Bahram Parvin

• Ph.D.
• Director of Bioengineering at University of Nevada, Reno

The detection and identification of microbial pathogens in meat and fresh produce play an essential role in food safety for reducing foodborne illnesses every year. A new approach based on targeting a specific sequence of the 16S rRNA region for each bacterium is proposed and validated. The probe complex consists of a C60, a conjugated RNA detector...

Motivation: Organization of the organoid models, imaged in 3D with a confocal microscope, is an essential morphometric index to assess responses to stress or therapeutic targets. In fact, differentiating malignant and normal cells is often difficult in monolayer cultures. But in 3D culture, colony organization can provide a clear set of indices fo...

Reprogramming the tumor stroma is an emerging approach to circumventing the challenges of conventional cancer therapies. This strategy, however, is hampered by the lack of a specific molecular target. We previously reported that stromal fibroblasts (FBs) with high expression of CD36 could be utilized for this purpose. These studies are now expanded...

Tumor and stroma coevolve to facilitate tumor growth. Hence, effective tumor therapeutics would not only induce growth suppression of tumor cells but also revert pro-tumor stroma into anti-tumoral type. Previously, we showed that coculturing triple-negative or luminal A breast cancer cells with CD36⁺ fibroblasts (FBs) in a three-dimensional extrace...

Simple Summary Identifying biomarkers of survival from a large-scale cohort of Glioblastoma Multiforme (GBM) pathology images is hindered by heterogeneity of tumor signature compounded by age being the single most important confounder in predicting survival in GBM. The main contributions of this manuscript are to define (i) metrics for identifying...

Profiling of Patient-Derived organoids is necessary for drug screening and precision medicine. This step requires accurate segmentation of three-dimensional cellular structures followed by protein readouts. While fully Convolutional Neural Networks are widely used in medical image segmentation, they struggle to capture long-range dependencies neces...

Vision Transformers have shown superior performance to the traditional convolutional-based frameworks in many vision applications, including but not limited to the segmentation of 3D medical images. To further advance this area, this study introduces the Multi-Aperture Fusion of Transformer-Convolutional Network (MFTC-Net), which integrates the out...

During space travel, astronauts will experience a unique environment that includes continuous exposure to microgravity and stressful living conditions. Physiological adaptation to this is a challenge and the effect of microgravity on organ development, architecture, and function is not well understood. How microgravity may impact the growth and dev...

High-resolution terrain models of open-pit mine highwalls and benches are essential in developing new automated slope monitoring systems for operational optimization. This paper presents several contributions to the field of remote sensing in surface mines providing a practical framework for generating high-resolution images using low-trim Unmanned...

Aerial imaging of an open-pit mine integrated with the visual analytics offers a novel approach for routine monitoring of tension cracks for mine safety. Tension cracks may occur on work- or catch-benches that are excavated according to a CAD model. The size of the tension cracks, their locations, and evolutions is commonly used to predict slope fa...

Human breast tumors are not fully autonomous. They are dependent on nutrients and growth-promoting signals provided by the supporting stromal cells. Within the tumor microenvironment, one of the secreted macromolecules by tumor cells is activin A, where we show to downregulate CD36 in fibroblasts. Downregulation of CD36 in fibroblasts also increase...

Motivation: Aberrant 3D colony organization of premalignant human mammary epithelial cells (HMEC) is one of the indices of dysplasia. An experiment has been designed where the stiffness of the microenvironment, in 3D culture, has been set at either low or high level of mammographic density and the organoid models are exposed to 50cGy X-ray radiati...

Motivation: Our previous study has shown that ERBB2 is overexpressed in the organoid model of MCF10A when the stiffness of the microenvironment is increased to that of high mammographic density (MD). We now aim to identify key transcription factors (TFs) and functional enhancers that regulate processes associated with increased stiffness of the mi...

Motivation: Nuclear delineation and phenotypic profiling are important steps in the automated analysis of histology sections. However, these are challenging problems due to (i) technical variations (e.g., fixation, staining) that originate as a result of sample preparation; (ii) biological heterogeneity (e.g., vesicular versus high chromatin pheno...

Background: Nuclear segmentation is an important step for profiling aberrant regions of histology sections. If nuclear segmentation can be resolved, then new biomarkers of nuclear phenotypes and their organization can be predicted for the application of precision medicine. However, segmentation is a complex problem as a result of variations in nuc...

Aberration in tissue architecture is an essential index for cancer diagnosis and tumor grading. Therefore, extracting features of aberrant phenotypes and classification of the histology tissue can provide a model for computer-aided pathology (CAP). As a case study, we investigate the application of convolutional neural networks (CNN)s for tumor gra...

Nuclear segmentation is an important step in quantitative profiling of colony organization in 3D cell culture models. However, complexities arise from technical variations and biological heterogeneities. We proposed a new 3D segmentation model based on convolutional neural networks for 3D nuclear segmentation, which overcome the complexities associ...

Document S1. Supplemental Experimental Procedures, Figures S1–S7, and Tables S1 and S2

Aging is associated with tissue-level changes in cellular composition that are correlated with increased susceptibility to disease. Aging human mammary tissue shows skewed progenitor cell potency, resulting in diminished tumor-suppressive cell types and the accumulation of defective epithelial progenitors. Quantitative characterization of these age...

Quantum Cascade Laser InfRared (QCL-IR) microscopy has the potential to emerge as a unique modality for the diagnostics of histology sections. A pilot experiment is designed to evaluate whether benign and malignant breast histology sections can be differentiated using chemical profiling and without the use of spatial information. The experiment con...

Nuclear segmentation is an important step for profiling aberrant regions of histology sections. However, segmentation is a complex problem as a result of variations in nuclear geometry (e.g., size, shape), nuclear type (e.g., epithelial, fibroblast), and nuclear phenotypes (e.g., vesicular, aneuploidy). The problem is further complicated as a resul...

Background Rapid identification of bacteria can play an important role at the point of care, evaluating the health of the ecosystem, and discovering spatiotemporal distributions of a bacterial community. We introduce a method for rapid identification of bacteria in live cell assays based on cargo delivery of a nucleic acid sequence and demonstrate...

Detection of nuclei is an important step in phenotypic profiling of (a) histology sections imaged in bright field; and (b) colony formation of the 3D cell culture models that are imaged using confocal microscopy. It is shown that feature-based representation of the original image improves color decomposition and subsequent nuclear detection using c...

Detection of nuclei is an important step in phe-notypic profiling of histology sections that are usually imaged in bright field. However, nuclei can have multiple phenotypes, which are difficult to model. It is shown that convolutional neu-ral networks (CNN)s can learn different phenotypic signatures for nuclear detection, and that the performance...

Detection of nuclei is an important step in phenotypic profiling of histology sections that are usually imaged in bright field. However, nuclei can have multiple phenotypes, which are difficult to model. It is shown that convolutional neural networks (CNN)s can learn different phenotypic signatures for nuclear detection, and that the performance is...

Integrative analysis based on quantitative representation of whole slide images (WSIs) in a large histology cohort may provide predictive models of clinical outcome. On one hand, the efficiency and effectiveness of such representation is hindered as a result of large technical variations (e.g., fixation, staining) and biological heterogeneities (e....

Classification of histology sections in large cohorts, in terms of distinct regions of microanatomy (e.g., stromal) and histopathology (e.g., tumor, necrosis), enables the quantification of tumor composition, and the construction of predictive models of genomics and clinical outcome. To tackle the large technical variations and biological heterogen...

Scientific Reports 6 : Article number: 28987 10.1038/srep28987 ; published online: 07 July 2016 ; updated: 24 August 2016 The original version of this Article contained a typographical error in the spelling of the author Gerald Fontenay, which was incorrectly given as Gerald Fonteney.

The effects of the stiffness of the microenvironment on the molecular response of 3D colony organization, at the maximum level of mammographic density (MD), are investigated. Phenotypic profiling reveals that 3D colony formation is heterogeneous and increased stiffness of the microenvironment, within the range of the MD, correlates with the increas...

BioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization...

BioSig3D Services. (DOCX)

(BioSig3D: Image linking video with the experimental variables) A video presenting how to use the java app to link images with experimental factors. (MP4)

(Biosig3D: Visualization and bioinformatics analysis) A video presenting visualization and bioinformatics analysis in BioSig3D. (MP4)

3D stack for a representative of MCF7 at day 12 with scale. (AVI)

3D stack for a representative of MDA-MB-468 at day 5 with scale. (AVI)

3D stack for a representative of MDA-MB-468 at day 7 with scale. (AVI)

Integration of image analysis and visualization modules. (DOCX)

(BioSig3D: Experimental Design Video) A video presenting the process of experimental design in BioSig3D. (MP4)

3D stack for a representative of MCF10A at day 2 with scale (second example). (AVI)

3D stack for a representative of MCF10A at day 7 with scale. (AVI)

3D stack for a representative of MCF7 at day 5 with scale. (AVI)

3D stack for a representative of MDA-MB-231at day 7 with scale. (AVI)

BioSig3D overview. (MP4)

Colony organization and computed indices. (DOCX)

(BioSig3D: Resource Manager Video): A video presenting the use and application of resource manager. (MP4)

(BioSig3D Uploading Images Video) A video presenting how to upload images into BioSig3D for visualization of processing. (MP4)

3D stack for a representative of MCF10A at day 2 with scale (first example). (AVI)

3D stack for a representative of MCF10A at day 12 with scale. (AVI)

3D stack for a representative of MCF7at day 2 with scale. (AVI)

3D stack for a representative of MCF7 at day 7 with scale. (AVI)

3D stack for a representative of MDA-MB-231at day 2 with scale. (AVI)

3D stack for a representative of MDA-MB-468 at day 2 with scale. (AVI)

Schema definition for computed indices. (PDF)

(BioSig3D: Plate Layout Video) A video presenting how to do plate layout for high content screening. (MP4)

3D stack for a representative of MCF10A at day 5 with scale. (AVI)

3D stack for a representative of MDA-MB-231at day 5 with scale. (AVI)

Cellular response to stress can be manifested and visualized by measuring induced DNA damage. However, cellular systems can repair the damage through a variety of DNA repair pathways. It is important to characterize the dynamics of DNA repair in a variety of model systems. Such a characterization is another example of the video bioinformatics throu...

To date, in situ visualization of microbial density has remained an open problem. Here, functionalized buckyballs (e.g., C60-pyrrolidine tris acid) are shown to be a versatile platform that allows internalization within a microorganism without either adhering to the cell wall and cell membrane or binding to a matrix substrate such as soil. These mo...

Presents the introductory editorial for this issue of the publication.

Determining at least one of a prognosis or a therapy for a patient based on a stained tissue section of the patient. An image of a stained tissue section of a patient is processed by a processing device. A set of features values for a set of cell-based features is extracted from the processed image, and the processed image is associated with a part...

Image-based classification of histology sections, in terms of distinct components (e.g., tumor, stroma, normal), provides a series of indices for histology composition (e.g., the percentage of each distinct components in histology sections), and enables the study of nuclear properties within each component. Furthermore, the study of these indices,...

The introduction of tools to study, control or expand the inner-workings of algae has been slow to develop. Provided are embodiments of a molecular method based on guanidinium-rich molecular transporters (GR-MoTrs) for bringing molecular cargos into algal cells. The methods of the disclosure have been shown to work in wild-type algae that have an i...

Embodiments disclosed herein provide methods and systems for delineating cell nuclei and classifying regions of histopathology or microanatomy while remaining invariant to batch effects. These systems and methods can include providing a plurality of reference images of histology sections. A first set of basis functions can then be determined from t...

Classification of histology sections from large cohorts, in terms of distinct regions of microanatomy (e.g., tumor, stroma, normal), enables the quantification of tumor composition, and the construction of predictive models of the clinical outcome. To tackle the batch effects and biological heterogeneities that are persistent in large co-horts, spa...

Automated profiling of nuclear architecture, in histology sections, can potentially help predict the clinical outcomes. However, the task is challenging as a result of nuclear pleomorphism and cellular states (e.g., cell fate, cell cycle), which are compounded by the batch effect (e.g., variations in fixation and staining). Present methods, for nuc...

http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=7045859

The current trend in high throughput screening is the utilization of more complex model systems that mimic both structural and functional properties of cellular processes in vivo. In this context, 3D cell culture models have emerged as effective systems to study tumor initiation and cancer be-havior, where colony organization represents distinct ph...

The articles in this special section focus on the interaction among researchers from the biological, optical, computer science, and signal processing communities by 1) presenting cutting-edge signal processing research in quantitative bioimaging and 2) bringing the vast scope of ongoing open problems and novel applications to the attention of the s...

Histology is the microscopic inspection of plant or animal tissue. It is a critical component in diagnostic medicine and a tool for studying the pathogenesis and biology of processes such as cancer and embryogenesis. Tissue processing for histology has become increasingly automated, drastically increasing the speed at which histology labs can produ...

Integrated analysis of tissue histology with the genome-wide array and clinical data has the potential to generate hypotheses as well as be prognostic. However, due to the inherent technical and biological variations, automated analysis of whole mount tissue sections is impeded in very large datasets, such as The Cancer Genome Atlas (TCGA), where t...

One minute video for CVPR2013

Membrane-bound macromolecules play an important role in tissue architecture and cell-cell communication, and is regulated by almost one-third of the genome. At the optical scale, one group of membrane proteins expresses themselves as linear structures along the cell surface boundaries, while others are sequestered; and this paper targets the former...

Telomere malfunction and other types of DNA damage induce an activin A-dependent stress response in mortal nontumorigenic human mammary epithelial cells that subsequently induces desmoplastic-like phenotypes in neighboring fibroblasts. Some characteristics of this fibroblast/stromal response, such as reduced adipocytes and increased extracellular m...

Image-based classification of histology sections plays an important role in predicting clinical outcomes. How-ever this task is very challenging due to the presence of large technical variations (e.g., fixation, staining) and bi-ological heterogeneities (e.g., cell type, cell state). In the field of biomedical imaging, for the purposes of vi-sualiz...

When the amount of labeled data are limited, semi-supervised learning can improve the learner's performance by also using the often easily available unlabeled data. In particular, a popular approach requires the learned function to be smooth on the underlying data manifold. By approximating this manifold as a weighted graph, such graph-based techni...

The field of bioengineering has pioneered the application of new precision fabrication technologies to model the different geometric, physical or molecular components of tissue microenvironments on solid-state substrata. Tissue engineering approaches building on these advances are used to assemble multicellular mimetic-tissues where cells reside wi...

Substituted rosamines are efficiently prepared through a new organometallic addition to an iminesubstituted xanthone as a novel primary amine equivalent. The synthesis reduces the number of synthetic steps to the targeted rosamines, for convenient and facile access to potential libraries of rosamine dyes. The prepared rosamine derivatives represent...

Image-based classification of tissue histology, in terms of distinct histopathology (e.g., tumor or necrosis regions), provides a series of indices for tumor composition. Furthermore, aggregation of these indices from each whole slide image (WSI) in a large cohort can provide predictive models of clinical outcome. However, the performance of the ex...

Image-based classification of tissue histology, in terms of different components (e.g., subtypes of aberrant phenotypic signatures), provides a set of indices for tumor composition. Subsequently, integration of these indices in whole slide images (WSI), from a large cohort, can provide predictive models of the clinical outcome. However, the perform...

Our goal is to develop a screening platform for quantitative profiling of colony organizations in three-dimensional (3D) cell culture models. The 3D cell culture models, which are also imaged in 3D, are functional assays that mimic the in-vivo characteristics of the tissue architecture more faithfully than the 2D cultures. However, they also introd...