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Analytical Modeling Is Enough for High-Performance BLIS

Tze Meng Low, Francisco D. Igual, Tyler M. Smith, Enrique S. Quintana-Orti
2016 ACM Transactions on Mathematical Software  
layered memories interact with high performance software.  ...  determine optimal tuning parameters for high-end instantiations of the matrix-matrix multiplication.  ...  This work was partially performed during their visit to The University of Texas at Austin (UT), funded by the JTO visitor applications programme from the Institute for Computational Engineering and Sciences  ... 
doi:10.1145/2925987 fatcat:bxzg2xmyvfgzjku5fccbfcldji

BLI-Based Functional Assay in Phage Display Benefits the Development of a PD-L1-Targeting Therapeutic Antibody

Jong Rip Choi, Min Jung Kim, Nara Tae, Tae Min Wi, Se-Ho Kim, Eung Suk Lee, Dae Hee Kim
2020 Viruses  
These results demonstrated that the BLI-based inhibition assay is an excellent technique for high-throughput scFv antibody screening in earlier stages and can make phage-display antibody screening more  ...  The same assays for IgG-format antibodies showed high efficiency of the BLI assay in the functional characterization of antibodies, and one candidate selected from the BLI assay resulted in highly efficacious  ...  We also thank Jeong-Im Sin, Kangwon National University, for providing MC38 murine colon carcinoma cells.  ... 
doi:10.3390/v12060684 pmid:32630442 pmcid:PMC7354572 fatcat:z5lihufyhjbtzppmzisgzne5ha

Recent Advances in Boundary Layer Ingestion Technology of Evolving Powertrain Systems

Dimitra Eirini Diamantidou, Md Lokman Hosain, Konstantinos G. Kyprianidis
2022 Sustainability  
The goal of this work is to review the current state-of-the-art of BLI evaluation studies.  ...  Boundary Layer Ingestion (BLI) is currently investigated as a potential technology to achieve different design goals such as energy efficiency improvement and noise emission reductions in the next generation  ...  The performance of an ultra-high bypass fan was investigated.  ... 
doi:10.3390/su14031731 fatcat:pmu4pb5iufda7dkesjgq4vodme

Characterization of new recombinant Immunoglobulins type-M binding to C1q by Biolayer Interferometry [article]

Anne Chouquet, Andrea J. Pinto, Wai Li W Ling, Julia Hennicke, Isabelle Bally, Linda Schwaigerlehner, Nicole M. Thielens, Renate Kunert, Jean-Baptiste REISER
2021 bioRxiv   pre-print
This biological function is the base for the huge therapeutic potential of IgMs but due to their high oligomeric complexity, in vitro production as well as biochemical and biophysical characterizations  ...  In the present study, we present new attempts of recombinant production of two IgM models (IgM617 and IgM012) and the evaluation of their polymer distribution using biophysical methods (AUC, SEC-MALLS,  ...  We would like to thank Véronique Rossi and Christine Gaboriaud from IBS for their expertise, helpful discussions and article proof reading.  ... 
doi:10.1101/2021.09.30.460443 fatcat:bqlor4xwbzgmzexmrihsezb4ru

Characterization and screening of IgG binding to the neonatal Fc receptor

Tobias Neuber, Katrin Frese, Jan Jaehrling, Sebastian Jäger, Daniela Daubert, Karin Felderer, Mechthild Linnemann, Anne Höhne, Stefan Kaden, Johanna Kölln, Thomas Tiller, Bodo Brocks (+2 others)
2014 mAbs  
Acknowledgments The authors thank MorphoSys' Physico-Chemical Analytics for characterization of Fc receptors, Martin Heßling for contribution of ideas, Stefanie Urlinger and Stefan Härtle for helpful comments  ...  Slonomics® is a registered trademark of Sloning BioTechnology GmbH, a subsidiary of MorphoSys AG.  ...  BLI is based on interferometry, i.e., it is a label-free method to measure interactions of soluble analytes with a sensor surface, onto which the corresponding interaction partner is immobilized.  ... 
doi:10.4161/mabs.28744 pmid:24802048 pmcid:PMC4171027 fatcat:sb3kcfzvc5eofgjtibibartspe

Qualified Biolayer Interferometry Avidity Measurements Distinguish the Heterogeneity of Antibody Interactions withPlasmodium falciparumCircumsporozoite Protein Antigens

S. Moses Dennison, Matthew Reichartz, Kelly E. Seaton, Sheetij Dutta, Ulrike Wille-Reece, Adrian V. S. Hill, Katie J. Ewer, Wes Rountree, Marcella Sarzotti-Kelsoe, Daniel A. Ozaki, S. Munir Alam, Georgia D. Tomaras
2018 Journal of Immunology  
Ab avidity is a measure of the overall strength of Ab-Ag interactions and hence is important for understanding the functional efficiency of Abs.  ...  The optimized BLI binding assay demonstrated 1) good precision (percentage of coefficient of variation <20), 2) high specificity, 3) a lower limit of detection and quantitation in the 0.3-3.3 nM range,  ...  We also thank GlaxoSmithKline for granting permission to include analysis of serum samples from the VAC055 study for BLI assay qualification.  ... 
doi:10.4049/jimmunol.1800323 pmid:30006374 pmcid:PMC6077849 fatcat:6tczwgc3erfjtpjamodl3q3xgq

Kinetic analysis of bacteriophage Sf6 binding to outer membrane protein a using whole virions

N. B. HUBBS, M. M. WHISBY-PITTS, J. L. MCMURRY
2019 Acta virologica  
For successful infection, viruses must recognize their respective host cells. A common mechanism of host recognition by viruses is to utilize a portion of the host cell as a receptor.  ...  Based on these data, we propose a model in which Sf6: Omp receptor recognition is not solely based on kinetics, but likely also on the ability of an Omp to induce a conformational change that results in  ...  Kristin Parent (MSU) for collaborative assistance, use of her laboratory and helpful comments on the manuscript, Dr. Xuefei Huang (MSU) and Peng Wang for time on their BLI instrument and Dr.  ... 
doi:10.4149/av_2019_412 pmid:31802688 fatcat:amknxa4b6zfmlgwyp6zx44mgoi

High Performance and Portable Convolution Operators for ARM-based Multicore Processors [article]

Pablo San Juan, Adrián Castelló, Manuel F. Dolz, Pedro Alonso-Jordá, Enrique S. Quintana-Ortí
2020 arXiv   pre-print
is not negligible for complex neural networks.  ...  This paper presents a portable high performance convolution algorithm based on the BLIS realization of the GEMM kernel that avoids the use of the intermediate memory by taking advantage of the BLIS structure  ...  Thus, provided m is large enough, the cost of the packing for B c is negligible compared with the amount of flops performed inside Loop L3.  ... 
arXiv:2005.06410v1 fatcat:omytbc6xbfasvaz3n3sco4nbra

Kinetic Analysis of Bacteriophage Sf6 Binding to Outer Membrane Protein A Using Whole Virions [article]

Natalia B. Hubbs, Mareena M. Whisby-Pitts, Jonathan L. McMurry
2019 bioRxiv   pre-print
For successful infection, viruses must recognize their respective host cells. A common mechanism of host recognition by viruses is to utilize a portion of the host cell as a receptor.  ...  Based on these data, we propose a model in which Sf6: Omp receptor recognition is not solely based on kinetics, but likely also on the ability of an Omp to induce a conformational change that results in  ...  Once Sf6 has cleaved enough LPS repeats [24, 48] , and is close enough to the surface of the cell it interacts with its secondary receptor, an Omp [25] .  ... 
doi:10.1101/509141 fatcat:v2b3lzhipvbv7ozjj22cdeup5u

Automating the Last-Mile for High Performance Dense Linear Algebra [article]

Richard Michael Veras, Tze Meng Low, Tyler Michael Smith, Robert van de Geijn, Franz Franchetti
2017 arXiv   pre-print
Thus,achieving high performance for the Gemm kernel translates into a high performance linear algebra stack above this kernel.  ...  This paper, instead, focuses on an analytical approach to code generation of the Gemm kernel for different architecture, in order to shed light on the details or voo-doo required for implementing a high  ...  We codify this effort as a model based code generation system for micro-kernels, thus automating the last-mile for producing high performance gemm routines. 2 Anatomy of a Gemm micro-kernel BLIS is a framework  ... 
arXiv:1611.08035v2 fatcat:oej3ze3xcraelblbipmqbxwzfq

Optimality considerations for propulsive fuselage power savings

Arne Seitz, Anaïs Luisa Habermann, Martijn van Sluis
2020 Proceedings of the Institution of Mechanical Engineers. Part G, Journal of Aerospace Engineering  
Analytical formulation for the power-saving coefficient metric is introduced, and, the classic Breguet–Coffin range equation is extended for the analytical assessment of boundary layer ingesting aircraft  ...  A common heuristic for the boundary layer ingesting efficiency factor is derived from the best aero-shaping cases of both projects.  ...  In case of turbofan engines, this is the outer fan. c.  ... 
doi:10.1177/0954410020916319 fatcat:cr37piddrre35a64m65y5psrim

Examining the role of context in statistical literacy outcomes using an isomorphic assessment instrument [article]

Sayali Phadke, Matthew D Beckman, Kari Lock Morgan
2022 arXiv   pre-print
ACKNOWLEDGEMENTS Work supported, in part, by Penn State's Centre for Social Data Analytics Accelerator Award Program Seed Grant.  ...  We wish to acknowledge the three expert reviewers of M-BLIS who provided valuable input. We wish to also thank Dr. Ziegler for her support during the adaptation of her original work.  ...  Residuals plot -Full model in Equation 1 Diagnostic plots for the model with interactions Diagnostic plots for the additive model process is called peerreview.  ... 
arXiv:2205.05608v1 fatcat:af2oapbnsvaide3bmlrn3kxjai

High Performance Code Generation in MLIR: An Early Case Study with GEMM [article]

Uday Bondhugula
2020 arXiv   pre-print
This article is primarily meant to present an early case study on using MLIR, a new compiler intermediate representation infrastructure, for high-performance code generation.  ...  This article is also aimed at showing the role compiler infrastructure could play in generating code that is competitive with highly tuned manually developed libraries, albeit in a more modular, reusable  ...  [12] have plugged in analytical models to drive such optimization with comparable performance. The work of Low et al. [7] makes a similar attempt with BLIS.  ... 
arXiv:2003.00532v1 fatcat:uxeea5zgsvctrg2udedajjibqa

Method for simulating the performance of a boundary layer ingesting propulsion system at design and off-design

C. Goldberg, D. Nalianda, D. MacManus, P. Pilidis, J. Felder
2018 Aerospace Science and Technology  
The performance of individual propulsors in the array is compared at off-design.  ...  The process is intended as a tool for design space exploration and the rapid analysis of concepts at the conceptualisation phase.  ...  Many thanks go also to staff at Cranfield University for their input and to Mr. Darrell Williams for many valuable discussions on developing the performance simulation methods.  ... 
doi:10.1016/j.ast.2018.04.026 fatcat:4kzibntgbfe4llialnijpuxgle

Analytical cache modeling and tilesize optimization for tensor contractions

Rui Li, Aravind Sukumaran-Rajam, Richard Veras, Tze Meng Low, Fabrice Rastello, Atanas Rountev, P. Sadayappan
2019 Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '19  
In this paper we provide an analytical model based approach to multi-level tile size optimization and permutation selection for tensor contractions.  ...  Data movement between processor and memory hierarchy is a fundamental bottleneck that limits the performance of many applications on modern computer architectures.  ...  ACKNOWLEDGMENTS We thank the reviewers for their valuable feedback. This work was supported in part by the U.S.  ... 
doi:10.1145/3295500.3356218 dblp:conf/sc/LiSVLRRS19 fatcat:376oo5hdqbehtfell2khswwv7i
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