@misc{15027, abstract = {This data repository underpins the paper, published in PNAS (doi pending) and bioarxiv (doi: https://doi.org/10.1101/2023.07.05.547777).}, author = {Curk, Samo}, publisher = {Figshare}, title = {{aggregation_data}}, year = {2023}, } @misc{23012, abstract = {The onset of turbulence in pipe flow has defied detailed understanding ever since Reynolds' first observations revealed the spatially-heterogeneous nature of the transition. While recent theoretical studies and experiments in simpler, shear-driven flows suggest that the onset of turbulence is a directed percolation non-equilibrium phase transition, whether these findings are generic and apply also to open or pressure-driven flows is unknown. In pipe flow, the extremely long time scales near the transition make direct observations of critical behavior virtually impossible. Here, we circumvent these limitations by experimentally characterizing all pairwise interactions between localized patches of turbulence ("puffs"), and using these interactions as input to renormalization group and computer simulations of minimal models that extrapolate to long length and time scales. We show that the universality class of the transition is directed percolation, from which emerges a jammed phase of puffs above the critical point. The stronger interactions in the jamming regime enable us to explicitly measure the turbulent fraction and confirm model predictions. Our work shows that directed percolation scaling applies beyond simple closed shear flows, and underscores how statistical mechanics can lead to profound, quantitative and predictive insights on turbulent flows and their phases.}, author = {Lemoult, Grégoire}, publisher = {Zenodo}, title = {{Directed percolation and puff jamming near the transition to pipe turbulence}}, doi = {10.5281/zenodo.10308791}, year = {2023}, } @misc{22961, abstract = {## Rationale: Differentiation trajectories to generate specialized cellular features rely on sets of transcription factors (TFs) whose temporal dynamics and coexistence underlie morphological and neurochemical divergence among neurons and neuroendocrine cells. Even though transcriptional programs were extensively studied in the developing nervous system, the coupling of TFs to effector gene networks that time and shape the morphogenesis of these polarized cells is less known. ## Results: Here, we make the curious observation that evolutionarily conserved Onecut3, a subordinate in the Onecut TF family known to control fate selection in progenitors, is instead expressed in fate-restricted neuroblasts in the vertebrate hypothalamus. In particular, a pool of Ascl1-containing progenitors in the midgestational mouse hypothalamus gives rise to both GABA and glutamate neurons destined to the periventricular and lateral hypothalamus, respectively, which uniformly upregulate Onecut3 only when exiting the proliferative zone of the 3rd ventricle. By combining single-cell RNA-seq, genetic Onecut3 reporters, gain-of-function models in vitro, and loss-of-function analysis in early-developing mice and C. elegans, we identify that Onecut3 instructs neuronal differentiation and maturation, through a Navigator-2 pathway to modulate neuritogenesis and leading process motility. ## Conclusion: Onecut3 executes an unexpected function by inducing cytoskeletal modifications of key importance for neuronal maturation and network integration during the morphogenesis of many neuronal phenotypes in the vertebrate hypothalamus.}, author = {Zupancic, Maja and Keimpema, Erik and Tretiakov, Evgenii and Bhandari, Pradeep and Eder, Stephanie and Lev, Itamar and Härtig, Wolfgang and Zimmer, Manuel and Clotman, Frederic and Harkany, Tibor}, publisher = {Repository}, title = {{Glutamate and GABA neurons share cascading Onecut3/NAV2-driven differentiation trajectories in the developing hypothalamus}}, doi = {10.6084/m9.figshare.22680433}, year = {2023}, } @article{14514, abstract = {The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous bouncing or steady-state floating. The effect embodies an unexplored interplay between thermodynamics, elasticity, and lubrication: despite being observed, its basic theoretical description remains a challenge. Here, we provide a theory of elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to the hot surface. By contrast, we discover an elasticity-dominated regime where the heavier the solid, the higher it floats. This geometry-governed behavior is reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this elastic regime is characterized by Hertzian behavior of the solid’s underbelly and derive how the float height scales with materials parameters. Introducing a dimensionless elastic Leidenfrost number, we capture the crossover between rigid and Hertzian behavior. Our results provide theoretical underpinning for recent experiments, and point to the design of novel soft machines.}, author = {Binysh, Jack and Chakraborty, Indrajit and Chubynsky, Mykyta V. and Diaz Melian, Vicente L and Waitukaitis, Scott R and Sprittles, James E. and Souslov, Anton}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {16}, publisher = {American Physical Society}, title = {{Modeling Leidenfrost levitation of soft elastic solids}}, doi = {10.1103/PhysRevLett.131.168201}, volume = {131}, year = {2023}, } @misc{14919, abstract = {GLACIER METEOROLOGICAL DATA SWISS ALPS -2022 }, author = {Shaw, Thomas and Buri, Pascal and McCarthy, Michael and Miles, Evan and Pellicciotti, Francesca}, publisher = {Zenodo}, title = {{Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer}}, doi = {10.5281/ZENODO.8277285}, year = {2023}, } @misc{23030, abstract = {%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% GLACIER METEOROLOGICAL DATA SWISS ALPS -2022 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Data gathered and structured by Thomas Shaw (WSL, Switzerland (until Oct 2022)). On and off-glacier meteorological data were gathered and analysed as part of a Marie-Curie project 'TEMPEST' (tempestglacier.com). The dataset consists of hourly low-cost AWS (Davis Vantage Pro2) and simple temperature ('T-')logger (Onset TidBitv2) sensor records on three glaciers in the Swiss Alps (Canton Valais). The glaciers are: Haut Glacier d'Arolla (45.967°N, 7.526°E) Glacier d'Otemma (45.956°N, 7.454°E) Glacier du Corbassière (45.975°N, 7.303°E) Data are provided in individual Excel files per glacier that contain all hourly data for the sub-period of comparison (11 August-18 September, 2022). Data are quality controlled and checked for obvious errors. Any uncertain values are set to NaN. Air temperature data at 'T-Logger' stations were corrected for heating errors using the comparison of measurements in artificially (AWS) and naturally ventilated (T-Logger) radiation shields on Arolla and Corbassiere glaciers. A multiple linear regression model was applied to estimate these differences at all T-Loggers on all glaciers as a function of incoming shortwave radiation (MeteoSwiss station-derived) and wind speed (measured at AWS). Each Excel file contains a 'META' tab for simple metadata related to station locations (latitude 'LAT' (°), longitude 'LON' (°), elevation 'ELE' (m a.s.l.) and flowpath length 'FPL' (m)) and a 'DATA' tab for the hourly data. Suffixes to the station names in each column provide the variable measured at that site: 'TA' - 2m air temperature (°C) 'TA_Hi' - Maximum air temperature for timestep (°C) 'TA_Lo' - Minimum air temperature for timestep (°C) 'RH' - 2m relative humiditiy (%) 'FF' - Wind speed (m s^-1) 'FF_Hi' - Maximum wind speed for timestep (m s^-1) 'FF_Lo' - Minimum wind speed for timestep (m s^-1) 'DIR' - Wind direction (°) 'DEW' - Dewpoint temperature (°C) 'PRESS' - Air pressure (mbar) 'CHILL' - Calculated wind chill temperature (°C) 'Heat_idx' - Calculated heat index (°C) 'THSW' - A calculated index that uses humidity and temperature like for the Heat Index, but also includes the heating effects of sunshine and the cooling effects of wind (like Wind Chill) to calculate an apparent temperature of what it "feels" like out in the shade Wind speeds and direction measured at off-glacier sites 'OG' are for the lower off-glacier station ('OG_Low'). }, author = {Shaw, Thomas E. and Buri, Pascal and McCarthy, Michael and Miles, Evan S. and Pelliciotti, Francesca}, publisher = {Zenodo}, title = {{Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer}}, doi = {10.5281/zenodo.8277284}, year = {2023}, } @misc{23031, abstract = {There are 4 tar.xz files with the result of the model for the paper: A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen, Svalbard. These archives can be unzipped on Linux using the tar command, or on other systems using a specific software. FrontPositions includes data files with the coordinates of the nodes of the front positons. CalvingStats includes txt files with some characteristics of the calving events. HydrologyOutput includes csv files with the main results of the hydrological model. ModelOutput include output and visualization files of the model results. The .vtu and .pvtu files are best viewed in the software Paraview.}, author = {Muñoz Hermosilla, José M}, publisher = {Zenodo}, title = {{A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen}}, doi = {10.5281/zenodo.8005257}, year = {2023}, } @misc{18634, abstract = {There are 4 tar.xz files with the result of the model for the paper: A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen, Svalbard. }, author = {Muñoz Hermosilla, José M}, publisher = {Zenodo}, title = {{A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen}}, doi = {10.5281/ZENODO.8005257}, year = {2023}, } @misc{23032, abstract = {Datasets in .csv or .xlsx format sorted into folders by figures. In some cases additional files with roi/well-to-sample mapping were provided. For more details contact authors.}, author = {Sarkisyan, Karen}, publisher = {Figshare}, title = {{A hybrid pathway for self-sustained luminescence - Raw data}}, doi = {10.6084/m9.figshare.24772872}, year = {2023}, } @inproceedings{14862, author = {Rella, Simon and Kulikova, Y and Minnegalieva, Aygul and Kondrashov, Fyodor}, booktitle = {European Journal of Public Health}, issn = {1464-360X}, keywords = {Public Health, Environmental and Occupational Health}, number = {Supplement_2}, publisher = {Oxford University Press}, title = {{Complex vaccination strategies prevent the emergence of vaccine resistance}}, doi = {10.1093/eurpub/ckad160.597}, volume = {33}, year = {2023}, } @unpublished{13312, 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 \left( 2 \varphi \right)$ CPR. Shapiro experiments complement this interpretation and the microwave drive allows to create a diode with $ \approx 100 \%$ efficiency. The reported results open up the path towards monolithic integration of spin qubit devices, microwave resonators and (protected) superconducting qubits on a silicon technology compatible platform.}, author = {Valentini, Marco and Sagi, Oliver and Baghumyan, Levon and Gijsel, Thijs de and Jung, Jason and Calcaterra, Stefano and Ballabio, Andrea and Servin, Juan Aguilera and Aggarwal, Kushagra and Janik, Marian and Adletzberger, Thomas and Souto, Rubén Seoane and Leijnse, Martin and Danon, Jeroen and Schrade, Constantin and Bakkers, Erik and Chrastina, Daniel and Isella, Giovanni and Katsaros, Georgios}, booktitle = {arXiv}, keywords = {Mesoscale and Nanoscale Physics}, title = {{Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas}}, doi = {10.48550/arXiv.2306.07109}, year = {2023}, } @misc{23036, author = {Valentini, Marco}, publisher = {Zenodo}, title = {{Data repository for 'Parity-conserving Cooper-pair transport and ideal superconducting diode in planar Germanium'}}, doi = {10.5281/zenodo.10119345}, year = {2023}, } @inproceedings{17378, abstract = {Generative Pre-trained Transformer models, known as GPT or OPT, set themselves apart through breakthrough performance across complex language modelling tasks, but also by their extremely high computational and storage costs. Specifically, due to their massive size, even inference for large, highly-accurate GPT models may require multiple performant GPUs, which limits the usability of such models. While there is emerging work on relieving this pressure via model compression, the applicability and performance of existing compression techniques is limited by the scale and complexity of GPT models. In this paper, we address this challenge, and propose OPTQ, a new one-shot weight quantization method based on approximate second-order information, that is both highly-accurate and highly-efficient. Specifically, OPTQ can quantize GPT models with 175 billion parameters in approximately four GPU hours, reducing the bitwidth down to 3 or 4 bits per weight, with negligible accuracy degradation relative to the uncompressed baseline. Our method more than doubles the compression gains relative to previously-proposed one-shot quantization methods, preserving accuracy, allowing us for the first time to execute an 175 billion-parameter model inside a single GPU for generative inference. Moreover, we also show that our method can still provide reasonable accuracy in the extreme quantization regime, in which weights are quantized to 2-bit or even ternary quantization levels. We show experimentally that these improvements can be leveraged for end-to-end inference speedups over FP16, of around 3.25x when using high-end GPUs (NVIDIA A100) and 4.5x when using more cost-effective ones (NVIDIA A6000). The implementation is available at https://github.com/IST-DASLab/gptq.}, author = {Frantar, Elias and Ashkboos, Saleh and Hoefler, Torsten and Alistarh, Dan-Adrian}, booktitle = {11th International Conference on Learning Representations }, location = {Kigali, Rwanda}, publisher = {International Conference on Learning Representations}, title = {{OPTQ: Accurate post-training quantization for generative pre-trained transformers}}, year = {2023}, } @inproceedings{14458, abstract = {We show for the first time that large-scale generative pretrained transformer (GPT) family models can be pruned to at least 50% sparsity in one-shot, without any retraining, at minimal loss of accuracy. This is achieved via a new pruning method called SparseGPT, specifically designed to work efficiently and accurately on massive GPT-family models. We can execute SparseGPT on the largest available open-source models, OPT-175B and BLOOM-176B, in under 4.5 hours, and can reach 60% unstructured sparsity with negligible increase in perplexity: remarkably, more than 100 billion weights from these models can be ignored at inference time. SparseGPT generalizes to semi-structured (2:4 and 4:8) patterns, and is compatible with weight quantization approaches. The code is available at: https://github.com/IST-DASLab/sparsegpt.}, author = {Frantar, Elias and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, issn = {2640-3498}, location = {Honolulu, Hawaii, HI, United States}, pages = {10323--10337}, publisher = {ML Research Press}, title = {{SparseGPT: Massive language models can be accurately pruned in one-shot}}, volume = {202}, year = {2023}, } @inproceedings{14461, abstract = {Communication-reduction techniques are a popular way to improve scalability in data-parallel training of deep neural networks (DNNs). The recent emergence of large language models such as GPT has created the need for new approaches to exploit data-parallelism. Among these, fully-sharded data parallel (FSDP) training is highly popular, yet it still encounters scalability bottlenecks. One reason is that applying compression techniques to FSDP is challenging: as the vast majority of the communication involves the model’s weights, direct compression alters convergence and leads to accuracy loss. We present QSDP, a variant of FSDP which supports both gradient and weight quantization with theoretical guarantees, is simple to implement and has essentially no overheads. To derive QSDP we prove that a natural modification of SGD achieves convergence even when we only maintain quantized weights, and thus the domain over which we train consists of quantized points and is, therefore, highly non-convex. We validate this approach by training GPT-family models with up to 1.3 billion parameters on a multi-node cluster. Experiments show that QSDP preserves model accuracy, while completely removing the communication bottlenecks of FSDP, providing end-to-end speedups of up to 2.2x.}, author = {Markov, Ilia and Vladu, Adrian and Guo, Qi and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, issn = {2640-3498}, location = {Honolulu, Hawaii, HI, United States}, pages = {24020--24044}, publisher = {ML Research Press}, title = {{Quantized distributed training of large models with convergence guarantees}}, volume = {202}, year = {2023}, } @article{12334, abstract = {Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.}, author = {Fäßler, Florian and Javoor, Manjunath and Datler, Julia and Döring, Hermann and Hofer, Florian and Dimchev, Georgi A and Hodirnau, Victor-Valentin and Faix, Jan and Rottner, Klemens and Schur, Florian KM}, issn = {2375-2548}, journal = {Science Advances}, keywords = {Multidisciplinary}, number = {3}, publisher = {American Association for the Advancement of Science}, title = {{ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning}}, doi = {10.1126/sciadv.add6495}, volume = {9}, year = {2023}, } @unpublished{17351, abstract = {Contractive coupling rates have been recently introduced by Conforti as a tool to establish convex Sobolev inequalities (including modified log-Sobolev and Poincar\'{e} inequality) for some classes of Markov chains. In this work, we show how contractive coupling rates can also be used to prove stronger inequalities, in the form of curvature lower bounds for Markov chains and geodesic convexity of entropic functionals. We illustrate this in several examples discussed by Conforti, where in particular, after appropriately choosing a parameter function, we establish positive curvature in the entropic and (discrete) Bakry--\'{E}mery sense. In addition, we recall and give straightforward generalizations of some notions of coarse Ricci curvature, and we discuss some of their properties and relations with the concepts of couplings and coupling rates: as an application, we show exponential contraction of the $p$-Wasserstein distance for the heat flow in the aforementioned examples.}, author = {Pedrotti, Francesco}, booktitle = {arXiv}, title = {{Contractive coupling rates and curvature lower bounds for Markov chains}}, doi = {10.48550/arXiv.2308.00516}, year = {2023}, } @article{13267, abstract = {Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.}, author = {Velicky, Philipp and Miguel Villalba, Eder and Michalska, Julia M and Lyudchik, Julia and Wei, Donglai and Lin, Zudi and Watson, Jake and Troidl, Jakob and Beyer, Johanna and Ben Simon, Yoav and Sommer, Christoph M and Jahr, Wiebke and Cenameri, Alban and Broichhagen, Johannes and Grant, Seth G.N. and Jonas, Peter M and Novarino, Gaia and Pfister, Hanspeter and Bickel, Bernd and Danzl, Johann G}, issn = {1548-7105}, journal = {Nature Methods}, pages = {1256--1265}, publisher = {Springer Nature}, title = {{Dense 4D nanoscale reconstruction of living brain tissue}}, doi = {10.1038/s41592-023-01936-6}, volume = {20}, year = {2023}, } @article{13227, abstract = {Currently available quantum processors are dominated by noise, which severely limits their applicability and motivates the search for new physical qubit encodings. In this work, we introduce the inductively shunted transmon, a weakly flux-tunable superconducting qubit that offers charge offset protection for all levels and a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting in a constant coherence over a full flux quantum. The parabolic confinement provided by the inductive shunt as well as the linearity of the geometric superinductor facilitates a high-power readout that resolves quantum jumps with a fidelity and QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover, the device reveals quantum tunneling physics between the two prepared fluxon ground states with a measured average decay time of up to 3.5 h. In the future, fast time-domain control of the transition matrix elements could offer a new path forward to also achieve full qubit control in the decay-protected fluxon basis.}, author = {Hassani, Farid and Peruzzo, Matilda and Kapoor, Lucky and Trioni, Andrea and Zemlicka, Martin and Fink, Johannes M}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours}}, doi = {10.1038/s41467-023-39656-2}, volume = {14}, year = {2023}, } @unpublished{17174, abstract = {We prove that a class of weakly perturbed Hamiltonians of the form $H_λ= H_0 + λW$, with $W$ being a Wigner matrix, exhibits prethermalization. That is, the time evolution generated by $H_λ$ relaxes to its ultimate thermal state via an intermediate prethermal state with a lifetime of order $λ^{-2}$. Moreover, we obtain a general relaxation formula, expressing the perturbed dynamics via the unperturbed dynamics and the ultimate thermal state. The proof relies on a two-resolvent law for the deformed Wigner matrix $H_λ$.}, author = {Erdös, László and Henheik, Sven Joscha and Reker, Jana and Riabov, Volodymyr}, booktitle = {arXiv}, title = {{Prethermalization for deformed Wigner Matrices}}, doi = {10.48550/arXiv.2310.06677}, year = {2023}, }