@misc{14926, author = {Hauschild, Robert}, publisher = {Institute of Science and Technology Austria}, title = {{Matlab script for analysis of clone dispersal}}, doi = {10.15479/AT:ISTA:14926}, year = {2024}, } @misc{22234, abstract = {Lists of nontrivial integral points on some (families of) cubic surfaces. (2024-07-18)}, author = {Browning, Timothy D and Sutherland, Andrew}, publisher = {Göttingen Research Online Data}, title = {{Data and code for: Integral points on cubic surfaces: heuristics and numerics}}, doi = {10.25625/4FLFH8}, year = {2024}, } @unpublished{19063, abstract = {Instruction-tuned Large Language Models (LLMs) show impressive results in numerous practical applications, but they lack essential safety features that are common in other areas of computer science, particularly an explicit separation of instructions and data. This makes them vulnerable to manipulations such as indirect prompt injections and generally unsuitable for safety-critical tasks. Surprisingly, there is currently no established definition or benchmark to quantify this phenomenon. In this work, we close this gap by introducing a formal measure for instruction-data separation and an empirical variant that is calculable from a model's outputs. We also present a new dataset, SEP, that allows estimating the measure for real-world models. Our results on various LLMs show that the problem of instruction-data separation is real: all models fail to achieve high separation, and canonical mitigation techniques, such as prompt engineering and fine-tuning, either fail to substantially improve separation or reduce model utility. The source code and SEP dataset are openly accessible at https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed. }, author = {Zverev, Egor and Abdelnabi, Sahar and Tabesh, Soroush and Fritz, Mario and Lampert, Christoph}, booktitle = {arXiv}, title = {{Can LLMs separate instructions from data? And what do we even mean by that?}}, doi = {10.48550/arXiv.2403.06833}, year = {2024}, } @phdthesis{15094, abstract = {Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in discrete geometry that have captivated mathematicians for centuries, if not millennia. This thesis seeks to cast new light on these structures by illustrating specific instances where a topological perspective, specifically through discrete Morse theory and persistent homology, provides valuable insights. At first glance, the topology of these geometric objects might seem uneventful: point sets essentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which is a contractible space, and the topology of a network primarily involves the enumeration of connected components and cycles within the network. However, beneath this apparent simplicity, there lies an array of intriguing structures, a small subset of which will be uncovered in this thesis. Focused on three case studies, each addressing one of the mentioned objects, this work will showcase connections that intertwine topology with diverse fields such as combinatorial geometry, algorithms and data structures, and emerging applications like spatial biology. }, author = {Cultrera di Montesano, Sebastiano}, issn = {2663-337X}, pages = {108}, publisher = {Institute of Science and Technology Austria}, title = {{Persistence and Morse theory for discrete geometric structures}}, doi = {10.15479/at:ista:15094}, year = {2024}, } @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}, pages = {1101--1119}, publisher = {Springer Nature}, title = {{Geometric characterization of the persistence of 1D maps}}, doi = {10.1007/s41468-023-00126-9}, volume = {8}, year = {2024}, } @article{14826, abstract = {The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.}, author = {Kuhn, Andre and Roosjen, Mark and Mutte, Sumanth and Dubey, Shiv Mani and Carrillo Carrasco, Vanessa Polet and Boeren, Sjef and Monzer, Aline and Koehorst, Jasper and Kohchi, Takayuki and Nishihama, Ryuichi and Fendrych, Matyas and Sprakel, Joris and Friml, Jiří and Weijers, Dolf}, issn = {1097-4172}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {1}, pages = {130--148.e17}, publisher = {Elsevier}, title = {{RAF-like protein kinases mediate a deeply conserved, rapid auxin response}}, doi = {10.1016/j.cell.2023.11.021}, volume = {187}, year = {2024}, } @article{17373, abstract = {Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating the electrostatic properties of material surfaces, enabling the imaging of variations in work function, topology, surface charge density, or combinations thereof. Regardless of the underlying signal source, SKPM results in a voltage image, which is spatially distorted due to the finite size of the probe, long-range electrostatic interactions, mechanical and electrical noise, and the finite response time of the electronics. In order to recover the underlying signal, it is necessary to deconvolve the measurement with an appropriate point spread function (PSF) that accounts the aforementioned distortions, but determining this PSF is difficult. Here, we describe how such PSFs can be determined experimentally and show how they can be used to recover the underlying information of interest. We first consider the physical principles that enable SKPM and discuss how these affect the system PSF. We then show how one can experimentally measure PSFs by looking at well-defined features, and that these compare well to simulated PSFs, provided scans are performed extremely slowly and carefully. Next, we work at realistic scan speeds and show that the idealized PSFs fail to capture temporal distortions in the scan direction. While simulating PSFs for these situations would be quite challenging, we show that measuring PSFs with similar scan conditions works well. Our approach clarifies the basic principles and inherent challenges to SKPM measurements and gives practical methods to improve results.}, author = {Lenton, Isaac C and Pertl, Felix and Shafeek, Lubuna B and Waitukaitis, Scott R}, issn = {1089-7550}, journal = {Journal of Applied Physics}, number = {4}, publisher = {AIP Publishing}, title = {{Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging}}, doi = {10.1063/5.0215151}, volume = {136}, year = {2024}, } @article{17103, abstract = {Phytoalexin sakuranetin functions in resistance against rice blast. However, the mechanisms underlying the effects of sakuranetin remains elusive. Here, we report that rice lines expressing resistance (R) genes were found to contain high levels of sakuranetin, which correlates with attenuated endocytic trafficking of plasma membrane (PM) proteins. Exogenous and endogenous sakuranetin attenuates the endocytosis of various PM proteins and the fungal effector PWL2. Moreover, accumulation of the avirulence protein AvrCO39, resulting from uptake into rice cells by Magnaporthe oryzae, was reduced following treatment with sakuranetin. Pharmacological manipulation of clathrin-mediated endocytic (CME) suggests that this pathway is targeted by sakuranetin. Indeed, attenuation of CME by sakuranetin is sufficient to convey resistance against rice blast. Our data reveals a mechanism of rice against M. oryzae by increasing sakuranetin levels and repressing the CME of pathogen effectors, which is distinct from the action of many R genes that mainly function by modulating transcription.}, author = {Jiang, Lihui and Zhang, Xiaoyan and Zhao, Yiting and Zhu, Haiyan and Fu, Qijing and Lu, Xinqi and Huang, Wuying and Yang, Xinyue and Zhou, Xuan and Wu, Lixia and Yang, Ao and He, Xie and Dong, Man and Peng, Ziai and Yang, Jing and Guo, Liwei and Wen, Jiancheng and Huang, Huichuan and Xie, Yong and Zhu, Shusheng and Li, Chengyun and He, Xiahong and Zhu, Youyong and Friml, Jiří and Du, Yunlong}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast}}, doi = {10.1038/s41467-024-47746-y}, volume = {15}, year = {2024}, } @misc{22776, author = {Du, Yunlong}, publisher = {Repository}, title = {{SeRrbJ609}}, doi = {10.6084/m9.figshare.25448191}, year = {2024}, } @inproceedings{18155, abstract = {We study the classical problem of verifying programs with respect to formal specifications given in the linear temporal logic (LTL). We first present novel sound and complete witnesses for LTL verification over imperative programs. Our witnesses are applicable to both verification (proving) and refutation (finding bugs) settings. We then consider LTL formulas in which atomic propositions can be polynomial constraints and turn our focus to polynomial arithmetic programs, i.e. programs in which every assignment and guard consists only of polynomial expressions. For this setting, we provide an efficient algorithm to automatically synthesize such LTL witnesses. Our synthesis procedure is both sound and semi-complete. Finally, we present experimental results demonstrating the effectiveness of our approach and that it can handle programs which were beyond the reach of previous state-of-the-art tools.}, author = {Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Goharshady, Ehsan and Karrabi, Mehrdad and Zikelic, Dorde}, booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)}, isbn = {9783031711619}, issn = {1611-3349}, location = {Milan, Italy}, pages = {600--619}, publisher = {Springer Nature}, title = {{Sound and complete witnesses for template-based verification of LTL properties on polynomial programs}}, doi = {10.1007/978-3-031-71162-6_31}, volume = {14933}, year = {2024}, } @misc{22798, abstract = {This repository contains the artifact of the paper titled "Sound and Complete Witnesses for Template-based Verification of LTL Properties on Polynomial Programs" accepted at FM 2024. The task of verifying an LTL formula on a program can be reduced to verifying a Büchi specification on the product transition system. This tool takes a non-deterministic transition system together with a Büchi specification as input and based on user preferences tries to either (i) prove the existence of a run in the program that satisfies the Büchi condition or (ii) demonstrate that every run of the program satisfies the Büchi condition. The tool is written in Java and works well with openjdk 11 on Ubuntu 22.04. Running all the experiments can take weeks to finish. We have provided a script for running the strongest configuration of our tool which solves most of the benchmarks and takes less than 48 hours. Detailed guidance is given in the readme file.}, author = {Chatterjee, Krishnendu and Kafshdar Goharshady, Amir and Kafshdar Goharshady, Ehsan and Karrabi, Mehrdad and Žikelić, Ðorđe}, publisher = {Repository}, title = {{Data for Sound and Complete Witnesses for Template-based Verification of LTL Properties on Polynomial Programs}}, doi = {10.5281/zenodo.12518216}, year = {2024}, } @article{18528, abstract = {The recent measurement of magnetic field strength inside the radiative interior of red giant stars has opened the way toward full 3D characterization of the geometry of stable large-scale magnetic fields. However, current measurements, which are limited to dipolar (ℓ = 1) mixed modes, do not properly constrain the topology of magnetic fields due to degeneracies on the observed magnetic field signature on such ℓ = 1 mode frequencies. Efforts focused toward unambiguous detections of magnetic field configurations are now key to better understand angular momentum transport in stars. We investigated the detectability of complex magnetic field topologies (such as the ones observed at the surface of stars with a radiative envelope with spectropolarimetry) inside the radiative interior of red giants. We focused on a field composed of a combination of a dipole and a quadrupole (quadrudipole) and on an offset field. We explored the potential of probing such magnetic field topologies from a combined measurement of magnetic signatures on ℓ = 1 and quadrupolar (ℓ = 2) mixed mode oscillation frequencies. We first derived the asymptotic theoretical formalism for computing the asymmetric signature in the frequency pattern for ℓ = 2 modes due to a quadrudipole magnetic field. To access asymmetry parameters for more complex magnetic field topologies, we numerically performed a grid search over the parameter space to map the degeneracy of the signatures of given topologies. We demonstrate the crucial role played by ℓ = 2 mixed modes in accessing internal magnetic fields with a quadrupolar component. The degeneracy of the quadrudipole compared to pure dipolar fields is lifted when considering magnetic asymmetries in both ℓ = 1 and ℓ = 2 mode frequencies. In addition to the analytical derivation for the quadrudipole, we present the prospect for complex magnetic field inversions using magnetic sensitivity kernels from standard perturbation analysis for forward modeling. Using this method, we explored the detectability of offset magnetic fields from ℓ = 1 and ℓ = 2 frequencies and demonstrate that offset fields may be mistaken for weak and centered magnetic fields, resulting in underestimating the magnetic field strength in stellar cores. We emphasize the need to characterize ℓ = 2 mixed-mode frequencies, (along with the currently characterized ℓ = 1 mixed modes), to unveil the higher-order components of the geometry of buried magnetic fields and to better constrain angular momentum transport inside stars.}, author = {Das, Srijan B and Einramhof, Lukas and Bugnet, Lisa Annabelle}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, title = {{Unveiling complex magnetic field configurations in red giant stars}}, doi = {10.1051/0004-6361/202450918}, volume = {690}, year = {2024}, } @misc{22802, abstract = {MESA inlist file for the paper "Unveiling complex magnetic field configurations in red giant stars" (10.1051/0004-6361/202450918)}, author = {Das, Srijan B and Einramhof, Lukas and Bugnet, Lisa}, publisher = {Institute of Science and Technology Austria}, title = {{MESA inlist file}}, doi = {10.5281/zenodo.12804810}, year = {2024}, } @misc{22803, abstract = {In this study, we analyzed the efficiency of different adeno-associated viral (AAV) injections in transfecting neurons in the salamander Pleurodeles waltl. To query sources of variation in AAV injection outcomes, we analyzed metadata and outcomes for an additional 68 intraparenchymal injections performed 39 in post-metamorphic Pleurodeles salamanders. This dataset included both quantitative variables (age, weight, viral genomes (v.g.) injected, and a cell transduction score ranging from 0 to 4, see STAR Methods) and categorical variables (here referred to as qualitative variables: serotype, promoter, reporter, single vs. dual injection, manufacturer, and injection site). To assess the associations between these variables, we performed a Factor Analysis for Mixed Data (FAMD), a principal component method that is designed to determine significant sources of variability within datasets that contain both quantitative and qualitative data types. This dataset contains the injection outcomes and metadata for AAV injections administered in the salamander Pleurodeles waltl. The RactoMineR package (https://CRAN.R-project.org/package=FactoMineR) was used to determine significant contributions of a number of variables contributing to injection outcomes. Analysis of these data revealed that, among other factors, age co-varies with injection score. Therefore, we conclude that increased animal age decreases the efficacy of this tool.}, author = {Jaeger, Eliza}, publisher = {Repository}, title = {{Multivariate analysis of Pleurodeles waltl injection outcomes using FAMD FactoMineR (RStudio 4.3.2) used to probe sources of variability during an Adeno-associated viral (AAV) screen}}, doi = {10.5061/dryad.mpg4f4r89}, year = {2024}, } @phdthesis{18088, abstract = {Instant messaging applications like Whatsapp, Signal or Telegram have become ubiquitous in today's society. Many of them provide not only end-to-end encryption, but also security guarantees even when the key material gets compromised. These are achieved through frequent key update performed by users. In particular, the compromise of a group key should preserve confidentiality of previously exchanged messages (forward secrecy), and a subsequent key update will ensure security for future ones (post-compromise security). Though great protocols for one-on-one communication have been known for some time, the design of ones that scale efficiently for larger groups while achieving akin security guarantees is a hard problem. A great deal of research has been aimed at this topic, much of it under the umbrella of the Messaging Layer Security (MLS) working group at the IETF. Started in 2018, this joint effort by academics and industry culminated in 2023 with the publication of the first standard for secure group messaging [IETF, RFC9420]. At the core of secure group messaging is a cryptographic primitive termed Continuous Group Key Agreement, or CGKA [Alwen et al. 2021], that essentially allows a changing group of users to agree on a common key with the added functionality security against compromises is achieved by users asynchronously issuing a key update. In this thesis we contribute to the understanding of CGKA across different angles. First, we present a new technique to effect dynamic operations in groups, i.e., add or remove members, that can be more efficient that the one employed by MLS in certain settings. Considering the setting of users belonging to multiple overlapping groups, we then show lowerbounds on the communication cost of constructions that leverage said overlap, at the same time showing protocols that are asymptotically optimal and efficient for practical settings, respectively. Along the way, we show that the communication cost of key updates in MLS is average-cost optimal. An important feature in CGKA protocols, particularly for big groups, is the possibility of executing several group operations concurrently. While later versions of MLS support this, they do at the cost of worsening the communication efficiency of future group operations. In this thesis we introduce two new protocols that permit concurrency without any negative effect on efficiency. Our protocols circumvent previously existing lower bounds by satisfying a new notion of post-compromise security that only asks for security to be re-established after a certain number of key updates have taken place. While this can be slower than MLS in terms of rounds of communication, we show that it leads to more efficient overall communication. Additionally, we introduce a new technique that allows group members to decrease the information they need to store and download, which makes one of our protocols enjoy much lower download cost than any other existing CGKA constructions. }, author = {Pascual Perez, Guillermo}, issn = {2663-337X}, pages = {239}, publisher = {Institute of Science and Technology Austria}, title = {{On the efficiency and security of secure group messaging}}, doi = {10.15479/at:ista:18088}, year = {2024}, } @inproceedings{18086, abstract = {Abstract. Continuous group key agreement (CGKA) allows a group of users to maintain a continuously updated shared key in an asynchronous setting where parties only come online sporadically and their messages are relayed by an untrusted server. CGKA captures the basic primitive underlying group messaging schemes. Current solutions including TreeKEM (“Messaging Layer Security” (MLS) IETF RFC 9420) cannot handle concurrent requests while retaining low communication complexity. The exception being CoCoA, which is concurrent while having extremely low communication complexity (in groups of size n and for m concurrent updates the communication per user is log(n), i.e., independent of m). The main downside of CoCoA is that in groups of size n, users might have to do up to log(n) update requests to the server to ensure their (potentially corrupted) key material has been refreshed. In this work we present a “fast healing” concurrent CGKA protocol, named DeCAF, where users will heal after at most log(t) requests, with t being the number of corrupted users. While also suitable for the standard central-server setting, our protocol is particularly interesting for realizing decentralized group messaging, where protocol messages (add, remove, update) are being posted on some append-only data structure rather than sent to a server. In this setting, concurrency is crucial once the rate of requests exceeds, say, the rate at which new blocks are added to a blockchain. In the central-server setting, CoCoA (the only alternative with concurrency, sub-linear communication and basic post-compromise security) enjoys much lower download communication. However, in the decentralized setting – where there is no server which can craft specific messages for different users to reduce their download communication – our protocol significantly outperforms CoCoA. DeCAF heals in fewer epochs (log(t) vs. log(n)) while incurring a similar per epoch per user communication cost.}, author = {Alwen, Joel F and Auerbach, Benedikt and Cueto Noval, Miguel and Klein, Karen and Pascual Perez, Guillermo and Pietrzak, Krzysztof Z}, booktitle = {Security and Cryptography for Networks: 14th International Conference}, editor = {Galdi, Clemente and Phan, Duong Hieu}, isbn = {9783031710728}, issn = {1611-3349}, location = {Amalfi, Italy}, pages = {294–313}, publisher = {Springer Nature}, title = {{DeCAF: Decentralizable CGKA with fast healing}}, doi = {10.1007/978-3-031-71073-5_14}, volume = {14974}, year = {2024}, } @inproceedings{18702, abstract = {In this work we prove lower bounds on the (communication) cost of maintaining a shared key among a dynamic group of users. Being “dynamic” means one can add and remove users from the group. This captures important protocols like multicast encryption (ME) and continuous group-key agreement (CGKA), which is the primitive underlying many group messaging applications. We prove our bounds in a combinatorial setting where the state of the protocol progresses in rounds. The state of the protocol in each round is captured by a set system, with each of its elements specifying a set of users who share a secret key. We show this combinatorial model implies bounds in symbolic models for ME and CGKA that capture, as building blocks, PRGs, PRFs, dual PRFs, secret sharing, and symmetric encryption in the setting of ME, and PRGs, PRFs, dual PRFs, secret sharing, public-key encryption, and key-updatable public-key encryption in the setting of CGKA. The models are related to the ones used by Micciancio and Panjwani (Eurocrypt’04) and Bienstock et al. (TCC’20) to analyze ME and CGKA, respectively. We prove – using the Bollobás’ Set Pairs Inequality – that the cost (number of uploaded ciphertexts) for replacing a set of d users in a group of size n is Ω(dln(n/d)). Our lower bound is asymptotically tight and both improves on a bound of Ω(d) by Bienstock et al. (TCC’20), and generalizes a result by Micciancio and Panjwani (Eurocrypt’04), who proved a lower bound of Ω(log(n)) for d=1. }, author = {Anastos, Michael and Auerbach, Benedikt and Baig, Mirza Ahad and Cueto Noval, Miguel and Kwan, Matthew Alan and Pascual Perez, Guillermo and Pietrzak, Krzysztof Z}, booktitle = {22nd International Conference on Theory of Cryptography}, isbn = {9783031780103}, issn = {1611-3349}, location = {Milan, Italy}, pages = {413--443}, publisher = {Springer Nature}, title = {{The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging}}, doi = {10.1007/978-3-031-78011-0_14}, volume = {15364}, year = {2024}, } @article{18480, abstract = {Caloric restriction (CR) can extend the organism life- and health-span by improving glucose homeostasis. How CR affects the structure-function of pancreatic beta cells remains unknown. We used single nucleus transcriptomics to show that CR increases the expression of genes for beta cell identity, protein processing, and organelle homeostasis. Gene regulatory network analysis reveal that CR activates transcription factors important for beta cell identity and homeostasis, while imaging metabolomics demonstrates that beta cells upon CR are more energetically competent. In fact, high-resolution microscopy show that CR reduces beta cell mitophagy to increase mitochondria mass and the potential for ATP generation. However, CR beta cells have impaired adaptive proliferation in response to high fat diet feeding. Finally, we show that long-term CR delays the onset of beta cell aging hallmarks and promotes cell longevity by reducing beta cell turnover. Therefore, CR could be a feasible approach to preserve compromised beta cell structure-function during aging and diabetes.}, author = {Dos Santos, Cristiane and Cambraia, Amanda and Shrestha, Shristi and Cutler, Melanie and Cottam, Matthew and Perkins, Guy and Lev-Ram, Varda and Roy, Birbickram and Acree, Christopher and Kim, Keun Young and Deerinck, Thomas and Dean, Danielle and Cartailler, Jean Philippe and Macdonald, Patrick E. and Hetzer, Martin W and Ellisman, Mark and Arrojo E Drigo, Rafael}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice}}, doi = {10.1038/s41467-024-53127-2}, volume = {15}, year = {2024}, } @misc{22865, abstract = {Dataset for Dos Santos et al, 2024}, author = {Arrojo e Drigo, Rafael}, publisher = {Repository}, title = {{Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity}}, doi = {10.5281/zenodo.6491943}, year = {2024}, } @misc{22866, author = {Hrast, Mateja}, publisher = {Repository}, title = {{Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl}}, doi = {10.5281/zenodo.13833474}, year = {2024}, }