@article{15141, abstract = {We reveal the cryo-electron microscopy structure of a type IV-B CRISPR ribonucleoprotein (RNP) complex (Csf) at 3.9-Å resolution. The complex best resembles the type III-A CRISPR Csm effector complex, consisting of a Cas7-like (Csf2) filament intertwined with a small subunit (Cas11) filament, but the complex lacks subunits for RNA processing and target DNA cleavage. Surprisingly, instead of assembling around a CRISPR-derived RNA (crRNA), the complex assembles upon heterogeneous RNA of a regular length arranged in a pseudo-A-form configuration. These findings provide a high-resolution glimpse into the assembly and function of enigmatic type IV CRISPR systems, expanding our understanding of class I CRISPR-Cas system architecture, and suggesting a function for type IV-B RNPs that may be distinct from other class 1 CRISPR-associated systems.}, author = {Zhou, Yi and Bravo, Jack Peter Kelly and Taylor, Hannah N. and Steens, Jurre A. and Jackson, Ryan N. and Staals, Raymond H.J. and Taylor, David W.}, issn = {2589-0042}, journal = {iScience}, keywords = {Multidisciplinary}, number = {3}, publisher = {Elsevier}, title = {{Structure of a type IV CRISPR-Cas ribonucleoprotein complex}}, doi = {10.1016/j.isci.2021.102201}, volume = {24}, year = {2021}, } @article{15150, abstract = {The majority of gene transcripts generated by RNA polymerase II in mammalian genomes initiate at CpG island (CGI) promoters1,2, yet our understanding of their regulation remains limited. This is in part due to the incomplete information that we have on transcription factors, their DNA-binding motifs and which genomic binding sites are functional in any given cell type3,4,5. In addition, there are orphan motifs without known binders, such as the CGCG element, which is associated with highly expressed genes across human tissues and enriched near the transcription start site of a subset of CGI promoters6,7,8. Here we combine single-molecule footprinting with interaction proteomics to identify BTG3-associated nuclear protein (BANP) as the transcription factor that binds this element in the mouse and human genome. We show that BANP is a strong CGI activator that controls essential metabolic genes in pluripotent stem and terminally differentiated neuronal cells. BANP binding is repelled by DNA methylation of its motif in vitro and in vivo, which epigenetically restricts most binding to CGIs and accounts for differential binding at aberrantly methylated CGI promoters in cancer cells. Upon binding to an unmethylated motif, BANP opens chromatin and phases nucleosomes. These findings establish BANP as a critical activator of a set of essential genes and suggest a model in which the activity of CGI promoters relies on methylation-sensitive transcription factors that are capable of chromatin opening.}, author = {Grand, Ralph S. and Burger, Lukas and Gräwe, Cathrin and Michael, Alicia and Isbel, Luke and Hess, Daniel and Hoerner, Leslie and Iesmantavicius, Vytautas and Durdu, Sevi and Pregnolato, Marco and Krebs, Arnaud R. and Smallwood, Sébastien A. and Thomä, Nicolas and Vermeulen, Michiel and Schübeler, Dirk}, issn = {1476-4687}, journal = {Nature}, pages = {133--137}, publisher = {Springer Nature}, title = {{BANP opens chromatin and activates CpG-island-regulated genes}}, doi = {10.1038/s41586-021-03689-8}, volume = {596}, year = {2021}, } @article{15151, abstract = {Eukaryotic DNA-binding proteins operate in the context of chromatin, where nucleosomes are the elementary building blocks. Nucleosomal DNA is wrapped around a histone core, thereby rendering a large fraction of the DNA surface inaccessible to DNA-binding proteins. Nevertheless, first responders in DNA repair and sequence-specific transcription factors bind DNA target sites obstructed by chromatin. While early studies examined protein binding to histone-free DNA, it is only now beginning to emerge how DNA sequences are interrogated on nucleosomes. These readout strategies range from the release of nucleosomal DNA from histones, to rotational/translation register shifts of the DNA motif, and nucleosome-specific DNA binding modes that differ from those observed on naked DNA. Since DNA motif engagement on nucleosomes strongly depends on position and orientation, we argue that motif location and nucleosome positioning co-determine protein access to DNA in transcription and DNA repair.}, author = {Michael, Alicia and Thomä, Nicolas H.}, issn = {0092-8674}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {14}, pages = {3599--3611}, publisher = {Elsevier}, title = {{Reading the chromatinized genome}}, doi = {10.1016/j.cell.2021.05.029}, volume = {184}, year = {2021}, } @article{15215, abstract = {AT2019wey (SRGA J043520.9+552226, SRGE J043523.3+552234) is a transient first reported by the ATLAS optical survey in 2019 December. It rose to prominence upon detection, three months later, by the Spektrum-Roentgen-Gamma (SRG) mission in its first all-sky survey. X-ray observations reported in Yao et al. suggest that AT2019wey is a Galactic low-mass X-ray binary (LMXB) with a black hole (BH) or neutron star (NS) accretor. Here we present ultraviolet, optical, near-infrared, and radio observations of this object. We show that the companion is a short-period (P ≲ 16 hr) low-mass (<1 M⊙) star. We consider AT2019wey to be a candidate BH system since its locations on the Lradio–LX and Lopt–LX diagrams are closer to BH binaries than NS binaries. We demonstrate that from 2020 June to August, despite the more than 10 times brightening at radio and X-ray wavelengths, the optical luminosity of AT2019wey only increased by 1.3–1.4 times. We interpret the UV/optical emission before the brightening as thermal emission from a truncated disk in a hot accretion flow and the UV/optical emission after the brightening as reprocessing of the X-ray emission in the outer accretion disk. AT2019wey demonstrates that combining current wide-field optical surveys and SRG provides a way to discover the emerging population of short-period BH LMXB systems with faint X-ray outbursts.}, author = {Yao, Yuhan and Kulkarni, S. R. and Burdge, Kevin B. and Caiazzo, Ilaria and De, Kishalay and Dong, Dillon and Fremling, C. and Kasliwal, Mansi M. and Kupfer, Thomas and van Roestel, Jan and Sollerman, Jesper and Bagdasaryan, Ashot and Bellm, Eric C. and Cenko, S. Bradley and Drake, Andrew J. and Duev, Dmitry A. and Graham, Matthew J. and Kaye, Stephen and Masci, Frank J. and Miranda, Nicolas and Prince, Thomas A. and Riddle, Reed and Rusholme, Ben and Soumagnac, Maayane T.}, issn = {1538-4357}, journal = {The Astrophysical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {2}, publisher = {American Astronomical Society}, title = {{Multi-wavelength observations of AT2019wey: A new candidate black hole low-mass X-ray binary}}, doi = {10.3847/1538-4357/ac15f9}, volume = {920}, year = {2021}, } @article{15216, abstract = {AM CVn systems are a rare type of accreting binary that consists of a white dwarf and a helium-rich, degenerate donor star. Using the Zwicky Transient Facility (ZTF), we searched for new AM CVn systems by focusing on blue, outbursting stars. We first selected outbursting stars using the ZTF alerts. We cross matched the candidates with Gaia and Pan-STARRS catalogs. The initial selection of candidates based on the Gaia BP-RP contains 1751 unknown objects. We used the Pan-STARRS g-r and r-i color in combination with the Gaia color to identify 59 strong AM CVn candidates. We obtained identification spectra of 35 sources, of which 18 are high-priority candidates, and discovered nine new AM CVn systems and one magnetic CV that shows only He-ii lines. Using the outburst recurrence time, we estimate the orbital periods of the nine new AM CVn systems that are in the range of 29–50 minutes. We conclude that targeted follow up of blue, outbursting sources is an efficient method to find new AM CVn systems and we plan to follow up all candidates we identified to systematically study the population of outbursting AM CVn systems.}, author = {van Roestel, Jan and Creter, Leah and Kupfer, Thomas and Szkody, Paula and Fuller, Jim and Green, Matthew J. and Rich, R. Michael and Sepikas, John and Burdge, Kevin and Caiazzo, Ilaria and Mróz, Przemek and Prince, Thomas A. and Duev, Dmitry A. and Graham, Matthew J. and Shupe, David L. and Laher, Russ R. and Mahabal, Ashish A. and Masci, Frank J.}, issn = {1538-3881}, journal = {The Astronomical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {3}, publisher = {American Astronomical Society}, title = {{A systematic search for outbursting AM CVn systems with the Zwicky transient facility}}, doi = {10.3847/1538-3881/ac0622}, volume = {162}, year = {2021}, } @article{15218, abstract = {White dwarfs represent the last stage of evolution of stars with mass less than about eight times that of the Sun and, like other stars, are often found in binaries1,2. If the orbital period of the binary is short enough, energy losses from gravitational-wave radiation can shrink the orbit until the two white dwarfs come into contact and merge3. Depending on the component masses, the merger can lead to a supernova of type Ia or result in a massive white dwarf4. In the latter case, the white dwarf remnant is expected to be highly magnetized5,6 because of the strong magnetic dynamo that should arise during the merger, and be rapidly spinning from the conservation of the orbital angular momentum7. Here we report observations of a white dwarf, ZTF J190132.9+145808.7, that exhibits these properties, but to an extreme: a rotation period of 6.94 minutes, a magnetic field ranging between 600 megagauss and 900 megagauss over its surface, and a stellar radius of kilometres, only slightly larger than the radius of the Moon. Such a small radius implies that the star’s mass is close to the maximum white dwarf mass, or Chandrasekhar mass. ZTF J190132.9+145808.7 is likely to be cooling through the Urca processes (neutrino emission from electron capture on sodium) because of the high densities reached in its core.}, author = {Caiazzo, Ilaria and Burdge, Kevin B. and Fuller, James and Heyl, Jeremy and Kulkarni, S. R. and Prince, Thomas A. and Richer, Harvey B. and Schwab, Josiah and Andreoni, Igor and Bellm, Eric C. and Drake, Andrew and Duev, Dmitry A. and Graham, Matthew J. and Helou, George and Mahabal, Ashish A. and Masci, Frank J. and Smith, Roger and Soumagnac, Maayane T.}, issn = {1476-4687}, journal = {Nature}, number = {7865}, pages = {39--42}, publisher = {Springer Nature}, title = {{A highly magnetized and rapidly rotating white dwarf as small as the Moon}}, doi = {10.1038/s41586-021-03615-y}, volume = {595}, year = {2021}, } @article{15219, abstract = {We have carried out a search for massive white dwarfs (WDs) in the direction of young open star clusters using the Gaia DR2 database. The aim of this survey was (1) to provide robust data for new and previously known high-mass WDs regarding cluster membership, (2) to highlight WDs previously included in the initial final mass relation (IFMR) that are unlikely members of their respective clusters according to Gaia astrometry, and (3) to select an unequivocal WD sample that could then be compared with the host clusters' turnoff masses. All promising WD candidates in each cluster color–magnitude diagram were followed up with spectroscopy from Gemini in order to determine whether they were indeed WDs and derive their masses, temperatures, and ages. In order to be considered cluster members, white dwarfs were required to (1) have proper motions and parallaxes within 2σ, 3σ, or 4σ of those of their potential parent cluster based on how contaminated the field was in their region of the sky, (2) have a cooling age that was less than the cluster age, and (3) have a mass that was broadly consistent with the IFMR. A number of WDs included in current versions of the IFMR turned out to be nonmembers, and a number of apparent members, based on Gaia's astrometric data alone, were rejected, as their mass and/or cooling times were incompatible with cluster membership. In this way, we developed a highly selected IFMR sample for high-mass WDs that, surprisingly, contained no precursor masses significantly in excess of ∼ 6 M⊙.}, author = {Richer, Harvey B. and Caiazzo, Ilaria and Du, Helen and Grondin, Steffani and Hegarty, James and Heyl, Jeremy and Kerr, Ronan and Miller, David R. and Thiele, Sarah}, issn = {1538-4357}, journal = {The Astrophysical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {2}, publisher = {American Astronomical Society}, title = {{Massive white dwarfs in young star clusters}}, doi = {10.3847/1538-4357/abdeb7}, volume = {912}, year = {2021}, } @inproceedings{15222, abstract = {We describe an implementation of a broad-band soft X-ray polarimeter, substantially based on previous designs. The Globe-Orbiting Soft X-ray Polarimeter (GOSoX) is a SmallSat. As in a related mission concept the PiSoX Polarimeter, the grating arrangement is designed optimally for the purpose of polarimetry matching the dispersion of a spectrometer to a laterally graded multilayer (LGML). For GOSoX, the optics are lightweight Si mirrors in a one-bounce parabolic configuration. The instrument covers the wavelength range from 31 A to 75 A (165 - 400 eV). Upon satellite rotation, the intensities of the dispersed spectra, after reflection and polarizing by the LGMLs, give the three Stokes parameters needed to determine a source's linear polarization fraction and orientation. The design can be extended to higher energies as LGMLs are developed further. We describe the potential scientific return and the proposed mission concept following the results of a JPL Team X concept study.}, author = {Marshall, Herman L. and Heine, Sarah and Davidson, Rosemary and Garner, Alan and Gullikson, Eric and Günther, Moritz and Leitz, Christopher and Masterson, Rebecca and Miller, Eric and Stenzel, June S. and Zhang, William W. and Boissay-Malaquin, Rozenn and Caiazzo, Ilaria and Chakrabarty, Deepto and Gallo, Luigi and Heilmann, Ralf and Heyl, Jeremy and Kara, Erin and Schulz, Norbert}, booktitle = {Optics for EUV, X-Ray, and Gamma-Ray Astronomy X}, location = {San Diego, CA, United States}, publisher = {SPIE}, title = {{The Globe Orbiting Soft X-ray (GOSoX) polarimeter concept study}}, doi = {10.1117/12.2596186}, volume = {11822}, year = {2021}, } @article{15254, abstract = {We consider the problem of reliable communication over a network containing a hidden myopic adversary who can eavesdrop on some zro links, jam some zwo links, and do both on some zrw links. We provide the first information-theoretically tight characterization of the optimal rate of communication possible under all possible settings of the tuple (zro,zwo,zrw) by providing a novel coding scheme/analysis for a subset of parameter regimes. In particular, our vanishing-error schemes bypass the Network Singleton Bound (which requires a zero-error recovery criteria) in a certain parameter regime where the capacity had been heretofore open. As a direct corollary we also obtain the capacity of the corresponding problem where information-theoretic secrecy against eavesdropping is required in addition to reliable communication.}, author = {Li, Sijie and Bitar, Rawad and Jaggi, Sidharth and Zhang, Yihan}, issn = {2641-8770}, journal = {IEEE Journal on Selected Areas in Information Theory}, number = {4}, pages = {1108--1119}, publisher = {IEEE}, title = {{Network coding with myopic adversaries}}, doi = {10.1109/JSAIT.2021.3126474}, volume = {2}, year = {2021}, } @article{15259, abstract = {We consider words Gi1⋯Gim involving i.i.d. complex Ginibre matrices and study tracial expressions of their eigenvalues and singular values. We show that the limit distribution of the squared singular values of every word of length m is a Fuss–Catalan distribution with parameter m+1. This generalizes previous results concerning powers of a complex Ginibre matrix and products of independent Ginibre matrices. In addition, we find other combinatorial parameters of the word that determine the second-order limits of the spectral statistics. For instance, the so-called coperiod of a word characterizes the fluctuations of the eigenvalues. We extend these results to words of general non-Hermitian matrices with i.i.d. entries under moment-matching assumptions, band matrices, and sparse matrices. These results rely on the moments method and genus expansion, relating Gaussian matrix integrals to the counting of compact orientable surfaces of a given genus. This allows us to derive a central limit theorem for the trace of any word of complex Ginibre matrices and their conjugate transposes, where all parameters are defined topologically.}, author = {Dubach, Guillaume and Peled, Yuval}, issn = {0091-1798}, journal = {The Annals of Probability}, keywords = {Statistics, Probability and Uncertainty, Statistics and Probability}, number = {4}, pages = {1886--1916}, publisher = {Institute of Mathematical Statistics}, title = {{On words of non-Hermitian random matrices}}, doi = {10.1214/20-aop1496}, volume = {49}, year = {2021}, } @article{15260, abstract = {Significant advances in the synthesis and processing of colloidal nanocrystals have given scientists and engineers access to a vast library of building blocks with precisely defined size, shape, and composition. These materials have inspired exciting prospects to enable bottom-up fabrication of programmable materials with properties by design. Successfully assembling and connecting the building blocks into superstructures in which constituent nanocrystals can purposefully interact requires robust understanding of and control over a complex interplay of dynamic physicochemical processes. Fluid interfaces provide an advantageous experimental workbench to both probe and control these processes. Despite the ostensible simplicity of fabricating nanocrystal assemblies at a fluid interface, sensitivity to processing conditions and limited reproducibility have underscored the complexity of this process. In situ studies have provided mechanistic insights into the competing dynamics of key subprocesses including solvent spreading and evaporation, superlattice formation, ligand detachment kinetics, and nanocrystal attachment. Understanding how these subprocesses influence the complex choreography of self-assembly, structure transformation, and oriented attachment processes presents a rich research challenge. In this context, we present a detailed methodology for self-assembly and attachment of lead chalcogenide nanocrystals at a liquid–gas interface as a model system for the fabrication of mono- and multilayer cubic connected superlattices. We discuss key experimental parameters such as the characteristics of the building blocks and processing conditions and detailed steps from colloidal nanocrystal injection to superlattice transfer. We hope that this Methods/Protocols paper will provide guidance for future advances in the exciting path toward bringing the prospect of nanocrystal-based programmable materials to fruition.}, author = {Cimada daSilva, Jessica and Balazs, Daniel and Dunbar, Tyler A. and Hanrath, Tobias}, issn = {1520-5002}, journal = {Chemistry of Materials}, keywords = {Materials Chemistry, General Chemical Engineering, General Chemistry}, number = {24}, pages = {9457--9472}, publisher = {American Chemical Society}, title = {{Fundamental processes and practical considerations of lead chalcogenide mesocrystals formed via self-assembly and directed attachment of nanocrystals at a fluid interface}}, doi = {10.1021/acs.chemmater.1c02910}, volume = {33}, year = {2021}, } @article{15261, abstract = {In this article, we study uniqueness of form extensions in a rather general setting. The method is based on the theory of ordered Hilbert spaces and the concept of domination of semigroups. Our main abstract result transfers uniqueness of form extension of a dominating form to that of a dominated form. This result can be applied to a multitude of examples including various magnetic Schrödinger forms on graphs and on manifolds.}, author = {Lenz, Daniel and Schmidt, Marcel and Wirth, Melchior}, issn = {1096-0783}, journal = {Journal of Functional Analysis}, keywords = {Analysis}, number = {6}, publisher = {Elsevier}, title = {{Uniqueness of form extensions and domination of semigroups}}, doi = {10.1016/j.jfa.2020.108848}, volume = {280}, year = {2021}, } @article{15262, abstract = {The Hunchback (Hb) transcription factor is crucial for anterior-posterior patterning of the Drosophila embryo. The maternal hb mRNA acts as a paradigm for translational regulation due to its repression in the posterior of the embryo. However, little is known about the translatability of zygotically transcribed hb mRNAs. Here, we adapt the SunTag system, developed for imaging translation at single-mRNA resolution in tissue culture cells, to the Drosophila embryo to study the translation dynamics of zygotic hb mRNAs. Using single-molecule imaging in fixed and live embryos, we provide evidence for translational repression of zygotic SunTag-hb mRNAs. Whereas the proportion of SunTag-hb mRNAs translated is initially uniform, translation declines from the anterior over time until it becomes restricted to a posterior band in the expression domain. We discuss how regulated hb mRNA translation may help establish the sharp Hb expression boundary, which is a model for precision and noise during developmental patterning. Overall, our data show how use of the SunTag method on fixed and live embryos is a powerful combination for elucidating spatiotemporal regulation of mRNA translation in Drosophila.}, author = {Vinter, Daisy J. and Hoppe, Caroline and Minchington, Thomas and Sutcliffe, Catherine and Ashe, Hilary L.}, issn = {1477-9129}, journal = {Development}, keywords = {Developmental Biology, Molecular Biology}, number = {18}, publisher = {The Company of Biologists}, title = {{Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo}}, doi = {10.1242/dev.196121}, volume = {148}, year = {2021}, } @inproceedings{15263, abstract = {We develop a new Riemannian descent algorithm that relies on momentum to improve over existing first-order methods for geodesically convex optimization. In contrast, accelerated convergence rates proved in prior work have only been shown to hold for geodesically strongly-convex objective functions. We further extend our algorithm to geodesically weakly-quasi-convex objectives. Our proofs of convergence rely on a novel estimate sequence that illustrates the dependency of the convergence rate on the curvature of the manifold. We validate our theoretical results empirically on several optimization problems defined on the sphere and on the manifold of positive definite matrices.}, author = {Alimisis, Foivos and Orvieto, Antonio and Becigneul, Gary and Lucchi, Aurelien}, booktitle = {Proceedings of the 24th International Conference on Artificial Intelligence and Statistics}, location = {San Diego, CA, United States; Virtual}, pages = {1351--1359}, publisher = {ML Research Press}, title = {{Momentum improves optimization on Riemannian manifolds}}, volume = {130}, year = {2021}, } @article{15264, abstract = {Signaling by the B cell antigen receptor (BCR) initiates actin remodeling. The assembly of branched actin networks that are nucleated by the Arp2/3 complex exert outward force on the plasma membrane, allowing B cells to form membrane protrusions that can scan the surface of antigen-presenting cells (APCs). The resulting Arp2/3 complex-dependent actin retrograde flow promotes the centripetal movement and progressive coalescence of BCR microclusters, which amplifies BCR signaling. Glia maturation factor γ (GMFγ) is an actin disassembly-protein that releases Arp2/3 complex-nucleated actin filaments from actin networks. By doing so, GMFγ could either oppose the actions of the Arp2/3 complex or support Arp2/3 complex-nucleated actin polymerization by contributing to the recycling of actin monomers and Arp2/3 complexes. We now show that reducing the levels of GMFγ in human B cell lines via transfection with a specific siRNA impairs the ability of B cells to spread on antigen-coated surfaces, decreases the velocity of actin retrograde flow, diminishes the coalescence of BCR microclusters into a central cluster at the B cell-APC contact site, and decreases APC-induced BCR signaling. These effects of depleting GMFγ are similar to what occurs when the Arp2/3 complex is inhibited. This suggests that GMFγ cooperates with the Arp2/3 complex to support BCR-induced actin remodeling and amplify BCR signaling at the immune synapse.}, author = {Deretic, Nikola and Bolger-Munro, Madison and Choi, Kate and Abraham, Libin and Gold, Michael R.}, issn = {2296-634X}, journal = {Frontiers in Cell and Developmental Biology}, keywords = {Cell Biology, Developmental Biology}, publisher = {Frontiers Media}, title = {{The actin-disassembly protein glia maturation factor γ enhances actin remodeling and B cell antigen receptor signaling at the immune synapse}}, doi = {10.3389/fcell.2021.647063}, volume = {9}, year = {2021}, } @article{15265, abstract = {The highly enhanced thermoelectric figure of merit, zT ≈ 2.6 at 573 K, obtained recently in Cd-doped polycrystalline AgSbTe2 by Roychowdhury et al. ( Science 2021, 371, 722) brings it to the forefront of thermoelectric and energy materials research. Ag/Sb cationic ordering in polycrystalline AgSbTe2 was a challenging issue for a long time: their ordered arrangement in the cationic sublattice in polycrystalline samples remained elusive despite multiple theoretical predictions and experimental studies. Recently, selective cation doping has been used to enhance the Ag/Sb ordering, and cation ordered nanoscale (2–4 nm) domains were observed in polycrystalline AgSbTe2, which reduce lattice thermal conductivity. The enhanced cation ordering also delocalizes disorder-induced localized electronic states, and consequently the electronic transport enhances. In this Focus Review, we provide the details of the rational design of a high-performance thermoelectric material using the recently developed atomic order–disorder optimization strategy with AgSbTe2 as an example. Atomic disorder is ubiquitous in most thermoelectric materials, and the atomic order–disorder optimization strategy applies to a large variety of thermoelectric materials.}, author = {Ghosh, Tanmoy and Roychowdhury, Subhajit and Dutta, Moinak and Biswas, Kanishka}, issn = {2380-8195}, journal = {ACS Energy Letters}, keywords = {Materials Chemistry, Energy Engineering and Power Technology, Fuel Technology, Renewable Energy, Sustainability and the Environment, Chemistry (miscellaneous)}, number = {8}, pages = {2825--2837}, publisher = {American Chemical Society}, title = {{High-performance thermoelectric energy conversion: A tale of atomic ordering in AgSbTe2}}, doi = {10.1021/acsenergylett.1c01184}, volume = {6}, year = {2021}, } @article{15266, abstract = {Plant pathogens often exploit a whole range of effectors to facilitate infection. The RXLR effector AVR1 produced by the oomycete plant pathogen Phytophthora infestans suppresses host defense by targeting Sec5. Sec5 is a subunit of the exocyst, a protein complex that is important for mediating polarized exocytosis during plant development and defense against pathogens. The mechanism by which AVR1 manipulates Sec5 functioning is unknown. In this study, we analyzed the effect of AVR1 on Sec5 localization and functioning in the moss Physcomitrium patens. P. patens has four Sec5 homologs. Two (PpSec5b and PpSec5d) were found to interact with AVR1 in yeast-two-hybrid assays while none of the four showed a positive interaction with AVR1ΔT, a truncated version of AVR1. In P. patens lines carrying β-estradiol inducible AVR1 or AVR1ΔT transgenes, expression of AVR1 or AVR1ΔT caused defects in the development of caulonemal protonema cells and abnormal morphology of chloronema cells. Similar phenotypes were observed in Sec5- or Sec6-silenced P. patens lines, suggesting that both AVR1 and AVR1ΔT affect exocyst functioning in P. patens. With respect to Sec5 localization we found no differences between β-estradiol-treated and untreated transgenic AVR1 lines. Sec5 localizes at the plasma membrane in growing caulonema cells, also during pathogen attack, and its subcellular localization is the same, with or without AVR1 in the vicinity.}, author = {Overdijk, Elysa J. R. and Putker, Vera and Smits, Joep and Tang, Han and Bouwmeester, Klaas and Govers, Francine and Ketelaar, Tijs}, issn = {1932-6203}, journal = {PLoS One}, keywords = {Multidisciplinary}, number = {4}, publisher = {Public Library of Science}, title = {{Phytophthora infestans RXLR effector AVR1 disturbs the growth of Physcomitrium patens without affecting Sec5 localization}}, doi = {10.1371/journal.pone.0249637}, volume = {16}, year = {2021}, } @article{15267, abstract = {We study two fundamental communication primitives: broadcasting and leader election in the classical model of multi-hop radio networks with unknown topology and without collision detection mechanisms. It has been known for almost 20 years that in undirected networks with n nodes and diameter D, randomized broadcasting requires Ω(D log n/D + log2 n) rounds, assuming that uninformed nodes are not allowed to communicate (until they are informed). Only very recently, Haeupler and Wajc (PODC'2016) showed that this bound can be improved for the model with spontaneous transmissions, providing an O(D log n log log n/log D + logO(1) n)-time broadcasting algorithm. In this article, we give a new and faster algorithm that completes broadcasting in O(D log n/log D + logO(1) n) time, succeeding with high probability. This yields the first optimal O(D)-time broadcasting algorithm whenever n is polynomial in D. Furthermore, our approach can be applied to design a new leader election algorithm that matches the performance of our broadcasting algorithm. Previously, all fast randomized leader election algorithms have used broadcasting as a subroutine and their complexity has been asymptotically strictly larger than the complexity of broadcasting. In particular, the fastest previously known randomized leader election algorithm of Ghaffari and Haeupler (SODA'2013) requires O(D log n/D min {log log n, log n/D} + logO(1) n)-time, succeeding with high probability. Our new algorithm again requires O(D log n/log D + logO(1) n) time, also succeeding with high probability.}, author = {Czumaj, Artur and Davies, Peter}, issn = {1557-735X}, journal = {Journal of the ACM}, keywords = {Artificial Intelligence, Hardware and Architecture, Information Systems, Control and Systems Engineering, Software}, number = {2}, publisher = {Association for Computing Machinery}, title = {{Exploiting spontaneous transmissions for broadcasting and leader election in radio networks}}, doi = {10.1145/3446383}, volume = {68}, year = {2021}, } @article{15269, abstract = {We study different aspects of quantum field theory at finite density using methods from quantum information theory. For simplicity we focus on massive Dirac fermions with nonzero chemical potential, and work in 1 + 1 space-time dimensions. Using the entanglement entropy on an interval, we construct an entropic c-function that is finite. Unlike what happens in Lorentz-invariant theories, this c-function exhibits a strong violation of monotonicity; it also encodes the creation of long-range entanglement from the Fermi surface. Motivated by previous works on lattice models, we next calculate numerically the Renyi entropies and find Friedel-type oscillations; these are understood in terms of a defect operator product expansion. Furthermore, we consider the mutual information as a measure of correlation functions between different regions. Using a long-distance expansion previously developed by Cardy, we argue that the mutual information detects Fermi surface correlations already at leading order in the expansion. We also analyze the relative entropy and its Renyi generalizations in order to distinguish states with different charge and/or mass. In particular, we show that states in different superselection sectors give rise to a super-extensive behavior in the relative entropy. Finally, we discuss possible extensions to interacting theories, and argue for the relevance of some of these measures for probing non-Fermi liquids.}, author = {Daguerre, Lucas and Medina Ramos, Raimel A and Solís, Mario and Torroba, Gonzalo}, issn = {1029-8479}, journal = {Journal of High Energy Physics}, keywords = {Nuclear and High Energy Physics}, number = {3}, publisher = {Springer Nature}, title = {{Aspects of quantum information in finite density field theory}}, doi = {10.1007/jhep03(2021)079}, volume = {2021}, year = {2021}, } @article{15270, abstract = {Various toxic compounds disrupt bacterial physiology. While bacteria harbor defense mechanisms to mitigate the toxicity, these mechanisms are often coupled to the physiological state of the cells and become ineffective when the physiology is severely disrupted.}, author = {Le, Dai and Krasnopeeva, Ekaterina and Sinjab, Faris and Pilizota, Teuta and Kim, Minsu}, issn = {2150-7511}, journal = {mBio}, keywords = {Virology, Microbiology}, number = {4}, publisher = {American Society for Microbiology}, title = {{Active efflux leads to heterogeneous dissipation of proton motive force by protonophores in bacteria}}, doi = {10.1128/mbio.00676-21}, volume = {12}, year = {2021}, }