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  1. Prostate cancer prognostication largely relies on visual assessment of a few thinly sectioned biopsy specimens under a microscope to assign a Gleason grade group (GG). Unfortunately, the assigned GG is not always associated with a patient’s outcome in part because of the limited sampling of spatially heterogeneous tumors achieved by 2-dimensional histopathology. In this study, open-top light-sheet microscopy was used to obtain 3-dimensional pathology data sets that were assessed by 4 human readers. Intrabiopsy variability was assessed by asking readers to perform Gleason grading of 5 different levels per biopsy for a total of 20 core needle biopsies (ie, 100 total images). Intrabiopsy variability (Cohen k) was calculated as the worst pairwise agreement in GG between individual levels within each biopsy and found to be 0.34, 0.34, 0.38, and 0.43 for the 4 pathologists. These preliminary results reveal that even within a 1-mm-diameter needle core, GG based on 2-dimensional images can vary dramatically depending on the location within a biopsy being analyzed. We believe that morphologic assessment of whole biopsies in 3 dimension has the potential to enable more reliable and consistent tumor grading. 
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    Free, publicly-accessible full text available December 1, 2024
  2. The transition between the gas-, supercritical-, and liquid-phase behavior is a fascinating topic, which still lacks molecular-level understanding. Recent ultrafast two-dimensional infrared spectroscopy experiments suggested that the vibrational spectroscopy of N 2 O embedded in xenon and SF 6 as solvents provides an avenue to characterize the transitions between different phases as the concentration (or density) of the solvent increases. The present work demonstrates that classical molecular dynamics (MD) simulations together with accurate interaction potentials allows us to (semi-)quantitatively describe the transition in rotational vibrational infrared spectra from the P-/R-branch line shape for the stretch vibrations of N 2 O at low solvent densities to the Q-branch-like line shapes at high densities. The results are interpreted within the classical theory of rigid-body rotation in more/less constraining environments at high/low solvent densities or based on phenomenological models for the orientational relaxation of rotational motion. It is concluded that classical MD simulations provide a powerful approach to characterize and interpret the ultrafast motion of solutes in low to high density solvents at a molecular level. 
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    Free, publicly-accessible full text available April 14, 2024
  3. The density dependence of rotational and vibrational energy relaxation (RER and VER) of the N 2 O ν 3 asymmetric stretch in dense gas and supercritical Xe and SF 6 solutions for near critical isotherms is measured by ultrafast 2DIR and infrared pump–probe spectroscopy. 2DIR analysis provides precise measurements of RER at all gas and supercritical solvent densities. An isolated binary collision (IBC) model is sufficient to describe RER for solvent densities ≤ ∼4M where rotational equilibrium is re-established in ∼1.5–2.5 collisions. N 2 O RER is ∼30% more efficient in SF 6 than in Xe due to additional relaxation pathways in SF 6 and electronic factor differences. 2DIR analysis revealed that N 2 O RER exhibits a critical slowing effect in SF 6 at near critical density ( ρ* ∼ 0.8) where the IBC model breaks down. This is attributable to the coupling of critical long-range density fluctuations to the local N 2 O free rotor environment. No such RER critical slowing is observed in Xe because IBC break down occurs much further from the Xe critical point. Many body interactions effectively shield N 2 O from these near critical Xe density fluctuations. The N 2 O ν 3 VER density dependence in SF 6 is different than that seen for RER, indicating a different coupling to the near critical environment than RER. N 2 O ν 3 VER is only about ∼7 times slower than RER in SF 6 . In contrast, almost no VER decay is observed in Xe over 200 ps. This VER solvent difference is due to a vibrationally resonant energy transfer pathway in SF 6 that is not possible for Xe. 
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  4. Abstract

    In recent years, technological advances in tissue preparation, high‐throughput volumetric microscopy, and computational infrastructure have enabled rapid developments in nondestructive 3D pathology, in which high‐resolution histologic datasets are obtained from thick tissue specimens, such as whole biopsies, without the need for physical sectioning onto glass slides. While 3D pathology generates massive datasets that are attractive for automated computational analysis, there is also a desire to use 3D pathology to improve the visual assessment of tissue histology. In this perspective, we discuss and provide examples of potential advantages of 3D pathology for the visual assessment of clinical specimens and the challenges of dealing with large 3D datasets (of individual or multiple specimens) that pathologists have not been trained to interpret. We discuss the need for artificial intelligence triaging algorithms and explainable analysis methods to assist pathologists or other domain experts in the interpretation of these novel, often complex, large datasets.

     
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  5. Abstract

    The diffuse radiation fertilization effect—the increase in plant productivity in the presence of higher diffuse radiation (K↓,d)—is an important yet understudied aspect of atmosphere‐biosphere interactions and can modify the terrestrial carbon, energy, and water budgets. TheK↓,dfertilization effect links the carbon cycle with clouds and aerosols, all of which are large sources of uncertainties for our current understanding of the Earth system and for future climate projections. Here we establish to what extent observational and modeling uncertainty in sunlight's diffuse fraction (kd) affects simulated gross primary productivity (GPP) and terrestrial evapotranspiration (λE). We find only 48 eddy covariance sites with simultaneous sufficient measurements ofK↓,dwith none in the tropical climate zone, making it difficult to constrain this mechanism globally using observations. Using a land modeling framework based on the latest version of the Community Land Model, we find that global GPP ranges from 114 Pg C year−1when usingkdforcing from the Modern‐Era Retrospective analysis for Research and Applications, version 2 reanalysis to a ∼7% higher value of 122 Pg C year−1when using the Clouds and the Earth's Radiant Energy System satellite product, with especially strong differences apparent over the tropical region (mean increase ∼9%). The differences inλE, although smaller (−0.4%) due to competing changes in shaded and sunlit leaf transpiration, can be greater than regional impacts of individual forcing agents like aerosols. Our results demonstrate the importance of comprehensively and systematically validating the simulatedkdby atmosphere modules as well as the response to differences inkdwithin land modules across Earth System Models.

     
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  6. For the last two decades, high-dimensional data and methods have proliferated throughout the literature. Yet, the classical technique of linear regression has not lost its usefulness in applications. In fact, many high-dimensional estimation techniques can be seen as variable selection that leads to a smaller set of variables (a “submodel”) where classical linear regression applies. We analyze linear regression estimators resulting from model selection by proving estimation error and linear representation bounds uniformly over sets of submodels. Based on deterministic inequalities, our results provide “good” rates when applied to both independent and dependent data. These results are useful in meaningfully interpreting the linear regression estimator obtained after exploring and reducing the variables and also in justifying post-model-selection inference. All results are derived under no model assumptions and are nonasymptotic in nature. 
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  7. Groundwater historically has been a critical but understudied, underfunded, and underappreciated natural resource, although recent challenges associated with both groundwater quantity and quality have raised its profile. This is particularly true in the Laurentian Great Lakes (LGL) region, where the rich abundance of surface water results in the perception of an unlimited water supply but limited attention on groundwater resources. As a consequence, groundwater management recommendations in the LGL have been severely constrained by our lack of information. To address this information gap, a virtual summit was held in June 2021 that included invited participants from local, state, and federal government entities, universities, non-governmental organizations, and private firms in the region. Both technical (e.g., hydrologists, geologists, ecologists) and policy experts were included, and participants were assigned to an agricultural, urban, or coastal wetland breakout group in advance, based on their expertise. The overall goals of this groundwater summit were fourfold: (1) inventory the key (grand) challenges facing groundwater in Michigan; (2) identify the knowledge gaps and scientific needs, as well as policy recommendations, associated with these challenges; (3) construct a set of conceptual models that elucidate these challenges; and (4) develop a list of (tractable) next steps that can be taken to address these challenges. Absent this type of information, the sustainability of this critical resource is imperiled. 
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