A5052563130- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Mathematical Biology Tumor Growth
- Cancer Genomics and Diagnostics
- Chromosomal and Genetic Variations
- Evolution and Genetic Dynamics
- Physics of Superconductivity and Magnetism
- Evolutionary Game Theory and Cooperation
- Mathematical and Theoretical Epidemiology and Ecology Models
- CAR-T cell therapy research
- Single-cell and spatial transcriptomics
- Cancer Immunotherapy and Biomarkers
- Cancer Cells and Metastasis
- Immune cells in cancer
- Renal cell carcinoma treatment
- Bladder and Urothelial Cancer Treatments
- Superconducting Materials and Applications
- Viral Infectious Diseases and Gene Expression in Insects
- Quantum and electron transport phenomena
- Natural Language Processing Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Topic Modeling
- Speech Recognition and Synthesis
- Microtubule and mitosis dynamics
- Pancreatic and Hepatic Oncology Research
Moffitt Cancer Center
2018-2023
Google (United States)
2022
Argonne National Laboratory
2017-2020
Northwestern University
2017-2019
Chimeric antigen receptor (CAR) T cell therapy is a remarkably effective immunotherapy that relies on in vivo expansion of engineered CAR cells, after lymphodepletion (LD) by chemotherapy. The quantitative laws underlying this and subsequent tumour eradication remain unknown. We develop mathematical model cell–tumour interactions demonstrate can be explained immune reconstitution dynamics LD competition among cells. cells rapidly grow engage but experience an emerging growth rate...
We examined the meaning of metabolically active lesions on 1-month restaging nuclear imaging patients with relapsed/refractory large B-cell lymphoma receiving axicabtagene ciloleucel (axi-cel) by assessing relationship between total metabolic tumor volume (MTV) positron emission tomography (PET) scans and circulating DNA (ctDNA) in plasma. In this prospective multicenter sample collection study, MTV was retrospectively calculated via commercial software at baseline, 1, 3 months after...
Introduction In clear cell renal carcinoma (ccRCC), tumor-associated macrophage (TAM) induction of CD8+T cells into a terminally exhausted state has been implicated as major mechanism immunotherapy resistance, but deeper biological understanding is necessary. Methods Primary ccRCC tumor samples were obtained from 97 patients between 2004 and 2018. Multiplex immunofluorescence using lymphoid myeloid markers was performed in seven regions interest per patient across three predefined zones,...
Neural Network Language Models (NNLMs) generate probability distributions by applying a softmax function to distance metric formed taking the dot product of prediction vector with all word vectors in high-dimensional embedding space. The dot-product forms part inductive bias NNLMs. Although NNLMs optimize well this bias, we show that results sub-optimal ordering space structurally impoverishes some words at expense others when assigning probability. We present numerical, theoretical and...
Abstract Summary Multiplex immunofluorescence (mIF) staining combined with quantitative digital image analysis is a novel and increasingly used technique that allows for the characterization of tumor immune microenvironment (TIME). Generally, mIF data to examine abundance cells in TIME; however, this does not capture spatial patterns throughout TIME, metric recognized as important prognosis. To address gap, we developed an R package spatialTIME enables data, well iTIME web application...
The phenotypic efficacy of somatic copy number alterations (SCNAs) stems from their incidence per base pair the genome, which is orders magnitudes greater than that point mutations. One mitotic event stands out in its potential to significantly change a cell’s SCNA burden–a chromosome missegregation. A stochastic model mis-segregations has been previously developed describe evolution SCNAs single type. Building upon this work, we derive general deterministic framework for modeling...
Significance Absolute zero resistance of superconducting materials is difficult to achieve in practice due the motion microscopic Abrikosov vortices, especially when external currents are applied. Even a partial reduction via vortex immobilization by material imperfections holy grail superconductivity research. It commonly believed that dissipation increases with applied magnetic field since number vortices as well. Through example molybdenum–germanium nanostrips, we show resistive losses...
Abstract An evolutionary game emerges when a subset of individuals incur costs to provide benefits all individuals. Public goods games (PGG) cover the essence such dilemmas in which cooperators are prone exploitation by defectors. We model population dynamics non-linear PGG and consider density-dependence on global level, while occurs within local neighborhoods. At low cooperation, increases public good increasing returns. high diminishing This mechanism leads diverse evolutionarily stable...
Immune infiltration is typically quantified using cellular density, not accounting for clustering. Tumor-associated macrophages (TAM) activate oncogenic signaling through paracrine interactions with tumor cells, which may be better reflected by local clustering than global density metrics. Using multiplex immunohistochemistry and digital pathologic analysis we myeloid cell markers in 129 regions of interest from 55 samples 35 patients metastatic ccRCC. CD68+ cells were found to clustered...
Cancer-associated fibroblasts (CAF) are highly prevalent cells in the tumor microenvironment clear cell renal carcinoma (ccRCC). CAFs exhibit a pro-tumor effect vitro and have been implicated proliferation, metastasis, treatment resistance. Our objective is to analyze geospatial distribution of with proliferating apoptotic ccRCC determine associations survival systemic treatment. Pre-treatment primary samples were collected from 96 patients metastatic ccRCC. Three adjacent slices obtained 2...
Transport characteristics of nano-sized superconducting strips and bridges are determined by an intricate interplay surface bulk pinning. In the limiting case a very narrow bridge, critical current is mostly defined its barrier, while in opposite wide it dominated pinning properties. Here we present detailed study intermediate regime, where determined, both, randomly placed centres Bean-Livingston barrier at edge strip external magnetic field. We use time-dependent Ginzburg-Landau equations...
ABSTRACT Chimeric antigen receptor (CAR) T cell therapy is a remarkably effective immunotherapy that relies on in vivo expansion of engineered CAR cells, after lymphodepletion by chemotherapy. The laws underlying this and subsequent tumor eradication remain unknown. Still, about 60% T-treated patients are likely to progress; their tumors not eradicated. Here we seek understand disentangle the multiple processes contribute eradication. We developed mathematical model cell-tumor interactions,...
For many technological applications of superconductors the performance a material is determined by highest current it can carry losslessly-the critical current. In turn, be controlled adding nonsuperconducting defects in superconductor matrix. Here we report on systematic comparison different local and global optimization strategies to predict optimal structures pinning centers leading possible currents. We demonstrate these methods for with randomly placed spherical, elliptical, columnar defects.
Breast cancer progresses in a multistep process from primary tumor growth and stroma invasion to metastasis. Nutrient-limiting environments promote chemotaxis with aggressive morphologies characteristic of invasion. It is unknown how coexisting cells differ their response nutrient limitations this impacts the metapopulation as whole. In study, we integrate mathematical modeling microenvironmental perturbation data investigate nutrient-limiting inhabited by one or two cell subpopulations....
The co-evolutionary dynamics of competing populations can be strongly affected by frequency-dependent selection and spatial population structure. As co-evolving grow into a domain, their initial arrangement growth rate differences are important factors that determine the long-term outcome. We here model producer free-rider co-evolution in context diffusive public good (PG) is produced producers at cost but evokes local concentration-dependent benefits to all. benefit PG non-linearly...
In this work, we present a kinetic Markov state Monte Carlo model designed to complement temperature-jump (T-jump) infrared spectroscopy experiments probing the kinetics and dynamics of short DNA oligonucleotides. The is be accessible experimental researchers in terms both computational simplicity expense while providing detailed insights beyond those provided by methods. an extension thermodynamic lattice for hybridization utilizing formalism nucleation-zipper mechanism. Association...
Superconducting vortices and phase slips are primary mechanisms of dissipation in superconducting, superfluid, cold atom systems. While the dynamics is fairly well described, occurring quasi-one dimensional superconducting wires still elude understanding. The main reason that strongly non-linear time-dependent phenomena cannot be cast terms small perturbations state. Here we study weak links. Thanks to partial suppression superconductivity links, employ a weakly nonlinear approximation for...
Abstract — Advances in molecular oncology research culminated the development of targeted therapies that act on defined targets either tumor cells directly (such as inhibitors oncogenic kinases), or indirectly by targeting microenvironment anti-angiogenesis drugs). These can induce strong clinical responses, when properly matched to patients. Unfortunately, most ultimately fail tumors evolve resistance. Tumors consist not only neoplastic cells, but also stroma, whereby “stroma” is umbrella...
Ecological and evolutionary dynamics can be strongly affected by population assortment frequency-dependent selection. In growing populations, a particular challenge is to disentangle global ecological effects from local effects. Here we implement logistic growth death model on the scale, coupled rates influenced public goods game between cooperators defectors. For each individual, good only effective within neighborhood of other individuals, good-growth rate relationship nonlinear. At low...
Public goods games (PGGs) describe situations in which individuals contribute to a good at private cost, but others can free-ride by receiving share of the public benefit no cost. The game occurs within local neighbourhoods, are subsets whole population. Free-riding and maximal production two extremes continuous spectrum traits. We study adaptive dynamics neighbourhood size. allow size coevolve observe evolutionary branching. explain how an initially monomorphic population undergoes...
We study the current-voltage characteristic of narrow superconducting strips in gapless regime near critical temperature framework Ginzburg-Landau model. Our focus is on its instabilities occurring at high current biases. The latter are consequences dynamical states with periodic phase-slip events space and time. analyze their structure derive value reentrance onset instability normal state. It expressed terms kinetic coefficient time-dependent equation calculated numerically.
Abstract Non-Hodgkin Lymphoma (NHL) is the most common hematologic malignancy in United States with an estimated 72,000 new cases (4.3% of all cancer cases) and 20,000 deaths (3.4% deaths) 2017; median 5-year survival rate 71%. Despite a possible cure, front-line chemotherapy, there exist patients that do not response or relapse develop refractory disease. These have overall less than seven months. Chimeric antigen receptor (CAR) T-cell therapy for NHL relies on expansion engineered T- cells...
Abstract The optimal Jacobi parameter (ω) in Jacobi's iterative method is obtained for specific classes of matrices. We define ω opt as the worst-case parameter. show that matrices with nonzero elements only along main diagonal and odd diagonals have = 1 . → holds size n d , ∞ where distance from diagonal. Finally, we an application which exploits these derived properties to reduce number required iterations. This especially useful physical problems involve 2nd order implicit PDEs (e.g....