a challenge for HIV. Comprehensive assessment of HIV vaccine-elicited CD8 + T cells, as well as comparisons between different vaccine platforms, will be critical to advance our understanding of how to design better CD8 + T cell-based vaccines for HIV.

Published
2023

14. Slow ramping emerges from spontaneous fluctuations in spiking neural networks

Author

Jake Gavenas, Ueli Rutishauser, Aaron Schurger, and Uri Maoz

Subjects
Science
Abstract

Abstract The capacity to initiate actions endogenously is critical for goal-directed behavior. Spontaneous voluntary actions are typically preceded by slow-ramping activity in medial frontal cortex that begins around two seconds before movement, which may reflect spontaneous fluctuations that influence action timing. However, the mechanisms by which these slow ramping signals emerge from single-neuron and network dynamics remain poorly understood. Here, we developed a spiking neural-network model that produces spontaneous slow ramping activity in single neurons and population activity with onsets ~2 s before threshold crossings. A key prediction of our model is that neurons that ramp together have correlated firing patterns before ramping onset. We confirmed this model-derived hypothesis in a dataset of human single neuron recordings from medial frontal cortex. Our results suggest that slow ramping signals reflect bounded spontaneous fluctuations that emerge from quasi-winner-take-all dynamics in clustered networks that are temporally stabilized by slow-acting synapses.

Published
2024
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16. ColibriUAV: An Ultra-Fast, Energy-Efficient Neuromorphic Edge Processing UAV-Platform with Event-Based and Frame-Based Cameras

Author

Bian, Sizhen, Schulthess, Lukas, Rutishauser, Georg, Di Mauro, Alfio, Benini, Luca, and Magno, Michele

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence, Computer Science - Hardware Architecture, Electrical Engineering and Systems Science - Systems and Control
Abstract

The interest in dynamic vision sensor (DVS)-powered unmanned aerial vehicles (UAV) is raising, especially due to the microsecond-level reaction time of the bio-inspired event sensor, which increases robustness and reduces latency of the perception tasks compared to a RGB camera. This work presents ColibriUAV, a UAV platform with both frame-based and event-based cameras interfaces for efficient perception and near-sensor processing. The proposed platform is designed around Kraken, a novel low-power RISC-V System on Chip with two hardware accelerators targeting spiking neural networks and deep ternary neural networks.Kraken is capable of efficiently processing both event data from a DVS camera and frame data from an RGB camera. A key feature of Kraken is its integrated, dedicated interface with a DVS camera. This paper benchmarks the end-to-end latency and power efficiency of the neuromorphic and event-based UAV subsystem, demonstrating state-of-the-art event data with a throughput of 7200 frames of events per second and a power consumption of 10.7 \si{\milli\watt}, which is over 6.6 times faster and a hundred times less power-consuming than the widely-used data reading approach through the USB interface. The overall sensing and processing power consumption is below 50 mW, achieving latency in the milliseconds range, making the platform suitable for low-latency autonomous nano-drones as well.

Published
2023

17. Marsellus: A Heterogeneous RISC-V AI-IoT End-Node SoC with 2-to-8b DNN Acceleration and 30%-Boost Adaptive Body Biasing

Author

Conti, Francesco, Paulin, Gianna, Rossi, Davide, Di Mauro, Alfio, Rutishauser, Georg, Ottavi, Gianmarco, Eggimann, Manuel, Okuhara, Hayate, and Benini, Luca

Subjects
Computer Science - Hardware Architecture, Computer Science - Artificial Intelligence, Computer Science - Machine Learning
Abstract

Emerging Artificial Intelligence-enabled Internet-of-Things (AI-IoT) System-on-a-Chip (SoC) for augmented reality, personalized healthcare, and nano-robotics need to run many diverse tasks within a power envelope of a few tens of mW over a wide range of operating conditions: compute-intensive but strongly quantized Deep Neural Network (DNN) inference, as well as signal processing and control requiring high-precision floating-point. We present Marsellus, an all-digital heterogeneous SoC for AI-IoT end-nodes fabricated in GlobalFoundries 22nm FDX that combines 1) a general-purpose cluster of 16 RISC-V Digital Signal Processing (DSP) cores attuned for the execution of a diverse range of workloads exploiting 4-bit and 2-bit arithmetic extensions (XpulpNN), combined with fused MAC&LOAD operations and floating-point support; 2) a 2-8bit Reconfigurable Binary Engine (RBE) to accelerate 3x3 and 1x1 (pointwise) convolutions in DNNs; 3) a set of On-Chip Monitoring (OCM) blocks connected to an Adaptive Body Biasing (ABB) generator and a hardware control loop, enabling on-the-fly adaptation of transistor threshold voltages. Marsellus achieves up to 180 Gop/s or 3.32 Top/s/W on 2-bit precision arithmetic in software, and up to 637 Gop/s or 12.4 Top/s/W on hardware-accelerated DNN layers., Comment: Post-print accepted by IEEE Journal of Solid-State Circuits

Published
2023

24. 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. Sebastián, Terborgh, John, Texier, Nicolas, Theilade, Ida, Thomas, Duncan W., Thomas, Raquel, Thomas, Sean C., Tirado, Milton, Toirambe, Benjamin, de Toledo, José Julio, Tomlinson, Kyle W., Torres-Lezama, Armando, Tran, Hieu Dang, Tshibamba Mukendi, John, Tumaneng, Roven D., Umaña, Maria Natalia, Umunay, Peter M., Urrego Giraldo, Ligia Estela, Valderrama Sandoval, Elvis H., Valenzuela Gamarra, Luis, Van Andel, Tinde R., van de Bult, Martin, van de Pol, Jaqueline, van der Heijden, Geertje, Vasquez, Rodolfo, Vela, César I. A., Venticinque, Eduardo Martins, Verbeeck, Hans, Veridiano, Rizza Karen A., Vicentini, Alberto, Vieira, Ima Célia Guimarães, Vilanova Torre, Emilio, Villarroel, Daniel, Villa Zegarra, Boris Eduardo, Vleminckx, Jason, von Hildebrand, Patricio, Vos, Vincent Antoine, Vriesendorp, Corine, Webb, Edward L., White, Lee J. T., Wich, Serge, Wittmann, Florian, Zagt, Roderick, Zang, Runguo, Zartman, Charles Eugene, Zemagho, Lise, Zent, Egleé L., and Zent, Stanford

Published
2024
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25. ColibriES: A Milliwatts RISC-V Based Embedded System Leveraging Neuromorphic and Neural Networks Hardware Accelerators for Low-Latency Closed-loop Control Applications

Author

Rutishauser, Georg, Hunziker, Robin, Di Mauro, Alfio, Bian, Sizhen, Benini, Luca, and Magno, Michele

Subjects
Computer Science - Hardware Architecture
Abstract

End-to-end event-based computation has the potential to push the envelope in latency and energy efficiency for edge AI applications. Unfortunately, event-based sensors (e.g., DVS cameras) and neuromorphic spike-based processors (e.g., Loihi) have been designed in a decoupled fashion, thereby missing major streamlining opportunities. This paper presents ColibriES, the first-ever neuromorphic hardware embedded system platform with dedicated event-sensor interfaces and full processing pipelines. ColibriES includes event and frame interfaces and data processing, aiming at efficient and long-life embedded systems in edge scenarios. ColibriES is based on the Kraken system-on-chip and contains a heterogeneous parallel ultra-low power (PULP) processor, frame-based and event-based camera interfaces, and two hardware accelerators for the computation of both event-based spiking neural networks and frame-based ternary convolutional neural networks. This paper explores and accurately evaluates the performance of event data processing on the example of gesture recognition on ColibriES, as the first step of full-system evaluation. In our experiments, we demonstrate a chip energy consumption of 7.7 \si{\milli\joule} and latency of 164.5 \si{\milli\second} of each inference with the DVS Gesture event data set as an example for closed-loop data processing, showcasing the potential of ColibriES for battery-powered applications such as wearable devices and UAVs that require low-latency closed-loop control.

Published
2023

26. Combining analytical techniques to assess the translocation of diesel particles across an alveolar tissue barrier in vitro

Author

Gowsinth Gunasingam, Ruiwen He, Patricia Taladriz-Blanco, Sandor Balog, Alke Petri-Fink, and Barbara Rothen-Rutishauser

Subjects
Diesel particles (DEPs), Translocation, Transmission electron microscopy (TEM), Ultraviolet – visible (UV-VIS), Lock-in thermography (LIT), A549 cells, Toxicology. Poisons, RA1190-1270, Industrial hygiene. Industrial welfare, HD7260-7780.8
Abstract

Abstract Background During inhalation, airborne particles such as particulate matter ≤ 2.5 μm (PM2.5), can deposit and accumulate on the alveolar epithelial tissue. In vivo studies have shown that fractions of PM2.5 can cross the alveolar epithelium to blood circulation, reaching secondary organs beyond the lungs. However, approaches to quantify the translocation of particles across the alveolar epithelium in vivo and in vitro are still not well established. In this study, methods to assess the translocation of standard diesel exhaust particles (DEPs) across permeable polyethylene terephthalate (PET) inserts at 0.4, 1, and 3 μm pore sizes were first optimized with transmission electron microscopy (TEM), ultraviolet-visible spectroscopy (UV-VIS), and lock-in thermography (LIT), which were then applied to study the translocation of DEPs across human alveolar epithelial type II (A549) cells. A549 cells that grew on the membrane (pore size: 3 μm) in inserts were exposed to DEPs at different concentrations from 0 to 80 µg.mL− 1 ( 0 to 44 µg.cm− 2) for 24 h. After exposure, the basal fraction was collected and then analyzed by combining qualitative (TEM) and quantitative (UV-VIS and LIT) techniques to assess the translocated fraction of the DEPs across the alveolar epithelium in vitro. Results We could detect the translocated fraction of DEPs across the PET membranes with 3 μm pore sizes and without cells by TEM analysis, and determine the percentage of translocation at approximatively 37% by UV-VIS (LOD: 1.92 µg.mL− 1) and 75% by LIT (LOD: 0.20 µg.cm− 2). In the presence of cells, the percentage of DEPs translocation across the alveolar tissue was determined around 1% at 20 and 40 µg.mL− 1 (11 and 22 µg.cm− 2), and no particles were detected at higher and lower concentrations. Interestingly, simultaneous exposure of A549 cells to DEPs and EDTA can increase the translocation of DEPs in the basal fraction. Conclusion We propose a combination of analytical techniques to assess the translocation of DEPs across lung tissues. Our results reveal a low percentage of translocation of DEPs across alveolar epithelial tissue in vitro and they correspond to in vivo findings. The combination approach can be applied to any traffic-generated particles, thus enabling us to understand their involvement in public health.

Published
2024
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27. Mapping the vertical heterogeneity of Greenland's firn from 2011–2019 using airborne radar and laser altimetry

Author

A. Rutishauser, K. M. Scanlan, B. Vandecrux, N. B. Karlsson, N. Jullien, A. P. Ahlstrøm, R. S. Fausto, and P. How

Subjects
Environmental sciences, GE1-350, Geology, QE1-996.5
Abstract

The firn layer on the Greenland Ice Sheet (GrIS) plays a crucial role in buffering surface meltwater runoff, which is constrained by the available firn pore space and impermeable ice layers that limit deeper meltwater percolation. Understanding these firn properties is essential for predicting current and future meltwater runoff and its contribution to global sea-level rise. While very-high-frequency (VHF) radars have been extensively used for surveying the GrIS, their lower bandwidth restricts direct firn stratigraphy extraction. In this study, we use concurrent VHF airborne radar and laser altimetry data collected as part of Operation IceBridge over the 2011–2019 period to investigate our hypothesis that vertical heterogeneities in firn (i.e. ice layers) cause vertical offsets in the radar surface reflection (dz). Our results, corroborated by modelling and firn core analyses, show that a dz larger than 1 m is strongly related to the vertical heterogeneity of a firn profile and effectively delineates between vertically homogeneous and vertically heterogeneous firn profiles over a depth range of ∼ 4 m. Temporal variations in dz align with climatic events and reveal an expansion of heterogeneous firn between 2011–2013 covering an area of ∼ 350 815 km2, followed by firn replenishment over the years 2014–2019 spanning an area of ∼ 667 725 km2. Our approach reveals the firn evolution of key regions on the Greenland Ice Sheet, providing valuable insights for detecting potential alterations in meltwater runoff patterns.

Published
2024
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30. TCN-CUTIE: A 1036 TOp/s/W, 2.72 uJ/Inference, 12.2 mW All-Digital Ternary Accelerator in 22 nm FDX Technology

Author

Scherer, Moritz, Di Mauro, Alfio, Fischer, Tim, Rutishauser, Georg, and Benini, Luca

Subjects
Computer Science - Hardware Architecture
Abstract

Tiny Machine Learning (TinyML) applications impose uJ/Inference constraints, with a maximum power consumption of tens of mW. It is extremely challenging to meet these requirements at a reasonable accuracy level. This work addresses the challenge with a flexible, fully digital Ternary Neural Network (TNN) accelerator in a RISC-V-based System-on-Chip (SoC). Besides supporting Ternary Convolutional Neural Networks, we introduce extensions to the accelerator design that enable the processing of time-dilated Temporal Convolutional Neural Networks (TCNs). The design achieves 5.5 uJ/Inference, 12.2 mW, 8000 Inferences/sec at 0.5 V for a Dynamic Vision Sensor (DVS) based TCN, and an accuracy of 94.5 % and 2.72 uJ/Inference, 12.2 mW, 3200 Inferences/sec at 0.5 V for a non-trivial 9-layer, 96 channels-per-layer convolutional network with CIFAR-10 accuracy of 86 %. The peak energy efficiency is 1036 TOp/s/W, outperforming the state-of-the-art silicon-proven TinyML quantized accelerators by 1.67x while achieving competitive accuracy., Comment: Accepted at IEEE MICRO Journal

Published
2022

31. A Mechanism for Ice Layer Formation in Glacial Firn

Author

Mohammad Afzal Shadab, Surendra Adhikari, Anja Rutishauser, Cyril Grima, and Marc Andre Hesse

Subjects
ice layer, formation mechanism and depth, firn hydrology, firn stratigraphy, climate variability, Geophysics. Cosmic physics, QC801-809
Abstract

Abstract There is ample evidence for ice layers and lenses within glacial firn. The standard model for ice layer formation localizes the refreezing by perching of meltwater on pre‐existing discontinuities. Here we argue that even extreme melting events provide insufficient flux for this mechanism. Using a thermomechanical model we demonstrate a different mechanism of ice layer formation. After a melting event when the drying front catches up with the wetting front and arrests melt percolation, conductive heat loss freezes the remaining melt in place to form an ice layer. This model reproduces the depth of a new ice layer at the Dye‐2 site in Greenland. It provides a deeper insight into the interpretation of firn stratigraphy and past climate variability. It also improves the simulation of firn densification processes, a key source of uncertainty in assessing and attributing ice sheet mass balance based on satellite altimetry and gravimetry data.

Published
2024
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34. 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 G. P., 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 H. S., 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 Y. H., 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, Jagodziński, Andrzej M., Jaroszewicz, Bogdan, Johannsen, Vivian Kvist, Joly, Carlos A., Jucker, Tommaso, Jung, Ilbin, Karminov, Viktor, Kartawinata, Kuswata, Kearsley, Elizabeth, Kenfack, David, Kennard, Deborah K., Kepfer-Rojas, Sebastian, Keppel, Gunnar, Khan, Mohammed Latif, Killeen, Timothy J., Kim, Hyun Seok, Kitayama, Kanehiro, Köhl, Michael, Korjus, Henn, Kraxner, Florian, Kucher, Dmitry, Laarmann, Diana, Lang, Mait, Lu, Huicui, Lukina, Natalia V., Maitner, Brian S., Malhi, Yadvinder, Marcon, Eric, Marimon, Beatriz Schwantes, Marimon-Junior, Ben Hur, Marshall, Andrew R., Martin, Emanuel H., Meave, Jorge A., Melo-Cruz, Omar, Mendoza, Casimiro, Mendoza-Polo, Irina, Miscicki, Stanislaw, Merow, Cory, Monteagudo Mendoza, Abel, Moreno, Vanessa S., Mukul, Sharif A., Mundhenk, Philip, Nava-Miranda, María Guadalupe, Neill, David, Neldner, Victor J., Nevenic, Radovan V., Ngugi, Michael R., Niklaus, Pascal A., Oleksyn, Jacek, Ontikov, Petr, Ortiz-Malavasi, Edgar, Pan, Yude, Paquette, Alain, Parada-Gutierrez, Alexander, Parfenova, Elena I., Park, Minjee, Parren, Marc, Parthasarathy, Narayanaswamy, Peri, Pablo L., Pfautsch, Sebastian, Picard, Nicolas, Piedade, Maria Teresa F., Piotto, Daniel, Pitman, Nigel C. A., Poulsen, Axel Dalberg, Poulsen, John R., Pretzsch, Hans, Ramirez Arevalo, Freddy, Restrepo-Correa, Zorayda, Rodeghiero, Mirco, Rolim, Samir G., Roopsind, Anand, Rovero, Francesco, Rutishauser, Ervan, Saikia, Purabi, Salas-Eljatib, Christian, Saner, Philippe, Schall, Peter, Schelhaas, Mart-Jan, Schepaschenko, Dmitry, Scherer-Lorenzen, Michael, Schmid, Bernhard, Schöngart, Jochen, Searle, Eric B., Seben, Vladimír, Serra-Diaz, Josep M., Sheil, Douglas, Shvidenko, Anatoly Z., Silva-Espejo, Javier E., Silveira, Marcos, Singh, James, Sist, Plinio, Slik, Ferry, Sonké, Bonaventure, Souza, Alexandre F., Stereńczak, Krzysztof J., Svenning, Jens-Christian, Svoboda, Miroslav, Swanepoel, Ben, Targhetta, Natalia, Tchebakova, Nadja, ter Steege, Hans, Thomas, Raquel, Tikhonova, Elena, Umunay, Peter M., Usoltsev, Vladimir A., Valencia, Renato, Valladares, Fernando, van der Plas, Fons, Van Do, Tran, van Nuland, Michael E., Vasquez, Rodolfo M., Verbeeck, Hans, Viana, Helder, Vibrans, Alexander C., Vieira, Simone, von Gadow, Klaus, Wang, Hua-Feng, Watson, James V., Werner, Gijsbert D. A., Wiser, Susan K., Wittmann, Florian, Woell, Hannsjoerg, Wortel, Verginia, Zagt, Roderik, Zawiła-Niedźwiecki, Tomasz, Zhang, Chunyu, Zhao, Xiuhai, Zhou, Mo, Zhu, Zhi-Xin, Zo-Bi, Irie C., Gann, George D., and Crowther, Thomas W.

Published
2023
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35. 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 H. S., 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 Y. H., 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 G. P., 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, Karminov, Viktor, Kartawinata, Kuswata, Kearsley, Elizabeth, Kenfack, David, Kennard, Deborah K., Kepfer-Rojas, Sebastian, Keppel, Gunnar, Khan, Mohammed Latif, Killeen, Timothy J., Kim, Hyun Seok, Kitayama, Kanehiro, Köhl, Michael, Korjus, Henn, Kraxner, Florian, Kucher, Dmitry, Laarmann, Diana, Lang, Mait, Lewis, Simon L., Lu, Huicui, Lukina, Natalia V., Maitner, Brian S., Malhi, Yadvinder, Marcon, Eric, Marimon, Beatriz Schwantes, Marimon-Junior, Ben Hur, Marshall, Andrew R., Martin, Emanuel H., Meave, Jorge A., Melo-Cruz, Omar, Mendoza, Casimiro, Merow, Cory, Monteagudo Mendoza, Abel, Moreno, Vanessa S., Mukul, Sharif A., Mundhenk, Philip, Nava-Miranda, María Guadalupe, Neill, David, Neldner, Victor J., Nevenic, Radovan V., Ngugi, Michael R., Niklaus, Pascal A., Oleksyn, Jacek, Ontikov, Petr, Ortiz-Malavasi, Edgar, Pan, Yude, Paquette, Alain, Parada-Gutierrez, Alexander, Parfenova, Elena I., Park, Minjee, Parren, Marc, Parthasarathy, Narayanaswamy, Peri, Pablo L., Pfautsch, Sebastian, Phillips, Oliver L., Picard, Nicolas, Piedade, Maria Teresa F., Piotto, Daniel, Pitman, Nigel C. A., Mendoza-Polo, Irina, Poulsen, Axel D., Poulsen, John R., Pretzsch, Hans, Ramirez Arevalo, Freddy, Restrepo-Correa, Zorayda, Rodeghiero, Mirco, Rolim, Samir G., Roopsind, Anand, Rovero, Francesco, Rutishauser, Ervan, Saikia, Purabi, Salas-Eljatib, Christian, Saner, Philippe, Schall, Peter, Schelhaas, Mart-Jan, Schepaschenko, Dmitry, Scherer-Lorenzen, Michael, Schmid, Bernhard, Schöngart, Jochen, Searle, Eric B., Seben, Vladimír, Serra-Diaz, Josep M., Sheil, Douglas, Shvidenko, Anatoly Z., Silva-Espejo, Javier E., Silveira, Marcos, Singh, James, Sist, Plinio, Slik, Ferry, Sonké, Bonaventure, Souza, Alexandre F., Miścicki, Stanislaw, Stereńczak, Krzysztof J., Svenning, Jens-Christian, Svoboda, Miroslav, Swanepoel, Ben, Targhetta, Natalia, Tchebakova, Nadja, ter Steege, Hans, Thomas, Raquel, Tikhonova, Elena, Umunay, Peter M., Usoltsev, Vladimir A., Valencia, Renato, Valladares, Fernando, van der Plas, Fons, Van Do, Tran, van Nuland, Michael E., Vasquez, Rodolfo M., Verbeeck, Hans, Viana, Helder, Vibrans, Alexander C., Vieira, Simone, von Gadow, Klaus, Wang, Hua-Feng, Watson, James V., Werner, Gijsbert D. A., Westerlund, Bertil, Wiser, Susan K., Wittmann, Florian, Woell, Hannsjoerg, Wortel, Verginia, Zagt, Roderick, Zawiła-Niedźwiecki, Tomasz, Zhang, Chunyu, Zhao, Xiuhai, Zhou, Mo, Zhu, Zhi-Xin, Zo-Bi, Irie C., and Zohner, Constantin M.

Published
2023
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36. Exploring synergies between B- and T-cell vaccine approaches to optimize immune responses against HIV—workshop report

Author

Milton Maciel, Rama R. Amara, Katharine J. Bar, Shane Crotty, Steven G. Deeks, Christopher Duplessis, Gaurav Gaiha, M. Juliana McElrath, Andrew McMichael, Amy Palin, Rachel Rutishauser, Stuart Shapiro, Stephen T. Smiley, and M. Patricia D’Souza

Subjects
Immunologic diseases. Allergy, RC581-607, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

The US National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institute of Health (NIH), convened a virtual workshop on August 8-9th, 2023 to explore potential synergies between HIV vaccine approaches that are designed to induce cellular or humoral immune responses. The goal of this workshop was to review data on leading vaccine candidates and to discuss the best strategies for combining these approaches to optimize immunity against HIV. Here, we summarize the findings reviewed at the workshop and discuss the knowledge gaps and priorities for future studies that will help accelerate the development of a preventive HIV vaccine.

Published
2024
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37. Multimodal single-neuron, intracranial EEG, and fMRI brain responses during movie watching in human patients

Author

Umit Keles, Julien Dubois, Kevin J. M. Le, J. Michael Tyszka, David A. Kahn, Chrystal M. Reed, Jeffrey M. Chung, Adam N. Mamelak, Ralph Adolphs, and Ueli Rutishauser

Subjects
Science
Abstract

Abstract We 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.

Published
2024
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38. Dataset of human-single neuron activity during a Sternberg working memory task

Author

Michael Kyzar, Jan Kamiński, Aneta Brzezicka, Chrystal M. Reed, Jeffrey M. Chung, Adam N. Mamelak, and Ueli Rutishauser

Subjects
Science
Abstract

Abstract We present a dataset of 1809 single neurons recorded from the human medial temporal lobe (amygdala and hippocampus) and medial frontal lobe (anterior cingulate cortex, pre-supplementary motor area, ventral medial prefrontal cortex) across 41 sessions from 21 patients that underwent seizure monitoring with depth electrodes. Subjects performed a screening task (907 neurons) to identify images for which highly selective cells were present. Subjects then performed a working memory task (902 neurons), in which they were sequentially presented with 1–3 images for which highly selective cells were present and, following a maintenance period, were asked if the probe was identical to one of the maintained images. This Neurodata Without Borders formatted dataset includes spike times, extracellular spike waveforms, stimuli presented, behavior, electrode locations, and subject demographics. As validation, we replicate previous findings on the selectivity of concept cells and their persistent activity during working memory maintenance. This large dataset of rare human single-neuron recordings and behavior enables the investigation of the neural mechanisms of working memory in humans.

Published
2024
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39. In vivo killing of primary HIV-infected cells by peripheral-injected early memory–enriched anti-HIV duoCAR T cells

Author

Anthony-Gonda, Kim, Ray, Alex, Su, Hang, Wang, Yuge, Xiong, Ying, Lee, Danica, Block, Ariele, Chilunda, Vanessa, Weiselberg, Jessica, Zemelko, Lily, Wang, Yen Y, Kleinsorge-Block, Sarah, Reese, Jane S, de Lima, Marcos, Ochsenbauer, Christina, Kappes, John C, Dimitrov, Dimiter S, Orentas, Rimas, Deeks, Steven G, Rutishauser, Rachel L, Berman, Joan W, Goldstein, Harris, and Dropulić, Boro

Subjects
Clinical Research, HIV/AIDS, Stem Cell Research - Nonembryonic - Human, Infectious Diseases, Genetics, Human Fetal Tissue, Immunization, Stem Cell Research, Development of treatments and therapeutic interventions, 5.2 Cellular and gene therapies, Infection, Animals, Mice, CD4-Positive T-Lymphocytes, HIV Infections, HIV-1, Leukocytes, Mononuclear, Receptors, Chimeric Antigen, Clinical Trials, Phase I as Topic, Clinical Trials, Phase II as Topic, AIDS/HIV, Immunotherapy, Therapeutics
Abstract

HIV-specific chimeric antigen receptor-T cell (CAR T cell) therapies are candidates to functionally cure HIV infection in people with HIV (PWH) by eliminating reactivated HIV-infected cells derived from latently infected cells within the HIV reservoir. Paramount to translating such therapeutic candidates successfully into the clinic will require anti-HIV CAR T cells to localize to lymphoid tissues in the body and eliminate reactivated HIV-infected cells such as CD4+ T cells and monocytes/macrophages. Here we show that i.v. injected anti-HIV duoCAR T cells, generated using a clinical-grade anti-HIV duoCAR lentiviral vector, localized to the site of active HIV infection in the spleen of humanized mice and eliminated HIV-infected PBMCs. CyTOF analysis of preinfusion duoCAR T cells revealed an early memory phenotype composed predominantly of CCR7+ stem cell-like/central memory T cells (TSCM/TCM) with expression of some effector-like molecules. In addition, we show that anti-HIV duoCAR T cells effectively sense and kill HIV-infected CD4+ T cells and monocytes/macrophages. Furthermore, we demonstrate efficient genetic modification of T cells from PWH on suppressive ART into anti-HIV duoCAR T cells that subsequently kill autologous PBMCs superinfected with HIV. These studies support the safety and efficacy of anti-HIV duoCAR T cell therapy in our presently open phase I/IIa clinical trial (NCT04648046).

Published
2022

40. Postacute sequelae and adaptive immune responses in people with HIV recovering from SARS-COV-2 infection

Author

Peluso, Michael J, Spinelli, Matthew A, Deveau, Tyler-Marie, Forman, Carrie A, Munter, Sadie E, Mathur, Sujata, Tang, Alex F, Lu, Scott, Goldberg, Sarah A, Arreguin, Mireya I, Hoh, Rebecca, Tai, Viva, Chen, Jessica Y, Martinez, Enrique O, Yee, Brandon C, Chenna, Ahmed, Winslow, John W, Petropoulos, Christos J, Sette, Alessandro, Weiskopf, Daniella, Kumar, Nitasha, Lynch, Kara L, Hunt, Peter W, Durstenfeld, Matthew S, Hsue, Priscilla Y, Kelly, J Daniel, Martin, Jeffrey N, Glidden, David V, Gandhi, Monica, Deeks, Steven G, Rutishauser, Rachel L, and Henrich, Timothy J

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Emerging Infectious Diseases, Clinical Research, Coronaviruses, Infectious Diseases, Sexually Transmitted Infections, HIV/AIDS, Infection, Inflammatory and immune system, Good Health and Well Being, Humans, Antibodies, Viral, CD4-Positive T-Lymphocytes, COVID-19, HIV Infections, Immunologic Memory, Programmed Cell Death 1 Receptor, SARS-CoV-2, Post-Acute COVID-19 Syndrome, coronavirus disease 2019, HIV, immune response, long coronavirus disease, postacute sequelae of SARS-CoV-2, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Virology, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundLimited data are available on the long-term clinical and immunologic consequences of SARS-CoV-2 infection in people with HIV (PWH).MethodsWe measured SARS-CoV-2-specific humoral and cellular responses in people with and without HIV recovering from COVID-19 ( n  = 39 and n  = 43, respectively) using binding antibody, surrogate virus neutralization, intracellular cytokine staining, and inflammatory marker assays. We identified individuals experiencing postacute sequelae of SARS-CoV-2 infection (PASC) and evaluated immunologic parameters. We used linear regression and generalized linear models to examine differences by HIV status in the magnitude of inflammatory and virus-specific antibody and T-cell responses, as well as differences in the prevalence of PASC.ResultsAmong PWH, we found broadly similar SARS-CoV-2-specific antibody and T-cell responses as compared with a well matched group of HIV-negative individuals. PWH had 70% lower relative levels of SARS-CoV-2-specific memory CD8 + T cells ( P  = 0.007) and 53% higher relative levels of PD-1+ SARS-CoV-2-specific CD4 + T cells ( P  = 0.007). Higher CD4 + /CD8 + ratio was associated with lower PD-1 expression on SARS-CoV-2-specific CD8 + T cells (0.34-fold effect, P  = 0.02). HIV status was strongly associated with PASC (odds ratio 4.01, P  = 0.008), and levels of certain inflammatory markers (IL-6, TNF-alpha, and IP-10) were associated with persistent symptoms.ConclusionWe identified potentially important differences in SARS-CoV-2-specific CD4 + and CD8 + T cells in PWH and HIV-negative participants that might have implications for long-term immunity conferred by natural infection. HIV status strongly predicted the presence of PASC. Larger and more detailed studies of PASC in PWH are urgently needed.

Published
2022

41. A Symptom-Checker for Adult Patients Visiting an Interdisciplinary Emergency Care Center and the Safety of Patient Self-Triage: Real-Life Prospective Evaluation

Author

Andreas Meer, Philipp Rahm, Markus Schwendinger, Michael Vock, Bettina Grunder, Jacopo Demurtas, and Jonas Rutishauser

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Public aspects of medicine, RA1-1270
Abstract

BackgroundSymptom-checkers have become important tools for self-triage, assisting patients to determine the urgency of medical care. To be safe and effective, these tools must be validated, particularly to avoid potentially hazardous undertriage without leading to inefficient overtriage. Only limited safety data from studies including small sample sizes have been available so far. ObjectiveThe objective of our study was to prospectively investigate the safety of patients’ self-triage in a large patient sample. We used SMASS (Swiss Medical Assessment System; in4medicine, Inc) pathfinder, a symptom-checker based on a computerized transparent neural network. MethodsWe recruited 2543 patients into this single-center, prospective clinical trial conducted at the cantonal hospital of Baden, Switzerland. Patients with an Emergency Severity Index of 1-2 were treated by the team of the emergency department, while those with an index of 3-5 were seen at the walk-in clinic by general physicians. We compared the triage recommendation obtained by the patients’ self-triage with the assessment of clinical urgency made by 3 successive interdisciplinary panels of physicians (panels A, B, and C). Using the Clopper-Pearson CI, we assumed that to confirm the symptom-checkers’ safety, the upper confidence bound for the probability of a potentially hazardous undertriage should lie below 1%. A potentially hazardous undertriage was defined as a triage in which either all (consensus criterion) or the majority (majority criterion) of the experts of the last panel (panel C) rated the triage of the symptom-checker to be “rather likely” or “likely” life-threatening or harmful. ResultsOf the 2543 patients, 1227 (48.25%) were female and 1316 (51.75%) male. None of the patients reached the prespecified consensus criterion for a potentially hazardous undertriage. This resulted in an upper 95% confidence bound of 0.1184%. Further, 4 cases met the majority criterion. This resulted in an upper 95% confidence bound for the probability of a potentially hazardous undertriage of 0.3616%. The 2-sided 95% Clopper-Pearson CI for the probability of overtriage (n=450 cases,17.69%) was 16.23% to 19.24%, which is considerably lower than the figures reported in the literature. ConclusionsThe symptom-checker proved to be a safe triage tool, avoiding potentially hazardous undertriage in a real-life clinical setting of emergency consultations at a walk-in clinic or emergency department without causing undesirable overtriage. Our data suggest the symptom-checker may be safely used in clinical routine. Trial RegistrationClinicalTrials.gov NCT04055298; https://clinicaltrials.gov/study/NCT04055298

Published
2024
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42. Understanding The Benefits and Risks of Sustainable Nanomaterials in a Research Environment

Author

Sandeep Keshavan, Alke Petri-Fink, and Barbara Rothen-Rutishauser

Subjects
Circular economy, Life cycle assessment, Nanomaterials, Risk assessment, Sustainable Nanotechnology, Chemistry, QD1-999
Abstract

Nanomaterials hold immense potential for numerous applications in energy, health care, and environmental sectors, playing an important role in our daily lives. Their utilization spans from improving energy efficiency to enhancing medical diagnostics, and mitigating environmental pollution, thus presenting a multifaceted approach towards achieving sustainability goals. To ensure the sustainable and safe utilization of nanomaterials, a thorough evaluation of potential hazards and risks is essential throughout their lifecycle—from resource extraction and production to use and disposal. In this review, we focus on understanding and addressing potential environmental and health risks associated with nanomaterial utilization. We advocate for a balanced approach with early hazard identification, safe-by-design principles, and life cycle assessments, while emphasizing safe handling and disposal practices, collaboration, and continuous improvement. Our goal is to ensure responsible nanotechnology development, fostering innovation alongside environmental and community well-being, through a holistic approach integrating science, ethics, and proactive risk assessment.

Published
2024
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44. CD8+ T-cell responses in HIV controllers: potential implications for novel HIV remission strategies

Author

Rutishauser, Rachel L and Trautmann, Lydie

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Vaccine Related (AIDS), Prevention, Immunization, Vaccine Related, HIV/AIDS, Infectious Diseases, Inflammatory and immune system, Infection, Good Health and Well Being, Animals, CD8-Positive T-Lymphocytes, HIV Infections, HIV Non-Progressors, Humans, Macaca mulatta, Simian Acquired Immunodeficiency Syndrome, Simian Immunodeficiency Virus, Viral Load, CD8(+) T cells, HIV controllers, HIV remission strategies, Simian immunodeficiency virus, Public Health and Health Services, Virology, Clinical sciences, Medical microbiology, Epidemiology
Abstract

Purpose of reviewImmunological studies of spontaneous HIV and simian virus (SIV) controllers have identified virus-specific CD8 +  T cells as a key immune mechanism of viral control. The purpose of this review is to consider how knowledge about the mechanisms that are associated with CD8 +  T cell control of HIV/SIV in natural infection can be harnessed in HIV remission strategies.Recent findingsWe discuss characteristics of CD8 +  T-cell responses that may be critical for suppressing HIV replication in spontaneous controllers comprising HIV antigen recognition including specific human leukocyte antigen types, broadly cross-reactive T cell receptors and epitope targeting, enhanced expansion and antiviral functions, and localization of virus-specific T cells near sites of reservoir persistence. We also discuss the need to better understand the timing of CD8 +  T-cell responses associated with viral control of HIV/SIV during acute infection and after treatment interruption as well as the mechanisms by which HIV/SIV-specific CD8 +  T cells coordinate with other immune responses to achieve control.SummaryWe propose implications as to how this knowledge from natural infection can be applied in the design and evaluation of CD8 +  T-cell-based remission strategies and offer questions to consider as these strategies target distinct CD8 +  T-cell-dependent mechanisms of viral control.

Published
2022

46. 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 H. S., Brandl, Susanne, Brienen, Roel, Broadbent, Eben N., Bruelheide, Helge, Bussotti, Filippo, Gatti, Roberto Cazzolla, César, Ricardo G., Cesljar, Goran, Chazdon, Robin, Chen, Han Y. H., 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 G. P., 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, Karminov, Viktor, Kartawinata, Kuswata, Kearsley, Elizabeth, Kenfack, David, Kennard, Deborah K., Kepfer-Rojas, Sebastian, Keppel, Gunnar, Khan, Mohammed Latif, Killeen, Timothy J., Kim, Hyun Seok, Kitayama, Kanehiro, Köhl, Michael, Korjus, Henn, Kraxner, Florian, Laarmann, Diana, Lang, Mait, Lewis, Simon L., Lu, Huicui, Lukina, Natalia V., Maitner, Brian S., Malhi, Yadvinder, Marcon, Eric, Marimon, Beatriz Schwantes, Marimon-Junior, Ben Hur, Marshall, Andrew R., Martin, Emanuel H., Martynenko, Olga, Meave, Jorge A., Melo-Cruz, Omar, Mendoza, Casimiro, Merow, Cory, Mendoza, Abel Monteagudo, Moreno, Vanessa S., Mukul, Sharif A., Mundhenk, Philip, Nava-Miranda, María Guadalupe, Neill, David, Neldner, Victor J., Nevenic, Radovan V., Ngugi, Michael R., Niklaus, Pascal A., Oleksyn, Jacek, Ontikov, Petr, Ortiz-Malavasi, Edgar, Pan, Yude, Paquette, Alain, Parada-Gutierrez, Alexander, Parfenova, Elena I., Park, Minjee, Parren, Marc, Parthasarathy, Narayanaswamy, Peri, Pablo L., Pfautsch, Sebastian, Phillips, Oliver L., Picard, Nicolas, Piedade, Maria Teresa T. F., Piotto, Daniel, Pitman, Nigel C. A., Polo, Irina, Poorter, Lourens, Poulsen, Axel D., Pretzsch, Hans, Ramirez Arevalo, Freddy, Restrepo-Correa, Zorayda, Rodeghiero, Mirco, Rolim, Samir G., Roopsind, Anand, Rovero, Francesco, Rutishauser, Ervan, Saikia, Purabi, Salas-Eljatib, Christian, Saner, Philippe, Schall, Peter, Schepaschenko, Dmitry, Scherer-Lorenzen, Michael, Schmid, Bernhard, Schöngart, Jochen, Searle, Eric B., Seben, Vladimír, Serra-Diaz, Josep M., Sheil, Douglas, Shvidenko, Anatoly Z., Silva-Espejo, Javier E., Silveira, Marcos, Singh, James, Sist, Plinio, Slik, Ferry, Sonké, Bonaventure, Souza, Alexandre F., Miscicki, Stanislaw, Stereńczak, Krzysztof J., Svenning, Jens-Christian, Svoboda, Miroslav, Swanepoel, Ben, Targhetta, Natalia, Tchebakova, Nadja, ter Steege, Hans, Thomas, Raquel, Tikhonova, Elena, Umunay, Peter M., Usoltsev, Vladimir A., Valencia, Renato, Valladares, Fernando, van der Plas, Fons, Do, Tran Van, van Nuland, Michael E., Vasquez, Rodolfo M., Verbeeck, Hans, Viana, Helder, Vibrans, Alexander C., Vieira, Simone, von Gadow, Klaus, Wang, Hua-Feng, Watson, James V., Werner, Gijsbert D. A., Wiser, Susan K., Wittmann, Florian, Woell, Hannsjoerg, Wortel, Verginia, Zagt, Roderik, Zawiła-Niedźwiecki, Tomasz, Zhang, Chunyu, Zhao, Xiuhai, Zhou, Mo, Zhu, Zhi-Xin, Zo-Bi, Irie C., and Maynard, Daniel S.

Published
2023
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48. The historical Greenland Climate Network (GC-Net) curated and augmented level-1 dataset

Author

B. Vandecrux, J. E. Box, A. P. Ahlstrøm, S. B. Andersen, N. Bayou, W. T. Colgan, N. J. Cullen, R. S. Fausto, D. Haas-Artho, A. Heilig, D. A. Houtz, P. How, I. Iosifescu Enescu, N. B. Karlsson, R. Kurup Buchholz, K. D. Mankoff, D. McGrath, N. P. Molotch, B. Perren, M. K. Revheim, A. Rutishauser, K. Sampson, M. Schneebeli, S. Starkweather, S. Steffen, J. Weber, P. J. Wright, H. J. Zwally, and K. Steffen

Subjects
Environmental sciences, GE1-350, Geology, QE1-996.5
Abstract

The Greenland Climate Network (GC-Net) consists of 31 automatic weather stations (AWSs) at 30 sites across the Greenland Ice Sheet. The first site was initiated in 1990, and the project has operated almost continuously since 1995 under the leadership of the late Konrad Steffen. The GC-Net AWS measured air temperature, relative humidity, wind speed, atmospheric pressure, downward and reflected shortwave irradiance, net radiation, and ice and firn temperatures. The majority of the GC-Net sites were located in the ice sheet accumulation area (17 AWSs), while 11 AWSs were located in the ablation area, and two sites (three AWSs) were located close to the equilibrium line altitude. Additionally, three AWSs of similar design to the GC-Net AWS were installed by Konrad Steffen's team on the Larsen C ice shelf, Antarctica. After more than 3 decades of operation, the GC-Net AWSs are being decommissioned and replaced by new AWSs operated by the Geological Survey of Denmark and Greenland (GEUS). Therefore, making a reassessment of the historical GC-Net AWS data is necessary. We present a full reprocessing of the historical GC-Net AWS dataset with increased attention to the filtering of erroneous measurements, data correction and derivation of additional variables: continuous surface height, instrument heights, surface albedo, turbulent heat fluxes, and 10 m ice and firn temperatures. This new augmented GC-Net level-1 (L1) AWS dataset is now available at https://doi.org/10.22008/FK2/VVXGUT (Steffen et al., 2023) and will continue to be refined. The processing scripts, latest data and a data user forum are available at https://github.com/GEUS-Glaciology-and-Climate/GC-Net-level-1-data-processing (last access: 30 November 2023). In addition to the AWS data, a comprehensive compilation of valuable metadata is provided: maintenance reports, yearly pictures of the stations and the station positions through time. This unique dataset provides more than 320 station years of high-quality atmospheric data and is available following FAIR (findable, accessible, interoperable, reusable) data and code practices.

Published
2023
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49. A uniform human multimodal dataset for emotion perception and judgment

Author

Sai Sun, Runnan Cao, Ueli Rutishauser, Rongjun Yu, and Shuo Wang

Subjects
Science
Abstract

Abstract Face perception is a fundamental aspect of human social interaction, yet most research on this topic has focused on single modalities and specific aspects of face perception. Here, we present a comprehensive multimodal dataset for examining facial emotion perception and judgment. This dataset includes EEG data from 97 unique neurotypical participants across 8 experiments, fMRI data from 19 neurotypical participants, single-neuron data from 16 neurosurgical patients (22 sessions), eye tracking data from 24 neurotypical participants, behavioral and eye tracking data from 18 participants with ASD and 15 matched controls, and behavioral data from 3 rare patients with focal bilateral amygdala lesions. Notably, participants from all modalities performed the same task. Overall, this multimodal dataset provides a comprehensive exploration of facial emotion perception, emphasizing the importance of integrating multiple modalities to gain a holistic understanding of this complex cognitive process. This dataset serves as a key missing link between human neuroimaging and neurophysiology literature, and facilitates the study of neuropsychiatric populations.

Published
2023
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50. A cytotoxic-skewed immune set point predicts low neutralizing antibody levels after Zika virus infection

Author

McCarthy, Elizabeth E, Odorizzi, Pamela M, Lutz, Emma, Smullin, Carolyn P, Tenvooren, Iliana, Stone, Mars, Simmons, Graham, Hunt, Peter W, Feeney, Margaret E, Norris, Philip J, Busch, Michael P, Spitzer, Matthew H, and Rutishauser, Rachel L

Subjects
Biological Sciences, Biotechnology, Prevention, Infectious Diseases, Immunization, HIV/AIDS, Rare Diseases, Vaccine Related, Infection, Inflammatory and immune system, Good Health and Well Being, Antibodies, Neutralizing, Antibodies, Viral, Humans, Vaccination, Zika Virus, Zika Virus Infection, CP: Immunology, CyTOF, Zika virus, immune signatures, neutralizing antibodies, systems immunology, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

Although generating high neutralizing antibody levels is a key component of protective immunity after acute viral infection or vaccination, little is known about why some individuals generate high versus low neutralizing antibody titers. Here, we leverage the high-dimensional single-cell profiling capacity of mass cytometry to characterize the longitudinal cellular immune response to Zika virus (ZIKV) infection in viremic blood donors in Puerto Rico. During acute ZIKV infection, we identify widely coordinated responses across innate and adaptive immune cell lineages. High frequencies of multiple activated cell types during acute infection are associated with high titers of ZIKV neutralizing antibodies 6 months post-infection, while stable immune features suggesting a cytotoxic-skewed immune set point are associated with low titers. Our study offers insight into the coordination of immune responses and identifies candidate cellular biomarkers that may offer predictive value in vaccine efficacy trials aimed at inducing high levels of antiviral neutralizing antibodies.

Published
2022

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