@article{9816,
abstract = {Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.
Methods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.
Results: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).
Conclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test.},
author = {Hledik, Michal and Polechova, Jitka and Beiglböck, Mathias and Herdina, Anna Nele and Strassl, Robert and Posch, Martin},
issn = {19326203},
journal = {PLoS ONE},
number = {7},
publisher = {Public Library of Science},
title = {{Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program}},
doi = {10.1371/journal.pone.0255267},
volume = {16},
year = {2021},
}
@article{9770,
abstract = {We study an effective one-dimensional quantum model that includes friction and spin-orbit coupling (SOC), and show that the model exhibits spin polarization when both terms are finite. Most important, strong spin polarization can be observed even for moderate SOC, provided that the friction is strong. Our findings might help to explain the pronounced effect of chirality on spin distribution and transport in chiral molecules. In particular, our model implies static magnetic properties of a chiral molecule, which lead to Shiba-like states when a molecule is placed on a superconductor, in accordance with recent experimental data.},
author = {Volosniev, Artem and Alpern, Hen and Paltiel, Yossi and Millo, Oded and Lemeshko, Mikhail and Ghazaryan, Areg},
issn = {2469-9969},
journal = {Physical Review B},
number = {2},
publisher = {American Physical Society},
title = {{Interplay between friction and spin-orbit coupling as a source of spin polarization}},
doi = {10.1103/physrevb.104.024430},
volume = {104},
year = {2021},
}
@article{9548,
abstract = {We extend the notion of the minimal volume ellipsoid containing a convex body in Rd to the setting of logarithmically concave functions. We consider a vast class of logarithmically concave functions whose superlevel sets are concentric ellipsoids. For a fixed function from this class, we consider the set of all its “affine” positions. For any log-concave function f on Rd, we consider functions belonging to this set of “affine” positions, and find the one with the minimal integral under the condition that it is pointwise greater than or equal to f. We study the properties of existence and uniqueness of the solution to this problem. For any s∈[0,+∞), we consider the construction dual to the recently defined John s-function (Ivanov and Naszódi in Functional John ellipsoids. arXiv preprint: arXiv:2006.09934, 2020). We prove that such a construction determines a unique function and call it the Löwner s-function of f. We study the Löwner s-functions as s tends to zero and to infinity. Finally, extending the notion of the outer volume ratio, we define the outer integral ratio of a log-concave function and give an asymptotically tight bound on it.},
author = {Ivanov, Grigory and Tsiutsiurupa, Igor},
issn = {1559-002X},
journal = {Journal of Geometric Analysis},
publisher = {Springer},
title = {{Functional Löwner ellipsoids}},
doi = {10.1007/s12220-021-00691-4},
year = {2021},
}
@article{9558,
abstract = {We show that turbulent dynamics that arise in simulations of the three-dimensional Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing can be described as transient visits to the neighborhoods of unstable time-periodic solutions. Based on this description, we reduce the original system with more than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds to the neighborhood of a periodic orbit. The model accurately reproduces long-term averages of the system's observables as weighted sums over the periodic orbits.
},
author = {Yalniz, Gökhan and Hof, Björn and Budanur, Nazmi B},
issn = {1079-7114},
journal = {Physical Review Letters},
number = {24},
publisher = {American Physical Society},
title = {{Coarse graining the state space of a turbulent flow using periodic orbits}},
doi = {10.1103/PhysRevLett.126.244502},
volume = {126},
year = {2021},
}
@article{9606,
abstract = {Sound propagation is a macroscopic manifestation of the interplay between the equilibrium thermodynamics and the dynamical transport properties of fluids. Here, for a two-dimensional system of ultracold fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover, and we analyze the system response to an external perturbation. In the low-temperature regime we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of the first sound velocity, which, due to the decoupling of density and entropy fluctuations, is the sole mode excited by a density probe. Conversely, a heat perturbation excites only the second sound, which, being sensitive to the superfluid depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the modes occurs only in the finite-temperature BEC regime, where our theory converges to the purely bosonic results.},
author = {Tononi, A. and Cappellaro, Alberto and Bighin, Giacomo and Salasnich, L.},
issn = {24699934},
journal = {Physical Review A},
number = {6},
publisher = {American Physical Society},
title = {{Propagation of first and second sound in a two-dimensional Fermi superfluid}},
doi = {10.1103/PhysRevA.103.L061303},
volume = {103},
year = {2021},
}
@article{9570,
abstract = {We present conductance-matrix measurements in long, three-terminal hybrid superconductor-semiconductor nanowires, and compare with theoretical predictions of a magnetic-field-driven, topological quantum phase transition. By examining the nonlocal conductance, we identify the closure of the excitation gap in the bulk of the semiconductor before the emergence of zero-bias peaks, ruling out spurious gap-closure signatures from localized states. We observe that after the gap closes, nonlocal signals and zero-bias peaks fluctuate strongly at both ends, inconsistent with a simple picture of clean topological superconductivity.},
author = {Puglia, Denise and Martinez, E. A. and Ménard, G. C. and Pöschl, A. and Gronin, S. and Gardner, G. C. and Kallaher, R. and Manfra, M. J. and Marcus, C. M. and Higginbotham, Andrew P and Casparis, L.},
issn = {24699969},
journal = {Physical Review B},
number = {23},
publisher = {American Physical Society},
title = {{Closing of the induced gap in a hybrid superconductor-semiconductor nanowire}},
doi = {10.1103/PhysRevB.103.235201},
volume = {103},
year = {2021},
}
@article{9815,
abstract = {The quantum bits (qubits) on which superconducting quantum computers are based have energy scales corresponding to photons with GHz frequencies. The energy of photons in the gigahertz domain is too low to allow transmission through the noisy room-temperature environment, where the signal would be lost in thermal noise. Optical photons, on the other hand, have much higher energies, and signals can be detected using highly efficient single-photon detectors. Transduction from microwave to optical frequencies is therefore a potential enabling technology for quantum devices. However, in such a device the optical pump can be a source of thermal noise and thus degrade the fidelity; the similarity of input microwave state to the output optical state. In order to investigate the magnitude of this effect we model the sub-Kelvin thermal behavior of an electro-optic transducer based on a lithium niobate whispering gallery mode resonator. We find that there is an optimum power level for a continuous pump, whilst pulsed operation of the pump increases the fidelity of the conversion.},
author = {Mobassem, Sonia and Lambert, Nicholas J. and Rueda Sanchez, Alfredo R and Fink, Johannes M and Leuchs, Gerd and Schwefel, Harald G.L.},
issn = {20589565},
journal = {Quantum Science and Technology},
number = {4},
publisher = {Quantum},
title = {{Thermal noise in electro-optic devices at cryogenic temperatures}},
doi = {10.1088/2058-9565/ac0f36},
volume = {6},
year = {2021},
}
@unpublished{9651,
abstract = {We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence.},
author = {Dymond, Michael and Kaluza, Vojtech},
booktitle = {arXiv},
title = {{Divergence of separated nets with respect to displacement equivalence}},
year = {2021},
}
@article{9827,
abstract = {The Nearest neighbour search (NNS) is a fundamental problem in many application domains dealing with multidimensional data. In a concurrent setting, where dynamic modifications are allowed, a linearizable implementation of the NNS is highly desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free concurrent kD-tree, which implements an abstract data type (ADT) that provides the operations Add, Remove, Contains, and NNS. Our implementation is linearizable. The operations in the LFkD-tree use single-word read and compare-and-swap (Image 1 ) atomic primitives, which are readily supported on available multi-core processors. We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world and synthetic datasets. The experiments show that the presented design is scalable and achieves significant speed-up compared to the implementations of an existing sequential kD-tree and a recently proposed multidimensional indexing structure, PH-tree.},
author = {Chatterjee, Bapi and Walulya, Ivan and Tsigas, Philippas},
issn = {03043975},
journal = {Theoretical Computer Science},
keywords = {Concurrent data structure, kD-tree, Nearest neighbor search, Similarity search, Lock-free, Linearizability},
publisher = {Elsevier},
title = {{Concurrent linearizable nearest neighbour search in LockFree-kD-tree}},
doi = {10.1016/j.tcs.2021.06.041},
year = {2021},
}
@article{9817,
abstract = {Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements.},
author = {Hafner, Christian and Bickel, Bernd},
issn = {15577368},
journal = {ACM Transactions on Graphics},
keywords = {Computing methodologies, shape modeling, modeling and simulation, theory of computation, computational geometry, mathematics of computing, mathematical optimization},
number = {4},
publisher = {Association for Computing Machinery},
title = {{The design space of plane elastic curves}},
doi = {10.1145/3450626.3459800},
volume = {40},
year = {2021},
}
@phdthesis{9623,
abstract = {Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.
We report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten.
We find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation.
},
author = {Caballero Mancebo, Silvia},
isbn = {978-3-99078-012-1},
issn = {2663-337X},
pages = {111},
publisher = {IST Austria},
title = {{Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes}},
doi = {10.15479/at:ista:9623},
year = {2021},
}
@article{9006,
abstract = {Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species.},
author = {Shamipour, Shayan and Caballero Mancebo, Silvia and Heisenberg, Carl-Philipp J},
issn = {18781551},
journal = {Developmental Cell},
number = {2},
pages = {P213--226},
publisher = {Elsevier},
title = {{Cytoplasm's got moves}},
doi = {10.1016/j.devcel.2020.12.002},
volume = {56},
year = {2021},
}
@article{9769,
abstract = {A few years ago, flow equations were introduced as a technique for calculating the ground-state energies of cold Bose gases with and without impurities. In this paper, we extend this approach to compute observables other than the energy. As an example, we calculate the densities, and phase fluctuations of one-dimensional Bose gases with one and two impurities. For a single mobile impurity, we use flow equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation. We show that the mean-field approximation is accurate for all values of the boson-impurity interaction strength as long as the phase coherence length is much larger than the healing length of the condensate. For two static impurities, we calculate impurity-impurity interactions induced by the Bose gas. We find that leading order perturbation theory fails when boson-impurity interactions are stronger than boson-boson interactions. The mean-field approximation reproduces the flow equation results for all values of the boson-impurity interaction strength as long as boson-boson interactions are weak.},
author = {Brauneis, Fabian and Hammer, Hans-Werner and Lemeshko, Mikhail and Volosniev, Artem},
issn = {2542-4653},
journal = {SciPost Physics},
number = {1},
publisher = {SciPost},
title = {{Impurities in a one-dimensional Bose gas: The flow equation approach}},
doi = {10.21468/scipostphys.11.1.008},
volume = {11},
year = {2021},
}
@inproceedings{9825,
abstract = {The dual attack has long been considered a relevant attack on lattice-based cryptographic schemes relying on the hardness of learning with errors (LWE) and its structured variants. As solving LWE corresponds to finding a nearest point on a lattice, one may naturally wonder how efficient this dual approach is for solving more general closest vector problems, such as the classical closest vector problem (CVP), the variants bounded distance decoding (BDD) and approximate CVP, and preprocessing versions of these problems. While primal, sieving-based solutions to these problems (with preprocessing) were recently studied in a series of works on approximate Voronoi cells [Laa16b, DLdW19, Laa20, DLvW20], for the dual attack no such overview exists, especially for problems with preprocessing. With one of the take-away messages of the approximate Voronoi cell line of work being that primal attacks work well for approximate CVP(P) but scale poorly for BDD(P), one may further wonder if the dual attack suffers the same drawbacks, or if it is perhaps a better solution when trying to solve BDD(P).
In this work we provide an overview of cost estimates for dual algorithms for solving these “classical” closest lattice vector problems. Heuristically we expect to solve the search version of average-case CVPP in time and space 20.293𝑑+𝑜(𝑑) in the single-target model. The distinguishing version of average-case CVPP, where we wish to distinguish between random targets and targets planted at distance (say) 0.99⋅𝑔𝑑 from the lattice, has the same complexity in the single-target model, but can be solved in time and space 20.195𝑑+𝑜(𝑑) in the multi-target setting, when given a large number of targets from either target distribution. This suggests an inequivalence between distinguishing and searching, as we do not expect a similar improvement in the multi-target setting to hold for search-CVPP. We analyze three slightly different decoders, both for distinguishing and searching, and experimentally obtain concrete cost estimates for the dual attack in dimensions 50 to 80, which confirm our heuristic assumptions, and show that the hidden order terms in the asymptotic estimates are quite small.
Our main take-away message is that the dual attack appears to mirror the approximate Voronoi cell line of work – whereas using approximate Voronoi cells works well for approximate CVP(P) but scales poorly for BDD(P), the dual approach scales well for BDD(P) instances but performs poorly on approximate CVP(P).},
author = {Laarhoven, Thijs and Walter, Michael},
booktitle = {Topics in Cryptology – CT-RSA 2021},
isbn = {9783030755386},
issn = {16113349},
location = {Virtual Event},
pages = {478--502},
publisher = {Springer Nature},
title = {{Dual lattice attacks for closest vector problems (with preprocessing)}},
doi = {10.1007/978-3-030-75539-3_20},
volume = {12704},
year = {2021},
}
@inproceedings{9826,
abstract = {Automated contract tracing aims at supporting manual contact tracing during pandemics by alerting users of encounters with infected people. There are currently many proposals for protocols (like the “decentralized” DP-3T and PACT or the “centralized” ROBERT and DESIRE) to be run on mobile phones, where the basic idea is to regularly broadcast (using low energy Bluetooth) some values, and at the same time store (a function of) incoming messages broadcasted by users in their proximity. In the existing proposals one can trigger false positives on a massive scale by an “inverse-Sybil” attack, where a large number of devices (malicious users or hacked phones) pretend to be the same user, such that later, just a single person needs to be diagnosed (and allowed to upload) to trigger an alert for all users who were in proximity to any of this large group of devices.
We propose the first protocols that do not succumb to such attacks assuming the devices involved in the attack do not constantly communicate, which we observe is a necessary assumption. The high level idea of the protocols is to derive the values to be broadcasted by a hash chain, so that two (or more) devices who want to launch an inverse-Sybil attack will not be able to connect their respective chains and thus only one of them will be able to upload. Our protocols also achieve security against replay, belated replay, and one of them even against relay attacks.},
author = {Auerbach, Benedikt and Chakraborty, Suvradip and Klein, Karen and Pascual Perez, Guillermo and Pietrzak, Krzysztof Z and Walter, Michael and Yeo, Michelle X},
booktitle = {Topics in Cryptology – CT-RSA 2021},
isbn = {9783030755386},
issn = {16113349},
location = {Virtual Event},
pages = {399--421},
publisher = {Springer Nature},
title = {{Inverse-Sybil attacks in automated contact tracing}},
doi = {10.1007/978-3-030-75539-3_17},
volume = {12704},
year = {2021},
}
@inproceedings{9823,
abstract = {Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a vertex of the graph as input and, if non-faulty, must output a vertex such that
all the outputs are within distance 1 of one another, and
each output value lies on a shortest path between two input values.
From prior work, it is known that there is no wait-free algorithm among 𝑛≥3 processes for this problem on any cycle of length 𝑐≥4 , by reduction from 2-set agreement (Castañeda et al. 2018).
In this work, we investigate the solvability and complexity of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length 𝑐≥4 , via a generalisation of Sperner’s Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a class of graphs that properly contains the class of chordal graphs.},
author = {Alistarh, Dan-Adrian and Ellen, Faith and Rybicki, Joel},
booktitle = {Structural Information and Communication Complexity},
isbn = {9783030795269},
issn = {16113349},
location = {Wrocław, Poland},
pages = {87--105},
publisher = {Springer Nature},
title = {{Wait-free approximate agreement on graphs}},
doi = {10.1007/978-3-030-79527-6_6},
volume = {12810},
year = {2021},
}
@article{9746,
abstract = {Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs.},
author = {Batra, Aditi and Römhild, Roderich and Rousseau, Emilie and Franzenburg, Sören and Niemann, Stefan and Schulenburg, Hinrich},
issn = {2050-084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{High potency of sequential therapy with only beta-lactam antibiotics}},
doi = {10.7554/elife.68876},
volume = {10},
year = {2021},
}
@article{8723,
abstract = {Deep learning at scale is dominated by communication time. Distributing samples across nodes usually yields the best performance, but poses scaling challenges due to global information dissemination and load imbalance across uneven sample lengths. State-of-the-art decentralized optimizers mitigate the problem, but require more iterations to achieve the same accuracy as their globally-communicating counterparts. We present Wait-Avoiding Group Model Averaging (WAGMA) SGD, a wait-avoiding stochastic optimizer that reduces global communication via subgroup weight exchange. The key insight is a combination of algorithmic changes to the averaging scheme and the use of a group allreduce operation. We prove the convergence of WAGMA-SGD, and empirically show that it retains convergence rates similar to Allreduce-SGD. For evaluation, we train ResNet-50 on ImageNet; Transformer for machine translation; and deep reinforcement learning for navigation at scale. Compared with state-of-the-art decentralized SGD variants, WAGMA-SGD significantly improves training throughput (e.g., 2.1× on 1,024 GPUs for reinforcement learning), and achieves the fastest time-to-solution (e.g., the highest score using the shortest training time for Transformer).},
author = {Li, Shigang and Tal Ben-Nun, Tal Ben-Nun and Nadiradze, Giorgi and Girolamo, Salvatore Di and Dryden, Nikoli and Alistarh, Dan-Adrian and Hoefler, Torsten},
issn = {10459219},
journal = {IEEE Transactions on Parallel and Distributed Systems},
number = {7},
publisher = {IEEE},
title = {{Breaking (global) barriers in parallel stochastic optimization with wait-avoiding group averaging}},
doi = {10.1109/TPDS.2020.3040606},
volume = {32},
year = {2021},
}
@article{9437,
abstract = {The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation.},
author = {Bhandari, Pradeep and Vandael, David H and Fernández-Fernández, Diego and Fritzius, Thorsten and Kleindienst, David and Önal, Hüseyin C and Montanaro-Punzengruber, Jacqueline-Claire and Gassmann, Martin and Jonas, Peter M and Kulik, Akos and Bettler, Bernhard and Shigemoto, Ryuichi and Koppensteiner, Peter},
issn = {2050-084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals}},
doi = {10.7554/ELIFE.68274},
volume = {10},
year = {2021},
}
@phdthesis{9562,
abstract = {Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.},
author = {Kleindienst, David},
issn = {2663-337X},
pages = {124},
publisher = {IST Austria},
title = {{2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning}},
doi = {10.15479/at:ista:9562},
year = {2021},
}