@article{10755, abstract = {We provide a definition of the effective mass for the classical polaron described by the Landau–Pekar (LP) equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by LP (1948 J. Exp. Theor. Phys. 18 419–423).}, author = {Feliciangeli, Dario and Rademacher, Simone Anna Elvira and Seiringer, Robert}, issn = {1751-8121}, journal = {Journal of Physics A: Mathematical and Theoretical}, number = {1}, publisher = {IOP Publishing}, title = {{The effective mass problem for the Landau-Pekar equations}}, doi = {10.1088/1751-8121/ac3947}, volume = {55}, year = {2022}, } @article{10758, abstract = {5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark.}, author = {Dubini, Romeo C. A. and Korytiaková, Eva and Schinkel, Thea and Heinrichs, Pia and Carell, Thomas and Rovo, Petra}, issn = {2694-2445}, journal = {ACS Physical Chemistry Au}, number = {3}, pages = {237--246}, publisher = {American Chemical Society}, title = {{1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives}}, doi = {10.1021/acsphyschemau.1c00050}, volume = {2}, year = {2022}, } @article{10765, abstract = {We establish the Hardy-Littlewood property (à la Borovoi-Rudnick) for Zariski open subsets in affine quadrics of the form q(x1,...,xn)=m, where q is a non-degenerate integral quadratic form in n>3 variables and m is a non-zero integer. This gives asymptotic formulas for the density of integral points taking coprime polynomial values, which is a quantitative version of the arithmetic purity of strong approximation property off infinity for affine quadrics.}, author = {Cao, Yang and Huang, Zhizhong}, issn = {1090-2082}, journal = {Advances in Mathematics}, number = {3}, publisher = {Elsevier}, title = {{Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics}}, doi = {10.1016/j.aim.2022.108236}, volume = {398}, year = {2022}, } @article{10768, abstract = {Among the most fascinated properties of the plant hormone auxin is its ability to promote formation of its own directional transport routes. These gradually narrowing auxin channels form from the auxin source toward the sink and involve coordinated, collective polarization of individual cells. Once established, the channels provide positional information, along which new vascular strands form, for example, during organogenesis, regeneration, or leave venation. The main prerequisite of this still mysterious auxin canalization mechanism is a feedback between auxin signaling and its directional transport. This is manifested by auxin-induced re-arrangements of polar, subcellular localization of PIN-FORMED (PIN) auxin exporters. Immanent open questions relate to how position of auxin source and sink as well as tissue context are sensed and translated into tissue polarization and how cells communicate to polarize coordinately. Recently, identification of the first molecular players opens new avenues into molecular studies of this intriguing example of self-organizing plant development.}, author = {Hajny, Jakub and Tan, Shutang and Friml, Jiří}, issn = {1369-5266}, journal = {Current Opinion in Plant Biology}, number = {2}, publisher = {Elsevier}, title = {{Auxin canalization: From speculative models toward molecular players}}, doi = {10.1016/j.pbi.2022.102174}, volume = {65}, year = {2022}, } @article{10772, abstract = {We introduce tropical corals, balanced trees in a half-space, and show that they correspond to holomorphic polygons capturing the product rule in Lagrangian Floer theory for the elliptic curve. We then prove a correspondence theorem equating counts of tropical corals to punctured log Gromov–Witten invariants of the Tate curve. This implies that the homogeneous coordinate ring of the mirror to the Tate curve is isomorphic to the degree-zero part of symplectic cohomology, confirming a prediction of homological mirror symmetry.}, author = {Arguez, Nuroemuer Huelya}, issn = {1469-7750}, journal = {Journal of the London Mathematical Society}, number = {1}, pages = {343--411}, publisher = {London Mathematical Society}, title = {{Mirror symmetry for the Tate curve via tropical and log corals}}, doi = {10.1112/jlms.12515}, volume = {105}, year = {2022}, } @article{10773, abstract = {The Voronoi tessellation in Rd is defined by locally minimizing the power distance to given weighted points. Symmetrically, the Delaunay mosaic can be defined by locally maximizing the negative power distance to other such points. We prove that the average of the two piecewise quadratic functions is piecewise linear, and that all three functions have the same critical points and values. Discretizing the two piecewise quadratic functions, we get the alpha shapes as sublevel sets of the discrete function on the Delaunay mosaic, and analogous shapes as superlevel sets of the discrete function on the Voronoi tessellation. For the same non-critical value, the corresponding shapes are disjoint, separated by a narrow channel that contains no critical points but the entire level set of the piecewise linear function.}, author = {Biswas, Ranita and Cultrera Di Montesano, Sebastiano and Edelsbrunner, Herbert and Saghafian, Morteza}, issn = {1432-0444}, journal = {Discrete and Computational Geometry}, pages = {811--842}, publisher = {Springer Nature}, title = {{Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics}}, doi = {10.1007/s00454-022-00371-2}, volume = {67}, year = {2022}, } @inproceedings{10774, abstract = {We study the problem of specifying sequential information-flow properties of systems. Information-flow properties are hyperproperties, as they compare different traces of a system. Sequential information-flow properties can express changes, over time, in the information-flow constraints. For example, information-flow constraints during an initialization phase of a system may be different from information-flow constraints that are required during the operation phase. We formalize several variants of interpreting sequential information-flow constraints, which arise from different assumptions about what can be observed of the system. For this purpose, we introduce a first-order logic, called Hypertrace Logic, with both trace and time quantifiers for specifying linear-time hyperproperties. We prove that HyperLTL, which corresponds to a fragment of Hypertrace Logic with restricted quantifier prefixes, cannot specify the majority of the studied variants of sequential information flow, including all variants in which the transition between sequential phases (such as initialization and operation) happens asynchronously. Our results rely on new equivalences between sets of traces that cannot be distinguished by certain classes of formulas from Hypertrace Logic. This presents a new approach to proving inexpressiveness results for HyperLTL.}, author = {Bartocci, Ezio and Ferrere, Thomas and Henzinger, Thomas A and Nickovic, Dejan and Da Costa, Ana Oliveira}, booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)}, isbn = {9783030945824}, issn = {16113349}, location = {Philadelphia, PA, United States}, pages = {1--19}, publisher = {Springer Nature}, title = {{Flavors of sequential information flow}}, doi = {10.1007/978-3-030-94583-1_1}, volume = {13182}, year = {2022}, } @article{10775, abstract = {List-decodability of Reed–Solomon codes has received a lot of attention, but the best-possible dependence between the parameters is still not well-understood. In this work, we focus on the case where the list-decoding radius is of the form r = 1-ε for ε tending to zero. Our main result states that there exist Reed–Solomon codes with rate Ω(ε) which are (1 - ε, O(1/ε))-list-decodable, meaning that any Hamming ball of radius 1-ε contains at most O(1/ε) codewords. This trade-off between rate and list-decoding radius is best-possible for any code with list size less than exponential in the block length. By achieving this trade-off between rate and list-decoding radius we improve a recent result of Guo, Li, Shangguan, Tamo, and Wootters, and resolve the main motivating question of their work. Moreover, while their result requires the field to be exponentially large in the block length, we only need the field size to be polynomially large (and in fact, almost-linear suffices). We deduce our main result from a more general theorem, in which we prove good list-decodability properties of random puncturings of any given code with very large distance.}, author = {Ferber, Asaf and Kwan, Matthew Alan and Sauermann, Lisa}, issn = {1557-9654}, journal = {IEEE Transactions on Information Theory}, number = {6}, pages = {3823--3828}, publisher = {IEEE}, title = {{List-decodability with large radius for Reed-Solomon codes}}, doi = {10.1109/TIT.2022.3148779}, volume = {68}, year = {2022}, } @article{10776, abstract = {Let K be a convex body in Rn (i.e., a compact convex set with nonempty interior). Given a point p in the interior of K, a hyperplane h passing through p is called barycentric if p is the barycenter of K∩h. In 1961, Grünbaum raised the question whether, for every K, there exists an interior point p through which there are at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly resolved affirmatively by showing that this is the case if p=p0 is the point of maximal depth in K. However, while working on a related question, we noticed that one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample; this re-opens Grünbaum’s question. It follows from known results that for n≥2, there are always at least three distinct barycentric cuts through the point p0∈K of maximal depth. Using tools related to Morse theory we are able to improve this bound: four distinct barycentric cuts through p0 are guaranteed if n≥3.}, author = {Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, issn = {1432-0444}, journal = {Discrete and Computational Geometry}, pages = {1133--1154}, publisher = {Springer Nature}, title = {{Barycentric cuts through a convex body}}, doi = {10.1007/s00454-021-00364-7}, volume = {68}, year = {2022}, } @unpublished{10788, abstract = {We determine an asymptotic formula for the number of integral points of bounded height on a certain toric variety, which is incompatible with part of a preprint by Chambert-Loir and Tschinkel. We provide an alternative interpretation of the asymptotic formula we get. To do so, we construct an analogue of Peyre's constant $\alpha$ and describe its relation to a new obstruction to the Zariski density of integral points in certain regions of varieties.}, author = {Wilsch, Florian Alexander}, booktitle = {arXiv}, keywords = {Integral point, toric variety, Manin's conjecture}, title = {{Integral points of bounded height on a certain toric variety}}, doi = {10.48550/arXiv.2202.10909}, year = {2022}, } @unpublished{10792, abstract = {Background Proper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology . Methods Here, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild type cells concomitantly in vivo using immunofluorescent techniques. Results We revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages. Limitations While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients. Conclusions Our genetic approach revealed several cell autonomous requirements of Wdfy3 in neuronal development that could underly the pathogenic mechanisms of WDFY3-related ASD conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for Wdfy3 in regulating neuronal function and interconnectivity in postnatal life.}, author = {Schaaf, Zachary and Tat, Lyvin and Cannizzaro, Noemi and Green, Ralph and Rülicke, Thomas and Hippenmeyer, Simon and Zarbalis, K}, issn = {2693-5015}, pages = {30}, publisher = {Research Square}, title = {{WDFY3 cell autonomously controls neuronal migration}}, doi = {10.21203/rs.3.rs-1316167/v1}, year = {2022}, } @article{10797, abstract = {We consider symmetric partial exclusion and inclusion processes in a general graph in contact with reservoirs, where we allow both for edge disorder and well-chosen site disorder. We extend the classical dualities to this context and then we derive new orthogonal polynomial dualities. From the classical dualities, we derive the uniqueness of the non-equilibrium steady state and obtain correlation inequalities. Starting from the orthogonal polynomial dualities, we show universal properties of n-point correlation functions in the non-equilibrium steady state for systems with at most two different reservoir parameters, such as a chain with reservoirs at left and right ends.}, author = {Floreani, Simone and Redig, Frank and Sau, Federico}, issn = {0246-0203}, journal = {Annales de l'institut Henri Poincare (B) Probability and Statistics}, number = {1}, pages = {220--247}, publisher = {Institute of Mathematical Statistics}, title = {{Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations}}, doi = {10.1214/21-AIHP1163}, volume = {58}, year = {2022}, } @article{10812, abstract = {Several promising strategies based on combining or cycling different antibiotics have been proposed to increase efficacy and counteract resistance evolution, but we still lack a deep understanding of the physiological responses and genetic mechanisms that underlie antibiotic interactions and the clinical applicability of these strategies. In antibiotic-exposed bacteria, the combined effects of physiological stress responses and emerging resistance mutations (occurring at different time scales) generate complex and often unpredictable dynamics. In this Review, we present our current understanding of bacterial cell physiology and genetics of responses to antibiotics. We emphasize recently discovered mechanisms of synergistic and antagonistic drug interactions, hysteresis in temporal interactions between antibiotics that arise from microbial physiology and interactions between antibiotics and resistance mutations that can cause collateral sensitivity or cross-resistance. We discuss possible connections between the different phenomena and indicate relevant research directions. A better and more unified understanding of drug and genetic interactions is likely to advance antibiotic therapy.}, author = {Römhild, Roderich and Bollenbach, Mark Tobias and Andersson, Dan I.}, issn = {1740-1534}, journal = {Nature Reviews Microbiology}, keywords = {General Immunology and Microbiology, Microbiology, Infectious Diseases}, pages = {478--490}, publisher = {Springer Nature}, title = {{The physiology and genetics of bacterial responses to antibiotic combinations}}, doi = {10.1038/s41579-022-00700-5}, volume = {20}, year = {2022}, } @article{10813, abstract = {Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li–S and Li–O2 batteries by shuttling electrons or holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics but with the lowest possible overpotential. However, the dependence of kinetics and overpotential is unclear, which hinders informed improvement. Here, we find that when the redox potentials of mediators are tuned via, for example, Li+ concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediator and electrolyte. The acceleration originates from the overpotentials required to activate fast Li+/e− extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids therefore requires careful consideration of the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents.}, author = {Cao, Deqing and Shen, Xiaoxiao and Wang, Aiping and Yu, Fengjiao and Wu, Yuping and Shi, Siqi and Freunberger, Stefan Alexander and Chen, Yuhui}, issn = {2520-1158}, journal = {Nature Catalysis}, keywords = {Process Chemistry and Technology, Biochemistry, Bioengineering, Catalysis}, pages = {193--201}, publisher = {Springer Nature}, title = {{Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries}}, doi = {10.1038/s41929-022-00752-z}, volume = {5}, year = {2022}, } @article{10818, abstract = {Microglia cells are active players in regulating synaptic development and plasticity in the brain. However, how they influence the normal functioning of synapses is largely unknown. In this study, we characterized the effects of pharmacological microglia depletion, achieved by administration of PLX5622, on hippocampal CA3-CA1 synapses of adult wild type mice. Following microglial depletion, we observed a reduction of spontaneous and evoked glutamatergic activity associated with a decrease of dendritic spine density. We also observed the appearance of immature synaptic features and higher levels of plasticity. Microglia depleted mice showed a deficit in the acquisition of the Novel Object Recognition task. These events were accompanied by hippocampal astrogliosis, although in the absence ofneuroinflammatory condition. PLX-induced synaptic changes were absent in Cx3cr1−/− mice, highlighting the role of CX3CL1/CX3CR1 axis in microglia control of synaptic functioning. Remarkably, microglia repopulation after PLX5622 withdrawal was associated with the recovery of hippocampal synapses and learning functions. Altogether, these data demonstrate that microglia contribute to normal synaptic functioning in the adult brain and that their removal induces reversible changes in organization and activity of glutamatergic synapses.}, author = {Basilico, Bernadette and Ferrucci, Laura and Ratano, Patrizia and Golia, Maria T. and Grimaldi, Alfonso and Rosito, Maria and Ferretti, Valentina and Reverte, Ingrid and Sanchini, Caterina and Marrone, Maria C. and Giubettini, Maria and De Turris, Valeria and Salerno, Debora and Garofalo, Stefano and St‐Pierre, Marie‐Kim and Carrier, Micael and Renzi, Massimiliano and Pagani, Francesca and Modi, Brijesh and Raspa, Marcello and Scavizzi, Ferdinando and Gross, Cornelius T. and Marinelli, Silvia and Tremblay, Marie‐Ève and Caprioli, Daniele and Maggi, Laura and Limatola, Cristina and Di Angelantonio, Silvia and Ragozzino, Davide}, issn = {1098-1136}, journal = {Glia}, keywords = {Cellular and Molecular Neuroscience, Neurology}, number = {1}, pages = {173--195}, publisher = {Wiley}, title = {{Microglia control glutamatergic synapses in the adult mouse hippocampus}}, doi = {10.1002/glia.24101}, volume = {70}, year = {2022}, } @inproceedings{10820, abstract = {Streaky structures in the boundary layers are often generated by surface roughness elements and/or free-stream turbulence, and are known to have significant effects on boundary-layer instability. In this paper, we investigate the impact of two forms of streaks on the instability of supersonic boundary layers. The first concerns the streaks generated by an array of spanwise periodic and streamwise elongated surface roughness elements, and our interest is how these streaks influence the lower-branch viscous first modes, whose characteristic wavelength and frequency are on the classical triple-deck scales. By adapting the triple-deck theory in the incompressible regime to the supersonic one, we first derived a simplified system which allows for efficient calculation of the streaks. The asymptotic analysis simplifies a bi-global eigenvalue problem to a one-dimensional problem in the spanwise direction, showing that the instability is controlled at leading order solely by the spanwise-dependent wall shear. In the fundamental configuration, the streaks stabilize first modes at low frequencies but destabilize the high-frequency ones. In the subharmonic configuration, the streaks generally destabilize the first mode across the entire frequency band. Importantly, the spanwise even modes are of radiating nature, i.e. they emit acoustic waves spontaneously to the far field. Streaks of the second form are generated by low-frequency vortical disturbances representing free-stream turbulence. They alter the flow in the entire layer and their effects on instability are investigated by solving the inviscid bi-global eigenvalue problem. Different from the incompressible case, a multitude of compressible instability modes exists, of which the dominant mode is an inviscid instability associated with the spanwise shear. In addition, there exists a separate branch of instability modes that have smaller growth rates but are spontaneously radiating.}, author = {Liu, Jianxin and Marensi, Elena and Wu, Xuesong}, booktitle = {IUTAM Laminar-Turbulent Transition}, isbn = {9783030679019}, issn = {1875-3493}, location = {London, United Kingdom}, pages = {587--598}, publisher = {Springer Nature}, title = {{Effects of streaky structures on the instability of supersonic boundary layers}}, doi = {10.1007/978-3-030-67902-6_51}, volume = {38}, year = {2022}, } @unpublished{10821, abstract = {Rhythmical cortical activity has long been recognized as a pillar in the architecture of brain functions. Yet, the dynamic organization of its underlying neuronal population activity remains elusive. Here we uncover a unique organizational principle regulating collective neural dynamics associated with the alpha rhythm in the awake resting-state. We demonstrate that cascades of neural activity obey attenuation-amplification dynamics (AAD), with a transition from the attenuation regime—within alpha cycles—to the amplification regime—across a few alpha cycles—that correlates with the characteristic frequency of the alpha rhythm. We find that this short-term AAD is part of a large-scale, size-dependent temporal structure of neural cascades that obeys the Omori law: Following large cascades, smaller cascades occur at a rate that decays as a power-law of the time elapsed from such events—a long-term AAD regulating brain activity over the timescale of seconds. We show that such an organization corresponds to the "waxing and waning" of the alpha rhythm. Importantly, we observe that short- and long-term AAD are unique to the awake resting-state, being absent during NREM sleep. These results provide a quantitative, dynamical description of the so-far-qualitative notion of the "waxing and waning" phenomenon, and suggest the AAD as a key principle governing resting-state dynamics across timescales.}, author = {Lombardi, Fabrizio and Herrmann, Hans J. and Parrino, Liborio and Plenz, Dietmar and Scarpetta, Silvia and Vaudano, Anna Elisabetta and de Arcangelis, Lucilla and Shriki, Oren}, booktitle = {bioRxiv}, pages = {25}, publisher = {Cold Spring Harbor Laboratory}, title = {{Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades}}, doi = {10.1101/2022.03.03.482657}, year = {2022}, } @article{10825, abstract = {In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages.}, author = {Yanagida, Ayaka and Corujo-Simon, Elena and Revell, Christopher K. and Sahu, Preeti and Stirparo, Giuliano G. and Aspalter, Irene M. and Winkel, Alex K. and Peters, Ruby and De Belly, Henry and Cassani, Davide A.D. and Achouri, Sarra and Blumenfeld, Raphael and Franze, Kristian and Hannezo, Edouard B and Paluch, Ewa K. and Nichols, Jennifer and Chalut, Kevin J.}, issn = {1097-4172}, journal = {Cell}, number = {5}, pages = {777--793.e20}, publisher = {Cell Press}, title = {{Cell surface fluctuations regulate early embryonic lineage sorting}}, doi = {10.1016/j.cell.2022.01.022}, volume = {185}, year = {2022}, } @article{10841, abstract = {In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.}, author = {Dahhan, DA and Reynolds, GD and Cárdenas, JJ and Eeckhout, D and Johnson, Alexander J and Yperman, K and Kaufmann, Walter and Vang, N and Yan, X and Hwang, I and Heese, A and De Jaeger, G and Friml, Jiří and Van Damme, D and Pan, J and Bednarek, SY}, issn = {1532-298x}, journal = {Plant Cell}, number = {6}, pages = {2150--2173}, publisher = {Oxford University Press}, title = {{Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components}}, doi = {10.1093/plcell/koac071}, volume = {34}, year = {2022}, } @article{10842, abstract = {We determine the unique factorization of some polynomials over a finite local commutative ring with identity explicitly. This solves and generalizes the main conjecture of Qian, Shi and Solé in [13]. We also give some applications to enumeration of certain generalized double circulant self-dual and linear complementary dual (LCD) codes over some finite rings together with an application in asymptotic coding theory.}, author = {Köse, Seyda and Özbudak, Ferruh}, issn = {1936-2455}, journal = {Cryptography and Communications}, keywords = {Applied Mathematics, Computational Theory and Mathematics, Computer Networks and Communications}, number = {4}, pages = {933--948}, publisher = {Springer Nature}, title = {{Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes}}, doi = {10.1007/s12095-022-00557-8}, volume = {14}, year = {2022}, }