@article{14605,
  abstract     = {The phonon transport mechanisms and ultralow lattice thermal conductivities (κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein, we study the lattice dynamics and thermal property of AgX under the framework of perturbation theory and the two-channel Wigner thermal transport model based on accurate machine learning potentials. We find that an accurate extraction of the third-order atomic force constants from largely displaced configurations is significant for the calculation of the κL of AgX, and the coherence thermal transport is also non-negligible. In AgI, however, the calculated κL still considerably overestimates the experimental values even including four-phonon scatterings. Molecular dynamics (MD) simulations using machine learning potential suggest an important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency phonon linewidths of AgI at room temperature, which can be related to the simultaneous restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated using MD phonon lifetimes including full-order lattice anharmonicity shows a better agreement with experiments.},
  author       = {Ouyang, Niuchang and Zeng, Zezhu and Wang, Chen and Wang, Qi and Chen, Yue},
  issn         = {2469-9969},
  journal      = {Physical Review B},
  number       = {17},
  publisher    = {American Physical Society},
  title        = {{Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I)}},
  doi          = {10.1103/PhysRevB.108.174302},
  volume       = {108},
  year         = {2023},
}

@inproceedings{14609,
  abstract     = {Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted party. DKG is an essential building block to many decentralized protocols such as randomness beacons, threshold signatures, Byzantine consensus, and multiparty computation. While significant progress has been made recently, existing asynchronous DKG constructions are inefficient when the reconstruction threshold is larger than one-third of the total nodes. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t + 1 nodes that can tolerate up to t malicious nodes and support any reconstruction threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where κ is the security parameter, and only assumes the hardness of the Discrete Logarithm. The
core ingredient of our ADKG protocol is an asynchronous protocol to secret share a random polynomial of degree ℓ ≥ t, which has other applications, such as asynchronous proactive secret sharing and asynchronous multiparty computation. We implement our high-threshold ADKG protocol and evaluate it using a network of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over the state-of-the-art.},
  author       = {Das, Sourav and Xiang, Zhuolun and Kokoris Kogias, Eleftherios and Ren, Ling},
  booktitle    = {32nd USENIX Security Symposium},
  isbn         = {9781713879497},
  location     = {Anaheim, CA, United States},
  pages        = {5359--5376},
  publisher    = {Usenix},
  title        = {{Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling}},
  volume       = {8},
  year         = {2023},
}

@article{14610,
  abstract     = {<jats:title>Abstract</jats:title><jats:p>Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells<jats:sup>1,2</jats:sup>. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis<jats:sup>3–7</jats:sup>. 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 <jats:italic>Mycobacterium tuberculosis</jats:italic>, a human pathogen that exploits endomembrane damage to survive within the host.</jats:p>},
  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},
  keywords     = {Multidisciplinary},
  publisher    = {Springer Nature},
  title        = {{Stress granules plug and stabilize damaged endolysosomal membranes}},
  doi          = {10.1038/s41586-023-06726-w},
  year         = {2023},
}

@article{14613,
  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 a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). 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 two 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 and Toups, Melissa A and Layana Franco, Lorena Alexandra and Macon, Ariana and Vicoso, Beatriz},
  issn         = {1537-1719},
  journal      = {Molecular Biology and Evolution},
  keywords     = {Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics},
  number       = {12},
  publisher    = {Oxford University Press},
  title        = {{The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome}},
  doi          = {10.1093/molbev/msad245},
  volume       = {40},
  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},
}

@misc{14619,
  abstract     = {Data underlying the publication "A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals" (DOI https://doi.org/10.1063/5.0173341).},
  author       = {Cheng, Bingqing},
  publisher    = {Zenodo},
  title        = {{BingqingCheng/solubility: V1.0}},
  doi          = {10.5281/ZENODO.8398094},
  year         = {2023},
}

@phdthesis{14622,
  author       = {Sack, Stefan},
  issn         = {2663 - 337X},
  pages        = {142},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems}},
  doi          = {10.15479/at:ista:14622},
  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         = {0730-0301},
  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},
}

@phdthesis{14641,
  author       = {Hennessey-Wesen, Mike},
  issn         = {2663 - 337X},
  keywords     = {microfluidics, miceobiology, mutations, quorum sensing},
  pages        = {104},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Adaptive mutation in E. coli modulated by luxS}},
  doi          = {10.15479/at:ista:14641},
  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},
}

@unpublished{14647,
  abstract     = {In the developing vertebrate central nervous system, neurons and glia typically arise sequentially from common progenitors. Here, we report that the transcription factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and in postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic ligand FGF18 in new born neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons increases Fgf18 expression and enhances gliogenesis in the progenitors. These results fit well with the model that new born neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex.},
  author       = {Bose, Mahima and Suresh, Varun and Mishra, Urvi and Talwar, Ishita and Yadav, Anuradha and Biswas, Shiona and Hippenmeyer, Simon and Tole, Shubha},
  booktitle    = {bioRxiv},
  publisher    = {Cold Spring Harbor Laboratory},
  title        = {{Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway}},
  doi          = {10.1101/2023.11.30.569337},
  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{14652,
  abstract     = {In order to demonstrate the stability of newly proposed iridium-based Ir2Cr(In,Sn) and IrRhCr(In,Sn) heusler alloys, we present ab-initio analysis of these alloys by examining various properties to prove their stability. The stability of these alloys can be inferred from different cohesive and formation energies as well as positive phonon frequencies. Their electronic structure results indicate that they are semi-metals in nature. The magnetic moments are computed using the Slater-Pauling formula and exhibit a high value, with the Cr atom contributing the most in all alloys. Mulliken’s charge analysis results show that our alloys contain a range of linkages, mainly ionic and covalent ones. The ductility and mechanical stability of these alloys are confirmed by elastic constants viz. Poisson’s ratio, Pugh’s ratio, and many different types of elastic moduli.},
  author       = {Gupta, Shyam Lal and Singh, Saurabh and Kumar, Sumit and Anupam, Unknown and Thakur, Samjeet Singh and Kumar, Ashish and Panwar, Sanjay and Diwaker, D.},
  issn         = {0921-4526},
  journal      = {Physica B: Condensed Matter},
  publisher    = {Elsevier},
  title        = {{Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys}},
  doi          = {10.1016/j.physb.2023.415539},
  volume       = {674},
  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{14656,
  abstract     = {Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.},
  author       = {Nardin, Michele and Csicsvari, Jozsef L and Tkačik, Gašper and Savin, Cristina},
  issn         = {1529-2401},
  journal      = {The Journal of Neuroscience},
  number       = {48},
  pages        = {8140--8156},
  publisher    = {Society of Neuroscience},
  title        = {{The structure of hippocampal CA1 interactions optimizes spatial coding across experience}},
  doi          = {10.1523/JNEUROSCI.0194-23.2023},
  volume       = {43},
  year         = {2023},
}

@article{14657,
  abstract     = {Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader’s fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader’s dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader’s connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader’s fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident.},
  author       = {Tkadlec, Josef and Kaveh, Kamran and Chatterjee, Krishnendu and Nowak, Martin A.},
  issn         = {1742-5662},
  journal      = {Journal of the Royal Society, Interface},
  number       = {208},
  publisher    = {The Royal Society},
  title        = {{Evolutionary dynamics of mutants that modify population structure}},
  doi          = {10.1098/rsif.2023.0355},
  volume       = {20},
  year         = {2023},
}