arXiv subjects

Andrew Baumgartner

Publications and source records attributed to Andrew Baumgartner.

10 recordsLinked to original sources

arXiv2026

T-cell repertoire response in individuals with post-acute sequelae of COVID-19

T-cells are central to SARS-CoV-2 clearance and immunological memory, yet their contribution to the persistence of post-acute sequelae of COVID-19 (PASC) remains poorly understood. The immunological features that distinguish individuals who develop PASC from those who recover fully are unresolved, in part due to the phenotypic heterogeneity of the condition and the likely multiplicity of its underlying mechanisms. Here, we profiled longitudinal bulk TCR$\beta$ repertoires from 120 individuals in the INCOV cohort--71 with PASC and 49 without--sampled at two to three time points spanning the acute and post-acute phases of infection. Using robust statistical modeling of repertoire composition and clonal dynamics, we found that global statistics such as V, J gene usage and CDR3 length do not differ between groups, but that locally enriched sequence motifs and differentially dynamic clones reveal distinct T-cell signatures associated with PASC status. Clones contracting following the peak of the acute response were significantly enriched for SARS-CoV-2 specificity in both groups. Interestingly, Influenza A-specific TCRs were disproportionately enriched among contracting clones in PASC{$^+$} repertoires, implicating viral co-infection as a potential contributor to early disease severity and, possibly, PASC pathogenesis. Rare public TCR clones were markedly enriched for SARS-CoV-2 specificity, with PASC{$^+$} individuals harboring a modestly but significantly higher proportion than PASC{$^-$} individuals. Together, we identified over 1,000 candidate TCR$\beta$ receptors potentially discriminating PASC{$^+$} from PASC{$^-$} immune responses, opening a path toward the identification of disease-relevant T-cell specificities and the development of T-cell-based immunological biomarkers for long COVID.

q-bio.GN↗

arXiv2024

Dimensional reduction of gradient-like stochastic systems with multiplicative noise via Fokker-Planck diffusion maps

Dimensional reduction techniques have long been used to visualize the structure and geometry of high dimensional data. However, most widely used techniques are difficult to interpret due to nonlinearities and opaque optimization processes. Here we present a specific graph based construction for dimensionally reducing continuous stochastic systems with multiplicative noise moving under the influence of a potential. To achieve this, we present a specific graph construction which generates the Fokker-Planck equation of the stochastic system in the continuum limit. The eigenvectors and eigenvalues of the normalized graph Laplacian are used as a basis for the dimensional reduction and yield a low dimensional representation of the dynamics which can be used for downstream analysis such as spectral clustering. We focus on the use case of single cell RNA sequencing data and show how current diffusion map implementations popular in the single cell literature fit into this framework.

q-bio.QM↗

arXiv2022

Imputing Missing Observations with Time Sliced Synthetic Minority Oversampling Technique

We present a simple yet novel time series imputation technique with the goal of constructing an irregular time series that is uniform across every sample in a data set. Specifically, we fix a grid defined by the midpoints of non-overlapping bins (dubbed "slices") of observation times and ensure that each sample has values for all of the features at that given time. This allows one to both impute fully missing observations to allow uniform time series classification across the entire data and, in special cases, to impute individually missing features. To do so, we slightly generalize the well-known class imbalance algorithm SMOTE \cite{smote} to allow component wise nearest neighbor interpolation that preserves correlations when there are no missing features. We visualize the method in the simplified setting of 2-dimensional uncoupled harmonic oscillators. Next, we use tSMOTE to train an Encoder/Decoder long-short term memory (LSTM) model with Logistic Regression for predicting and classifying distinct trajectories of different 2D oscillators. After illustrating the the utility of tSMOTE in this context, we use the same architecture to train a clinical model for COVID-19 disease severity on an imputed data set. Our experiments show an improvement over standard mean and median imputation techniques by allowing a wider class of patient trajectories to be recognized by the model, as well as improvement over aggregated classification models.

cs.LG↗

arXiv2020

Flavor Broken QCD$_3$ at Large N

We examine the vacuum structure of QCD$_3$ with flavor group $U(f)\times U(N_f-f)$ in the limit $N\to\infty$ with $g^2N=$fixed. We find that, generically, the resolution of critical points into a series of first order pahse transitions persists at special locations in the phase diagram. In particular, the number of Grassmannians that one traverses and their locations in the phase diagram is a function of $f$.

hep-th↗

arXiv2019

Generalization of QCD$_3$ Symmetry-Breaking and Flavored Quiver Dualities

We extend the recently proposed symmetry breaking scenario of QCD$_3$ to the so-called "master" $(2+1)$d bosonization duality, which has bosonic and fermionic matter on both ends. Using anomaly arguments, a phase diagram emerges with several novel regions. We then construct $2+1$ dimensional dualities for flavored quivers using node-by-node dualization. Such dualities are applicable to theories which live on domain walls in QCD$_4$-like theories with dynamical quarks. We also derive dualities for quivers based on orthogonal and symplectic gauge groups. Lastly, we support the conjectured dualities using holographic constructions, even though several aspects of this holographic construction remain mostly qualitative.

hep-th↗

arXiv2019

Phases of Flavor Broken QCD$_3$

We map out the phase diagram of QCD$_3$ with a product flavor group of the form $U(f)\times U(F)$. We find interesting structures emerge when $f+F>k$ depending on the relative sizes of $f$,$F$ and $k$. In particular, there exists phase transitions in which a Grassmannian phase will disappear and reappear in a different part of the phase diagram.

hep-th↗

arXiv2018

Novel 3d bosonic dualities from bosonization and holography

We use 3d bosonization dualities to derive new non-supersymmetric dualities between bosonic quiver theories in $2+1$ dimensions. It is shown that such dualities are a natural non-Abelian generalization of the bosonic particle-vortex duality. A special case of such dualities is applicable to Chern-Simons theories living on interfaces in $3+1$ dimensional $SU(N)$ Yang-Mills theory across which the theta angle jumps. We also analyze such interfaces in a holographic construction which provides further evidence for novel dualities between quiver gauge theories and gauge theories with adjoint scalars. These conjectured dualities pass some stringent consistency tests.

hep-th↗

arXiv2018

Phase Transitions and Conductivties of Floquet Fluids

We investigate the phase structure and conductivity of a relativistic fluid in a circulating electric field with a transverse magnetic field. This system exhibits behavior similar to other driven systems such as strongly coupled driven CFTs [Rangamani2015] or a simple anharmonic oscillator. We identify distinct regions of fluid behavior as a function of driving frequency, and argue that a "phase" transition will occur. Such a transition could be measurable in graphene, and may be characterized by sudden discontinuous increase in the Hall conductivity. The presence of the discontinuity depends on how the boundary is approached as the frequency or amplitude is dialed. In the region where two solution exists the measured conductivity will depend on how the system is prepared.

hep-th↗

arXiv2017

3d Abelian Dualities with Boundaries

We establish the action of three-dimensional bosonization and particle-vortex duality in the presence of a boundary, which supports a non-anomalous two-dimensional theory. We confirm our prescription using a microscopic realization of the duality in terms of a Euclidean lattice.

hep-th↗

arXiv2017

Magnetoresistance in relativistic hydrodynamics without anomalies

We present expressions for the magnetoconductivity and the magnetoresistance of a strongly interacting metal in 3+1 dimensions, derivable from relativistic hydrodynamics. Such an approach is suitable for ultraclean metals with emergent Lorentz invariance. When this relativistic fluid contains chiral anomalies, it is known to exhibit longitudinal negative magnetoresistance. We show that similar effects can arise in non-anomalous relativistic fluids due to the distinctive gradient expansion. In contrast with a Galilean-invariant fluid, the resistivity tensor of a dirty relativistic fluid exhibits similar angular dependence to negative magnetoresistance, even when the constitutive relations and momentum relaxation rate are isotropic. We further account for the effect of magnetic field-dependent corrections to the gradient expansion and the effects of long-wavelength impurities on magnetoresistance. We note that the holographic D3/D7 system exhibits negative magnetoresistance.

hep-th↗