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Creators/Authors contains: "Xu, Jie"

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  1. Free, publicly-accessible full text available January 1, 2025
  2. Abstract Overly restrictive eligibility criteria for clinical trials may limit the generalizability of the trial results to their target real-world patient populations. We developed a novel machine learning approach using large collections of real-world data (RWD) to better inform clinical trial eligibility criteria design. We extracted patients’ clinical events from electronic health records (EHRs), which include demographics, diagnoses, and drugs, and assumed certain compositions of these clinical events within an individual’s EHRs can determine the subphenotypes—homogeneous clusters of patients, where patients within each subgroup share similar clinical characteristics. We introduced an outcome-guided probabilistic model to identify those subphenotypes, such that the patients within the same subgroup not only share similar clinical characteristics but also at similar risk levels of encountering severe adverse events (SAEs). We evaluated our algorithm on two previously conducted clinical trials with EHRs from the OneFlorida+ Clinical Research Consortium. Our model can clearly identify the patient subgroups who are more likely to suffer or not suffer from SAEs as subphenotypes in a transparent and interpretable way. Our approach identified a set of clinical topics and derived novel patient representations based on them. Each clinical topic represents a certain clinical event composition pattern learned from the patient EHRs. Tested on both trials, patient subgroup (#SAE=0) and patient subgroup (#SAE>0) can be well-separated by k-means clustering using the inferred topics. The inferred topics characterized as likely to align with the patient subgroup (#SAE>0) revealed meaningful combinations of clinical features and can provide data-driven recommendations for refining the exclusion criteria of clinical trials. The proposed supervised topic modeling approach can infer the clinical topics from the subphenotypes with or without SAEs. The potential rules for describing the patient subgroups with SAEs can be further derived to inform the design of clinical trial eligibility criteria. 
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    Free, publicly-accessible full text available December 1, 2024
  3. Free, publicly-accessible full text available August 1, 2024
  4. We derived equations and closed-form solutions of transit time for a viscous droplet squeezing through a small circular pore with a finite length at microscale under constant pressures. Our analyses were motivated by the vital processes of biological cells squeezing through small pores in blood vessels and sinusoids and droplets squeezing through pores in microfluidics. First, we derived ordinary differential equations (ODEs) of a droplet squeezing through a circular pore by combining Sampson flow, Poiseuille flow, and Young–Laplace equations and took into account the lubrication layer between the droplet and the pore wall. Second, for droplets wetting the wall with small surface tension, we derived the closed-form solutions of transit time. For droplets with finite surface tension, we solved the original ODEs numerically to predict the transit time. After validations against experiments and finite element simulations, we studied the effects of pressure, viscosity, pore/droplet dimensions, and surface tension on the transit time. We found that the transit time is inversely linearly proportional to pressure when the surface tension is low compared to the critical surface tension for preventing the droplet to pass and becomes nonlinear when it approaches the critical tension. Remarkably, we showed that when a fixed percentage of surface tension to critical tension is applied, the transit time is always inversely linearly proportional to pressure, and the dependence of transit time on surface tension is nonmonotonic. Our results provided a quick way of quantitative calculations of transit time for designing droplet microfluidics and understanding cells passing through constrictions.

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    Free, publicly-accessible full text available August 1, 2024
  5. With the increase of multi-view graph data, multi-view graph clustering (MVGC) that can discover the hidden clusters without label supervision has attracted growing attention from researchers. Existing MVGC methods are often sensitive to the given graphs, especially influenced by the low quality graphs, i.e., they tend to be limited by the homophily assumption. However, the widespread real-world data hardly satisfy the homophily assumption. This gap limits the performance of existing MVGC methods on low homophilous graphs. To mitigate this limitation, our motivation is to extract high-level view-common information which is used to refine each view's graph, and reduce the influence of non-homophilous edges. To this end, we propose dual label-guided graph refinement for multi-view graph clustering (DuaLGR), to alleviate the vulnerability in facing low homophilous graphs. Specifically, DuaLGR consists of two modules named dual label-guided graph refinement module and graph encoder module. The first module is designed to extract the soft label from node features and graphs, and then learn a refinement matrix. In cooperation with the pseudo label from the second module, these graphs are refined and aggregated adaptively with different orders. Subsequently, a consensus graph can be generated in the guidance of the pseudo label. Finally, the graph encoder module encodes the consensus graph along with node features to produce the high-level pseudo label for iteratively clustering. The experimental results show the superior performance on coping with low homophilous graph data. The source code for DuaLGR is available at 
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    Free, publicly-accessible full text available June 27, 2024
  6. Abstract

    Stretchable polymer semiconductors (PSCs) have seen great advancements alongside the development of soft electronics. But it remains a challenge to simultaneously achieve high charge carrier mobility and stretchability. Herein, we report the finding that stretchable PSC thin films (<100-nm-thick) with high stretchability tend to exhibit multi-modal energy dissipation mechanisms and have a large relative stretchability (rS) defined by the ratio of the entropic energy dissipation to the enthalpic energy dissipation under strain. They effectively recovered the original molecular ordering, as well as electrical performance, after strain was released. The highestrSvalue with a model polymer (P4) exhibited an average charge carrier mobility of 0.2 cm2V−1s−1under 100% biaxial strain, while PSCs with lowrSvalues showed irreversible morphology changes and rapid degradation of electrical performance under strain. These results suggestrScan be used as a parameter to compare the reliability and reversibility of stretchable PSC thin films.

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