@inproceedings{14758,
abstract = {We present a flexible and efficient toolchain to symbolically solve (standard) Rabin games, fair-adversarial Rabin games, and 2 1/2 license type-player Rabin games. To our best knowledge, our tools are the first ones to be able to solve these problems. Furthermore, using these flexible game solvers as a back-end, we implemented a tool for computing correct-by-construction controllers for stochastic dynamical systems under LTL specifications. Our implementations use the recent theoretical result that all of these games can be solved using the same symbolic fixpoint algorithm but utilizing different, domain specific calculations of the involved predecessor operators. The main feature of our toolchain is the utilization of two programming abstractions: one to separate the symbolic fixpoint computations from the predecessor calculations, and another one to allow the integration of different BDD libraries as back-ends. In particular, we employ a multi-threaded execution of the fixpoint algorithm by using the multi-threaded BDD library Sylvan, which leads to enormous computational savings.},
author = {Majumdar, Rupak and Mallik, Kaushik and Rychlicki, Mateusz and Schmuck, Anne-Kathrin and Soudjani, Sadegh},
booktitle = {35th International Conference on Computer Aided Verification},
isbn = {9783031377082},
issn = {1611-3349},
location = {Paris, France},
pages = {3--15},
publisher = {Springer Nature},
title = {{A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties}},
doi = {10.1007/978-3-031-37709-9_1},
volume = {13966},
year = {2023},
}
@article{14654,
abstract = {Two assumptions commonly applied in convection schemes—the diagnostic and quasi-equilibrium assumptions—imply that convective activity (e.g., convective precipitation) is controlled only by the large-scale (macrostate) environment at the time. In contrast, numerical experiments indicate a “memory” or dependence of convection also on its own previous activity whereby subgrid-scale (microstate) structures boost but are also boosted by convection. In this study we investigated this memory by comparing single-column model behavior in two idealized tests previously executed by a cloud-resolving model (CRM). Conventional convection schemes that employ the diagnostic assumption fail to reproduce the CRM behavior. The memory-capable org and Laboratoire de Météorologie Dynamique Zoom cold pool schemes partially capture the behavior, but fail to fully exhibit the strong reinforcing feedbacks implied by the CRM. Analysis of this failure suggests that it is because the CRM supports a linear (or superlinear) dependence of the subgrid structure growth rate on the precipitation rate, while the org scheme assumes a sublinear dependence. Among varying versions of the org scheme, the growth rate of the org variable representing subgrid structure is strongly associated with memory strength. These results demonstrate the importance of parameterizing convective memory, and the ability of idealized tests to reveal shortcomings of convection schemes and constrain model structural assumptions.},
author = {Hwong, Yi-Ling and Colin, M. and Aglas, Philipp and Muller, Caroline J and Sherwood, S. C.},
issn = {1942-2466},
journal = {Journal of Advances in Modeling Earth Systems},
number = {12},
publisher = {Wiley},
title = {{Assessing memory in convection schemes using idealized tests}},
doi = {10.1029/2023MS003726},
volume = {15},
year = {2023},
}
@inproceedings{13139,
abstract = {A classical problem for Markov chains is determining their stationary (or steady-state) distribution. This problem has an equally classical solution based on eigenvectors and linear equation systems. However, this approach does not scale to large instances, and iterative solutions are desirable. It turns out that a naive approach, as used by current model checkers, may yield completely wrong results. We present a new approach, which utilizes recent advances in partial exploration and mean payoff computation to obtain a correct, converging approximation.},
author = {Meggendorfer, Tobias},
booktitle = {TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems},
isbn = {9783031308222},
issn = {1611-3349},
location = {Paris, France},
pages = {489--507},
publisher = {Springer Nature},
title = {{Correct approximation of stationary distributions}},
doi = {10.1007/978-3-031-30823-9_25},
volume = {13993},
year = {2023},
}
@misc{14991,
abstract = {This repository contains the data, scripts, WRF codes and files required to reproduce the results of the manuscript "Assessing Memory in Convection Schemes Using Idealized Tests" submitted to the Journal of Advances in Modeling Earth Systems (JAMES).},
author = {Hwong, Yi-Ling and Colin, Maxime and Aglas, Philipp and Muller, Caroline J and Sherwood, Steven C.},
publisher = {Zenodo},
title = {{Data-assessing memory in convection schemes using idealized tests}},
doi = {10.5281/ZENODO.7757041},
year = {2023},
}
@misc{14990,
abstract = {The software artefact to evaluate the approximation of stationary distributions implementation.},
author = {Meggendorfer, Tobias},
publisher = {Zenodo},
title = {{Artefact for: Correct Approximation of Stationary Distributions}},
doi = {10.5281/ZENODO.7548214},
year = {2023},
}
@inproceedings{14260,
abstract = {This paper presents Lincheck, a new practical and user-friendly framework for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck provides a simple and declarative way to write concurrent tests: instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. The framework automatically generates a set of concurrent scenarios, examines them using stress-testing or bounded model checking, and verifies that the results of each invocation are correct. Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow trace to reproduce it, significantly simplifying the bug investigation.
To the best of our knowledge, Lincheck is the first production-ready tool on the JVM that offers such a simple way of writing concurrent tests, without requiring special skills or expertise. We successfully integrated Lincheck in the development process of several large projects, such as Kotlin Coroutines, and identified new bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is used in most of the synchronization primitives. We believe that Lincheck can significantly improve the quality and productivity of concurrent algorithms research and development and become the state-of-the-art tool for checking their correctness.},
author = {Koval, Nikita and Fedorov, Alexander and Sokolova, Maria and Tsitelov, Dmitry and Alistarh, Dan-Adrian},
booktitle = {35th International Conference on Computer Aided Verification },
isbn = {9783031377051},
issn = {1611-3349},
location = {Paris, France},
pages = {156--169},
publisher = {Springer Nature},
title = {{Lincheck: A practical framework for testing concurrent data structures on JVM}},
doi = {10.1007/978-3-031-37706-8_8},
volume = {13964},
year = {2023},
}
@misc{14995,
abstract = {Lincheck is a new practical and user-friendly framework for testing concurrent data structures on the Java Virtual Machine (JVM). It provides a simple and declarative way to write concurrent tests. Instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand.
The artifact presents a collection of Lincheck tests that discover new bugs in popular libraries and implementations from the concurrency literature -- they are listed in Table 1, Section 3. To evaluate the performance of Lincheck analysis, the collection of tests also includes those which check correct data structures and, thus, always succeed. Similarly to Table 2, Section 3, the experiments demonstrate the reasonable time to perform a test. Finally, Lincheck provides user-friendly output with an easy-to-follow trace to reproduce a detected error, significantly simplifying further investigation.},
author = {Koval, Nikita and Fedorov, Alexander and Sokolova, Maria and Tsitelov, Dmitry and Alistarh, Dan-Adrian},
publisher = {Zenodo},
title = {{Lincheck: A practical framework for testing concurrent data structures on JVM}},
doi = {10.5281/ZENODO.7877757},
year = {2023},
}
@misc{14994,
abstract = {This resource contains the artifacts for reproducing the experimental results presented in the paper titled "A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties" that has been submitted in CAV 2023.},
author = {Majumdar, Rupak and Mallik, Kaushik and Rychlicki, Mateusz and Schmuck, Anne-Kathrin and Soudjani, Sadegh},
publisher = {Zenodo},
title = {{A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties}},
doi = {10.5281/ZENODO.7877790},
year = {2023},
}
@inproceedings{15023,
abstract = {Reinforcement learning has shown promising results in learning neural network policies for complicated control tasks. However, the lack of formal guarantees about the behavior of such policies remains an impediment to their deployment. We propose a novel method for learning a composition of neural network policies in stochastic environments, along with a formal certificate which guarantees that a specification over the policy's behavior is satisfied with the desired probability. Unlike prior work on verifiable RL, our approach leverages the compositional nature of logical specifications provided in SpectRL, to learn over graphs of probabilistic reach-avoid specifications. The formal guarantees are provided by learning neural network policies together with reach-avoid supermartingales (RASM) for the graph’s sub-tasks and then composing them into a global policy. We also derive a tighter lower bound compared to previous work on the probability of reach-avoidance implied by a RASM, which is required to find a compositional policy with an acceptable probabilistic threshold for complex tasks with multiple edge policies. We implement a prototype of our approach and evaluate it on a Stochastic Nine Rooms environment.},
author = {Zikelic, Dorde and Lechner, Mathias and Verma, Abhinav and Chatterjee, Krishnendu and Henzinger, Thomas A},
booktitle = {37th Conference on Neural Information Processing Systems},
location = {New Orleans, LO, United States},
title = {{Compositional policy learning in stochastic control systems with formal guarantees}},
year = {2023},
}
@inproceedings{14993,
abstract = {Traditional top-down approaches for global health have historically failed to achieve social progress (Hoffman et al., 2015; Hoffman & Røttingen, 2015). Recently, however, a more holistic, multi-level approach termed One Health (OH) (Osterhaus et al., 2020) is being adopted. Several sets of challenges have been identified for the implementation of OH (dos S. Ribeiro et al., 2019), including policy and funding, education and training, and multi-actor, multi-domain, and multi-level collaborations. These exist despite the increasing accessibility to
knowledge and digital collaborative research tools through the internet. To address some of these challenges, we propose a general framework for grassroots community-based means of participatory research. Additionally, we present a specific roadmap to create a Machine Learning for Global Health community in Africa. The proposed framework aims to enable any small group of individuals with scarce resources to build and sustain an online community within approximately two years. We provide a discussion on the potential impact of the proposed framework for global health research collaborations.},
author = {Currin, Christopher and Asiedu , Mercy Nyamewaa and Fourie, Chris and Rosman, Benjamin and Turki, Houcemeddine and Lambebo Tonja, Atnafu and Abbott, Jade and Ajala, Marvellous and Adedayo, Sadiq Adewale and Emezue, Chris Chinenye and Machangara, Daphne},
booktitle = {1st Workshop on Machine Learning & Global Health},
location = {Kigali, Rwanda},
publisher = {OpenReview},
title = {{A framework for grassroots research collaboration in machine learning and global health}},
year = {2023},
}
@inproceedings{12979,
abstract = {Color and gloss are fundamental aspects of surface appearance. State-of-the-art fabrication techniques can manipulate both properties of the printed 3D objects. However, in the context of appearance reproduction, perceptual aspects of color and gloss are usually handled separately, even though previous perceptual studies suggest their interaction. Our work is motivated by previous studies demonstrating a perceived color shift due to a change in the object's gloss, i.e., two samples with the same color but different surface gloss appear as they have different colors. In this paper, we conduct new experiments which support this observation and provide insights into the magnitude and direction of the perceived color change. We use the observations as guidance to design a new method that estimates and corrects the color shift enabling the fabrication of objects with the same perceived color but different surface gloss. We formulate the problem as an optimization procedure solved using differentiable rendering. We evaluate the effectiveness of our method in perceptual experiments with 3D objects fabricated using a multi-material 3D printer and demonstrate potential applications. },
author = {Condor, Jorge and Piovarci, Michael and Bickel, Bernd and Didyk, Piotr},
booktitle = {SIGGRAPH ’23 Conference Proceedings},
isbn = {9798400701597},
keywords = {color, gloss, perception, color compensation, color management},
location = {Los Angeles, CA, United States},
publisher = {Association for Computing Machinery},
title = {{Gloss-aware color correction for 3D printing}},
doi = {10.1145/3588432.3591546},
year = {2023},
}
@inproceedings{14076,
abstract = {Hyperproperties are properties that relate multiple execution traces. Previous work on monitoring hyperproperties focused on synchronous hyperproperties, usually specified in HyperLTL. When monitoring synchronous hyperproperties, all traces are assumed to proceed at the same speed. We introduce (multi-trace) prefix transducers and show how to use them for monitoring synchronous as well as, for the first time, asynchronous hyperproperties. Prefix transducers map multiple input traces into one or more output traces by incrementally matching prefixes of the input traces against expressions similar to regular expressions. The prefixes of different traces which are consumed by a single matching step of the monitor may have different lengths. The deterministic and executable nature of prefix transducers makes them more suitable as an intermediate formalism for runtime verification than logical specifications, which tend to be highly non-deterministic, especially in the case of asynchronous hyperproperties. We report on a set of experiments about monitoring asynchronous version of observational determinism.},
author = {Chalupa, Marek and Henzinger, Thomas A},
booktitle = {23nd International Conference on Runtime Verification},
isbn = {978-3-031-44266-7},
location = {Thessaloniki, Greek},
pages = {168--190},
publisher = {Springer Nature},
title = {{Monitoring hyperproperties with prefix transducers}},
doi = {10.1007/978-3-031-44267-4_9},
volume = {14245},
year = {2023},
}
@inproceedings{14743,
abstract = {Leader-based consensus algorithms are fast and efficient under normal conditions, but lack robustness to adverse conditions due to their reliance on timeouts for liveness. We present QuePaxa, the first protocol offering state-of-the-art normal-case efficiency without depending on timeouts. QuePaxa uses a novel randomized asynchronous consensus core to tolerate adverse conditions such as denial-of-service (DoS) attacks, while a one-round-trip fast path preserves the normal-case efficiency of Multi-Paxos or Raft. By allowing simultaneous proposers without destructive interference, and using short hedging delays instead of conservative timeouts to limit redundant effort, QuePaxa permits rapid recovery after leader failure without risking costly view changes due to false timeouts. By treating leader choice and hedging delay as a multi-armed-bandit optimization, QuePaxa achieves responsiveness to prevalent conditions, and can choose the best leader even if the current one has not failed. Experiments with a prototype confirm that QuePaxa achieves normal-case LAN and WAN performance of 584k and 250k cmd/sec in throughput, respectively, comparable to Multi-Paxos. Under conditions such as DoS attacks, misconfigurations, or slow leaders that severely impact existing protocols, we find that QuePaxa remains live with median latency under 380ms in WAN experiments.},
author = {Tennage, Pasindu and Basescu, Cristina and Kokoris Kogias, Eleftherios and Syta, Ewa and Jovanovic, Philipp and Estrada-Galinanes, Vero and Ford, Bryan},
booktitle = {Proceedings of the 29th Symposium on Operating Systems Principles},
isbn = {9798400702297},
location = {Koblenz, Germany},
pages = {281--297},
publisher = {Association for Computing Machinery},
title = {{QuePaxa: Escaping the tyranny of timeouts in consensus}},
doi = {10.1145/3600006.3613150},
year = {2023},
}
@inproceedings{14748,
author = {Chen, Yi-Lu and Ly, Mickaël and Wojtan, Christopher J},
booktitle = {Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation},
isbn = {9798400702686},
location = {Los Angeles, CA, United States},
publisher = {Association for Computing Machinery},
title = {{Unified treatment of contact, friction and shock-propagation in rigid body animation}},
doi = {10.1145/3606037.3606836},
year = {2023},
}
@misc{15035,
abstract = {This artifact aims to reproduce experiments from the paper Monitoring Hyperproperties With Prefix Transducers accepted at RV'23, and give further pointers to implementation of prefix transducers.
It has two parts: a pre-compiled docker image and sources that one can use to compile (locally or in docker) the software and run the experiments.},
author = {Chalupa, Marek and Henzinger, Thomas A},
publisher = {Zenodo},
title = {{Monitoring hyperproperties with prefix transducers}},
doi = {10.5281/ZENODO.8191723},
year = {2023},
}
@phdthesis{13984,
abstract = {Social insects fight disease using their individual immune systems and the cooperative
sanitary behaviors of colony members. These social defenses are well explored against
externally-infecting pathogens, but little is known about defense strategies against
internally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades
it has become evident that also many ant species harbor viruses. We present one of the first
studies addressing transmission dynamics and collective disease defenses against viruses in
ants on a mechanistic level. I successfully established an experimental ant host – viral
pathogen system as a model for the defense strategies used by social insects against internal
pathogen infections, as outlined in the third chapter. In particular, we studied how garden ants
(Lasius neglectus) defend themselves and their colonies against the generalist insect virus
CrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’
hemolymph because it allowed us to use a defined exposure dose. Here we show that this is a
good model system, as the virus is replicating and thus infecting the host. The ants mount a
clear individual immune response against the viral infection, which is characterized by a
specific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21
and 22 bp long fragments. The onset of this immune response is consistent with the timeline
of viral replication that starts already within two days post injection. The disease manifests in
decreased survival over a course of two to three weeks.
Regarding group living, we find that infected ants show a strong individual immune response,
but that their course of disease is little affected by nestmate presence, as described in chapter
four. Hence, we do not find social immunity in the context of viral infections in ants.
Nestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we
showed that 94 % of the nestmates contract active virus within four days of social contact to
an infected individual. Virus is transmitted in low doses, thus not causing disease
transmission within the colony. While virus can be transmitted during short direct contacts,
we also assume transmission from deceased ants and show that the nestmates’ immune
system gets activated after contracting a low viral dose. We find considerable potential for
indirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one
week and is also picked up by other ants. Apart from that, we want to underline the potential
of ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV
in vitro. However, we found no evidence for effective poison use to sanitize the nest space.
On the other hand, local application of ant poison by oral poison uptake, which is part of the
ants prophylactic behavioral repertoire, probably contributes to keeping the gut of each
individual sanitized. We hypothesize that oral poison uptake might be the reason why we did
not find viable virus in the trophallactic fluid.
The fifth chapter encompasses preliminary data on potential social immunization. However,
our experiments do not confirm an actual survival benefit for the nestmates upon pathogen
challenge under the given experimental settings. Nevertheless, we do not want to rule out the
possibility for nestmate immunization, but rather emphasize that considering different
experimental timelines and viral doses would provide a multitude of options for follow-up
experiments.
In conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,
might play a role in preventing viral disease transmission. Compared to colony defense
against external pathogens, internal pathogen infections require a stronger component of
individual physiological immunity than behavioral social immunity, yet could still lead to
collective protection.},
author = {Franschitz, Anna},
isbn = {978-3-99078-034-3},
issn = {2663 - 337X},
pages = {89},
publisher = {Institute of Science and Technology Austria},
title = {{Individual and social immunity against viral infections in ants}},
doi = {10.15479/at:ista:13984},
year = {2023},
}
@unpublished{15039,
abstract = {A crucial property for achieving secure, trustworthy and interpretable deep learning systems is their robustness: small changes to a system's inputs should not result in large changes to its outputs. Mathematically, this means one strives for networks with a small Lipschitz constant. Several recent works have focused on how to construct such Lipschitz networks, typically by imposing constraints on the weight matrices. In this work, we study an orthogonal aspect, namely the role of the activation function. We show that commonly used activation functions, such as MaxMin, as well as all piece-wise linear ones with two segments unnecessarily restrict the class of representable functions, even in the simplest one-dimensional setting. We furthermore introduce the new N-activation function that is provably more expressive than currently popular activation functions. We provide code at this https URL.},
author = {Prach, Bernd and Lampert, Christoph},
booktitle = {arXiv},
title = {{1-Lipschitz neural networks are more expressive with N-activations}},
doi = {10.48550/ARXIV.2311.06103},
year = {2023},
}
@misc{14812,
abstract = {This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode},
author = {Stankowski, Sean},
publisher = {Zenodo},
title = {{Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails}},
doi = {10.5281/ZENODO.8318995},
year = {2023},
}
@article{13214,
abstract = {Nitrogen is an important macronutrient required for plant growth and development, thus directly impacting agricultural productivity. In recent years, numerous studies have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen homeostasis and hormonal networks that act both locally and systemically to coordinate growth and development of plant organs. In this review, we will focus on recent advances in understanding the role of the plant hormones auxin and cytokinin and their crosstalk in nitrate-regulated growth and discuss the significance of novel findings and possible missing links.},
author = {Abualia, R and Riegler, Stefan and Benková, Eva},
issn = {2073-4409},
journal = {Cells},
number = {12},
publisher = {MDPI},
title = {{Nitrate, auxin and cytokinin - a trio to tango}},
doi = {10.3390/cells12121613},
volume = {12},
year = {2023},
}
@phdthesis{14323,
abstract = {Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.},
author = {Kuzmicz-Kowalska, Katarzyna},
issn = {2663 - 337X},
pages = {151},
publisher = {Institute of Science and Technology Austria},
title = {{Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord}},
doi = {10.15479/at:ista:14323},
year = {2023},
}
@inproceedings{14974,
abstract = {The field of machine learning and AI has witnessed remarkable breakthroughs with the emergence of LLMs, which have also sparked a lively debate in the causal community. As researchers in this field, we are interested in exploring how LLMs relate to causality research, and how we can leverage the technology to advance it. In the second conference of Causal Learning and Reasoning (CLeaR), 2023, we held a round table discussion to gather and integrate the diverse perspectives of the CLeaR community on this topic.
There is a general consensus that LLMs are not yet capable of causal reasoning at the current
stage but has a lot of potential with public available information by CLeaR 2023. Enhancing causal machine learning is vital not only for its own sake but also to help LLMs improve their performance, especially regarding trustworthiness. In this document, we present both the summary and the raw outcome of the round table discussion. We acknowledge that with the progress of both fields, the opportunities and impact may rapidly change. We will repeat the same exercise in CLeaR 2024 to document the evolution.},
author = {Zhang, Cheng and Janzing, Dominik and van der Schaar, Mihaela and Locatello, Francesco and Spirtes, Peter and Zhang, Kun and Schölkopf, Bernhard and Uhler, Caroline},
booktitle = {2nd Conference on Causal Learning and Reasoning},
location = {Tübingen, Germany},
title = {{Causality in the time of LLMs: Round table discussion results of CLeaR 2023}},
year = {2023},
}
@misc{13173,
abstract = {GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles at the presynaptic active zone (AZ). Strikingly, tonic and phasic release exhibit distinct coupling distances and are selectively affected by deletion of synaptoporin (SPO) and Ca2+-dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. Double pre-embedding immunolabeling confirmed the co-localization of CAPS2 and SPO inside the same terminal. The cytosolic protein CAPS2 showed a synaptic vesicle (SV)-associated distribution similar to the vesicular transmembrane protein SPO. A newly developed “Flash and Freeze-fracture” method revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to a persistent RRP increase. Thus, we discovered structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.},
author = {Shigemoto, Ryuichi},
keywords = {medial habenula, GABAB receptor, vesicle release, Flash and Freeze, Flash and Freeze-fracture},
publisher = {Institute of Science and Technology Austria},
title = {{Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals}},
doi = {10.15479/AT:ISTA:13173},
year = {2023},
}
@article{15085,
abstract = {The hydrogen-rich outer layers of massive stars can be removed by interactions with a binary companion. Theoretical models predict that this stripping produces a population of hot helium stars of ~2 to 8 solar masses (M☉), however, only one such system has been identified thus far. We used ultraviolet photometry to identify potential stripped helium stars then investigated 25 of them using optical spectroscopy. We identified stars with high temperatures (~60,000 to 100,000 kelvin), high surface gravities, and hydrogen-depleted surfaces; 16 stars also showed binary motion. These properties match expectations for stars with initial masses of 8 to 25 M☉ that were stripped by binary interaction. Their masses fall in the gap between subdwarf helium stars and Wolf-Rayet stars. We propose that these stars could be progenitors of stripped-envelope supernovae.},
author = {Drout, M. R. and Götberg, Ylva Louise Linsdotter and Ludwig, B. A. and Groh, J. H. and de Mink, S. E. and O’Grady, A. J. G. and Smith, N.},
issn = {1095-9203},
journal = {Science},
keywords = {Stellar Astrophysics},
number = {6676},
pages = {1287--1291},
publisher = {American Association for the Advancement of Science},
title = {{An observed population of intermediate-mass helium stars that have been stripped in binaries}},
doi = {10.1126/science.ade4970},
volume = {382},
year = {2023},
}
@inproceedings{13236,
abstract = {We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1−ε)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time O(mε−1log(ε−1)), matching the running time of the linear-time approximation algorithm of Duan and Pettie [JACM ’14]. Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1−ε)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is O(mε−1log(ε−1)), where m is the sum of the number of initially existing and inserted edges.},
author = {Zheng, Da Wei and Henzinger, Monika H},
booktitle = {International Conference on Integer Programming and Combinatorial Optimization},
isbn = {9783031327254},
issn = {1611-3349},
location = {Madison, WI, United States},
pages = {453--465},
publisher = {Springer Nature},
title = {{Multiplicative auction algorithm for approximate maximum weight bipartite matching}},
doi = {10.1007/978-3-031-32726-1_32},
volume = {13904},
year = {2023},
}
@article{13182,
abstract = {We characterize critical points of 1-dimensional maps paired in persistent homology
geometrically and this way get elementary proofs of theorems about the symmetry
of persistence diagrams and the variation of such maps. In particular, we identify
branching points and endpoints of networks as the sole source of asymmetry and
relate the cycle basis in persistent homology with a version of the stable marriage
problem. Our analysis provides the foundations of fast algorithms for maintaining a
collection of sorted lists together with its persistence diagram.},
author = {Biswas, Ranita and Cultrera Di Montesano, Sebastiano and Edelsbrunner, Herbert and Saghafian, Morteza},
issn = {2367-1734},
journal = {Journal of Applied and Computational Topology},
publisher = {Springer Nature},
title = {{Geometric characterization of the persistence of 1D maps}},
doi = {10.1007/s41468-023-00126-9},
year = {2023},
}
@article{13044,
abstract = {Singlet oxygen (1O2) formation is now recognised as a key aspect of non-aqueous oxygen redox chemistry. For identifying 1O2, chemical trapping via 9,10-dimethylanthracene (DMA) to form the endoperoxide (DMA-O2) has become the mainstay method due to its sensitivity, selectivity, and ease of use. While DMA has been shown to be selective for 1O2, rather than forming DMA-O2 with a wide variety of potentially reactive O-containing species, false positives might hypothetically be obtained in the presence of previously overlooked species. Here, we first give unequivocal direct spectroscopic proof by the 1O2-specific near infrared (NIR) emission at 1270 nm for the previously proposed 1O2 formation pathways, which centre around superoxide disproportionation. We then show that peroxocarbonates, common intermediates in metal-O2 and metal carbonate electrochemistry, do not produce false-positive DMA-O2. Moreover, we identify a previously unreported 1O2-forming pathway through the reaction of CO2 with superoxide. Overall, we give unequivocal proof for 1O2 formation in non-aqueous oxygen redox and show that chemical trapping with DMA is a reliable method to assess 1O2 formation.},
author = {Mondal, Soumyadip and Jethwa, Rajesh B and Pant, Bhargavi and Hauschild, Robert and Freunberger, Stefan Alexander},
issn = {1364-5498},
journal = {Faraday Discussions},
keywords = {Physical and Theoretical Chemistry},
publisher = {Royal Society of Chemistry},
title = {{Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes}},
doi = {10.1039/d3fd00088e},
year = {2023},
}
@phdthesis{14641,
author = {Hennessey-Wesen, Mike},
issn = {2663 - 337X},
keywords = {microfluidics, miceobiology, mutations, quorum sensing},
pages = {104},
publisher = {Institute of Science and Technology Austria},
title = {{Adaptive mutation in E. coli modulated by luxS}},
doi = {10.15479/at:ista:14641},
year = {2023},
}
@phdthesis{14587,
abstract = {This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.
First, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.
The core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.
This thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.
In the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.
At last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero.},
author = {Marveggio, Alice},
issn = {2663 - 337X},
pages = {228},
publisher = {Institute of Science and Technology Austria},
title = {{Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences}},
doi = {10.15479/at:ista:14587},
year = {2023},
}
@inproceedings{14922,
abstract = {We propose a novel approach to concentration for non-independent random variables. The main idea is to ``pretend'' that the random variables are independent and pay a multiplicative price measuring how far they are from actually being independent. This price is encapsulated in the Hellinger integral between the joint and the product of the marginals, which is then upper bounded leveraging tensorisation properties. Our bounds represent a natural generalisation of concentration inequalities in the presence of dependence: we recover exactly the classical bounds (McDiarmid's inequality) when the random variables are independent. Furthermore, in a ``large deviations'' regime, we obtain the same decay in the probability as for the independent case, even when the random variables display non-trivial dependencies. To show this, we consider a number of applications of interest. First, we provide a bound for Markov chains with finite state space. Then, we consider the Simple Symmetric Random Walk, which is a non-contracting Markov chain, and a non-Markovian setting in which the stochastic process depends on its entire past. To conclude, we propose an application to Markov Chain Monte Carlo methods, where our approach leads to an improved lower bound on the minimum burn-in period required to reach a certain accuracy. In all of these settings, we provide a regime of parameters in which our bound fares better than what the state of the art can provide.},
author = {Esposito, Amedeo Roberto and Mondelli, Marco},
booktitle = {Proceedings of 2023 IEEE International Symposium on Information Theory},
issn = {2157-8117},
location = {Taipei, Taiwan},
pages = {400--405},
publisher = {IEEE},
title = {{Concentration without independence via information measures}},
doi = {10.1109/isit54713.2023.10206899},
year = {2023},
}
@article{15173,
abstract = {We show that the number of linear spaces on a set of n points and the number of rank-3 matroids on a ground set of size n are both of the form (cn+o(n))n2/6, where c=e3√/2−3(1+3–√)/2. This is the final piece of the puzzle for enumerating fixed-rank matroids at this level of accuracy: the numbers of rank-1 and rank-2 matroids on a ground set of size n have exact representations in terms of well-known combinatorial functions, and it was recently proved by van der Hofstad, Pendavingh, and van der Pol that for constant r≥4 there are (e1−rn+o(n))nr−1/r! rank-r matroids on a ground set of size n. In our proof, we introduce a new approach for bounding the number of clique decompositions of a complete graph, using quasirandomness instead of the so-called entropy method that is common in this area.},
author = {Kwan, Matthew Alan and Sah, Ashwin and Sawhney, Mehtaab},
issn = {1778-3569},
journal = {Comptes Rendus Mathematique},
number = {G2},
pages = {565--575},
publisher = {Academie des Sciences},
title = {{Enumerating matroids and linear spaces}},
doi = {10.5802/crmath.423},
volume = {361},
year = {2023},
}
@article{14772,
abstract = {Many coupled evolution equations can be described via 2×2-block operator matrices of the form A=[
A B
C D
] in a product space X=X1×X2 with possibly unbounded entries. Here, the case of diagonally dominant block operator matrices is considered, that is, the case where the full operator A can be seen as a relatively bounded perturbation of its diagonal part with D(A)=D(A)×D(D) though with possibly large relative bound. For such operators the properties of sectoriality, R-sectoriality and the boundedness of the H∞-calculus are studied, and for these properties perturbation results for possibly large but structured perturbations are derived. Thereby, the time dependent parabolic problem associated with A can be analyzed in maximal Lpt
-regularity spaces, and this is applied to a wide range of problems such as different theories for liquid crystals, an artificial Stokes system, strongly damped wave and plate equations, and a Keller-Segel model.},
author = {Agresti, Antonio and Hussein, Amru},
issn = {0022-1236},
journal = {Journal of Functional Analysis},
keywords = {Analysis},
number = {11},
publisher = {Elsevier},
title = {{Maximal Lp-regularity and H∞-calculus for block operator matrices and applications}},
doi = {10.1016/j.jfa.2023.110146},
volume = {285},
year = {2023},
}
@article{15148,
abstract = {The basic helix–loop–helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members1. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. 2,3). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry–exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A–H2B acidic patch4, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes5–7 at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors.},
author = {Michael, Alicia and Stoos, Lisa and Crosby, Priya and Eggers, Nikolas and Nie, Xinyu Y. and Makasheva, Kristina and Minnich, Martina and Healy, Kelly L. and Weiss, Joscha and Kempf, Georg and Cavadini, Simone and Kater, Lukas and Seebacher, Jan and Vecchia, Luca and Chakraborty, Deyasini and Isbel, Luke and Grand, Ralph S. and Andersch, Florian and Fribourgh, Jennifer L. and Schübeler, Dirk and Zuber, Johannes and Liu, Andrew C. and Becker, Peter B. and Fierz, Beat and Partch, Carrie L. and Menet, Jerome S. and Thomä, Nicolas H.},
issn = {1476-4687},
journal = {Nature},
number = {7969},
pages = {385--393},
publisher = {Springer Nature},
title = {{Cooperation between bHLH transcription factors and histones for DNA access}},
doi = {10.1038/s41586-023-06282-3},
volume = {619},
year = {2023},
}
@article{15149,
abstract = {The genomic binding sites of the transcription factor (TF) and tumor suppressor p53 are unusually diverse with regard to their chromatin features, including histone modifications, raising the possibility that the local chromatin environment can contextualize p53 regulation. Here, we show that epigenetic characteristics of closed chromatin, such as DNA methylation, do not influence the binding of p53 across the genome. Instead, the ability of p53 to open chromatin and activate its target genes is locally restricted by its cofactor Trim24. Trim24 binds to both p53 and unmethylated histone 3 lysine 4 (H3K4), thereby preferentially localizing to those p53 sites that reside in closed chromatin, whereas it is deterred from accessible chromatin by H3K4 methylation. The presence of Trim24 increases cell viability upon stress and enables p53 to affect gene expression as a function of the local chromatin state. These findings link H3K4 methylation to p53 function and illustrate how specificity in chromatin can be achieved, not by TF-intrinsic sensitivity to histone modifications, but by employing chromatin-sensitive cofactors that locally modulate TF function.},
author = {Isbel, Luke and Iskar, Murat and Durdu, Sevi and Weiss, Joscha and Grand, Ralph S. and Hietter-Pfeiffer, Eric and Kozicka, Zuzanna and Michael, Alicia and Burger, Lukas and Thomä, Nicolas H. and Schübeler, Dirk},
issn = {1545-9985},
journal = {Nature Structural & Molecular Biology},
keywords = {Molecular Biology, Structural Biology},
number = {7},
pages = {948--957},
publisher = {Springer Nature},
title = {{Readout of histone methylation by Trim24 locally restricts chromatin opening by p53}},
doi = {10.1038/s41594-023-01021-8},
volume = {30},
year = {2023},
}
@unpublished{15128,
abstract = {We prove a universal mesoscopic central limit theorem for linear eigenvalue statistics of a Wigner-type matrix inside the bulk of the spectrum with compactly supported twice continuously differentiable test functions. The main novel ingredient is an optimal local law for the two-point function $T(z,\zeta)$ and a general class of related quantities involving two resolvents
at nearby spectral parameters. },
author = {Riabov, Volodymyr},
booktitle = {arXiv},
title = {{Mesoscopic eigenvalue statistics for Wigner-type matrices}},
doi = {10.48550/arXiv.2301.01712},
year = {2023},
}
@phdthesis{12491,
abstract = {The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate.
Despite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment.
In this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET).
To this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants.
In order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness.
High-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment.
In summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.},
author = {Zens, Bettina},
isbn = {978-3-99078-027-5},
issn = {2663-337X},
keywords = {cryo-EM, cryo-ET, FIB milling, method development, FIBSEM, extracellular matrix, ECM, cell-derived matrices, CDMs, cell culture, high pressure freezing, HPF, structural biology, tomography, collagen},
pages = {187},
publisher = {Institute of Science and Technology Austria},
title = {{Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography}},
doi = {10.15479/at:ista:12491},
year = {2023},
}
@article{13201,
abstract = {As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability.},
author = {Wang, Yalu and Yuan, Zhi and Wang, Jinyi and Xiao, Huixin and Wan, Lu and Li, Lanxin and Guo, Yan and Gong, Zhizhong and Friml, Jiří and Zhang, Jing},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {25},
publisher = {National Academy of Sciences},
title = {{The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation}},
doi = {10.1073/pnas.2221313120},
volume = {120},
year = {2023},
}
@phdthesis{14226,
abstract = {We introduce the notion of a Faustian interchange in a 1-parameter family of smooth
functions to generalize the medial axis to critical points of index larger than 0.
We construct and implement a general purpose algorithm for approximating such
generalized medial axes.},
author = {Stephenson, Elizabeth R},
issn = {2791-4585},
pages = {43},
publisher = {Institute of Science and Technology Austria},
title = {{Generalizing medial axes with homology switches}},
doi = {10.15479/at:ista:14226},
year = {2023},
}
@phdthesis{12470,
abstract = {The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of
connections that orchestrate our cognition and behavior. To decode its complex connectivity, it is
pivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of
nm-small synapses.
To achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across
Scales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (superresolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular
space, that is compatible with chemical fixation, with information on molecular markers, superresolved data acquisition and machine-learning based data analysis for segmentation and synapse
identification.
I used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue
architecture, neuronal in- and output-fields, down to synapse morphology.
Focusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy
fiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3
pyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal
connectivity with light microscopy.},
author = {Michalska, Julia M},
isbn = { 978-3-99078-026-8},
issn = {2663-337X},
pages = {201},
publisher = {Institute of Science and Technology Austria},
title = {{A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy}},
doi = {10.15479/at:ista:12470},
year = {2023},
}
@phdthesis{12531,
abstract = {All visual experiences of the vertebrates begin with light being converted into electrical signals
by the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the
mammal retina, and they transmit visual information to the rest of the brain.
It has been shown that RGCs vary in their morphology and genetic profiles, moreover they can
be unambiguously grouped into subtypes that share the same morphological and/or molecular
properties. However, in terms of RGCs function, it remains unclear how many distinct types
there are and what response properties their typology relies on. Even given the recent studies
that successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the
question remains whether the found subtypes persist across the entire retina.
In this work, using a novel imaging method, we show that, when sampled from a large portion
of the retina, RGCs can not be clearly divided into functional subtypes. We found that in
photopic conditions, which implies more prominent natural scene statistic differences across
the visual field, response properties can be exhibited by cells differently depending on their
location in the retina, which leads to formation of a gradient of features rather than distinct
classes.
This finding suggests that RGCs follow a global organization across the visual field of the
animal, adapting each RGC subtype to the requirements imposed by the natural scene statistics.},
author = {Kirillova, Kseniia},
issn = {2791-4585},
pages = {46},
publisher = {Institute of Science and Technology Austria},
title = {{Panoramic functional gradients across the mouse retina}},
doi = {10.15479/at:ista:12531},
year = {2023},
}
@phdthesis{12800,
abstract = {The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. },
author = {Julseth, Mara},
issn = {2791-4585},
pages = {21},
publisher = {Institute of Science and Technology Austria},
title = {{The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone}},
doi = {10.15479/at:ista:12800},
year = {2023},
}
@phdthesis{14510,
author = {Gnyliukh, Nataliia},
isbn = {978-3-99078-037-4},
issn = {2663-337X},
keywords = {Clathrin-Mediated Endocytosis, vesicle scission, Dynamin-Related Protein 2, SH3P2, TPLATE complex, Total internal reflection fluorescence microscopy, Arabidopsis thaliana},
pages = {180},
publisher = {Institute of Science and Technology Austria},
title = {{Mechanism of clathrin-coated vesicle formation during endocytosis in plants}},
doi = {10.15479/at:ista:14510},
year = {2023},
}
@phdthesis{12897,
abstract = {Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.
The first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.
We show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping.
The second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will.},
author = {Hafner, Christian},
isbn = {978-3-99078-031-2},
issn = {2663-337X},
pages = {180},
publisher = {Institute of Science and Technology Austria},
title = {{Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models}},
doi = {10.15479/at:ista:12897},
year = {2023},
}
@article{13188,
abstract = {The Kirchhoff rod model describes the bending and twisting of slender elastic rods in three dimensions, and has been widely studied to enable the prediction of how a rod will deform, given its geometry and boundary conditions. In this work, we study a number of inverse problems with the goal of computing the geometry of a straight rod that will automatically deform to match a curved target shape after attaching its endpoints to a support structure. Our solution lets us finely control the static equilibrium state of a rod by varying the cross-sectional profiles along its length.
We also show that the set of physically realizable equilibrium states admits a concise geometric description in terms of linear line complexes, which leads to very efficient computational design algorithms. Implemented in an interactive software tool, they allow us to convert three-dimensional hand-drawn spline curves to elastic rods, and give feedback about the feasibility and practicality of a design in real time. We demonstrate the efficacy of our method by designing and manufacturing several physical prototypes with applications to interior design and soft robotics.},
author = {Hafner, Christian and Bickel, Bernd},
issn = {1557-7368},
journal = {ACM Transactions on Graphics},
keywords = {Computer Graphics, Computational Design, Computational Geometry, Shape Modeling},
number = {5},
publisher = {Association for Computing Machinery},
title = {{The design space of Kirchhoff rods}},
doi = {10.1145/3606033},
volume = {42},
year = {2023},
}
@article{10652,
abstract = {Finding a feasible scheme for testing the quantum mechanical nature of the gravitational interaction has been attracting an increasing level of attention. Gravity mediated entanglement generation so far appears to be the key ingredient for a potential experiment. In a recent proposal [D. Carney et al., PRX Quantum 2, 030330 (2021)] combining an atom interferometer with a low-frequency mechanical oscillator, a coherence revival test is proposed for verifying this entanglement generation. With measurements performed only on the atoms, this protocol bypasses the need for correlation measurements. Here, we explore formulations of such a protocol, and specifically find that in the envisioned regime of operation with high thermal excitation, semiclassical models, where there is no concept of entanglement, also give the same experimental signatures. We elucidate in a fully quantum mechanical calculation that entanglement is not the source of the revivals in the relevant parameter regime. We argue that, in its current form, the suggested test is only relevant if the oscillator is nearly in a pure quantum state, and in this regime the effects are too small to be measurable. We further discuss potential open ends. The results highlight the importance and subtleties of explicitly considering how the quantum case differs from the classical expectations when testing for the quantum mechanical nature of a physical system.},
author = {Hosten, Onur},
issn = {2643-1564},
journal = {Physical Review Research},
number = {1},
publisher = {American Physical Society},
title = {{Constraints on probing quantum coherence to infer gravitational entanglement}},
doi = {10.1103/PhysRevResearch.4.013023},
volume = {4},
year = {2022},
}
@article{10758,
abstract = {5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark.},
author = {Dubini, Romeo C. A. and Korytiaková, Eva and Schinkel, Thea and Heinrichs, Pia and Carell, Thomas and Rovo, Petra},
issn = {2694-2445},
journal = {ACS Physical Chemistry Au},
number = {3},
pages = {237--246},
publisher = {American Chemical Society},
title = {{1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives}},
doi = {10.1021/acsphyschemau.1c00050},
volume = {2},
year = {2022},
}
@inproceedings{10774,
abstract = {We study the problem of specifying sequential information-flow properties of systems. Information-flow properties are hyperproperties, as they compare different traces of a system. Sequential information-flow properties can express changes, over time, in the information-flow constraints. For example, information-flow constraints during an initialization phase of a system may be different from information-flow constraints that are required during the operation phase. We formalize several variants of interpreting sequential information-flow constraints, which arise from different assumptions about what can be observed of the system. For this purpose, we introduce a first-order logic, called Hypertrace Logic, with both trace and time quantifiers for specifying linear-time hyperproperties. We prove that HyperLTL, which corresponds to a fragment of Hypertrace Logic with restricted quantifier prefixes, cannot specify the majority of the studied variants of sequential information flow, including all variants in which the transition between sequential phases (such as initialization and operation) happens asynchronously. Our results rely on new equivalences between sets of traces that cannot be distinguished by certain classes of formulas from Hypertrace Logic. This presents a new approach to proving inexpressiveness results for HyperLTL.},
author = {Bartocci, Ezio and Ferrere, Thomas and Henzinger, Thomas A and Nickovic, Dejan and Da Costa, Ana Oliveira},
booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
isbn = {9783030945824},
issn = {16113349},
location = {Philadelphia, PA, United States},
pages = {1--19},
publisher = {Springer Nature},
title = {{Flavors of sequential information flow}},
doi = {10.1007/978-3-030-94583-1_1},
volume = {13182},
year = {2022},
}
@article{10769,
abstract = {studiamos aspectos de Teoría Cuántica de Campos a densidad finita usando técnicas y conceptos de información cuántica. Nos enfocamos en fermiones de Dirac masivos con potencial químico en 1+1 dimensiones espacio-temporales. Usando la entropía de entrelazamiento en un intervalo, construimos la función c entrópica que es finita. Esta función c no es monótona, e incorpora el entrelazamiento de largo alcance proveniente de la superficie de Fermi. Motivados por trabajos previos de modelos en la red, calculamos numéricamente las entropías de Renyi y encontramos oscilaciones de Friedel. Seguidamente, analizamos la información mutua como una medida de correlación entre diferentes regiones. Usando una expansión de distancia grande desarrollada por Cardy, argumentamos que la información mutua detecta las correlaciones inducidas por la superficie de Fermi todavía al orden dominante en la expansión. Finalmente, analizamos la entropía relativa y sus generalizaciones de Renyi para distinguir estados con diferente carga. Encontramos que estados en diferentes sectores de superselección dan origen a un comportamiento super-extensivo en la entropía relativa.},
author = {Daguerre, L. and Torroba, G. and Medina Ramos, Raimel A and Solís, M.},
issn = {18501168},
journal = {Anales de la Asociacion Fisica Argentina},
number = {4},
pages = {93--98},
publisher = {Asociación Física Argentina},
title = {{Non relativistic quantum field theory: Dynamics and irreversibility}},
doi = {10.31527/analesafa.2021.32.4.93},
volume = {32},
year = {2022},
}
@unpublished{10821,
abstract = {Rhythmical cortical activity has long been recognized as a pillar in the architecture of brain functions. Yet, the dynamic organization of its underlying neuronal population activity remains elusive. Here we uncover a unique organizational principle regulating collective neural dynamics associated with the alpha rhythm in the awake resting-state. We demonstrate that cascades of neural activity obey attenuation-amplification dynamics (AAD), with a transition from the attenuation regime—within alpha cycles—to the amplification regime—across a few alpha cycles—that correlates with the characteristic frequency of the alpha rhythm. We find that this short-term AAD is part of a large-scale, size-dependent temporal structure of neural cascades that obeys the Omori law: Following large cascades, smaller cascades occur at a rate that decays as a power-law of the time elapsed from such events—a long-term AAD regulating brain activity over the timescale of seconds. We show that such an organization corresponds to the "waxing and waning" of the alpha rhythm. Importantly, we observe that short- and long-term AAD are unique to the awake resting-state, being absent during NREM sleep. These results provide a quantitative, dynamical description of the so-far-qualitative notion of the "waxing and waning" phenomenon, and suggest the AAD as a key principle governing resting-state dynamics across timescales.},
author = {Lombardi, Fabrizio and Herrmann, Hans J. and Parrino, Liborio and Plenz, Dietmar and Scarpetta, Silvia and Vaudano, Anna Elisabetta and de Arcangelis, Lucilla and Shriki, Oren},
booktitle = {bioRxiv},
pages = {25},
publisher = {Cold Spring Harbor Laboratory},
title = {{Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades}},
doi = {10.1101/2022.03.03.482657},
year = {2022},
}
@article{10845,
abstract = {We study an impurity with a resonance level whose position coincides with the Fermi energy of the surrounding Fermi gas. An impurity causes a rapid variation of the scattering phase shift for fermions at the Fermi surface, introducing a new characteristic length scale into the problem. We investigate manifestations of this length scale in the self-energy of the impurity and in the density of the bath. Our calculations reveal a model-independent deformation of the density of the Fermi gas, which is determined by the width of the resonance. To provide a broader picture, we investigate time evolution of the density in quench dynamics, and study the behavior of the system at finite temperatures. Finally, we briefly discuss implications of our findings for the Fermi-polaron problem.},
author = {Maslov, Mikhail and Lemeshko, Mikhail and Volosniev, Artem},
issn = {2643-1564},
journal = {Physical Review Research},
publisher = {American Physical Society},
title = {{Impurity with a resonance in the vicinity of the Fermi energy}},
doi = {10.1103/PhysRevResearch.4.013160},
volume = {4},
year = {2022},
}
@article{10939,
abstract = {Understanding and characterising biochemical processes inside single cells requires experimental platforms that allow one to perturb and observe the dynamics of such processes as well as computational methods to build and parameterise models from the collected data. Recent progress with experimental platforms and optogenetics has made it possible to expose each cell in an experiment to an individualised input and automatically record cellular responses over days with fine time resolution. However, methods to infer parameters of stochastic kinetic models from single-cell longitudinal data have generally been developed under the assumption that experimental data is sparse and that responses of cells to at most a few different input perturbations can be observed. Here, we investigate and compare different approaches for calculating parameter likelihoods of single-cell longitudinal data based on approximations of the chemical master equation (CME) with a particular focus on coupling the linear noise approximation (LNA) or moment closure methods to a Kalman filter. We show that, as long as cells are measured sufficiently frequently, coupling the LNA to a Kalman filter allows one to accurately approximate likelihoods and to infer model parameters from data even in cases where the LNA provides poor approximations of the CME. Furthermore, the computational cost of filtering-based iterative likelihood evaluation scales advantageously in the number of measurement times and different input perturbations and is thus ideally suited for data obtained from modern experimental platforms. To demonstrate the practical usefulness of these results, we perform an experiment in which single cells, equipped with an optogenetic gene expression system, are exposed to various different light-input sequences and measured at several hundred time points and use parameter inference based on iterative likelihood evaluation to parameterise a stochastic model of the system.},
author = {Davidović, Anđela and Chait, Remy P and Batt, Gregory and Ruess, Jakob},
issn = {1553-7358},
journal = {PLoS Computational Biology},
number = {3},
publisher = {Public Library of Science},
title = {{Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level}},
doi = {10.1371/journal.pcbi.1009950},
volume = {18},
year = {2022},
}
@article{11051,
abstract = {Nuclear pore complexes (NPCs) bridge the nucleus and the cytoplasm and are indispensable for crucial cellular activities, such as bidirectional molecular trafficking and gene transcription regulation. The discovery of long-lived proteins (LLPs) in NPCs from postmitotic cells raises the exciting possibility that the maintenance of NPC integrity might play an inherent role in lifelong cell function. Age-dependent deterioration of NPCs and loss of nuclear integrity have been linked to age-related decline in postmitotic cell function and degenerative diseases. In this review, we discuss our current understanding of NPC maintenance in proliferating and postmitotic cells, and how malfunction of nucleoporins (Nups) might contribute to the pathogenesis of various neurodegenerative and cardiovascular diseases.},
author = {Liu, Jinqiang and HETZER, Martin W},
issn = {0962-8924},
journal = {Trends in Cell Biology},
keywords = {Cell Biology},
number = {3},
pages = {P216--227},
publisher = {Elsevier},
title = {{Nuclear pore complex maintenance and implications for age-related diseases}},
doi = {10.1016/j.tcb.2021.10.001},
volume = {32},
year = {2022},
}
@inproceedings{11184,
abstract = {Let G be a graph on n nodes. In the stochastic population protocol model, a collection of n indistinguishable, resource-limited nodes collectively solve tasks via pairwise interactions. In each interaction, two randomly chosen neighbors first read each other’s states, and then update their local states. A rich line of research has established tight upper and lower bounds on the complexity of fundamental tasks, such as majority and leader election, in this model, when G is a clique. Specifically, in the clique, these tasks can be solved fast, i.e., in n polylog n pairwise interactions, with high probability, using at most polylog n states per node.
In this work, we consider the more general setting where G is an arbitrary regular graph, and present a technique for simulating protocols designed for fully-connected networks in any connected regular graph. Our main result is a simulation that is efficient on many interesting graph families: roughly, the simulation overhead is polylogarithmic in the number of nodes, and quadratic in the conductance of the graph. As a sample application, we show that, in any regular graph with conductance φ, both leader election and exact majority can be solved in φ^{-2} ⋅ n polylog n pairwise interactions, with high probability, using at most φ^{-2} ⋅ polylog n states per node. This shows that there are fast and space-efficient population protocols for leader election and exact majority on graphs with good expansion properties. We believe our results will prove generally useful, as they allow efficient technology transfer between the well-mixed (clique) case, and the under-explored spatial setting.},
author = {Alistarh, Dan-Adrian and Gelashvili, Rati and Rybicki, Joel},
booktitle = {25th International Conference on Principles of Distributed Systems},
editor = {Bramas, Quentin and Gramoli, Vincent and Milani, Alessia},
isbn = {9783959772198},
issn = {1868-8969},
location = {Strasbourg, France},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Fast graphical population protocols}},
doi = {10.4230/LIPIcs.OPODIS.2021.14},
volume = {217},
year = {2022},
}
@inproceedings{11183,
abstract = {Subgraph detection has recently been one of the most studied problems in the CONGEST model of distributed computing. In this work, we study the distributed complexity of problems closely related to subgraph detection, mainly focusing on induced subgraph detection. The main line of this work presents lower bounds and parameterized algorithms w.r.t structural parameters of the input graph:
- On general graphs, we give unconditional lower bounds for induced detection of cycles and patterns of treewidth 2 in CONGEST. Moreover, by adapting reductions from centralized parameterized complexity, we prove lower bounds in CONGEST for detecting patterns with a 4-clique, and for induced path detection conditional on the hardness of triangle detection in the congested clique.
- On graphs of bounded degeneracy, we show that induced paths can be detected fast in CONGEST using techniques from parameterized algorithms, while detecting cycles and patterns of treewidth 2 is hard.
- On graphs of bounded vertex cover number, we show that induced subgraph detection is easy in CONGEST for any pattern graph. More specifically, we adapt a centralized parameterized algorithm for a more general maximum common induced subgraph detection problem to the distributed setting. In addition to these induced subgraph detection results, we study various related problems in the CONGEST and congested clique models, including for multicolored versions of subgraph-detection-like problems.},
author = {Nikabadi, Amir and Korhonen, Janne},
booktitle = {25th International Conference on Principles of Distributed Systems},
editor = {Bramas, Quentin and Gramoli, Vincent and Milani, Alessia},
isbn = {9783959772198},
issn = {1868-8969},
location = {Strasbourg, France},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters}},
doi = {10.4230/LIPIcs.OPODIS.2021.15},
volume = {217},
year = {2022},
}
@article{11182,
abstract = {Immune cells are constantly on the move through multicellular organisms to explore and respond to pathogens and other harmful insults. While moving, immune cells efficiently traverse microenvironments composed of tissue cells and extracellular fibers, which together form complex environments of various porosity, stiffness, topography, and chemical composition. In this protocol we describe experimental procedures to investigate immune cell migration through microenvironments of heterogeneous porosity. In particular, we describe micro-channels, micro-pillars, and collagen networks as cell migration paths with alternative pore size choices. Employing micro-channels or micro-pillars that divide at junctions into alternative paths with initially differentially sized pores allows us to precisely (1) measure the cellular translocation time through these porous path junctions, (2) quantify the cellular preference for individual pore sizes, and (3) image cellular components like the nucleus and the cytoskeleton. This reductionistic experimental setup thus can elucidate how immune cells perform decisions in complex microenvironments of various porosity like the interstitium. The setup further allows investigation of the underlying forces of cellular squeezing and the consequences of cellular deformation on the integrity of the cell and its organelles. As a complementary approach that does not require any micro-engineering expertise, we describe the usage of three-dimensional collagen networks with different pore sizes. Whereas we here focus on dendritic cells as a model for motile immune cells, the described protocols are versatile as they are also applicable for other immune cell types like neutrophils and non-immune cell types such as mesenchymal and cancer cells. In summary, we here describe protocols to identify the mechanisms and principles of cellular probing, decision making, and squeezing during cellular movement through microenvironments of heterogeneous porosity.},
author = {Kroll, Janina and Ruiz-Fernandez, Mauricio J.A. and Braun, Malte B. and Merrin, Jack and Renkawitz, Jörg},
issn = {2691-1299},
journal = {Current Protocols},
number = {4},
publisher = {Wiley},
title = {{Quantifying the probing and selection of microenvironmental pores by motile immune cells}},
doi = {10.1002/cpz1.407},
volume = {2},
year = {2022},
}
@inproceedings{11428,
abstract = {The medial axis of a set consists of the points in the ambient space without a unique closest point on the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a topologically equivalent skeleton. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities various prunings of the medial axis have been proposed. Here, we examine one type of pruning, called burning. Because of the good experimental results, it was hoped that the burning method of simplifying the medial axis would be stable. In this work we show a simple example that dashes such hopes based on Bing’s house with two rooms, demonstrating an isotopy of a shape where the medial axis goes from collapsible to non-collapsible.},
author = {Chambers, Erin and Fillmore, Christopher D and Stephenson, Elizabeth R and Wintraecken, Mathijs},
booktitle = {38th International Symposium on Computational Geometry},
editor = {Goaoc, Xavier and Kerber, Michael},
isbn = {978-3-95977-227-3},
issn = {1868-8969},
location = {Berlin, Germany},
pages = {66:1--66:9},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{A cautionary tale: Burning the medial axis is unstable}},
doi = {10.4230/LIPIcs.SoCG.2022.66},
volume = {224},
year = {2022},
}
@article{11420,
abstract = {Understanding the properties of neural networks trained via stochastic gradient descent (SGD) is at the heart of the theory of deep learning. In this work, we take a mean-field view, and consider a two-layer ReLU network trained via noisy-SGD for a univariate regularized regression problem. Our main result is that SGD with vanishingly small noise injected in the gradients is biased towards a simple solution: at convergence, the ReLU network implements a piecewise linear map of the inputs, and the number of “knot” points -- i.e., points where the tangent of the ReLU network estimator changes -- between two consecutive training inputs is at most three. In particular, as the number of neurons of the network grows, the SGD dynamics is captured by the solution of a gradient flow and, at convergence, the distribution of the weights approaches the unique minimizer of a related free energy, which has a Gibbs form. Our key technical contribution consists in the analysis of the estimator resulting from this minimizer: we show that its second derivative vanishes everywhere, except at some specific locations which represent the “knot” points. We also provide empirical evidence that knots at locations distinct from the data points might occur, as predicted by our theory.},
author = {Shevchenko, Aleksandr and Kungurtsev, Vyacheslav and Mondelli, Marco},
issn = {1533-7928},
journal = {Journal of Machine Learning Research},
number = {130},
pages = {1--55},
publisher = {Journal of Machine Learning Research},
title = {{Mean-field analysis of piecewise linear solutions for wide ReLU networks}},
volume = {23},
year = {2022},
}
@book{11429,
abstract = {This book constitutes the refereed proceedings of the 18th International Symposium on Web and Wireless Geographical Information Systems, W2GIS 2022, held in Konstanz, Germany, in April 2022.
The 7 full papers presented together with 6 short papers in the volume were carefully reviewed and selected from 16 submissions. The papers cover topics that range from mobile GIS and Location-Based Services to Spatial Information Retrieval and Wireless Sensor Networks.},
editor = {Karimipour, Farid and Storandt, Sabine},
isbn = {9783031062445},
issn = {1611-3349},
pages = {153},
publisher = {Springer Nature},
title = {{Web and Wireless Geographical Information Systems}},
doi = {10.1007/978-3-031-06245-2},
volume = {13238},
year = {2022},
}
@inbook{11440,
abstract = {To compute the persistent homology of a grayscale digital image one needs to build a simplicial or cubical complex from it. For cubical complexes, the two commonly used constructions (corresponding to direct and indirect digital adjacencies) can give different results for the same image. The two constructions are almost dual to each other, and we use this relationship to extend and modify the cubical complexes to become dual filtered cell complexes. We derive a general relationship between the persistent homology of two dual filtered cell complexes, and also establish how various modifications to a filtered complex change the persistence diagram. Applying these results to images, we derive a method to transform the persistence diagram computed using one type of cubical complex into a persistence diagram for the other construction. This means software for computing persistent homology from images can now be easily adapted to produce results for either of the two cubical complex constructions without additional low-level code implementation.},
author = {Bleile, Bea and Garin, Adélie and Heiss, Teresa and Maggs, Kelly and Robins, Vanessa},
booktitle = {Research in Computational Topology 2},
editor = {Gasparovic, Ellen and Robins, Vanessa and Turner, Katharine},
isbn = {9783030955182},
pages = {1--26},
publisher = {Springer Nature},
title = {{The persistent homology of dual digital image constructions}},
doi = {10.1007/978-3-030-95519-9_1},
volume = {30},
year = {2022},
}
@article{11444,
abstract = {This article investigates library-related documents written by Gerard van Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through a textual analysis. Handwritten letters were deconstructed in terms of their appearance, layout, and tone in order to mine them for meaning. Furthermore, the contents were examined for library matters such as censorship, catalogues, and collection development. The Imperial Court Library held a prominent role as a repository for rare and valuable works, later becoming the National Library of Austria.
Gerard van Swieten’s work as a librarian tends to be overlooked, perhaps because he is better known as the private physician of Maria Theresia, as well as a medical reformer. Nevertheless, he was a hard-working chief librarian deeply involved in all aspects of librarianship. Van Swieten endorsed modern scientific works, which were otherwise banned officially by the censorship commission, for the use of scholars in the library, expanded the collection by acquiring books through his network of scholars and publishers, and reissued library catalogues. He also provided for the comfort of users in the library reading room, at a time when such considerations were unusual. In conclusion, a proposal is made that van Swieten viewed his role as librarian with some importance and pride.},
author = {Chlebak, Clara A and Reid, Peter H.},
issn = {1758-3497},
journal = {Library and Information History},
number = {1},
pages = {23--41},
publisher = {Edinburgh University Press},
title = {{From the prefect’s desk: Gerard van Swieten’s library correspondence}},
doi = {10.3366/lih.2022.0097},
volume = {38},
year = {2022},
}
@inbook{11456,
abstract = {The proteomes of specialized structures, and the interactomes of proteins of interest, provide entry points to elucidate the functions of molecular machines. Here, we review a proximity-labeling strategy that uses the improved E. coli biotin ligase TurboID to characterize C. elegans protein complexes. Although the focus is on C. elegans neurons, the method is applicable regardless of cell type. We describe detailed extraction procedures that solubilize the bulk of C. elegans proteins and highlight the importance of tagging endogenous genes, to ensure physiological expression levels. We review issues associated with non-specific background noise and the importance of appropriate controls. As proof of principle, we review our analysis of the interactome of a presynaptic active zone protein, ELKS-1. Our aim is to provide a detailed protocol for TurboID-based proximity labeling in C. elegans and to highlight its potential and its limitations to characterize protein complexes and subcellular compartments in this animal.},
author = {Artan, Murat and de Bono, Mario},
booktitle = {Behavioral Neurogenetics},
editor = {Yamamoto, Daisuke},
isbn = {9781071623206},
issn = {1940-6045},
pages = {277--294},
publisher = {Springer Nature},
title = {{Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling}},
doi = {10.1007/978-1-0716-2321-3_15},
volume = {181},
year = {2022},
}
@article{11488,
abstract = {Hydrogen Lyα haloes (LAHs) are commonly used as a tracer of the circumgalactic medium (CGM) at high redshifts. In this work, we aim to explore the existence of Lyα haloes around individual UV-selected galaxies, rather than around Lyα emitters (LAEs), at high redshifts. Our sample was continuum-selected with F775W ≤ 27.5, and spectroscopic redshifts were assigned or constrained for all the sources thanks to the deepest (100- to 140-h) existing Very Large Telescope (VLT)/Multi-Unit Spectroscopic Explorer (MUSE) data with adaptive optics. The final sample includes 21 galaxies that are purely F775W-magnitude selected within the redshift range z ≈ 2.9 − 4.4 and within a UV magnitude range −20 ≤ M1500 ≤ −18, thus avoiding any bias toward LAEs. We tested whether galaxy’s Lyα emission is significantly more extended than the MUSE PSF-convolved continuum component. We find 17 LAHs and four non-LAHs. We report the first individual detections of extended Lyα emission around non-LAEs. The Lyα halo fraction is thus as high as 81.0−11.2+10.3%, which is close to that for LAEs at z = 3 − 6 in the literature. This implies that UV-selected galaxies generally have a large amount of hydrogen in their CGM. We derived the mean surface brightness (SB) profile for our LAHs with cosmic dimming corrections and find that Lyα emission extends to 5.4 arcsec (≃40 physical kpc at the midpoint redshift z = 3.6) above the typical 1σ SB limit. The incidence rate of surrounding gas detected in Lyα per one-dimensional line of sight per unit redshift, dn/dz, is estimated to be 0.76−0.09+0.09 for galaxies with M1500 ≤ −18 mag at z ≃ 3.7. Assuming that Lyα emission and absorption arise in the same gas, this suggests, based on abundance matching, that LAHs trace the same gas as damped Lyα systems (DLAs) and sub-DLAs.},
author = {Kusakabe, Haruka and Verhamme, Anne and Blaizot, Jérémy and Garel, Thibault and Wisotzki, Lutz and Leclercq, Floriane and Bacon, Roland and Schaye, Joop and Gallego, Sofia G. and Kerutt, Josephine and Matthee, Jorryt J and Maseda, Michael and Nanayakkara, Themiya and Pelló, Roser and Richard, Johan and Tresse, Laurence and Urrutia, Tanya and Vitte, Eloïse},
issn = {1432-0746},
journal = {Astronomy & Astrophysics},
keywords = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations},
publisher = {EDP Sciences},
title = {{The MUSE eXtremely Deep Field: Individual detections of Lyα haloes around rest-frame UV-selected galaxies at z ≃ 2.9–4.4}},
doi = {10.1051/0004-6361/202142302},
volume = {660},
year = {2022},
}
@article{11497,
abstract = {Context. The hydrogen Lyman α line is often the only measurable feature in optical spectra of high-redshift galaxies. Its shape and strength are influenced by radiative transfer processes and the properties of the underlying stellar population. High equivalent widths of several hundred Å are especially hard to explain by models and could point towards unusual stellar populations, for example with low metallicities, young stellar ages, and a top-heavy initial mass function. Other aspects influencing equivalent widths are the morphology of the galaxy and its gas properties.
Aims. The aim of this study is to better understand the connection between the Lyman α rest-frame equivalent width (EW0) and spectral properties as well as ultraviolet (UV) continuum morphology by obtaining reliable EW0 histograms for a statistical sample of galaxies and by assessing the fraction of objects with large equivalent widths.
Methods. We used integral field spectroscopy from the Multi Unit Spectroscopic Explorer (MUSE) combined with broad-band data from the Hubble Space Telescope (HST) to measure EW0. We analysed the emission lines of 1920 Lyman α emitters (LAEs) detected in the full MUSE-Wide (one hour exposure time) and MUSE-Deep (ten hour exposure time) surveys and found UV continuum counterparts in archival HST data. We fitted the UV continuum photometric images using the Galfit software to gain morphological information on the rest-UV emission and fitted the spectra obtained from MUSE to determine the double peak fraction, asymmetry, full-width at half maximum, and flux of the Lyman α line.
Results. The two surveys show different histograms of Lyman α EW0. In MUSE-Wide, 20% of objects have EW0 > 240 Å, while this fraction is only 11% in MUSE-Deep and ≈16% for the full sample. This includes objects without HST continuum counterparts (one-third of our sample), for which we give lower limits for EW0. The object with the highest securely measured EW0 has EW0 = 589 ± 193 Å (the highest lower limit being EW0 = 4464 Å). We investigate the connection between EW0 and Lyman α spectral or UV continuum morphological properties.
Conclusions. The survey depth has to be taken into account when studying EW0 distributions. We find that in general, high EW0 objects can have a wide range of spectral and UV morphological properties, which might reflect that the underlying causes for high EW0 values are equally varied.},
author = {Kerutt, J. and Wisotzki, L. and Verhamme, A. and Schmidt, K. B. and Leclercq, F. and Herenz, E. C. and Urrutia, T. and Garel, T. and Hashimoto, T. and Maseda, M. and Matthee, Jorryt J and Kusakabe, H. and Schaye, J. and Richard, J. and Guiderdoni, B. and Mauerhofer, V. and Nanayakkara, T. and Vitte, E.},
issn = {1432-0746},
journal = {Astronomy & Astrophysics},
keywords = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations},
publisher = {EDP Sciences},
title = {{Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep}},
doi = {10.1051/0004-6361/202141900},
volume = {659},
year = {2022},
}
@article{11490,
abstract = {Directly characterising the first generations of stars in distant galaxies is a key quest of observational cosmology. We present a case study of ID53 at z = 4.77, the UV-brightest (but L⋆) star-forming galaxy at z > 3 in the MUSE eXtremely Deep Field with a mass of ≈109 M⊙. In addition to very strong Lyman-α (Lyα) emission, we clearly detect the (stellar) continuum and an N V P Cygni feature, interstellar absorption, fine-structure emission and nebular C IV emission lines in the 140 h spectrum. Continuum emission from two spatially resolved components in Hubble Space Telescope data are blended in the MUSE data, but we show that the nebular C IV emission originates from a subcomponent of the galaxy. The UV spectrum can be fit with recent BPASS stellar population models combined with single-burst or continuous star formation histories (SFHs), a standard initial mass function, and an attenuation law. Models with a young age and low metallicity (log10(age/yr) = 6.5–7.6 and [Z/H] = −2.15 to −1.15) are preferred, but the details depend on the assumed SFH. The intrinsic Hα luminosity of the best-fit models is an order of magnitude higher than the Hα luminosity inferred from Spitzer/IRAC data, which either suggests a high escape fraction of ionising photons, a high relative attenuation of nebular to stellar dust, or a complex SFH. The metallicity appears lower than the metallicity in more massive galaxies at z = 3 − 5, consistent with the scenario according to which younger galaxies have lower metallicities. This chemical immaturity likely facilitates Lyα escape, explaining why the Lyα equivalent width is anti-correlated with stellar metallicity. Finally, we stress that uncertainties in SFHs impose a challenge for future inferences of the stellar metallicity of young galaxies. This highlights the need for joint (spatially resolved) analyses of stellar spectra and photo-ionisation models.},
author = {Matthee, Jorryt J and Feltre, Anna and Maseda, Michael and Nanayakkara, Themiya and Boogaard, Leindert and Bacon, Roland and Verhamme, Anne and Leclercq, Floriane and Kusakabe, Haruka and Urrutia, Tanya and Wisotzki, Lutz},
issn = {1432-0746},
journal = {Astronomy & Astrophysics},
keywords = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: high-redshift / techniques: spectroscopic / galaxies: stellar content / galaxies: formation},
publisher = {EDP Sciences},
title = {{Deciphering stellar metallicities in the early universe: Case study of a young galaxy at z = 4.77 in the MUSE eXtremely Deep Field}},
doi = {10.1051/0004-6361/202142187},
volume = {660},
year = {2022},
}
@article{11509,
abstract = {We present Keck/LRIS follow-up spectroscopy for 13 photometric candidates of extremely metal-poor galaxies (EMPGs) selected by a machine-learning technique applied to the deep (∼26 AB mag) optical and wide-area (∼500 deg2) Subaru imaging data in the EMPRESS survey. Nine out of the 13 candidates are EMPGs with an oxygen abundance (O/H) less than ∼10% solar value (O/H)⊙, and four sources are contaminants of moderately metal-rich galaxies or no emission-line objects. Notably, two out of the nine EMPGs have extremely low stellar masses and oxygen abundances of 5 × 10⁴x–7 × -10⁵ M⊙ and 2%–3% (O/H)⊙, respectively. With a sample of five EMPGs with (Fe/O) measurements, two (three) of which are taken from this study (the literature), we confirm that two EMPGs with the lowest (O/H) ratios of ∼2% (O/H)⊙ show high (Fe/O) ratios of ∼0.1, close to the solar abundance ratio. Comparing galaxy chemical enrichment models, we find that the two EMPGs cannot be explained by a scenario of metal-poor gas accretion/episodic star formation history due to their low (N/O) ratios. We conclude that the two EMPGs can be reproduced by the inclusion of bright hypernovae and/or hypothetical pair-instability supernovae (SNe) preferentially produced in a metal-poor environment. This conclusion implies that primordial galaxies at z ∼ 10 could have a high abundance of Fe that did not originate from Type Ia SNe with delays and that Fe may not serve as a cosmic clock for primordial galaxies.},
author = {Isobe, Yuki and Ouchi, Masami and Suzuki, Akihiro and Moriya, Takashi J. and Nakajima, Kimihiko and Nomoto, Ken’ichi and Rauch, Michael and Harikane, Yuichi and Kojima, Takashi and Ono, Yoshiaki and Fujimoto, Seiji and Inoue, Akio K. and Kim, Ji Hoon and Komiyama, Yutaka and Kusakabe, Haruka and Lee, Chien-Hsiu and Maseda, Michael and Matthee, Jorryt J and Michel-Dansac, Leo and Nagao, Tohru and Nanayakkara, Themiya and Nishigaki, Moka and Onodera, Masato and Sugahara, Yuma and Xu, Yi},
issn = {1538-4357},
journal = {The Astrophysical Journal},
keywords = {Space and Planetary Science, Astronomy and Astrophysics},
number = {2},
publisher = {IOP Publishing},
title = {{EMPRESS. IV. Extremely metal-poor galaxies including very low-mass primordial systems with M∗= 10⁴-10⁵⊙ and 2%–3% (O/H): High (Fe/O) suggestive of metal enrichment by hypernovae/pair-instability supernovae}},
doi = {10.3847/1538-4357/ac3509},
volume = {925},
year = {2022},
}
@article{11510,
abstract = {Galaxy evolution is driven by a variety of physical processes that are predicted to proceed at different rates for different dark matter haloes and environments across cosmic times. A record of this evolution is preserved in galaxy stellar populations, which we can access using absorption-line spectroscopy. Here we explore the large LEGA-C survey (DR3) to investigate the role of the environment and stellar mass on stellar populations at z ∼ 0.6–1 in the COSMOS field. Leveraging the statistical power and depth of LEGA-C, we reveal significant gradients in Dn4000 and Hδ equivalent widths (EWs) distributions over the stellar mass versus environment 2D spaces for the massive galaxy population (M > 1010 M⊙) at z ∼ 0.6–1.0. Dn4000 and Hδ EWs primarily depend on stellar mass, but they also depend on environment at fixed stellar mass. By splitting the sample into centrals and satellites, and in terms of star-forming galaxies and quiescent galaxies, we reveal that the significant environmental trends of Dn4000 and Hδ EW, when controlling for stellar mass, are driven by quiescent galaxies. Regardless of being centrals or satellites, star-forming galaxies reveal Dn4000 and Hδ EWs, which depend strongly on their stellar mass and are completely independent of the environment at 0.6 < z < 1.0. The environmental trends seen for satellite galaxies are fully driven by the trends that hold only for quiescent galaxies, combined with the strong environmental dependency of the quiescent fraction at fixed stellar mass. Our results are consistent with recent predictions from simulations that point toward massive galaxies forming first in overdensities or the most compact dark matter haloes.},
author = {Sobral, David and van der Wel, Arjen and Bezanson, Rachel and Bell, Eric and Muzzin, Adam and D’Eugenio, Francesco and Darvish, Behnam and Gallazzi, Anna and Wu, Po-Feng and Maseda, Michael and Matthee, Jorryt J and Paulino-Afonso, Ana and Straatman, Caroline and van Dokkum, Pieter G.},
issn = {1538-4357},
journal = {The Astrophysical Journal},
keywords = {Space and Planetary Science, Astronomy and Astrophysics},
number = {2},
publisher = {IOP Publishing},
title = {{The LEGA-C of nature and nurture in stellar populations at z ∼ 0.6–1.0: Dn4000 and Hδ reveal different assembly histories for quiescent galaxies in different environments}},
doi = {10.3847/1538-4357/ac4419},
volume = {926},
year = {2022},
}
@article{11511,
abstract = {The ratio of α-elements to iron in galaxies holds valuable information about the star formation history (SFH) since their enrichment occurs on different timescales. The fossil record of stars in galaxies has mostly been excavated for passive galaxies, since the light of star-forming galaxies is dominated by young stars, which have much weaker atmospheric absorption features. Here we use the largest reference cosmological simulation of the EAGLE project to investigate the origin of variations in stellar α-enhancement among star-forming galaxies at z = 0, and their impact on integrated spectra. The definition of α-enhancement in a composite stellar population is ambiguous. We elucidate two definitions—termed “mean” and “galactic” α-enhancement—in more detail. While a star-forming galaxy has a high “mean” α-enhancement when its stars formed rapidly, a galaxy with a large “galactic” α-enhancement generally had a delayed SFH. We find that absorption-line strengths of Mg and Fe correlate with variations in α-enhancement. These correlations are strongest for the “galactic” α-enhancement. However, we show that these are mostly caused by other effects that are cross-correlated with α-enhancement, such as variations in the light-weighted age. This severely complicates the retrieval of α-enhancements in star-forming galaxies. The ambiguity is not severe for passive galaxies, and we confirm that spectral variations in these galaxies are caused by measurable variations in α-enhancements. We suggest that this more complex coupling between α-enhancement and SFHs can guide the interpretation of new observations of star-forming galaxies.},
author = {Gebek, Andrea and Matthee, Jorryt J},
issn = {1538-4357},
journal = {The Astrophysical Journal},
keywords = {Space and Planetary Science, Astronomy and Astrophysics},
number = {2},
publisher = {IOP Publishing},
title = {{On the variation in stellar α-enhancements of star-forming galaxies in the EAGLE simulation}},
doi = {10.3847/1538-4357/ac350b},
volume = {924},
year = {2022},
}
@article{11521,
abstract = {The cosmic ionizing emissivity from star-forming galaxies has long been anchored to UV luminosity functions. Here, we introduce an emissivity framework based on Lyα emitters (LAEs), which naturally hones in on the subset of galaxies responsible for the ionizing background due to the intimate connection between production and escape of Lyα and LyC photons. Using constraints on the escape fractions of bright LAEs (LLyα > 0.2L*) at z ≈ 2 obtained from resolved Lyα profiles, and arguing for their redshift-invariance, we show that: (i) quasars and LAEs together reproduce the relatively flat emissivity at z ≈ 2–6, which is non-trivial given the strong evolution in both the star formation density and quasar number density at these epochs and (ii) LAEs produce late and rapid reionization between z ≈ 6−9 under plausible assumptions. Within this framework, the >10 × rise in the UV population-averaged fesc between z ≈ 3–7 naturally arises due to the same phenomena that drive the growing LAE fraction with redshift. Generally, a LAE dominated emissivity yields a peak in the distribution of the ionizing budget with UV luminosity as reported in latest simulations. Using our adopted parameters (fesc=50 per cent, ξion = 1025.9 Hz erg−1 for half the bright LAEs), a highly ionizing minority of galaxies with MUV < −17 accounts for the entire ionizing budget from star-forming galaxies. Rapid flashes of LyC from such rare galaxies produce a ‘disco’ ionizing background. We conclude proposing tests to further develop our suggested Lyα-anchored formalism.},
author = {Matthee, Jorryt J and Naidu, Rohan P. and Pezzulli, Gabriele and Gronke, Max and Sobral, David and Oesch, Pascal A. and Hayes, Matthew and Erb, Dawn and Schaerer, Daniel and Amorín, Ricardo and Tacchella, Sandro and Ana Paulino-Afonso, Ana Paulino-Afonso and Llerena, Mario and Calhau, João and Röttgering, Huub},
issn = {1365-2966},
journal = {Monthly Notices of the Royal Astronomical Society},
keywords = {galaxies: high-redshift, intergalactic medium, cosmology: observations, dark ages, reionization, first stars, ultraviolet: galaxies},
number = {4},
pages = {5960--5977},
publisher = {Oxford University Press},
title = {{(Re)Solving reionization with Lyα: How bright Lyα emitters account for the z ≈ 2 − 8 cosmic ionizing background}},
doi = {10.1093/mnras/stac801},
volume = {512},
year = {2022},
}
@article{11553,
abstract = {In holomorphic dynamics, complex box mappings arise as first return maps to wellchosen domains. They are a generalization of polynomial-like mapping, where the domain of the return map can have infinitely many components. They turned out to be extremely useful in tackling diverse problems. The purpose of this paper is:
• To illustrate some pathologies that can occur when a complex box mapping is not induced by a globally defined map and when its domain has infinitely many components, and to give conditions to avoid these issues.
• To show that once one has a box mapping for a rational map, these conditions can be assumed to hold in a very natural setting. Thus, we call such complex box mappings dynamically natural. Having such box mappings is the first step in tackling many problems in one-dimensional dynamics.
• Many results in holomorphic dynamics rely on an interplay between combinatorial and analytic techniques. In this setting, some of these tools are:
• the Enhanced Nest (a nest of puzzle pieces around critical points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred to below as KSS;
• the Covering Lemma (which controls the moduli of pullbacks of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009);
• the QC-Criterion and the Spreading Principle from KSS.
The purpose of this paper is to make these tools more accessible so that they can be used as a ‘black box’, so one does not have to redo the proofs in new settings.
• To give an intuitive, but also rather detailed, outline of the proof from KSS and Kozlovski and van Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for non-renormalizable dynamically natural complex box mappings:
• puzzle pieces shrink to points,
• (under some assumptions) topologically conjugate non-renormalizable polynomials and box mappings are quasiconformally conjugate.
• We prove the fundamental ergodic properties for dynamically natural box mappings. This leads to some necessary conditions for when such a box mapping supports a measurable invariant line field on its filled Julia set. These mappings
are the analogues of Lattès maps in this setting.
• We prove a version of Mañé’s Theorem for complex box mappings concerning expansion along orbits of points that avoid a neighborhood of the set of critical points.},
author = {Clark, Trevor and Drach, Kostiantyn and Kozlovski, Oleg and Strien, Sebastian Van},
issn = {2199-6806},
journal = {Arnold Mathematical Journal},
number = {2},
pages = {319--410},
publisher = {Springer Nature},
title = {{The dynamics of complex box mappings}},
doi = {10.1007/s40598-022-00200-7},
volume = {8},
year = {2022},
}
@article{11601,
abstract = {We present the third and final data release of the K2 Galactic Archaeology Program (K2 GAP) for Campaigns C1–C8 and C10–C18. We provide asteroseismic radius and mass coefficients, κR and κM, for ∼19,000 red giant stars, which translate directly to radius and mass given a temperature. As such, K2 GAP DR3 represents the largest asteroseismic sample in the literature to date. K2 GAP DR3 stellar parameters are calibrated to be on an absolute parallactic scale based on Gaia DR2, with red giant branch and red clump evolutionary state classifications provided via a machine-learning approach. Combining these stellar parameters with GALAH DR3 spectroscopy, we determine asteroseismic ages with precisions of ∼20%–30% and compare age-abundance relations to Galactic chemical evolution models among both low- and high-α populations for α, light, iron-peak, and neutron-capture elements. We confirm recent indications in the literature of both increased Ba production at late Galactic times as well as significant contributions to r-process enrichment from prompt sources associated with, e.g., core-collapse supernovae. With an eye toward other Galactic archeology applications, we characterize K2 GAP DR3 uncertainties and completeness using injection tests, suggesting that K2 GAP DR3 is largely unbiased in mass/age, with uncertainties of 2.9% (stat.) ± 0.1% (syst.) and 6.7% (stat.) ± 0.3% (syst.) in κR and κM for red giant branch stars and 4.7% (stat.) ± 0.3% (syst.) and 11% (stat.) ± 0.9% (syst.) for red clump stars. We also identify percent-level asteroseismic systematics, which are likely related to the time baseline of the underlying data, and which therefore should be considered in TESS asteroseismic analysis.},
author = {Zinn, Joel C. and Stello, Dennis and Elsworth, Yvonne and García, Rafael A. and Kallinger, Thomas and Mathur, Savita and Mosser, Benoît and Hon, Marc and Bugnet, Lisa Annabelle and Jones, Caitlin and Reyes, Claudia and Sharma, Sanjib and Schönrich, Ralph and Warfield, Jack T. and Luger, Rodrigo and Vanderburg, Andrew and Kobayashi, Chiaki and Pinsonneault, Marc H. and Johnson, Jennifer A. and Huber, Daniel and Buder, Sven and Joyce, Meridith and Bland-Hawthorn, Joss and Casagrande, Luca and Lewis, Geraint F. and Miglio, Andrea and Nordlander, Thomas and Davies, Guy R. and Silva, Gayandhi De and Chaplin, William J. and Silva Aguirre, Victor},
issn = {1538-4357},
journal = {The Astrophysical Journal},
keywords = {Space and Planetary Science, Astronomy and Astrophysics},
number = {2},
publisher = {IOP Publishing},
title = {{The K2 Galactic Archaeology Program data release 3: Age-abundance patterns in C1–C8 and C10–C18}},
doi = {10.3847/1538-4357/ac2c83},
volume = {926},
year = {2022},
}
@article{11602,
abstract = {During the survey phase of the Kepler mission, several thousand stars were observed in short cadence, allowing for the detection of solar-like oscillations in more than 500 main-sequence and subgiant stars. These detections showed the power of asteroseismology in determining fundamental stellar parameters. However, the Kepler Science Office discovered an issue in the calibration that affected half of the store of short-cadence data, leading to a new data release (DR25) with corrections on the light curves. In this work, we re-analyzed the one-month time series of the Kepler survey phase to search for solar-like oscillations that might have been missed when using the previous data release. We studied the seismic parameters of 99 stars, among which there are 46 targets with new reported solar-like oscillations, increasing, by around 8%, the known sample of solar-like stars with an asteroseismic analysis of the short-cadence data from this mission. The majority of these stars have mid- to high-resolution spectroscopy publicly available with the LAMOST and APOGEE surveys, respectively, as well as precise Gaia parallaxes. We computed the masses and radii using seismic scaling relations and we find that this new sample features massive stars (above 1.2 M⊙ and up to 2 M⊙) and subgiants. We determined the granulation parameters and amplitude of the modes, which agree with the scaling relations derived for dwarfs and subgiants. The stars studied here are slightly fainter than the previously known sample of main-sequence and subgiants with asteroseismic detections. We also studied the surface rotation and magnetic activity levels of those stars. Our sample of 99 stars has similar levels of activity compared to the previously known sample and is in the same range as the Sun between the minimum and maximum of its activity cycle. We find that for seven stars, a possible blend could be the reason for the non-detection with the early data release. Finally, we compared the radii obtained from the scaling relations with the Gaia ones and we find that the Gaia radii are overestimated by 4.4%, on average, compared to the seismic radii, with a scatter of 12.3% and a decreasing trend according to the evolutionary stage. In addition, for homogeneity purposes, we re-analyzed the DR25 of the main-sequence and subgiant stars with solar-like oscillations that were previously detected and, as a result, we provide the global seismic parameters for a total of 525 stars.},
author = {Mathur, S. and García, R. A. and Breton, S. and Santos, A. R. G. and Mosser, B. and Huber, D. and Sayeed, M. and Bugnet, Lisa Annabelle and Chontos, A.},
issn = {1432-0746},
journal = {Astronomy & Astrophysics},
keywords = {Space and Planetary Science, Astronomy and Astrophysics},
publisher = {EDP Sciences},
title = {{Detections of solar-like oscillations in dwarfs and subgiants with Kepler DR25 short-cadence data}},
doi = {10.1051/0004-6361/202141168},
volume = {657},
year = {2022},
}
@article{11600,
abstract = {The Sun’s surface hosts varying magnetic activities and rotation rates (from equator to pole), and unique solar weather. Now, a combination of ground and space observations has unveiled a previously undetected magnetized plasma current.},
author = {Bugnet, Lisa Annabelle},
issn = {2397-3366},
journal = {Nature Astronomy},
keywords = {Astronomy and Astrophysics},
pages = {631--632},
publisher = {Springer Nature},
title = {{Hidden currents at the Sun’s surface}},
doi = {10.1038/s41550-022-01683-2},
volume = {6},
year = {2022},
}
@article{11621,
abstract = {Context. Asteroseismology has revealed small core-to-surface rotation contrasts in stars in the whole Hertzsprung–Russell diagram. This is the signature of strong transport of angular momentum (AM) in stellar interiors. One of the plausible candidates to efficiently carry AM is magnetic fields with various topologies that could be present in stellar radiative zones. Among them, strong axisymmetric azimuthal (toroidal) magnetic fields have received a lot of interest. Indeed, if they are subject to the so-called Tayler instability, the accompanying triggered Maxwell stresses can transport AM efficiently. In addition, the electromotive force induced by the fluctuations of magnetic and velocity fields could potentially sustain a dynamo action that leads to the regeneration of the initial strong axisymmetric azimuthal magnetic field.
Aims. The key question we aim to answer is whether we can detect signatures of these deep strong azimuthal magnetic fields. The only way to answer this question is asteroseismology, and the best laboratories of study are intermediate-mass and massive stars with external radiative envelopes. Most of these are rapid rotators during their main sequence. Therefore, we have to study stellar pulsations propagating in stably stratified, rotating, and potentially strongly magnetised radiative zones, namely magneto-gravito-inertial (MGI) waves.
Methods. We generalise the traditional approximation of rotation (TAR) by simultaneously taking general axisymmetric differential rotation and azimuthal magnetic fields into account. Both the Coriolis acceleration and the Lorentz force are therefore treated in a non-perturbative way. Using this new formalism, we derive the asymptotic properties of MGI waves and their period spacings.
Results. We find that toroidal magnetic fields induce a shift in the period spacings of gravity (g) and Rossby (r) modes. An equatorial azimuthal magnetic field with an amplitude of the order of 105 G leads to signatures that are detectable in period spacings for high-radial-order g and r modes in γ Doradus (γ Dor) and slowly pulsating B (SPB) stars. More complex hemispheric configurations are more difficult to observe, particularly when they are localised out of the propagation region of MGI modes, which can be localised in an equatorial belt.
Conclusions. The magnetic TAR, which takes into account toroidal magnetic fields in a non-perturbative way, is derived. This new formalism allows us to assess the effects of the magnetic field in γ Dor and SPB stars on g and r modes. We find that these effects should be detectable for equatorial fields thanks to modern space photometry using observations from Kepler, TESS CVZ, and PLATO.},
author = {Dhouib, H. and Mathis, S. and Bugnet, Lisa Annabelle and Van Reeth, T. and Aerts, C.},
issn = {1432-0746},
journal = {Astronomy & Astrophysics},
keywords = {Space and Planetary Science, Astronomy and Astrophysics, magnetohydrodynamics (MHD) / waves / stars, rotation / stars: magnetic field / stars, oscillations / methods},
publisher = {EDP Sciences},
title = {{Detecting deep axisymmetric toroidal magnetic fields in stars: The traditional approximation of rotation for differentially rotating deep spherical shells with a general azimuthal magnetic field}},
doi = {10.1051/0004-6361/202142956},
volume = {661},
year = {2022},
}
@article{11638,
abstract = {Statistical inference is central to many scientific endeavors, yet how it works remains unresolved. Answering this requires a quantitative understanding of the intrinsic interplay between statistical models, inference methods, and the structure in the data. To this end, we characterize the efficacy of direct coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence data—in inferring pairwise interactions from samples of ferromagnetic Ising models on random graphs. Our approach allows for physically motivated exploration of qualitatively distinct data regimes separated by phase transitions. We show that inference quality depends strongly on the nature of data-generating distributions: optimal accuracy occurs at an intermediate temperature where the detrimental effects from macroscopic order and thermal noise are minimal. Importantly our results indicate that DCA does not always outperform its local-statistics-based predecessors; while DCA excels at low temperatures, it becomes inferior to simple correlation thresholding at virtually all temperatures when data are limited. Our findings offer insights into the regime in which DCA operates so successfully, and more broadly, how inference interacts with the structure in the data.},
author = {Ngampruetikorn, Vudtiwat and Sachdeva, Vedant and Torrence, Johanna and Humplik, Jan and Schwab, David J. and Palmer, Stephanie E.},
issn = {2643-1564},
journal = {Physical Review Research},
number = {2},
publisher = {American Physical Society},
title = {{Inferring couplings in networks across order-disorder phase transitions}},
doi = {10.1103/PhysRevResearch.4.023240},
volume = {4},
year = {2022},
}
@article{11662,
abstract = {We give a fully dynamic (Las-Vegas style) algorithm with constant expected amortized time per update that maintains a proper (Δ +1)-vertex coloring of a graph with maximum degree at most Δ. This improves upon the previous O(log Δ)-time algorithm by Bhattacharya et al. (SODA 2018). Our algorithm uses an approach based on assigning random ranks to vertices and does not need to maintain a hierarchical graph decomposition. We show that our result does not only have optimal running time but is also optimal in the sense that already deciding whether a Δ-coloring exists in a dynamically changing graph with maximum degree at most Δ takes Ω (log n) time per operation.},
author = {Henzinger, Monika H and Peng, Pan},
issn = {1549-6333},
journal = {ACM Transactions on Algorithms},
number = {2},
publisher = {Association for Computing Machinery (ACM)},
title = {{Constant-time Dynamic (Δ +1)-Coloring}},
doi = {10.1145/3501403},
volume = {18},
year = {2022},
}
@article{11702,
abstract = {When Mendel’s work was rediscovered in 1900, and extended to establish classical genetics, it was initially seen in opposition to Darwin’s theory of evolution by natural selection on continuous variation, as represented by the biometric research program that was the foundation of quantitative genetics. As Fisher, Haldane, and Wright established a century ago, Mendelian inheritance is exactly what is needed for natural selection to work efficiently. Yet, the synthesis remains unfinished. We do not understand why sexual reproduction and a fair meiosis predominate in eukaryotes, or how far these are responsible for their diversity and complexity. Moreover, although quantitative geneticists have long known that adaptive variation is highly polygenic, and that this is essential for efficient selection, this is only now becoming appreciated by molecular biologists—and we still do not have a good framework for understanding polygenic variation or diffuse function.},
author = {Barton, Nicholas H},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {30},
publisher = {Proceedings of the National Academy of Sciences},
title = {{The "New Synthesis"}},
doi = {10.1073/pnas.2122147119},
volume = {119},
year = {2022},
}
@article{11713,
abstract = {Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA).
Results: Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes.},
author = {Nikolic, Nela and Sauert, Martina and Albanese, Tanino G. and Moll, Isabella},
issn = {1756-0500},
journal = {BMC Research Notes},
keywords = {General Biochemistry, Genetics and Molecular Biology, General Medicine},
publisher = {Springer Nature},
title = {{Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli}},
doi = {10.1186/s13104-022-06061-9},
volume = {15},
year = {2022},
}
@inproceedings{11812,
abstract = {This paper presents a comprehensive study of algorithms for maintaining the number of all connected four-vertex subgraphs in a dynamic graph. Specifically, our algorithms maintain the number of paths of length three in deterministic amortized O(m^{1/2}) update time, and any other connected four-vertex subgraph which is not a clique in deterministic amortized update time O(m^{2/3}). Queries can be answered in constant time. We also study the query times for subgraphs containing an arbitrary edge that is supplied only with the query as well as the case where only subgraphs containing a vertex s that is fixed beforehand are considered. For length-3 paths, paws, 4-cycles, and diamonds our bounds match or are not far from (conditional) lower bounds: Based on the OMv conjecture we show that any dynamic algorithm that detects the existence of paws, diamonds, or 4-cycles or that counts length-3 paths takes update time Ω(m^{1/2-δ}).
Additionally, for 4-cliques and all connected induced subgraphs, we show a lower bound of Ω(m^{1-δ}) for any small constant δ > 0 for the amortized update time, assuming the static combinatorial 4-clique conjecture holds. This shows that the O(m) algorithm by Eppstein et al. [David Eppstein et al., 2012] for these subgraphs cannot be improved by a polynomial factor.},
author = {Hanauer, Kathrin and Henzinger, Monika H and Hua, Qi Cheng},
booktitle = {1st Symposium on Algorithmic Foundations of Dynamic Networks},
isbn = {9783959772242},
issn = {1868-8969},
location = {Virtual},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Fully dynamic four-vertex subgraph counting}},
doi = {10.4230/LIPIcs.SAND.2022.18},
volume = {221},
year = {2022},
}
@inproceedings{11808,
abstract = {In recent years, significant advances have been made in the design and analysis of fully dynamic algorithms. However, these theoretical results have received very little attention from the practical perspective. Few of the algorithms are implemented and tested on real datasets, and their practical potential is far from understood. Here, we present a quick reference guide to recent engineering and theory results in the area of fully dynamic graph algorithms.},
author = {Hanauer, Kathrin and Henzinger, Monika H and Schulz, Christian},
booktitle = {1st Symposium on Algorithmic Foundations of Dynamic Networks},
isbn = {9783959772242},
issn = {1868-8969},
location = {Virtual},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Recent advances in fully dynamic graph algorithms}},
doi = {10.4230/LIPIcs.SAND.2022.1},
volume = {221},
year = {2022},
}
@article{11916,
abstract = {A domain is called Kac regular for a quadratic form on L2 if every functions vanishing almost everywhere outside the domain can be approximated in form norm by functions with compact support in the domain. It is shown that this notion is stable under domination of quadratic forms. As applications measure perturbations of quasi-regular Dirichlet forms, Cheeger energies on metric measure spaces and Schrödinger operators on manifolds are studied. Along the way a characterization of the Sobolev space with Dirichlet boundary conditions on domains in infinitesimally Riemannian metric measure spaces is obtained.},
author = {Wirth, Melchior},
issn = {2538-225X},
journal = {Advances in Operator Theory},
keywords = {Algebra and Number Theory, Analysis},
number = {3},
publisher = {Springer Nature},
title = {{Kac regularity and domination of quadratic forms}},
doi = {10.1007/s43036-022-00199-w},
volume = {7},
year = {2022},
}
@inproceedings{11918,
abstract = {Statistics of small subgraph counts such as triangles, four-cycles, and s-t paths of short lengths reveal important structural properties of the underlying graph. These problems have been widely studied in social network analysis. In most relevant applications, the graphs are not only massive but also change dynamically over time. Most of these problems become hard in the dynamic setting when considering the worst case. In this paper, we ask whether the question of small subgraph counting over dynamic graphs is hard also in the average case.
We consider the simplest possible average case model where the updates follow an Erdős-Rényi graph: each update selects a pair of vertices (u, v) uniformly at random and flips the existence of the edge (u, v). We develop new lower bounds and matching algorithms in this model for counting four-cycles, counting triangles through a specified point s, or a random queried point, and st paths of length 3, 4 and 5. Our results indicate while computing st paths of length 3, and 4 are easy in the average case with O(1) update time (note that they are hard in the worst case), it becomes hard when considering st paths of length 5.
We introduce new techniques which allow us to get average-case hardness for these graph problems from the worst-case hardness of the Online Matrix vector problem (OMv). Our techniques rely on recent advances in fine-grained average-case complexity. Our techniques advance this literature, giving the ability to prove new lower bounds on average-case dynamic algorithms.},
author = {Henzinger, Monika H and Lincoln, Andrea and Saha, Barna},
booktitle = {33rd Annual ACM-SIAM Symposium on Discrete Algorithms},
location = {Alexandria, VA, United States},
pages = {459--498},
publisher = {Society for Industrial and Applied Mathematics},
title = {{The complexity of average-case dynamic subgraph counting}},
doi = {10.1137/1.9781611977073.23},
year = {2022},
}
@inproceedings{11930,
abstract = {We present a practically efficient algorithm for maintaining a global minimum cut in large dynamic graphs under both edge insertions and deletions. While there has been theoretical work on this problem, our algorithm is the first implementation of a fully-dynamic algorithm. The algorithm uses the theoretical foundation and combines it with efficient and finely-tuned implementations to give an algorithm that can maintain the global minimum cut of a graph with rapid update times. We show that our algorithm gives up to multiple orders of magnitude speedup compared to static approaches both on edge insertions and deletions.},
author = {Henzinger, Monika H and Noe, Alexander and Schulz, Christian},
booktitle = {2022 Proceedings of the Symposium on Algorithm Engineering and Experiments},
location = {Alexandria, VA, United States},
pages = {13--26},
publisher = {Society for Industrial and Applied Mathematics},
title = {{Practical fully dynamic minimum cut algorithms}},
doi = {10.1137/1.9781611977042.2},
year = {2022},
}
@article{11955,
abstract = {Covalent organic frameworks (COFs) are structurally tuneable, porous and crystalline polymers constructed through the covalent attachment of small organic building blocks as elementary units. Using the myriad of such building blocks, a broad spectrum of functionalities has been applied for COF syntheses for broad applications, including heterogeneous catalysis. Herein, we report the synthesis of a new family of porous and crystalline COFs using a novel acridine linker and benzene-1,3,5-tricarbaldehyde derivatives bearing a variable number of hydroxy groups. With the broad absorption in the visible light region, the COFs were applied as photocatalysts in metallaphotocatalytic C−N cross-coupling. The fully β-ketoenamine linked COF showed the highest activity, due to the increased charge separation upon irradiation. The COF showed good to excellent yields for several aryl bromides, good recyclability and even catalyzed the organic transformation in presence of green light as energy source.},
author = {Traxler, Michael and Gisbertz, Sebastian and Pachfule, Pradip and Schmidt, Johannes and Roeser, Jérôme and Reischauer, Susanne and Rabeah, Jabor and Pieber, Bartholomäus and Thomas, Arne},
issn = {1521-3773},
journal = {Angewandte Chemie International Edition},
number = {21},
publisher = {Wiley},
title = {{Acridine‐functionalized covalent organic frameworks (COFs) as photocatalysts for metallaphotocatalytic C−N cross‐coupling}},
doi = {10.1002/anie.202117738},
volume = {61},
year = {2022},
}
@article{11991,
abstract = {The study of the complexity of the constraint satisfaction problem (CSP), centred around the Feder-Vardi Dichotomy Conjecture, has been very prominent in the last two decades. After a long concerted effort and many partial results, the Dichotomy Conjecture has been proved in 2017 independently by Bulatov and Zhuk. At about the same time, a vast generalisation of CSP, called promise CSP, has started to gain prominence. In this survey, we explain the importance of promise CSP and highlight many new very interesting features that the study of promise CSP has brought to light. The complexity classification quest for the promise CSP is wide open, and we argue that, despite the promise CSP being more general, this quest is rather more accessible to a wide range of researchers than the dichotomy-led study of the CSP has been.},
author = {Krokhin, Andrei and Opršal, Jakub},
issn = {2372-3491},
journal = {ACM SIGLOG News},
number = {3},
pages = {30--59},
publisher = {Association for Computing Machinery},
title = {{An invitation to the promise constraint satisfaction problem}},
doi = {10.1145/3559736.3559740},
volume = {9},
year = {2022},
}
@article{11996,
abstract = {If you mix fruit syrups with alcohol to make a schnapps, the two liquids will remain perfectly blended forever. But if you mix oil with vinegar to make a vinaigrette, the oil and vinegar will soon separate back into their previous selves. Such liquid-liquid phase separation is a thermodynamically driven phenomenon and plays an important role in many biological processes (1). Although energy injection at the macroscale can reverse the phase separation—a strong shake is the normal response to a separated vinaigrette—little is known about the effect of energy added at the microscopic level on phase separation. This fundamental question has deep ramifications, notably in biology, because active processes also make the interior of a living cell different from a dead one. On page 768 of this issue, Adkins et al. (2) examine how mechanical activity at the microscopic scale affects liquid-liquid phase separation and allows liquids to climb surfaces.},
author = {Palacci, Jérémie A},
issn = {1095-9203},
journal = {Science},
number = {6607},
pages = {710--711},
publisher = {American Association for the Advancement of Science},
title = {{A soft active matter that can climb walls}},
doi = {10.1126/science.adc9202},
volume = {377},
year = {2022},
}
@inproceedings{12010,
abstract = {World models learn behaviors in a latent imagination space to enhance the sample-efficiency of deep reinforcement learning (RL) algorithms. While learning world models for high-dimensional observations (e.g., pixel inputs) has become practicable on standard RL benchmarks and some games, their effectiveness in real-world robotics applications has not been explored. In this paper, we investigate how such agents generalize to real-world autonomous vehicle control tasks, where advanced model-free deep RL algorithms fail. In particular, we set up a series of time-lap tasks for an F1TENTH racing robot, equipped with a high-dimensional LiDAR sensor, on a set of test tracks with a gradual increase in their complexity. In this continuous-control setting, we show that model-based agents capable of learning in imagination substantially outperform model-free agents with respect to performance, sample efficiency, successful task completion, and generalization. Moreover, we show that the generalization ability of model-based agents strongly depends on the choice of their observation model. We provide extensive empirical evidence for the effectiveness of world models provided with long enough memory horizons in sim2real tasks.},
author = {Brunnbauer, Axel and Berducci, Luigi and Brandstatter, Andreas and Lechner, Mathias and Hasani, Ramin and Rus, Daniela and Grosu, Radu},
booktitle = {2022 International Conference on Robotics and Automation},
isbn = {9781728196817},
issn = {1050-4729},
location = {Philadelphia, PA, United States},
pages = {7513--7520},
publisher = {IEEE},
title = {{Latent imagination facilitates zero-shot transfer in autonomous racing}},
doi = {10.1109/ICRA46639.2022.9811650},
year = {2022},
}
@article{12007,
abstract = {The Tibetan plateau (TP) plays an important role in the Asian summer monsoon (ASM) dynamics as a heat source during the pre-monsoon and monsoon seasons. A significant contribution to the pre-monsoon TP heating comes from the sensible heat flux (SHF), which depend on the surface properties. A glaciated surface would have a different SHF compared to a non-glaciated surface. Therefore, the TP glaciers potentially can also impact the hydrological cycle in the Asian continent by impacting the ASM rainfall via its contribution to the total plateau heating. However, there is no assessment of this putative link available. Here, we attempt to qualitatively study the role of TP glaciers on ASM by analyzing the sensitivity of an atmospheric model to the absence of TP glaciers. We find that the absence of the glaciers is most felt in climatologically less snowy regions (which are mostly located at the south-central boundary of the TP during the pre-monsoon season), which leads to positive SHF anomalies. The resulting positive diabatic heating leads to rising air in the eastern TP and sinking air in the western TP. This altered circulation in turn leads to a positive SHF memory in the western TP, which persists until the end of the monsoon season. The impact of SHF anomalies on diabatic heating results in a large-scale subsidence over the ASM domain. The net result is a reduced seasonal ASM rainfall. Given the relentless warming and the vulnerability of glaciers to warming, this is another flag in the ASM variability and change that needs further attention.},
author = {GOSWAMI, BIDYUT B and An, Soon-Il and Murtugudde, Raghu},
issn = {0165-0009},
journal = {Climatic Change},
keywords = {Atmospheric Science, Global and Planetary Change},
number = {3-4},
publisher = {Springer Nature},
title = {{Role of the Tibetan plateau glaciers in the Asian summer monsoon}},
doi = {10.1007/s10584-022-03426-8},
volume = {173},
year = {2022},
}
@inproceedings{12011,
abstract = {We characterize the capacity for the discrete-time arbitrarily varying channel with discrete inputs, outputs, and states when (a) the encoder and decoder do not share common randomness, (b) the input and state are subject to cost constraints, (c) the transition matrix of the channel is deterministic given the state, and (d) at each time step the adversary can only observe the current and past channel inputs when choosing the state at that time. The achievable strategy involves stochastic encoding together with list decoding and a disambiguation step. The converse uses a two-phase "babble-and-push" strategy where the adversary chooses the state randomly in the first phase, list decodes the output, and then chooses state inputs to symmetrize the channel in the second phase. These results generalize prior work on specific channels models (additive, erasure) to general discrete alphabets and models.},
author = {Zhang, Yihan and Jaggi, Sidharth and Langberg, Michael and Sarwate, Anand D.},
booktitle = {2022 IEEE International Symposium on Information Theory},
isbn = {9781665421591},
issn = {2157-8095},
location = {Espoo, Finland},
pages = {2523--2528},
publisher = {IEEE},
title = {{The capacity of causal adversarial channels}},
doi = {10.1109/ISIT50566.2022.9834709},
volume = {2022},
year = {2022},
}
@inproceedings{12017,
abstract = {In the classic adversarial communication problem, two parties communicate over a noisy channel in the presence of a malicious jamming adversary. The arbitrarily varying channels (AVCs) offer an elegant framework to study a wide range of interesting adversary models. The optimal throughput or capacity over such AVCs is intimately tied to the underlying adversary model; in some cases, capacity is unknown and the problem is known to be notoriously hard. The omniscient adversary, one which knows the sender’s entire channel transmission a priori, is one of such classic models of interest; the capacity under such an adversary remains an exciting open problem. The myopic adversary is a generalization of that model where the adversary’s observation may be corrupted over a noisy discrete memoryless channel. Through the adversary’s myopicity, one can unify the slew of different adversary models, ranging from the omniscient adversary to one that is completely blind to the transmission (the latter is the well known oblivious model where the capacity is fully characterized).In this work, we present new results on the capacity under both the omniscient and myopic adversary models. We completely characterize the positive capacity threshold over general AVCs with omniscient adversaries. The characterization is in terms of two key combinatorial objects: the set of completely positive distributions and the CP-confusability set. For omniscient AVCs with positive capacity, we present non-trivial lower and upper bounds on the capacity; unlike some of the previous bounds, our bounds hold under fairly general input and jamming constraints. Our lower bound improves upon the generalized Gilbert-Varshamov bound for general AVCs while the upper bound generalizes the well known Elias-Bassalygo bound (known for binary and q-ary alphabets). For the myopic AVCs, we build on prior results known for the so-called sufficiently myopic model, and present new results on the positive rate communication threshold over the so-called insufficiently myopic regime (a completely insufficient myopic adversary specializes to an omniscient adversary). We present interesting examples for the widely studied models of adversarial bit-flip and bit-erasure channels. In fact, for the bit-flip AVC with additive adversarial noise as well as random noise, we completely characterize the omniscient model capacity when the random noise is sufficiently large vis-a-vis the adversary’s budget.},
author = {Yadav, Anuj Kumar and Alimohammadi, Mohammadreza and Zhang, Yihan and Budkuley, Amitalok J. and Jaggi, Sidharth},
booktitle = {2022 IEEE International Symposium on Information Theory},
isbn = {9781665421591},
issn = {2157-8095},
location = {Espoo, Finland},
pages = {2535--2540},
publisher = {Institute of Electrical and Electronics Engineers},
title = {{New results on AVCs with omniscient and myopic adversaries}},
doi = {10.1109/ISIT50566.2022.9834632},
volume = {2022},
year = {2022},
}
@inproceedings{12013,
abstract = {We consider the problem of communication over adversarial channels with feedback. Two parties comprising sender Alice and receiver Bob seek to communicate reliably. An adversary James observes Alice's channel transmission entirely and chooses, maliciously, its additive channel input or jamming state thereby corrupting Bob's observation. Bob can communicate over a one-way reverse link with Alice; we assume that transmissions over this feedback link cannot be corrupted by James. Our goal in this work is to study the optimum throughput or capacity over such channels with feedback. We first present results for the quadratically-constrained additive channel where communication is known to be impossible when the noise-to-signal (power) ratio (NSR) is at least 1. We present a novel achievability scheme to establish that positive rate communication is possible even when the NSR is as high as 8/9. We also present new converse upper bounds on the capacity of this channel under potentially stochastic encoders and decoders. We also study feedback communication over the more widely studied q-ary alphabet channel under additive noise. For the q -ary channel, where q > 2, it is well known that capacity is positive under full feedback if and only if the adversary can corrupt strictly less than half the transmitted symbols. We generalize this result and show that the same threshold holds for positive rate communication when the noiseless feedback may only be partial; our scheme employs a stochastic decoder. We extend this characterization, albeit partially, to fully deterministic schemes under partial noiseless feedback. We also present new converse upper bounds for q-ary channels under full feedback, where the encoder and/or decoder may privately randomize. Our converse results bring to the fore an interesting alternate expression for the well known converse bound for the q—ary channel under full feedback which, when specialized to the binary channel, also equals its known capacity.},
author = {Joshi, Pranav and Purkayastha, Amritakshya and Zhang, Yihan and Budkuley, Amitalok J. and Jaggi, Sidharth},
booktitle = {2022 IEEE International Symposium on Information Theory},
isbn = {9781665421591},
issn = {2157-8095},
location = {Espoo, Finland},
pages = {504--509},
publisher = {IEEE},
title = {{On the capacity of additive AVCs with feedback}},
doi = {10.1109/ISIT50566.2022.9834850},
volume = {2022},
year = {2022},
}
@inproceedings{12016,
abstract = {We consider the problem of coded distributed computing using polar codes. The average execution time of a coded computing system is related to the error probability for transmission over the binary erasure channel in recent work by Soleymani, Jamali and Mahdavifar, where the performance of binary linear codes is investigated. In this paper, we focus on polar codes and unveil a connection between the average execution time and the scaling exponent μ of the family of codes. In the finite-length characterization of polar codes, the scaling exponent is a key object capturing the speed of convergence to capacity. In particular, we show that (i) the gap between the normalized average execution time of polar codes and that of optimal MDS codes is O(n –1/μ ), and (ii) this upper bound can be improved to roughly O(n –1/2 ) by considering polar codes with large kernels. We conjecture that these bounds could be improved to O(n –2/μ ) and O(n –1 ), respectively, and provide a heuristic argument as well as numerical evidence supporting this view.},
author = {Fathollahi, Dorsa and Mondelli, Marco},
booktitle = {2022 IEEE International Symposium on Information Theory},
isbn = {9781665421591},
issn = {2157-8095},
location = {Espoo, Finland},
pages = {2154--2159},
publisher = {IEEE},
title = {{Polar coded computing: The role of the scaling exponent}},
doi = {10.1109/ISIT50566.2022.9834712},
volume = {2022},
year = {2022},
}
@inproceedings{12012,
abstract = {This paper is eligible for the Jack Keil Wolf ISIT Student Paper Award. We generalize a previous framework for designing utility-optimal differentially private (DP) mechanisms via graphs, where datasets are vertices in the graph and edges represent dataset neighborhood. The boundary set contains datasets where an individual’s response changes the binary-valued query compared to its neighbors. Previous work was limited to the homogeneous case where the privacy parameter ε across all datasets was the same and the mechanism at boundary datasets was identical. In our work, the mechanism can take different distributions at the boundary and the privacy parameter ε is a function of neighboring datasets, which recovers an earlier definition of personalized DP as special case. The problem is how to extend the mechanism, which is only defined at the boundary set, to other datasets in the graph in a computationally efficient and utility optimal manner. Using the concept of strongest induced DP condition we solve this problem efficiently in polynomial time (in the size of the graph).},
author = {Torkamani, Sahel and Ebrahimi, Javad B. and Sadeghi, Parastoo and D'Oliveira, Rafael G.L. and Médard, Muriel},
booktitle = {2022 IEEE International Symposium on Information Theory},
isbn = {9781665421591},
issn = {2157-8095},
location = {Espoo, Finland},
pages = {1623--1628},
publisher = {IEEE},
title = {{Heterogeneous differential privacy via graphs}},
doi = {10.1109/ISIT50566.2022.9834711},
volume = {2022},
year = {2022},
}
@inproceedings{12018,
abstract = {We study the problem of characterizing the maximal rates of list decoding in Euclidean spaces for finite list sizes. For any positive integer L ≥ 2 and real N > 0, we say that a subset C⊂Rn is an (N,L – 1)-multiple packing or an (N,L– 1)-list decodable code if every Euclidean ball of radius nN−−−√ in ℝ n contains no more than L − 1 points of C. We study this problem with and without ℓ 2 norm constraints on C, and derive the best-known lower bounds on the maximal rate for (N,L−1) multiple packing. Our bounds are obtained via error exponents for list decoding over Additive White Gaussian Noise (AWGN) channels. We establish a curious inequality which relates the error exponent, a quantity of average-case nature, to the list-decoding radius, a quantity of worst-case nature. We derive various bounds on the error exponent for list decoding in both bounded and unbounded settings which could be of independent interest beyond multiple packing.},
author = {Zhang, Yihan and Vatedka, Shashank},
booktitle = {2022 IEEE International Symposium on Information Theory},
isbn = {9781665421591},
issn = {2157-8095},
location = {Espoo, Finland},
pages = {1324--1329},
publisher = {Institute of Electrical and Electronics Engineers},
title = {{Lower bounds on list decoding capacity using error exponents}},
doi = {10.1109/ISIT50566.2022.9834815},
volume = {2022},
year = {2022},
}
@inproceedings{12015,
abstract = {We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let P, N > 0 and L∈Z≥2. A multiple packing is a set C of points in Bn(0–,nP−−−√) such that any point in ℝ n lies in the intersection of at most L – 1 balls of radius nN−−−√ around points in C. 1 In this paper, we derive two lower bounds on the largest possible density of a multiple packing. These bounds are obtained through a stronger notion called average-radius multiple packing. Specifically, we exactly pin down the asymptotics of (expurgated) Gaussian codes and (expurgated) spherical codes under average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory. The bound for spherical codes matches the previous best known bound which was obtained for the standard (weaker) notion of multiple packing through a curious connection with error exponents [Bli99], [ZV21]. The bound for Gaussian codes suggests that they are strictly inferior to spherical codes.},
author = {Zhang, Yihan and Vatedka, Shashank},
booktitle = {2022 IEEE International Symposium on Information Theory},
isbn = {9781665421591},
issn = {2157-8095},
location = {Espoo, Finland},
pages = {3085--3090},
publisher = {IEEE},
title = {{Lower bounds for multiple packing}},
doi = {10.1109/ISIT50566.2022.9834443},
volume = {2022},
year = {2022},
}
@inproceedings{12014,
abstract = {We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let N > 0 and L∈Z≥2. A multiple packing is a set C of points in Rn such that any point in Rn lies in the intersection of at most L – 1 balls of radius nN−−−√ around points in C. Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied for finite fields. In this paper, we exactly pin down the asymptotic density of (expurgated) Poisson Point Processes under a stronger notion called average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory. This gives rise to the best known lower bound on the largest multiple packing density. Our result corrects a mistake in a previous paper by Blinovsky [Bli05].},
author = {Zhang, Yihan and Vatedka, Shashank},
booktitle = {2022 IEEE International Symposium on Information Theory},
isbn = {9781665421591},
issn = {2157-8095},
location = {Espoo, Finland},
pages = {2559--2564},
publisher = {IEEE},
title = {{List-decodability of Poisson Point Processes}},
doi = {10.1109/ISIT50566.2022.9834512},
volume = {2022},
year = {2022},
}
@inproceedings{12019,
abstract = {This paper studies combinatorial properties of codes for the Z-channel. A Z-channel with error fraction τ takes as input a length-n binary codeword and injects in an adversarial manner up to nτ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest (L − 1)-list-decodable code for the Z-channel with error fraction τ has exponential (in n) size if τ is less than a critical value that we call the Plotkin point and has constant size if τ is larger than the threshold. The (L−1)-list-decoding Plotkin point is known to be L−1L−1−L−LL−1. In this paper, we show that the largest (L−1)-list-decodable code ε-above the Plotkin point has size Θ L (ε −3/2 ) for any L − 1 ≥ 1.},
author = {Polyanskii, Nikita and Zhang, Yihan},
booktitle = {2022 IEEE International Symposium on Information Theory},
isbn = {9781665421591},
issn = {2157-8095},
location = {Espoo, Finland},
pages = {2553--2558},
publisher = {Institute of Electrical and Electronics Engineers},
title = {{List-decodable zero-rate codes for the Z-channel}},
doi = {10.1109/ISIT50566.2022.9834829},
volume = {2022},
year = {2022},
}
@phdthesis{12072,
abstract = {In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm
form associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations.
In the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or
integral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points.
More precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in
the power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture. },
author = {Shute, Alec L},
isbn = {978-3-99078-023-7},
issn = {2663-337X},
pages = {208},
publisher = {Institute of Science and Technology Austria},
title = {{Existence and density problems in Diophantine geometry: From norm forms to Campana points}},
doi = {10.15479/at:ista:12072},
year = {2022},
}
@inproceedings{12088,
abstract = {We present a quantum-enabled microwave-telecom interface with bidirectional conversion efficiencies up to 15% and added input noise quanta as low as 0.16. Moreover, we observe evidence for electro-optic laser cooling and vacuum amplification.},
author = {Sahu, Rishabh and Hease, William J and Rueda Sanchez, Alfredo R and Arnold, Georg M and Qiu, Liu and Fink, Johannes M},
booktitle = {Conference on Lasers and Electro-Optics},
isbn = {9781557528209},
location = {San Jose, CA, United States},
publisher = {Optica Publishing Group},
title = {{Realizing a quantum-enabled interconnect between microwave and telecom light}},
doi = {10.1364/CLEO_QELS.2022.FW4D.4},
year = {2022},
}
@inproceedings{12102,
abstract = {Given a Markov chain M = (V, v_0, δ), with state space V and a starting state v_0, and a probability threshold ε, an ε-core is a subset C of states that is left with probability at most ε. More formally, C ⊆ V is an ε-core, iff ℙ[reach (V\C)] ≤ ε. Cores have been applied in a wide variety of verification problems over Markov chains, Markov decision processes, and probabilistic programs, as a means of discarding uninteresting and low-probability parts of a probabilistic system and instead being able to focus on the states that are likely to be encountered in a real-world run. In this work, we focus on the problem of computing a minimal ε-core in a Markov chain. Our contributions include both negative and positive results: (i) We show that the decision problem on the existence of an ε-core of a given size is NP-complete. This solves an open problem posed in [Jan Kretínský and Tobias Meggendorfer, 2020]. We additionally show that the problem remains NP-complete even when limited to acyclic Markov chains with bounded maximal vertex degree; (ii) We provide a polynomial time algorithm for computing a minimal ε-core on Markov chains over control-flow graphs of structured programs. A straightforward combination of our algorithm with standard branch prediction techniques allows one to apply the idea of cores to find a subset of program lines that are left with low probability and then focus any desired static analysis on this core subset.},
author = {Ahmadi, Ali and Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Meggendorfer, Tobias and Safavi Hemami, Roodabeh and Zikelic, Dorde},
booktitle = {42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science},
isbn = {9783959772617},
issn = {1868-8969},
location = {Madras, India},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Algorithms and hardness results for computing cores of Markov chains}},
doi = {10.4230/LIPIcs.FSTTCS.2022.29},
volume = {250},
year = {2022},
}
@inproceedings{12101,
abstract = {Spatial games form a widely-studied class of games from biology and physics modeling the evolution of social behavior. Formally, such a game is defined by a square (d by d) payoff matrix M and an undirected graph G. Each vertex of G represents an individual, that initially follows some strategy i ∈ {1,2,…,d}. In each round of the game, every individual plays the matrix game with each of its neighbors: An individual following strategy i meeting a neighbor following strategy j receives a payoff equal to the entry (i,j) of M. Then, each individual updates its strategy to its neighbors' strategy with the highest sum of payoffs, and the next round starts. The basic computational problems consist of reachability between configurations and the average frequency of a strategy. For general spatial games and graphs, these problems are in PSPACE. In this paper, we examine restricted setting: the game is a prisoner’s dilemma; and G is a subgraph of grid. We prove that basic computational problems for spatial games with prisoner’s dilemma on a subgraph of a grid are PSPACE-hard.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Jecker, Ismael R and Svoboda, Jakub},
booktitle = {42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science},
isbn = {9783959772617},
issn = {1868-8969},
location = {Madras, India},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Complexity of spatial games}},
doi = {10.4230/LIPIcs.FSTTCS.2022.11},
volume = {250},
year = {2022},
}
@article{12111,
abstract = {Quantum impurities exhibit fascinating many-body phenomena when the small interacting impurity changes the physics of a large noninteracting environment. The characterisation of such strongly correlated nonperturbative effects is particularly challenging due to the infinite size of the environment, and the inability of local correlators to capture the buildup of long-ranged entanglement in the system. Here, we harness an entanglement-based observable—the purity of the impurity—as a witness for the formation of strong correlations. We showcase the utility of our scheme by exactly solving the open Kondo box model in the small box limit, and thus describe all-electronic dot-cavity devices. Specifically, we conclusively characterize the metal-to-insulator phase transition in the system and identify how the (conducting) dot-lead Kondo singlet is quenched by an (insulating) intraimpurity singlet formation. Furthermore, we propose an experimentally feasible tomography protocol for the measurement of the purity, which motivates the observation of impurity physics through their entanglement build up.},
author = {Stocker, Lidia and Sack, Stefan and Ferguson, Michael S. and Zilberberg, Oded},
issn = {2643-1564},
journal = {Physical Review Research},
number = {4},
publisher = {American Physical Society},
title = {{Entanglement-based observables for quantum impurities}},
doi = {10.1103/PhysRevResearch.4.043177},
volume = {4},
year = {2022},
}