Circular representative volume element for discrete model of concrete

Support of the project FAST-J-23-8323 is gratefully acknowledged. The first author is Brno Ph.D. Talent Scholarship Holder – Funded by the Brno City Municipality, Czech Republic

Development of meso-scale discrete model for simulations of ballistic experiments

The authors gratefully acknowledge financial support provided by the Faculty of Civil Engineering, Brno University of Technology under project No. FAST-T-J-23-8329

Differentially private correlation clustering

Correlation clustering is a widely used technique in unsupervised machine learning. Motivated by applications where individual privacy is a concern, we initiate the study of differentially private correlation clustering. We propose an algorithm that achieves subquadratic additive error compared to the optimal cost. In contrast, straightforward adaptations of existing non-private algorithms all lead to a trivial quadratic error. Finally, we give a lower bound showing that any pure differentially private algorithm for correlation clustering requires additive error of Ω(n)

Differentially private correlation clustering

Correlation clustering is a widely used technique in unsupervised machine learning. Motivated by applications where individual privacy is a concern, we initiate the study of differentially private correlation clustering. We propose an algorithm that achieves subquadratic additive error compared to the optimal cost. In contrast, straightforward adaptations of existing non-private algorithms all lead to a trivial quadratic error. Finally, we give a lower bound showing that any pure differentially private algorithm for correlation clustering requires additive error of $\Omega(n)$

Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase

Rheb is a conserved and widespread Ras-like GTPase involved in cell growth regulation mediated by the (m)TORC1 kinase complex and implicated in tumourigenesis in humans. Rheb function depends on its association with membranes via prenylated C-terminus, a mechanism shared with many other eukaryotic GTPases. Strikingly, our analysis of a phylogenetically rich sample of Rheb sequences revealed that in multiple lineages this canonical and ancestral membrane attachment mode has been variously altered. The modifications include: (1) accretion to the N-terminus of two different phosphatidylinositol 3-phosphate-binding domains, PX in Cryptista (the fusion being the first proposed synapomorphy of this clade), and FYVE in Euglenozoa and the related undescribed flagellate SRT308; (2) acquisition of lipidic modifications of the N-terminal region, namely myristoylation and/or S-palmitoylation in seven different protist lineages; (3) acquisition of S-palmitoylation in the hypervariable C-terminal region of Rheb in apusomonads, convergently to some other Ras family proteins; (4) replacement of the C-terminal prenylation motif with four transmembrane segments in a novel Rheb paralog in the SAR clade; (5) loss of an evident C-terminal membrane attachment mechanism in Tremellomycetes and some Rheb paralogs of Euglenozoa. Rheb evolution is thus surprisingly dynamic and presents a spectacular example of molecular tinkering

Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase

Rheb is a conserved and widespread Ras-like GTPase involved in cell growth regulation mediated by the (m)TORC1 kinase complex and implicated in tumourigenesis in humans. Rheb function depends on its association with membranes via prenylated C-terminus, a mechanism shared with many other eukaryotic GTPases. Strikingly, our analysis of a phylogenetically rich sample of Rheb sequences revealed that in multiple lineages this canonical and ancestral membrane attachment mode has been variously altered. The modifications include: (1) accretion to the N-terminus of two different phosphatidylinositol 3-phosphate-binding domains, PX in Cryptista (the fusion being the first proposed synapomorphy of this clade), and FYVE in Euglenozoa and the related undescribed flagellate SRT308; (2) acquisition of lipidic modifications of the N-terminal region, namely myristoylation and/or S-palmitoylation in seven different protist lineages; (3) acquisition of S-palmitoylation in the hypervariable C-terminal region of Rheb in apusomonads, convergently to some other Ras family proteins; (4) replacement of the C-terminal prenylation motif with four transmembrane segments in a novel Rheb paralog in the SAR clade; (5) loss of an evident C-terminal membrane attachment mechanism in Tremellomycetes and some Rheb paralogs of Euglenozoa. Rheb evolution is thus surprisingly dynamic and presents a spectacular example of molecular tinkering

Formin homology 2 domains occur in multiple contexts in angiosperms

BACKGROUND: Involvement of conservative molecular modules and cellular mechanisms in the widely diversified processes of eukaryotic cell morphogenesis leads to the intriguing question: how do similar proteins contribute to dissimilar morphogenetic outputs. Formins (FH2 proteins) play a central part in the control of actin organization and dynamics, providing a good example of evolutionarily versatile use of a conserved protein domain in the context of a variety of lineage-specific structural and signalling interactions. RESULTS: In order to identify possible plant-specific sequence features within the FH2 protein family, we performed a detailed analysis of angiosperm formin-related sequences available in public databases, with particular focus on the complete Arabidopsis genome and the nearly finished rice genome sequence. This has led to revision of the current annotation of half of the 22 Arabidopsis formin-related genes. Comparative analysis of the two plant genomes revealed a good conservation of the previously described two subfamilies of plant formins (Class I and Class II), as well as several subfamilies within them that appear to predate the separation of monocot and dicot plants. Moreover, a number of plant Class II formins share an additional conserved domain, related to the protein phosphatase/tensin/auxilin fold. However, considerable inter-species variability sets limits to generalization of any functional conclusions reached on a single species such as Arabidopsis. CONCLUSIONS: The plant-specific domain context of the conserved FH2 domain, as well as plant-specific features of the domain itself, may reflect distinct functional requirements in plant cells. The variability of formin structures found in plants far exceeds that known from both fungi and metazoans, suggesting a possible contribution of FH2 proteins in the evolution of the plant type of multicellularity

Constraining long-term denudation and faulting history in intraplate regions by multisystem thermochronology: An example of the Sudetic Marginal Fault (Bohemian Massif, central Europe)

The Rychlebské hory Mountain region in the Sudetes (NE Bohemian Massif) provides a natural laboratory for studies of postorogenic landscape evolution. This work reveals both the exhumation history of the region and the paleoactivity along the Sudetic Marginal Fault (SMF) using zircon (U-Th)/He (ZHe), apatite fission track (AFT), and apatite (U-Th)/He (AHe) dating of crystalline basement and postorogenic sedimentary samples. Most significantly, and in direct contradiction of traditional paleogeographic reconstructions, this work has found evidence of a large Cretaceous sea and regional burial (to >6.5 km) of the Carboniferous-Permian basement in the Late Cretaceous (~95–80 Ma). During the burial by sediments of the Bohemian Cretaceous Basin System, the SMF acted as a normal fault as documented by offset ZHe ages across the fault. At 85–70 Ma, the basin was inverted, Cretaceous strata eroded, and basement blocks were exhumed to the near surface at a rate of ~300 m/Ma as evidenced by Late Cretaceous–Paleocene AFT ages and thermal modeling results. There is no appreciable difference in AFT and AHe ages across the fault, suggesting that the SMF acted as a reverse fault during exhumation. In the late Eocene–Oligocene, the basement was locally heated to <70°C by magmatic activity related to opening of the Eger rift system. Neogene or younger thermal activity was not recorded in the thermochronological data, confirming that late Cenozoic uplift and erosion of the basement blocks was limited to less than ∼1.5 km in the study area