Publications

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1687 Publications visible to you, out of a total of 1687

Abstract

Not specified

Authors: Zheng-Wei Liu, Friedrich K. Röpke, Yaotian Zeng

Date Published: 4th Apr 2022

Publication Type: Journal

Abstract

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Authors: Patrick A. Ondratschek, Friedrich K. Röpke, Fabian R. N. Schneider, Christian Fendt, Christian Sand, Sebastian T. Ohlmann, Rüdiger Pakmor, Volker Springel

Date Published: 1st Apr 2022

Publication Type: Journal

Abstract

Not specified

Authors: Patrick A. Ondratschek, Friedrich K. Röpke, Fabian R. N. Schneider, Christian Fendt, Christian Sand, Sebastian T. Ohlmann, Rüdiger Pakmor, Volker Springel

Date Published: 1st Apr 2022

Publication Type: Journal

Abstract

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Authors: Richard Miller, Marco Ajello, Katie Auchettl, John Beacom, Peter Bloser, Adam Burrows, Anna Frebel, Chris Fryer, Dieter Hartmann, Peter Hoeflich, Aimee Hungerford, Mark Leising, Laura Lopez, Peter Milne, Patrick Peplowski, Friedrich Roepke, Daniel Scolnic, Ivo Seitenzahl, LihSin The, C. Young

Date Published: 1st Apr 2022

Publication Type: InProceedings

Abstract

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Authors: Richard Miller, Marco Ajello, Katie Auchettl, John Beacom, Peter Bloser, Adam Burrows, Anna Frebel, Chris Fryer, Dieter Hartmann, Peter Hoeflich, Aimee Hungerford, Mark Leising, Laura Lopez, Peter Milne, Patrick Peplowski, Friedrich Roepke, Daniel Scolnic, Ivo Seitenzahl, Lih-Sin The, C. Alex Young, LOX Team

Date Published: 1st Apr 2022

Publication Type: InProceedings

Abstract (Expand)

ecause of rounding errors, parallel floating-point summation can produce different results on different core-counts. For some algorithms like hill climbing, RAxML-NG [7] or greedy algorithms, this implies that results may be irreproducible with different core-counts. We present the Binary Tree Reduction algorithm, which follows a distributed binary tree scheme that keeps the calculation order fixed and independent of the core-count 푝. A naive implementation requires up to (푝 − 1) ∗ (log2 ( 푁 −1 푝 ) + 1) messages to sum 푁 floating-point numbers. To reduce the message count, we introduce a message buffer and optimize data distribution across the cores, the latter results in a runtime decrease of 18 %. We find that for 푝 = 256, Binary Tree Reduction has a slowdown of less than 2 compared to a naive, irreproducible solution. It is able to compute the sum of 푁 ≈ 21 ∗ 106 summands on 푝 = 256 cores in about 248 μs.

Authors: Christoph Stelz, Lukas Hübner, Alexandros Stamatakis

Date Published: 1st Apr 2022

Publication Type: Bachelor's Thesis

Abstract (Expand)

Macrophage-1 antigen or Mac-1 (CD11b/CD18, αMβ2) is a leukocyte integrin essential for firm adhesion of neutrophils, lymphocytes and monocytes against flow when recruited to the endothelium. To migrate to the site of inflammation, leukocytes require coordinated adhesion and de-adhesion for directional movement. The vascular thiol isomerase, protein disulfide isomerase (PDI), was found by fluorescence microscopy to colocalize with high affinity Mac-1 at the trailing edge of stimulated neutrophils when adhered to ICAM-1 under fluid shear. From differential cysteine alkylation and mass spectrometry studies, PDI cleaves two allosteric disulfide bonds, C169-C176 and C224-C264, in the βI domain of the β2 subunit, and in mutagenesis and cell transfection studies, cleavage of the C224-C264 disulfide bond was shown to selectively control Mac-1 dis-engagement from ICAM-1 under fluid shear. Molecular dynamics simulations and binding of conformation-specific antibodies reveal that cleavage of the C224-C264 bond induces conformational change and mechanical stress in the βI domain that allosterically alters exposure of an αI domain epitope and shifts Mac-1 to a lower affinity state. From studies of neutrophil adherence to ICAM-1 under fluid shear, these molecular events promote neutrophil motility in the direction of flow at high shear stress. In summary, shear-dependent PDI cleavage of neutrophil Mac-1 C224-C264 disulfide bond triggers Mac-1 de-adherence from ICAM-1 at the trailing edge of the cell and enables directional movement of neutrophils during inflammation.

Authors: Alexander Dupuy, Camilo Aponte-Santamaría, Adva Yeheskel, Frauke Gräter, Philip J. Hogg, Freda H. Passam, Joyce Chiu

Date Published: 30th Mar 2022

Publication Type: Journal

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