@article{15169, abstract = {Interpretation of extracellular recordings can be challenging due to the long range of electric field. This challenge can be mitigated by estimating the current source density (CSD). Here we introduce kCSD-python, an open Python package implementing Kernel Current Source Density (kCSD) method and related tools to facilitate CSD analysis of experimental data and the interpretation of results. We show how to counter the limitations imposed by noise and assumptions in the method itself. kCSD-python allows CSD estimation for an arbitrary distribution of electrodes in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in a single cell, and includes a range of diagnostic aids. We demonstrate its features in a Jupyter Notebook tutorial which illustrates a typical analytical workflow and main functionalities useful in validating analysis results.}, author = {Chintaluri, Chaitanya and Bejtka, Marta and Sredniawa, Wladyslaw and Czerwinski, Michal and Dzik, Jakub M. and Jedrzejewska-Szmek, Joanna and Wojciki, Daniel K.}, issn = {1553-7358}, journal = {PLoS Computational Biology}, number = {3}, publisher = {Public Library of Science}, title = {{kCSD-python, reliable current source density estimation with quality control}}, doi = {10.1371/journal.pcbi.1011941}, volume = {20}, year = {2024}, } @inproceedings{17147, abstract = {Efficient utilization of large-scale biobank data is crucial for inferring the genetic basis of disease and predicting health outcomes from the DNA. Yet we lack efficient, accurate methods that scale to data where electronic health records are linked to whole genome sequence information. To address this issue, our paper develops a new algorithmic paradigm based on Approximate Message Passing (AMP), which is specifically tailored for genomic prediction and association testing. Our method yields comparable out-of-sample prediction accuracy to the state of the art on UK Biobank traits, whilst dramatically improving computational complexity, with a 8x-speed up in the run time. In addition, AMP theory provides a joint association testing framework, which outperforms the currently used REGENIE method, in roughly a third of the compute time. This first, truly large-scale application of the AMP framework lays the foundations for a far wider range of statistical analyses for hundreds of millions of variables measured on millions of people.}, author = {Depope, Al and Mondelli, Marco and Robinson, Matthew Richard}, booktitle = {2024 IEEE International Conference on Acoustics, Speech, and Signal Processing}, isbn = {9798350344851}, issn = {1520-6149}, location = {Seoul, Korea}, pages = {13151--13155}, publisher = {IEEE}, title = {{Inference of genetic effects via approximate message passing}}, doi = {10.1109/ICASSP48485.2024.10447198}, year = {2024}, } @article{22179, abstract = {Burr and Erd˝os in 1975 conjectured, and Chv´atal, R¨odl, Szemer´edi and Trotter later proved, that the Ramsey number of any bounded degree graph is linear in the number of vertices. In this paper, we disprove the natural directed analogue of the Burr–Erd˝os conjecture, answering a question of Buci´c, Letzter, and Sudakov. If H is an acyclic digraph, the oriented Ramsey number of H, denoted −→r1(H), is the least N such that every tournament on N vertices contains a copy of H. We show that for any Δ ≥ 2 and any sufficiently large n, there exists an acyclic digraph H with n vertices and maximum degree Δ such that −→r1(H) ≥ nΩ(Δ2/3/ log5/3 Δ). This proves that −→r1(H) is not always linear in the number of vertices for bounded-degree H. On the other hand, we show that −→r1(H) is nearly linear in the number of vertices for typical bounded-degree acyclic digraphs H, and obtain linear or nearly linear bounds for several natural families of bounded-degree acyclic digraphs. For multiple colors, we prove a quasi-polynomial upper bound −→rk(H)= 2(log n)Ok(1) for all bounded-degree acyclic digraphs H on n vertices, where −→rk(H) is the least N such that every k-edge-colored tournament on N vertices contains a monochromatic copy of H. For k ≥ 2 and n ≥ 4, we exhibit an acyclic digraph H with n vertices and maximum degree 3 such that −→rk(H) ≥ nΩ(log n/ log log n), showing that these Ramsey numbers can grow faster than any polynomial in the number of vertices.}, author = {Fox, Jacob and He, Xiaoyu and Wigderson, Yuval}, issn = {1565-8511}, journal = {Israel Journal of Mathematics}, number = {1}, pages = {1--48}, publisher = {Springer Nature}, title = {{Ramsey numbers of sparse digraphs}}, doi = {10.1007/s11856-024-2624-y}, volume = {263}, year = {2024}, } @article{22180, abstract = {Given a graph , its Ramsey number is the minimum so that every two‐coloring of contains a monochromatic copy of . It was conjectured by Conlon, Fox, and Sudakov that if one deletes a single vertex from , the Ramsey number can change by at most a constant factor. We disprove this conjecture, exhibiting an infinite family of graphs such that deleting a single vertex from each decreases the Ramsey number by a super‐constant factor. One consequence of this result is the following. There exists a family of graphs so that in any Ramsey coloring for (i.e., a coloring of a clique on vertices with no monochromatic copy of ), one of the color classes has density .}, author = {Wigderson, Yuval}, issn = {1097-0118}, journal = {Journal of Graph Theory}, number = {3}, pages = {663--675}, publisher = {Wiley}, title = {{Ramsey numbers upon vertex deletion}}, doi = {10.1002/jgt.23093}, volume = {106}, year = {2024}, } @article{22190, abstract = {We consider the set of 𝑚×𝑛 matrices with rational entries having numerator and denominator of size at most H and obtain various upper bounds on the number of such matrices of a given rank, or with a given determinant, or a given characteristic polynomial. We also consider similar questions for matrices whose entries are Egyptian fractions.}, author = {Afifurrahman, Muhammad and Kuperberg, Vivian Zieve and Ostafe, Alina and Shparlinski, Igor E.}, issn = {1435-5337}, journal = {Forum Mathematicum}, number = {4}, publisher = {De Gruyter}, title = {{Statistics of ranks, determinants and characteristic polynomials of rational matrices}}, doi = {10.1515/forum-2024-0114}, volume = {37}, year = {2024}, } @article{22209, abstract = {The curvature of elongated microscopic building blocks plays a crucial role on their self-assembly into orientationally ordered phases. While rod-like molecules form a handful of liquid crystal (LC) phases, curved or banana-shaped molecules show more than fifty phases, with fascinating physical properties, such as chirality or polarity. Despite the fundamental and technological importance of these so-called ‘banana-shaped liquid crystals’, little is known about their microscopic details at the single-molecule level. Curved colloidal liquid crystals—liquid crystals formed by curved colloidal rods—are excellent model systems to optically resolve the structure and dynamics of curved building blocks within these condensed phases. Recent advances in the synthesis of curved rod-like particles have unlocked the potential for studying—at the single-particle level—the intimate relationship between shape and phase symmetry, and even confirmed the stability of elusive LC phases. Further developments in this nascent field promise exciting findings, such as the first observation of the colloidal twist-bend nematic phase or the fabrication of functional materials with curvature-dependent properties. In this Report on Progress, we will highlight recent advances in the synthesis and assembly of curved colloidal liquid crystals and discuss the upcoming challenges and opportunities of this field.}, author = {Fernández-Rico, Carla and Dullens, Roel P A}, issn = {1361-6633}, journal = {Reports on Progress in Physics}, number = {9}, publisher = {IOP Publishing}, title = {{Liquid crystals from curved colloidal rods: Waves, twists and more}}, doi = {10.1088/1361-6633/ad627b}, volume = {87}, year = {2024}, } @article{22219, abstract = {Bicontinuous microstructures are essential to the function of diverse natural and synthetic systems. Their synthesis has been based on two approaches: arrested phase separation or self-assembly of block copolymers. The former is attractive for its chemical simplicity and the latter, for its thermodynamic robustness. Here we introduce elastic microphase separation (EMPS) as an alternative approach to make bicontinuous microstructures. Conceptually, EMPS balances the molecular-scale forces that drive demixing with large-scale elasticity to encode a thermodynamic length scale. This process features a continuous phase transition, reversible without hysteresis. Practically, EMPS is triggered by simply supersaturating an elastomeric matrix with a liquid, resulting in uniform bicontinuous materials with a well-defined microscopic length scale tuned by the matrix stiffness. The versatility of EMPS is further demonstrated by fabricating bicontinuous materials with superior mechanical properties and controlled anisotropy and microstructural gradients. Overall, EMPS presents a robust alternative for the bulk fabrication of homogeneous bicontinuous materials.}, author = {Fernández-Rico, Carla and Schreiber, Sanjay and Oudich, Hamza and Lorenz, Charlotta and Sicher, Alba and Sai, Tianqi and Bauernfeind, Viola and Heyden, Stefanie and Carrara, Pietro and Lorenzis, Laura De and Style, Robert W. and Dufresne, Eric R.}, issn = {1476-4660}, journal = {Nature Materials}, pages = {124--130}, publisher = {Springer Nature}, title = {{Elastic microphase separation produces robust bicontinuous materials}}, doi = {10.1038/s41563-023-01703-0}, volume = {23}, year = {2024}, } @article{15182, abstract = {Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications.}, author = {Kleinhanns, Tobias and Milillo, Francesco and Calcabrini, Mariano and Fiedler, Christine and Horta, Sharona and Balazs, Daniel and Strumolo, Marissa J. and Hasler, Roger and Llorca, Jordi and Tkadletz, Michael and Brutchey, Richard L. and Ibáñez, Maria}, issn = {1614-6840}, journal = {Advanced Energy Materials}, number = {22}, publisher = {Wiley}, title = {{A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se}}, doi = {10.1002/aenm.202400408}, volume = {14}, year = {2024}, } @article{18951, abstract = {We consider local dynamics of the dimer model (perfect matchings) on hypercubic boxes [n] d . These consist of successively switching the dimers along alternating cycles of prescribed (small) lengths. We study the connectivity properties of the dimer configuration space equipped with these transitions. Answering a question of Freire, Klivans, Milet, and Saldanha, we show that in three dimensions any configuration admits an alternating cycle of length at most 6. We further establish that any configuration on [n] d features order n d−2 alternating cycles of length at most 4d−2. We also prove that the dynamics of dimer configurations on the unit hypercube of dimension d is ergodic when switching alternating cycles of length at most 4d−4. Finally, in the planar but non-bipartite case, we show that parallelogram-shaped boxes in the triangular lattice are ergodic for switching alternating cycles of lengths 4 and 6 only, thus improving a result of Kenyon and Rémila, which also uses 8-cycles. None of our proofs make reference to height functions.}, author = {Hartarsky, Ivailo and Lichev, Lyuben and Toninelli, Fabio Lucio}, issn = {2308-5835}, journal = {Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions}, publisher = {EMS Press}, title = {{Local dimer dynamics in higher dimensions}}, doi = {10.4171/aihpd/200}, year = {2024}, } @inproceedings{18917, abstract = {An eight-partition of a finite set of points (respectively, of a continuous mass distribution) in ℝ³ consists of three planes that divide the space into 8 octants, such that each open octant contains at most 1/8 of the points (respectively, of the mass). In 1966, Hadwiger showed that any mass distribution in ℝ³ admits an eight-partition; moreover, one can prescribe the normal direction of one of the three planes. The analogous result for finite point sets follows by a standard limit argument. We prove the following variant of this result: Any mass distribution (or point set) in ℝ³ admits an eight-partition for which the intersection of two of the planes is a line with a prescribed direction. Moreover, we present an efficient algorithm for calculating an eight-partition of a set of n points in ℝ³ (with prescribed normal direction of one of the planes) in time O^*(n^{5/2}).}, author = {Aronov, Boris and Basit, Abdul and Ramesh, Indu and Tasinato, Gianluca and Wagner, Uli}, booktitle = {40th International Symposium on Computational Geometry}, isbn = {9783959773164}, location = {Athens, Greece}, pages = {8:1--8:15}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Eight-partitioning points in 3D, and efficiently too}}, doi = {10.4230/LIPIcs.SoCG.2024.8}, volume = {293}, year = {2024}, } @inproceedings{18557, abstract = {Broadcast and Consensus are most fundamental tasks in distributed computing. These tasks are particularly challenging in dynamic networks where communication across the network links may be unreliable, e.g., due to mobility or failures. Over the last years, researchers have derived several impossibility results and high time complexity lower bounds for these tasks. Specifically for the setting where in each round of communication the adversary is allowed to choose one rooted tree along which the information is disseminated, there is a lower as well as an upper bound that is linear in the number n of nodes for Broadcast and for n ≥ 3 the adversary can guarantee that Consensus never happens. This setting is called the oblivious message adversary for rooted trees. Also note that if the adversary is allowed to choose a graph that does not contain a rooted tree, then it can guarantee that Broadcast and Consensus will never happen. However, such deterministic adversarial models may be overly pessimistic, as many processes in real-world settings are stochastic in nature rather than worst-case. This paper studies Broadcast on stochastic dynamic networks and shows that the situation is very different to the deterministic case. In particular, we show that if information dissemination occurs along random rooted trees and directed Erdős–Rényi graphs, Broadcast completes in O(log n) rounds of communication with high probability. The fundamental insight in our analysis is that key variables are mutually independent. We then study two adversarial models, (a) one with Byzantine nodes and (b) one where an adversary controls the edges. (a) Our techniques without Byzantine nodes are general enough so that they can be extended to Byzantine nodes. (b) In the spirit of smoothed analysis, we introduce the notion of randomized oblivious message adversary, where in each round, an adversary picks k ≤ 2n/3 edges to appear in the communication network, and then a graph (e.g. rooted tree or directed Erdős–Rényi graph) is chosen uniformly at random among the set of all such graphs that include these edges. We show that Broadcast completes in a finite number of rounds, which is, e.g., O(k+log n) rounds in rooted trees. We then extend these results to All-to-All Broadcast, and Consensus, and give lower bounds that show that most of our upper bounds are tight.}, author = {El-Hayek, Antoine and Henzinger, Monika H and Schmid, Stefan}, booktitle = {38th International Symposium on Distributed Computing}, isbn = {9783959773522}, issn = {1868-8969}, location = {Madrid, Spain}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Broadcast and Consensus in stochastic dynamic networks with Byzantine nodes and adversarial edges}}, doi = {10.4230/LIPIcs.DISC.2024.21}, volume = {319}, year = {2024}, } @inproceedings{17146, abstract = {The Upper Bound Theorem for convex polytopes implies that the p-th Betti number of the Čech complex of any set of N points in ℝ^d and any radius satisfies β_p = O(N^m), with m = min{p+1, ⌈d/2⌉}. We construct sets in even and odd dimensions, which prove that this upper bound is asymptotically tight. For example, we describe a set of N = 2(n+1) points in ℝ³ and two radii such that the first Betti number of the Čech complex at one radius is (n+1)² - 1, and the second Betti number of the Čech complex at the other radius is n². In particular, there is an arrangement of n contruent balls in ℝ³ that enclose a quadratic number of voids, which answers a long-standing open question in computational geometry.}, author = {Edelsbrunner, Herbert and Pach, János}, booktitle = {40th International Symposium on Computational Geometry}, isbn = {9783959773164}, issn = {1868-8969}, location = {Athens, Greece}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Maximum Betti numbers of Čech complexes}}, doi = {10.4230/LIPIcs.SoCG.2024.53}, volume = {293}, year = {2024}, } @inproceedings{17426, abstract = {The robustness of neural networks against input perturbations with bounded magnitude represents a serious concern in the deployment of deep learning models in safety-critical systems. Recently, the scientific community has focused on enhancing certifiable robustness guarantees by crafting 1-Lipschitz neural networks that leverage Lipschitz bounded dense and convolutional layers. Although different methods have been proposed in the literature to achieve this goal, understanding the performance of such methods is not straightforward, since different metrics can be relevant (e.g., training time, memory usage, accuracy, certifiable robustness) for different applications. For this reason, this work provides a thorough theoretical and empirical comparison between methods by evaluating them in terms of memory usage, speed, and certifiable robust accuracy. The paper also provides some guidelines and recommendations to support the user in selecting the methods that work best depending on the available resources. We provide code at https://github.com/berndprach/1LipschitzLayersCompared.}, author = {Prach, Bernd and Brau, Fabio and Buttazzo, Giorgio and Lampert, Christoph}, booktitle = {Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition}, location = {Seattle, WA, United States}, pages = {24574--24583}, publisher = {Computer Vision Foundation}, title = {{1-Lipschitz layers compared: Memory, speed, and certifiable robustness}}, doi = {10.1109/CVPR52733.2024.02320}, year = {2024}, } @unpublished{18874, abstract = {Despite extensive research since the community learned about adversarial examples 10 years ago, we still do not know how to train high-accuracy classifiers that are guaranteed to be robust to small perturbations of their inputs. Previous works often argued that this might be because no classifier exists that is robust and accurate at the same time. However, in computer vision this assumption does not match reality where humans are usually accurate and robust on most tasks of interest. We offer an alternative explanation and show that in certain settings robust generalization is only possible with unrealistically large amounts of data. More precisely we find a setting where a robust classifier exists, it is easy to learn an accurate classifier, yet it requires an exponential amount of data to learn a robust classifier. Based on this theoretical result, we explore how well robust classifiers generalize on datasets such as CIFAR-10. We come to the conclusion that on this datasets, the limitation of current robust models also lies in the generalization, and that they require a lot of data to do well on the test set. We also show that the problem is not in the expressiveness or generalization capabilities of current architectures, and that there are low magnitude features in the data which are useful for non-robust generalization but are not available for robust classifiers.}, author = {Prach, Bernd and Lampert, Christoph}, booktitle = {arXiv}, title = {{Intriguing properties of robust classification}}, doi = {10.48550/arXiv.2412.04245}, year = {2024}, } @inproceedings{17634, abstract = {System behaviors are traditionally evaluated through binary classifications of correctness, which do not suffice for properties involving quantitative aspects of systems and executions. Quantitative automata offer a more nuanced approach, mapping each execution to a real number by incorporating weighted transitions and value functions generalizing acceptance conditions. In this paper, we introduce QuAK, the first tool designed to automate the analysis of quantitative automata. QuAK currently supports a variety of quantitative automaton types, including Inf, Sup, LimInf, LimSup, LimInfAvg, and LimSupAvg automata, and implements decision procedures for problems such as emptiness, universality, inclusion, equivalence, as well as for checking whether an automaton is safe, live, or constant. Additionally, QuAK is able to compute extremal values when possible, construct safety-liveness decompositions, and monitor system behaviors. We demonstrate the effectiveness of QuAK through experiments focusing on the inclusion, constant-function check, and monitoring problems.}, author = {Chalupa, Marek and Henzinger, Thomas A and Mazzocchi, Nicolas Adrien and Sarac, Naci E}, booktitle = {12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation}, isbn = {9783031753862}, issn = {1611-3349}, location = {Crete, Greece}, pages = {3--20}, publisher = {Springer Nature}, title = {{QuAK: Quantitative Automata Kit}}, doi = {10.1007/978-3-031-75387-9_1}, volume = {15222}, year = {2024}, } @inproceedings{18121, abstract = {It is known that sparsity can improve interpretability for deep neural networks. However, existing methods in the area either require networks that are pre-trained with sparsity constraints, or impose sparsity after the fact, altering the network’s general behavior. In this paper, we demonstrate, for the first time, that sparsity can instead be incorporated into the interpretation process itself, as a sample-specific preprocessing step. Unlike previous work, this approach, which we call SPADE, does not place constraints on the trained model and does not affect its behavior during inference on the sample. Given a trained model and a target sample, SPADE uses sample-targeted pruning to provide a "trace" of the network’s execution on the sample, reducing the network to the most important connections prior to computing an interpretation. We demonstrate that preprocessing with SPADE significantly increases the accuracy of image saliency maps across several interpretability methods. Additionally, SPADE improves the usefulness of neuron visualizations, aiding humans in reasoning about network behavior. Our code is available at https://github.com/IST-DASLab/SPADE.}, author = {Moakhar, Arshia Soltani and Iofinova, Eugenia B and Frantar, Elias and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 41st International Conference on Machine Learning}, issn = {2640-3498}, location = {Vienna, Austria}, pages = {45955--45987}, publisher = {ML Research Press}, title = {{SPADE: Sparsity-guided debugging for deep neural networks}}, volume = {235}, year = {2024}, } @unpublished{18689, abstract = {Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.}, author = {Gallei, Michelle C and Truckenbrodt, Sven M and Kreuzinger, Caroline and Inumella, Syamala and Vistunou, Vitali and Sommer, Christoph M and Tavakoli, Mojtaba and Agudelo Duenas, Nathalie and Vorlaufer, Jakob and Jahr, Wiebke and Randuch, Marek and Johnson, Alexander J and Benková, Eva and Friml, Jiří and Danzl, Johann G}, booktitle = {bioRxiv}, title = {{Super-resolution expansion microscopy in plant roots}}, doi = {10.1101/2024.02.21.581330}, year = {2024}, } @unpublished{18688, abstract = {The human brain has remarkable computational power. It generates sophisticated behavioral sequences, stores engrams over an individual’s lifetime, and produces higher cognitive functions up to the level of consciousness. However, so little of our neuroscience knowledge covers the human brain, and it remains unknown whether this organ is truly unique, or is a scaled version of the extensively studied rodent brain. To address this fundamental question, we determined the cellular, synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using multicellular patch clamp-recording. This circuit is the largest autoassociative network in the brain, and plays a key role in memory and higher-order computations such as pattern separation and pattern completion. We demonstrate that human hippocampal CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks. Connectivity sparsifies from rodents to humans, providing a circuit architecture that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses showed both distinct species-specific and circuit-dependent properties, with high reliability, unique amplitude precision, and long integration times. We also identify differential scaling rules between hippocampal pathways from rodents to humans, with a moderate increase in the convergence of CA3 inputs per cell, but a marked increase in human mossy fiber innervation. Anatomically guided full-scale modeling suggests that the human brain’s sparse connectivity, expanded neuronal number, and reliable synaptic signaling combine to enhance the associative memory storage capacity of CA3. Together, our results reveal unique rules of connectivity and synaptic signaling in the human hippocampus, demonstrating the absolute necessity of human brain research and beginning to unravel the remarkable performance of our autoassociative memory circuits.}, author = {Watson, Jake F. and Vargas-Barroso, Victor and Morse-Mora, Rebecca J. and Navas-Olive, Andrea and Tavakoli, Mojtaba and Danzl, Johann G and Tomschik, Matthias and Rössler, Karl and Jonas, Peter M}, booktitle = {bioRxiv}, title = {{Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory}}, doi = {10.1101/2024.05.02.592169}, year = {2024}, } @unpublished{18677, abstract = {The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labeling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner.}, author = {Tavakoli, Mojtaba and Lyudchik, Julia and Januszewski, Michał and Vistunou, Vitali and Agudelo Duenas, Nathalie and Vorlaufer, Jakob and Sommer, Christoph M and Kreuzinger, Caroline and Oliveira, Bárbara and Cenameri, Alban and Novarino, Gaia and Jain, Viren and Danzl, Johann G}, booktitle = {bioRxiv}, title = {{Light-microscopy based dense connectomic reconstruction of mammalian brain tissue}}, doi = {10.1101/2024.03.01.582884}, year = {2024}, } @article{14793, abstract = {Superconductor/semiconductor hybrid devices have attracted increasing interest in the past years. Superconducting electronics aims to complement semiconductor technology, while hybrid architectures are at the forefront of new ideas such as topological superconductivity and protected qubits. In this work, we engineer the induced superconductivity in two-dimensional germanium hole gas by varying the distance between the quantum well and the aluminum. We demonstrate a hard superconducting gap and realize an electrically and flux tunable superconducting diode using a superconducting quantum interference device (SQUID). This allows to tune the current phase relation (CPR), to a regime where single Cooper pair tunneling is suppressed, creating a sin(2y) CPR. Shapiro experiments complement this interpretation and the microwave drive allows to create a diode with ≈ 100% efficiency. The reported results open up the path towards integration of spin qubit devices, microwave resonators and (protected) superconducting qubits on the same silicon technology compatible platform.}, author = {Valentini, Marco and Sagi, Oliver and Baghumyan, Levon and de Gijsel, Thijs and Jung, Jason and Calcaterra, Stefano and Ballabio, Andrea and Aguilera Servin, Juan L and Aggarwal, Kushagra and Janik, Marian and Adletzberger, Thomas and Seoane Souto, Rubén and Leijnse, Martin and Danon, Jeroen and Schrade, Constantin and Bakkers, Erik and Chrastina, Daniel and Isella, Giovanni and Katsaros, Georgios}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium}}, doi = {10.1038/s41467-023-44114-0}, volume = {15}, year = {2024}, }