TY - JOUR AB - Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality. AU - Gurel, Nezihe Merve AU - Kara, Kaan AU - Stojanov, Alen AU - Smith, Tyler AU - Lemmin, Thomas AU - Alistarh, Dan-Adrian AU - Puschel, Markus AU - Zhang, Ce ID - 8268 JF - IEEE Transactions on Signal Processing SN - 1053587X TI - Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications VL - 68 ER - TY - JOUR AU - He, Peng AU - Zhang, Yuzhou AU - Xiao, Guanghui ID - 8271 IS - 9 JF - Molecular Plant SN - 16742052 TI - Origin of a subgenome and genome evolution of allotetraploid cotton species VL - 13 ER - TY - JOUR AB - By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature. AU - Grosjean, Galien M AU - Wald, Sebastian AU - Sobarzo Ponce, Juan Carlos A AU - Waitukaitis, Scott R ID - 8101 IS - 8 JF - Physical Review Materials KW - electric charge KW - tribocharging KW - soft matter KW - granular materials KW - polymers SN - 2475-9953 TI - Quantitatively consistent scale-spanning model for same-material tribocharging VL - 4 ER - TY - JOUR AB - Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. AU - Kalinin, Nikita AU - Shkolnikov, Mikhail ID - 8325 IS - 9 JF - Communications in Mathematical Physics SN - 00103616 TI - Sandpile solitons via smoothing of superharmonic functions VL - 378 ER - TY - JOUR AB - Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I. AU - Gutierrez-Fernandez, Javier AU - Kaszuba, Karol AU - Minhas, Gurdeep S. AU - Baradaran, Rozbeh AU - Tambalo, Margherita AU - Gallagher, David T. AU - Sazanov, Leonid A ID - 8318 IS - 1 JF - Nature Communications TI - Key role of quinone in the mechanism of respiratory complex I VL - 11 ER - TY - JOUR AB - The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications. AU - Mukba, S. A. AU - Vlasov, Petr AU - Kolosov, P. M. AU - Shuvalova, E. Y. AU - Egorova, T. V. AU - Alkalaeva, E. Z. ID - 8320 IS - 4 JF - Molecular Biology SN - 00268933 TI - Expanding the genetic code: Unnatural base pairs in biological systems VL - 54 ER - TY - JOUR AB - The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications. AU - Mukba, S. A. AU - Vlasov, Petr AU - Kolosov, P. M. AU - Shuvalova, E. Y. AU - Egorova, T. V. AU - Alkalaeva, E. Z. ID - 8321 IS - 4 JF - Molekuliarnaia biologiia SN - 00268984 TI - Expanding the genetic code: Unnatural base pairs in biological systems VL - 54 ER - TY - JOUR AU - Pach, János ID - 8323 JF - Discrete and Computational Geometry SN - 01795376 TI - A farewell to Ricky Pollack VL - 64 ER - TY - JOUR AB - Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER. AU - Kubiasova, Karolina AU - Montesinos López, Juan C AU - Šamajová, Olga AU - Nisler, Jaroslav AU - Mik, Václav AU - Semeradova, Hana AU - Plíhalová, Lucie AU - Novák, Ondřej AU - Marhavý, Peter AU - Cavallari, Nicola AU - Zalabák, David AU - Berka, Karel AU - Doležal, Karel AU - Galuszka, Petr AU - Šamaj, Jozef AU - Strnad, Miroslav AU - Benková, Eva AU - Plíhal, Ondřej AU - Spíchal, Lukáš ID - 8336 JF - Nature Communications TI - Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum VL - 11 ER - TY - JOUR AB - Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses. AU - Antoniadi, Ioanna AU - Novák, Ondřej AU - Gelová, Zuzana AU - Johnson, Alexander J AU - Plíhal, Ondřej AU - Simerský, Radim AU - Mik, Václav AU - Vain, Thomas AU - Mateo-Bonmatí, Eduardo AU - Karady, Michal AU - Pernisová, Markéta AU - Plačková, Lenka AU - Opassathian, Korawit AU - Hejátko, Jan AU - Robert, Stéphanie AU - Friml, Jiří AU - Doležal, Karel AU - Ljung, Karin AU - Turnbull, Colin ID - 8337 JF - Nature Communications TI - Cell-surface receptors enable perception of extracellular cytokinins VL - 11 ER - TY - GEN AB - With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7. AU - Varzi, Alberto AU - Thanner, Katharina AU - Scipioni, Roberto AU - Di Lecce, Daniele AU - Hassoun, Jusef AU - Dörfler, Susanne AU - Altheus, Holger AU - Kaskel, Stefan AU - Prehal, Christian AU - Freunberger, Stefan Alexander ID - 8067 KW - Battery KW - Lithium metal KW - Lithium-sulphur KW - Lithium-air KW - All-solid-state SN - 2664-1690 TI - Current status and future perspectives of Lithium metal batteries ER - TY - JOUR AB - With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, Li metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries. A particular attention is paid to recent developments of these battery technologies and their current state with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7. AU - Varzi, Alberto AU - Thanner, Katharina AU - Scipioni, Roberto AU - Di Lecce, Daniele AU - Hassoun, Jusef AU - Dörfler, Susanne AU - Altheus, Holger AU - Kaskel, Stefan AU - Prehal, Christian AU - Freunberger, Stefan Alexander ID - 8361 IS - 12 JF - Journal of Power Sources SN - 0378-7753 TI - Current status and future perspectives of lithium metal batteries VL - 480 ER - TY - GEN AB - The present review addresses the technical advances and the theoretical developments to realize and rationalize attosecond-science experiments that reveal a new dynamical time scale (10−15-10−18 s), with a particular emphasis on molecular systems and the implications of attosecond processes for chemical dynamics. After a brief outline of the theoretical framework for treating non-perturbative phenomena in Section 2, we introduce the physical mechanisms underlying high-harmonic generation and attosecond technology. The relevant technological developments and experimental schemes are covered in Section 3. Throughout the remainder of the chapter, we report on selected applications in molecular attosecond physics, thereby addressing specific phenomena mediated by purely electronic dynamics: charge localization in molecular hydrogen, charge migration in biorelevant molecules, high-harmonic spectroscopy, and delays in molecular photoionization. AU - Baykusheva, Denitsa Rangelova AU - Wörner, Hans Jakob ID - 14028 TI - Attosecond molecular spectroscopy and dynamics ER - TY - JOUR AB - Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform. AU - Arnold, Georg M AU - Wulf, Matthias AU - Barzanjeh, Shabir AU - Redchenko, Elena AU - Rueda Sanchez, Alfredo R AU - Hease, William J AU - Hassani, Farid AU - Fink, Johannes M ID - 8529 JF - Nature Communications KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Physics and Astronomy KW - General Chemistry SN - 2041-1723 TI - Converting microwave and telecom photons with a silicon photonic nanomechanical interface VL - 11 ER - TY - JOUR AB - We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation. AU - Skrivan, Tomas AU - Soderstrom, Andreas AU - Johansson, John AU - Sprenger, Christoph AU - Museth, Ken AU - Wojtan, Christopher J ID - 8535 IS - 4 JF - ACM Transactions on Graphics SN - 07300301 TI - Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces VL - 39 ER - TY - JOUR AB - Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions. AU - Su, C. AU - Zhao, Gufang AU - Zhong, C. ID - 8539 IS - 3 JF - Annales Scientifiques de l'Ecole Normale Superieure SN - 0012-9593 TI - On the K-theory stable bases of the springer resolution VL - 53 ER - TY - CHAP AB - This chapter presents an overview of the state of the art in attosecond time-resolved spectroscopy. The theoretical foundations of strong-field light–matter interaction and attosecond pulse generation are described. The enabling laser technologies are reviewed from chirped-pulse amplification and carrier-envelope-phase stabilization to the generation and characterization of attosecond pulses. The applications of attosecond pulses and pulse trains in electron- or ion-imaging experiments are presented, followed by attosecond electron spectroscopy in larger molecules. After this, high-harmonic spectroscopy and its applications to probing charge migration on attosecond time scales is reviewed. The rapidly evolving field of molecular photoionization delays is discussed. Finally, the applications of attosecond transient absorption to probing molecular dynamics are presented. AU - Baykusheva, Denitsa Rangelova AU - Wörner, Hans Jakob ED - Marquardt, Roberto ED - Quack, Martin ID - 14000 SN - 9780128172353 T2 - Molecular Spectroscopy and Quantum Dynamics TI - Attosecond Molecular Dynamics and Spectroscopy ER - TY - GEN AB - This datasets comprises all data shown in plots of the submitted article "Converting microwave and telecom photons with a silicon photonic nanomechanical interface". Additional raw data are available from the corresponding author on reasonable request. AU - Arnold, Georg M AU - Wulf, Matthias AU - Barzanjeh, Shabir AU - Redchenko, Elena AU - Rueda Sanchez, Alfredo R AU - Hease, William J AU - Hassani, Farid AU - Fink, Johannes M ID - 13056 TI - Converting microwave and telecom photons with a silicon photonic nanomechanical interface ER - TY - JOUR AB - Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells. AU - Andrei, Andreea AU - Öztürk, Yavuz AU - Khalfaoui-Hassani, Bahia AU - Rauch, Juna AU - Marckmann, Dorian AU - Trasnea, Petru Iulian AU - Daldal, Fevzi AU - Koch, Hans-Georg ID - 8579 IS - 9 JF - Membranes TI - Cu homeostasis in bacteria: The ins and outs VL - 10 ER - TY - JOUR AB - The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the ‘proton translocation cluster’ attached to the c-ring and a more distant ‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine. AU - Pinke, Gergely AU - Zhou, Long AU - Sazanov, Leonid A ID - 8581 IS - 11 JF - Nature Structural and Molecular Biology SN - 15459993 TI - Cryo-EM structure of the entire mammalian F-type ATP synthase VL - 27 ER - TY - CONF AB - We evaluate the usefulness of persistent homology in the analysis of heart rate variability. In our approach we extract several topological descriptors characterising datasets of RR-intervals, which are later used in classical machine learning algorithms. By this method we are able to differentiate the group of patients with the history of transient ischemic attack and the group of hypertensive patients. AU - Graff, Grzegorz AU - Graff, Beata AU - Jablonski, Grzegorz AU - Narkiewicz, Krzysztof ID - 8580 SN - 9781728157511 T2 - 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, TI - The application of persistent homology in the analysis of heart rate variability ER - TY - JOUR AB - Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma. AU - Tian, Anhao AU - Kang, Bo AU - Li, Baizhou AU - Qiu, Biying AU - Jiang, Wenhong AU - Shao, Fangjie AU - Gao, Qingqing AU - Liu, Rui AU - Cai, Chengwei AU - Jing, Rui AU - Wang, Wei AU - Chen, Pengxiang AU - Liang, Qinghui AU - Bao, Lili AU - Man, Jianghong AU - Wang, Yan AU - Shi, Yu AU - Li, Jin AU - Yang, Minmin AU - Wang, Lisha AU - Zhang, Jianmin AU - Hippenmeyer, Simon AU - Zhu, Junming AU - Bian, Xiuwu AU - Wang, Ying‐Jie AU - Liu, Chong ID - 8592 IS - 21 JF - Advanced Science KW - General Engineering KW - General Physics and Astronomy KW - General Materials Science KW - Medicine (miscellaneous) KW - General Chemical Engineering KW - Biochemistry KW - Genetics and Molecular Biology (miscellaneous) SN - 2198-3844 TI - Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting VL - 7 ER - TY - JOUR AB - Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries. AU - Prehal, Christian AU - Fitzek, Harald AU - Kothleitner, Gerald AU - Presser, Volker AU - Gollas, Bernhard AU - Freunberger, Stefan Alexander AU - Abbas, Qamar ID - 8568 JF - Nature Communications KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Physics and Astronomy KW - General Chemistry SN - 2041-1723 TI - Persistent and reversible solid iodine electrodeposition in nanoporous carbons VL - 11 ER - TY - JOUR AB - The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors. AU - Deichler, Alfonso AU - Carrasco, Denisse AU - Lopez-Jury, Luciana AU - Vega Zuniga, Tomas A AU - Marquez, Natalia AU - Mpodozis, Jorge AU - Marin, Gonzalo ID - 8643 JF - Scientific Reports TI - A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents VL - 10 ER - TY - JOUR AB - Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data. AU - Esteban, Laura A AU - Lonishin, Lyubov R AU - Bobrovskiy, Daniil M AU - Leleytner, Gregory AU - Bogatyreva, Natalya S AU - Kondrashov, Fyodor AU - Ivankov, Dmitry N ID - 8645 IS - 6 JF - Bioinformatics SN - 1367-4803 TI - HypercubeME: Two hundred million combinatorially complete datasets from a single experiment VL - 36 ER - TY - JOUR AB - Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy. AU - Merrin, Jack ID - 8597 IS - 6 JF - Physical Biology TI - Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide VL - 17 ER - TY - JOUR AB - Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections. AU - Henneberger, Christian AU - Bard, Lucie AU - Panatier, Aude AU - Reynolds, James P. AU - Kopach, Olga AU - Medvedev, Nikolay I. AU - Minge, Daniel AU - Herde, Michel K. AU - Anders, Stefanie AU - Kraev, Igor AU - Heller, Janosch P. AU - Rama, Sylvain AU - Zheng, Kaiyu AU - Jensen, Thomas P. AU - Sanchez-Romero, Inmaculada AU - Jackson, Colin J. AU - Janovjak, Harald L AU - Ottersen, Ole Petter AU - Nagelhus, Erlend Arnulf AU - Oliet, Stephane H.R. AU - Stewart, Michael G. AU - Nägerl, U. VAlentin AU - Rusakov, Dmitri A. ID - 8674 IS - 5 JF - Neuron SN - 08966273 TI - LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia VL - 108 ER - TY - JOUR AB - Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules. AU - Ghazaryan, Areg AU - Lemeshko, Mikhail AU - Volosniev, Artem ID - 8652 JF - Communications Physics SN - 2399-3650 TI - Filtering spins by scattering from a lattice of point magnets VL - 3 ER - TY - JOUR AB - Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development. AU - Sznurkowska, Magdalena K. AU - Hannezo, Edouard B AU - Azzarelli, Roberta AU - Chatzeli, Lemonia AU - Ikeda, Tatsuro AU - Yoshida, Shosei AU - Philpott, Anna AU - Simons, Benjamin D ID - 8669 JF - Nature Communications TI - Tracing the cellular basis of islet specification in mouse pancreas VL - 11 ER - TY - JOUR AB - Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions. AU - Chaigne, Agathe AU - Labouesse, Céline AU - White, Ian J. AU - Agnew, Meghan AU - Hannezo, Edouard B AU - Chalut, Kevin J. AU - Paluch, Ewa K. ID - 8672 IS - 2 JF - Developmental Cell SN - 15345807 TI - Abscission couples cell division to embryonic stem cell fate VL - 55 ER - TY - JOUR AB - In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest. AU - Fischer, Julian L AU - Kniely, Michael ID - 8697 IS - 11 JF - Nonlinearity SN - 09517715 TI - Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model VL - 33 ER - TY - JOUR AB - Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning. AU - Tsai, Tony Y.-C. AU - Sikora, Mateusz K AU - Xia, Peng AU - Colak-Champollion, Tugba AU - Knaut, Holger AU - Heisenberg, Carl-Philipp J AU - Megason, Sean G. ID - 8680 IS - 6512 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - An adhesion code ensures robust pattern formation during tissue morphogenesis VL - 370 ER - TY - JOUR AB - Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data. AU - Galan, Silvia AU - Machnik, Nick N AU - Kruse, Kai AU - Díaz, Noelia AU - Marti-Renom, Marc A AU - Vaquerizas, Juan M ID - 8707 JF - Nature Genetics SN - 10614036 TI - CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction VL - 52 ER - TY - JOUR AB - A central goal of artificial intelligence in high-stakes decision-making applications is to design a single algorithm that simultaneously expresses generalizability by learning coherent representations of their world and interpretable explanations of its dynamics. Here, we combine brain-inspired neural computation principles and scalable deep learning architectures to design compact neural controllers for task-specific compartments of a full-stack autonomous vehicle control system. We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated input features to outputs by 253 synapses, learns to map high-dimensional inputs into steering commands. This system shows superior generalizability, interpretability and robustness compared with orders-of-magnitude larger black-box learning systems. The obtained neural agents enable high-fidelity autonomy for task-specific parts of a complex autonomous system. AU - Lechner, Mathias AU - Hasani, Ramin AU - Amini, Alexander AU - Henzinger, Thomas A AU - Rus, Daniela AU - Grosu, Radu ID - 8679 JF - Nature Machine Intelligence TI - Neural circuit policies enabling auditable autonomy VL - 2 ER - TY - JOUR AB - The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)]. AU - Zhang, Haonan ID - 8670 IS - 10 JF - Journal of Mathematical Physics SN - 00222488 TI - Equality conditions of data processing inequality for α-z Rényi relative entropies VL - 61 ER - TY - JOUR AB - The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation. AU - Maoz, Ori AU - Tkačik, Gašper AU - Esteki, Mohamad Saleh AU - Kiani, Roozbeh AU - Schneidman, Elad ID - 8698 IS - 40 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 00278424 TI - Learning probabilistic neural representations with randomly connected circuits VL - 117 ER - TY - CONF AB - Traditional robotic control suits require profound task-specific knowledge for designing, building and testing control software. The rise of Deep Learning has enabled end-to-end solutions to be learned entirely from data, requiring minimal knowledge about the application area. We design a learning scheme to train end-to-end linear dynamical systems (LDS)s by gradient descent in imitation learning robotic domains. We introduce a new regularization loss component together with a learning algorithm that improves the stability of the learned autonomous system, by forcing the eigenvalues of the internal state updates of an LDS to be negative reals. We evaluate our approach on a series of real-life and simulated robotic experiments, in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures. Our results show that our stabilizing method significantly improves test performance of LDS, enabling such linear models to match the performance of contemporary nonlinear RNN architectures. A video of the obstacle avoidance performance of our method on a mobile robot, in unseen environments, compared to other methods can be viewed at https://youtu.be/mhEsCoNao5E. AU - Lechner, Mathias AU - Hasani, Ramin AU - Rus, Daniela AU - Grosu, Radu ID - 8704 SN - 10504729 T2 - Proceedings - IEEE International Conference on Robotics and Automation TI - Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme ER - TY - JOUR AB - Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency. AU - Sokolova, E. E. AU - Vlasov, Petr AU - Egorova, T. V. AU - Shuvalov, A. V. AU - Alkalaeva, E. Z. ID - 8700 IS - 5 JF - Molecular Biology SN - 00268933 TI - The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes VL - 54 ER - TY - JOUR AB - Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency. AU - Sokolova, E. E. AU - Vlasov, Petr AU - Egorova, T. V. AU - Shuvalov, A. V. AU - Alkalaeva, E. Z. ID - 8701 IS - 5 JF - Molekuliarnaia biologiia SN - 00268984 TI - The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes VL - 54 ER - TY - GEN AB - A binary neutron star merger has been observed in a multi-messenger detection of gravitational wave (GW) and electromagnetic (EM) radiation. Binary neutron stars that merge within a Hubble time, as well as many other compact binaries, are expected to form via common envelope evolution. Yet five decades of research on common envelope evolution have not yet resulted in a satisfactory understanding of the multi-spatial multi-timescale evolution for the systems that lead to compact binaries. In this paper, we report on the first successful simulations of common envelope ejection leading to binary neutron star formation in 3D hydrodynamics. We simulate the dynamical inspiral phase of the interaction between a 12M⊙ red supergiant and a 1.4M⊙ neutron star for different initial separations and initial conditions. For all of our simulations, we find complete envelope ejection and final orbital separations of af≈1.3-5.1R⊙ depending on the simulation and criterion, leading to binary neutron stars that can merge within a Hubble time. We find αCE-equivalent efficiencies of ≈0.1-2.7 depending on the simulation and criterion, but this may be specific for these extended progenitors. We fully resolve the core of the star to ≲0.005R⊙ and our 3D hydrodynamics simulations are informed by an adjusted 1D analytic energy formalism and a 2D kinematics study in order to overcome the prohibitive computational cost of simulating these systems. The framework we develop in this paper can be used to simulate a wide variety of interactions between stars, from stellar mergers to common envelope episodes leading to GW sources. AU - Jamie A. P. Law-Smith, Jamie A. P. Law-Smith AU - Everson, Rosa Wallace AU - Enrico Ramirez-Ruiz, Enrico Ramirez-Ruiz AU - Mink, Selma E. de AU - Son, Lieke A. C. van AU - Götberg, Ylva Louise Linsdotter AU - Zellmann, Stefan AU - Alejandro Vigna-Gómez, Alejandro Vigna-Gómez AU - Renzo, Mathieu AU - Wu, Samantha AU - Schrøder, Sophie L. AU - Foley, Ryan J. AU - Tenley Hutchinson-Smith, Tenley Hutchinson-Smith ID - 14096 T2 - arXiv TI - Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics ER - TY - JOUR AB - In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling. AU - Paris, Eugenio AU - Tseng, Yi AU - Paerschke, Ekaterina AU - Zhang, Wenliang AU - Upton, Mary H AU - Efimenko, Anna AU - Rolfs, Katharina AU - McNally, Daniel E AU - Maurel, Laura AU - Naamneh, Muntaser AU - Caputo, Marco AU - Strocov, Vladimir N AU - Wang, Zhiming AU - Casa, Diego AU - Schneider, Christof W AU - Pomjakushina, Ekaterina AU - Wohlfeld, Krzysztof AU - Radovic, Milan AU - Schmitt, Thorsten ID - 8699 IS - 40 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 00278424 TI - Strain engineering of the charge and spin-orbital interactions in Sr2IrO4 VL - 117 ER - TY - JOUR AB - Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions. AU - Kampjut, Domen AU - Sazanov, Leonid A ID - 8737 IS - 6516 JF - Science TI - The coupling mechanism of mammalian respiratory complex I VL - 370 ER - TY - CONF AB - Load imbalance pervasively exists in distributed deep learning training systems, either caused by the inherent imbalance in learned tasks or by the system itself. Traditional synchronous Stochastic Gradient Descent (SGD) achieves good accuracy for a wide variety of tasks, but relies on global synchronization to accumulate the gradients at every training step. In this paper, we propose eager-SGD, which relaxes the global synchronization for decentralized accumulation. To implement eager-SGD, we propose to use two partial collectives: solo and majority. With solo allreduce, the faster processes contribute their gradients eagerly without waiting for the slower processes, whereas with majority allreduce, at least half of the participants must contribute gradients before continuing, all without using a central parameter server. We theoretically prove the convergence of the algorithms and describe the partial collectives in detail. Experimental results on load-imbalanced environments (CIFAR-10, ImageNet, and UCF101 datasets) show that eager-SGD achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing accuracy. AU - Li, Shigang AU - Tal Ben-Nun, Tal Ben-Nun AU - Girolamo, Salvatore Di AU - Alistarh, Dan-Adrian AU - Hoefler, Torsten ID - 8722 T2 - Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming TI - Taming unbalanced training workloads in deep learning with partial collective operations ER - TY - JOUR AB - Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding. AU - Schulte, Linda AU - Mao, Jiafei AU - Reitz, Julian AU - Sreeramulu, Sridhar AU - Kudlinzki, Denis AU - Hodirnau, Victor-Valentin AU - Meier-Credo, Jakob AU - Saxena, Krishna AU - Buhr, Florian AU - Langer, Julian D. AU - Blackledge, Martin AU - Frangakis, Achilleas S. AU - Glaubitz, Clemens AU - Schwalbe, Harald ID - 8744 JF - Nature Communications KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Physics and Astronomy KW - General Chemistry SN - 2041-1723 TI - Cysteine oxidation and disulfide formation in the ribosomal exit tunnel VL - 11 ER - TY - JOUR AB - Appropriately designed nanocomposites allow improving the thermoelectric performance by several mechanisms, including phonon scattering, modulation doping and energy filtering, while additionally promoting better mechanical properties than those of crystalline materials. Here, a strategy for producing Bi2Te3–Cu2xTe nanocomposites based on the consolidation of heterostructured nanoparticles is described and the thermoelectric properties of the obtained materials are investigated. We first detail a two-step solution-based process to produce Bi2Te3–Cu2xTe heteronanostructures, based on the growth of Cu2xTe nanocrystals on the surface of Bi2Te3 nanowires. We characterize the structural and chemical properties of the synthesized nanostructures and of the nanocomposites produced by hot-pressing the particles at moderate temperatures. Besides, the transport properties of the nanocomposites are investigated as a function of the amount of Cu introduced. Overall, the presence of Cu decreases the material thermal conductivity through promotion of phonon scattering, modulates the charge carrier concentration through electron spillover, and increases the Seebeck coefficient through filtering of charge carriers at energy barriers. These effects result in an improvement of over 50% of the thermoelectric figure of merit of Bi2Te3. AU - Zhang, Yu AU - Liu, Yu AU - Calcabrini, Mariano AU - Xing, Congcong AU - Han, Xu AU - Arbiol, Jordi AU - Cadavid, Doris AU - Ibáñez, Maria AU - Cabot, Andreu ID - 8747 IS - 40 JF - Journal of Materials Chemistry C TI - Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks VL - 8 ER - TY - GEN AB - The Habitable Exoplanet Observatory, or HabEx, has been designed to be the Great Observatory of the 2030s. For the first time in human history, technologies have matured sufficiently to enable an affordable space-based telescope mission capable of discovering and characterizing Earthlike planets orbiting nearby bright sunlike stars in order to search for signs of habitability and biosignatures. Such a mission can also be equipped with instrumentation that will enable broad and exciting general astrophysics and planetary science not possible from current or planned facilities. HabEx is a space telescope with unique imaging and multi-object spectroscopic capabilities at wavelengths ranging from ultraviolet (UV) to near-IR. These capabilities allow for a broad suite of compelling science that cuts across the entire NASA astrophysics portfolio. HabEx has three primary science goals: (1) Seek out nearby worlds and explore their habitability; (2) Map out nearby planetary systems and understand the diversity of the worlds they contain; (3) Enable new explorations of astrophysical systems from our own solar system to external galaxies by extending our reach in the UV through near-IR. This Great Observatory science will be selected through a competed GO program, and will account for about 50% of the HabEx primary mission. The preferred HabEx architecture is a 4m, monolithic, off-axis telescope that is diffraction-limited at 0.4 microns and is in an L2 orbit. HabEx employs two starlight suppression systems: a coronagraph and a starshade, each with their own dedicated instrument. AU - Gaudi, B. Scott AU - Seager, Sara AU - Mennesson, Bertrand AU - Kiessling, Alina AU - Warfield, Keith AU - Cahoy, Kerri AU - Clarke, John T. AU - Shawn Domagal-Goldman, Shawn Domagal-Goldman AU - Feinberg, Lee AU - Guyon, Olivier AU - Kasdin, Jeremy AU - Mawet, Dimitri AU - Plavchan, Peter AU - Robinson, Tyler AU - Rogers, Leslie AU - Scowen, Paul AU - Somerville, Rachel AU - Stapelfeldt, Karl AU - Stark, Christopher AU - Stern, Daniel AU - Turnbull, Margaret AU - Amini, Rashied AU - Kuan, Gary AU - Martin, Stefan AU - Morgan, Rhonda AU - Redding, David AU - Stahl, H. Philip AU - Webb, Ryan AU - Oscar Alvarez-Salazar, Oscar Alvarez-Salazar AU - Arnold, William L. AU - Arya, Manan AU - Balasubramanian, Bala AU - Baysinger, Mike AU - Bell, Ray AU - Below, Chris AU - Benson, Jonathan AU - Blais, Lindsey AU - Booth, Jeff AU - Bourgeois, Robert AU - Bradford, Case AU - Brewer, Alden AU - Brooks, Thomas AU - Cady, Eric AU - Caldwell, Mary AU - Calvet, Rob AU - Carr, Steven AU - Chan, Derek AU - Cormarkovic, Velibor AU - Coste, Keith AU - Cox, Charlie AU - Danner, Rolf AU - Davis, Jacqueline AU - Dewell, Larry AU - Dorsett, Lisa AU - Dunn, Daniel AU - East, Matthew AU - Effinger, Michael AU - Eng, Ron AU - Freebury, Greg AU - Garcia, Jay AU - Gaskin, Jonathan AU - Greene, Suzan AU - Hennessy, John AU - Hilgemann, Evan AU - Hood, Brad AU - Holota, Wolfgang AU - Howe, Scott AU - Huang, Pei AU - Hull, Tony AU - Hunt, Ron AU - Hurd, Kevin AU - Johnson, Sandra AU - Kissil, Andrew AU - Knight, Brent AU - Kolenz, Daniel AU - Kraus, Oliver AU - Krist, John AU - Li, Mary AU - Lisman, Doug AU - Mandic, Milan AU - Mann, John AU - Marchen, Luis AU - Colleen Marrese-Reading, Colleen Marrese-Reading AU - McCready, Jonathan AU - McGown, Jim AU - Missun, Jessica AU - Miyaguchi, Andrew AU - Moore, Bradley AU - Nemati, Bijan AU - Nikzad, Shouleh AU - Nissen, Joel AU - Novicki, Megan AU - Perrine, Todd AU - Pineda, Claudia AU - Polanco, Otto AU - Putnam, Dustin AU - Qureshi, Atif AU - Richards, Michael AU - Riggs, A. J. Eldorado AU - Rodgers, Michael AU - Rud, Mike AU - Saini, Navtej AU - Scalisi, Dan AU - Scharf, Dan AU - Schulz, Kevin AU - Serabyn, Gene AU - Sigrist, Norbert AU - Sikkia, Glory AU - Singleton, Andrew AU - Shaklan, Stuart AU - Smith, Scott AU - Southerd, Bart AU - Stahl, Mark AU - Steeves, John AU - Sturges, Brian AU - Sullivan, Chris AU - Tang, Hao AU - Taras, Neil AU - Tesch, Jonathan AU - Therrell, Melissa AU - Tseng, Howard AU - Valente, Marty AU - Buren, David Van AU - Villalvazo, Juan AU - Warwick, Steve AU - Webb, David AU - Westerhoff, Thomas AU - Wofford, Rush AU - Wu, Gordon AU - Woo, Jahning AU - Wood, Milana AU - Ziemer, John AU - Arney, Giada AU - Anderson, Jay AU - Jesús Maíz-Apellániz, Jesús Maíz-Apellániz AU - Bartlett, James AU - Belikov, Ruslan AU - Bendek, Eduardo AU - Cenko, Brad AU - Douglas, Ewan AU - Dulz, Shannon AU - Evans, Chris AU - Faramaz, Virginie AU - Feng, Y. Katherina AU - Ferguson, Harry AU - Follette, Kate AU - Ford, Saavik AU - García, Miriam AU - Geha, Marla AU - Gelino, Dawn AU - Götberg, Ylva Louise Linsdotter AU - Hildebrandt, Sergi AU - Hu, Renyu AU - Jahnke, Knud AU - Kennedy, Grant AU - Kreidberg, Laura AU - Isella, Andrea AU - Lopez, Eric AU - Marchis, Franck AU - Macri, Lucas AU - Marley, Mark AU - Matzko, William AU - Mazoyer, Johan AU - McCandliss, Stephan AU - Meshkat, Tiffany AU - Mordasini, Christoph AU - Morris, Patrick AU - Nielsen, Eric AU - Newman, Patrick AU - Petigura, Erik AU - Postman, Marc AU - Reines, Amy AU - Roberge, Aki AU - Roederer, Ian AU - Ruane, Garreth AU - Schwieterman, Edouard AU - Sirbu, Dan AU - Spalding, Christopher AU - Teplitz, Harry AU - Tumlinson, Jason AU - Turner, Neal AU - Werk, Jessica AU - Wofford, Aida AU - Wyatt, Mark AU - Young, Amber AU - Zellem, Rob ID - 14095 T2 - arXiv TI - The habitable exoplanet observatory (HabEx) mission concept study final report ER - TY - JOUR AB - Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring. AU - Kaveh, Kamran AU - McAvoy, Alex AU - Chatterjee, Krishnendu AU - Nowak, Martin A. ID - 8767 IS - 11 JF - PLOS Computational Biology KW - Ecology KW - Modelling and Simulation KW - Computational Theory and Mathematics KW - Genetics KW - Ecology KW - Evolution KW - Behavior and Systematics KW - Molecular Biology KW - Cellular and Molecular Neuroscience SN - 1553-734X TI - The Moran process on 2-chromatic graphs VL - 16 ER - TY - CONF AB - Efficiently handling time-triggered and possibly nondeterministic switches for hybrid systems reachability is a challenging task. In this paper we present an approach based on conservative set-based enclosure of the dynamics that can handle systems with uncertain parameters and inputs, where the uncertainties are bound to given intervals. The method is evaluated on the plant model of an experimental electro-mechanical braking system with periodic controller. In this model, the fast-switching controller dynamics requires simulation time scales of the order of nanoseconds. Accurate set-based computations for relatively large time horizons are known to be expensive. However, by appropriately decoupling the time variable with respect to the spatial variables, and enclosing the uncertain parameters using interval matrix maps acting on zonotopes, we show that the computation time can be lowered to 5000 times faster with respect to previous works. This is a step forward in formal verification of hybrid systems because reduced run-times allow engineers to introduce more expressiveness in their models with a relatively inexpensive computational cost. AU - Forets, Marcelo AU - Freire, Daniel AU - Schilling, Christian ID - 8750 SN - 9781728191485 T2 - 18th ACM-IEEE International Conference on Formal Methods and Models for System Design TI - Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions ER - TY - JOUR AB - We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where the microscopic system satisfies the detailed-balance condition. The latter allows us to enrich the systems with a gradient structure, i.e. the evolution is given by a gradient-flow equation. We present the arising links between the associated gradient structures that are driven by the relative entropy of the detailed-balance steady state. The limit of large volumes is studied in the sense of evolutionary Γ-convergence of gradient flows. Moreover, we use the gradient structures to derive hybrid models for coupling different modeling levels. AU - Maas, Jan AU - Mielke, Alexander ID - 8758 IS - 6 JF - Journal of Statistical Physics SN - 00224715 TI - Modeling of chemical reaction systems with detailed balance using gradient structures VL - 181 ER - TY - GEN AB - This dataset comprises all data shown in the figures of the submitted article "Surpassing the resistance quantum with a geometric superinductor". Additional raw data are available from the corresponding author on reasonable request. AU - Peruzzo, Matilda AU - Trioni, Andrea AU - Hassani, Farid AU - Zemlicka, Martin AU - Fink, Johannes M ID - 13070 TI - Surpassing the resistance quantum with a geometric superinductor ER -