21,285 results on '"Daum, A"'
Search Results
2. 2. Constantly on the Move: Practices and Ideas, 1792-1799
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Savage, Robert and Daum, Andreas W.
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- 2024
3. Index
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Savage, Robert and Daum, Andreas W.
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- 2024
4. Half Title Page, Title Page, Copyright, Dedication
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Savage, Robert and Daum, Andreas W.
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- 2024
5. 5. Delivering to the Public: In Paris and Civil Society, 1804-1827
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Savage, Robert and Daum, Andreas W.
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- 2024
6. 7. Between Cosmos and Fragments: The Final Years, 1840-1859
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Savage, Robert and Daum, Andreas W.
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- 2024
7. 4. Gaining a Picture of the Whole: The American Journey, 1799-1804
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Savage, Robert and Daum, Andreas W.
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- 2024
8. 1. Training the Mind: From Childhood to University, 1769-1792
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Savage, Robert and Daum, Andreas W.
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- 2024
9. 3. The Interaction of All Forces: Humboldt's Science
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Savage, Robert and Daum, Andreas W.
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- 2024
10. Notes
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Savage, Robert and Daum, Andreas W.
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- 2024
11. Acknowledgments
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Savage, Robert and Daum, Andreas W.
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- 2024
12. Introduction: Revisiting Alexander von Humboldt
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Savage, Robert and Daum, Andreas W.
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- 2024
13. Guide to Sources and Further Reading
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Savage, Robert and Daum, Andreas W.
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- 2024
14. 6. I Love What I Comprehend: In Changing Worlds, 1827-1840
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Savage, Robert and Daum, Andreas W.
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- 2024
15. Selected Bibliography
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Savage, Robert and Daum, Andreas W.
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- 2024
16. The Politics of Oil: A Study of Private Power and Democratic Directions by Robert Engler (review)
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Daum, Arnold R.
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- 2023
17. Oil on Stream! A History of Interstate Oil Pipe Line Company, 1909–1959 by John L. Loos (review)
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Daum, Arnold R.
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- 2023
18. A Century of Oil and Gas in Books: A Descriptive Bibliography comp. by E. B. Swanson (review)
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Daum, Arnold R.
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- 2023
19. Under Pressure: Altimeter-Aided ICP for 3D Maps Consistency
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Dubois, William, Samson, Nicolas, Daum, Effie, Laconte, Johann, and Pomerleau, François
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Computer Science - Robotics - Abstract
We propose a novel method to enhance the accuracy of the Iterative Closest Point (ICP) algorithm by integrating altitude constraints from a barometric pressure sensor. While ICP is widely used in mobile robotics for Simultaneous Localization and Mapping ( SLAM ), it is susceptible to drift, especially in underconstrained environments such as vertical shafts. To address this issue, we propose to augment ICP with altimeter measurements, reliably constraining drifts along the gravity vector. To demonstrate the potential of altimetry in SLAM , we offer an analysis of calibration procedures and noise sensitivity of various pressure sensors, improving measurements to centimeter-level accuracy. Leveraging this accuracy, we propose a novel ICP formulation that integrates altitude measurements along the gravity vector, thus simplifying the optimization problem to 3-Degree Of Freedom (DOF). Experimental results from real-world deployments demonstrate that our method reduces vertical drift by 84% and improves overall localization accuracy compared to state-of-the-art methods in non-planar environments., Comment: 6 pages + references, 5 figures, submitted to ICRA25
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- 2024
20. UAV-Assisted Self-Supervised Terrain Awareness for Off-Road Navigation
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Fortin, Jean-Michel, Gamache, Olivier, Fecteau, William, Daum, Effie, Larrivée-Hardy, William, Pomerleau, François, and Giguère, Philippe
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Computer Science - Robotics - Abstract
Terrain awareness is an essential milestone to enable truly autonomous off-road navigation. Accurately predicting terrain characteristics allows optimizing a vehicle's path against potential hazards. Recent methods use deep neural networks to predict traversability-related terrain properties in a self-supervised manner, relying on proprioception as a training signal. However, onboard cameras are inherently limited by their point-of-view relative to the ground, suffering from occlusions and vanishing pixel density with distance. This paper introduces a novel approach for self-supervised terrain characterization using an aerial perspective from a hovering drone. We capture terrain-aligned images while sampling the environment with a ground vehicle, effectively training a simple predictor for vibrations, bumpiness, and energy consumption. Our dataset includes 2.8 km of off-road data collected in forest environment, comprising 13 484 ground-based images and 12 935 aerial images. Our findings show that drone imagery improves terrain property prediction by 21.37 % on the whole dataset and 37.35 % in high vegetation, compared to ground robot images. We conduct ablation studies to identify the main causes of these performance improvements. We also demonstrate the real-world applicability of our approach by scouting an unseen area with a drone, planning and executing an optimized path on the ground., Comment: 7 pages, 5 figures, submitted to ICRA 2025
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- 2024
21. Neurospora intermedia from a traditional fermented food enables waste-to-food conversion.
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Maini Rekdal, Vayu, Villalobos-Escobedo, José, Rodriguez-Valeron, Nabila, Olaizola Garcia, Mikel, Prado Vásquez, Diego, Rosales, Alexander, Sörensen, Pia, Baidoo, Edward, Calheiros de Carvalho, Ana, Riley, Robert, Lipzen, Anna, He, Guifen, Yan, Mi, Haridas, Sajeet, Daum, Christopher, Yoshinaga, Yuko, Ng, Vivian, Grigoriev, Igor, Munk, Rasmus, Wijaya, Christofora, Nuraida, Lilis, Damayanti, Isty, Cruz-Morales, Pablo, and Keasling, Jay
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Fermentation ,Fermented Foods ,Neurospora ,Phylogeny ,Indonesia ,Food Microbiology ,Metagenomics ,Humans ,Metabolomics - Abstract
Fungal fermentation of food and agricultural by-products holds promise for improving food sustainability and security. However, the molecular basis of fungal waste-to-food upcycling remains poorly understood. Here we use a multi-omics approach to characterize oncom, a fermented food traditionally produced from soymilk by-products in Java, Indonesia. Metagenomic sequencing of samples from small-scale producers in Western Java indicated that the fungus Neurospora intermedia dominates oncom. Further transcriptomic, metabolomic and phylogenomic analysis revealed that oncom-derived N. intermedia utilizes pectin and cellulose degradation during fermentation and belongs to a genetically distinct subpopulation associated with human-generated by-products. Finally, we found that N. intermedia grew on diverse by-products such as fruit and vegetable pomace and plant-based milk waste, did not encode mycotoxins, and could create foods that were positively perceived by consumers outside Indonesia. These results showcase the traditional significance and future potential of fungal fermentation for creating delicious and nutritious foods from readily available by-products.
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- 2024
22. On Differentially Private 3D Medical Image Synthesis with Controllable Latent Diffusion Models
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Daum, Deniz, Osuala, Richard, Riess, Anneliese, Kaissis, Georgios, Schnabel, Julia A., and Di Folco, Maxime
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Generally, the small size of public medical imaging datasets coupled with stringent privacy concerns, hampers the advancement of data-hungry deep learning models in medical imaging. This study addresses these challenges for 3D cardiac MRI images in the short-axis view. We propose Latent Diffusion Models that generate synthetic images conditioned on medical attributes, while ensuring patient privacy through differentially private model training. To our knowledge, this is the first work to apply and quantify differential privacy in 3D medical image generation. We pre-train our models on public data and finetune them with differential privacy on the UK Biobank dataset. Our experiments reveal that pre-training significantly improves model performance, achieving a Fr\'echet Inception Distance (FID) of 26.77 at $\epsilon=10$, compared to 92.52 for models without pre-training. Additionally, we explore the trade-off between privacy constraints and image quality, investigating how tighter privacy budgets affect output controllability and may lead to degraded performance. Our results demonstrate that proper consideration during training with differential privacy can substantially improve the quality of synthetic cardiac MRI images, but there are still notable challenges in achieving consistent medical realism.
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- 2024
23. Non-uniformity is All You Need: Efficient and Timely Encrypted Traffic Classification With ECHO
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Daum, Shilo, Shapira, Tal, Bremler-Barr, Anat, and Hay, David
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Computer Science - Networking and Internet Architecture ,Computer Science - Cryptography and Security ,Computer Science - Machine Learning - Abstract
With 95% of Internet traffic now encrypted, an effective approach to classifying this traffic is crucial for network security and management. This paper introduces ECHO -- a novel optimization process for ML/DL-based encrypted traffic classification. ECHO targets both classification time and memory utilization and incorporates two innovative techniques. The first component, HO (Hyperparameter Optimization of binnings), aims at creating efficient traffic representations. While previous research often uses representations that map packet sizes and packet arrival times to fixed-sized bins, we show that non-uniform binnings are significantly more efficient. These non-uniform binnings are derived by employing a hyperparameter optimization algorithm in the training stage. HO significantly improves accuracy given a required representation size, or, equivalently, achieves comparable accuracy using smaller representations. Then, we introduce EC (Early Classification of traffic), which enables faster classification using a cascade of classifiers adapted for different exit times, where classification is based on the level of confidence. EC reduces the average classification latency by up to 90\%. Remarkably, this method not only maintains classification accuracy but also, in certain cases, improves it. Using three publicly available datasets, we demonstrate that the combined method, Early Classification with Hyperparameter Optimization (ECHO), leads to a significant improvement in classification efficiency.
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- 2024
24. Metatranscriptomes of California grassland soil microbial communities in response to rewetting.
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Chuckran, Peter, Estera-Molina, Katerina, Huntemann, Marcel, Foster, Brian, Roux, Simon, Mukherjee, Supratim, Hajek, Patrick, Reddy, TBK, Daum, Chris, Chen, I-Min, Pennacchio, Christa, Eloe-Fadrosh, Emiley, Dijkstra, Paul, Firestone, Mary, Blazewicz, Steven, and Pett-Ridge, Jennifer
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biogeochemistry ,metatranscriptomics - Abstract
When very dry soil is rewet, rapid stimulation of microbial activity has important implications for ecosystem biogeochemistry, yet associated changes in microbial transcription are poorly known. Here, we present metatranscriptomes of California annual grassland soil microbial communities, collected over 1 week from soils rewet after a summer drought-providing a time series of short-term transcriptional response during rewetting.
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- 2024
25. FoMo: A Proposal for a Multi-Season Dataset for Robot Navigation in For\^et Montmorency
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Boxan, Matěj, Krawciw, Alexander, Daum, Effie, Qiao, Xinyuan, Lilge, Sven, Barfoot, Timothy D., and Pomerleau, François
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Computer Science - Robotics - Abstract
In this paper, we propose the FoMo (For\^et Montmorency) dataset: a comprehensive, multi-season data collection. Located in the Montmorency Forest, Quebec, Canada, our dataset will capture a rich variety of sensory data over six distinct trajectories totaling 6 kilometers, repeated through different seasons to accumulate 42 kilometers of recorded data. The boreal forest environment increases the diversity of datasets for mobile robot navigation. This proposed dataset will feature a broad array of sensor modalities, including lidar, radar, and a navigation-grade Inertial Measurement Unit (IMU), against the backdrop of challenging boreal forest conditions. Notably, the FoMo dataset will be distinguished by its inclusion of seasonal variations, such as changes in tree canopy and snow depth up to 2 meters, presenting new challenges for robot navigation algorithms. Alongside, we will offer a centimeter-level accurate ground truth, obtained through Post Processed Kinematic (PPK) Global Navigation Satellite System (GNSS) correction, facilitating precise evaluation of odometry and localization algorithms. This work aims to spur advancements in autonomous navigation, enabling the development of robust algorithms capable of handling the dynamic, unstructured environments characteristic of boreal forests. With a public odometry and localization leaderboard and a dedicated software suite, we invite the robotics community to engage with the FoMo dataset by exploring new frontiers in robot navigation under extreme environmental variations. We seek feedback from the community based on this proposal to make the dataset as useful as possible. For further details and supplementary materials, please visit https://norlab-ulaval.github.io/FoMo-website/., Comment: Accepted to the IEEE ICRA Workshop on Field Robotics 2024
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- 2024
26. Migrating Software Systems towards Post-Quantum-Cryptography -- A Systematic Literature Review
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Näther, Christian, Herzinger, Daniel, Gazdag, Stefan-Lukas, Steghöfer, Jan-Philipp, Daum, Simon, and Loebenberger, Daniel
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Computer Science - Cryptography and Security - Abstract
Networks such as the Internet are essential for our connected world. Quantum computing poses a threat to this heterogeneous infrastructure since it threatens fundamental security mechanisms. Therefore, a migration to post-quantum-cryptography (PQC) is necessary for networks and their components. At the moment, there is little knowledge on how such migrations should be structured and implemented in practice. Our systematic literature review addresses migration approaches for IP networks towards PQC. It surveys papers about the migration process and exemplary real-world software system migrations. On the process side, we found that terminology, migration steps, and roles are not defined precisely or consistently across the literature. Still, we identified four major phases and appropriate substeps which we matched with also emerging archetypes of roles. In terms of real-world migrations, we see that reports used several different PQC implementations and hybrid solutions for migrations of systems belonging to a wide range of system types. Across all papers we noticed three major challenges for adopters: missing experience of PQC and a high realization effort, concerns about the security of the upcoming system, and finally, high complexity. Our findings indicate that recent standardization efforts already push quantum-safe networking forward. However, the literature is still not in consensus about definitions and best practices. Implementations are mostly experimental and not necessarily practical, leading to an overall chaotic situation. To better grasp this fast moving field of (applied) research, our systematic literature review provides a comprehensive overview of its current state and serves as a starting point for delving into the matter of PQC migration., Comment: 2 figures, 12 tables, 21 pages
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- 2024
27. Measurement of groomed event shape observables in deep-inelastic electron-proton scattering at HERA
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The H1 collaboration, Andreev, V., Arratia, M., Baghdasaryan, A., Baty, A., Begzsuren, K., Bolz, A., Boudry, V., Brandt, G., Britzger, D., Buniatyan, A., Bystritskaya, L., Campbell, A. J., Avila, K. B. Cantun, Cerny, K., Chekelian, V., Chen, Z., Contreras, J. G., Cvach, J., Dainton, J. B., Daum, K., Deshpande, A., Diaconu, C., Drees, A., Eckerlin, G., Egli, S., Elsen, E., Favart, L., Fedotov, A., Feltesse, J., Fleischer, M., Fomenko, A., Gal, C., Gayler, J., Goerlich, L., Gogitidze, N., Gouzevitch, M., Grab, C., Greenshaw, T., Grindhammer, G., Haidt, D., Henderson, R. C. W., Hessler, J., Hladký, J., Hoffmann, D., Horisberger, R., Hreus, T., Huber, F., Jacobs, P. M., Jacquet, M., Janssen, T., Jung, A. W., Katzy, J., Kiesling, C., Klein, M., Kleinwort, C., Klest, H. T., Kogler, R., Kostka, P., Kretzschmar, J., Krücker, D., Krüger, K., Landon, M. P. J., Lange, W., Laycock, P., Lee, S. H., Levonian, S., Li, W., Lin, J., Lipka, K., List, B., List, J., Lobodzinski, B., Long, O. R., Malinovski, E., Martyn, H. -U., Maxfield, S. J., Mehta, A., Meyer, A. B., Meyer, J., Mikocki, S., Mikuni, V. M., Mondal, M. M., Müller, K., Nachman, B., Naumann, Th., Newman, P. R., Niebuhr, C., Nowak, G., Olsson, J. E., Ozerov, D., Park, S., Pascaud, C., Patel, G. D., Perez, E., Petrukhin, A., Picuric, I., Pitzl, D., Polifka, R., Preins, S., Radescu, V., Raicevic, N., Ravdandorj, T., Reichelt, D., Reimer, P., Rizvi, E., Robmann, P., Roosen, R., Rostovtsev, A., Rotaru, M., Sankey, D. P. C., Sauter, M., Sauvan, E., Schmitt, S., Schmookler, B. A., Schnell, G., Schoeffel, L., Schöning, A., Schumann, S., Sefkow, F., Shushkevich, S., Soloviev, Y., Sopicki, P., South, D., Specka, A., Steder, M., Stella, B., Stöcker, L., Straumann, U., Sun, C., Sykora, T., Thompson, P. D., Acosta, F. Torales, Traynor, D., Tseepeldorj, B., Tu, Z., Tustin, G., Valkárová, A., Vallée, C., Van Mechelen, P., Wegener, D., Wünsch, E., Žáček, J., Zhang, J., Zhang, Z., Žlebčík, R., Zohrabyan, H., and Zomer, F.
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High Energy Physics - Experiment ,High Energy Physics - Phenomenology ,Nuclear Experiment - Abstract
The H1 Collaboration at HERA reports the first measurement of groomed event shape observables in deep inelastic electron-proton scattering (DIS) at $\sqrt{s}=319$ GeV, using data recorded between the years 2003 and 2007 with an integrated luminosity of $351$ pb$^{-1}$. Event shapes provide incisive probes of perturbative and non-perturbative QCD. Grooming techniques have been used for jet measurements in hadronic collisions; this paper presents the first application of grooming to DIS data. The analysis is carried out in the Breit frame, utilizing the novel Centauro jet clustering algorithm that is designed for DIS event topologies. Events are required to have squared momentum-transfer $Q^2 > 150$ GeV$^2$ and inelasticity $ 0.2 < y < 0.7$. We report measurements of the production cross section of groomed event 1-jettiness and groomed invariant mass for several choices of grooming parameter. Monte Carlo model calculations and analytic calculations based on Soft Collinear Effective Theory are compared to the measurements., Comment: 32 pages, 17 tables, 7 figures, version as accepted by EPJ C
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- 2024
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28. Measurement of the 1-jettiness event shape observable in deep-inelastic electron-proton scattering at HERA
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The H1 collaboration, Andreev, V., Arratia, M., Baghdasaryan, A., Baty, A., Begzsuren, K., Bolz, A., Boudry, V., Brandt, G., Britzger, D., Buniatyan, A., Bystritskaya, L., Campbell, A. J., Avila, K. B. Cantun, Cerny, K., Chekelian, V., Chen, Z., Contreras, J. G., Cvach, J., Dainton, J. B., Daum, K., Deshpande, A., Diaconu, C., Drees, A., Eckerlin, G., Egli, S., Elsen, E., Favart, L., Fedotov, A., Feltesse, J., Fleischer, M., Fomenko, A., Gal, C., Gayler, J., Goerlich, L., Gogitidze, N., Gouzevitch, M., Grab, C., Greenshaw, T., Grindhammer, G., Haidt, D., Henderson, R. C. W., Hessler, J., Hladký, J., Hoffmann, D., Horisberger, R., Hreus, T., Huber, F., Jacobs, P. M., Jacquet, M., Janssen, T., Jung, A. W., Katzy, J., Kiesling, C., Klein, M., Kleinwort, C., Klest, H. T., Kluth, S., Kogler, R., Kostka, P., Kretzschmar, J., Krücker, D., Krüger, K., Landon, M. P. J., Lange, W., Laycock, P., Lee, S. H., Levonian, S., Li, W., Lin, J., Lipka, K., List, B., List, J., Lobodzinski, B., Long, O. R., Malinovski, E., Martyn, H. -U., Maxfield, S. J., Mehta, A., Meyer, A. B., Meyer, J., Mikocki, S., Mikuni, V. M., Mondal, M. M., Müller, K., Nachman, B., Naumann, Th., Newman, P. R., Niebuhr, C., Nowak, G., Olsson, J. E., Ozerov, D., Park, S., Pascaud, C., Patel, G. D., Perez, E., Petrukhin, A., Picuric, I., Pitzl, D., Polifka, R., Preins, S., Radescu, V., Raicevic, N., Ravdandorj, T., Reichelt, D., Reimer, P., Rizvi, E., Robmann, P., Roosen, R., Rostovtsev, A., Rotaru, M., Sankey, D. P. C., Sauter, M., Sauvan, E., Schmitt, S., Schmookler, B. A., Schnell, G., Schoeffel, L., Schöning, A., Schumann, S., Sefkow, F., Shushkevich, S., Soloviev, Y., Sopicki, P., South, D., Specka, A., Steder, M., Stella, B., Stöcker, L., Straumann, U., Sun, C., Sykora, T., Thompson, P. D., Acosta, F. Torales, Traynor, D., Tseepeldorj, B., Tu, Z., Tustin, G., Valkárová, A., Vallée, C., Van Mechelen, P., Wegener, D., Wünsch, E., Žáček, J., Zhang, J., Zhang, Z., Žlebčík, R., Zohrabyan, H., and Zomer, F.
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High Energy Physics - Experiment ,High Energy Physics - Phenomenology ,Nuclear Experiment - Abstract
The H1 Collaboration reports the first measurement of the 1-jettiness event shape observable $\tau_1^b$ in neutral-current deep-inelastic electron-proton scattering (DIS). The observable $\tau_1^b$ is equivalent to a thrust observable defined in the Breit frame. The data sample was collected at the HERA $ep$ collider in the years 2003-2007 with center-of-mass energy of $\sqrt{s}=319\,\text{GeV}$, corresponding to an integrated luminosity of $351.1\,\text{pb}^{-1}$. Triple differential cross sections are provided as a function of $\tau_1^b$, event virtuality $Q^2$, and inelasticity $y$, in the kinematic region $Q^2>150\,\text{GeV}^{2}$. Single differential cross section are provided as a function of $\tau_1^b$ in a limited kinematic range. Double differential cross sections are measured, in contrast, integrated over $\tau_1^b$ and represent the inclusive neutral-current DIS cross section measured as a function of $Q^2$ and $y$. The data are compared to a variety of predictions and include classical and modern Monte Carlo event generators, predictions in fixed-order perturbative QCD where calculations up to $\mathcal{O}(\alpha_s^3)$ are available for $\tau_1^b$ or inclusive DIS, and resummed predictions at next-to-leading logarithmic accuracy matched to fixed order predictions at $\mathcal{O}(\alpha_s^2)$. These comparisons reveal sensitivity of the 1-jettiness observable to QCD parton shower and resummation effects, as well as the modeling of hadronization and fragmentation. Within their range of validity, the fixed-order predictions provide a good description of the data. Monte Carlo event generators are predictive over the full measured range and hence their underlying models and parameters can be constrained by comparing to the presented data., Comment: 45 pages, 38 tables, 13 figures
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- 2024
29. Observation and differential cross section measurement of neutral current DIS events with an empty hemisphere in the Breit frame
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The H1 collaboration, Andreev, V., Arratia, M., Baghdasaryan, A., Baty, A., Begzsuren, K., Bolz, A., Boudry, V., Brandt, G., Britzger, D., Buniatyan, A., Bystritskaya, L., Campbell, A. J., Avila, K. B. Cantun, Cerny, K., Chekelian, V., Chen, Z., Contreras, J. G., Cvach, J., Dainton, J. B., Daum, K., Deshpande, A., Diaconu, C., Drees, A., Eckerlin, G., Egli, S., Elsen, E., Favart, L., Fedotov, A., Feltesse, J., Fleischer, M., Fomenko, A., Gal, C., Gayler, J., Goerlich, L., Gogitidze, N., Gouzevitch, M., Grab, C., Greenshaw, T., Grindhammer, G., Haidt, D., Henderson, R. C. W., Hessler, J., Hladký, J., Hoffmann, D., Horisberger, R., Hreus, T., Huber, F., Jacobs, P. M., Jacquet, M., Janssen, T., Jung, A. W., Katzy, J., Kiesling, C., Klein, M., Kleinwort, C., Klest, H. T., Kluth, S., Kogler, R., Kostka, P., Kretzschmar, J., Krücker, D., Krüger, K., Landon, M. P. J., Lange, W., Laycock, P., Lee, S. H., Levonian, S., Li, W., Lin, J., Lipka, K., List, B., List, J., Lobodzinski, B., Long, O. R., Malinovski, E., Martyn, H. -U., Maxfield, S. J., Mehta, A., Meyer, A. B., Meyer, J., Mikocki, S., Mikuni, V. M., Mondal, M. M., Müller, K., Nachman, B., Naumann, Th., Newman, P. R., Niebuhr, C., Nowak, G., Olsson, J. E., Ozerov, D., Park, S., Pascaud, C., Patel, G. D., Perez, E., Petrukhin, A., Picuric, I., Pitzl, D., Polifka, R., Preins, S., Radescu, V., Raicevic, N., Ravdandorj, T., Reichelt, D., Reimer, P., Rizvi, E., Robmann, P., Roosen, R., Rostovtsev, A., Rotaru, M., Sankey, D. P. C., Sauter, M., Sauvan, E., Schmitt, S., Schmookler, B. A., Schnell, G., Schoeffel, L., Schöning, A., Schumann, S., Sefkow, F., Shushkevich, S., Soloviev, Y., Sopicki, P., South, D., Specka, A., Steder, M., Stella, B., Stöcker, L., Straumann, U., Sun, C., Sykora, T., Thompson, P. D., Acosta, F. Torales, Traynor, D., Tseepeldorj, B., Tu, Z., Tustin, G., Valkárová, A., Vallée, C., Van Mechelen, P., Wegener, D., Wünsch, E., Žáček, J., Zhang, J., Zhang, Z., Žlebčík, R., Zohrabyan, H., and Zomer, F.
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High Energy Physics - Experiment ,High Energy Physics - Phenomenology ,Nuclear Experiment - Abstract
The Breit frame provides a natural frame to analyze lepton-proton scattering events. In this reference frame, the parton model hard interactions between a quark and an exchanged boson defines the coordinate system such that the struck quark is back-scattered along the virtual photon momentum direction. In Quantum Chromodynamics (QCD), higher order perturbative or non-perturbative effects can change this picture drastically. As Bjorken-$x$ decreases below one half, a rather peculiar event signature is predicted with increasing probability, where no radiation is present in one of the two Breit-frame hemispheres and all emissions are to be found in the other hemisphere. At higher orders in $\alpha_s$ or in the presence of soft QCD effects, predictions of the rate of these events are far from trivial, and that motivates measurements with real data. We report on the first observation of the empty current hemisphere events in electron-proton collisions at the HERA collider using data recorded with the H1 detector at a center-of-mass energy of 319 GeV. The fraction of inclusive neutral-current DIS events with an empty hemisphere is found to be $0.0112 \pm 3.9\,\%_\text{stat} \pm 4.5\,\%_\text{syst} \pm 1.6\,\%_\text{mod}$ in the selected kinematic region of $150< Q^2<1500$ GeV$^2$ and inelasticity $0.14< y<0.7$. The data sample corresponds to an integrated luminosity of 351.1 pb$^{-1}$, sufficient to enable differential cross section measurements of these events. The results show an enhanced discriminating power at lower Bjorken-$x$ among different Monte Carlo event generator predictions., Comment: 13 pages, 5 figures, 2 Tables. This version as accepted for publication
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- 2024
- Full Text
- View/download PDF
30. Incident Beamline Design for a Modern Cold Triple Axis Spectrometer at the High Flux Isotope Reactor
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Granroth, G. E., Daum, M., Aczel, A. A., Williams, T. J., Winn, B., Fernandez-Baca, J. A., Mourigal, M., and Lumsden, M. D.
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Physics - Instrumentation and Detectors - Abstract
A modern cold triple axis spectrometer is being planned for the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory. Here, we describe the design of an incident beamline that will put a flux of $\sim 10^8\mathrm{\frac{n}{cm^2 s}}$ on a sample with an area of 2 cm x 2 cm. It takes current physical constraints at HFIR into account and it can accommodate both single and multiplexed analyzer-detector secondary spectrometers and large superconducting magnets. The proposed incident beamline includes a multi-channel guide with horizontal focusing, a neutron velocity selector, components to facilitate an incident beam polarization option, and a double-focusing pyrolytic graphite monochromator. This work describes the process of optimizing the guide system and monochromator and summarizes the expected performance of the incident beamline for non-polarized operation.
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- 2024
- Full Text
- View/download PDF
31. Genomes of multicellular algal sisters to land plants illuminate signaling network evolution
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Feng, Xuehuan, Zheng, Jinfang, Irisarri, Iker, Yu, Huihui, Zheng, Bo, Ali, Zahin, de Vries, Sophie, Keller, Jean, Fürst-Jansen, Janine MR, Dadras, Armin, Zegers, Jaccoline MS, Rieseberg, Tim P, Dhabalia Ashok, Amra, Darienko, Tatyana, Bierenbroodspot, Maaike J, Gramzow, Lydia, Petroll, Romy, Haas, Fabian B, Fernandez-Pozo, Noe, Nousias, Orestis, Li, Tang, Fitzek, Elisabeth, Grayburn, W Scott, Rittmeier, Nina, Permann, Charlotte, Rümpler, Florian, Archibald, John M, Theißen, Günter, Mower, Jeffrey P, Lorenz, Maike, Buschmann, Henrik, von Schwartzenberg, Klaus, Boston, Lori, Hayes, Richard D, Daum, Chris, Barry, Kerrie, Grigoriev, Igor V, Wang, Xiyin, Li, Fay-Wei, Rensing, Stefan A, Ben Ari, Julius, Keren, Noa, Mosquna, Assaf, Holzinger, Andreas, Delaux, Pierre-Marc, Zhang, Chi, Huang, Jinling, Mutwil, Marek, de Vries, Jan, and Yin, Yanbin
- Subjects
Plant Biology ,Biological Sciences ,Genetics ,Life on Land ,Signal Transduction ,Embryophyta ,Evolution ,Molecular ,Phylogeny ,Gene Regulatory Networks ,Genome ,Genome ,Plant ,Medical and Health Sciences ,Developmental Biology ,Agricultural biotechnology ,Bioinformatics and computational biology - Abstract
Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.
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- 2024
32. Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems
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Auer, Lucas, Buée, Marc, Fauchery, Laure, Lombard, Vincent, Barry, Kerry W, Clum, Alicia, Copeland, Alex, Daum, Chris, Foster, Brian, LaButti, Kurt, Singan, Vasanth, Yoshinaga, Yuko, Martineau, Christine, Alfaro, Manuel, Castillo, Federico J, Imbert, J Bosco, Ramírez, Lucia, Castanera, Raúl, Pisabarro, Antonio G, Finlay, Roger, Lindahl, Björn, Olson, Ake, Séguin, Armand, Kohler, Annegret, Henrissat, Bernard, Grigoriev, Igor V, and Martin, Francis M
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Microbiology ,Biological Sciences ,Ecology ,Genetics ,Life on Land ,Forests ,Fungi ,Soil Microbiology ,Transcriptome ,Mycorrhizae ,Gene Expression Profiling ,Gene Expression Regulation ,Fungal ,Nitrogen ,Soil ,Ecosystem ,RNA ,Messenger ,forest soil ,functional traits ,fungal guilds ,metatranscriptomics ,organic matter degradation ,Agricultural and Veterinary Sciences ,Plant Biology & Botany ,Plant biology ,Climate change impacts and adaptation ,Ecological applications - Abstract
Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.
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- 2024
33. Major impacts of widespread structural variation on sorghum.
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Zhang, Zhihai, Gomes Viana, Joao, Zhang, Bosen, Walden, Kimberly, Müller Paul, Hans, Moose, Stephen, Morris, Geoffrey, Daum, Chris, Barry, Kerrie, Shakoor, Nadia, and Hudson, Matthew
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Genetic Variation ,Sorghum ,Genome-Wide Association Study ,Plant Breeding ,Phenotype ,Edible Grain ,Polymorphism ,Single Nucleotide - Abstract
Genetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent genome analyses in plants reveal many structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent of the impact of SVs on global trait variation, as well as their utility in genome-wide selection, is not yet understood. In this study, we built an SV data set based on whole-genome resequencing of diverse sorghum lines (n = 363), validated the correlation of photoperiod sensitivity and variety type, and identified SV hotspots underlying the divergent evolution of cellulosic and sweet sorghum. In addition, we showed the complementary contribution of SVs for heritability of traits related to sorghum adaptation. Importantly, inclusion of SV polymorphisms in association studies revealed genotype-phenotype associations not observed with SNPs alone. Three-way genome-wide association studies (GWAS) based on whole-genome SNP, SV, and integrated SNP + SV data sets showed substantial associations between SVs and sorghum traits. The addition of SVs to GWAS substantially increased heritability estimates for some traits, indicating their important contribution to functional allelic variation at the genome level. Our discovery of the widespread impacts of SVs on heritable gene expression variation could render a plausible mechanism for their disproportionate impact on phenotypic variation. This study expands our knowledge of SVs and emphasizes the extensive impacts of SVs on sorghum.
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- 2024
34. A large sequenced mutant library – valuable reverse genetic resource that covers 98% of sorghum genes
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Jiao, Yinping, Nigam, Deepti, Barry, Kerrie, Daum, Chris, Yoshinaga, Yuko, Lipzen, Anna, Khan, Adil, Parasa, Sai‐Praneeth, Wei, Sharon, Lu, Zhenyuan, Tello‐Ruiz, Marcela K, Dhiman, Pallavi, Burow, Gloria, Hayes, Chad, Chen, Junping, Brandizzi, Federica, Mortimer, Jenny, Ware, Doreen, and Xin, Zhanguo
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Human Genome ,Sorghum ,Reverse Genetics ,Plant Breeding ,Mutation ,Phenotype ,Edible Grain ,Ethyl Methanesulfonate ,Genome ,Plant ,ethyl methyl sulfone mutants ,sorghum ,resequencing ,Biochemistry and Cell Biology ,Plant Biology ,Plant Biology & Botany ,Biochemistry and cell biology ,Plant biology - Abstract
Mutant populations are crucial for functional genomics and discovering novel traits for crop breeding. Sorghum, a drought and heat-tolerant C4 species, requires a vast, large-scale, annotated, and sequenced mutant resource to enhance crop improvement through functional genomics research. Here, we report a sorghum large-scale sequenced mutant population with 9.5 million ethyl methane sulfonate (EMS)-induced mutations that covered 98% of sorghum's annotated genes using inbred line BTx623. Remarkably, a total of 610 320 mutations within the promoter and enhancer regions of 18 000 and 11 790 genes, respectively, can be leveraged for novel research of cis-regulatory elements. A comparison of the distribution of mutations in the large-scale mutant library and sorghum association panel (SAP) provides insights into the influence of selection. EMS-induced mutations appeared to be random across different regions of the genome without significant enrichment in different sections of a gene, including the 5' UTR, gene body, and 3'-UTR. In contrast, there were low variation density in the coding and UTR regions in the SAP. Based on the Ka /Ks value, the mutant library (~1) experienced little selection, unlike the SAP (0.40), which has been strongly selected through breeding. All mutation data are publicly searchable through SorbMutDB (https://www.depts.ttu.edu/igcast/sorbmutdb.php) and SorghumBase (https://sorghumbase.org/). This current large-scale sequence-indexed sorghum mutant population is a crucial resource that enriched the sorghum gene pool with novel diversity and a highly valuable tool for the Poaceae family, that will advance plant biology research and crop breeding.
- Published
- 2024
35. Monte-Carlo ray-tracing studies of multiplexed prismatic graphite analyzers for the cold-neutron triple-axis spectrometer at the High Flux Isotope Reactor
- Author
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Desai, Adit S., Williams, Travis J., Daum, Marcus, Sala, Gabriele, Aczel, Adam A., Granroth, Garrett E., and Mourigal, Martin
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Physics - Instrumentation and Detectors ,Condensed Matter - Materials Science ,Condensed Matter - Strongly Correlated Electrons - Abstract
A modern cold triple-axis spectrometer to study quantum condensed matter systems is planned for the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory. Here, we describe the conceptual principles and design of a secondary spectrometer using a multiplexed, prismatic analyzer system relying on graphite crystals and inspired by the successful implementation of the Continuous Angle Multiple Energy Analysis (CAMEA) spectrometers at the Paul Scherrer Institute. This project is currently known as MANTA for Multi-analyzer Neutron Triple-Axis. We report Monte-Carlo ray-tracing simulations on a simple but realistic sample scattering kernel to further illustrate the prismatic analyzer concept's workings, calibration, and performance. Then, we introduce a new statistical analysis approach based on the prismatic analyzer concept to improve the number of final energies measured on the spectrometer. We also study possible evolutions in the CAMEA design relevant for MANTA., Comment: 11 pages, 11 figures
- Published
- 2023
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36. Introduction
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Daum, Andreas W., Hake, Sabine, and Prager, Brad
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- 2016
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37. On Differentially Private 3D Medical Image Synthesis with Controllable Latent Diffusion Models
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Daum, Deniz, Osuala, Richard, Riess, Anneliese, Kaissis, Georgios, Schnabel, Julia A., Di Folco, Maxime, Goos, Gerhard, Series Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Mukhopadhyay, Anirban, editor, Oksuz, Ilkay, editor, Engelhardt, Sandy, editor, Mehrof, Dorit, editor, and Yuan, Yixuan, editor
- Published
- 2025
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38. Physical Fitness Testing Concerns: Bullying and Inclusion
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Bittner, Melissa, Daum, David N., Moore, Tonya, Patterson, Debra, Wilson-Graham, Dianne, and Suppe, Patricia
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California. Department of Education -- Analysis -- Surveys ,United States. Centers for Disease Control and Prevention -- Surveys -- Analysis ,Disability -- Surveys -- Analysis ,Bullying -- Surveys -- Analysis ,Disabled students -- Surveys ,Discrimination in education -- Analysis -- Surveys ,Physical fitness -- Surveys -- Analysis ,Education ,Sports and fitness ,United Kingdom. Gender Recognition Act 2004 - Abstract
In February 2020, California Governor Gavin Newsom's proposed budget recommended suspending the state-mandated physical fitness test (Fitness Gram*) for three years due to concerns over bullying and test discrimination against students who identify as gender non-binary and students with disabilities. The purpose of this study was to gain an understanding of California physical educators' perceptions of the state-mandated physical fitness assessment. Snowball sampling was used to recruit 1,082 participants who completed a survey with quantitative and open-ended questions. Analysis of the open-ended questions indicated the two main themes were 'how to improve fitness testing' and 'challenges in fitness testing.' It is imperative to consider the needs of all students, including those who identify as gender non-binary or have a disability, and ensure physical fitness testing is conducted in a, Introduction The FitnessGram[R] was developed by The Cooper Institute and is used to identify student progress related to the Healthy Fitness Zone[R]. It is estimated that FitnessGram[R] is used by [...]
- Published
- 2024
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39. A surgical activity model of laparoscopic cholecystectomy for co-operation with collaborative robots
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Younis, R., Yamlahi, A., Bodenstedt, S., Scheikl, PM., Kisilenko, A., Daum, M., Schulze, A., Wise, P. A., Nickel, F., Mathis-Ullrich, F., Maier-Hein, L., Müller-Stich, BP., Speidel, S., Distler, M., Weitz, J., and Wagner, M.
- Published
- 2024
- Full Text
- View/download PDF
40. RTS-GT: Robotic Total Stations Ground Truthing dataset
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Vaidis, Maxime, Shahraji, Mohsen Hassanzadeh, Daum, Effie, Dubois, William, Giguère, Philippe, and Pomerleau, François
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Computer Science - Robotics - Abstract
Numerous datasets and benchmarks exist to assess and compare Simultaneous Localization and Mapping (SLAM) algorithms. Nevertheless, their precision must follow the rate at which SLAM algorithms improved in recent years. Moreover, current datasets fall short of comprehensive data-collection protocol for reproducibility and the evaluation of the precision or accuracy of the recorded trajectories. With this objective in mind, we proposed the Robotic Total Stations Ground Truthing dataset (RTS-GT) dataset to support localization research with the generation of six-Degrees Of Freedom (DOF) ground truth trajectories. This novel dataset includes six-DOF ground truth trajectories generated using a system of three Robotic Total Stations (RTSs) tracking moving robotic platforms. Furthermore, we compare the performance of the RTS-based system to a Global Navigation Satellite System (GNSS)-based setup. The dataset comprises around sixty experiments conducted in various conditions over a period of 17 months, and encompasses over 49 kilometers of trajectories, making it the most extensive dataset of RTS-based measurements to date. Additionally, we provide the precision of all poses for each experiment, a feature not found in the current state-of-the-art datasets. Our results demonstrate that RTSs provide measurements that are 22 times more stable than GNSS in various environmental settings, making them a valuable resource for SLAM benchmark development., Comment: 7 pages; Accepted to ICRA 2024
- Published
- 2023
41. Benchmarking ground truth trajectories with robotic total stations
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Daum, Effie, Vaidis, Maxime, and Pomerleau, François
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Computer Science - Robotics - Abstract
Benchmarks stand as vital cornerstones in elevating SLAM algorithms within mobile robotics. Consequently, ensuring accurate and reproducible ground truth generation is vital for fair evaluation. A majority of outdoor ground truths are generated by GNSS, which can lead to discrepancies over time, especially in covered areas. However, research showed that RTS setups are more precise and can alternatively be used to generate these ground truths. In our work, we compare both RTS and GNSS systems' precision and repeatability through a set of experiments conducted weeks and months apart in the same area. We demonstrated that RTS setups give more reproducible results, with disparities having a median value of 8.6 mm compared to a median value of 10.6 cm coming from a GNSS setup. These results highlight that RTS can be considered to benchmark process for SLAM algorithms with higher precision., Comment: Accepted and presented at IROS23, Workshop on Methods for Objective Comparison of Results in Intelligent Robotics Research
- Published
- 2023
42. Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert.
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Nguyen, Thuy M, Pombubpa, Nuttapon, Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Roux, Simon, Palaniappan, Krishnaveni, Varghese, Neha, Mukherjee, Supratim, Reddy, TBK, Daum, Chris, Copeland, Alex, Chen, I-Min A, Ivanova, Natalia N, Kyrpides, Nikos C, Harmon-Smith, Miranda, Eloe-Fadrosh, Emiley A, Pietrasiak, Nicole, Stajich, Jason E, and Hom, Erik FY
- Subjects
metagenomics ,soil crusts ,Biochemistry and Cell Biology ,Genetics ,Microbiology - Abstract
We present six whole community shotgun metagenomic sequencing data sets of two types of biological soil crusts sampled at the ecotone of the Mojave Desert and Colorado Desert in California. These data will help us understand the diversity and function of biocrust microbial communities, which are essential for desert ecosystems.
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- 2024
43. Metatranscriptomes of two biological soil crust types from the Mojave desert in response to wetting.
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Nguyen, Thuy M, Pombubpa, Nuttapon, Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Roux, Simon, Palaniappan, Krishnaveni, Varghese, Neha, Mukherjee, Supratim, Reddy, TBK, Daum, Chris, Copeland, Alex, Chen, I-Min A, Ivanova, Natalia N, Kyrpides, Nikos C, Harmon-Smith, Miranda, Eloe-Fadrosh, Emiley A, Pietrasiak, Nicole, Stajich, Jason E, and Hom, Erik FY
- Subjects
Microbiology ,Biological Sciences ,Genetics ,RNA ,biocrust ,desert ,soil ,transcriptome ,wetting ,Biochemistry and Cell Biology - Abstract
We present eight metatranscriptomic datasets of light algal and cyanolichen biological soil crusts from the Mojave Desert in response to wetting. These data will help us understand gene expression patterns in desert biocrust microbial communities after they have been reactivated by the addition of water.
- Published
- 2024
44. Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota
- Author
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Oliver, Tiffany, Varghese, Neha, Roux, Simon, Schulz, Frederik, Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Riley, Robert, LaButti, Kurt, Egan, Robert, Hajek, Patrick, Mukherjee, Supratim, Ovchinnikova, Galina, Reddy, TBK, Calhoun, Sara, Hayes, Richard D, Rohwer, Robin R, Zhou, Zhichao, Daum, Chris, Copeland, Alex, Chen, I-Min A, Ivanova, Natalia N, Kyrpides, Nikos C, Mouncey, Nigel J, del Rio, Tijana Glavina, Grigoriev, Igor V, Hofmeyr, Steven, Oliker, Leonid, Yelick, Katherine, Anantharaman, Karthik, McMahon, Katherine D, Woyke, Tanja, and Eloe-Fadrosh, Emiley A
- Subjects
Microbiology ,Biological Sciences ,Ecology ,Bacteria ,Lakes ,Metagenome ,Metagenomics ,Phylogeny - Abstract
The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.
- Published
- 2024
45. Draft genome sequencing and assembly of Favolaschia claudopus CIRM-BRFM 2984 isolated from oak limbs
- Author
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Navarro, David, Drula, Elodie, Chaduli, Delphine, Cazenave, Robert, Ahrendt, Steven, Wang, Jie, Lipzen, Anna, Daum, Chris, Barry, Kerrie, Grigoriev, Igor V, Favel, Anne, Rosso, Marie-Noëlle, and Martin, Francis
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,Agaricales ,Favolaschia ,Invasive species ,Mycenaceae ,decayed wood ,genome - Abstract
Favolaschia claudopus, a wood-inhabiting basidiomycete of the Mycenaceae family, is considered an invasive species that has recently spread from Oceania to Europe. The CIRM-BRFM 2984 strain of this fungus was originally isolated from a basidiome collected from the fallen limb of a decayed oak tree in Southwest France. The genome sequence of this strain shared characteristics with other Mycenaceae species, including a large genome size and enriched content of protein-coding genes. The genome sequence provided here will facilitate further investigation on the factors that contribute to the successful global dissemination of F. claudopus.
- Published
- 2024
46. Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus.
- Author
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Zhang, Jin, Wang, Xiaqin, Wang, Hsin-Tzu, Qiao, Zhenzhen, Yao, Tao, Xie, Meng, Urbanowicz, Breeanna, Zeng, Wei, Jawdy, Sara, Gunter, Lee, Yang, Xiaohan, Czarnecki, Olaf, Regan, Sharon, Seguin, Armand, Rottmann, William, Winkeler, Kimberly, Sykes, Robert, Lipzen, Anna, Daum, Chris, Barry, Kerrie, Lu, Meng-Zhu, Tuskan, Gerald, Muchero, Wellington, and Chen, Jin-Gui
- Subjects
Populus ,Xylans ,Acetylation ,Biomass ,Biofuels ,Plants ,Cell Wall ,Lignin - Abstract
Plant lignocellulosic biomass, i.e. secondary cell walls of plants, is a vital alternative source for bioenergy. However, the acetylation of xylan in secondary cell walls impedes the conversion of biomass to biofuels. Previous studies have shown that REDUCED WALL ACETYLATION (RWA) proteins are directly involved in the acetylation of xylan but the regulatory mechanism of RWAs is not fully understood. In this study, we demonstrate that overexpression of a Populus trichocarpa PtRWA-C gene increases the level of xylan acetylation and increases the lignin content and S/G ratio, ultimately yielding poplar woody biomass with reduced saccharification efficiency. Furthermore, through gene coexpression network and expression quantitative trait loci (eQTL) analysis, we found that PtRWA-C was regulated not only by the secondary cell wall hierarchical regulatory network but also by an AP2 family transcription factor HARDY (HRD). Specifically, HRD activates PtRWA-C expression by directly binding to the PtRWA-C promoter, which is also the cis-eQTL for PtRWA-C. Taken together, our findings provide insights into the functional roles of PtRWA-C in xylan acetylation and consequently saccharification and shed light on synthetic biology approaches to manipulate this gene and alter cell wall properties. These findings have substantial implications for genetic engineering of woody species, which could be used as a sustainable source of biofuels, valuable biochemicals, and biomaterials.
- Published
- 2023
47. Draft genome sequence of Yarrowia lipolytica NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates.
- Author
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Jagtap, Sujit, Liu, Jing-Jing, Walukiewicz, Hanna, Ahrendt, Steven, Koriabine, Maxim, Cobaugh, Kelly, Salamov, Asaf, Yoshinaga, Yuko, Ng, Vivian, Daum, Chris, Grigoriev, Igor, Slininger, Patricia, Dien, Bruce, Jin, Yong-Su, Rao, Christopher, and Riley, Robert
- Subjects
Yarrowia lipolytica ,genome analysis ,oleaginous yeast - Abstract
Yarrowia lipolytica is an oleaginous yeast that produces high titers of fatty acid-derived biofuels and biochemicals. It can grow on hydrophobic carbon sources and lignocellulosic hydrolysates. The genome sequence of Y. lipolytica NRRL Y-64008 is reported to aid in its development as a biotechnological chassis for producing biofuels and bioproducts.
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- 2023
48. Genome-scale phylogeny and comparative genomics of the fungal order Sordariales
- Author
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Hensen, Noah, Bonometti, Lucas, Westerberg, Ivar, Brännström, Ioana Onut, Guillou, Sonia, Cros-Aarteil, Sandrine, Calhoun, Sara, Haridas, Sajeet, Kuo, Alan, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, LaButti, Kurt, Andreopoulos, Bill, Lipzen, Anna, Chen, Cindy, Yan, Mi, Daum, Chris, Ng, Vivian, Clum, Alicia, Steindorff, Andrei, Ohm, Robin A, Martin, Francis, Silar, Philippe, Natvig, Donald O, Lalanne, Christophe, Gautier, Valérie, Ament-Velásquez, Sandra Lorena, Kruys, Åsa, Hutchinson, Miriam I, Powell, Amy Jo, Barry, Kerrie, Miller, Andrew N, Grigoriev, Igor V, Debuchy, Robert, Gladieux, Pierre, Hiltunen Thorén, Markus, and Johannesson, Hanna
- Subjects
Microbiology ,Biological Sciences ,Evolutionary Biology ,Genetics ,Biotechnology ,Human Genome ,Humans ,Phylogeny ,Genomics ,Genome ,Sordariales ,Base Sequence ,Evolution ,Molecular ,Whole-genome phylogeny ,Podosporaceae ,Chaetomiaceae ,Sordariaceae ,Genome evolution ,Zoology ,Evolutionary biology - Abstract
The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chaetomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.
- Published
- 2023
49. The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses
- Author
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Collier, Jackie L, Rest, Joshua S, Gallot-Lavallée, Lucie, Lavington, Erik, Kuo, Alan, Jenkins, Jerry, Plott, Chris, Pangilinan, Jasmyn, Daum, Chris, Grigoriev, Igor V, Filloramo, Gina V, Novák Vanclová, Anna MG, and Archibald, John M
- Subjects
Microbiology ,Biological Sciences ,Genetics ,2.2 Factors relating to the physical environment ,Life Below Water ,DNA ,Ribosomal ,Viruses ,Genome ,Heterochromatin ,Eukaryota ,Telomere ,Phylogeny ,LORE-TEARS ,duplodnaviria ,endogenous viruses ,host-virus co-evolution ,labyrinthulomycetes ,long repeated-telomere and rDNA spacers ,protist genome assembly ,subtelomeric rDNAs ,thraustochytrids ,varidnaviria ,viral episome ,Medical and Health Sciences ,Psychology and Cognitive Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences ,Psychology - Abstract
Viruses are the most abundant biological entities in the world's oceans, where they play important ecological and biogeochemical roles. Metagenomics is revealing new groups of eukaryotic viruses, although disconnected from known hosts. Among these are the recently described mirusviruses, which share some similarities with herpesviruses.1 50 years ago, "herpes-type" viral particles2 were found in a thraustochytrid member of the labyrinthulomycetes, a diverse group of abundant and ecologically important marine eukaryotes,3,4 but could not be further characterized by methods then available. Long-read sequencing has allowed us to connect the biology of mirusviruses and thraustochytrids. We sequenced the genome of the genetically tractable model thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381 and found that its 26 linear chromosomes have an extraordinary configuration. Subtelomeric ribosomal DNAs (rDNAs) found at all chromosome ends are interspersed with long repeated sequence elements denoted as long repeated-telomere and rDNA spacers (LORE-TEARS). We identified two genomic elements that are related to mirusvirus genomes. The first is a ∼300-kbp episome (circular element 1 [CE1]) present at a high copy number. Strikingly, the second, distinct, mirusvirus-like element is integrated between two sets of rDNAs and LORE-TEARS at the left end of chromosome 15 (LE-Chr15). Similar to metagenomically derived mirusviruses, these putative A. limacinum mirusviruses have a virion module related to that of herpesviruses along with an informational module related to nucleocytoplasmic large DNA viruses (NCLDVs). CE1 and LE-Chr15 bear striking similarities to episomal and endogenous latent forms of herpesviruses, respectively, and open new avenues of research into marine virus-host interactions.
- Published
- 2023
50. Simply the green: Urban refuges
- Author
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Johanna L. Berger, Sonja N.K. Daum, and Margarita Hartlieb
- Subjects
Arthropods ,City ,Environmental ethics ,Green space ,Humans ,Insects ,Ecology ,QH540-549.5 - Abstract
Large refugia and small refuges have always been crucial for species survival, particularly during periods like the Ice Age. When their original habitats became uninhabitable, they provided important shelters in space and time. Drawing from a biological and philosophical perspective, we propose creating and preserving refuges as socio-ecological solutions in an epoch primarily shaped by human activity, the Anthropocene. Our focus lies on green refuges within urban settings, given that urbanization is one of the large drivers of insect decline and has adverse effects on humans, such as increased heat. Refuges can be beneficial for both biodiversity and human well-being.After clarifying the relevant terminology on four levels of abstraction, we conducted a systematic biological literature review - as a case study. Here, we summarize the current state of research on the effects of unmown refuges on insects and spiders. The mere existence of refuges proved beneficial for arthropods, with over 70 % of studies reporting positive responses among these species.While insects and spiders have specific habitat requirements, humans are able to create a habitable environment for themselves. However, ecological crises for humans and arthropods are increasing, as are human populations. Therefore, refuges offer a way to address both ecological and social challenges simultaneously, enhancing biodiversity and human well-being.
- Published
- 2024
- Full Text
- View/download PDF
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