@article{12163, abstract = {Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time.}, author = {Loose, Martin and Auer, Albert and Brognara, Gabriel and Budiman, Hanifatul R and Kowalski, Lukasz M and Matijevic, Ivana}, issn = {1873-3468}, journal = {FEBS Letters}, keywords = {Cell Biology, Genetics, Molecular Biology, Biochemistry, Structural Biology, Biophysics}, number = {6}, pages = {762--777}, publisher = {Wiley}, title = {{In vitro reconstitution of small GTPase regulation}}, doi = {10.1002/1873-3468.14540}, volume = {597}, year = {2023}, } @article{12164, abstract = {A shared-memory counter is a widely-used and well-studied concurrent object. It supports two operations: An Inc operation that increases its value by 1 and a Read operation that returns its current value. In Jayanti et al (SIAM J Comput, 30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case step complexity of obstruction-free implementations, from read-write registers, of a large class of shared objects that includes counters. The lower bound leaves open the question of finding counter implementations with sub-linear amortized step complexity. In this work, we address this gap. We show that n-process, wait-free and linearizable counters can be implemented from read-write registers with O(log2n) amortized step complexity. This is the first counter algorithm from read-write registers that provides sub-linear amortized step complexity in executions of arbitrary length. Since a logarithmic lower bound on the amortized step complexity of obstruction-free counter implementations exists, our upper bound is within a logarithmic factor of the optimal. The worst-case step complexity of the construction remains linear, which is optimal. This is obtained thanks to a new max register construction with O(logn) amortized step complexity in executions of arbitrary length in which the value stored in the register does not grow too quickly. We then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel [1] in which we “plug” our max register implementation to show that it remains linearizable while achieving O(log2n) amortized step complexity.}, author = {Baig, Mirza Ahad and Hendler, Danny and Milani, Alessia and Travers, Corentin}, issn = {1432-0452}, journal = {Distributed Computing}, keywords = {Computational Theory and Mathematics, Computer Networks and Communications, Hardware and Architecture, Theoretical Computer Science}, pages = {29--43}, publisher = {Springer Nature}, title = {{Long-lived counters with polylogarithmic amortized step complexity}}, doi = {10.1007/s00446-022-00439-5}, volume = {36}, year = {2023}, } @article{12515, abstract = {Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents. Methods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques. Results: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity. Discussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues.}, author = {Ortiz-Leal, Irene and Torres, Mateo V. and Vargas Barroso, Victor M and Fidalgo, Luis Eusebio and López-Beceiro, Ana María and Larriva-Sahd, Jorge A. and Sánchez-Quinteiro, Pablo}, issn = {1662-5129}, journal = {Frontiers in Neuroanatomy}, publisher = {Frontiers}, title = {{The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway}}, doi = {10.3389/fnana.2022.1097467}, volume = {16}, year = {2023}, } @article{12106, abstract = {Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.}, author = {Yeung, Jake and Florescu, Maria and Zeller, Peter and De Barbanson, Buys Anton and Wellenstein, Max D. and Van Oudenaarden, Alexander}, issn = {1546-1696}, journal = {Nature Biotechnology}, pages = {813–823}, publisher = {Springer Nature}, title = {{scChIX-seq infers dynamic relationships between histone modifications in single cells}}, doi = {10.1038/s41587-022-01560-3}, volume = {41}, year = {2023}, } @article{12183, abstract = {We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii regime, with an optimal bound on the condensate depletion. Moreover, our lower bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann bracketing) a lower bound for the ground state energy of N bosons in a large box [−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit.}, author = {Boccato, Chiara and Seiringer, Robert}, issn = {1424-0637}, journal = {Annales Henri Poincare}, pages = {1505--1560}, publisher = {Springer Nature}, title = {{The Bose Gas in a box with Neumann boundary conditions}}, doi = {10.1007/s00023-022-01252-3}, volume = {24}, year = {2023}, }