@article{14610,
abstract = {Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3–7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host.},
author = {Bussi, Claudio and Mangiarotti, Agustín and Vanhille-Campos, Christian Eduardo and Aylan, Beren and Pellegrino, Enrica and Athanasiadi, Natalia and Fearns, Antony and Rodgers, Angela and Franzmann, Titus M. and Šarić, Anđela and Dimova, Rumiana and Gutierrez, Maximiliano G.},
issn = {1476-4687},
journal = {Nature},
pages = {1062--1069},
publisher = {Springer Nature},
title = {{Stress granules plug and stabilize damaged endolysosomal membranes}},
doi = {10.1038/s41586-023-06726-w},
volume = {623},
year = {2023},
}
@misc{14614,
abstract = {Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.},
author = {Lasne, Clementine and Elkrewi, Marwan N},
keywords = {Panorpa, scorpionfly, genome, transcriptome},
publisher = {Institute of Science and Technology Austria},
title = {{The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome}},
doi = {10.15479/AT:ISTA:14614},
year = {2023},
}
@misc{14616,
abstract = {Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.},
author = {Toups, Melissa A and Vicoso, Beatriz},
publisher = {Dryad},
title = {{The X chromosome of insects likely predates the origin of Class Insecta}},
doi = {10.5061/DRYAD.HX3FFBGKT},
year = {2023},
}
@misc{14617,
abstract = {Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.},
author = {Toups, Melissa A and Vicoso, Beatriz},
publisher = {Zenodo},
title = {{The X chromosome of insects likely predates the origin of Class Insecta}},
doi = {10.5281/ZENODO.8138705},
year = {2023},
}
@article{14628,
abstract = {We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration.},
author = {Makatura, Liane and Wang, Bohan and Chen, Yi-Lu and Deng, Bolei and Wojtan, Christopher J and Bickel, Bernd and Matusik, Wojciech},
issn = {1557-7368},
journal = {ACM Transactions on Graphics},
keywords = {Computer Graphics and Computer-Aided Design},
number = {5},
publisher = {Association for Computing Machinery},
title = {{Procedural metamaterials: A unified procedural graph for metamaterial design}},
doi = {10.1145/3605389},
volume = {42},
year = {2023},
}
@unpublished{14644,
abstract = {Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression.},
author = {Tluckova, Katarina and Testa Salmazo, Anita P and Bernecky, Carrie A},
publisher = {Institute of Science and Technology Austria},
title = {{Mechanism of mammalian transcriptional repression by noncoding RNA}},
doi = {10.15479/AT:ISTA:14644},
year = {2023},
}
@article{14650,
abstract = {We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e., impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the impurity-boson interaction. We show that the dipolar nature of the condensate and of the impurity results in anisotropic relaxation dynamics, in particular, anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench dynamics is strongly affected by the interplay between dipolar anisotropy and trap geometry. Our findings pave the way for simulating impurities in anisotropic media utilizing experiments with dipolar mixtures.},
author = {Volosniev, Artem and Bighin, Giacomo and Santos, Luis and Peña Ardila, Luisllu A.},
issn = {2542-4653},
journal = {SciPost Physics},
keywords = {General Physics and Astronomy},
number = {6},
publisher = {SciPost Foundation},
title = {{Non-equilibrium dynamics of dipolar polarons}},
doi = {10.21468/scipostphys.15.6.232},
volume = {15},
year = {2023},
}
@phdthesis{14651,
abstract = {For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.},
author = {Arathoon, Louise S},
issn = {2663-337X},
pages = {96},
publisher = {Institute of Science and Technology Austria},
title = {{Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus}},
doi = {10.15479/at:ista:14651},
year = {2023},
}
@article{14654,
abstract = {Two assumptions commonly applied in convection schemes—the diagnostic and quasi-equilibrium assumptions—imply that convective activity (e.g., convective precipitation) is controlled only by the large-scale (macrostate) environment at the time. In contrast, numerical experiments indicate a “memory” or dependence of convection also on its own previous activity whereby subgrid-scale (microstate) structures boost but are also boosted by convection. In this study we investigated this memory by comparing single-column model behavior in two idealized tests previously executed by a cloud-resolving model (CRM). Conventional convection schemes that employ the diagnostic assumption fail to reproduce the CRM behavior. The memory-capable org and Laboratoire de Météorologie Dynamique Zoom cold pool schemes partially capture the behavior, but fail to fully exhibit the strong reinforcing feedbacks implied by the CRM. Analysis of this failure suggests that it is because the CRM supports a linear (or superlinear) dependence of the subgrid structure growth rate on the precipitation rate, while the org scheme assumes a sublinear dependence. Among varying versions of the org scheme, the growth rate of the org variable representing subgrid structure is strongly associated with memory strength. These results demonstrate the importance of parameterizing convective memory, and the ability of idealized tests to reveal shortcomings of convection schemes and constrain model structural assumptions.},
author = {Hwong, Yi-Ling and Colin, M. and Aglas, Philipp and Muller, Caroline J and Sherwood, S. C.},
issn = {1942-2466},
journal = {Journal of Advances in Modeling Earth Systems},
number = {12},
publisher = {Wiley},
title = {{Assessing memory in convection schemes using idealized tests}},
doi = {10.1029/2023MS003726},
volume = {15},
year = {2023},
}
@article{14655,
abstract = {The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments’ ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division.},
author = {Sorichetti, Valerio and Lenz, Martin},
issn = {1079-7114},
journal = {Physical Review Letters},
number = {22},
publisher = {American Physical Society},
title = {{Transverse fluctuations control the assembly of semiflexible filaments}},
doi = {10.1103/PhysRevLett.131.228401},
volume = {131},
year = {2023},
}
@article{14658,
abstract = {We investigate spin-charge separation of a spin-
1
2
Fermi system confined in a triple well where multiple bands are occupied. We assume that our finite fermionic system is close to fully spin polarized while being doped by a hole and an impurity fermion with opposite spin. Our setup involves ferromagnetic couplings among the particles in different bands, leading to the development of strong spin-transport correlations in an intermediate interaction regime. Interactions are then strong enough to lift the degeneracy among singlet and triplet spin configurations in the well of the spin impurity but not strong enough to prohibit hole-induced magnetic excitations to the singlet state. Despite the strong spin-hole correlations, the system exhibits spin-charge deconfinement allowing for long-range entanglement of the spatial and spin degrees of freedom.},
author = {Becker, J. M. and Koutentakis, Georgios and Schmelcher, P.},
issn = {2643-1564},
journal = {Physical Review Research},
number = {4},
publisher = {American Physical Society},
title = {{Spin-charge correlations in finite one-dimensional multiband Fermi systems}},
doi = {10.1103/PhysRevResearch.5.043039},
volume = {5},
year = {2023},
}
@article{14659,
abstract = {Understanding the response of Himalayan glaciers to global warming is vital because of their role as a water source for the Asian subcontinent. However, great uncertainties still exist on the climate drivers of past and present glacier changes across scales. Here, we analyse continuous hourly climate station data from a glacierized elevation (Pyramid station, Mount Everest) since 1994 together with other ground observations and climate reanalysis. We show that a decrease in maximum air temperature and precipitation occurred during the last three decades at Pyramid in response to global warming. Reanalysis data suggest a broader occurrence of this effect in the glacierized areas of the Himalaya. We hypothesize that the counterintuitive cooling is caused by enhanced sensible heat exchange and the associated increase in glacier katabatic wind, which draws cool air downward from higher elevations. The stronger katabatic winds have also lowered the elevation of local wind convergence, thereby diminishing precipitation in glacial areas and negatively affecting glacier mass balance. This local cooling may have partially preserved glaciers from melting and could help protect the periglacial environment.},
author = {Salerno, Franco and Guyennon, Nicolas and Yang, Kun and Shaw, Thomas and Lin, Changgui and Colombo, Nicola and Romano, Emanuele and Gruber, Stephan and Bolch, Tobias and Alessandri, Andrea and Cristofanelli, Paolo and Putero, Davide and Diolaiuti, Guglielmina and Tartari, Gianni and Verza, Gianpietro and Thakuri, Sudeep and Balsamo, Gianpaolo and Miles, Evan S. and Pellicciotti, Francesca},
issn = {1752-0908},
journal = {Nature Geoscience},
pages = {1120--1127},
publisher = {Springer Nature},
title = {{Local cooling and drying induced by Himalayan glaciers under global warming}},
doi = {10.1038/s41561-023-01331-y},
volume = {16},
year = {2023},
}
@article{14661,
abstract = {This paper is concerned with equilibrium configurations of one-dimensional particle systems with non-convex nearest-neighbour and next-to-nearest-neighbour interactions and its passage to the continuum. The goal is to derive compactness results for a Γ-development of the energy with the novelty that external forces are allowed. In particular, the forces may depend on Lagrangian or Eulerian coordinates and thus may model dead as well as live loads. Our result is based on a new technique for deriving compactness results which are required for calculating the first-order Γ-limit in the presence of external forces: instead of comparing a configuration of n atoms to a global minimizer of the Γ-limit, we compare the configuration to a minimizer in some subclass of functions which in some sense are "close to" the configuration. The paper is complemented with the study of the minimizers of the Γ-limit.},
author = {Carioni, Marcello and Fischer, Julian L and Schlömerkemper, Anja},
issn = {2363-6394},
journal = {Journal of Convex Analysis},
number = {1},
pages = {217--247},
publisher = {Heldermann Verlag},
title = {{External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development}},
volume = {30},
year = {2023},
}
@article{14662,
abstract = {We consider a class of polaron models, including the Fröhlich model, at zero total momentum, and show that at sufficiently weak coupling there are no excited eigenvalues below the essential spectrum.},
author = {Seiringer, Robert},
issn = {1664-0403},
journal = {Journal of Spectral Theory},
number = {3},
pages = {1045--1055},
publisher = {EMS Press},
title = {{Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling}},
doi = {10.4171/JST/469},
volume = {13},
year = {2023},
}
@article{14663,
abstract = {As a bottleneck in the direct synthesis of hydrogen peroxide, the development of an efficient palladium-based catalyst has garnered great attention. However, elusive active centers and reaction mechanism issues inhibit further optimization of its performance. In this work, advanced microkinetic modeling with the adsorbate–adsorbate interaction and nanoparticle size effect based on first-principles calculations is developed. A full mechanism uncovering the significance of adsorbate–adsorbate interaction is determined on Pd nanoparticles. We demonstrate unambiguously that Pd(100) with main coverage species of O2 and H is beneficial to H2O2 production, being consistent with experimental operando observation, while H2O forms on Pd(111) covered by O species and Pd(211) covered by O and OH species. Kinetic analyses further enable quantitative estimation of the influence of temperature, pressure, and particle size. Large-size Pd nanoparticles are found to achieve a high H2O2 reaction rate when the operating conditions are moderate temperature and higher oxygen partial pressure. We reveal that specific facets of the Pd nanoparticles are crucial factors for their selectivity and activity. Consistent with the experiment, the production of H2O2 is discovered to be more favorable on Pd nanoparticles containing Pd(100) facets. The ratio of H2/O2 induces substantial variations in the coverage of intermediates of O2 and H on Pd(100), resulting in a change in product selectivity.},
author = {Zhao, Jinyan and Yao, Zihao and Bunting, Rhys and Hu, P. and Wang, Jianguo},
issn = {2155-5435},
journal = {ACS Catalysis},
number = {22},
pages = {15054--15073},
publisher = {American Chemical Society},
title = {{Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles}},
doi = {10.1021/acscatal.3c03893},
volume = {13},
year = {2023},
}
@article{14664,
abstract = {The architecture of self-assembled host molecules can profoundly affect the properties of the encapsulated guests. For example, a rigid cage with small windows can efficiently protect its contents from the environment; in contrast, tube-shaped, flexible hosts with large openings and an easily accessible cavity are ideally suited for catalysis. Here, we report a “Janus” nature of a Pd6L4 coordination host previously reported to exist exclusively as a tube isomer (T). We show that upon encapsulating various tetrahedrally shaped guests, T can reconfigure into a cage-shaped host (C) in quantitative yield. Extracting the guest affords empty C, which is metastable and spontaneously relaxes to T, and the T⇄C interconversion can be repeated for multiple cycles. Reversible toggling between two vastly different isomers paves the way toward controlling functional properties of coordination hosts “on demand”.},
author = {Hema, Kuntrapakam and Grommet, Angela B. and Białek, Michał J. and Wang, Jinhua and Schneider, Laura and Drechsler, Christoph and Yanshyna, Oksana and Diskin-Posner, Yael and Clever, Guido H. and Klajn, Rafal},
issn = {1520-5126},
journal = {Journal of the American Chemical Society},
number = {45},
pages = {24755--24764},
publisher = {American Chemical Society},
title = {{Guest encapsulation alters the thermodynamic landscape of a coordination host}},
doi = {10.1021/jacs.3c08666},
volume = {145},
year = {2023},
}
@article{14667,
abstract = {For large dimensional non-Hermitian random matrices X with real or complex independent, identically distributed, centered entries, we consider the fluctuations of f (X) as a matrix where f is an analytic function around the spectrum of X. We prove that for a generic bounded square matrix A, the quantity Tr f (X)A exhibits Gaussian fluctuations as the matrix size grows to infinity, which consists of two independent modes corresponding to the tracial and traceless parts of A. We find a new formula for the variance of the traceless part that involves the Frobenius norm of A and the L2-norm of f on the boundary of the limiting spectrum. },
author = {Erdös, László and Ji, Hong Chang},
issn = {0246-0203},
journal = {Annales de l'institut Henri Poincare (B) Probability and Statistics},
number = {4},
pages = {2083--2105},
publisher = {Institute of Mathematical Statistics},
title = {{Functional CLT for non-Hermitian random matrices}},
doi = {10.1214/22-AIHP1304},
volume = {59},
year = {2023},
}
@article{14689,
author = {Ing-Simmons, Elizabeth and Machnik, Nick N and Vaquerizas, Juan M.},
issn = {1546-1718},
journal = {Nature Genetics},
number = {12},
pages = {2053--2055},
publisher = {Springer Nature},
title = {{Reply to: Revisiting the use of structural similarity index in Hi-C}},
doi = {10.1038/s41588-023-01595-5},
volume = {55},
year = {2023},
}
@article{14690,
abstract = {Generalized multifractality characterizes system size dependence of pure scaling local observables at Anderson transitions in all 10 symmetry classes of disordered systems. Recently, the concept of generalized multifractality has been extended to boundaries of critical disordered noninteracting systems. Here we study the generalized boundary multifractality in the presence of electron-electron interaction, focusing on the spin quantum Hall symmetry class (class C). Employing the two-loop renormalization group analysis within the Finkel'stein nonlinear sigma model, we compute the anomalous dimensions of the pure scaling operators located at the boundary of the system. We find that generalized boundary multifractal exponents are twice larger than their bulk counterparts. Exact symmetry relations between generalized boundary multifractal exponents in the case of noninteracting systems are explicitly broken by the interaction.},
author = {Babkin, Serafim and Burmistrov, I},
issn = {2469-9969},
journal = {Physical Review B},
number = {20},
publisher = {American Physical Society},
title = {{Boundary multifractality in the spin quantum Hall symmetry class with interaction}},
doi = {10.1103/PhysRevB.108.205429},
volume = {108},
year = {2023},
}
@inproceedings{14693,
abstract = {Lucas sequences are constant-recursive integer sequences with a long history of applications in cryptography, both in the design of cryptographic schemes and cryptanalysis. In this work, we study the sequential hardness of computing Lucas sequences over an RSA modulus.
First, we show that modular Lucas sequences are at least as sequentially hard as the classical delay function given by iterated modular squaring proposed by Rivest, Shamir, and Wagner (MIT Tech. Rep. 1996) in the context of time-lock puzzles. Moreover, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring. In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring.
Second, we demonstrate the feasibility of constructing practically-efficient verifiable delay functions based on the sequential hardness of modular Lucas sequences. Our construction builds on the work of Pietrzak (ITCS 2019) by leveraging the intrinsic connection between the problem of computing modular Lucas sequences and exponentiation in an appropriate extension field.},
author = {Hoffmann, Charlotte and Hubáček, Pavel and Kamath, Chethan and Krňák, Tomáš},
booktitle = {21st International Conference on Theory of Cryptography},
isbn = {9783031486234},
issn = {1611-3349},
location = {Taipei, Taiwan},
pages = {336--362},
publisher = {Springer Nature},
title = {{(Verifiable) delay functions from Lucas sequences}},
doi = {10.1007/978-3-031-48624-1_13},
volume = {14372},
year = {2023},
}