- Purdue University
Bindley Bioscience Center
1203 W. State Street
West Lafayette, IN 47907
Bartek Rajwa
Purdue University, Bindley Bioscience Center, Faculty Member
- Bartek Rajwa’s expertise is in cytomics, a newly emerged research field, integrating a variety of linked technologies... moreBartek Rajwa’s expertise is in cytomics, a newly emerged research field, integrating a variety of linked technologies from flow cytometry through biological imaging to proteomics. The unifying theme for cytomics is an integrated study of the functional role of cellular systems. The research in which Bartek is involved has a direct impact on progress in cytomics, especially in areas of biological cytometry (quantitative cell measurements), but also in biodetection, and consequently biosecurity. Bartek has published over 35 peer-reviewed papers and a number of conferences proceeding papers, and has presented his research at numerous national and international meetings including those of the International Society for Analytical Cytology (ISAC), the International Society for Optical Engineering (SPIE), the American Society for Cell Biology (ASCB), the Society for Biomolecular Sciences (SBS), and others.edit
Motivation: We investigate whether a template-based classification pipeline could be used to identify immunophenotypes in (and thereby classify) a heterogeneous disease with many subtypes. The disease we consider here is Acute Myeloid... more
Motivation: We investigate whether a template-based classification pipeline could be used to identify immunophenotypes in (and thereby classify) a heterogeneous disease with many subtypes. The disease we consider here is Acute Myeloid Leukemia, which is heterogeneous at the morphologic, cytogenetic and molecular levels, with several known subtypes. The prognosis and treatment for AML depends on the subtype. Results: We apply flowMatch, an algorithmic pipeline for flow cytometry data created in earlier work, to compute templates succinctly summarizing classes of AML and healthy samples. We develop a scoring function that accounts for features of the AML data such as heterogeneity to identify immunophenotypes corresponding to various AML subtypes, including APL. All of the AML samples in the test set are classified correctly with high confidence. Availability: flowMatch is available at www.bioconductor.org/packages/devel/bioc/html/flowMatch.html; programs specific to immunophenotyping...
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Dirichlet process mixture of Gaussians (DPMG) has been used in the literature for clustering and density estimation problems. However, many real-world data exhibit cluster distributions that cannot be captured by a single Gaussian.... more
Dirichlet process mixture of Gaussians (DPMG) has been used in the literature for clustering and density estimation problems. However, many real-world data exhibit cluster distributions that cannot be captured by a single Gaussian. Modeling such data sets by DPMG creates several extraneous clusters even when clusters are relatively well-defined. Herein, we present the infinite mixture of infinite Gaussian mixtures (I2GMM) for more flexible modeling of data sets with skewed and multi-modal cluster distributions. Instead of using a single Gaussian for each cluster as in the standard DPMG model, the generative model of I2GMM uses a single DPMG for each cluster. The individual DPMGs are linked together through centering of their base distributions at the atoms of a higher level DP prior. Inference is performed by a collapsed Gibbs sampler that also enables partial parallelization. Experimental results on several artificial and real-world data sets suggest the proposed I2GMM model can pr...
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Non-exhaustive learning (NEL) is an emerging machine-learning paradigm designed to confront the challenge of non-stationary environments characterized by anon-exhaustive training sets lacking full information about the available... more
Non-exhaustive learning (NEL) is an emerging machine-learning paradigm designed to confront the challenge of non-stationary environments characterized by anon-exhaustive training sets lacking full information about the available classes.Unlike traditional supervised learning that relies on fixed models, NEL utilizes self-adjusting machine learning to better accommodate the non-stationary nature of the real-world problem, which is at the root of many recently discovered limitations of deep learning. Some of these hurdles led to a surge of interest in several research areas relevant to NEL such as open set classification or zero-shot learning. The presented study which has been motivated by two important applications proposes a NEL algorithm built on a highly flexible, doubly non-parametric Bayesian Gaussian mixture model that can grow arbitrarily large in terms of the number of classes and their components. We report several experiments that demonstrate the promising performance of t...
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Numerous algorithms are used for nonnegative matrix factorization under the assumption that the matrix is nearly separable. In this paper, we show how to make these algorithms scalable for data matrices that have many more rows than... more
Numerous algorithms are used for nonnegative matrix factorization under the assumption that the matrix is nearly separable. In this paper, we show how to make these algorithms scalable for data matrices that have many more rows than columns, so-called "tall-and-skinny matrices." One key component to these improved methods is an orthogonal matrix transformation that preserves the separability of the NMF problem. Our final methods need to read the data matrix only once and are suitable for streaming, multi-core, and MapReduce architectures. We demonstrate the efficacy of these algorithms on terabyte-sized matrices from scientific computing and bioinformatics.
Lipids play a critical role in the skin as components of the epidermal barrier and as signaling and antimicrobial molecules. Atopic dermatitis in dogs is associated with changes in the lipid composition of the skin, but whether these... more
Lipids play a critical role in the skin as components of the epidermal barrier and as signaling and antimicrobial molecules. Atopic dermatitis in dogs is associated with changes in the lipid composition of the skin, but whether these precede or follow the onset of dermatitis is unclear. We applied rapid lipid-profiling mass spectrometry to skin and blood of 30 control and 30 atopic dogs. Marked differences in lipid profiles were observed between control, nonlesional, and lesional skin. The lipid composition of blood from control and atopic dogs was different, indicating systemic changes in lipid metabolism. Female and male dogs differed in the degree of changes in the skin and blood lipid profiles. Treatment with oclacitinib or lokivetmab ameliorated the skin condition and caused changes in skin and blood lipids. A set of lipid features of the skin was selected as a biomarker that classified samples as control or atopic dermatitis with 95% accuracy, whereas blood lipids discriminate...
Research Interests: Medicine and metabolites
Excipients serve as vehicles, preservatives, solubilizers, and colorants for drugs, food, and cosmetics. They are considered to be inert at biological targets; however, several reports suggest that some could interact with human targets... more
Excipients serve as vehicles, preservatives, solubilizers, and colorants for drugs, food, and cosmetics. They are considered to be inert at biological targets; however, several reports suggest that some could interact with human targets and cause unwanted effects. We investigated 40 commonly used drug excipients for cellular stress in the AsedaSciences® SYSTEMETRIC® Cell Health Screen, which was developed to estimate toxicity risk of small molecular entities (SMEs). The screen uses supervised machine learning (ML) to classify test compound cell stress phenotypes relative to a training set of on-market and withdrawn drugs. While 80% (n = 32) of the excipients did not show elevated risk in a broad, but pharmacologically relevant, concentration range (5 nM to 100 μM), we identified 20% (n = 8) with elevated risk. This group included two mercury containing preservatives, propyl gallate, methylene blue, benzethonium chloride, and cetylpyridinium chloride, all known for previously reported safety issues. All compounds were tested in parallel in an in vitro assay panel regularly used to investigate off-target effects of drug candidates. Target engagement in this assay panel confirmed risk-indicative biological activity for the same excipients, except propyl gallate, which may have a separate, interesting mechanism. We conclude that the SYSTEMETRIC Cell Health Screen, in conjunction with in vitro pharmacological profiling, can provide a fast and cost effective methodology for first line testing of SMEs, including excipients, to avoid cellular damage, particularly in the GI, where they are represented in high concentrations.
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Evaluation of signaling lipids is essential for measuring biological processes. There is a lack of experimental data regarding the proper storage of extracts for signaling lipid analysis, potentially impacting the procedures that can lead... more
Evaluation of signaling lipids is essential for measuring biological processes. There is a lack of experimental data regarding the proper storage of extracts for signaling lipid analysis, potentially impacting the procedures that can lead to accurate and reproducible evaluation. In this study, the importance of pre-analytical conditions for analyzing ion transitions for phosphatidylethanolamines (PEs), an abundant signaling phospholipid, was systematically assessed. A novel workflow was utilized involving an MRM-based experimental approach followed by statistical analysis. Specifically, lipids were extracted from the brain, heart, lungs, and serum of C57BL/6 mice. Extract subsets were resuspended in organic solvents prior to storage in various temperature conditions. Mass spectrometry analysis by multiple reaction monitoring (MRM) profiling was performed at four time points (1 day, 2 weeks, 2 months, or 6 months) to measure relative amounts of PEs in distinct lipid extract aliquots. We introduce an innovative statistical workflow to measure the changes in relative amounts of PEs in the profiles over time to determine lipid extract storage conditions in which fewer profile changes occur. Results demonstrated that time is the most significant factor affecting the changes in lipid samples, with temperature and solvent having comparatively minor effects. We conclude that for lipid extracts obtained by Bligh & Dyer extraction, storage at − 80.0 °C without solvent for less than 2 weeks before analysis is ideal. By considering the data generated by this study, lipid extract storage practices may be optimized and standardized, enhancing the validity and reproducibility of lipid assessments.
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Atopic dermatitis (AD) is a multifactorial disease associated with alterations in lipid composition and organization in the epidermis. Multiple variants of AD exist with different outcomes in response to therapies. The evaluation of... more
Atopic dermatitis (AD) is a multifactorial disease associated with alterations in lipid composition and organization in the epidermis. Multiple variants of AD exist with different outcomes in response to therapies. The evaluation of disease progression and response to treatment are observational assessments with poor inter-observer agreement highlighting the need for molecular markers. SHARPIN-deficient mice (Sharpincpdm) spontaneously develop chronic proliferative dermatitis with features similar to AD in humans. To study the changes in the epidermal lipid-content during disease progression, we tested 72 epidermis samples from three groups (5-, 7-, and 10-weeks old) of cpdm mice and their WT littermates. An agnostic mass-spectrometry strategy for biomarker discovery termed multiple-reaction monitoring (MRM)-profiling was used to detect and monitor 1,030 lipid ions present in the epidermis samples. In order to select the most relevant ions, we utilized a two-tiered filter/wrapper fe...
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BACKGROUND Gastric electrical stimulation (GES) can be a life-changing, device-based treatment option for drug-resistant nausea and vomiting associated with diabetic or idiopathic gastroparesis (GP). Despite over two decades of clinical... more
BACKGROUND Gastric electrical stimulation (GES) can be a life-changing, device-based treatment option for drug-resistant nausea and vomiting associated with diabetic or idiopathic gastroparesis (GP). Despite over two decades of clinical use, the mechanism of action remains unclear. We hypothesize a vagal mechanism. NEW METHOD Here, we describe a noninvasive method to investigate vagal nerve involvement in GES therapy in 66 human subjects through the compound nerve action potential (CNAP). RESULTS Of the 66 subjects, 28 had diabetic GP, 35 had idiopathic GP, and 3 had postsurgical GP. Stimulus charge per pulse did not predict treatment efficacy, but did predict a significant increase in total symptom score in type 1 diabetics as GES stimulus charge per pulse increased (p < 0.01), representing a notable side effect and providing a method to identify it. In contrast, the number of significant left and right vagal fiber responses that were recorded directly related to patient symptom improvement. Increased vagal responses correlated with significant decreases in total symptom score (p < 0.05). COMPARISON WITH EXISTING METHOD(S) We have developed transcutaneous recording of cervical vagal activity that is synchronized with GES in conscious human subjects, along with methods of discriminating the activity of different nerve fiber groups with respect to conduction speed and treatment response. CONCLUSIONS Cutaneous vagal CNAP analysis is a useful technique to unmask relationships among GES parameters, vagal recruitment, efficacy and side-effect management. Our results suggest that CNAP-guided GES optimization will provide the most benefit to patients with idiopathic and type 1 diabetic gastroparesis.
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Flow cytometry has well-established methods for data analysis based on traditional data collection techniques. These techniques typically involved manual insertion of tube samples into an instrument that, historically, could only measure... more
Flow cytometry has well-established methods for data analysis based on traditional data collection techniques. These techniques typically involved manual insertion of tube samples into an instrument that, historically, could only measure 1-3 colors. The field has since evolved to incorporate new technologies for faster and highly automated sample preparation and data collection. For example, the use of microwell plates on benchtop instruments is now a standard on virtually every new instrument, and so users can easily accumulate multiple data sets quickly. Further, because the user must carefully define the layout of the plate, this information is already defined when considering the analytical process, expanding the opportunities for automated analysis. Advances in multi-parametric data collection, as demonstrated by the development of hyperspectral flow-cytometry, 20-40 color polychromatic flow cytometry, and mass cytometry (CyTOF), are game-changing. As data and assay complexity ...
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Compounds that modulate the heat shock protein (HSP) network have potential in a broad range of research applications and diseases. A yeast-based liquid culture assay that measured time-dependent turbidity enabled the high-throughput... more
Compounds that modulate the heat shock protein (HSP) network have potential in a broad range of research applications and diseases. A yeast-based liquid culture assay that measured time-dependent turbidity enabled the high-throughput screening of different Saccharomyces cerevisae strains to identify HSP modulators with unique molecular mechanisms. A focused set of four strains, with differing sensitivities to Hsp90 inhibitors, was used to screen a compound library of 3680 compounds. Computed turbidity curve functions were used to classify strain responses and sensitivity to chemical effects across the compound library. Filtering based on single-strain selectivity identified nine compounds as potential heat shock modulators, including the known Hsp90 inhibitor macbecin. Haploid yeast deletion strains (360), mined from previous Hsp90 inhibitor yeast screens and heat shock protein interaction data, were screened for differential sensitivities to known N-terminal ATP site-directed Hsp90...
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Comparing phenotypes of heterogeneous cell populations from multiple biological conditions is at the heart of scientific discovery based on flow cytometry (FC). When the biological signal is measured by the average expression of a... more
Comparing phenotypes of heterogeneous cell populations from multiple biological conditions is at the heart of scientific discovery based on flow cytometry (FC). When the biological signal is measured by the average expression of a biomarker, standard statistical methods require that variance be approximately stabilized in populations to be compared. Since the mean and variance of a cell population are often correlated in fluorescence-based FC measurements, a preprocessing step is needed to stabilize the within-population variances. We present a variance-stabilization algorithm, called flowVS, that removes the mean-variance correlations from cell populations identified in each fluorescence channel. flowVS transforms each channel from all samples of a data set by the inverse hyperbolic sine (asinh) transformation. For each channel, the parameters of the transformation are optimally selected by Bartlett's likelihood-ratio test so that the populations attain homogeneous variances. T...
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We report a multispectral elastic-light-scatter instrument that can simultaneously detect three-wavelength scatter patterns and associated optical densities from individual bacterial colonies, overcoming the limits of the... more
We report a multispectral elastic-light-scatter instrument that can simultaneously detect three-wavelength scatter patterns and associated optical densities from individual bacterial colonies, overcoming the limits of the single-wavelength predecessor. Absorption measurements on liquid bacterial samples revealed that the spectroscopic information can indeed contribute to sample differentiability. New optical components, including a pellicle beam splitter and an optical cage system, were utilized for robust acquisition of multispectral images. Four different genera and seven shiga toxin producing E. coli serovars were analyzed; the acquired images showed differences in scattering characteristics among the tested organisms. In addition, colony-based spectral optical-density information was also collected. The optical model, which was developed using diffraction theory, correctly predicted wavelength-related differences in scatter patterns, and was matched with the experimental results...
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Flow cytometry (FC) is a widely acknowledged technology in diagnosis of acute myeloid leukemia (AML) and has been indispensable in determining progression of the disease. Although FC plays a key role as a post-therapy prognosticator and... more
Flow cytometry (FC) is a widely acknowledged technology in diagnosis of acute myeloid leukemia (AML) and has been indispensable in determining progression of the disease. Although FC plays a key role as a post-therapy prognosticator and evaluator of therapeutic efficacy, the manual analysis of cytometry data is a barrier to optimization of reproducibility and objectivity. This study investigates the utility of our recently introduced non-parametric Bayesian framework in accurately predicting the direction of change in disease progression in AML patients using FC data. The highly flexible non-parametric Bayesian model based on the infinite mixture of infinite Gaussian mixtures is used for jointly modeling data from multiple FC samples to automatically identify functionally distinct cell populations and their local realizations. Phenotype vectors are obtained by characterizing each sample by the proportions of recovered cell populations, which are in turn used to predict the direction...
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Despite the advancement of recent molecular technologies, culturing is still considered the gold standard for microbial sample analysis. Here we review three different bacterial colony-based screening modalities that provide significant... more
Despite the advancement of recent molecular technologies, culturing is still considered the gold standard for microbial sample analysis. Here we review three different bacterial colony-based screening modalities that provide significant information beyond the simple shape and color of the colony. The plate imaging technique provides numeration and quantitative spectral reflectance information for each colony, while Raman spectroscopic analysis of bacteria colonies relates the Raman-shifted peaks to specific chemical bonding. Finally, the elastic-light-scatter technique provides a volumetric interaction of the whole colony through laser-bacteria interactions, instantly capturing the morphological traits of the colony and allowing quantitative classifications.
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The aim of this work has been to test the biocompatibility of four bioactive, gel derived glass-ceramic materials of CaO-PO2-SiO2 system, modified by addition of boron, aluminum and magnesium compounds. We have examined the growth,... more
The aim of this work has been to test the biocompatibility of four bioactive, gel derived glass-ceramic materials of CaO-PO2-SiO2 system, modified by addition of boron, aluminum and magnesium compounds. We have examined the growth, collagen synthesis, adhesion and morphology of NRK rat fibroblasts cultured in direct and indirect contact with biomaterials. The growth of cells cultures has been quantified by two methods: [3H]thymidine incorporation and direct counting of cells. The level of collagen synthesis has been used as a parameter describing metabolic activity of cells. Cellular morphology has been assessed following 24 h and 4 days of culturing cells on biomaterials by using SEM and confocal microscopy, respectively. Additionally, in order to obtain information about the attachment of cells to substratum the presence of focal contacts has been examined. The results of all the experiments have demonstrated that none of the materials under study significantly altered cellular functions that were tested. This indicates that additions of MgO, Al2O3 and B2O3 have not induced cytotoxicity of the materials under study. This qualifies them for further in vivo experiments.
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n Press: Hyperspectral Cytometry, Gérald Grégori, Bartek Rajwa, Valery Patsekin, James Jones, Motohiro Furuki, Masanobu Yamamoto and J. Paul Robinson: in " Novel techniques of multiparametric cytometry and large scale data analysis... more
n Press: Hyperspectral Cytometry, Gérald Grégori, Bartek Rajwa, Valery Patsekin, James Jones, Motohiro Furuki, Masanobu Yamamoto and J. Paul Robinson: in " Novel techniques of multiparametric cytometry and large scale data analysis " Eds. Fienberg, H & Nolan, G., Publisher Springer, Heidelberg, 2013
Interacting melanocytes and keratinocytes in the epidermis create a unique structure in which keratinocytes regulate the growth of melanocytes and the expression of cell surface molecules. The critical role of communication between these... more
Interacting melanocytes and keratinocytes in the epidermis create a unique structure in which keratinocytes regulate the growth of melanocytes and the expression of cell surface molecules. The critical role of communication between these cells means that any anti-melanoma drug should be studied in the context of its possible influence on keratinocytes. For that reason, this study focused on comparing the influence of daunomycin on human melanoma cells and on keratinocytes in vitro. The effects were studied by cytochemical methods (TUNEL, FITC-Annexin V labelling, endocytosis activity assay, measurements of DNA content) and morphological methods (measurements of cell surface area, perimeter, extension, dispersion and elongation) to verify the hypothesis of differential response. The results of our research demonstrate that keratinocytes are less susceptible than melanoma cells to daunomycin treatment in vitro. Keratinocytes are also able to resume growth when the drug is removed from...
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CD44H is a transmembrane protein involved in cell-cell and cell-matrix interactions. In melanoma cells CD44H influences motility and invasiveness. Daunomycin (daunorubicin) is an anthracycline antibiotic, capable to inducing apoptosis in... more
CD44H is a transmembrane protein involved in cell-cell and cell-matrix interactions. In melanoma cells CD44H influences motility and invasiveness. Daunomycin (daunorubicin) is an anthracycline antibiotic, capable to inducing apoptosis in many cell lines. The data presented in this report show that 12-hours treatment with clinically applied concentration of daunomycin led to apoptotic death of a portion of the investigated melanoma cell population. Surviving cells showed random distribution of CD44H and decreased expression of the protein on the cell surface, but no cell blebbing or changes in nuclei. Hypothetical mechanisms concerning a role of CD44H in induction of apoptosis are discussed.
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Research Interests: Computer Science, Algorithms, Biofilms, Fluorescence, Medicine, and 3 moreSoftware, Humans, and Tooth
We previously described a population of lymphoid progenitor cells (LPCs) in canine B-cell lymphoma defined by retention of the early progenitor markers CD34 and CD117 and “slow proliferation” molecular signatures that persist in the... more
We previously described a population of lymphoid progenitor cells (LPCs) in canine B-cell lymphoma defined by retention of the early progenitor markers CD34 and CD117 and “slow proliferation” molecular signatures that persist in the xenotransplantation setting. We examined whether valspodar, a selective inhibitor of the ATP binding cassette B1 transporter (ABCB1, a.k.a., p-glycoprotein/multidrug resistance protein-1) used in the neoadjuvant setting would sensitize LPCs to doxorubicin and extend the length of remission in dogs with therapy naïve large B-cell lymphoma. Twenty dogs were enrolled into a double-blinded, placebo controlled study where experimental and control groups received oral valspodar (7.5 mg/kg) or placebo, respectively, twice daily for five days followed by five treatments with doxorubicin 21 days apart with a reduction in the first dose to mitigate the potential side effects of ABCB1 inhibition. Lymph node and blood LPCs were quantified at diagnosis, on the fourth...
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Multispectral imaging has been in use for over half a century. Owing to advances in digital photographic technology, multispectral imaging is now used in settings ranging from clinical medicine to industrial quality control. Our efforts... more
Multispectral imaging has been in use for over half a century. Owing to advances in digital photographic technology, multispectral imaging is now used in settings ranging from clinical medicine to industrial quality control. Our efforts focus on the use of multispectral imaging coupled with spectral deconvolution for measurement of endogenous tissue fluorophores and for animal tissue analysis by multispectral fluorescence,
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Protein body-free maize zein, when mixed at 35 degrees C (above its glass transition temperature range), significantly (p &amp;amp;amp;amp;amp;amp;lt; 0.01) improved the rheological and leavening properties of sorghum-wheat composite... more
Protein body-free maize zein, when mixed at 35 degrees C (above its glass transition temperature range), significantly (p &amp;amp;amp;amp;amp;amp;lt; 0.01) improved the rheological and leavening properties of sorghum-wheat composite flour dough, resulting in improved loaf volume. Confocal laser scanning microscopy was used to observe the structure of zein fibrils and the interaction between zein and gluten proteins in the composite dough and bread systems. Autofluorescence and immunolocalization techniques were used to locate gluten and zein, respectively. Optical sections were collected every 0.4 microm through the samples and digitally processed to produce reconstructed three-dimensional images. Results showed that zein fibrils form an outer layer that intermittently coats the gluten networks, thereby strengthening them. This type of microstructure is able to withstand the pressure exerted by gas cell expansion during yeast fermentation to increase loaf volume.
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Biology-driven advances in photonic detection systems have been dramatic in the last several years. Three specific aspects are of particular interest: molecular detection, cellular detection, and whole-organ or small-animal imaging. Each... more
Biology-driven advances in photonic detection systems have been dramatic in the last several years. Three specific aspects are of particular interest: molecular detection, cellular detection, and whole-organ or small-animal imaging. Each area of study requires specific probes, detectors, and analytical processes. The purpose of this paper is to provide an overview of many of the options available today. a. Molecular Detection
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Modern applications of biological microscopy such as high-content screening (HCS), 4D imaging, and multispectral imaging may involve collection of thousands of images in every experiment making efficient image-compression techniques... more
Modern applications of biological microscopy such as high-content screening (HCS), 4D imaging, and multispectral imaging may involve collection of thousands of images in every experiment making efficient image-compression techniques necessary. Reversible compression algorithms, when used with biological micrographs, provide only a moderate compression ratio, while irreversible techniques obtain better ratios at the cost of removing some information from images and introducing artifacts. We construct a model of ...
Research Interests: Computer Science, Algorithms, Biomedical Engineering, Fluorescence Microscopy, Medicine, and 15 moreHigh Content Screening, Image coding, Image compression, Animals, Vascular endothelium, Cattle, Information Content, Theoretical Models, Reproducibility of Results, Computer Methods, Multispectral Images, Compression Ratio, Single Channel, imaging system, and Compression Algorithm
Multispectral imaging has been in use for over half a century. Owing to advances in digital photographic technology, multispectral imaging is now used in settings ranging from clinical medicine to industrial quality control. Our efforts... more
Multispectral imaging has been in use for over half a century. Owing to advances in digital photographic technology, multispectral imaging is now used in settings ranging from clinical medicine to industrial quality control. Our efforts focus on the use of multispectral imaging coupled with spectral deconvolution for measurement of endogenous tissue fluorophores and for animal tissue analysis by multispectral fluorescence, absorbance, and reflectance data. Multispectral reflectance and fluorescence images may be useful in evaluation of ...
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Abstract: We present a framework for online inference in the presence of a nonexhaustively defined set of classes that incorporates supervised classification with class discovery and modeling. A Dirichlet process prior (DPP) model defined... more
Abstract: We present a framework for online inference in the presence of a nonexhaustively defined set of classes that incorporates supervised classification with class discovery and modeling. A Dirichlet process prior (DPP) model defined over class distributions ensures that both known and unknown class distributions originate according to a common base distribution. In an attempt to automatically discover potentially interesting class formations, the prior model is coupled with a suitably chosen data model, and sequential Monte Carlo ...
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Interacting melanocytes and keratinocytes in the epidermis create a unique structure in which keratinocytes regulate the growth of melanocytes and the expression of cell surface molecules. The critical role of communication between these... more
Interacting melanocytes and keratinocytes in the epidermis create a unique structure in which keratinocytes regulate the growth of melanocytes and the expression of cell surface molecules. The critical role of communication between these cells means that any anti-melanoma drug should be studied in the context of its possible influence on keratinocytes. For that reason, this study focused on comparing the influence of daunomycin on human melanoma cells and on keratinocytes in vitro. The effects were studied by cytochemical ...
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Protein body-free maize zein, when mixed at 35 C (above its glass transition temperature range), significantly (p< 0.01) improved the rheological and leavening properties of sorghum-wheat composite flour dough, resulting in improved... more
Protein body-free maize zein, when mixed at 35 C (above its glass transition temperature range), significantly (p< 0.01) improved the rheological and leavening properties of sorghum-wheat composite flour dough, resulting in improved loaf volume. Confocal laser scanning microscopy was used to observe the structure of zein fibrils and the interaction between zein and gluten proteins in the composite dough and bread systems. Autofluorescence and immunolocalization techniques were used to locate gluten and zein ...
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Research Interests: Engineering, Physics, Chemistry, Biology, Medicine, and 3 moreMultidisciplinary, Light, and PLoS one
Disease outbreaks due to contaminated food are a major concern not only for the food-processing industry but also for the public at large. Techniques for automated detection and classification of microorganisms can be a great help in... more
Disease outbreaks due to contaminated food are a major concern not only for the food-processing industry but also for the public at large. Techniques for automated detection and classification of microorganisms can be a great help in preventing outbreaks and maintaining the safety of the nations food supply. Identification and classification of foodborne pathogens using colony scatter patterns is a promising new label-free technique that utilizes image-analysis and machine-learning tools. However, the feature-extraction tools employed for this approach are computationally complex, and choosing the right combination of scatter-related features requires extensive testing with different feature combinations. In the presented work we used computer clusters to speed up the feature-extraction process, which enables us to analyze the contribution of different scatter-based features to the overall classification accuracy. A set of 1000 scatter patterns representing ten different bacterial strains was used. Zernike and Chebyshev moments as well as Haralick texture features were computed from the available light-scatter patterns. The most promising features were first selected using Fishers discriminant analysis, and subsequently a support-vector-machine (SVM) classifier with a linear kernel was used. With extensive testing we were able to identify a small subset of features that produced the desired results in terms of classification accuracy and execution speed. The use of distributed computing for scatter-pattern analysis, feature extraction, and selection provides a feasible mechanism for large-scale deployment of a light scatter-based approach to bacterial classification.