@misc{19800, abstract = {This archive contains all the code and data necessary to reproduce the results presented in the "Mapping the attractor landscape of Boolean networks" paper.}, author = {trinh, Van Giang and Park, Kyu Hyong and Pastva, Samuel and Rozum, Jordan}, publisher = {Zenodo}, title = {{Mapping the attractor landscape of Boolean networks}}, doi = {10.5281/ZENODO.13854759}, year = {2024}, } @misc{19884, abstract = {This is Marlin, a Mixed Auto-Regressive Linear kernel (and the name of one of the planet's fastest fish), an extremely optimized FP16xINT4 matmul kernel aimed at LLM inference that can deliver close to ideal (4x) speedups up to batchsizes of 16-32 tokens (in contrast to the 1-2 tokens of prior work with comparable speedup). Additionally, it includes Sparse-Marlin, an extension of the MARLIN kernels adding support to 2:4 weight sparsity, achieving 5.3x speedups on NVIDIA GPUs (Ampere/Ada).}, author = {Frantar, Elias and Castro, Roberto and Chen, Jiale and Hoefler, Torsten and Alistarh, Dan-Adrian}, publisher = {Zenodo}, title = {{MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models}}, doi = {10.5281/ZENODO.14213091}, year = {2024}, } @article{20039, abstract = {This Comment presents a high-level protocol for data harmonization within large cohorts, in which it postulates four main steps including (1) expert review, (2) pre-statistical harmonization, (3) statistical harmonization, and (4) validation.}, author = {Neidhart, Maja and Kjelkenes, Rikka and Jansone, Karina and Rehák Bučková, Barbora and Holz, Nathalie and Nees, Frauke and Walter, Henrik and Schumann, Gunter and Rapp, Michael A. and Banaschewski, Tobias and Schwarz, Emanuel and Marquand, Andre and Ogoh, George and Stahl, Bernd and Young, Allan H. and Desrivières, Sylvane and Clinton, Nicholas and Thompson, Paul and Schwalber, Ameli and Liu, Jingyu and Calhoun, Vince and Chang, Xiao and Xia, Yunman and Gong, Yanting and Jia, Tianye and Renner, Paul and Hese, Sören and Giner, Arantxa and Sanchez, Mavi and Alvarez, Elena and Spanlang, Bernhard and Pearmund, Charlie and Athanasiadis, Anastasios Polykarpos and Otten, Lisa and Pitel, Séverine and Petkoski, Spase and Jirsa, Viktor and Schmitt, Karen and Wilbertz, Johannes and Patraskaki, Myrto and Sommer, Peter and Heilmann-Heimbach, Stefanie and Mathey, Carina M. and Miller, Abigail and Claus, Isabelle and Nöthen, Markus M. and Hoffmann, Per and Forstner, Andreas J. and Pastor, Alvaro and Gallego, Jaime and Orosa, Francisco Eiroa and Viapiana, Guillem Feixas and Slater, Mel and Marr, Lena and Novarino, Gaia and Böttger, Sarah Jane and Tschorn, Mira and Rapp, Michael and Ask, Helga and Fernandez, Sara and Van Der Meer, Dennis and Westlye, Lars T. and Andreassen, Ole A. and Aden, Rieke and Seefried, Beke and Siehl, Sebastian and Nees, Frauke and Stringaris, Argyris and Tost, Heike and Meyer-Lindenberg, Andreas and Christmann, Nina and Banks, Jamie and Schepanski, Kerstin and Schütz, Tatjana and Taron, Ulrike Helene and Eils, Roland and Roy, Jean Charles and Lett, Tristram A. and Kebir, Hedi and Polemiti, Elli and Hitchen, Esther and Jentsch, Marcel and Serin, Emin and Bernas, Antoine and Vaidya, Nilakshi and Twardziok, Sven and Ralser, Markus and Heinz, Andreas}, issn = {2731-6076}, journal = {Nature Mental Health}, number = {10}, pages = {1134--1137}, publisher = {Springer Nature}, title = {{A protocol for data harmonization in large cohorts}}, doi = {10.1038/s44220-024-00315-0}, volume = {2}, year = {2024}, } @misc{20057, abstract = {In article number 2305128, Qing Sun, Shang Wang, Yanhong Tian, Andreu Cabot, and co-workers report an investigation of the energy-storage mechanism of a layered Bi2Te3-based cathode for aqueous zinc-ion batteries (ZIBs). They demonstrate that the zinc ion is not inserted into the cathode as previously assumed; in contrast, proton charge-storage dominates the process. They also demonstrate the great application prospects of aqueous ZIBs in flexible electronics via jet printing technology.}, author = {Zeng, Guifang and Sun, Qing and Horta, Sharona and Wang, Shang and Lu, Xuan and Zhang, Chao Yue and Li, Jing and Li, Junshan and Ci, Lijie and Tian, Yanhong and Ibáñez, Maria and Cabot, Andreu}, booktitle = {Advanced Materials}, issn = {1521-4095}, number = {1}, publisher = {Wiley}, title = {{A layered Bi2Te3@PPy cathode for aqueous Zinc‐Ion batteries: Mechanism and application in printed flexible batteries}}, doi = {10.1002/adma.202470004}, volume = {36}, year = {2024}, } @unpublished{20071, abstract = {Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take "infinite values".}, author = {Dvorak, Martin and Kolmogorov, Vladimir}, booktitle = {arXiv}, keywords = {Farkas lemma, linear programming, extended reals, calculus of inductive constructions}, title = {{Duality theory in linear optimization and its extensions -- formally verified}}, doi = {10.48550/arXiv.2409.08119}, year = {2024}, } @misc{20121, abstract = {PyDaddy is an open source package which is a key contribution of the manuscript Nabeel et al, arXiv:2205.02645. The basic scientific premise for this package is to discover the nature of stochasticity in ecological time series datasets. It is well known that the stochasticity can affect the dynamics of ecological systems in counter-intuitive ways. Without understanding the equations (typically, in the form of stochastic differential equations or SDEs, in short) that govern the dynamics of populations or ecosystems, it's challenging to determine the impact of randomness on real datasets. In this manuscript and accompanying package, we introduce a methodology for discovering equations (SDEs) that transforms time series data of state variables into stochastic differential equations. This approach merges traditional stochastic calculus with modern equation-discovery techniques. We showcase the generality of our method through various applications and discuss its limitations and potential pitfalls, offering diagnostic measures to address these challenges.}, author = {Nabeel, Arshed and Karichannavar, Ashwin and Palathingal, Shuaib and Jhawar, Jitesh and Brückner, David and Danny Raj, Masila and Guttal, Vishwesha}, publisher = {Zenodo}, title = {{PyDaddy: A Python Package for Discovering SDEs from Time Series Data}}, doi = {10.5281/ZENODO.7137151}, year = {2024}, } @article{20156, abstract = {Integrative analyses that incorporate different levels of ‘-omics’ data represent a powerful tool for deciphering the biological mechanisms that underlie environmental influences on mental health and disease. This Comment highlights various aspects of such multi-omics approaches, using the example of the EU-funded environMENTAL project.}, author = {Desrivières, Sylvane and Miller, Abigail and Mathey, Carina M. and Yu, Xinyang and Chen, Di and Agunbiade, Kofoworola and Heilmann-Heimbach, Stefanie and Forstner, Andreas J. and Schumann, Gunter and Hoffmann, Per and Nöthen, Markus M. and Ogoh, George and Stahl, Bernd and Young, Allan H. and Clinton, Nicholas and Thompson, Paul and Schwalber, Ameli and Liu, Jingyu and Calhoun, Vince and Chang, Xiao and Xia, Yunman and Gong, Yanting and Jia, Tianye and Renner, Paul and Hese, Sören and Giner, Arantxa and Sanchez, Mavi and Alvarez, Elena and Spanlang, Bernhard and Pearmund, Charlie and Athanasiadis, Anastasios Polykarpos and Otten, Lisa and Pitel, Séverine and Petkoski, Spase and Jirsa, Viktor and Schmitt, Karen and Wilbertz, Johannes and Patraskaki, Myrto and Sommer, Peter and Claus, Isabelle and Pastor, Alvaro and Gallego, Jaime and Orosa, Francisco Eiroa and Viapiana, Guillem Feixas and Slater, Mel and Marr, Lena and Novarino, Gaia and Marquand, Andre and Böttger, Sarah Jane and Tschorn, Mira and Rapp, Michael and Ask, Helga and Kjelkenes, Rikka and Fernandez, Sara and Van Der Meer, Dennis and Westlye, Lars T. and Andreassen, Ole A. and Aden, Rieke and Seefried, Beke and Siehl, Sebastian and Nees, Frauke and Neidhart, Maja and Stringaris, Argyris and Schwarz, Emanuel and Holz, Nathalie and Tost, Heike and Meyer-Lindenberg, Andreas and Christmann, Nina and Jansone, Karina and Banaschewski, Tobias and Banks, Jamie and Schepanski, Kerstin and Schütz, Tatjana and Taron, Ulrike Helene and Eils, Roland and Roy, Jean Charles and Lett, Tristram A. and Kebir, Hedi and Polemiti, Elli and Hitchen, Esther and Jentsch, Marcel and Serin, Emin and Bernas, Antoine and Vaidya, Nilakshi and Twardziok, Sven and Ralser, Markus and Heinz, Andreas and Walter, Henrik}, issn = {2731-6076}, journal = {Nature Mental Health}, number = {10}, pages = {1131--1133}, publisher = {Springer Nature}, title = {{Multi-omics analyses of the environMENTAL project provide insights into mental health and disease}}, doi = {10.1038/s44220-024-00317-y}, volume = {2}, year = {2024}, } @article{20157, abstract = {The focus of much of contemporary research ethics is on compliance with established protocols. However, large data-driven neuroscience research raises new ethical concerns that have no agreed-upon solution. Here we reflect on these challenges and propose better integration of public and patient involvement in this evolving landscape.}, author = {Stahl, Bernd and Ogoh, George and Schumann, Gunter and Walter, Henrik and Stahl, Bernd and Young, Allan H. and Desrivières, Sylvane and Clinton, Nicholas and Thompson, Paul and Schwalber, Ameli and Liu, Jingyu and Calhoun, Vince and Chang, Xiao and Xia, Yunman and Gong, Yanting and Jia, Tianye and Renner, Paul and Hese, Sören and Giner, Arantxa and Sanchez, Mavi and Alvarez, Elena and Spanlang, Bernhard and Pearmund, Charlie and Athanasiadis, Anastasios Polykarpos and Otten, Lisa and Pitel, Séverine and Petkoski, Spase and Jirsa, Viktor and Schmitt, Karen and Wilbertz, Johannes and Patraskaki, Myrto and Sommer, Peter and Heilmann-Heimbach, Stefanie and Mathey, Carina M. and Miller, Abigail and Claus, Isabelle and Nöthen, Markus M. and Hoffmann, Per and Forstner, Andreas J. and Pastor, Alvaro and Gallego, Jaime and Orosa, Francisco Eiroa and Viapiana, Guillem Feixas and Slater, Mel and Marr, Lena and Novarino, Gaia and Marquand, Andre and Böttger, Sarah Jane and Tschorn, Mira and Rapp, Michael and Ask, Helga and Kjelkenes, Rikka and Fernandez, Sara and Van Der Meer, Dennis and Westlye, Lars T. and Andreassen, Ole A. and Aden, Rieke and Seefried, Beke and Siehl, Sebastian and Nees, Frauke and Neidhart, Maja and Stringaris, Argyris and Schwarz, Emanuel and Holz, Nathalie and Tost, Heike and Meyer-Lindenberg, Andreas and Christmann, Nina and Jansone, Karina and Banaschewski, Tobias and Banks, Jamie and Schepanski, Kerstin and Schütz, Tatjana and Taron, Ulrike Helene and Eils, Roland and Roy, Jean Charles and Lett, Tristram A. and Kebir, Hedi and Polemiti, Elli and Hitchen, Esther and Jentsch, Marcel and Serin, Emin and Bernas, Antoine and Vaidya, Nilakshi and Twardziok, Sven and Ralser, Markus and Heinz, Andreas and Walter, Henrik}, issn = {2731-6076}, journal = {Nature Mental Health}, number = {10}, publisher = {Springer Nature}, title = {{Rethinking ethics in interdisciplinary and big data-driven neuroscience projects}}, doi = {10.1038/s44220-024-00320-3}, volume = {2}, year = {2024}, } @article{10018, abstract = {In order to study integral points of bounded log-anticanonical height on weak del Pezzo surfaces, we classify weak del Pezzo pairs. As a representative example, we consider a quartic del Pezzo surface of singularity type A1 + A3 and prove an analogue of Manin's conjecture for integral points with respect to its singularities and its lines.}, author = {Derenthal, Ulrich and Wilsch, Florian Alexander}, issn = {1475-3030 }, journal = {Journal of the Institute of Mathematics of Jussieu}, keywords = {Integral points, del Pezzo surface, universal torsor, Manin’s conjecture}, number = {3}, pages = {1259--1294}, publisher = {Cambridge University Press}, title = {{Integral points on singular del Pezzo surfaces}}, doi = {10.1017/S1474748022000482}, volume = {23}, year = {2024}, } @article{17202, abstract = {Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for hybrid quantum circuits. In this study, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material.}, author = {Sagi, Oliver and Crippa, Alessandro and Valentini, Marco and Janik, Marian and Baghumyan, Levon and Fabris, Giorgio and Kapoor, Lucky and Hassani, Farid and Fink, Johannes M and Calcaterra, Stefano and Chrastina, Daniel and Isella, Giovanni and Katsaros, Georgios}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{A gate tunable transmon qubit in planar Ge}}, doi = {10.1038/s41467-024-50763-6}, volume = {15}, year = {2024}, } @article{17203, abstract = {The behavior of a rigid body primarily depends on its mass moments, which consist of the mass, center of mass, and moments of inertia. It is possible to manipulate these quantities without altering the geometric appearance of an object by introducing cavities in its interior. Algorithms that find cavities of suitable shapes and sizes have enabled the computational design of spinning tops, yo-yos, wheels, buoys, and statically balanced objects. Previous work is based, for example, on topology optimization on voxel grids, which introduces a large number of optimization variables and box constraints, or offset surface computation, which cannot guarantee that solutions to a feasible problem will always be found. In this work, we provide a mathematical analysis of constrained topology optimization problems that depend only on mass moments. This class of problems covers, among others, all applications mentioned above. Our main result is to show that no matter the outer shape of the rigid body to be optimized or the optimization objective and constraints considered, the optimal solution always features a quadric-shaped interface between material and cavities. This proves that optimal interfaces are always ellipsoids, hyperboloids, paraboloids, or one of a few degenerate cases, such as planes. This insight lets us replace a difficult topology optimization problem with a provably equivalent non-linear equation system in a small number (<10) of variables, which represent the coefficients of the quadric. This system can be solved in a few seconds for most examples, provides insights into the geometric structure of many specific applications, and lets us describe their solution properties. Finally, our method integrates seamlessly into modern fabrication workflows because our solutions are analytical surfaces that are native to the CAD domain.}, author = {Hafner, Christian and Ly, Mickaël and Wojtan, Christopher J}, issn = {1557-7368}, journal = {Transactions on Graphics}, keywords = {Topology Optimization, Mass Moments, Computational Geometry}, location = {Denver, Colorado}, number = {4}, publisher = {Association for Computing Machinery}, title = {{Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments}}, doi = {10.1145/3658194}, volume = {43}, year = {2024}, } @article{17207, author = {Fouqueau, Louise and Polechova, Jitka}, issn = {1420-9101}, journal = {Journal of evolutionary biology}, number = {6}, pages = {579--587}, publisher = {Oxford University Press}, title = {{Eco-evolutionary dynamics in changing environments: Integrating theory with data}}, doi = {10.1093/jeb/voae067}, volume = {37}, year = {2024}, } @phdthesis{17208, abstract = {Can current quantum computers provide a speedup over their classical counterparts for some kinds of problems? In this thesis, with a focus on ground state search/preparation, we address some of the challenges that both quantum annealing and variational quantum algorithms suffer from, hindering any possible practical speedup in comparison to the best classical counterparts. In the first part of the thesis, we study the performance of quantum annealing for solving a particular combinatorial optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$. We consider how modifying the initial problem, by adding more interaction terms to the corresponding Hamiltonian, leads to the emergence of a first-order phase transition during the annealing process. This phenomenon causes the total annealing duration, $T$, required to prepare the ground state of $H_C$ with a high probability to increase exponentially with the size of the problem. Our findings indicate that with the growing complexity of problem instances, the likelihood of encountering first-order phase transitions also increases, making quantum annealing an impractical solution for these types of combinatorial optimization problems. In the second part, we focus on the problem of barren plateaus in generic variational quantum algorithms. Barren plateaus correspond to flat regions in the parameter space where the gradient of the cost function is zero in expectation, and with the variance decaying exponentially with the system size, thus obstructing an efficient parameter optimization. We propose an algorithm to circumvent Barren Plateaus by monitoring the entanglement entropy of k-local reduced density matrices, alongside a method for estimating entanglement entropy via classical shadow tomography. We illustrate the approach with the paradigmatic example of the variational quantum eigensolver, and show that our algorithm effectively avoids barren plateaus in the initialization as well as during the optimization stage. Lastly, in the last two Chapters of this thesis, we focus on the quantum approximate optimization algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial optimization problems in near-term quantum devices. Specifically, we focus on how to develop rigorous initialization strategies with guarantee improvement. Our motivation for this study lies in that for random initialization, the optimization typically leads to local minima with poor performance. Our main result corresponds to the analytical construction of index-1 saddle points or transition states, stationary points with a single direction of descent, as a tool for systematically exploring the QAOA optimization landscape. This leads us to propose a novel greedy parameter initialization strategy that guarantees for the energy to decrease with an increasing number of circuit layers. Furthermore, with precise estimates for the negative Hessian eigenvalue and its eigenvector, we establish a lower bound for energy improvement following a QAOA iteration.}, author = {Medina Ramos, Raimel A}, issn = {2663-337X}, keywords = {Quantum computing, Variational Quantum Algorithms, Optimization}, pages = {133}, publisher = {Institute of Science and Technology Austria}, title = {{Exploring the optimization landscape of variational quantum algorithms}}, doi = {10.15479/at:ista:17208}, year = {2024}, } @inproceedings{17214, abstract = {Current numerical algorithms for simulating friction fall in one of two camps: smooth solvers sacrifice the stable treatment of static friction in exchange for fast convergence, and non-smooth solvers accurately compute friction at convergence rates that are often prohibitive for large graphics applications. We introduce a novel bridge between these two ideas that computes static and dynamic friction stably and efficiently. Our key idea is to convert the highly constrained non-smooth problem into an unconstrained smooth problem using logarithmic barriers that converges to the exact solution as accuracy increases. We phrase the problem as an interior point primal-dual problem that can be solved efficiently with Newton iteration. We observe quadratic convergence despite the non-smooth nature of the original problem, and our method is well-suited for large systems of tightly packed objects with many contact points. We demonstrate the efficacy of our method with stable piles of grains and stacks of objects, complex granular flows, and robust interlocking assemblies of rigid bodies.}, author = {Chen, Yi-Lu and Ly, Mickaël and Wojtan, Christopher J}, booktitle = {Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24}, isbn = {9798400705250}, keywords = {physical simulation, frictional contact, rigid body mechanics, non-smooth dynamics}, location = {Denver, United States}, publisher = {Association for Computing Machinery}, title = {{Primal-dual non-smooth friction for rigid body animation}}, doi = {10.1145/3641519.3657485}, year = {2024}, } @article{17219, abstract = {We introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts self-intersections into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations with thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting of millions of triangles.}, author = {Synak, Peter and Kalinov, Aleksei and Strugaru, Irina-Malina and Etemadihaghighi, Arian and Yang, Huidong and Wojtan, Christopher J}, issn = {1557-7368}, journal = {ACM Transactions on Graphics}, keywords = {surface tracking, topology change, non- manifold meshes, multi-material flows, solid modeling}, number = {4}, publisher = {Association for Computing Machinery}, title = {{Multi-material mesh-based surface tracking with implicit topology changes}}, doi = {10.1145/3658223}, volume = {43}, year = {2024}, } @unpublished{17222, abstract = {The quantum approximate optimization algorithm (QAOA) uses a quantum computer to implement a variational method with $2p$ layers of alternating unitary operators, optimized by a classical computer to minimize a cost function. While rigorous performance guarantees exist for the QAOA at small depths $p$, the behavior at large depths remains less clear, though simulations suggest exponentially fast convergence for certain problems. In this work, we gain insights into the deep QAOA using an analytic expansion of the cost function around transition states. Transition states are constructed in a recursive manner: from the local minima of the QAOA with $p$ layers we obtain transition states of the QAOA with $p+1$ layers, which are stationary points characterized by a unique direction of negative curvature. We construct an analytic estimate of the negative curvature and the corresponding direction in parameter space at each transition state. The expansion of the QAOA cost function along the negative direction to the quartic order gives a lower bound of the QAOA cost function improvement. We provide physical intuition behind the analytic expressions for the local curvature and quartic expansion coefficient. Our numerical study confirms the accuracy of our approximations and reveals that the obtained bound and the true value of the QAOA cost function gain have a characteristic exponential decrease with the number of layers $p$, with the bound decreasing more rapidly. Our study establishes an analytical method for recursively studying the QAOA that is applicable in the regime of high circuit depth.}, author = {Medina Ramos, Raimel A and Serbyn, Maksym}, booktitle = {arXiv}, title = {{A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm}}, doi = {10.48550/arXiv.2405.10125}, year = {2024}, } @article{17231, abstract = {In the class of projective billiards, which contains the usual billiards, we exhibit counter-examples to Ivrii's conjecture, which states that in any planar billiard with smooth boundary the set of periodic orbits has zero measure. The counter-examples are polygons admitting a 2-parameters family of n-periodic orbits, with n being either 3 or any even integer greater than 4.}, author = {Fiorebe, Corentin}, issn = {1553-5231}, journal = {Discrete and Continuous Dynamical Systems- Series A}, number = {11}, pages = {3287--3301}, publisher = {American Institute of Mathematical Sciences}, title = {{Examples of projective billiards with open sets of periodic orbits}}, doi = {10.3934/dcds.2024059}, volume = {44}, year = {2024}, } @article{17232, abstract = {The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing. For complete details on the use and execution of this protocol, please refer to Cheung et al. 1}, author = {Cheung, Giselle T and Pauler, Florian and Koppensteiner, Peter and Hippenmeyer, Simon}, issn = {2666-1667}, journal = {STAR Protocols}, number = {3}, publisher = {Elsevier}, title = {{Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq}}, doi = {10.1016/j.xpro.2024.103168}, volume = {5}, year = {2024}, } @article{17233, abstract = {CRISPR-Cas9 technology has become an essential tool for plant genome editing. Recent advancements have significantly improved the ability to target multiple genes simultaneously within the same genetic background through various strategies. Additionally, there has been significant progress in developing methods for inducible or tissue-specific editing. These advancements offer numerous possibilities for tailored genome modifications. Building upon existing research, we have developed an optimized and modular strategy allowing the targeting of several genes simultaneously in combination with the synchronized expression of the Cas9 endonuclease in the egg cell. This system allows significant editing efficiency while avoiding mosaicism. In addition, the versatile system we propose allows adaptation to inducible and/or tissue-specific edition according to the promoter chosen to drive the expression of the Cas9 gene. Here, we describe a step-by-step protocol for generating the binary vector necessary for establishing Arabidopsis edited lines using a versatile cloning strategy that combines Gateway® and Golden Gate technologies. We describe a versatile system that allows the cloning of as many guides as needed to target DNA, which can be multiplexed into a polycistronic gene and combined in the same construct with sequences for the expression of the Cas9 endonuclease. The expression of Cas9 is controlled by selecting from among a collection of promoters, including constitutive, inducible, ubiquitous, or tissue-specific promoters. Only one vector containing the polycistronic gene (tRNA-sgRNA) needs to be constructed. For that, sgRNA (composed of protospacers chosen to target the gene of interest and sgRNA scaffold) is cloned in tandem with the pre-tRNA sequence. Then, a single recombination reaction is required to assemble the promoter, the zCas9 coding sequence, and the tRNA-gRNA polycistronic gene. Each element is cloned in an entry vector and finally assembled according to the Multisite Gateway® Technology. Here, we detail the process to express zCas9 under the control of egg cell promoter fused to enhancer sequence (EC1.2en-EC1.1p) and to simultaneously target two multiple C2 domains and transmembrane region protein genes (MCTP3 and MCTP4, respectively at3g57880 and at1g51570), using one or two sgRNA per gene.}, author = {Li, Ziqiang and Huard, Jennifer and Bayer, Emmanuelle M. and Wattelet-Boyer, Valérie}, issn = {2331-8325}, journal = {Bio-protocol}, number = {13}, publisher = {Bio-Protocol}, title = {{Versatile cloning strategy for efficient multigene editing in Arabidopsis}}, doi = {10.21769/BioProtoc.5029}, volume = {14}, year = {2024}, } @article{17234, abstract = {The identification of red, apparently massive galaxies at z > 7 in early James Webb Space Telescope (JWST) photometry suggests a strongly accelerated time line compared to standard models of galaxy growth. A major uncertainty in the interpretation is whether the red colors are caused by evolved stellar populations, dust, or other effects such as emission lines or active galactic nuclei (AGNs). Here we show that three of the massive galaxy candidates at z = 6.7–8.4 have prominent Balmer breaks in JWST/NIRSpec spectroscopy from the RUBIES program. The Balmer breaks demonstrate unambiguously that stellar emission dominates at λrest = 0.4 μm and require formation histories extending hundreds of millions of years into the past in galaxies only 600–800 Myr after the big bang. Two of the three galaxies also show broad Balmer lines, with Hβ FWHM > 2500 km s−1, suggesting that dust-reddened AGNs contribute to, or even dominate, the spectral energy distributions of these galaxies at λrest ≳ 0.6 μm. All three galaxies have relatively narrow [O iii] lines, seemingly ruling out a high-mass interpretation if the lines arise in dynamically relaxed, inclined disks. Yet the inferred masses also remain highly uncertain. We model the high-quality spectra using Prospector to decompose the continuum into stellar and AGN components and explore limiting cases in stellar/AGN contribution. This produces a wide range of possible stellar masses, spanning M⋆ ∼ 109−1011M⊙. Nevertheless, all fits suggest a very early and rapid formation, most of which follow with a truncation in star formation. Potential origins and evolutionary tracks for these objects are discussed, from the cores of massive galaxies to low-mass galaxies with overmassive black holes. Intriguingly, we find all of these explanations to be incomplete; deeper and redder data are needed to understand the physics of these systems.}, author = {Wang, Bingjie and Leja, Joel and De Graaff, Anna and Brammer, Gabriel B. and Weibel, Andrea and Van Dokkum, Pieter and Baggen, Josephine F.W. and Suess, Katherine A. and Greene, Jenny E. and Bezanson, Rachel and Cleri, Nikko J. and Hirschmann, Michaela and Labbé, Ivo and Matthee, Jorryt J and Mcconachie, Ian and Naidu, Rohan P. and Nelson, Erica and Oesch, Pascal A. and Setton, David J. and Williams, Christina C.}, issn = {2041-8213}, journal = {Astrophysical Journal Letters}, number = {1}, publisher = {IOP Publishing}, title = {{RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec}}, doi = {10.3847/2041-8213/ad55f7}, volume = {969}, year = {2024}, }