Aaron S. Meyer
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View article: Tensor-Based Integration of Time-Series Measurements Reveals Relationships Between Underlying Disease, Early Injury, and CD4+ Polarization in Liver Transplantation
Tensor-Based Integration of Time-Series Measurements Reveals Relationships Between Underlying Disease, Early Injury, and CD4+ Polarization in Liver Transplantation Open
For patients with end-stage liver failure, liver transplantation (LT) remains the standard-of-care, though five-year allograft survival rates remain below 80%. Liver ischemia reperfusion injuries (LIRI) arise during transplant and contribu…
View article: Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE
Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE Open
Effective exploration and analysis tools are vital for the extraction of insights from single-cell data. However, current techniques for modeling single-cell studies performed across experimental conditions (e.g., samples) require restrict…
View article: Signs of Non-Monotonic Finite-Volume Corrections to $g_A$
Signs of Non-Monotonic Finite-Volume Corrections to $g_A$ Open
We study finite-volume (FV) corrections to determinations of $g_A$ via lattice quantum chromodynamics (QCD) using analytic results and numerical analysis. We observe that $SU(2)$ Heavy Baryon Chiral Perturbation Theory does not provide an …
View article: Finite Temperature Transition in Hyper Stealth Dark Matter using Möbius Domain Wall Fermions
Finite Temperature Transition in Hyper Stealth Dark Matter using Möbius Domain Wall Fermions Open
The first-order confinement transition of a strongly coupled composite dark matter theory can provide a possible source of gravitational waves in the early universe. In this work, on behalf of the Lattice Strong Dynamics (LSD) Collaboratio…
View article: Machine-learning-guided design of electroanalytical pulse waveforms
Machine-learning-guided design of electroanalytical pulse waveforms Open
Bayesian optimization outperforms random- and human-designed waveforms for electrochemical detection of serotonin in physiologically-relevant environments.
View article: Human Retinal Progenitor Cell (hRPC) Migration in Three‐Dimensional (3D) Environments of Varying Stiffness and Composition
Human Retinal Progenitor Cell (hRPC) Migration in Three‐Dimensional (3D) Environments of Varying Stiffness and Composition Open
Retinal degeneration is the leading cause of blindness worldwide. Subretinal implantation of human retinal progenitor cells (hRPCs) has shown great promise in models of retinal degeneration for restoration of vision but is limited by extre…
View article: A multivalent binding model infers antibody Fc species from systems serology
A multivalent binding model infers antibody Fc species from systems serology Open
Systems serology aims to broadly profile the antigen binding, Fc biophysical features, immune receptor engagement, and effector functions of antibodies. This experimental approach excels at identifying antibody functional features that are…
View article: Machine-learning-guided design of electroanalytical pulse waveforms
Machine-learning-guided design of electroanalytical pulse waveforms Open
Voltammetry is widely used to detect and quantify oxidizable or reducible species in complex environments. The neurotransmitter serotonin epitomizes an analyte that is challenging to detect in situ due to low concentrations and co-existing…
View article: Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood Open
View article: The structure is the message: Preserving experimental context through tensor decomposition
The structure is the message: Preserving experimental context through tensor decomposition Open
View article: Integrative, high-resolution analysis of single cell gene expression across experimental conditions with PARAFAC2-RISE
Integrative, high-resolution analysis of single cell gene expression across experimental conditions with PARAFAC2-RISE Open
Effective and scalable exploration and analysis tools are vital for the extraction of insights from large-scale single-cell data. However, current techniques for modeling single-cell studies performed across experimental conditions (e.g., …
View article: Censored Least Squares for Imputing Missing Values in PARAFAC Tensor Factorization
Censored Least Squares for Imputing Missing Values in PARAFAC Tensor Factorization Open
Tensor factorization is a dimensionality reduction method applied to multidimensional arrays. These methods are useful for identifying patterns within a variety of biomedical datasets due to their ability to preserve the organizational str…
View article: Tensor modeling of MRSA bacteremia cytokine and transcriptional patterns reveals coordinated, outcome-associated immunological programs
Tensor modeling of MRSA bacteremia cytokine and transcriptional patterns reveals coordinated, outcome-associated immunological programs Open
Methicillin-resistant Staphylococcus aureus (MRSA) bacteremia is a common and life-threatening infection that imposes up to 30% mortality even when appropriate therapy is used. Despite in vitro efficacy determined by minimum inhibitory con…
View article: The structure is the message: preserving experimental context through tensor decomposition
The structure is the message: preserving experimental context through tensor decomposition Open
Recent biological studies have been revolutionized in scale and granularity by multiplex and high-throughput assays. Profiling cell responses across several experimental parameters, such as perturbations, time, and genetic contexts, leads …
View article: Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood Open
Cytokines mediate cell-to-cell communication across the immune system and therefore are critical to immunosurveillance in cancer and other diseases. Several cytokines show dysregulated abundance or signaling responses in breast cancer, ass…
View article: Dissecting signaling regulators driving AXL-mediated bypass resistance and associated phenotypes by phosphosite perturbations
Dissecting signaling regulators driving AXL-mediated bypass resistance and associated phenotypes by phosphosite perturbations Open
Receptor tyrosine kinase (RTK)-targeted therapies are often effective but invariably limited by drug resistance. A major mechanism of acquired resistance involves “bypass” switching to alternative pathways driven by non-targeted RTKs that …
View article: Multivalent, asymmetric IL-2–Fc fusions show enhanced selectivity for regulatory T cells
Multivalent, asymmetric IL-2–Fc fusions show enhanced selectivity for regulatory T cells Open
The cytokine interleukin-2 (IL-2) has the potential to treat autoimmune disease but is limited by its modest specificity toward immunosuppressive regulatory T (T reg ) cells. IL-2 receptors consist of combinations of α, β, and γ chains of …
View article: Disulfide-HMGB1 signals through TLR4 and TLR9 to induce inflammatory macrophages capable of innate-adaptive crosstalk in human liver transplantation
Disulfide-HMGB1 signals through TLR4 and TLR9 to induce inflammatory macrophages capable of innate-adaptive crosstalk in human liver transplantation Open
View article: Mixed IgG Fc immune complexes exhibit blended binding profiles and refine FcR affinity estimates
Mixed IgG Fc immune complexes exhibit blended binding profiles and refine FcR affinity estimates Open
Immunoglobulin G (IgG) antibodies coordinate immune effector responses by interacting with effector cells via fragment crystallizable γ (Fcγ) receptors. The IgG Fc domain directs effector responses through subclass and glycosylation variat…
View article: Analysis and modeling of cancer drug responses using cell cycle phase-specific rate effects
Analysis and modeling of cancer drug responses using cell cycle phase-specific rate effects Open
View article: Design of cell-type-specific hyperstable IL-4 mimetics via modular de novo scaffolds
Design of cell-type-specific hyperstable IL-4 mimetics via modular de novo scaffolds Open
View article: Supplementary Figure S1 from Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance
Supplementary Figure S1 from Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance Open
Supplementary Figure S1. U0126 treatment reduces p-Erk1/2 while increasing p-cJUN in a panel of cell lines, measured by bead-based immunoassay.
View article: Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration Open
Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
View article: Supplementary Figure S2 from Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance
Supplementary Figure S2 from Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance Open
Supplementary Figure S2. Correlation between plasma RTK changes with MAPKi, PFS, and initial tumor shrinkage (using RECIST) in melanoma patients.
View article: Supplementary Figure S3 from Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance
Supplementary Figure S3 from Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance Open
Supplementary Figure 3. Corresponds to Fig. 3C, showing U0126 and PD325901 elicit AXL upregulation to a degree that correlates with AXLi/MEKi synergy across a panel of cell lines.
View article: Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration Open
Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
View article: Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration Open
Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
View article: Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration Open
Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
View article: Data from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
Data from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration Open
To better understand the signaling complexity of AXL, a member of the tumor-associated macrophage (TAM) receptor tyrosine kinase family, we created a physical and functional map of AXL signaling interactions, phosphorylation events, and ta…
View article: Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration Open
Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration