@misc{8254,
  abstract     = {Here are the research data underlying the publication "Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)". Further information are summed up in the README document.
The files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192.},
  author       = {Arathoon, Louise S},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)}},
  doi          = {10.15479/AT:ISTA:8254},
  year         = {2020},
}

@article{8261,
  abstract     = {Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion.},
  author       = {Zhang, Xiaomin and Schlögl, Alois and Jonas, Peter M},
  issn         = {0896-6273},
  journal      = {Neuron},
  number       = {6},
  pages        = {1212--1225},
  publisher    = {Elsevier},
  title        = {{Selective routing of spatial information flow from input to output in hippocampal granule cells}},
  doi          = {10.1016/j.neuron.2020.07.006},
  volume       = {107},
  year         = {2020},
}

@article{8268,
  abstract     = {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.},
  author       = {Gurel, Nezihe Merve and Kara, Kaan and Stojanov, Alen and Smith, Tyler and Lemmin, Thomas and Alistarh, Dan-Adrian and Puschel, Markus and Zhang, Ce},
  issn         = {1941-0476},
  journal      = {IEEE Transactions on Signal Processing},
  pages        = {4268--4282},
  publisher    = {IEEE},
  title        = {{Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications}},
  doi          = {10.1109/TSP.2020.3010355},
  volume       = {68},
  year         = {2020},
}

@article{8271,
  author       = {He, Peng and Zhang, Yuzhou and Xiao, Guanghui},
  issn         = {1752-9867},
  journal      = {Molecular Plant},
  number       = {9},
  pages        = {1238--1240},
  publisher    = {Elsevier},
  title        = {{Origin of a subgenome and genome evolution of allotetraploid cotton species}},
  doi          = {10.1016/j.molp.2020.07.006},
  volume       = {13},
  year         = {2020},
}

@article{8285,
  abstract     = {We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200  μm radius and falls roughly 300  μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively.},
  author       = {Malia, Benjamin K. and Martínez-Rincón, Julián and Wu, Yunfan and Hosten, Onur and Kasevich, Mark A.},
  issn         = {1079-7114},
  journal      = {Physical Review Letters},
  number       = {4},
  publisher    = {American Physical Society},
  title        = {{Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit}},
  doi          = {10.1103/PhysRevLett.125.043202},
  volume       = {125},
  year         = {2020},
}

@misc{8294,
  abstract     = {Automated root growth analysis and tracking of root tips. },
  author       = {Hauschild, Robert},
  publisher    = {IST Austria},
  title        = {{RGtracker}},
  doi          = {10.15479/AT:ISTA:8294},
  year         = {2020},
}

@unpublished{8307,
  abstract     = {Classic Byzantine fault-tolerant consensus protocols forfeit liveness in the face of asynchrony in order to preserve safety, whereas most deployed blockchain protocols forfeit safety in order to remain live. In this work, we achieve the best of both worlds by proposing a novel abstractions called the finality gadget. A finality gadget allows for transactions to always optimistically commit but informs the clients that these transactions might be unsafe. As a result, a blockchain can execute transactions optimistically and only commit them after they have been sufficiently and provably audited. In
this work, we formally model the finality gadget abstraction, prove that it is impossible to solve it deterministically in full asynchrony (even though it is stronger than consensus) and provide a partially synchronous protocol which is currently securing a major blockchain. This way we show that the protocol designer can decouple safety and liveness in order to speed up recovery from failures. We believe that there can be other types of finality gadgets that provide weaker safety (e.g., probabilistic) in order to gain more efficiency and this can depend on the probability that the network is not in synchrony.},
  author       = {Stewart, Alistair and Kokoris Kogias, Eleftherios},
  booktitle    = {arXiv},
  title        = {{GRANDPA: A Byzantine finality gadget}},
  doi          = {10.48550/arXiv.2007.01560},
  year         = {2020},
}

@article{8319,
  abstract     = {We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated.},
  author       = {Wu, Yunfan and Krishnakumar, Rajiv and Martínez-Rincón, Julián and Malia, Benjamin K. and Hosten, Onur and Kasevich, Mark A.},
  issn         = {2469-9934},
  journal      = {Physical Review A},
  number       = {1},
  publisher    = {American Physical Society},
  title        = {{Retrieval of cavity-generated atomic spin squeezing after free-space release}},
  doi          = {10.1103/PhysRevA.102.012224},
  volume       = {102},
  year         = {2020},
}

@article{8320,
  abstract     = {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.},
  author       = {Mukba, S. A. and Vlasov, Petr and Kolosov, P. M. and Shuvalova, E. Y. and Egorova, T. V. and Alkalaeva, E. Z.},
  issn         = {1608-3245},
  journal      = {Molecular Biology},
  number       = {4},
  pages        = {475--484},
  publisher    = {Springer Nature},
  title        = {{Expanding the genetic code: Unnatural base pairs in biological systems}},
  doi          = {10.1134/S0026893320040111},
  volume       = {54},
  year         = {2020},
}

@article{8321,
  abstract     = {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.},
  author       = {Mukba, S. A. and Vlasov, Petr and Kolosov, P. M. and Shuvalova, E. Y. and Egorova, T. V. and Alkalaeva, E. Z.},
  issn         = {0026-8984},
  journal      = {Molekuliarnaia biologiia},
  number       = {4},
  pages        = {531--541},
  publisher    = {Russian Academy of Sciences},
  title        = {{Expanding the genetic code: Unnatural base pairs in biological systems}},
  doi          = {10.31857/S0026898420040126},
  volume       = {54},
  year         = {2020},
}

@article{8323,
  author       = {Pach, János},
  issn         = {14320444},
  journal      = {Discrete and Computational Geometry},
  pages        = {571--574},
  publisher    = {Springer Nature},
  title        = {{A farewell to Ricky Pollack}},
  doi          = {10.1007/s00454-020-00237-5},
  volume       = {64},
  year         = {2020},
}

@inproceedings{8324,
  abstract     = {The notion of program sensitivity (aka Lipschitz continuity) specifies that changes in the program input result in proportional changes to the program output. For probabilistic programs the notion is naturally extended to expected sensitivity. A previous approach develops a relational program logic framework for proving expected sensitivity of probabilistic while loops, where the number of iterations is fixed and bounded. In this work, we consider probabilistic while loops where the number of iterations is not fixed, but randomized and depends on the initial input values. We present a sound approach for proving expected sensitivity of such programs. Our sound approach is martingale-based and can be automated through existing martingale-synthesis algorithms. Furthermore, our approach is compositional for sequential composition of while loops under a mild side condition. We demonstrate the effectiveness of our approach on several classical examples from Gambler's Ruin, stochastic hybrid systems and stochastic gradient descent. We also present experimental results showing that our automated approach can handle various probabilistic programs in the literature.},
  author       = {Wang, Peixin and Fu, Hongfei and Chatterjee, Krishnendu and Deng, Yuxin and Xu, Ming},
  booktitle    = {Proceedings of the ACM on Programming Languages},
  issn         = {2475-1421},
  number       = {POPL},
  publisher    = {ACM},
  title        = {{Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time}},
  doi          = {10.1145/3371093},
  volume       = {4},
  year         = {2020},
}

@article{8325,
  abstract     = {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. },
  author       = {Kalinin, Nikita and Shkolnikov, Mikhail},
  issn         = {1432-0916},
  journal      = {Communications in Mathematical Physics},
  number       = {9},
  pages        = {1649--1675},
  publisher    = {Springer Nature},
  title        = {{Sandpile solitons via smoothing of superharmonic functions}},
  doi          = {10.1007/s00220-020-03828-8},
  volume       = {378},
  year         = {2020},
}

@article{8329,
  abstract     = {We show the synthesis of a redox‐active quinone, 2‐methoxy‐1,4‐hydroquinone (MHQ), from a bio‐based feedstock and its suitability as electrolyte in aqueous redox flow batteries. We identified semiquinone intermediates at insufficiently low pH and quinoid radicals as responsible for decomposition of MHQ under electrochemical conditions. Both can be avoided and/or stabilized, respectively, using H 3 PO 4 electrolyte, allowing for reversible cycling in a redox flow battery for hundreds of cycles.},
  author       = {Schlemmer, Werner and Nothdurft, Philipp and Petzold, Alina and Frühwirt, Philipp and Schmallegger, Max and Gescheidt-Demner, Georg and Fischer, Roland and Freunberger, Stefan Alexander and Kern, Wolfgang and Spirk, Stefan},
  issn         = {1521-3773},
  journal      = {Angewandte Chemie International Edition},
  number       = {51},
  pages        = {22943--22946},
  publisher    = {Wiley},
  title        = {{2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries}},
  doi          = {10.1002/anie.202008253},
  volume       = {59},
  year         = {2020},
}

@article{8361,
  abstract     = {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.},
  author       = {Varzi, Alberto and Thanner, Katharina and Scipioni, Roberto and Di Lecce, Daniele and Hassoun, Jusef and Dörfler, Susanne and Altheus, Holger and Kaskel, Stefan and Prehal, Christian and Freunberger, Stefan Alexander},
  issn         = {0378-7753},
  journal      = {Journal of Power Sources},
  number       = {12},
  publisher    = {Elsevier},
  title        = {{Current status and future perspectives of lithium metal batteries}},
  doi          = {10.1016/j.jpowsour.2020.228803},
  volume       = {480},
  year         = {2020},
}

@inproceedings{8382,
  abstract     = {We present the first deterministic wait-free long-lived snapshot algorithm, using only read and write operations, that guarantees polylogarithmic amortized step complexity in all executions. This is the first non-blocking snapshot algorithm, using reads and writes only, that has sub-linear amortized step complexity in executions of arbitrary length. The key to our construction is a novel implementation of a 2-component max array object which may be of independent interest.},
  author       = {Baig, Mirza Ahad and Hendler, Danny and Milani, Alessia and Travers, Corentin},
  booktitle    = {Proceedings of the 39th Symposium on Principles of Distributed Computing},
  isbn         = {9781450375825},
  location     = {Virtual, Italy},
  pages        = {31--40},
  publisher    = {Association for Computing Machinery},
  title        = {{Long-lived snapshots with polylogarithmic amortized step complexity}},
  doi          = {10.1145/3382734.3406005},
  year         = {2020},
}

@inproceedings{8383,
  abstract     = {We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We explain why this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power.},
  author       = {Alistarh, Dan-Adrian and Aspnes, James and Ellen, Faith and Gelashvili, Rati and Zhu, Leqi},
  booktitle    = {Proceedings of the 39th Symposium on Principles of Distributed Computing},
  isbn         = {9781450375825},
  location     = {Virtual, Italy},
  pages        = {54--56},
  publisher    = {Association for Computing Machinery},
  title        = {{Brief Announcement: Why Extension-Based Proofs Fail}},
  doi          = {10.1145/3382734.3405743},
  year         = {2020},
}

@article{8402,
  abstract     = {Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway.
Results: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins.
Conclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins.},
  author       = {Rampelt, Heike and Sucec, Iva and Bersch, Beate and Horten, Patrick and Perschil, Inge and Martinou, Jean-Claude and van der Laan, Martin and Wiedemann, Nils and Schanda, Paul and Pfanner, Nikolaus},
  issn         = {1741-7007},
  journal      = {BMC Biology},
  keywords     = {Biotechnology, Plant Science, General Biochemistry, Genetics and Molecular Biology, Developmental Biology, Cell Biology, Physiology, Ecology, Evolution, Behavior and Systematics, Structural Biology, General Agricultural and Biological Sciences},
  publisher    = {Springer Nature},
  title        = {{The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments}},
  doi          = {10.1186/s12915-019-0733-6},
  volume       = {18},
  year         = {2020},
}

@unpublished{8403,
  abstract     = {Chaperones are essential for assisting protein folding, and for transferring poorly soluble proteins to their functional locations within cells. Hydrophobic interactions drive promiscuous chaperone–client binding, but our understanding of how additional interactions enable client specificity is sparse. Here we decipher what determines binding of two chaperones (TIM8·13, TIM9·10) to different integral membrane proteins, the all-transmembrane mitochondrial carrier Ggc1, and Tim23 which has an additional disordered hydrophilic domain. Combining NMR, SAXS and molecular dynamics simulations, we determine the structures of Tim23/TIM8·13 and Tim23/TIM9·10 complexes. TIM8·13 uses transient salt bridges to interact with the hydrophilic part of its client, but its interactions to the transmembrane part are weaker than in TIM9·10. Consequently, TIM9·10 outcompetes TIM8·13 in binding hydrophobic clients, while TIM8·13 is tuned to few clients with both hydrophilic and hydrophobic parts. Our study exemplifies how chaperones fine-tune the balance of promiscuity <jats:italic>vs.</jats:italic> specificity.},
  author       = {Sučec, Iva and Wang, Yong and Dakhlaoui, Ons and Weinhäupl, Katharina and Jores, Tobias and Costa, Doriane and Hessel, Audrey and Brennich, Martha and Rapaport, Doron and Lindorff-Larsen, Kresten and Bersch, Beate and Schanda, Paul},
  booktitle    = {bioRxiv},
  publisher    = {Cold Spring Harbor Laboratory},
  title        = {{Structural basis of client specificity in mitochondrial membrane-protein chaperones}},
  doi          = {10.1101/2020.06.08.140772},
  year         = {2020},
}

@unpublished{8404,
  abstract     = {<jats:p>The mitochondrial Tim chaperones are responsible for the transport of membrane proteins across the inter-membrane space to the inner and outer mitochondrial membranes. TIM9·10, a hexameric 70 kDa protein complex formed by 3 copies of Tim9 and Tim10, guides its clients across the aqueous compartment. The TIM9·10·12 complex is the anchor point at the inner-membrane insertase complex TIM22. The mechanism of client transport by TIM9·10 has been resolved recently, but the structure and subunit composition of the TIM9·10·12 complex remains largely unresolved. Furthermore, the assembly process of the hexameric TIM chaperones from its subunits remained elusive. We investigate the structural and dynamical properties of the Tim subunits, and show that they are highly dynamic. In their non-assembled form, the subunits behave as intrinsically disordered proteins; when the conserved cysteines of the CX<jats:sub>3</jats:sub>C-X<jats:sub><jats:italic>n</jats:italic></jats:sub>-CX<jats:sub>3</jats:sub>C motifs are formed, short marginally stable <jats:italic>α</jats:italic>-helices are formed, which are only fully stabilized upon hexamer formation to the mature chaperone. Subunits are in equilibrium between their hexamer-embedded and a free form, with exchange kinetics on a minutes time scale. Joint NMR, small-angle X-ray scattering and MD simulation data allow us to derive a structural model of the TIM9·10·12 assembly, which has a 2:3:1 stoichiometry (Tim9:Tim10:Tim12) with a conserved hydrophobic client-binding groove and flexible N- and C-terminal tentacles.</jats:p>},
  author       = {Weinhäupl, Katharina and Wang, Yong and Hessel, Audrey and Brennich, Martha and Lindorff-Larsen, Kresten and Schanda, Paul},
  booktitle    = {bioRxiv},
  publisher    = {Cold Spring Harbor Laboratory},
  title        = {{Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone}},
  doi          = {10.1101/2020.03.13.990150},
  year         = {2020},
}