@article{13166, abstract = {Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans.}, author = {Vetrova, Alexandra A. and Kupaeva, Daria M. and Kizenko, Alena and Lebedeva, Tatiana S. and Walentek, Peter and Tsikolia, Nikoloz and Kremnyov, Stanislav V.}, issn = {2045-2322}, journal = {Scientific Reports}, publisher = {Springer Nature}, title = {{The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization}}, doi = {10.1038/s41598-023-35979-8}, volume = {13}, year = {2023}, } @article{13138, abstract = {We consider the spin- 1 2 Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain.}, author = {Orlov, Pavel and Tiutiakina, Anastasiia and Sharipov, Rustem and Petrova, Elena and Gritsev, Vladimir and Kurlov, Denis V.}, issn = {2469-9969}, journal = {Physical Review B}, number = {18}, publisher = {American Physical Society}, title = {{Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain}}, doi = {10.1103/PhysRevB.107.184312}, volume = {107}, year = {2023}, } @article{13213, abstract = {The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in the root epidermis–cortex and cortex–endodermis junctions. A decrease in ROS level or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5 sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment, and iron over-accumulated in the walls between the root epidermis and cortex cell layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial for membrane association and functionality of SKU5 and SKS1. Overall, our results identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation of cell wall structure and root cell growth.}, author = {Chen, C and Zhang, Y and Cai, J and Qiu, Y and Li, L and Gao, C and Gao, Y and Ke, M and Wu, S and Wei, C and Chen, J and Xu, T and Friml, Jiří and Wang, J and Li, R and Chao, D and Zhang, B and Chen, X and Gao, Z}, issn = {1532-2548}, journal = {Plant Physiology}, number = {3}, pages = {2243--2260}, publisher = {American Society of Plant Biologists}, title = {{Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots}}, doi = {10.1093/plphys/kiad207}, volume = {192}, year = {2023}, } @article{12478, abstract = {In Gram negative bacteria, the multiple antibiotic resistance or mar operon, is known to control the expression of multi-drug efflux genes that protect bacteria from a wide range of drugs. As many different chemical compounds can induce this operon, identifying the parameters that govern the dynamics of its induction is crucial to better characterize the processes of tolerance and resistance. Most experiments have assumed that the properties of the mar transcriptional network can be inferred from population measurements. However, measurements from an asynchronous population of cells can mask underlying phenotypic variations of single cells. We monitored the activity of the mar promoter in single Escherichia coli cells in linear micro-colonies and established that the response to a steady level of inducer was most heterogeneous within individual colonies for an intermediate value of inducer. Specifically, sub-lineages defined by contiguous daughter-cells exhibited similar promoter activity, whereas activity was greatly variable between different sub-lineages. Specific sub-trees of uniform promoter activity persisted over several generations. Statistical analyses of the lineages suggest that the presence of these sub-trees is the signature of an inducible memory of the promoter state that is transmitted from mother to daughter cells. This single-cell study reveals that the degree of epigenetic inheritance changes as a function of inducer concentration, suggesting that phenotypic inheritance may be an inducible phenotype.}, author = {Guet, Calin C and Bruneaux, L and Oikonomou, P and Aldana, M and Cluzel, P}, issn = {1664-302X}, journal = {Frontiers in Microbiology}, publisher = {Frontiers}, title = {{Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression}}, doi = {10.3389/fmicb.2023.1049255}, volume = {14}, year = {2023}, } @article{13229, abstract = {Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation.}, author = {Shamipour, Shayan and Hofmann, Laura and Steccari, Irene and Kardos, Roland and Heisenberg, Carl-Philipp J}, issn = {1545-7885}, journal = {PLoS Biology}, number = {6}, pages = {e3002146}, publisher = {Public Library of Science}, title = {{Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes}}, doi = {10.1371/journal.pbio.3002146}, volume = {21}, year = {2023}, } @article{13197, abstract = {Nominally identical materials exchange net electric charge during contact through a mechanism that is still debated. ‘Mosaic models’, in which surfaces are presumed to consist of a random patchwork of microscopic donor/acceptor sites, offer an appealing explanation for this phenomenon. However, recent experiments have shown that global differences persist even between same-material samples, which the standard mosaic framework does not account for. Here, we expand the mosaic framework by incorporating global differences in the densities of donor/acceptor sites. We develop an analytical model, backed by numerical simulations, that smoothly connects the global and deterministic charge transfer of different materials to the local and stochastic mosaic picture normally associated with identical materials. Going further, we extend our model to explain the effect of contact asymmetries during sliding, providing a plausible explanation for reversal of charging sign that has been observed experimentally.}, author = {Grosjean, Galien M and Waitukaitis, Scott R}, issn = {2475-9953}, journal = {Physical Review Materials}, keywords = {Physics and Astronomy (miscellaneous), General Materials Science}, number = {6}, publisher = {American Physical Society}, title = {{Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts}}, doi = {10.1103/physrevmaterials.7.065601}, volume = {7}, year = {2023}, } @article{13230, abstract = {To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals.}, author = {Charlton, Julie A. and Mlynarski, Wiktor F and Bai, Yoon H. and Hermundstad, Ann M. and Goris, Robbe L.T.}, issn = {1553-7358}, journal = {PLoS Computational Biology}, number = {6}, publisher = {Public Library of Science}, title = {{Environmental dynamics shape perceptual decision bias}}, doi = {10.1371/journal.pcbi.1011104}, volume = {19}, year = {2023}, } @article{13232, abstract = {The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study.}, author = {Dormeshkin, Dmitri and Katsin, Mikalai and Stegantseva, Maria and Golenchenko, Sergey and Shapira, Michail and Dubovik, Simon and Lutskovich, Dzmitry and Kavaleuski, Anton and Meleshko, Alexander}, issn = {2076-393X}, journal = {Vaccines}, number = {6}, publisher = {MDPI}, title = {{Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein}}, doi = {10.3390/vaccines11061014}, volume = {11}, year = {2023}, } @article{13231, abstract = {We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles.}, author = {Schörner, Maximilian and Bethkenhagen, Mandy and Döppner, Tilo and Kraus, Dominik and Fletcher, Luke B. and Glenzer, Siegfried H. and Redmer, Ronald}, issn = {2470-0053}, journal = {Physical Review E}, number = {6}, publisher = {American Physical Society}, title = {{X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula}}, doi = {10.1103/PhysRevE.107.065207}, volume = {107}, year = {2023}, } @article{13233, abstract = {We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters.}, author = {Agafonova, Sofya and Lemeshko, Mikhail and Volosniev, Artem}, issn = {2469-9934}, journal = {Physical Review A}, number = {6}, publisher = {American Physical Society}, title = {{Finite-range bias in fitting three-body loss to the zero-range model}}, doi = {10.1103/PhysRevA.107.L061304}, volume = {107}, year = {2023}, } @article{13256, abstract = {The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate.}, author = {Goswami, Bidyut B and An, Soon Il}, issn = {2397-3722}, journal = {npj Climate and Atmospheric Science}, publisher = {Springer Nature}, title = {{An assessment of the ENSO-monsoon teleconnection in a warming climate}}, doi = {10.1038/s41612-023-00411-5}, volume = {6}, year = {2023}, } @article{13260, abstract = {Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines.}, author = {De Castro Barbosa Rodrigues Barata, Carolina and Snook, Rhonda R. and Ritchie, Michael G. and Kosiol, Carolin}, issn = {1759-6653}, journal = {Genome biology and evolution}, number = {7}, publisher = {Oxford Academic}, title = {{Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura}}, doi = {10.1093/gbe/evad113}, volume = {15}, year = {2023}, } @article{13346, abstract = {The self-assembly of nanoparticles driven by small molecules or ions may produce colloidal superlattices with features and properties reminiscent of those of metals or semiconductors. However, to what extent the properties of such supramolecular crystals actually resemble those of atomic materials often remains unclear. Here, we present coarse-grained molecular simulations explicitly demonstrating how a behavior evocative of that of semiconductors may emerge in a colloidal superlattice. As a case study, we focus on gold nanoparticles bearing positively charged groups that self-assemble into FCC crystals via mediation by citrate counterions. In silico ohmic experiments show how the dynamically diverse behavior of the ions in different superlattice domains allows the opening of conductive ionic gates above certain levels of applied electric fields. The observed binary conductive/nonconductive behavior is reminiscent of that of conventional semiconductors, while, at a supramolecular level, crossing the “band gap” requires a sufficient electrostatic stimulus to break the intermolecular interactions and make ions diffuse throughout the superlattice’s cavities.}, author = {Lionello, Chiara and Perego, Claudio and Gardin, Andrea and Klajn, Rafal and Pavan, Giovanni M.}, issn = {1936-086X}, journal = {ACS Nano}, keywords = {General Physics and Astronomy, General Engineering, General Materials Science}, number = {1}, pages = {275--287}, publisher = {American Chemical Society}, title = {{Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices}}, doi = {10.1021/acsnano.2c07558}, volume = {17}, year = {2023}, } @unpublished{13447, abstract = {Asteroseismology has transformed stellar astrophysics. Red giant asteroseismology is a prime example, with oscillation periods and amplitudes that are readily detectable with time-domain space-based telescopes. These oscillations can be used to infer masses, ages and radii for large numbers of stars, providing unique constraints on stellar populations in our galaxy. The cadence, duration, and spatial resolution of the Roman galactic bulge time-domain survey (GBTDS) are well-suited for asteroseismology and will probe an important population not studied by prior missions. We identify photometric precision as a key requirement for realizing the potential of asteroseismology with Roman. A precision of 1 mmag per 15-min cadence or better for saturated stars will enable detections of the populous red clump star population in the Galactic bulge. If the survey efficiency is better than expected, we argue for repeat observations of the same fields to improve photometric precision, or covering additional fields to expand the stellar population reach if the photometric precision for saturated stars is better than 1 mmag. Asteroseismology is relatively insensitive to the timing of the observations during the mission, and the prime red clump targets can be observed in a single 70 day campaign in any given field. Complementary stellar characterization, particularly astrometry tied to the Gaia system, will also dramatically expand the diagnostic power of asteroseismology. We also highlight synergies to Roman GBTDS exoplanet science using transits and microlensing.}, author = {Huber, Daniel and Pinsonneault, Marc and Beck, Paul and Bedding, Timothy R. and Joss Bland-Hawthorn, Joss Bland-Hawthorn and Breton, Sylvain N. and Bugnet, Lisa Annabelle and Chaplin, William J. and Garcia, Rafael A. and Grunblatt, Samuel K. and Guzik, Joyce A. and Hekker, Saskia and Kawaler, Steven D. and Mathis, Stephane and Mathur, Savita and Metcalfe, Travis and Mosser, Benoit and Ness, Melissa K. and Piro, Anthony L. and Serenelli, Aldo and Sharma, Sanjib and Soderblom, David R. and Stassun, Keivan G. and Stello, Dennis and Tayar, Jamie and Belle, Gerard T. van and Zinn, Joel C.}, booktitle = {arXiv}, title = {{Asteroseismology with the Roman galactic bulge time-domain survey}}, doi = {10.48550/arXiv.2307.03237}, year = {2023}, } @article{13354, abstract = {Integrating light-sensitive molecules within nanoparticle (NP) assemblies is an attractive approach to fabricate new photoresponsive nanomaterials. Here, we describe the concept of photocleavable anionic glue (PAG): small trianions capable of mediating interactions between (and inducing the aggregation of) cationic NPs by means of electrostatic interactions. Exposure to light converts PAGs into dianionic products incapable of maintaining the NPs in an assembled state, resulting in light-triggered disassembly of NP aggregates. To demonstrate the proof-of-concept, we work with an organic PAG incorporating the UV-cleavable o-nitrobenzyl moiety and an inorganic PAG, the photosensitive trioxalatocobaltate(III) complex, which absorbs light across the entire visible spectrum. Both PAGs were used to prepare either amorphous NP assemblies or regular superlattices with a long-range NP order. These NP aggregates disassembled rapidly upon light exposure for a specific time, which could be tuned by the incident light wavelength or the amount of PAG used. Selective excitation of the inorganic PAG in a system combining the two PAGs results in a photodecomposition product that deactivates the organic PAG, enabling nontrivial disassembly profiles under a single type of external stimulus.}, author = {Wang, Jinhua and Peled, Tzuf Shay and Klajn, Rafal}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {7}, pages = {4098--4108}, publisher = {American Chemical Society}, title = {{Photocleavable anionic glues for light-responsive nanoparticle aggregates}}, doi = {10.1021/jacs.2c11973}, volume = {145}, year = {2023}, } @phdthesis{13074, abstract = {Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties. The focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks.}, author = {Peste, Elena-Alexandra}, issn = {2663-337X}, pages = {147}, publisher = {Institute of Science and Technology Austria}, title = {{Efficiency and generalization of sparse neural networks}}, doi = {10.15479/at:ista:13074}, year = {2023}, } @article{13963, abstract = {The many-body localization (MBL) proximity effect is an intriguing phenomenon where a thermal bath localizes due to the interaction with a disordered system. The interplay of thermal and nonergodic behavior in these systems gives rise to a rich phase diagram, whose exploration is an active field of research. In this paper, we study a bosonic Hubbard model featuring two particle species representing the bath and the disordered system. Using state-of-the-art numerical techniques, we investigate the dynamics of the model in different regimes, based on which we obtain a tentative phase diagram as a function of coupling strength and bath size. When the bath is composed of a single particle, we observe clear signatures of a transition from an MBL proximity effect to a delocalized phase. Increasing the bath size, however, its thermalizing effect becomes stronger and eventually the whole system delocalizes in the range of moderate interaction strengths studied. In this regime, we characterize particle transport, revealing diffusive behavior of the originally localized bosons.}, author = {Brighi, Pietro and Ljubotina, Marko and Abanin, Dmitry A. and Serbyn, Maksym}, issn = {2469-9969}, journal = {Physical Review B}, number = {5}, publisher = {American Physical Society}, title = {{Many-body localization proximity effect in a two-species bosonic Hubbard model}}, doi = {10.1103/physrevb.108.054201}, volume = {108}, year = {2023}, } @article{13966, abstract = {We present a low-scaling diagrammatic Monte Carlo approach to molecular correlation energies. Using combinatorial graph theory to encode many-body Hugenholtz diagrams, we sample the Møller-Plesset (MPn) perturbation series, obtaining accurate correlation energies up to n=5, with quadratic scaling in the number of basis functions. Our technique reduces the computational complexity of the molecular many-fermion correlation problem, opening up the possibility of low-scaling, accurate stochastic computations for a wide class of many-body systems described by Hugenholtz diagrams.}, author = {Bighin, Giacomo and Ho, Quoc P and Lemeshko, Mikhail and Tscherbul, T. V.}, issn = {2469-9969}, journal = {Physical Review B}, number = {4}, publisher = {American Physical Society}, title = {{Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling}}, doi = {10.1103/PhysRevB.108.045115}, volume = {108}, year = {2023}, } @article{13970, author = {Madani, Amiera and Sletten, Eric T. and Cavedon, Cristian and Seeberger, Peter H. and Pieber, Bartholomäus}, issn = {2333-3553}, journal = {Organic Syntheses}, pages = {271--286}, publisher = {Organic Syntheses}, title = {{Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose}}, doi = {10.15227/orgsyn.100.0271}, volume = {100}, year = {2023}, } @article{13127, abstract = {Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense.}, author = {Casillas Perez, Barbara E and Bod'Ová, Katarína and Grasse, Anna V and Tkačik, Gašper and Cremer, Sylvia}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Dynamic pathogen detection and social feedback shape collective hygiene in ants}}, doi = {10.1038/s41467-023-38947-y}, volume = {14}, year = {2023}, }