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Hartman TW, Radichev E, Ali HM, Alaba MO, Hoffman M, Kassa G, Sani R, Gadhamshetty V, Ragi S, Messerli SM, de la Puente P, Sandhurst ES, Do T, Lushbough C, Gnimpieba EZ. BASIN: A Semi-automatic Workflow, with Machine Learning Segmentation, for Objective Statistical Analysis of Biomedical and Biofilm Image Datasets. J Mol Biol 2023; 435:167895. [PMID: 36463932 PMCID: PMC10280363 DOI: 10.1016/j.jmb.2022.167895] [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: 07/12/2022] [Revised: 11/01/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
Micrograph comparison remains useful in bioscience. This technology provides researchers with a quick snapshot of experimental conditions. But sometimes a two- condition comparison relies on researchers' eyes to draw conclusions. Our Bioimage Analysis, Statistic, and Comparison (BASIN) software provides an objective and reproducible comparison leveraging inferential statistics to bridge image data with other modalities. Users have access to machine learning-based object segmentation. BASIN provides several data points such as images' object counts, intensities, and areas. Hypothesis testing may also be performed. To improve BASIN's accessibility, we implemented it using R Shiny and provided both an online and offline version. We used BASIN to process 498 image pairs involving five bioscience topics. Our framework supported either direct claims or extrapolations 57% of the time. Analysis results were manually curated to determine BASIN's accuracy which was shown to be 78%. Additionally, each BASIN version's initial release shows an average 82% FAIR compliance score.
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Affiliation(s)
- Timothy W Hartman
- Biomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States
| | - Evgeni Radichev
- Biomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States
| | - Hafiz Munsub Ali
- Biomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States
| | - Mathew Olakunle Alaba
- Biomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States
| | - Mariah Hoffman
- Biomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States
| | - Gideon Kassa
- Biomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States
| | - Rajesh Sani
- Chemical and Biological Engineering Department, South Dakota School of Mines and Technology, 501 E St. Joseph Street, Rapid City, SD 57701, United States
| | - Venkata Gadhamshetty
- Civil and Environmental Engineering Department, South Dakota School of Mines and Technology, 501 E St. Joseph Street, Rapid City, SD 57701, United States
| | - Shankarachary Ragi
- Electrical Engineering Department, South Dakota School of Mines and Technology, 501 E St. Joseph Street, Rapid City, SD 57701, United States
| | - Shanta M Messerli
- Biomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States; Cancer Biology and Immunotherapies Group, Sanford Research, 2301 E 60(th) Street North, Sioux Falls, SD 57104, United States; Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, United States
| | - Pilar de la Puente
- Cancer Biology and Immunotherapies Group, Sanford Research, 2301 E 60(th) Street North, Sioux Falls, SD 57104, United States
| | - Eric S Sandhurst
- Biomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States
| | - Tuyen Do
- Biomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States
| | - Carol Lushbough
- Biomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States
| | - Etienne Z Gnimpieba
- Biomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States.
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Welfare JG, Mortelliti MJ, McGlade CA, Hartman TW, Dempsey JL, Lawrence DS. Assessment of Photoreleasable Linkers and Light-Capturing Antennas on a Photoresponsive Cobalamin Scaffold. J Org Chem 2022; 87:5076-5084. [PMID: 35353509 PMCID: PMC9727707 DOI: 10.1021/acs.joc.1c02931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cobalamin has shown promise as a light-sensitive drug delivery platform owing to its ease of modification and the high quantum yields for drug photorelease. However, studies to date on the general photochemistry of alkyl cobalamins have primarily focused on methyl and adenosyl-substituted derivatives, the natural cofactors present in various enzymatic species. We describe the synthesis and photolytic behavior of cobalamin conjugates comprised of different combinations of fluorophores and β-axial ligands. In general, cobalamin conjugates containing β-axial alkyl substituents undergo efficient photolysis under aqueous conditions, with quantum yields up to >40%. However, substituents that are large and hydrophobic, or unable to readily support the presumed radical intermediate, suffer less efficient photolysis (<15%) than smaller, water-soluble, analogs. By contrast, quantum yields improve by 2-fold in DMF for cobalamins containing large hydrophobic β-axial substituents. This suggests that drug release from carriers comprised of membranous compartments, such as liposomes, may be significantly more efficient than the corresponding photorelease in an aqueous environment. Finally, we explored the impact of fluorophores on the photolysis of alkyl cobalamins under tissue-mimetic conditions. Cobalamins substituted with efficient photon-capturing fluorophores display up to 4-fold enhancements in photolysis relative to unsubstituted derivatives. In summary, we have shown that the photosensitivity of alkyl cobalamin conjugates can be tuned by altering the Co-appended alkyl moiety, modulating the polarity of the environment (solvent), and installing photon-capturing fluorophores onto the cobalamin framework.
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Hoffman MM, Zylla JS, Bhattacharya S, Calar K, Hartman TW, Bhardwaj RD, Miskimins WK, de la Puente P, Gnimpieba EZ, Messerli SM. Analysis of Dual Class I Histone Deacetylase and Lysine Demethylase Inhibitor Domatinostat (4SC-202) on Growth and Cellular and Genomic Landscape of Atypical Teratoid/Rhabdoid. Cancers (Basel) 2020; 12:cancers12030756. [PMID: 32210076 PMCID: PMC7140080 DOI: 10.3390/cancers12030756] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/07/2020] [Accepted: 03/19/2020] [Indexed: 12/12/2022] Open
Abstract
Central nervous system atypical teratoid/rhabdoid tumors (ATRTs) are rare and aggressive tumors with a very poor prognosis. Current treatments for ATRT include resection of the tumor, followed by systemic chemotherapy and radiation therapy, which have toxic side effects for young children. Gene expression analyses of human ATRTs and normal brain samples indicate that ATRTs have aberrant expression of epigenetic markers including class I histone deacetylases (HDAC’s) and lysine demethylase (LSD1). Here, we investigate the effect of a small molecule epigenetic modulator known as Domatinostat (4SC-202), which inhibits both class I HDAC’s and Lysine Demethylase (LSD1), on ATRT cell survival and single cell heterogeneity. Our findings suggest that 4SC-202 is both cytotoxic and cytostatic to ATRT in 2D and 3D scaffold cell culture models and may target cancer stem cells. Single-cell RNA sequencing data from ATRT-06 spheroids treated with 4SC-202 have a reduced population of cells overexpressing stem cell-related genes, including SOX2. Flow cytometry and immunofluorescence on 3D ATRT-06 scaffold models support these results suggesting that 4SC-202 reduces expression of cancer stem cell markers SOX2, CD133, and FOXM1. Drug-induced changes to the systems biology landscape are also explored by multi-omics enrichment analyses. In summary, our data indicate that 4SC-202 has both cytotoxic and cytostatic effects on ATRT, targets specific cell sub-populations, including those with cancer stem-like features, and is an important potential cancer therapeutic to be investigated in vivo.
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Affiliation(s)
- Mariah M. Hoffman
- Department of Biomedical Engineering, University of South Dakota, Sioux Falls, SD 57107, USA; (M.M.H.); (E.Z.G.)
- Department of Biomedical Engineering, University of South Dakota, BioSNTR, Sioux Falls, SD 57107, USA
| | - Jessica S. Zylla
- Department of Biomedical Engineering, University of South Dakota, Sioux Falls, SD 57107, USA; (M.M.H.); (E.Z.G.)
| | | | - Kristin Calar
- Cancer Biology & Immunotherapies, Sanford Research, Sioux Falls, SD 57104, USA (P.P.)
| | - Timothy W. Hartman
- Department of Biomedical Engineering, University of South Dakota, Sioux Falls, SD 57107, USA; (M.M.H.); (E.Z.G.)
| | - Ratan D. Bhardwaj
- Cancer Biology & Immunotherapies, Sanford Research, Sioux Falls, SD 57104, USA (P.P.)
| | - W. Keith Miskimins
- Cancer Biology & Immunotherapies, Sanford Research, Sioux Falls, SD 57104, USA (P.P.)
| | - Pilar de la Puente
- Cancer Biology & Immunotherapies, Sanford Research, Sioux Falls, SD 57104, USA (P.P.)
- Department of Surgery, University of South Dakota Sanford School of Medicine, Sioux Falls, SD 57105, USA
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57006, USA
| | - Etienne Z. Gnimpieba
- Department of Biomedical Engineering, University of South Dakota, Sioux Falls, SD 57107, USA; (M.M.H.); (E.Z.G.)
- Department of Biomedical Engineering, University of South Dakota, BioSNTR, Sioux Falls, SD 57107, USA
| | - Shanta M. Messerli
- Department of Biomedical Engineering, University of South Dakota, Sioux Falls, SD 57107, USA; (M.M.H.); (E.Z.G.)
- Department of Biomedical Engineering, University of South Dakota, BioSNTR, Sioux Falls, SD 57107, USA
- Cancer Biology & Immunotherapies, Sanford Research, Sioux Falls, SD 57104, USA (P.P.)
- Correspondence: ; Tel.: +1-508-364-1181
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Clayton AE, McNutt LA, Homestead HL, Hartman TW, Senecal S. Public health in managed care: a randomized controlled trial of the effectiveness of postcard reminders. Am J Public Health 1999; 89:1235-7. [PMID: 10432913 PMCID: PMC1508682 DOI: 10.2105/ajph.89.8.1235] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES This study evaluated the effectiveness of an annual public health intervention in a managed care setting. METHODS Managed care organization members 65 years and older who received influenza immunization in 1996 were randomized to an intervention group (mailed a postcard reminder to receive an influenza vaccination in 1997) or a control group (no postcard). Vaccination rates for both groups were assessed monthly. RESULTS Members receiving the intervention were no more likely to be immunized (78.6%) than members of the control group (77.2%, P = .222). Members were vaccinated at the same pace regardless of vaccination history and postcard intervention status. CONCLUSIONS Postcard reminders were not an effective intervention among seniors who had been vaccinated the previous year.
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Affiliation(s)
- A E Clayton
- Kaiser Permanente Northeast Division, Quality Management Department, Latham, NY 12110, USA.
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Abstract
After becoming alarmed about seven unusual and severe complications reported by New York State hospitals after laparoscopic cholecystectomy, the Department of Health of New York State tabulated all reported adverse incidents. After observing unusual injuries to the great vessels of the abdomen and an increase in major bile duct injury during laparoscopic cholecystectomy, the Department of Health prepared a memorandum to New York State hospitals advising closer attention to education, credentialing, proctoring, and outcome after these operations. The frequency of cholecystectomy has increased sharply, by 21%, since the advent of laparoscopic cholecystectomy. The serious injury rate may be approximately 15 times that observed after an open cholecystectomy. Recognizing the theoretic advantages of the procedure, the Department of Health reminded hospital Boards of Trustees of their obligation to establish mechanisms for credentialing and privileging surgeons and surgical teams so that the risks do not exceed those expected of the open procedure and to detect and correct deviations from this standard.
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Affiliation(s)
- H R Bernard
- New York State Department of Health, Albany, New York 12237
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