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  1. Free, publicly-accessible full text available December 31, 2024
  2. Abstract Background Modeling of single cell RNA-sequencing (scRNA-seq) data remains challenging due to a high percentage of zeros and data heterogeneity, so improved modeling has strong potential to benefit many downstream data analyses. The existing zero-inflated or over-dispersed models are based on aggregations at either the gene or the cell level. However, they typically lose accuracy due to a too crude aggregation at those two levels. Results We avoid the crude approximations entailed by such aggregation through proposing an independent Poisson distribution (IPD) particularly at each individual entry in the scRNA-seq data matrix. This approach naturally and intuitively models the large number of zeros as matrix entries with a very small Poisson parameter. The critical challenge of cell clustering is approached via a novel data representation as Departures from a simple homogeneous IPD (DIPD) to capture the per-gene-per-cell intrinsic heterogeneity generated by cell clusters. Our experiments using real data and crafted experiments show that using DIPD as a data representation for scRNA-seq data can uncover novel cell subtypes that are missed or can only be found by careful parameter tuning using conventional methods. Conclusions This new method has multiple advantages, including (1) no need for prior feature selection or manual optimization of hyperparameters; (2) flexibility to combine with and improve upon other methods, such as Seurat. Another novel contribution is the use of crafted experiments as part of the validation of our newly developed DIPD-based clustering pipeline. This new clustering pipeline is implemented in the R (CRAN) package scpoisson . 
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    Free, publicly-accessible full text available December 1, 2024
  3. The accurate and efficient determination of hydrologic connectivity has garnered significant attention from both academic and industrial sectors due to its critical implications for environmental management. While recent studies have leveraged the spatial characteristics of hydrologic features, the use of elevation models for identifying drainage paths can be influenced by flow barriers. To address these challenges, our focus in this study is on detecting drainage crossings through the application of advanced convolutional neural networks (CNNs). In pursuit of this goal, we use neural architecture search to automatically explore CNN models for identifying drainage crossings. Our approach not only attains high accuracy (over 97% for average precision) in object detection but also excels in efficiently inferring correct drainage crossings within a remarkably short time frame (0.268 ms). Furthermore, we perform a detailed profiling of our approach on GPU systems to analyze performance bottlenecks. 
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  4. Abstract

    Traditional histochemical staining of post-mortem samples often confronts inferior staining quality due to autolysis caused by delayed fixation of cadaver tissue, and such chemical staining procedures covering large tissue areas demand substantial labor, cost and time. Here, we demonstrate virtual staining of autopsy tissue using a trained neural network to rapidly transform autofluorescence images of label-free autopsy tissue sections into brightfield equivalent images, matching hematoxylin and eosin (H&E) stained versions of the same samples. The trained model can effectively accentuate nuclear, cytoplasmic and extracellular features in new autopsy tissue samples that experienced severe autolysis, such as COVID-19 samples never seen before, where the traditional histochemical staining fails to provide consistent staining quality. This virtual autopsy staining technique provides a rapid and resource-efficient solution to generate artifact-free H&E stains despite severe autolysis and cell death, also reducing labor, cost and infrastructure requirements associated with the standard histochemical staining.

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  5. Free, publicly-accessible full text available July 16, 2024
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  9. Free, publicly-accessible full text available June 21, 2024
  10. The conductivity and charge transport mobility of conjugated polymers (CPs) are largely correlated with their degree of crystallinity, rendering the crystallization of CPs an important endeavour. However, such tasks can be challenging, especially in the absence of sidechain functionalization. In this study, we demonstrate that the incorporation of a small amount of oligomers, specifically tetraaniline, can induce crystallization of the parent polymer, polyaniline, through a single-step self-assembly process. The resulting crystals are compositionally homogeneous because the oligomers and their parent polymer share the same repeating unit and are both electroactive. Mechanistic studies reveal that the tetraaniline forms a crystalline seed that subsequently guides the assembly of polyaniline due to their structural similarities. Applying this oligomer-assisted crystallization approach to polyaniline with defined molecular weights resulted in single crystalline nanowires for 5000 Da polyaniline, and nanowires with strong preferential chain orientation for those with molecular weights between 10 000 and 100 000 Da. Absorption studies reveal that the polymer chains are in an expanded conformation, which likely contributed to the high degree of packing order. Two-probe, single nanowire measurements show that the crystals have conductivity as high as 19.5 S cm −1 . This method is simple, general, and can potentially be applied to other CPs. 
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    Free, publicly-accessible full text available April 3, 2024