@article{9093, abstract = {We employ the Gross-Pitaevskii equation to study acoustic emission generated in a uniform Bose gas by a static impurity. The impurity excites a sound-wave packet, which propagates through the gas. We calculate the shape of this wave packet in the limit of long wave lengths, and argue that it is possible to extract properties of the impurity by observing this shape. We illustrate here this possibility for a Bose gas with a trapped impurity atom -- an example of a relevant experimental setup. Presented results are general for all one-dimensional systems described by the nonlinear Schrödinger equation and can also be used in nonatomic systems, e.g., to analyze light propagation in nonlinear optical media. Finally, we calculate the shape of the sound-wave packet for a three-dimensional Bose gas assuming a spherically symmetric perturbation.}, author = {Marchukov, Oleksandr and Volosniev, Artem}, issn = {2542-4653}, journal = {SciPost Physics}, number = {2}, publisher = {SciPost Foundation}, title = {{Shape of a sound wave in a weakly-perturbed Bose gas}}, doi = {10.21468/scipostphys.10.2.025}, volume = {10}, year = {2021}, } @article{9094, abstract = {Dendritic cells (DCs) are crucial for the priming of naive T cells and the initiation of adaptive immunity. Priming is initiated at a heterologous cell–cell contact, the immunological synapse (IS). While it is established that F-actin dynamics regulates signaling at the T cell side of the contact, little is known about the cytoskeletal contribution on the DC side. Here, we show that the DC actin cytoskeleton is decisive for the formation of a multifocal synaptic structure, which correlates with T cell priming efficiency. DC actin at the IS appears in transient foci that are dynamized by the WAVE regulatory complex (WRC). The absence of the WRC in DCs leads to stabilized contacts with T cells, caused by an increase in ICAM1-integrin–mediated cell–cell adhesion. This results in lower numbers of activated and proliferating T cells, demonstrating an important role for DC actin in the regulation of immune synapse functionality.}, author = {Leithner, Alexander F and Altenburger, LM and Hauschild, R and Assen, Frank P and Rottner, K and TEB, Stradal and Diz-Muñoz, A and Stein, JV and Sixt, Michael K}, issn = {1540-8140}, journal = {Journal of Cell Biology}, number = {4}, publisher = {Rockefeller University Press}, title = {{Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse}}, doi = {10.1083/jcb.202006081}, volume = {220}, year = {2021}, } @article{9097, abstract = {Psoriasis is a chronic inflammatory skin disease clinically characterized by the appearance of red colored, well-demarcated plaques with thickened skin and with silvery scales. Recent studies have established the involvement of a complex signalling network of interactions between cytokines, immune cells and skin cells called keratinocytes. Keratinocytes form the cells of the outermost layer of the skin (epidermis). Visible plaques in psoriasis are developed due to the fast proliferation and unusual differentiation of keratinocyte cells. Despite that, the exact mechanism of the appearance of these plaques in the cytokine-immune cell network is not clear. A mathematical model embodying interactions between key immune cells believed to be involved in psoriasis, keratinocytes and relevant cytokines has been developed. The complex network formed of these interactions poses several challenges. Here, we choose to study subnetworks of this complex network and initially focus on interactions involving TNFα, IL-23/IL-17, and IL-15. These are chosen based on known evidence of their therapeutic efficacy. In addition, we explore the role of IL-15 in the pathogenesis of psoriasis and its potential as a future drug target for a novel treatment option. We perform steady state analyses for these subnetworks and demonstrate that the interactions between cells, driven by cytokines could cause the emergence of a psoriasis state (hyper-proliferation of keratinocytes) when levels of TNFα, IL-23/IL-17 or IL-15 are increased. The model results explain and support the clinical potentiality of anti-cytokine treatments. Interestingly, our results suggest different dynamic scenarios underpin the pathogenesis of psoriasis, depending upon the dominant cytokines of subnetworks. We observed that the increase in the level of IL-23/IL-17 and IL-15 could lead to psoriasis via a bistable route, whereas an increase in the level of TNFα would lead to a monotonic and gradual disease progression. Further, we demonstrate how this insight, bistability, could be exploited to improve the current therapies and develop novel treatment strategies for psoriasis.}, author = {Pandey, Rakesh and Al-Nuaimi, Yusur and Mishra, Rajiv Kumar and Spurgeon, Sarah K. and Goodfellow, Marc}, issn = {20452322}, journal = {Scientific Reports}, publisher = {Springer Nature}, title = {{Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis}}, doi = {10.1038/s41598-020-80507-7}, volume = {11}, year = {2021}, } @article{9098, abstract = {We study properties of the volume of projections of the n-dimensional cross-polytope $\crosp^n = \{ x \in \R^n \mid |x_1| + \dots + |x_n| \leqslant 1\}.$ We prove that the projection of $\crosp^n$ onto a k-dimensional coordinate subspace has the maximum possible volume for k=2 and for k=3. We obtain the exact lower bound on the volume of such a projection onto a two-dimensional plane. Also, we show that there exist local maxima which are not global ones for the volume of a projection of $\crosp^n$ onto a k-dimensional subspace for any n>k⩾2.}, author = {Ivanov, Grigory}, issn = {0012365X}, journal = {Discrete Mathematics}, number = {5}, publisher = {Elsevier}, title = {{On the volume of projections of the cross-polytope}}, doi = {10.1016/j.disc.2021.112312}, volume = {344}, year = {2021}, } @article{9099, abstract = {We show that on an Abelian variety over an algebraically closed field of positive characteristic, the obstruction to lifting an automorphism to a field of characteristic zero as a morphism vanishes if and only if it vanishes for lifting it as a derived autoequivalence. We also compare the deformation space of these two types of deformations.}, author = {Srivastava, Tanya K}, issn = {14208938}, journal = {Archiv der Mathematik}, number = {5}, pages = {515--527}, publisher = {Springer Nature}, title = {{Lifting automorphisms on Abelian varieties as derived autoequivalences}}, doi = {10.1007/s00013-020-01564-y}, volume = {116}, year = {2021}, } @article{9100, abstract = {Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.}, author = {Faria, Rui and Johannesson, Kerstin and Stankowski, Sean}, issn = {14209101}, journal = {Journal of Evolutionary Biology}, number = {1}, pages = {4--15}, publisher = {Wiley}, title = {{Speciation in marine environments: Diving under the surface}}, doi = {10.1111/jeb.13756}, volume = {34}, year = {2021}, } @article{9101, abstract = {Behavioral predispositions are innate tendencies of animals to behave in a given way without the input of learning. They increase survival chances and, due to environmental and ecological challenges, may vary substantially even between closely related taxa. These differences are likely to be especially pronounced in long-lived species like crocodilians. This order is particularly relevant for comparative cognition due to its phylogenetic proximity to birds. Here we compared early life behavioral predispositions in two Alligatoridae species. We exposed American alligator and spectacled caiman hatchlings to three different novel situations: a novel object, a novel environment that was open and a novel environment with a shelter. This was then repeated a week later. During exposure to the novel environments, alligators moved around more and explored a larger range of the arena than the caimans. When exposed to the novel object, the alligators reduced the mean distance to the novel object in the second phase, while the caimans further increased it, indicating diametrically opposite ontogenetic development in behavioral predispositions. Although all crocodilian hatchlings face comparable challenges, e.g., high predation pressure, the effectiveness of parental protection might explain the observed pattern. American alligators are apex predators capable of protecting their offspring against most dangers, whereas adult spectacled caimans are frequently predated themselves. Their distancing behavior might be related to increased predator avoidance and also explain the success of invasive spectacled caimans in the natural habitats of other crocodilians.}, author = {Reber, Stephan A. and Oh, Jinook and Janisch, Judith and Stevenson, Colin and Foggett, Shaun and Wilkinson, Anna}, issn = {14359456}, journal = {Animal Cognition}, number = {4}, pages = {753--764}, publisher = {Springer Nature}, title = {{Early life differences in behavioral predispositions in two Alligatoridae species}}, doi = {10.1007/s10071-020-01461-5}, volume = {24}, year = {2021}, } @article{9111, abstract = {We study the probabilistic convergence between the mapper graph and the Reeb graph of a topological space X equipped with a continuous function f:X→R. We first give a categorification of the mapper graph and the Reeb graph by interpreting them in terms of cosheaves and stratified covers of the real line R. We then introduce a variant of the classic mapper graph of Singh et al. (in: Eurographics symposium on point-based graphics, 2007), referred to as the enhanced mapper graph, and demonstrate that such a construction approximates the Reeb graph of (X,f) when it is applied to points randomly sampled from a probability density function concentrated on (X,f). Our techniques are based on the interleaving distance of constructible cosheaves and topological estimation via kernel density estimates. Following Munch and Wang (In: 32nd international symposium on computational geometry, volume 51 of Leibniz international proceedings in informatics (LIPIcs), Dagstuhl, Germany, pp 53:1–53:16, 2016), we first show that the mapper graph of (X,f), a constructible R-space (with a fixed open cover), approximates the Reeb graph of the same space. We then construct an isomorphism between the mapper of (X,f) to the mapper of a super-level set of a probability density function concentrated on (X,f). Finally, building on the approach of Bobrowski et al. (Bernoulli 23(1):288–328, 2017b), we show that, with high probability, we can recover the mapper of the super-level set given a sufficiently large sample. Our work is the first to consider the mapper construction using the theory of cosheaves in a probabilistic setting. It is part of an ongoing effort to combine sheaf theory, probability, and statistics, to support topological data analysis with random data.}, author = {Brown, Adam and Bobrowski, Omer and Munch, Elizabeth and Wang, Bei}, issn = {2367-1734}, journal = {Journal of Applied and Computational Topology}, number = {1}, pages = {99--140}, publisher = {Springer Nature}, title = {{Probabilistic convergence and stability of random mapper graphs}}, doi = {10.1007/s41468-020-00063-x}, volume = {5}, year = {2021}, } @article{9113, abstract = {“Hydrogen economy” could enable a carbon-neutral sustainable energy chain. However, issues with safety, storage, and transport of molecular hydrogen impede its realization. Alcohols as liquid H2 carriers could be enablers, but state-of-the-art reforming is difficult, requiring high temperatures >200 °C and pressures >25 bar, and the resulting H2 is carbonized beyond tolerance levels for direct use in fuel cells. Here, we demonstrate ambient temperature and pressure alcohol reforming in a fuel cell (ARFC) with a simultaneous electrical power output. The alcohol is oxidized at the alkaline anode, where the resulting CO2 is sequestrated as carbonate. Carbon-free H2 is liberated at the acidic cathode. The neutralization energy between the alkaline anode and the acidic cathode drives the process, particularly the unusually high entropy gain (1.27-fold ΔH). The significantly positive temperature coefficient of the resulting electromotive force allows us to harvest a large fraction of the output energy from the surrounding, achieving a thermodynamic efficiency as high as 2.27. MoS2 as the cathode catalyst allows alcohol reforming even under open-air conditions, a challenge that state-of-the-art alcohol reforming failed to overcome. We further show reforming of a wide range of alcohols. The ARFC offers an unprecedented route toward hydrogen economy as CO2 is simultaneously captured and pure H2 produced at mild conditions.}, author = {Manzoor Bhat, Zahid Manzoor and Thimmappa, Ravikumar and Dargily, Neethu Christudas and Raafik, Abdul and Kottaichamy, Alagar Raja and Devendrachari, Mruthyunjayachari Chattanahalli and Itagi, Mahesh and Makri Nimbegondi Kotresh, Harish and Freunberger, Stefan Alexander and Ottakam Thotiyl, Musthafa }, issn = {2168-0485}, journal = {ACS Sustainable Chemistry and Engineering}, number = {8}, pages = {3104--3111}, publisher = {American Chemical Society}, title = {{Ambient condition alcohol reforming to hydrogen with electricity output}}, doi = {10.1021/acssuschemeng.0c07547}, volume = {9}, year = {2021}, } @article{9118, abstract = {Cesium lead halides have intrinsically unstable crystal lattices and easily transform within perovskite and nonperovskite structures. In this work, we explore the conversion of the perovskite CsPbBr3 into Cs4PbBr6 in the presence of PbS at 450 °C to produce doped nanocrystal-based composites with embedded Cs4PbBr6 nanoprecipitates. We show that PbBr2 is extracted from CsPbBr3 and diffuses into the PbS lattice with a consequent increase in the concentration of free charge carriers. This new doping strategy enables the adjustment of the density of charge carriers between 1019 and 1020 cm–3, and it may serve as a general strategy for doping other nanocrystal-based semiconductors.}, author = {Calcabrini, Mariano and Genc, Aziz and Liu, Yu and Kleinhanns, Tobias and Lee, Seungho and Dirin, Dmitry N. and Akkerman, Quinten A. and Kovalenko, Maksym V. and Arbiol, Jordi and Ibáñez, Maria}, issn = {2380-8195}, journal = {ACS Energy Letters}, number = {2}, pages = {581--587}, publisher = {American Chemical Society}, title = {{Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites}}, doi = {10.1021/acsenergylett.0c02448}, volume = {6}, year = {2021}, } @article{9119, abstract = {We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.}, author = {Fraisse, Christelle and Popovic, Iva and Mazoyer, Clément and Spataro, Bruno and Delmotte, Stéphane and Romiguier, Jonathan and Loire, Étienne and Simon, Alexis and Galtier, Nicolas and Duret, Laurent and Bierne, Nicolas and Vekemans, Xavier and Roux, Camille}, issn = {17550998}, journal = {Molecular Ecology Resources}, pages = {2629--2644}, publisher = {Wiley}, title = {{DILS: Demographic inferences with linked selection by using ABC}}, doi = {10.1111/1755-0998.13323}, volume = {21}, year = {2021}, } @article{9158, abstract = {While several tools have been developed to study the ground state of many-body quantum spin systems, the limitations of existing techniques call for the exploration of new approaches. In this manuscript we develop an alternative analytical and numerical framework for many-body quantum spin ground states, based on the disentanglement formalism. In this approach, observables are exactly expressed as Gaussian-weighted functional integrals over scalar fields. We identify the leading contribution to these integrals, given by the saddle point of a suitable effective action. Analytically, we develop a field-theoretical expansion of the functional integrals, performed by means of appropriate Feynman rules. The expansion can be truncated to a desired order to obtain analytical approximations to observables. Numerically, we show that the disentanglement approach can be used to compute ground state expectation values from classical stochastic processes. While the associated fluctuations grow exponentially with imaginary time and the system size, this growth can be mitigated by means of an importance sampling scheme based on knowledge of the saddle point configuration. We illustrate the advantages and limitations of our methods by considering the quantum Ising model in 1, 2 and 3 spatial dimensions. Our analytical and numerical approaches are applicable to a broad class of systems, bridging concepts from quantum lattice models, continuum field theory, and classical stochastic processes.}, author = {De Nicola, Stefano}, issn = {1742-5468}, journal = {Journal of Statistical Mechanics: Theory and Experiment}, keywords = {Statistics, Probability and Uncertainty, Statistics and Probability, Statistical and Nonlinear Physics}, number = {1}, publisher = {IOP Publishing}, title = {{Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation}}, doi = {10.1088/1742-5468/abc7c7}, volume = {2021}, year = {2021}, } @article{9168, abstract = {Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.}, author = {Fraisse, Christelle and Sachdeva, Himani}, issn = {1943-2631}, journal = {Genetics}, number = {2}, publisher = {Genetics Society of America}, title = {{The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes}}, doi = {10.1093/genetics/iyaa025}, volume = {217}, year = {2021}, } @article{9173, abstract = {We show that Hilbert schemes of points on supersingular Enriques surface in characteristic 2, Hilbn(X), for n ≥ 2 are simply connected, symplectic varieties but are not irreducible symplectic as the hodge number h2,0 > 1, even though a supersingular Enriques surface is an irreducible symplectic variety. These are the classes of varieties which appear only in characteristic 2 and they show that the hodge number formula for G¨ottsche-Soergel does not hold over haracteristic 2. It also gives examples of varieties with trivial canonical class which are neither irreducible symplectic nor Calabi-Yau, thereby showing that there are strictly more classes of simply connected varieties with trivial canonical class in characteristic 2 than over C as given by Beauville-Bogolomov decomposition theorem.}, author = {Srivastava, Tanya K}, issn = {0007-4497}, journal = {Bulletin des Sciences Mathematiques}, number = {03}, publisher = {Elsevier}, title = {{Pathologies of the Hilbert scheme of points of a supersingular Enriques surface}}, doi = {10.1016/j.bulsci.2021.102957}, volume = {167}, year = {2021}, } @article{9188, abstract = {Genomic imprinting is an epigenetic mechanism that results in parental allele-specific expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental regulators and play pivotal roles in many biological processes such as nutrient transfer from the mother to offspring and neuronal development. Imprinted genes are also involved in human disease, including neurodevelopmental disorders, and often occur in clusters that are regulated by a common imprint control region (ICR). In extra-embryonic tissues ICRs can act over large distances, with the largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical imprinted expression that shows near exclusive maternal or paternal expression, widespread biased imprinted expression has been identified mainly in brain. In this review we discuss recent developments mapping cell type specific imprinted expression in extra-embryonic tissues and neocortex in the mouse. We highlight the advantages of using an inducible uniparental chromosome disomy (UPD) system to generate cells carrying either two maternal or two paternal copies of a specific chromosome to analyze the functional consequences of genomic imprinting. Mosaic Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant induction of UPD sparsely in specific cell types, and thus to over-express or suppress all imprinted genes on that chromosome. To illustrate the utility of this technique, we explain how MADM-induced UPD revealed new insights about the function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs led to identification of highly cell type specific phenotypes related to perturbed imprinted expression in the mouse neocortex. Finally, we give an outlook on how MADM could be used to probe cell type specific imprinted expression in other tissues in mouse, particularly in extra-embryonic tissues.}, author = {Pauler, Florian and Hudson, Quanah and Laukoter, Susanne and Hippenmeyer, Simon}, issn = {0197-0186}, journal = {Neurochemistry International}, keywords = {Cell Biology, Cellular and Molecular Neuroscience}, number = {5}, publisher = {Elsevier}, title = {{Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond}}, doi = {10.1016/j.neuint.2021.104986}, volume = {145}, year = {2021}, } @article{9189, abstract = {Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses.}, author = {Zhao, Y and Wu, L and Fu, Q and Wang, D and Li, J and Yao, B and Yu, S and Jiang, L and Qian, J and Zhou, X and Han, L and Zhao, S and Ma, C and Zhang, Y and Luo, C and Dong, Q and Li, S and Zhang, L and Jiang, X and Li, Y and Luo, H and Li, K and Yang, J and Luo, Q and Li, L and Peng, S and Huang, H and Zuo, Z and Liu, C and Wang, L and Li, C and He, X and Friml, Jiří and Du, Y}, issn = {1365-3040}, journal = {Plant, Cell & Environment}, number = {6}, pages = {1846--1857}, publisher = {Wiley}, title = {{INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance}}, doi = {10.1111/pce.14029}, volume = {44}, year = {2021}, } @misc{9192, abstract = {Here are the research data underlying the publication " Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus)." Further information are summed up in the README document.}, author = {Surendranadh, Parvathy and Arathoon, Louise S and Baskett, Carina and Field, David and Pickup, Melinda and Barton, Nicholas H}, publisher = {Institute of Science and Technology Austria}, title = {{Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus}}, doi = {10.15479/AT:ISTA:9192}, year = {2021}, } @inproceedings{9200, abstract = {Formal design of embedded and cyber-physical systems relies on mathematical modeling. In this paper, we consider the model class of hybrid automata whose dynamics are defined by affine differential equations. Given a set of time-series data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting behavior that is close to the data, up to a specified precision, and changes in synchrony with the data. A fundamental problem in our synthesis algorithm is to check membership of a time series in a hybrid automaton. Our solution integrates reachability and optimization techniques for affine dynamical systems to obtain both a sufficient and a necessary condition for membership, combined in a refinement framework. The algorithm processes one time series at a time and hence can be interrupted, provide an intermediate result, and be resumed. We report experimental results demonstrating the applicability of our synthesis approach.}, author = {Garcia Soto, Miriam and Henzinger, Thomas A and Schilling, Christian}, booktitle = {HSCC '21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control}, isbn = {9781450383394}, keywords = {hybrid automaton, membership, system identification}, location = {Nashville, TN, United States}, pages = {2102.12734}, publisher = {Association for Computing Machinery}, title = {{Synthesis of hybrid automata with affine dynamics from time-series data}}, doi = {10.1145/3447928.3456704}, year = {2021}, } @article{9205, abstract = {Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins.}, author = {Kampjut, Domen and Steiner, Julia and Sazanov, Leonid A}, issn = {25890042}, journal = {iScience}, number = {3}, publisher = {Elsevier}, title = {{Cryo-EM grid optimization for membrane proteins}}, doi = {10.1016/j.isci.2021.102139}, volume = {24}, year = {2021}, } @article{9206, abstract = {The precise engineering of thermoelectric materials using nanocrystals as their building blocks has proven to be an excellent strategy to increase energy conversion efficiency. Here we present a synthetic route to produce Sb-doped PbS colloidal nanoparticles. These nanoparticles are then consolidated into nanocrystalline PbS:Sb using spark plasma sintering. We demonstrate that the introduction of Sb significantly influences the size, geometry, crystal lattice and especially the carrier concentration of PbS. The increase of charge carrier concentration achieved with the introduction of Sb translates into an increase of the electrical and thermal conductivities and a decrease of the Seebeck coefficient. Overall, PbS:Sb nanomaterial were characterized by two-fold higher thermoelectric figures of merit than undoped PbS. }, author = {Cadavid, Doris and Wei, Kaya and Liu, Yu and Zhang, Yu and Li, Mengyao and Genç, Aziz and Berestok, Taisiia and Ibáñez, Maria and Shavel, Alexey and Nolas, George S. and Cabot, Andreu}, issn = {1996-1944}, journal = {Materials}, number = {4}, publisher = {MDPI}, title = {{Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks}}, doi = {10.3390/ma14040853}, volume = {14}, year = {2021}, }