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1. Error Diffusion: Post Training Quantization with Block-Scaled Number Formats for Neural Networks

Author

Khodamoradi, Alireza, Denolf, Kristof, and Dellinger, Eric

Subjects
Computer Science - Machine Learning
Abstract

Quantization reduces the model's hardware costs, such as data movement, storage, and operations like multiply and addition. It also affects the model's behavior by degrading the output quality. Therefore, there is a need for methods that preserve the model's behavior when quantizing model parameters. More exotic numerical encodings, such as block-scaled number formats, have shown advantages for utilizing a fixed bit budget to encode model parameters. This paper presents error diffusion (ED), a hyperparameter-free method for post-training quantization with support for block-scaled data formats. Our approach does not rely on backpropagation or Hessian information. We describe how to improve the quantization process by viewing the neural model as a composite function and diffusing the quantization error in every layer. In addition, we introduce TensorCast, an open-source library based on PyTorch to emulate a variety of number formats, including the block-scaled ones, to aid the research in neural model quantization. We demonstrate the efficacy of our algorithm through rigorous testing on various architectures, including vision and large language models (LLMs), where it consistently delivers competitive results. Our experiments confirm that block-scaled data formats provide a robust choice for post-training quantization and could be used effectively to enhance the practical deployment of advanced neural networks.

Published
2024

4. Microscaling Data Formats for Deep Learning

Author

Rouhani, Bita Darvish, Zhao, Ritchie, More, Ankit, Hall, Mathew, Khodamoradi, Alireza, Deng, Summer, Choudhary, Dhruv, Cornea, Marius, Dellinger, Eric, Denolf, Kristof, Dusan, Stosic, Elango, Venmugil, Golub, Maximilian, Heinecke, Alexander, James-Roxby, Phil, Jani, Dharmesh, Kolhe, Gaurav, Langhammer, Martin, Li, Ada, Melnick, Levi, Mesmakhosroshahi, Maral, Rodriguez, Andres, Schulte, Michael, Shafipour, Rasoul, Shao, Lei, Siu, Michael, Dubey, Pradeep, Micikevicius, Paulius, Naumov, Maxim, Verrilli, Colin, Wittig, Ralph, Burger, Doug, and Chung, Eric

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

Narrow bit-width data formats are key to reducing the computational and storage costs of modern deep learning applications. This paper evaluates Microscaling (MX) data formats that combine a per-block scaling factor with narrow floating-point and integer types for individual elements. MX formats balance the competing needs of hardware efficiency, model accuracy, and user friction. Empirical results on over two dozen benchmarks demonstrate practicality of MX data formats as a drop-in replacement for baseline FP32 for AI inference and training with low user friction. We also show the first instance of training generative language models at sub-8-bit weights, activations, and gradients with minimal accuracy loss and no modifications to the training recipe.

Published
2023

5. Tailor: Altering Skip Connections for Resource-Efficient Inference

Author

Weng, Olivia, Marcano, Gabriel, Loncar, Vladimir, Khodamoradi, Alireza, G, Abarajithan, Sheybani, Nojan, Meza, Andres, Koushanfar, Farinaz, Denolf, Kristof, Duarte, Javier Mauricio, and Kastner, Ryan

Subjects
Information and Computing Sciences, Engineering, Electrical Engineering, Machine Learning, Electrical and Electronic Engineering, Computer Hardware, Electronics, sensors and digital hardware, Distributed computing and systems software
Abstract

Deep neural networks use skip connections to improve training convergence. However, these skip connections are costly in hardware, requiring extra buffers and increasing on- and off-chip memory utilization and bandwidth requirements. In this paper, we show that skip connections can be optimized for hardware when tackled with a hardware-software codesign approach. We argue that while a network’s skip connections are needed for the network to learn, they can later be removed or shortened to provide a more hardware efficient implementation with minimal to no accuracy loss. We introduce Tailor , a codesign tool whose hardware-aware training algorithm gradually removes or shortens a fully trained network’s skip connections to lower their hardware cost. Tailor improves resource utilization by up to 34% for BRAMs, 13% for FFs, and 16% for LUTs for on-chip, dataflow-style architectures. Tailor increases performance by 30% and reduces memory bandwidth by 45% for a 2D processing element array architecture.

Published
2023

6. SPARTA: Spatial Acceleration for Efficient and Scalable Horizontal Diffusion Weather Stencil Computation

Author

Singh, Gagandeep, Khodamoradi, Alireza, Denolf, Kristof, Lo, Jack, Gómez-Luna, Juan, Melber, Joseph, Bisca, Andra, Corporaal, Henk, and Mutlu, Onur

Subjects
Computer Science - Hardware Architecture
Abstract

Fast and accurate climate simulations and weather predictions are critical for understanding and preparing for the impact of climate change. Real-world weather and climate modeling consist of complex compound stencil kernels that do not perform well on conventional architectures. Horizontal diffusion is one such important compound stencil found in many climate and weather prediction models. Recent works propose using FPGAs as an alternative to traditional CPU and GPU-based systems to accelerate compound stencil kernels. However, we observe that compound stencil computations cannot leverage the bit-level flexibility available on an FPGA because of its complex memory access patterns, leading to high hardware resource utilization and low peak performance. We introduce SPARTA, a novel spatial accelerator for horizontal diffusion weather stencil computation. We exploit the two-dimensional spatial architecture to efficiently accelerate horizontal diffusion stencil by designing the first scaled-out spatial accelerator using MLIR (Multi-Level Intermediate Representation) compiler framework. We evaluate its performance on a real cutting-edge AMD-Xilinx Versal AI Engine spatial architecture. Our real-system evaluation results demonstrate that SPARTA outperforms the state-of-the-art CPU, GPU, and FPGA implementations by 17.1x, 1.2x, and 2.1x, respectively. Our results reveal that balancing workload across the available processing resources is crucial in achieving high performance on spatial architectures. We also implement and evaluate five elementary stencils that are commonly used as benchmarks for stencil computation research. We freely open-source all our implementations to aid future research in stencil computation and spatial computing systems at https://github.com/CMU-SAFARI/SPARTA.

Published
2023

7. CHARM: Composing Heterogeneous Accelerators for Matrix Multiply on Versal ACAP Architecture

Author

Zhuang, Jinming, Lau, Jason, Ye, Hanchen, Yang, Zhuoping, Du, Yubo, Lo, Jack, Denolf, Kristof, Neuendorffer, Stephen, Jones, Alex, Hu, Jingtong, Chen, Deming, Cong, Jason, and Zhou, Peipei

Subjects
Computer Science - Hardware Architecture
Abstract

Dense matrix multiply (MM) serves as one of the most heavily used kernels in deep learning applications. To cope with the high computation demands of these applications, heterogeneous architectures featuring both FPGA and dedicated ASIC accelerators have emerged as promising platforms. For example, the AMD/Xilinx Versal ACAP architecture combines general-purpose CPU cores and programmable logic with AI Engine processors optimized for AI/ML. With 400 AIEs, it provides up to 6.4 TFLOPs performance for 32-bit floating-point data. However, machine learning models often contain both large and small MM operations. While large MM operations can be parallelized efficiently across many cores, small MM operations typically cannot. We observe that executing some small MM layers from the BERT natural language processing model on a large, monolithic MM accelerator in Versal ACAP achieved less than 5% of the theoretical peak performance. Therefore, one key question arises: How can we design accelerators to fully use the abundant computation resources under limited communication bandwidth for applications with multiple MM layers of diverse sizes? We identify the biggest system throughput bottleneck resulting from the mismatch of massive computation resources of one monolithic accelerator and the various MM layers of small sizes in the application. To resolve this problem, we propose the CHARM framework to compose multiple diverse MM accelerator architectures working concurrently towards different layers in one application. We deploy the CHARM framework for four different applications, including BERT, ViT, NCF, MLP, on the AMD Versal ACAP VCK190 evaluation board. Our experiments show that we achieve 1.46 TFLOPs, 1.61 TFLOPs, 1.74 TFLOPs, and 2.94 TFLOPs inference throughput for BERT, ViT, NCF and MLP, which obtain 5.40x, 32.51x, 1.00x and 1.00x throughput gains compared to one monolithic accelerator.

Published
2023

8. In Memoriam: Peter J. Urcuioli (1952-2022).

Author

Vasconcelos, Marco, Lionello-DeNolf, Karen M, Swisher, Melissa, and Sweeney, Mary M

Subjects
Psychology, Cognitive Sciences, Behavioral Science & Comparative Psychology
Published
2023

9. RUBICON: A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers

Author

Singh, Gagandeep, Alser, Mohammed, Denolf, Kristof, Firtina, Can, Khodamoradi, Alireza, Cavlak, Meryem Banu, Corporaal, Henk, and Mutlu, Onur

Subjects
Computer Science - Hardware Architecture, Computer Science - Distributed, Parallel, and Cluster Computing, Quantitative Biology - Genomics
Abstract

Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The accuracy and speed of basecalling have critical implications for all later steps in genome analysis. Many researchers adopt complex deep learning-based models to perform basecalling without considering the compute demands of such models, which leads to slow, inefficient, and memory-hungry basecallers. Therefore, there is a need to reduce the computation and memory cost of basecalling while maintaining accuracy. Our goal is to develop a comprehensive framework for creating deep learning-based basecallers that provide high efficiency and performance. We introduce RUBICON, a framework to develop hardware-optimized basecallers. RUBICON consists of two novel machine-learning techniques that are specifically designed for basecalling. First, we introduce the first quantization-aware basecalling neural architecture search (QABAS) framework to specialize the basecalling neural network architecture for a given hardware acceleration platform while jointly exploring and finding the best bit-width precision for each neural network layer. Second, we develop SkipClip, the first technique to remove the skip connections present in modern basecallers to greatly reduce resource and storage requirements without any loss in basecalling accuracy. We demonstrate the benefits of RUBICON by developing RUBICALL, the first hardware-optimized basecaller that performs fast and accurate basecalling. Compared to the fastest state-of-the-art basecaller, RUBICALL provides a 3.96x speedup with 2.97% higher accuracy. We show that RUBICON helps researchers develop hardware-optimized basecallers that are superior to expert-designed models.

Published
2022

10. Vision, challenges and opportunities for a Plant Cell Atlas.

Author

Plant Cell Atlas Consortium, Jha, Suryatapa Ghosh, Borowsky, Alexander T, Cole, Benjamin J, Fahlgren, Noah, Farmer, Andrew, Huang, Shao-Shan Carol, Karia, Purva, Libault, Marc, Provart, Nicholas J, Rice, Selena L, Saura-Sanchez, Maite, Agarwal, Pinky, Ahkami, Amir H, Anderton, Christopher R, Briggs, Steven P, Brophy, Jennifer An, Denolf, Peter, Di Costanzo, Luigi F, Exposito-Alonso, Moises, Giacomello, Stefania, Gomez-Cano, Fabio, Kaufmann, Kerstin, Ko, Dae Kwan, Kumar, Sagar, Malkovskiy, Andrey V, Nakayama, Naomi, Obata, Toshihiro, Otegui, Marisa S, Palfalvi, Gergo, Quezada-Rodríguez, Elsa H, Singh, Rajveer, Uhrig, R Glen, Waese, Jamie, Van Wijk, Klaas, Wright, R Clay, Ehrhardt, David W, Birnbaum, Kenneth D, and Rhee, Seung Y

Subjects
Plant Cell Atlas Consortium, 4D imaging, A. thaliana, Plant Cell Atlas, cell biology, chlamydomonas reinhardtii, location-to-function, maize, science forum, single-cell omics, translational research, Biochemistry and Cell Biology
Abstract

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

Published
2021

11. Vision, challenges and opportunities for a Plant Cell Atlas

Author

Ahmed, Jahed, Alaba, Oluwafemi, Ameen, Gazala, Arora, Vaishali, Arteaga-Vazquez, Mario A, Arun, Alok, Bailey-Serres, Julia, Bartley, Laura E, Bassel, George W, Bergmann, Dominique C, Bertolini, Edoardo, Bhati, Kaushal Kumar, Blanco-Touriñán, Noel, Briggs, Steven P, Brumos, Javier, Buer, Benjamin, Burlaocot, Adrien, Cervantes-Pérez, Sergio Alan, Chen, Sixue, Contreras-Moreira, Bruno, CORPAS, Francisco J, Cruz-Ramirez, Alfredo, Cuevas-Velazquez, Cesar L, Cuperus, Josh T, David, Lisa I, de Folter, Stefan, Denolf, Peter H, Ding, Pingtao, Dwyer, William P, Evans, Matthew MS, George, Nancy, Handakumbura, Pubudu P, Harrison, Maria J, Haswell, Elizabeth S, Herath, Venura, Jiao, Yuling, Jinkerson, Robert E, John, Uwe, Joshi, Sanjay, Joshi, Abhishek, Joubert, Lydia-Marie, Katam, Ramesh, Kaur, Harmanpreet, Kazachkova, Yana, Raju, Sunil K Kenchanmane, Khan, Mather A, Khangura, Rajdeep, Kumar, Ajay, Kumar, Arun, Kumar, Pankaj, Kumar, Pradeep, Lavania, Dhruv, Lew, Tedrick Thomas Salim, Lewsey, Mathew G, Lin, Chien-Yuan, Liu, Dianyi, Liu, Le, Liu, Tie, Lokdarshi, Ansul, Luong, Ai My, Macaulay, Iain C, Mahmud, Sakil, Mähönen, Ari Pekka, Malukani, Kamal Kumar, Marand, Alexandre P, Martin, Carly A, McWhite, Claire D, Mehta, Devang, Martín, Miguel Miñambres, Mortimer, Jenny C, Nikolov, Lachezar A, Nobori, Tatsuya, Nolan, Trevor M, Ogden, Aaron J, Otegui, Marisa S, Ott, Mark-Christoph, Palma, José M, Paul, Puneet, Rehman, Atique U, Romera-Branchat, Maida, Romero, Luis C, Roth, Ronelle, Sah, Saroj K, Shahan, Rachel, Solanki, Shyam, Song, Bao-Hua, Sozzani, Rosangela, Stacey, Gary, Stepanova, Anna N, Taylor, Nicolas L, Tello-Ruiz, Marcela K, Tran, Tuan M, Tripathi, Rajiv Kumar, Vadde, Batthula Vijaya Lakshmi Vadde, Varga, Tamas, Vidovic, Marija, Walley, Justin W, Wang, Zhiyong, Weizbauer, Renate A, and Whelan, James

Subjects
Plant Biology, Biological Sciences, Agriculture, Chlamydomonas reinhardtii, Chloroplasts, Computational Biology, Image Processing, Computer-Assisted, Plant Cells, Plant Development, Plants, Zea mays, Plant Cell Atlas Consortium, 4D imaging, A. thaliana, Plant Cell Atlas, cell biology, chlamydomonas reinhardtii, location-to-function, maize, science forum, single-cell omics, translational research, Biochemistry and Cell Biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

Published
2021

12. Comparing Energy Efficiency of CPU, GPU and FPGA Implementations for Vision Kernels

Author

Qasaimeh, Murad, Denolf, Kristof, Lo, Jack, Vissers, Kees, Zambreno, Joseph, and Jones, Phillip H.

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

Developing high performance embedded vision applications requires balancing run-time performance with energy constraints. Given the mix of hardware accelerators that exist for embedded computer vision (e.g. multi-core CPUs, GPUs, and FPGAs), and their associated vendor optimized vision libraries, it becomes a challenge for developers to navigate this fragmented solution space. To aid with determining which embedded platform is most suitable for their application, we conduct a comprehensive benchmark of the run-time performance and energy efficiency of a wide range of vision kernels. We discuss rationales for why a given underlying hardware architecture innately performs well or poorly based on the characteristics of a range of vision kernel categories. Specifically, our study is performed for three commonly used HW accelerators for embedded vision applications: ARM57 CPU, Jetson TX2 GPU and ZCU102 FPGA, using their vendor optimized vision libraries: OpenCV, VisionWorks and xfOpenCV. Our results show that the GPU achieves an energy/frame reduction ratio of 1.1-3.2x compared to the others for simple kernels. While for more complicated kernels and complete vision pipelines, the FPGA outperforms the others with energy/frame reduction ratios of 1.2-22.3x. It is also observed that the FPGA performs increasingly better as a vision application's pipeline complexity grows., Comment: 8 pages, Design Automation Conference (DAC), The 15th IEEE International Conference on Embedded Software and Systems, 2019

Published
2019

17. Case Study: Extension of a Systematic Data-Based Reinforcement System to Increase Independence in Public-School Inclusion Settings to a Student with Down Syndrome and Intellectual Disability

Author

Gifford, Audrey, Redpath, Caroline C., and Lionello-DeNolf, Karen M.

Abstract

Prompt dependency in inclusion-setting students with intellectual disabilities is a challenge. Using a scientist-practitioner model, an intervention to shape independent responding was implemented by paraprofessionals for a student with Down syndrome. It included systematic reinforcement-schedule thinning, reduced paraprofessional proximity, and incorporation of peer models into prompting strategies. Independence on nine pre-academic skills improved by 25-100% (mean = 68.1%) as reinforcement criteria increased and paraprofessional proximity decreased. Although the intervention significantly departed from treatment as usual, social validity among stakeholders was high.

Published
2018

21. Contextual Influences on Resistance to Disruption in Children with Intellectual Disabilities

Author

Lionello-DeNolf, Karen and Dube, William V.

Abstract

Training context can influence resistance to disruption under differing reinforcement schedules. With nonhumans, when relatively lean and rich reinforcement schedules are experienced in the context of a multiple schedule, greater resistance is found in the rich than the lean component, as described by behavioral momentum theory. By contrast, when the schedules are experienced in separated blocks of sessions (i.e., as single schedules), resistance is not consistently greater in either component. In the current study, two groups of 6 children with intellectual disabilities responded to stimuli presented in relatively lean or rich components. For both, reinforcers were delivered according to the same variable-interval reinforcement schedule; additionally, the rich component included the delivery of response-independent reinforcers. The Within group was trained on a multiple schedule in which lean and rich components alternated regularly within sessions; the Blocked group was trained on two single schedules in which sessions with either the lean or rich schedule were conducted in successive blocks. Disruption tests presented a concurrently available alternative stimulus disrupter signaling the availability of tangible reinforcers. All 6 Within participants showed greater resistance to disruption in the rich component, consistent with behavioral momentum theory. By contrast, there was no consistent or significant difference in resistance for Blocked participants. This finding is potentially relevant to the development of interventions in applied settings, where such interventions often approximate single schedules and include response-independent reinforcers. (Contains 4 tables and 2 figures.)

Published
2011

22. Evaluation of Resistance to Change under Different Disrupter Conditions in Children with Autism and Severe Intellectual Disability

Author

Lionello-DeNolf, Karen M., Dube, William V., and McIlvane, William J.

Abstract

Translational research inspired by behavioral momentum theory in the area of developmental disabilities has shown effects in individuals over a range of functioning levels. In the current study, behavioral momentum was assessed in 6 children diagnosed with autism and severe intellectual disability. In a repeated measures design, participants were exposed to relatively rich versus lean reinforcement contingencies in a multiple schedule with food reinforcers. This was followed by exposure to each of four disrupting conditions: prefeeding, presentation of a concurrent alternative stimulus, presentation of a movie, and the presence of a researcher dispensing response-independent reinforcers on a variable-time schedule. Consistently greater resistance to disruption in the component with the richer schedule occurred with the alternative stimulus disrupter but not with the other disrupters. These results suggest parameters that may be more (or less) effective if behavioral momentum inspired techniques are to be exploited in therapeutic environments. (Contains 5 tables and 5 figures.)

Published
2010

23. A Novel Method for Teaching the First Instances of Simple Discrimination to Nonverbal Children with Autism in a Laboratory Environment

Author

Lionello-DeNolf, Karen M., da Silva Barros, Romariz, and McIlvane, William J.

Abstract

A novel method for initiating discrimination training with nonverbal children combines a delayed S+ procedure that requires children to refrain from responding to either of 2 physically different choice stimuli until a prompt stimulus is added onto 1 of the choices, and a delayed prompting procedure that presents the same 2-choice stimulus display, but stimuli are initially added onto both choices. After a short delay, the added stimulus on the S- is removed, and the choice of the S+ is thus prompted. If the children learn to observe and respond to the defining features of the S+ choice stimulus, then they may respond to the S+ prior to the added-stimulus removal. Implementation was successful with 8 nonverbal children who had not previously exhibited simple simultaneous discrimination, suggesting a useful methodology for initiating discrimination training with populations for whom verbal instruction is ineffective. (Contains 2 tables and 5 figures.)

Published
2008

24. Failure to Replicate the 'Work Ethic' Effect in Pigeons

Author

Vasconcelos, Marco, Urcuioli, Peter J., and Lionello-DeNolf, Karen M.

Abstract

We report six unsuccessful attempts to replicate the "work ethic" phenomenon reported by Clement, Feltus, Kaiser, and Zentall (2000). In Experiments 1-5, pigeons learned two simultaneous discriminations in which the S+ and S- stimuli were obtained by pecking an initial stimulus once or multiple (20 or 40) times. Subsequent preference tests between the S+ stimuli and between the S- stimuli mostly revealed indifference, on average, between the S+ from the multiple-peck (high-effort) trials and the S+ from the one-peck (low-effort) trials, and likewise between the two respective S- stimuli. Using a slightly different procedure that permitted assessment of the relative aversiveness of low versus high effort, Experiment 6 again revealed a pattern of indifference despite showing that pigeons took considerably longer to begin pecking on high- than on low-effort trials. Our findings call into question the reliability of the original findings and the sufficiency of the hypothesized within-trial contrast mechanism to produce them. (Contains 6 figures and 1 footnote.)

Published
2007

25. Some Tests of Response Membership in Acquired Equivalence Classes

Author

Urcuioli, Peter J., Lionello-DeNolf, Karen, and Michalek, Sarah

Abstract

Pigeons were trained on many-to-one matching in which pairs of samples, each consisting of a visual stimulus and a distinctive pattern of center-key responding, occasioned the same reinforced comparison choice. Acquired equivalence between the visual and response samples then was evaluated by reinforcing new comparison choices to one set of samples, and examining generalization of these choices to the other samples. Three separate experiments found no evidence of such generalization, as indexed by performance on class-consistent versus class-inconsistent tests. Other tests showed that the pigeons' center-key response patterns during training had indeed served as a conditional cue for choice. These results do not support the hypothesis that different defined responses can become members of acquired equivalence classes. (Contains 10 figures and 2 tables.)

Published
2006
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26. Science forum: vision, challenges and opportunities for a Plant Cell Atlas

Author

Jha, SG, Borowsky, AT, Cole, BJ, Fahlgren, N, Farmer, A, Huang, S-SC, Karia, P, Libault, M, Provart, NJ, Rice, SL, Saura-Sanchez, M, Agarwal, P, Ahkami, AH, Anderton, CR, Briggs, SP, Brophy, JA, Denolf, P, Di Costanzo, LF, Exposito-Alonso, M, Giacomello, S, Gomez-Cano, F, Kaufmann, K, Ko, DK, Kumar, S, Malkovskiy, A, Nakayama, N, Obata, T, Otegui, MS, Palfalvi, G, Quezada-Rodriguez, EH, Singh, R, Uhrig, RG, Waese, J, Van Wijk, K, Wright, RC, Ehrhardt, DW, Birnbaum, KD, Rhee, SY, Royal Society, and The Royal Society

Subjects
Life Sciences & Biomedicine - Other Topics, chlamydomonas reinhardtii, Chloroplasts, DATABASE, Plant Development, maize, 0601 Biochemistry and Cell Biology, Zea mays, MECHANISMS, Plant Cells, cell biology, Image Processing, Computer-Assisted, Plant Cell Atlas Consortium, Biology, Science & Technology, Computational Biology, Agriculture, Plants, ARABIDOPSIS, GENE, C-4 PHOTOSYNTHESIS, Plant Cell Atlas, science forum, single-cell omics, translational research, VOCABULARY, A. thaliana, SYSTEMS BIOLOGY, PLASTIDS, location-to-function, Life Sciences & Biomedicine, 4D imaging, GENERATION
Abstract

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

Published
2021

28. When Is a Failure to Replicate Not a Type II Error?

Author

Vasconcelos, Marco, Urcuioli, Peter J., and Lionello-DeNolf, Karen M.

Abstract

Zentall and Singer (2007) challenge our conclusion that the work-ethic effect reported by Clement, Feltus, Kaiser, and Zentall (2000) may have been a Type I error by arguing that (a) the effect has been extensively replicated and (b) the amount of overtraining our pigeons received may not have been sufficient to produce it. We believe that our conclusion is warranted because (a) the original effect has not been replicated despite multiple attempts to do so and (b) the statement that more extended overtraining may be needed itself suggests that the original effect is not reliable.

Published
2007

33. Vision, challenges and opportunities for a Plant Cell Atlas

Author

National Science Foundation (US), Plant Cell Atlas, Consortium, Romero, Luis C., Brumós Fuentes, Javier, Corpas, Francisco J., Palma Martínez, José Manuel, Jha, S. G., Borowsky, A. T., Cole, B. J., Fahlgren, N., Farmer, Andrew, Huang, S. C., Karia, P., Libault, M., Provart, N. J., Rice, S. L., Saura-Sanchez, M., Agarwal, P., Ahkami, A. H., Anderton, C. R., Briggs, S. P., Brophy, J. A., Denolf, P., Di Costanzo, L. F., Exposito-Alonso, Moises, Giacomello, S., Gomez-Cano, F., Kaufmann, K., Ko, D. K., Kumar, Sumit, Malkovskiy, A. V., Nakayama, N., Obata, T., Otegui, M. S., Palfalvi, G., Quezada-Rodriguez, E. H., Singh, R., Uhrig, R. G., Waese, J., Van Wijk, K., Wright, R. C., Ehrhardt, D. W., Birnbaum, K. D., Rhee, S. Y., National Science Foundation (US), Plant Cell Atlas, Consortium, Romero, Luis C., Brumós Fuentes, Javier, Corpas, Francisco J., Palma Martínez, José Manuel, Jha, S. G., Borowsky, A. T., Cole, B. J., Fahlgren, N., Farmer, Andrew, Huang, S. C., Karia, P., Libault, M., Provart, N. J., Rice, S. L., Saura-Sanchez, M., Agarwal, P., Ahkami, A. H., Anderton, C. R., Briggs, S. P., Brophy, J. A., Denolf, P., Di Costanzo, L. F., Exposito-Alonso, Moises, Giacomello, S., Gomez-Cano, F., Kaufmann, K., Ko, D. K., Kumar, Sumit, Malkovskiy, A. V., Nakayama, N., Obata, T., Otegui, M. S., Palfalvi, G., Quezada-Rodriguez, E. H., Singh, R., Uhrig, R. G., Waese, J., Van Wijk, K., Wright, R. C., Ehrhardt, D. W., Birnbaum, K. D., and Rhee, S. Y.

Abstract

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

Published
2021

36. Sports injury prevention programmes from the sports physical therapist's perspective: An international expert Delphi approach.

Author

Mendonça, Luciana De Michelis, Schuermans, Joke, Denolf, Sander, Napier, Christopher, Bittencourt, Natália F.N., Romanuk, Andrés, Tak, Igor, Thorborg, Kristian, Bizzini, Mario, Ramponi, Carlo, Paterson, Colin, Hägglund, Martin, Malisoux, Laurent, Al Attar, Wesam Saleh A., Samukawa, Mina, Esteve, Ernest, Bakare, Ummkulthoum, Constantinou, Maria, Schneiders, Anthony, and Cavallieri Gomes, Alexandre

Abstract

To provide consensus on how to plan, organize and implement exercise-based injury prevention program (IPP) in sports. Delphi. LimeSurvey platform. Experienced sports physical therapists from the International Federation of Sports Physical Therapy member countries. Factors related to sports IPP planning, organization and implementation. We included 305 participants from 32 countries. IPP planning should be based on an athlete's injury history, on pre-season screening results, and on injury rates (respectively, 98%, 92%, 89% agreement). In total 97% participants agreed that IPP organization should depend on the athlete's age, 93% on the competition level, and 93% on the availability of low-cost materials. It was agreed that IPP should mainly be implemented in warm-up sessions delivered by the head or strength/conditioning coach, with physical training sessions and individual physical therapy sessions (respectively, 94%, 92%, 90% agreement). Strong consensus was reached on (1) IPP based on the athlete's injury history, pre-season screening and evidence-based sports-specific injury rates; (2) IPP organization based on the athlete's age, competition level, and the availability of low-cost materials and (3) IPP implementation focussing on warm-up sessions implemented by the strength/conditioning coach, and/or individual prevention sessions by the physical therapist. • IPP structuring involve injury rates, history and screening outcome as main factors. • IPP organization involve injury risk profile, low-cost material and financial resources. • IPP implementation is delivered mainly by warm-up or physical therapy sessions. • Coach's support, athlete's routine and the work environment are considered for implementation. [ABSTRACT FROM AUTHOR]

Published
2022
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39. Biotinylation of Bacillus thuringiensis insecticidal crystal proteins

Author

Denolf, P., Jansens, S., Houdt, S. van, Peferoen, M., Degheele, D., and Rie, J. van

Subjects
Biotin -- Usage, Biological sciences
Abstract

The usefulness of Bacillus thuringiensis insecticidal crystal protein (ICP) is studied. An alternative method is established by it for the screening of novel ICPs toxic to pest insects, and for ICP receptor characterization. The results of heterologous competition experiments performed with biotinylated and native ICPs confirms the relationship between different ICP receptor types in Plutella xylostella which is inferred from radioligand binding studies.

Published
1993

40. Two different Bacillus thuringiensis delta-endotoxin receptors in the midgut brush border membrane of the European corn borer, Ostrinia nubilalis (Hubner)(Lepidoptera: Pyralidae)

Author

Denolf, P., Jansens, S., Peferoen, M., Degheele, M., and Rie, J. van

Subjects
Endotoxins -- Research, European corn borer -- Physiological aspects, Biological sciences
Abstract

The presence of insecticidal crystal protein (ICP) receptors in the European corn borer, Ostrinia nubilalis (Hubner) (Lepidoptera: Pyralidae), the major lepidopteran pest of maize in southern Europe and North America, is studied. Two independent ICP receptors are present in the brush border of O.nubilalis gut epithelium. The interactions of B-thuringiensis ICPs with the larval gut of O.nubilalis is investigated by the experiments performed to determine binding of ICPs to both isolated brush border membrane vesicles and tissue sections.

Published
1993

43. Association between SARS‐COV‐2 infection and muscle strain injury occurrence in elite male football players: a prospective study of 29 weeks including three teams from the Belgian professional football league

Author

Wezenbeek, Evi, Denolf, Sander, Willems, Tine Marieke, Pieters, Dries, Bourgois, Jan G, Philippaerts, Renaat M, De Winne, Bram, Wieme, Matthias, Van Hecke, Robbe, Markey, Laurence, Schuermans, Joke, Witvrouw, Erik, and Verstockt, Steven

Abstract

ObjectivesThe aim of this study was to investigate the association between SARS-CoV-2 infection and muscle strain injury in elite athletes.MethodsA prospective cohort study in three Belgian professional male football teams was performed during the first half of the 2020–2021 season (June 2020–January 2021). Injury data were collected using established surveillance methods. Assessment of SARS-CoV-2 infection was performed by a PCR test before each official game.ResultsOf the 84 included participants, 22 were infected with SARS-CoV-2 and 14 players developed a muscle strain during the follow-up period. Cox’s proportional hazards regression analyses demonstrated a significant association between SARS-CoV-2 infection and the development of muscle strain (HR 5.1; 95% CI 1.1 to 23.1; p=0.037), indicating an increased risk of developing muscle strains following SARS-CoV-2 infection. All athletes who sustained a muscle strain after infection were injured within the first month (15.71±11.74 days) after sports resumption and completed a longer time in quarantine (14.57±6.50 days) compared with the infected players who did not develop a muscle strain (11.18±5.25 days).ConclusionThis study reported a five times higher risk of developing a muscle strain after a SARS-CoV-2 infection in elite male football players. Although this association should be examined further, it is possible that short-term detraining effects due to quarantine, and potentially pathological effects of the SARS-CoV-2 infection are associated with a higher risk of muscle strain injury.

Published
2022
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46. An update on the search for symmetry in nonhumans

Author

Lionello‐DeNolf, Karen M.

Abstract

Sidman et al.'s (1982) failure to find evidence for symmetry (bidirectional associations between stimuli) in monkeys and baboons set the stage for decades of work on emergent relations in nonhumans. They attributed the failure to the use of procedures that did not (1) promote stimulus control based on the relation between the sample and correct comparison and (2) reduce control by irrelevant stimulus features. Previous reviews of symmetry in nonhumans indicated that multiple exemplar training and successive matching might encourage appropriate stimulus control. This review examined 16 studies that investigated symmetry in 94 subjects, including pigeons, rats, capuchin monkeys, and baboons. Several studies used alternative training procedures to minimize sources of irrelevant stimulus control, and many combined multiple exemplar training with other procedural modifications. Symmetry was observed in approximately 30% of subjects. Studies that reported the strongest evidence for symmetry used successive matching‐to‐sample procedures that included training on both symbolic and identity relations, and studies finding mixed evidence employed alternative methods. These studies highlight the challenge in creating training procedures that promote symmetry and the need to assess the underlying sources of control on positive demonstrations.

Published
2021
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47. The establishment of auditory–visual equivalence classes with a go/no‐go successive matching‐to‐sample procedure

Author

Zhelezoglo, Karina N., Hanson, Robbie J., Miguel, Caio F., and Lionello‐DeNolf, Karen M.

Abstract

The current study evaluated the effectiveness of a go/no‐go successive matching‐to‐sample procedure (S‐MTS) to establish auditory–visual equivalence classes with college students. A sample and a comparison were presented, one at a time, in the same location. During training, after an auditory stimulus was presented, a green box appeared in the center of the screen for participants to touch to produce the comparison. Touching the visual comparison that was related to the auditory sample (e.g., A1B1) produced points, while touching or refraining from touching an unrelated comparison (e.g., A1B2) produced no consequences. Following AB/AC training, participants were tested on untrained relations (i.e., BA/CA and BC/CB), as well as tacting and sorting. During BA/CA relations tests, after touching the visual sample, the auditory stimulus was presented along with a white box for participants to respond. During BC/CB relations tests, after touching the visual sample, a visual comparison appeared. Across 2 experiments, all participants met emergence criterion for untrained relations and for sorting. Additionally, 14 out of 24 participants tacted all visual stimuli correctly. Results suggest the auditory–visual S‐MTS procedure is an effective alternative to simultaneous MTS for establishing conditional relations and auditory‐visual equivalence classes.

Published
2021
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48. Expansion of Sidman's theory: The inclusion of prompt stimuli in equivalence classes

Author

Palmer, Simone K., Maguire, R. W., Lionello‐DeNolf, Karen M., and Braga‐Kenyon, Paula

Abstract

Stimulus equivalence is defined as the ability to relate stimuli in novel ways after training in which not all of the stimuli had been directly linked to one another. Sidman (2000) suggested all elements of conditional discrimination training contingencies that result in equivalence potentially become class members. Research has demonstrated the inclusion of samples, comparisons, responses, and reinforcers in equivalence classes. Given the evidence that all elements of a conditional discrimination become part of the class, the purpose of this study was to determine if class‐specific prompts would also enter into their relevant equivalence classes. Experiment 1 investigated the inclusion of prompts in an equivalence class using abstract stimuli with neurotypical students enrolled in higher education courses. Experiment 2 systematically replicated Experiment 1 using meaningful stimuli and individuals diagnosed with autism spectrum disorder. The results of both experiments demonstrated that class‐specific prompts became part of equivalence classes with the other positive elements of the contingency. The results are discussed in terms of class expansion and the potential impact on equivalence‐based instruction.

Published
2021
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