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Creators/Authors contains: "Cooper, John"

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  1. Subtelomeres are imperfect repeats adjacent to telomeres that are repressed by heterochromatin. Although essential for genome integrity, their repetitive nature has thwarted dissection of local heterochromatin assembly and maintenance mechanisms. Here, we engineeredSchizosaccharomyces pombestrains carrying fluorescent reporters at a single subtelomere. We find that subtelomeric heterochromatin is organized into discrete subdomains that nucleate at telomere-proximal and cryptic internal sites. Telomere-proximal regions depend on canonical shelterin or RNA interference nucleation pathways, while telomere-distal regions require nucleosome remodelers, histone chaperones, and boundary-associated factors. Using multi-generational live imaging and targeted perturbations, we show that subtelomeric subdomains display position-specific, clonally variable silencing across a spectrum of robust to fragile epigenetic states. This clonal variegation is also induced by naturally occurring subtelomeric structural variants. These findings demonstrate that subtelomeric heterochromatin maintenance is not uniform but rather governed by local chromatin context and architecture. 
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    Free, publicly-accessible full text available September 25, 2026
  2. The weak-to-strong generalization phenomenon is the driver for important machine learning applications including highly data-efficient learning and, most recently, performing superalignment. While decades of research have resulted in numerous algorithms that produce strong empirical performance, understanding what aspects of data enable weak-to-strong generalization has been understudied. We propose a simple data-centric mechanism that characterizes weak-to-strong generalization: the overlap density. Intuitively, generalization tracks the number of points that contain overlaps, i.e., both easy patterns (learnable by a weak model) and challenging patterns (only learnable by a stronger model), as with such points, weak predictions can be used to learn challenging patterns by stronger models. We provide a practical overlap detection algorithm to find such points in datasets and leverage them to learn, among multiple sources of data, which to query when seeking to maximize overlap density and thereby enhance weak-to-strong generalization. We present a theoretical result showing that the generalization benefit is a function of the overlap density and a regret bound for our data selection algorithm. Empirically, we validate the mechanism and the overlap detection algorithm on a wide array of settings. 
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    Free, publicly-accessible full text available April 28, 2026
  3. The weak-to-strong generalization phenomenon is the driver for important machine learning applications including highly data-efficient learning and, most recently, performing superalignment. While decades of research have resulted in numerous algorithms that produce strong empirical performance, understanding what aspects of data enable weak-to-strong generalization has been understudied. We propose a simple data-centric mechanism that characterizes weak-to-strong generalization: the overlap density. Intuitively, generalization tracks the number of points that contain overlaps, i.e., both easy patterns (learnable by a weak model) and challenging patterns (only learnable by a stronger model), as with such points, weak predictions can be used to learn challenging patterns by stronger models. We provide a practical overlap detection algorithm to find such points in datasets and leverage them to learn, among multiple sources of data, which to query when seeking to maximize overlap density and thereby enhance weak-to-strong generalization. We present a theoretical result showing that the generalization benefit is a function of the overlap density and a regret bound for our data selection algorithm. Empirically, we validate the mechanism and the overlap detection algorithm on a wide array of settings. 
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    Free, publicly-accessible full text available April 24, 2026
  4. Free, publicly-accessible full text available January 3, 2026
  5. We present a simple and effective method to create highly entangled spin states on a faster timescale than that of the commonly employed one-axis twisting (OAT) model. We demonstrate that by periodically driving the Dicke Hamiltonian at a resonance frequency, the system effectively becomes a two-axis countertwisting Hamiltonian, which is known to quickly create Heisenberg limit scaled entangled states. For these states we show that simple quadrature measurements can saturate the ultimate precision limit for parameter estimation determined by the quantum Cramér-Rao bound. An example experimental realization of the periodically driven scheme is discussed with the potential to quickly generate momentum entanglement in a recently described experimental vertical cavity system. We analyze effects of collective dissipation in this vertical cavity system and find that our squeezing protocol can be more robust than the previous realization of OAT. Published by the American Physical Society2024 
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  6. Abstract The quest to improve transparent conductors balances two key goals: increasing electrical conductivity and increasing optical transparency. To improve both simultaneously is hindered by the physical limitation that good metals with high electrical conductivity have large carrier densities that push the plasma edge into the ultra-violet range. Technological solutions reflect this trade-off, achieving the desired transparencies only by reducing the conductor thickness or carrier density at the expense of a lower conductance. Here we demonstrate that highly anisotropic crystalline conductors offer an alternative solution, avoiding this compromise by separating the directions of conduction and transmission. We demonstrate that slabs of the layered oxides Sr2RuO4and Tl2Ba2CuO6+δare optically transparent even at macroscopic thicknesses >2 μm for c-axis polarized light. Underlying this observation is the fabrication of out-of-plane slabs by focused ion beam milling. This work provides a glimpse into future technologies, such as highly polarized and addressable optical screens. 
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  7. null (Ed.)