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3. Diffraction as scattering under the Born approximation

Author

Goswami, Neha and Popescu, Gabriel

Subjects
Physics - Optics
Abstract

Light diffraction at an aperture is a basic problem that has generated a tremendous amount of interest in optics. Some of the most significant diffraction results are the Fresnel-Kirchhoff and Rayleigh-Sommerfeld formulas. These theories are based on solving the wave equation using Green's theorem and result in slightly different expressions depending on the particular boundary conditions employed. In this paper, we propose another approach for solving the diffraction by a thin screen, which includes apertures, gratings, transparencies etc. We show that, applying the first order Born approximation to 2D objects, we obtain a general diffraction formula, without angular approximations. We discuss several common approximations and place our results in the context of existing theories.

Published
2021
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7. Roadmap on Label‐Free Super‐Resolution Imaging (Laser Photonics Rev. 17(12)/2023)

Author

Astratov, Vasily N., primary, Sahel, Yair Ben, additional, Eldar, Yonina C., additional, Huang, Luzhe, additional, Ozcan, Aydogan, additional, Zheludev, Nikolay, additional, Zhao, Junxiang, additional, Burns, Zachary, additional, Liu, Zhaowei, additional, Narimanov, Evgenii, additional, Goswami, Neha, additional, Popescu, Gabriel, additional, Pfitzner, Emanuel, additional, Kukura, Philipp, additional, Hsiao, Yi‐Teng, additional, Hsieh, Chia‐Lung, additional, Abbey, Brian, additional, Diaspro, Alberto, additional, LeGratiet, Aymeric, additional, Bianchini, Paolo, additional, Shaked, Natan T., additional, Simon, Bertrand, additional, Verrier, Nicolas, additional, Debailleul, Matthieu, additional, Haeberlé, Olivier, additional, Wang, Sheng, additional, Liu, Mengkun, additional, Bai, Yeran, additional, Cheng, Ji‐Xin, additional, Kariman, Behjat S., additional, Fujita, Katsumasa, additional, Sinvani, Moshe, additional, Zalevsky, Zeev, additional, Li, Xiangping, additional, Huang, Guan‐Jie, additional, Chu, Shi‐Wei, additional, Tzang, Omer, additional, Hershkovitz, Dror, additional, Cheshnovsky, Ori, additional, Huttunen, Mikko J., additional, Stanciu, Stefan G., additional, Smolyaninova, Vera N., additional, Smolyaninov, Igor I., additional, Leonhardt, Ulf, additional, Sahebdivan, Sahar, additional, Wang, Zengbo, additional, Luk'yanchuk, Boris, additional, Wu, Limin, additional, Maslov, Alexey V., additional, Jin, Boya, additional, Simovski, Constantin R., additional, Perrin, Stephane, additional, Montgomery, Paul, additional, and Lecler, Sylvain, additional

Published
2023
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10. MicroRNA-146a modulates B-cell oncogenesis by regulating Egr1

Author

Contreras, Jorge R, Palanichamy, Jayanth Kumar, Tran, Tiffany M, Fernando, Thilini R, Rodriguez-Malave, Norma I, Goswami, Neha, Arboleda, Valerie A, Casero, David, and Rao, Dinesh S

Subjects
Cancer, Biotechnology, Genetics, Aetiology, 2.1 Biological and endogenous factors, Animals, Apoptosis, B-Lymphocytes, Biomarkers, Tumor, Blotting, Western, Cell Proliferation, Cell Transformation, Neoplastic, Cells, Cultured, Early Growth Response Protein 1, Flow Cytometry, Gene Expression Regulation, Neoplastic, High-Throughput Nucleotide Sequencing, Humans, Lymphoma, B-Cell, Mice, Mice, Knockout, Mice, Transgenic, MicroRNAs, NF-kappa B, Proto-Oncogene Proteins c-myc, RNA, Messenger, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, microRNA, B-cell, lymphoma, leukemia, c-Myc, Oncology and Carcinogenesis
Abstract

miR-146a is a NF-κB induced microRNA that serves as a feedback regulator of this critical pathway. In mice, deficiency of miR-146a results in hematolymphoid cancer at advanced ages as a consequence of constitutive NF-κB activity. In this study, we queried whether the deficiency of miR-146a contributes to B-cell oncogenesis. Combining miR-146a deficiency with transgenic expression of c-Myc led to the development of highly aggressive B-cell malignancies. Mice transgenic for c-Myc and deficient for miR-146a were characterized by significantly shortened survival, increased lymph node involvement, differential involvement of the spleen and a mature B-cell phenotype. High-throughput sequencing of the tumors revealed significant dysregulation of approximately 250 genes. Amongst these, the transcription factor Egr1 was consistently upregulated in mice deficient for miR-146a. Interestingly, transcriptional targets of Egr1 were enriched in both the high-throughput dataset and in a larger set of miR-146a-deficient tumors. miR-146a overexpression led to downregulation of Egr1 and downstream targets with concomitant decrease in cell growth. Direct targeting of the human EGR1 by miR-146a was seen by luciferase assay. Together our findings illuminate a bona fide role for miR-146a in the modulation of B-cell oncogenesis and reveal the importance of understanding microRNA function in a cell- and disease-specific context.

Published
2015

24. Detection and classification of SARS-CoV-2 through phase imaging with computational specificity (PICS)

Author

Goswami, Neha, primary, He, Yuchen R., additional, Deng, Yu-Heng, additional, Oh, Chamteut, additional, Chowdhury, Sajeeb Roy, additional, Sobh, Nahil, additional, Valera, Enrique, additional, Bashir, Rashid, additional, Ismail, Nahed, additional, Kong, Hyun Joon, additional, Nguyen, Thanh H., additional, Best-Popescu, Catherine, additional, and Popescu, Gabriel, additional

Published
2022
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38. STXBP6, reciprocally regulated with autophagy, reduces triple negative breast cancer aggressiveness

Author

Lenka, Govinda, primary, Shan, Jingxuan, additional, Halabi, Najeeb, additional, Abuaqel, Sirin W J, additional, Goswami, Neha, additional, Schmidt, Frank, additional, Zaghlool, Shaza, additional, Romero, Atilio Reyes, additional, Subramanian, Murugan, additional, Boujassoum, Salha, additional, Al‐Bozom, Issam, additional, Gehani, Salah, additional, Khori, Noor Al, additional, Bedognetti, Davide, additional, Suhre, Karsten, additional, Ma, Xiaojing, additional, Dömling, Alexander, additional, Rafii, Arash, additional, and Chouchane, Lotfi, additional

Published
2020
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40. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells*[S]

Author

Billing, Anja M., primary, Dib, Shaima S., additional, Bhagwat, Aditya M., additional, da Silva, Israel T., additional, Drummond, Rodrigo D., additional, Hayat, Shahina, additional, Al-Mismar, Rasha, additional, Ben-Hamidane, Hisham, additional, Goswami, Neha, additional, Engholm-Keller, Kasper, additional, Larsen, Martin R., additional, Suhre, Karsten, additional, Rafii, Arash, additional, and Graumann, Johannes, additional

Published
2019
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43. Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers

Author

Billing, Anja M., primary, Ben Hamidane, Hisham, additional, Dib, Shaima S., additional, Cotton, Richard J., additional, Bhagwat, Aditya M., additional, Kumar, Pankaj, additional, Hayat, Shahina, additional, Yousri, Noha A., additional, Goswami, Neha, additional, Suhre, Karsten, additional, Rafii, Arash, additional, and Graumann, Johannes, additional

Published
2016
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44. SIRT1 Limits Adipocyte Hyperplasia through c-Myc Inhibition

Author

Abdesselem, Houari, primary, Madani, Aisha, additional, Hani, Ahmad, additional, Al-Noubi, Muna, additional, Goswami, Neha, additional, Ben Hamidane, Hisham, additional, Billing, Anja M., additional, Pasquier, Jennifer, additional, Bonkowski, Michael S., additional, Halabi, Najeeb, additional, Dalloul, Rajaa, additional, Sheriff, Mohamed Z., additional, Mesaeli, Nasrin, additional, ElRayess, Mohamed, additional, Sinclair, David A., additional, Graumann, Johannes, additional, and Mazloum, Nayef A., additional

Published
2016
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45. Comprehensive Characterization Of The Differentiation Of Human Embryonic Stem Cells Into Mesenchymal Stem Cells

Author

Billing, Anja M, primary, Dib, Shaima S., additional, Ben Hamidane, Hisham, additional, Goswami, Neha, additional, Al-mismar, Rasha, additional, Cotton, Richard, additional, Kumar, Pankaj, additional, Hayat, Shahina, additional, Pasquier, Jennifer, additional, Suhre, Karsten, additional, Rafii, Arash, additional, and Graumann, Johannes, additional

Published
2014
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48. Comprehensive Proteomic Profiling of Converted Adipocyte-like Cells from Normal Human Dermal Fibroblasts Using Data-Independent Acquisition Mass Spectrometry.

Author

Choi S, Dalloul RSD, Vemulapalli PB, Yousef S, Goswami N, and Schmidt F

Abstract

Adipocytes play an important role in the regulation of systemic energy homeostasis and are closely related to metabolic disorders, such as type-2 diabetes and inflammatory bowel diseases. Particularly, there is an increasing need for a human adipocyte model for studying metabolic diseases and obesity. However, utilizing human primary adipocyte culture and stem-cell-based models presents several practical limitations due to their time-consuming nature, requirement for relatively intensive labor, and high cost. Here, we applied direct conversion of normal human dermal fibroblasts (NHDFs) into adipocyte-like cells using an adipogenic cocktail containing 3-isobutyl-1-methylxanthine (IBMX), dexamethasone, insulin, and rosiglitazone and confirmed prominent lipid droplet accumulation in the converted cells. For profiling the proteome changes in the converted cells, we conducted a comprehensive quantitative proteome analysis of both the intracellular and extracellular proteome fractions using data-independent acquisition mass spectrometry. We observed that several proteins, which are known to be highly expressed in adipocytes specifically, were dominantly increased in the converted cells. In this study, we suggest that NHDFs can be converted into adipocyte-like cells by an adipogenic cocktail and can serve as a useful tool for studying human adipocytes and their metabolism., Competing Interests: The authors declare no competing financial interest., (© 2024 American Chemical Society.)

Published
2024
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49. Quantitative phase imaging techniques for measuring scattering properties of cells and tissues: a review-part II.

Author

Goswami N, Anastasio MA, and Popescu G

Subjects
Humans, Animals, Light, Quantitative Phase Imaging, Imaging, Three-Dimensional methods, Scattering, Radiation
Abstract

Significance: Quantitative phase imaging (QPI) is a non-invasive, label-free technique that provides intrinsic information about the sample under study. Such information includes the structure, function, and dynamics of the sample. QPI overcomes the limitations of conventional fluorescence microscopy in terms of phototoxicity to the sample and photobleaching of the fluorophore. As such, the application of QPI in estimating the three-dimensional (3D) structure and dynamics is well-suited for a range of samples from intracellular organelles to highly scattering multicellular samples while allowing for longer observation windows., Aim: We aim to provide a comprehensive review of 3D QPI and related phase-based measurement techniques along with a discussion of methods for the estimation of sample dynamics., Approach: We present information collected from 106 publications that cover the theoretical description of 3D light scattering and the implementation of related measurement techniques for the study of the structure and dynamics of the sample. We conclude with a discussion of the applications of the reviewed techniques in the biomedical field., Results: QPI has been successfully applied to 3D sample imaging. The scattering-based contrast provides measurements of intrinsic quantities of the sample that are indicative of disease state, stage of growth, or overall dynamics., Conclusions: We reviewed state-of-the-art QPI techniques for 3D imaging and dynamics estimation of biological samples. Both theoretical and experimental aspects of various techniques were discussed. We also presented the applications of the discussed techniques as applied to biomedicine and biology research., (© 2024 The Authors.)

Published
2024
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50. Machine learning assisted health viability assay for mouse embryos with artificial confocal microscopy (ACM).

Author

Goswami N, Winston N, Choi W, Lai NZE, Arcanjo RB, Chen X, Sobh N, Nowak RA, Anastasio MA, and Popescu G

Abstract

The combination of a good quality embryo and proper maternal health factors promise higher chances of a successful in vitro fertilization (IVF) procedure leading to clinical pregnancy and live birth. Of these two factors, selection of a good embryo is a controllable aspect. The current gold standard in clinical practice is visual assessment of an embryo based on its morphological appearance by trained embryologists. More recently, machine learning has been incorporated into embryo selection "packages". Here, we report a machine-learning assisted embryo health assessment tool utilizing a quantitative phase imaging technique called artificial confocal microscopy (ACM). We present a label-free nucleus detection method with novel quantitative embryo health biomarkers. Two viability assessment models are presented for grading embryos into two classes: healthy/intermediate (H/I) or sick (S) class. The models achieve a weighted F1 score of 1.0 and 0.99 respectively on the in-distribution test set of 72 fixed embryos and a weighted F1 score of 0.9 and 0.95 respectively on the out-of-distribution test dataset of 19 time-instances from 8 live embryos.

Published
2023
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