1
|
Goswami N, Winston N, Choi W, Lai NZE, Arcanjo RB, Chen X, Sobh N, Nowak RA, Anastasio MA, Popescu G. EVATOM: an optical, label-free, machine learning assisted embryo health assessment tool. Commun Biol 2024; 7:268. [PMID: 38443460 PMCID: PMC10915136 DOI: 10.1038/s42003-024-05960-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/22/2024] [Indexed: 03/07/2024] Open
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 EVATOM: a machine-learning assisted embryo health assessment tool utilizing an optical quantitative phase imaging technique called artificial confocal microscopy (ACM). We present a label-free nucleus detection method with, to the best of our knowledge, 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.
Collapse
Affiliation(s)
- Neha Goswami
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Beckman Institute of Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Nicola Winston
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of Illinois at Chicago College of Medicine, Chicago, IL, 60612, USA
| | - Wonho Choi
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Nastasia Z E Lai
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Rachel B Arcanjo
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Xi Chen
- Beckman Institute of Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, 14850, USA
| | - Nahil Sobh
- NCSA Center for Artificial Intelligence Innovation, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Romana A Nowak
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Mark A Anastasio
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Beckman Institute of Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Gabriel Popescu
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute of Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
2
|
Goswami N, Winston N, Choi W, Lai NZE, Arcanjo RB, Chen X, Sobh N, Nowak RA, Anastasio MA, Popescu G. Machine learning assisted health viability assay for mouse embryos with artificial confocal microscopy (ACM). bioRxiv 2023:2023.07.30.550591. [PMID: 37547014 PMCID: PMC10402120 DOI: 10.1101/2023.07.30.550591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
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.
Collapse
|
3
|
Bashir ST, Redden CR, Raj K, Arcanjo RB, Stasiak S, Li Q, Steelman AJ, Nowak RA. Endometriosis leads to central nervous system-wide glial activation in a mouse model of endometriosis. J Neuroinflammation 2023; 20:59. [PMID: 36879305 PMCID: PMC9987089 DOI: 10.1186/s12974-023-02713-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/31/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND Chronic pelvic pain (CPP) is a common symptom of endometriosis. Women with endometriosis are also at a high risk of suffering from anxiety, depression, and other psychological disorders. Recent studies indicate that endometriosis can affect the central nervous system (CNS). Changes in the functional activity of neurons, functional magnetic resonance imaging signals, and gene expression have been reported in the brains of rat and mouse models of endometriosis. The majority of the studies thus far have focused on neuronal changes, whereas changes in the glial cells in different brain regions have not been studied. METHODS Endometriosis was induced in female mice (45-day-old; n = 6-11/timepoint) by syngeneic transfer of donor uterine tissue into the peritoneal cavity of recipient animals. Brains, spines, and endometriotic lesions were collected for analysis at 4, 8, 16, and 32 days post-induction. Sham surgery mice were used as controls (n = 6/timepoint). The pain was assessed using behavioral tests. Using immunohistochemistry for microglia marker ionized calcium-binding adapter molecule-1 (IBA1) and machine learning "Weka trainable segmentation" plugin in Fiji, we evaluated the morphological changes in microglia in different brain regions. Changes in glial fibrillary acidic protein (GFAP) for astrocytes, tumor necrosis factor (TNF), and interleukin-6 (IL6) were also evaluated. RESULTS We observed an increase in microglial soma size in the cortex, hippocampus, thalamus, and hypothalamus of mice with endometriosis compared to sham controls on days 8, 16, and 32. The percentage of IBA1 and GFAP-positive area was increased in the cortex, hippocampus, thalamus, and hypothalamus in mice with endometriosis compared to sham controls on day 16. The number of microglia and astrocytes did not differ between endometriosis and sham control groups. We observed increased TNF and IL6 expression when expression levels from all brain regions were combined. Mice with endometriosis displayed reduced burrowing behavior and hyperalgesia in the abdomen and hind-paw. CONCLUSION We believe this is the first report of central nervous system-wide glial activation in a mouse model of endometriosis. These results have significant implications for understanding chronic pain associated with endometriosis and other issues such as anxiety and depression in women with endometriosis.
Collapse
Affiliation(s)
- Shah Tauseef Bashir
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Room 314 ASL, Urbana, IL, 61801, USA
| | - Catherine R Redden
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Room 314 ASL, Urbana, IL, 61801, USA
| | - Kishori Raj
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Room 314 ASL, Urbana, IL, 61801, USA
| | - Rachel B Arcanjo
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Room 314 ASL, Urbana, IL, 61801, USA
| | - Sandra Stasiak
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Room 314 ASL, Urbana, IL, 61801, USA
| | - Quanxi Li
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andrew J Steelman
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Room 314 ASL, Urbana, IL, 61801, USA
| | - Romana A Nowak
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Room 314 ASL, Urbana, IL, 61801, USA.
| |
Collapse
|
4
|
Bashir ST, Chiu K, Zheng E, Martinez A, Chiu J, Raj K, Stasiak S, Lai NZE, Arcanjo RB, Flaws JA, Nowak RA. Subchronic exposure to environmentally relevant concentrations of di-(2-ethylhexyl) phthalate differentially affects the colon and ileum in adult female mice. Chemosphere 2022; 309:136680. [PMID: 36209858 DOI: 10.1016/j.chemosphere.2022.136680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Di(2-ethylhexyl) phthalate (DEHP) is a large-molecular-weight phthalate added to plastics to impart versatile properties. DEHP can be found in medical equipment and devices, food containers, building materials, and children's toys. Although DEHP exposure occurs most commonly by ingesting contaminated foods in the majority of the population, its effects on the gastrointestinal tract have not been well studied. Therefore, we analyzed the effects of subchronic exposure to DEHP on the ileum and colon morphology, gene expression, and immune microenvironment. Adult C57BL/6 female mice were orally dosed with corn oil (control, n = 7) or DEHP (0.02, 0.2, or 30 mg/kg, n = 7/treatment dose) for 30-34 days. Mice were euthanized during diestrus, and colon and ileum tissues were collected for RT-qPCR and immunohistochemistry. Subchronic DEHP exposure in the ileum altered the expression of several immune-mediating factors (Muc1, Lyz1, Cldn1) and cell viability factors (Bcl2 and Aifm1). Similarly, DEHP exposure in the colon impacted the gene expression of factors involved in mediating immune responses (Muc3a, Zo2, Ocln, Il6, and Il17a); and also altered the expression of cell viability factors (Ki67, Bcl2, Cdk4, and Aifm1) as well as a specialized epithelial cell marker (Vil1). Immunohistochemical analysis of the ileum showed DEHP increased expression of VIL1, CLDN1, and TNF and decreased number of T-cells in the villi. Histological analysis of the colon showed DEHP altered morphology and reduced cell proliferation. Moreover, in the colon, DEHP increased the expression of MUC2, MUC1, VIL1, CLDN1, and TNF. DEHP also increased the number of T-cells and Type 2 immune cells in the colon. These data suggest that subchronic DEHP exposure differentially affects the ileum and colon and alters colonic morphology and the intestinal immune microenvironment. These results have important implications for understanding the effects of DEHP on the gastrointestinal system.
Collapse
Affiliation(s)
- Shah Tauseef Bashir
- Department of Molecular and Integrative Physiology, College of Liberal Arts & Sciences, University of Illinois, Urbana, IL, USA; Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL, USA
| | - Karen Chiu
- Division of Nutritional Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL, USA; Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Eileen Zheng
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL, USA
| | - Angel Martinez
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL, USA
| | - Justin Chiu
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL, USA; Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Kishori Raj
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL, USA
| | - Sandra Stasiak
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL, USA
| | - Nastasia Zhen Ee Lai
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL, USA
| | - Rachel B Arcanjo
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL, USA
| | - Jodi A Flaws
- Division of Nutritional Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL, USA; Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA; Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Romana A Nowak
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL, USA; Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana, IL, USA.
| |
Collapse
|
5
|
B Arcanjo R, Richardson KA, Yang S, Patel S, Flaws JA, Nowak RA. Effects of Chronic Dietary Exposure to Phytoestrogen Genistein on Uterine Morphology in Mice. J Agric Food Chem 2021; 69:1693-1704. [PMID: 33528250 DOI: 10.1021/acs.jafc.0c07456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Genistein is naturally occurring in plants and binds to estrogen receptors. Humans are mainly exposed through diet, but the use of supplements is increasing as genistein is claimed to promote health and alleviate menopausal symptoms. We analyzed diverse uterine features in adult mice chronically fed genistein for different times. The luminal epithelium height was increased in females treated with 500 and 1000 ppm at PND 95, and the width of the outer myometrium was increased in females treated with 1000 ppm at PND 65 compared to that in controls. An increase in proliferation was noted in the inner myometrium layer of animals exposed to 300 ppm genistein at PND 185 compared to that in controls. Luminal hyperplasia was greater in the 1000 ppm group at PND 65, 95, and 185, although not statistically different from control. These results indicate that genistein may exert estrogenic activity in the uterus, without persistent harm to the organ.
Collapse
Affiliation(s)
- Rachel B Arcanjo
- Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - Kadeem A Richardson
- Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - Shuhong Yang
- Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801, United States
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, People's Republic of China
| | - Shreya Patel
- Department of Comparative Biosciences, University of Illinois, Urbana, Illinois 61820, United States
| | - Jodi A Flaws
- Department of Comparative Biosciences, University of Illinois, Urbana, Illinois 61820, United States
| | - Romana A Nowak
- Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801, United States
| |
Collapse
|
6
|
Arcanjo RB, de Souza LP, Rezende CF, Silva JRF. Embryonic development and nourishment in the viviparous fishPoecilia vivipara(Cyprinodontiformes: Poeciliidae). ACTA ZOOL-STOCKHOLM 2013. [DOI: 10.1111/azo.12046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Rachel B. Arcanjo
- Departamento de Biologia; Universidade Federal do Ceará (UFC); Av. Mister Hull, s/n CEP: 60455-760 Fortaleza Ceará Brazil
| | - Leonardo P. de Souza
- Departamento de Biologia; Instituto de Biociências; Universidade Estadual Paulista (UNESP); Av. 24 A, n. 1515 CEP: 13506-900 Rio Claro São Paulo Brazil
| | - Carla F. Rezende
- Departamento de Biologia; Universidade Federal do Ceará (UFC); Av. Mister Hull, s/n CEP: 60455-760 Fortaleza Ceará Brazil
| | - José R. F. Silva
- Departamento de Biologia; Universidade Federal do Ceará (UFC); Av. Mister Hull, s/n CEP: 60455-760 Fortaleza Ceará Brazil
| |
Collapse
|