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  1. Abstract

    Predicting and elucidating the impacts of materials on human health and the environment is an unending task that has taken on special significance in the context of nanomaterials research over the last two decades. The properties of materials in environmental and physiological media are dynamic, reflecting the complex interactions between materials and these media. This dynamic behavior requires special consideration in the design of databases and data curation that allow for subsequent comparability and interrogation of the data from potentially diverse sources. We present two data processing methods that can be integrated into the experimental process to encourage pre-mediated interoperability of disparate material data: Knowledge Mapping and Instance Mapping. Originally developed as a framework for the NanoInformatics Knowledge Commons (NIKC) database, this architecture and associated methods can be used independently of the NIKC and applied across multiple subfields of nanotechnology and material science.

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  2. Accommodating long-running deep learning (DL) training and inference jobs is challenging on GPU clusters that use traditional batch schedulers, such as Slurm. Given fixed wall clock time limits, DL researchers usually need to run a sequence of batch jobs and experience long interruptions on overloaded machines. Such interruptions significantly lower the research productivity and QoS for services that are deployed in production. To mitigate the issues from interruption, we propose the design of a proactive provisioner and investigate a set of statistical learning and reinforcement learning (RL) techniques, including random forest, xgboost, Deep Q-Network, and policy gradient. Using production job traces from three GPU clusters, we train each model using a subset of the trace and then evaluate their generality using the remaining validation subset. We introduce Mirage, a Slurm-compatible resource provisioner that integrates the candidate ML methods. Our experiments show that the Mirage can reduce interruption by 17--100% and safeguard 23%-76% of jobs with zero interruption across varying load levels on the three clusters. 
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  3. Free, publicly-accessible full text available October 1, 2024
  4. Free, publicly-accessible full text available October 20, 2024
  5. A burst buffer is a common method to bridge the performance gap between the I/O needs of modern supercomputing applications and the performance of the shared file system on large-scale supercomputers. However, existing I/O sharing methods require resource isolation, offline profiling, or repeated execution that significantly limit the utilization and applicability of these systems. Here we present ThemisIO, a policy-driven I/O sharing framework for a remote-shared burst buffer: a dedicated group of I/O nodes, each with a local storage device. ThemisIO preserves high utilization by implementing opportunity fairness so that it can reallocate unused I/O resources to other applications. ThemisIO accurately and efficiently allocates I/O cycles among applications, purely based on real-time I/O behavior without requiring user-supplied information or offline-profiled application characteristics. ThemisIO supports a variety of fair sharing policies, such as user-fair, size-fair, as well as composite policies, e.g., group-then-user-fair. All these features are enabled by its statistical token design. ThemisIO can alter the execution order of incoming I/O requests based on assigned tokens to precisely balance I/O cycles between applications via time slicing, thereby enforcing processing isolation. Experiments using I/O benchmarks show that ThemisIO sustains 13.5--13.7% higher I/O throughput and 19.5--40.4% lower performance variation than existing algorithms. For real applications, ThemisIO significantly reduces the slowdown by 59.1--99.8% caused by I/O interference. 
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  6. Autofluorescence (AF) poses challenges for detecting proteins of interest in situ when employing immunofluorescence (IF) microscopy. This interference is particularly pronounced in strongly autofluorescent tissues such as myocardium, where tissue AF can be comparable to IF. Although various histochemical methods have been developed to achieve effective AF suppression in different types of tissue, their applications on myocardial  samples have not been well validated. Due to inconsistency across different autofluorescent structures in sometypes of tissue, it is unclear if these methods can effectively suppress AF across all autofluorescent structures within the myocardium. Here, we quantitatively evaluated the performance of several commonly used quenching treatments on formaldehyde-fixed myocardial samples, including 0.3 M glycine, 0.3% Sudan Black B (SBB), 0.1% and 1% sodium borohydride (NaBH4), TrueVIEW® and TrueBlack®. We further assessed their quenching performance by employing the pre-treatment and post-treatment protocols, designed to cover two common IF staining scenarios where buffers contained detergents or not. The results suggest that SBB and TrueBlack® outperform other reagents in AF suppression on formaldehyde-fixed myocardial samples in both protocols. Furthermore, we inspected the quenching performance of SBB and TrueBlack® on major autofluorescent myocardial structures and evaluated their influence on IF imaging. The results suggest that SBB outperforms TrueBlack® in quenching major autofluorescent structures, while TrueBlack® excels in preserving IF labeling signal. Surprisingly, we found the treatment of NaBH4 increased AF signal and enhanced the AF contrast of major autofluorescent structures. This finding suggests that NaBH4 has the potential to act as an AF enhancer and may facilitate the interpretation of myocardial structures without the need for counterstaining.

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    Free, publicly-accessible full text available October 2, 2024
  7. We generalize the area-law violating models of Fredkin and Motzkin spin chains into two dimensions by building quantum six- and nineteen-vertex models with correlated interactions. The Hamiltonian is frustration free, and its projectors generate ergodic dynamics within the subspace of height configuration that are non negative. The ground state is a volume- and color-weighted superposition of classical bi-color vertex configurations with non-negative heights in the bulk and zero height on the boundary. The entanglement entropy between subsystems has a phase transition as the q q -deformation parameter is tuned, which is shown to be robust in the presence of an external field acting on the color degree of freedom. The ground state undergoes a quantum phase transition between area- and volume-law entanglement phases with a critical point where entanglement entropy scales as a function L\log L L log L of the linear system size L L . Intermediate power law scalings between L\log L L log L and L^2 L 2 can be achieved with an inhomogeneous deformation parameter that approaches 1 at different rates in the thermodynamic limit. For the q>1 q > 1 phase, we construct a variational wave function that establishes an upper bound on the spectral gap that scales as q^{-L^3/8} q − L 3 / 8 . 
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  8. Abstract

    Polymer‐derived amorphous SiCN has excellent high‐temperature stability and properties. To reduce the shrinkage during pyrolysis and to improve the high‐temperature oxidation resistance, Y2O3was added as a filler. In this study, polymer‐derived SiCN–Y2O3composites were fabricated by mixing a polymeric precursor of SiCN with Y2O3submicron powders in different ratios. The mixtures were cross‐linked and pyrolyzed in argon. SiCN–Y2O3composites were processed using field‐assisted sintering technology at 1350°C for 5 min under vacuum. Dense SiCN–Y2O3composite pellets were successfully made with relative density higher than 98% and homogeneous microstructure. Due to low temperature and short time of the heat‐treatment, the grain growth of Y2O3was substantially inhibited. The Y2O3grain size was ∼1 μm after sintering. The composites’ heat capacity, thermal diffusivity, and thermal expansion coefficients were characterized as a function of temperature. The thermal conductivity of the composites ceramics decreased as the amount of amorphous SiCN increased and the coefficient of thermal expansion (CTE) of the composites increased with Y2O3content. However, the thermal conductivity and CTE did not follow the rule of mixture. This is likely due to the partial oxidation of SiCN and the resultant impurity phases such as Y2SiO5, Y2Si2O7, and Y4.67(SiO4)3O.

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