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Work 1-10 of 92

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Article

DNA-Barcoded pMHC Tetramers for Detection of Single Antigen-Specific T Cells by Digital PCR

by Shreyas N. Dahotre; Yun Min Chang; Anna M. Romanov; Gabe Kwong

2019

Subjects
  • Chemistry, Analytical
  • Biology, Microbiology
  • Engineering, Biomedical
  • File Download
  • View Abstract

Abstract:Close

Antigen-specific T cells are found at low frequencies in circulation but carry important diagnostic information as liquid biomarkers in numerous biomedical settings, such as monitoring the efficacy of vaccines and cancer immunotherapies. To enable detection of antigen-specific T cells with high sensitivity, we develop peptide-MHC (pMHC) tetramers labeled with DNA barcodes to detect single T cells by droplet digital PCR (ddPCR). We show that site-specific conjugation of DNA via photocleavable linkers allows barcoded tetramers to stain T cells with similar avidity compared to conventional fluorescent tetramers and efficient recovery of barcodes by light with no loss in cell viability. We design an orthogonal panel of DNA-barcoded tetramers to simultaneously detect multiple antigen-specific T cell populations, including from a mouse model of viral infection, and discriminate single cancer-specific T cells with high diagnostic sensitivity and specificity. This approach of DNA-barcoding can be broadened to encompass additional rare cells for monitoring immunological health at the single cell level.

Article

Semiconductor Quantum Dots for Bioimaging and Biodiagnostic Applications

by Brad Anthony Kairdolf; Andrew M. Smith; Todd H. Stokes; May D. Wang; Andrew N Young; Shuming Nie

2013

Subjects
  • Chemistry, General
  • Engineering, Biomedical
  • Health Sciences, Pathology
  • View on PubMed Central
  • View Abstract

Abstract:Close

Semiconductor quantum dots (QDs) are light-emitting particles on the nanometer scale that have emerged as a new class of fluorescent labels for chemical analysis, molecular imaging, and biomedical diagnostics. Compared with traditional fluorescent probes, QDs have unique optical and electronic properties such as size-tunable light emission, narrow and symmetric emission spectra, and broad absorption spectra that enable the simultaneous excitation of multiple fluorescence colors. QDs are also considerably brighter and more resistant to photobleaching than are organic dyes and fluorescent proteins. These properties are well suited for dynamic imaging at the single-molecule level and for multiplexed biomedical diagnostics at ultrahigh sensitivity. Here, we discuss the fundamental properties of QDs; the development of next-generation QDs; and their applications in bioanalytical chemistry, dynamic cellular imaging, and medical diagnostics. For in vivo and clinical imaging, the potential toxicity of QDs remains a major concern. However, the toxic nature of cadmium-containing QDs is no longer a factor for in vitro diagnostics, so the use of multicolor QDs for molecular diagnostics and pathology is probably the most important and clinically relevant application for semiconductor QDs in the immediate future.

Article

Quasi-periodic patterns (QPP): Large-scale dynamics in resting state fMRI that correlate with local infraslow electrical activity

by Garth John Thompson; Wenju Pan; Matthew Evan Magnuson; Dieter Jaeger; Shella D Keilholz

2014

Subjects
  • Biology, Neuroscience
  • Engineering, Biomedical
  • File Download
  • View Abstract

Abstract:Close

Functional connectivity measurements from resting state blood-oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI) are proving a powerful tool to probe both normal brain function and neuropsychiatric disorders. However, the neural mechanisms that coordinate these large networks are poorly understood, particularly in the context of the growing interest in network dynamics. Recent work in anesthetized rats has shown that the spontaneous BOLD fluctuations are tightly linked to infraslow local field potentials (LFPs) that are seldom recorded but comparable in frequency to the slow BOLD fluctuations. These findings support the hypothesis that long-range coordination involves low frequency neural oscillations and establishes infraslow LFPs as an excellent candidate for probing the neural underpinnings of the BOLD spatiotemporal patterns observed in both rats and humans. To further examine the link between large-scale network dynamics and infraslow LFPs, simultaneous fMRI and microelectrode recording were performed in anesthetized rats. Using an optimized filter to isolate shared components of the signals, we found that time-lagged correlation between infraslow LFPs and BOLD is comparable in spatial extent and timing to a quasi-periodic pattern (QPP) found from BOLD alone, suggesting that fMRI-measured QPPs and the infraslow LFPs share a common mechanism. As fMRI allows spatial resolution and whole brain coverage not available with electroencephalography, QPPs can be used to better understand the role of infraslow oscillations in normal brain function and neurological or psychiatric disorders.

Article

Neural correlates of time-varying functional connectivity in the rat

by Garth John Thompson; Michael Donelyn Merritt; Wenju Pan; Matthew Evan Magnuson; Joshua Koehler Grooms; Dieter Jaeger; Shella Keilholz

2013

Subjects
  • Biology, Neuroscience
  • Engineering, Biomedical
  • File Download
  • View Abstract

Abstract:Close

Functional connectivity between brain regions, measured with resting state functional magnetic resonance imaging, holds great potential for understanding the basis of behavior and neuropsychiatric diseases. Recently it has become clear that correlations between the blood oxygenation level dependent (BOLD) signals from different areas vary over the course of a typical scan (6-10. min in length), though the changes are obscured by standard methods of analysis that assume the relationships are stationary. Unfortunately, because similar variability is observed in signals that share no temporal information, it is unclear which dynamic changes are related to underlying neural events. To examine this question, BOLD data were recorded simultaneously with local field potentials (LFP) from interhemispheric primary somatosensory cortex (SI) in anesthetized rats. LFP signals were converted into band-limited power (BLP) signals including delta, theta, alpha, beta and gamma. Correlation between signals from interhemispheric SI was performed in sliding windows to produce signals of correlation over time for BOLD and each BLP band. Both BOLD and BLP signals showed large changes in correlation over time and the changes in BOLD were significantly correlated to the changes in BLP. The strongest relationship was seen when using the theta, beta and gamma bands. Interestingly, while steady-state BOLD and BLP correlate with the global fMRI signal, dynamic BOLD becomes more like dynamic BLP after the global signal is regressed. As BOLD sliding window connectivity is partially reflecting underlying LFP changes, the present study suggests it may be a valuable method of studying dynamic changes in brain states.

Article

Gain Control of Synaptic Response Function in Cerebellar Nuclear Neurons by a Calcium-Activated Potassium Conductance

by Steven Si Feng; Risa Lin; Volker Gauck; Dieter Jaeger

2013

Subjects
  • Biology, Neuroscience
  • Engineering, Biomedical
  • File Download
  • View Abstract

Abstract:Close

Small conductance Ca2+-activated potassium (SK) current provides an important modulator of excitatory synaptic transmission, which undergoes plastic regulation via multiple mechanisms. We examined whether inhibitory input processing is also dependent on SK current in the cerebellar nuclei (CN) where inhibition provides the only route of information transfer from the cerebellar cortical Purkinje cells. We employed dynamic clamping in conjunction with computer simulations to address this question. We found that SK current plays a critical role in the inhibitory synaptic control of spiking output. Specifically, regulation of SK current density resulted in a gain control of spiking output, such that low SK current promoted large output signaling for large inhibitory cell input fluctuations due to Purkinje cell synchronization. In contrast, smaller nonsynchronized Purkinje cell input fluctuations were not amplified. Regulation of SK density in the CN therefore would likely lead to important consequences for the transmission of synchronized Purkinje cell activity to the motor system.

Article

Infraslow LFP correlates to resting-state fMRI BOLD signals

by Wenju Pan; Garth John Thompson; Matthew Evan Magnuson; Dieter Jaeger; Shella Keilholz

2013

Subjects
  • Engineering, Biomedical
  • Biology, Neuroscience
  • File Download
  • View Abstract

Abstract:Close

The slow fluctuations of the blood-oxygenation-level dependent (BOLD) signal in resting-state fMRI are widely utilized as a surrogate marker of ongoing neural activity. Spontaneous neural activity includes a broad range of frequencies, from infraslow (< 0.5. Hz) fluctuations to fast action potentials. Recent studies have demonstrated a correlative relationship between the BOLD fluctuations and power modulations of the local field potential (LFP), particularly in the gamma band. However, the relationship between the BOLD signal and the infraslow components of the LFP, which are directly comparable in frequency to the BOLD fluctuations, has not been directly investigated. Here we report a first examination of the temporal relation between the resting-state BOLD signal and infraslow LFPs using simultaneous fMRI and full-band LFP recording in rat. The spontaneous BOLD signal at the recording sites exhibited significant localized correlation with the infraslow LFP signals as well as with the slow power modulations of higher-frequency LFPs (1-100. Hz) at a delay comparable to the hemodynamic response time under anesthesia. Infraslow electrical activity has been postulated to play a role in attentional processes, and the findings reported here suggest that infraslow LFP coordination may share a mechanism with the large-scale BOLD-based networks previously implicated in task performance, providing new insight into the mechanisms contributing to the resting state fMRI signal.

Article

Disentangling Multispectral Functional Connectivity With Wavelets

by Jacob C.W. Billings; Garth J. Thompson; Wenju Pan; Matthew E. Magnuson; Alessio Medda; Shella Keilholz

2018

Subjects
  • Biology, Neuroscience
  • Engineering, Biomedical
  • File Download
  • View Abstract

Abstract:Close

The field of brain connectomics develops our understanding of the brain's intrinsic organization by characterizing trends in spontaneous brain activity. Linear correlations in spontaneous blood-oxygen level dependent functional magnetic resonance imaging (BOLD-fMRI) fluctuations are often used as measures of functional connectivity (FC), that is, as a quantity describing how similarly two brain regions behave over time. Given the natural spectral scaling of BOLD-fMRI signals, it may be useful to represent BOLD-fMRI as multiple processes occurring over multiple scales. The wavelet domain presents a transform space well suited to the examination of multiscale systems as the wavelet basis set is constructed from a self-similar rescaling of a time and frequency delimited kernel. In the present study, we utilize wavelet transforms to examine fluctuations in whole-brain BOLD-fMRI connectivity as a function of wavelet spectral scale in a sample (N = 31) of resting healthy human volunteers. Information theoretic criteria measure relatedness between spectrally-delimited FC graphs. Voxelwise comparisons of between-spectra graph structures illustrate the development of preferential functional networks across spectral bands.

Article

Multiscale network representation of physiological time series for early prediction of sepsis

by Supreeth P. Shashikumar; Gari Clifford; Qiao Li; Shamim Nemati

2017

Subjects
  • Engineering, Biomedical
  • File Download
  • View Abstract

Abstract:Close

Objective and Approach: Sepsis, a dysregulated immune-mediated host response to infection, is the leading cause of morbidity and mortality in critically ill patients. Indices of heart rate variability and complexity (such as entropy) have been proposed as surrogate markers of neuro-immune system dysregulation with diseases such as sepsis. However, these indices only provide an average, one dimensional description of complex neuro-physiological interactions. We propose a novel multiscale network construction and analysis method for multivariate physiological time series, and demonstrate its utility for early prediction of sepsis. Main results: We show that features derived from a multiscale heart rate and blood pressure time series network provide approximately 20% improvement in the area under the receiver operating characteristic (AUROC) for four-hour advance prediction of sepsis over traditional indices of heart rate entropy ( versus ). Our results indicate that this improvement is attributable to both the improved network construction method proposed here, as well as the information embedded in the higher order interaction of heart rate and blood pressure time series dynamics. Our final model, which included the most commonly available clinical measurements in patients' electronic medical records and multiscale entropy features, as well as the proposed network-based features, achieved an AUROC of . Significance: Prediction of the onset of sepsis prior to clinical recognition will allow for meaningful earlier interventions (e.g. antibiotic and fluid administration), which have the potential to decrease sepsis-related morbidity, mortality and healthcare costs.

Article

Modeling Left Ventricular Blood Flow Using Smoothed Particle Hydrodynamics

by Andres Caballero; Wenbin Mao; Liang Liang; John Oshinski; Charles Primiano; Raymond McKay; Susheel Kodali; Wei Sun

2017

Subjects
  • Health Sciences, Epidemiology
  • Engineering, Biomedical
  • File Download
  • View Abstract

Abstract:Close

This study aims to investigate the capability of smoothed particle hydrodynamics (SPH), a fully Lagrangian mesh-free method, to simulate the bulk blood flow dynamics in two realistic left ventricular (LV) models. Three dimensional geometries and motion of the LV, proximal left atrium and aortic root are extracted from cardiac magnetic resonance imaging and multi-slice computed tomography imaging data. SPH simulation results are analyzed and compared with those obtained using a traditional finite volume-based numerical method, and to in vivo phase contrast magnetic resonance imaging and echocardiography data, in terms of the large-scale blood flow phenomena usually clinically measured. A quantitative comparison of the velocity fields and global flow parameters between the in silico models and the in vivo data shows a reasonable agreement, given the inherent uncertainties and limitations in the modeling and imaging techniques. The results indicate the capability of SPH as a promising tool for predicting clinically relevant large-scale LV flow information.

Article

Template-based quality assessment of the Doppler Ultrasound signal for fetal monitoring

by Camilo E. Valderrama; Faezeh Marzbanrad; Lisa Stroux; Gari Clifford

2017

Subjects
  • Computer Science
  • Engineering, Electronics and Electrical
  • Engineering, Biomedical
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One dimensional Doppler Ultrasound (DUS) is a low cost method for fetal auscultation. However, accuracy of any metrics derived from the DUS signals depends on their quality, which relies heavily on operator skills. In low resource settings, where skill levels are sparse, it is important for the device to provide real time signal quality feedback to allow the re-recording of data. Retrospectively, signal quality assessment can help remove low quality recordings when processing large amounts of data. To this end, we proposed a novel template-based method, to assess DUS signal quality. Data used in this study were collected from 17 pregnant women using a low-cost transducer connected to a smart phone. Recordings were split into 1990 segments of 3.75 s duration, and hand labeled for quality by three independent annotators. The proposed template-based method uses Empirical Mode Decomposition (EMD) to allow detection of the fetal heart beats and segmentation into short, time-aligned temporal windows. Templates were derived for each 15 s window of the recordings. The DUS signal quality index (SQI) was calculated by correlating the segments in each window with the corresponding running template using four different pre-processing steps: (i) no additional preprocessing, (ii) linear resampling of each beat, (iii) dynamic time warping (DTW) of each beat and (iv) weighted DTW of each beat. The template-based SQIs were combined with additional features based on sample entropy and power spectral density. To assess the performance of the method, the dataset was split into training and test subsets. The training set was used to obtain the best combination of features for predicting the DUS quality using cross validation, and the test set was used to estimate the classification accuracy using bootstrap resampling. A median out of sample classification accuracy on the test set of 85.8% was found using three features; template-based SQI, sample entropy and the relative power in the 160 to 660 Hz range. The results suggest that the new automated method can reliably assess the DUS quality, thereby helping users to consistently record DUS signals with acceptable quality for fetal monitoring.
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