@article{12776, abstract = {An improved asymptotic formula is established for the number of rational points of bounded height on the split smooth del Pezzo surface of degree 5. The proof uses the five conic bundle structures on the surface.}, author = {Browning, Timothy D}, issn = {1076-9803}, journal = {New York Journal of Mathematics}, pages = {1193 -- 1229}, publisher = {State University of New York}, title = {{Revisiting the Manin–Peyre conjecture for the split del Pezzo surface of degree 5}}, volume = {28}, year = {2022}, } @article{12793, abstract = {Let F be a global function field with constant field Fq. Let G be a reductive group over Fq. We establish a variant of Arthur's truncated kernel for G and for its Lie algebra which generalizes Arthur's original construction. We establish a coarse geometric expansion for our variant truncation. As applications, we consider some existence and uniqueness problems of some cuspidal automorphic representations for the functions field of the projective line P1Fq with two points of ramifications.}, author = {Yu, Hongjie}, issn = {1945-5844}, journal = {Pacific Journal of Mathematics}, keywords = {Arthur–Selberg trace formula, cuspidal automorphic representations, global function fields}, number = {1}, pages = {193--237}, publisher = {Mathematical Sciences Publishers}, title = {{ A coarse geometric expansion of a variant of Arthur's truncated traces and some applications}}, doi = {10.2140/pjm.2022.321.193}, volume = {321}, year = {2022}, } @unpublished{12860, abstract = {Memorization of the relation between entities in a dataset can lead to privacy issues when using a trained model for question answering. We introduce Relational Memorization (RM) to understand, quantify and control this phenomenon. While bounding general memorization can have detrimental effects on the performance of a trained model, bounding RM does not prevent effective learning. The difference is most pronounced when the data distribution is long-tailed, with many queries having only few training examples: Impeding general memorization prevents effective learning, while impeding only relational memorization still allows learning general properties of the underlying concepts. We formalize the notion of Relational Privacy (RP) and, inspired by Differential Privacy (DP), we provide a possible definition of Differential Relational Privacy (DrP). These notions can be used to describe and compute bounds on the amount of RM in a trained model. We illustrate Relational Privacy concepts in experiments with large-scale models for Question Answering.}, author = {Bombari, Simone and Achille, Alessandro and Wang, Zijian and Wang, Yu-Xiang and Xie, Yusheng and Singh, Kunwar Yashraj and Appalaraju, Srikar and Mahadevan, Vijay and Soatto, Stefano}, booktitle = {arXiv}, title = {{Towards differential relational privacy and its use in question answering}}, doi = {10.48550/arXiv.2203.16701}, year = {2022}, } @inproceedings{12894, author = {Schlögl, Alois and Hornoiu, Andrei and Elefante, Stefano and Stadlbauer, Stephan}, booktitle = {ASHPC22 - Austrian-Slovenian HPC Meeting 2022}, isbn = {978-3-200-08499-5}, location = {Grundlsee, Austria}, pages = {7}, publisher = {EuroCC Austria c/o Universität Wien}, title = {{Where is the sweet spot? A procurement story of general purpose compute nodes}}, doi = {10.25365/phaidra.337}, year = {2022}, } @misc{13064, abstract = {Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R 2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h SNP 2 . We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies.}, author = {Orliac, Etienne and Trejo Banos, Daniel and Ojavee, Sven and Läll, Kristi and Mägi, Reedik and Visscher, Peter and Robinson, Matthew Richard}, publisher = {Dryad}, title = {{Improving genome-wide association discovery and genomic prediction accuracy in biobank data}}, doi = {10.5061/DRYAD.GTHT76HMZ}, year = {2022}, } @misc{13066, abstract = {Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.}, author = {Koch, Eva and Ravinet, Mark and Westram, Anja M and Jonannesson, Kerstin and Butlin, Roger}, publisher = {Dryad}, title = {{Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution}}, doi = {10.5061/DRYAD.M905QFV4B}, year = {2022}, } @misc{13076, abstract = {The source code for replicating experiments presented in the paper. The implementation of the designed priority schedulers can be found in Galois-2.2.1/include/Galois/WorkList/: StealingMultiQueue.h is the StealingMultiQueue. MQOptimized/ contains MQ Optimized variants. We provide images that contain all the dependencies and datasets. Images can be pulled from npostnikova/mq-based-schedulers repository, or downloaded from Zenodo. See readme for more detail.}, author = {Postnikova, Anastasiia and Koval, Nikita and Nadiradze, Giorgi and Alistarh, Dan-Adrian}, publisher = {Zenodo}, title = {{Multi-queues can be state-of-the-art priority schedulers}}, doi = {10.5281/ZENODO.5733408}, year = {2022}, } @inproceedings{13239, abstract = {Brains are thought to engage in predictive learning - learning to predict upcoming stimuli - to construct an internal model of their environment. This is especially notable for spatial navigation, as first described by Tolman’s latent learning tasks. However, predictive learning has also been observed in sensory cortex, in settings unrelated to spatial navigation. Apart from normative frameworks such as active inference or efficient coding, what could be the utility of learning to predict the patterns of occurrence of correlated stimuli? Here we show that prediction, and thereby the construction of an internal model of sequential stimuli, can bootstrap the learning process of a working memory task in a recurrent neural network. We implemented predictive learning alongside working memory match-tasks, and networks emerged to solve the prediction task first by encoding information across time to predict upcoming stimuli, and then eavesdropped on this solution to solve the matching task. Eavesdropping was most beneficial when neural resources were limited. Hence, predictive learning acts as a general neural mechanism to learn to store sensory information that can later be essential for working memory tasks.}, author = {Van Der Plas, Thijs L. and Vogels, Tim P and Manohar, Sanjay G.}, booktitle = {Proceedings of Machine Learning Research}, issn = {2640-3498}, pages = {518--531}, publisher = {ML Research Press}, title = {{Predictive learning enables neural networks to learn complex working memory tasks}}, volume = {199}, year = {2022}, } @article{13240, abstract = {Ustilago maydis is a biotrophic phytopathogenic fungus that causes corn smut disease. As a well-established model system, U. maydis is genetically fully accessible with large omics datasets available and subject to various biological questions ranging from DNA-repair, RNA-transport, and protein secretion to disease biology. For many genetic approaches, tight control of transgene regulation is important. Here we established an optimised version of the Tetracycline-ON (TetON) system for U. maydis. We demonstrate the Tetracycline concentration-dependent expression of fluorescent protein transgenes and the system’s suitability for the induced expression of the toxic protein BCL2 Associated X-1 (Bax1). The Golden Gate compatible vector system contains a native minimal promoter from the mating factor a-1 encoding gene, mfa with ten copies of the tet-regulated operator (tetO) and a codon optimised Tet-repressor (tetR*) which is translationally fused to the native transcriptional corepressor Mql1 (UMAG_05501). The metabolism-independent transcriptional regulator system is functional both, in liquid culture as well as on solid media in the presence of the inducer and can become a useful tool for toxin-antitoxin studies, identification of antifungal proteins, and to study functions of toxic gene products in Ustilago maydis.}, author = {Ingole, Kishor D. and Nagarajan, Nithya and Uhse, Simon and Giannini, Caterina and Djamei, Armin}, issn = {2673-6128}, journal = {Frontiers in Fungal Biology}, publisher = {Frontiers Media}, title = {{Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis}}, doi = {10.3389/ffunb.2022.1029114}, volume = {3}, year = {2022}, } @inproceedings{13241, abstract = {Addressing fairness concerns about machine learning models is a crucial step towards their long-term adoption in real-world automated systems. Many approaches for training fair models from data have been developed and an implicit assumption about such algorithms is that they are able to recover a fair model, despite potential historical biases in the data. In this work we show a number of impossibility results that indicate that there is no learning algorithm that can recover a fair model when a proportion of the dataset is subject to arbitrary manipulations. Specifically, we prove that there are situations in which an adversary can force any learner to return a biased classifier, with or without degrading accuracy, and that the strength of this bias increases for learning problems with underrepresented protected groups in the data. Our results emphasize on the importance of studying further data corruption models of various strength and of establishing stricter data collection practices for fairness-aware learning.}, author = {Konstantinov, Nikola H and Lampert, Christoph}, booktitle = {Proceedings of Machine Learning Research}, issn = {2640-3498}, pages = {59--83}, publisher = {ML Research Press}, title = {{On the impossibility of fairness-aware learning from corrupted data}}, volume = {171}, year = {2022}, } @inbook{19984, abstract = {The first part of this paper is a survey of mathematical results on mirror symmetry phenomena between Hitchin systems for Langlands dual groups. The second part introduces and discusses multiplicity algebras of the Hitchin system on Lagrangians, and considers corresponding conjectural structures on their mirror.}, author = {Hausel, Tamás}, booktitle = {International Congress of Mathematicians}, isbn = {9783985470587}, location = {virtuel}, pages = {2228--2249}, publisher = {EMS Press}, title = {{Enhanced mirror symmetry for Langlands dual Hitchin systems}}, doi = {10.4171/icm2022/164}, year = {2022}, } @article{15268, abstract = {Apolipoprotein A‐I (apoA‐I) has a key function in the reverse cholesterol transport. However, aggregation of apoA‐I single point mutants can lead to hereditary amyloid pathology. Although several studies have tackled the biophysical and structural consequences introduced by these mutations, there is little information addressing the relationship between the evolutionary and structural features that contribute to the amyloid behavior of apoA‐I. We combined evolutionary studies, in silico mutagenesis and molecular dynamics (MD) simulations to provide a comprehensive analysis of the conservation and pathogenic role of the aggregation‐prone regions (APRs) present in apoA‐I. Sequence analysis demonstrated that among the four amyloidogenic regions described for human apoA‐I, only two (APR1 and APR4) are evolutionary conserved across different species of Sarcopterygii. Moreover, stability analysis carried out with the FoldX engine showed that APR1 contributes to the marginal stability of apoA‐I. Structural properties of full‐length apoA‐I models suggest that aggregation is avoided by placing APRs into highly packed and rigid portions of its native fold. Compared to silent variants extracted from the gnomAD database, the thermodynamic and pathogenic impact of amyloid mutations showed evidence of a higher destabilizing effect. MD simulations of the amyloid variant G26R evidenced the partial unfolding of the alpha‐helix bundle with the concomitant exposure of APR1 to the solvent, suggesting an insight into the early steps involved in its aggregation. Our findings highlight APR1 as a relevant component for apoA‐I structural integrity and emphasize a destabilizing effect of amyloid variants that leads to the exposure of this region.}, author = {Gisonno, Romina A. and Masson, Tomas and Ramella, Nahuel A. and Barrera, Exequiel E. and Romanowski, Víctor and Tricerri, M. Alejandra}, issn = {1097-0134}, journal = {Proteins: Structure, Function, and Bioinformatics}, keywords = {Molecular Biology, Biochemistry, Structural Biology}, number = {1}, pages = {258--269}, publisher = {Wiley}, title = {{Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior}}, doi = {10.1002/prot.26217}, volume = {90}, year = {2022}, } @article{10566, abstract = {A versatile, scalable, room temperature and surfactant-free route for the synthesis of metal chalcogenide nanoparticles in aqueous solution is detailed here for the production of PbS and Cu-doped PbS nanoparticles. Subsequently, nanoparticles are annealed in a reducing atmosphere to remove surface oxide, and consolidated into dense polycrystalline materials by means of spark plasma sintering. By characterizing the transport properties of the sintered material, we observe the annealing step and the incorporation of Cu to play a key role in promoting the thermoelectric performance of PbS. The presence of Cu allows improving the electrical conductivity by increasing the charge carrier concentration and simultaneously maintaining a large charge carrier mobility, which overall translates into record power factors at ambient temperature, 2.3 mWm-1K−2. Simultaneously, the lattice thermal conductivity decreases with the introduction of Cu, leading to a record high ZT = 0.37 at room temperature and ZT = 1.22 at 773 K. Besides, a record average ZTave = 0.76 is demonstrated in the temperature range 320–773 K for n-type Pb0.955Cu0.045S.}, author = {Li, Mengyao and Liu, Yu and Zhang, Yu and Chang, Cheng and Zhang, Ting and Yang, Dawei and Xiao, Ke and Arbiol, Jordi and Ibáñez, Maria and Cabot, Andreu}, issn = {1385-8947}, journal = {Chemical Engineering Journal}, publisher = {Elsevier}, title = {{Room temperature aqueous-based synthesis of copper-doped lead sulfide nanoparticles for thermoelectric application}}, doi = {10.1016/j.cej.2021.133837}, volume = {433}, year = {2022}, } @article{10583, abstract = {The synthetic strigolactone (SL) analog, rac-GR24, has been instrumental in studying the role of SLs as well as karrikins because it activates the receptors DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2) of their signaling pathways, respectively. Treatment with rac-GR24 modifies the root architecture at different levels, such as decreasing the lateral root density (LRD), while promoting root hair elongation or flavonol accumulation. Previously, we have shown that the flavonol biosynthesis is transcriptionally activated in the root by rac-GR24 treatment, but, thus far, the molecular players involved in that response have remained unknown. To get an in-depth insight into the changes that occur after the compound is perceived by the roots, we compared the root transcriptomes of the wild type and the more axillary growth2 (max2) mutant, affected in both SL and karrikin signaling pathways, with and without rac-GR24 treatment. Quantitative reverse transcription (qRT)-PCR, reporter line analysis and mutant phenotyping indicated that the flavonol response and the root hair elongation are controlled by the ELONGATED HYPOCOTYL 5 (HY5) and MYB12 transcription factors, but HY5, in contrast to MYB12, affects the LRD as well. Furthermore, we identified the transcription factors TARGET OF MONOPTEROS 5 (TMO5) and TMO5 LIKE1 as negative and the Mediator complex as positive regulators of the rac-GR24 effect on LRD. Altogether, hereby, we get closer toward understanding the molecular mechanisms that underlay the rac-GR24 responses in the root.}, author = {Struk, Sylwia and Braem, Lukas and Matthys, Cedrick and Walton, Alan and Vangheluwe, Nick and Van Praet, Stan and Jiang, Lingxiang and Baster, Pawel and De Cuyper, Carolien and Boyer, Francois-Didier and Stes, Elisabeth and Beeckman, Tom and Friml, Jiří and Gevaert, Kris and Goormachtig, Sofie}, issn = {1471-9053}, journal = {Plant & Cell Physiology}, keywords = {flavonols, MAX2, rac-Gr24, RNA-seq, root development, transcriptional regulation}, number = {1}, pages = {104--119}, publisher = {Oxford University Press}, title = {{Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density}}, doi = {10.1093/pcp/pcab149}, volume = {63}, year = {2022}, } @article{10584, abstract = {Electrically tunable lenses (ETLs) are those with the ability to alter their optical power in response to an electric signal. This feature allows such systems to not only image the areas of interest but also obtain spatial depth perception (depth of field, DOF). The aim of the present study was to develop an ETL-based imaging system for quantitative surface analysis. Firstly, the system was calibrated to achieve high depth resolution, warranting the accurate measurement of the depth and to account for and correct any influences from external factors on the ETL. This was completed using the Tenengrad operator which effectively identified the plane of best focus as demonstrated by the linear relationship between the control current applied to the ETL and the height at which the optical system focuses. The system was then employed to measure amplitude, spatial, hybrid, and volume surface texture parameters of a model material (pharmaceutical dosage form) which were validated against the parameters obtained using a previously validated surface texture analysis technique, optical profilometry. There were no statistically significant differences between the surface texture parameters measured by the techniques, highlighting the potential application of ETL-based imaging systems as an easily adaptable and low-cost alternative surface texture analysis technique to conventional microscopy techniques}, author = {Nirwan, Jorabar Singh and Lou, Shan and Hussain, Saqib and Nauman, Muhammad and Hussain, Tariq and Conway, Barbara R. and Ghori, Muhammad Usman}, issn = {2072-666X}, journal = {Micromachines}, keywords = {surface texture, electrically tunable lens, materials, hypromellose, surface topography, surface roughness, pharmaceutical tablet, variable focus imaging}, number = {1}, publisher = {MDPI}, title = {{Electrically tunable lens (ETL) - based variable focus imaging system for parametric surface texture analysis of materials}}, doi = {10.3390/mi13010017}, volume = {13}, year = {2022}, } @article{10587, abstract = {Access to a blossoming library of colloidal nanomaterials provides building blocks for complex assembled materials. The journey to bring these prospects to fruition stands to benefit from the application of advanced processing methods. Epitaxially connected nanocrystal (or quantum dot) superlattices present a captivating model system for mesocrystals with intriguing emergent properties. The conventional processing approach to creating these materials involves assembling and attaching the constituent nanocrystals at the interface between two immiscible fluids. Processing small liquid volumes of the colloidal nanocrystal solution involves several complexities arising from the concurrent spreading, evaporation, assembly, and attachment. The ability of inkjet printers to deliver small (typically picoliter) liquid volumes with precise positioning is attractive to advance fundamental insights into the processing science, and thereby potentially enable new routes to incorporate the epitaxially connected superlattices into technology platforms. In this study, we identified the processing window of opportunity, including nanocrystal ink formulation and printing approach to enable delivery of colloidal nanocrystals from an inkjet nozzle onto the surface of a sessile droplet of the immiscible subphase. We demonstrate how inkjet printing can be scaled-down to enable the fabrication of epitaxially connected superlattices on patterned sub-millimeter droplets. We anticipate that insights from this work will spur on future advances to enable more mechanistic insights into the assembly processes and new avenues to create high-fidelity superlattices.}, author = {Balazs, Daniel and Erkan, N. Deniz and Quien, Michelle and Hanrath, Tobias}, issn = {1998-0000}, journal = {Nano Research}, keywords = {interfacial assembly, colloidal nanocrystal, superlattice, inkjet printing}, number = {5}, pages = {4536–4543}, publisher = {Springer Nature}, title = {{Inkjet printing of epitaxially connected nanocrystal superlattices}}, doi = {10.1007/s12274-021-4022-7}, volume = {15}, year = {2022}, } @article{10588, abstract = {We prove the Sobolev-to-Lipschitz property for metric measure spaces satisfying the quasi curvature-dimension condition recently introduced in Milman (Commun Pure Appl Math, to appear). We provide several applications to properties of the corresponding heat semigroup. In particular, under the additional assumption of infinitesimal Hilbertianity, we show the Varadhan short-time asymptotics for the heat semigroup with respect to the distance, and prove the irreducibility of the heat semigroup. These results apply in particular to large classes of (ideal) sub-Riemannian manifolds.}, author = {Dello Schiavo, Lorenzo and Suzuki, Kohei}, issn = {1432-1807}, journal = {Mathematische Annalen}, keywords = {quasi curvature-dimension condition, sub-riemannian geometry, Sobolev-to-Lipschitz property, Varadhan short-time asymptotics}, pages = {1815--1832}, publisher = {Springer Nature}, title = {{Sobolev-to-Lipschitz property on QCD- spaces and applications}}, doi = {10.1007/s00208-021-02331-2}, volume = {384}, year = {2022}, } @article{10589, abstract = {Superconducting devices ubiquitously have an excess of broken Cooper pairs, which can hamper their performance. It is widely believed that external radiation is responsible but a study now suggests there must be an additional, unknown source.}, author = {Higginbotham, Andrew P}, issn = {1745-2481}, journal = {Nature Physics}, keywords = {superconducting devices, superconducting properties and materials}, pages = {126}, publisher = {Springer Nature}, title = {{A secret source}}, doi = {10.1038/s41567-021-01459-x}, volume = {18}, year = {2022}, } @article{10600, abstract = {We show that recent results on adiabatic theory for interacting gapped many-body systems on finite lattices remain valid in the thermodynamic limit. More precisely, we prove a generalized super-adiabatic theorem for the automorphism group describing the infinite volume dynamics on the quasi-local algebra of observables. The key assumption is the existence of a sequence of gapped finite volume Hamiltonians, which generates the same infinite volume dynamics in the thermodynamic limit. Our adiabatic theorem also holds for certain perturbations of gapped ground states that close the spectral gap (so it is also an adiabatic theorem for resonances and, in this sense, “generalized”), and it provides an adiabatic approximation to all orders in the adiabatic parameter (a property often called “super-adiabatic”). In addition to the existing results for finite lattices, we also perform a resummation of the adiabatic expansion and allow for observables that are not strictly local. Finally, as an application, we prove the validity of linear and higher order response theory for our class of perturbations for infinite systems. While we consider the result and its proof as new and interesting in itself, we also lay the foundation for the proof of an adiabatic theorem for systems with a gap only in the bulk, which will be presented in a follow-up article.}, author = {Henheik, Sven Joscha and Teufel, Stefan}, issn = {1089-7658}, journal = {Journal of Mathematical Physics}, keywords = {mathematical physics, statistical and nonlinear physics}, number = {1}, publisher = {AIP Publishing}, title = {{Adiabatic theorem in the thermodynamic limit: Systems with a uniform gap}}, doi = {10.1063/5.0051632}, volume = {63}, year = {2022}, } @article{10602, abstract = {Transforming ω-automata into parity automata is traditionally done using appearance records. We present an efficient variant of this idea, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and show that our method produces significantly smaller automata than previous approaches.}, author = {Kretinsky, Jan and Meggendorfer, Tobias and Waldmann, Clara and Weininger, Maximilian}, issn = {1432-0525}, journal = {Acta Informatica}, keywords = {computer networks and communications, information systems, software}, pages = {585--618}, publisher = {Springer Nature}, title = {{Index appearance record with preorders}}, doi = {10.1007/s00236-021-00412-y}, volume = {59}, year = {2022}, }