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Aslam M, AL-Marshadi AH. Dietary Fat and Prostate Cancer Relationship Using Trimmed Regression Under Uncertainty. Front Nutr 2022; 9:799375. [PMID: 35360700 PMCID: PMC8961509 DOI: 10.3389/fnut.2022.799375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/14/2022] [Indexed: 12/27/2022] Open
Abstract
In this paper, a new trimmed regression model under the neutrosophic environment is introduced. The mathematical model of the new regression model along with its neutrosophic form is given. The methods to find the error sum of square and trended values are also given. The trimmed neutrosophic correlation is also introduced in the paper. The proposed trimmed regression is applied to prostate cancer. From the analysis, it is concluded that the proposed model provides the minimum error sum of square as compared to the existing regression model under neutrosophic statistics. It is found that the proposed model is quite effective to forecast prostate cancer patients under an indeterminacy setting.
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Affiliation(s)
- Muhammad Aslam
- *Correspondence: Muhammad Aslam ; ; orcid.org/0000-0003-0644-1950
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Arthurs C, Ahmed A. QuArray: an application for tissue array whole slide image export and signal analysis. Bioinformatics 2021; 37:3082-3083. [PMID: 33690813 DOI: 10.1093/bioinformatics/btab119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 02/04/2021] [Accepted: 03/02/2021] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Tissue array (TA) staining, combined with whole slide imaging (WSI) methods facilitate discovery of biomarkers for diagnosis, prognostication and disease stratification. A key impediment in TA WSI analysis is handling missing tissue and artefacts when identifying tissue cores before quantitative, standardized downstream analysis. There is a need for an open access, user friendly, integrated analysis of the WSI generated using TAs in clinical and scientific research laboratories. RESULTS We have developed QuArray (Quantitative Array Application) for image export and signal analysis of TAs using WSI. The application input is a WSI and a corresponding TA configuration file. QuArray identifies and exports core images and analyses chromogen staining in a simple graphical user interface. Output data is saved to file for further analysis including indexed data. AVAILABILITYAND IMPLEMENTATION Available for download from https://github.com/c-arthurs/QuArray under an MIT licence. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Callum Arthurs
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, SE1 9RT London, UK
| | - Aamir Ahmed
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, SE1 9RT London, UK
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Gevaert T, Van Eycke YR, Vanden Broeck T, Van Poppel H, Salmon I, Rorive S, Muilwijk T, Claessens F, De Ridder D, Joniau S, Decaestecker C. The potential of tumour microenvironment markers to stratify the risk of recurrence in prostate cancer patients. PLoS One 2020; 15:e0244663. [PMID: 33370412 PMCID: PMC7769484 DOI: 10.1371/journal.pone.0244663] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/15/2020] [Indexed: 12/21/2022] Open
Abstract
The tumour micro-environment (TME) plays a crucial role in the onset and progression of prostate cancer (PCa). Here we studied the potential of a selected panel of TME-markers to predict clinical recurrence (CLR) in PCa. Patient cohorts were matched for the presence or absence of CLR 5 years post-prostatectomy. Tissue micro-arrays (TMA) were composed with both prostate non-tumour (PNT) and PCa tissue and subsequently processed for immunohistochemistry (IHC). The IHC panel included markers for cancer activated fibroblasts (CAFs), blood vessels and steroid hormone receptors ((SHR): androgen receptor (AR), progesterone receptor (PR) and estrogen receptor (ER)). Stained slides were digitalised, selectively annotated and analysed for percentage of marker expression with standardized and validated image analysis algorithms. A univariable analysis identified several TME markers with significant impact on CR: expression of CD31 (vascular marker) in PNT stroma, expression of alpha smooth muscle actin (αSMA) in PCa stroma, and PR expression ratio between PCa stroma and PNT stroma. A multivariable model, which included CD31 expression (vascular marker) in PNT stroma and PR expression ratio between PCa stroma and PNT stroma, could significantly stratify patients for CLR, with the identification of a low risk and high-risk subgroup. If validated and confirmed in an independent prospective series, this subgroup might have clinical potential for PCa patient stratification.
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Affiliation(s)
- Thomas Gevaert
- Department of Urology, UZ Leuven, Leuven, Belgium
- Organ Systems, KU Leuven, Leuven, Belgium
- Department of Pathology, AZ Klina, Brasschaat, Belgium
- P.E.A.R.L. (ProstatE cAncer Research Leuven), Leuven, Belgium
| | - Yves-Rémi Van Eycke
- Laboratories of Image, Synthesis and Analysis (LISA), Brussels School of Engineering/École polytechnique de Bruxelles, ULB, Brussels, Belgium
- DIAPath-Center for Microscopy and Molecular Imaging (CMMI), ULB, Gosselies, Belgium
| | - Thomas Vanden Broeck
- Department of Urology, UZ Leuven, Leuven, Belgium
- P.E.A.R.L. (ProstatE cAncer Research Leuven), Leuven, Belgium
- Department of Molecular and Cellular Medicine, KU Leuven, Leuven, Belgium
| | - Hein Van Poppel
- Department of Urology, UZ Leuven, Leuven, Belgium
- Organ Systems, KU Leuven, Leuven, Belgium
- P.E.A.R.L. (ProstatE cAncer Research Leuven), Leuven, Belgium
| | - Isabelle Salmon
- DIAPath-Center for Microscopy and Molecular Imaging (CMMI), ULB, Gosselies, Belgium
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Centre Universitaire Inter Régional d'Expertise en Anatomie Pathologique Hospitalière (CurePath), Jumet, Belgium
| | - Sandrine Rorive
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Centre Universitaire Inter Régional d'Expertise en Anatomie Pathologique Hospitalière (CurePath), Jumet, Belgium
| | - Tim Muilwijk
- Department of Urology, UZ Leuven, Leuven, Belgium
- Organ Systems, KU Leuven, Leuven, Belgium
| | - Frank Claessens
- P.E.A.R.L. (ProstatE cAncer Research Leuven), Leuven, Belgium
- Department of Molecular and Cellular Medicine, KU Leuven, Leuven, Belgium
| | - Dirk De Ridder
- Department of Urology, UZ Leuven, Leuven, Belgium
- Organ Systems, KU Leuven, Leuven, Belgium
- P.E.A.R.L. (ProstatE cAncer Research Leuven), Leuven, Belgium
| | - Steven Joniau
- Department of Urology, UZ Leuven, Leuven, Belgium
- Organ Systems, KU Leuven, Leuven, Belgium
- P.E.A.R.L. (ProstatE cAncer Research Leuven), Leuven, Belgium
| | - Christine Decaestecker
- Laboratories of Image, Synthesis and Analysis (LISA), Brussels School of Engineering/École polytechnique de Bruxelles, ULB, Brussels, Belgium
- DIAPath-Center for Microscopy and Molecular Imaging (CMMI), ULB, Gosselies, Belgium
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Arthurs C, Suarez-Bonnet A, Willis C, Xie B, Machulla N, Mair TS, Cao K, Millar M, Thrasivoulou C, Priestnall SL, Ahmed A. Equine penile squamous cell carcinoma: expression of biomarker proteins and EcPV2. Sci Rep 2020; 10:7863. [PMID: 32398763 PMCID: PMC7217868 DOI: 10.1038/s41598-020-64014-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 03/27/2020] [Indexed: 02/07/2023] Open
Abstract
Equine penile squamous cell carcinoma (EpSCC) is a relatively common cutaneous neoplasm with a poor prognosis. In this study, we aimed to determine the protein expression and colocalisation of FRA1, c-Myc, Cyclin D1, and MMP7 in normal (NT), tumour (T), hyperplastic epidermis and/or squamous papilloma (Hyp/Pap), poorly-differentiated (PDSCC), or well-differentiated (WDSCC) EpSCC using a tissue array approach. Further objectives were to correlate protein expression to (i) levels of inflammation, using a convolutional neural network (ii) equine papillomavirus 2 (EcPV2) infection, detected using PCR amplification. We found an increase in expression of FRA1 in EpSCC compared to NT samples. c-Myc expression was higher in Hyp/Pap and WDSCC but not PDSCC whereas MMP7 was reduced in WDSCC compared with NT. There was a significant increase in the global intersection coefficient (GIC) of FRA1 with MMP7, c-Myc, and Cyclin D1 in EpSCC. Conversely, GIC for MMP7 with c-Myc was reduced in EpSCC tissue. Inflammation was positively associated with EcPV2 infection in both NT and EpSCC but not Hyp/Pap. Changes in protein expression could be correlated with EcPV2 for Cyclin D1 and c-Myc. Our results evaluate novel biomarkers of EpSCC and a putative correlation between the expression of biomarkers, EcPV2 infection and inflammation.
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Affiliation(s)
- Callum Arthurs
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Alejandro Suarez-Bonnet
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, UK
| | - Claire Willis
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, UK
| | - Boyu Xie
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Natalie Machulla
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Tim S Mair
- Bell Equine Veterinary Clinic, Maidstone, UK
| | - Kevin Cao
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Michael Millar
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Christopher Thrasivoulou
- Research Department of Cell and Developmental Biology, The Centre for Cell and Molecular Dynamics, Rockefeller Building, University College London, London, United Kingdom
| | - Simon L Priestnall
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, UK
| | - Aamir Ahmed
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom.
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Santos PB, Patel H, Henrique R, Félix A. Can epigenetic and inflammatory biomarkers identify clinically aggressive prostate cancer? World J Clin Oncol 2020; 11:43-52. [PMID: 32133274 PMCID: PMC7046922 DOI: 10.5306/wjco.v11.i2.43] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 12/13/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer (PCa) is a highly prevalent malignancy and constitutes a major cause of cancer-related morbidity and mortality. It emerges through the acquisition of genetic and epigenetic alterations. Epigenetic modifications include DNA methylation, histone modifications and microRNA deregulation. These generate heritable transformations in the expression of genes but do not change the DNA sequence. Alterations in DNA methylation (hypo and hypermethylation) are the most characterized in PCa. They lead to genomic instability and inadequate gene expression. Major and minor-specific modifications in chromatin recasting are involved in PCa, with signs suggesting a dysfunction of enzymes modified by histones. MicroRNA deregulation also contributes to the initiation of PCa, including involvement in androgen receptor signalization and apoptosis. The influence of inflammation on prostate tumor carcinogenesis is currently much better known. Recent discoveries about microbial species resident in the urinary tract suggest that these are the initiators of chronic inflammation, promoting prostate inflammatory atrophy and eventually leading to PCa. Complete characterization of the relationship between the urinary microbiome and prostatic chronic inflammation will be crucial to develop plans for the prevention of PCa. The prevalent nature of epigenetic and inflammatory alterations may provide potential biomarkers for PCa diagnosis, treatment decisions, evaluation of prognosis and posttreatment surveillance.
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Affiliation(s)
- Pedro Bargão Santos
- Department of Urology, Prof. Doutor Fernando Fonseca Hospital, Amadora 2720-276, Portugal
| | - Hitendra Patel
- Department of Urology, University Hospital North Norway, Tromsø 9019, Norway
- Department of Urology, St George’s University Hospitals, Tooting, London SW17 0QT, United Kingdom
| | - Rui Henrique
- Departments of Pathology and Cancer Biology and Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto, Porto 4200-072, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4099-002, Portugal
| | - Ana Félix
- Department of Pathology, Portuguese Oncology Institute of Lisbon, Lisbon 1099-023, Portugal
- Department of Pathology, NOVA Medical School, Lisbon 1169-056, Portugal
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Krijgsman D, Van Vlierberghe RLP, Evangelou V, Vahrmeijer AL, Van de Velde CJH, Sier CFM, Kuppen PJK. A method for semi-automated image analysis of HLA class I tumour epithelium expression in rectal cancer. Eur J Histochem 2019; 63. [PMID: 31113192 PMCID: PMC6536912 DOI: 10.4081/ejh.2019.3028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/20/2019] [Indexed: 12/11/2022] Open
Abstract
Biomarkers may hold the key towards development and improvement of personalized cancer treatment. For instance, tumour expression of immune system-related proteins may reveal the tumour immune status and, accordingly, determine choice for type of immunotherapy. Therefore, objective evaluation of tumour biomarker expression is needed but often challenging. For instance, human leukocyte antigen (HLA) class I tumour epithelium expression is cumbersome to quantify by eye due to its presence on both tumour epithelial cells and tumour stromal cells, as well as tumourinfiltrating immune cells. In this study, we solved this problem by setting up an immunohistochemical (IHC) double staining using a tissue microarray (TMA) of rectal tumours wherein HLA class I expression was coloured with a blue chromogen, whereas non-epithelial tissue was visualized with a brown chromogen. We subsequently developed a semi-automated image analysis method that identified tumour epithelium as well as the percentage of HLA class I-positive tumour epithelium. Using this technique, we compared HCA2/HC10 and EMR8-5 antibodies for the assessment of HLA class I tumour expression and concluded that EMR8-5 is the superior antibody for this purpose. This IHC double staining can in principle be used for scoring of any biomarker expressed by tumour epithelium.
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Application of Neutrosophic Logic to Evaluate Correlation between Prostate Cancer Mortality and Dietary Fat Assumption. Symmetry (Basel) 2019. [DOI: 10.3390/sym11030330] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
This paper presents an epidemiological study on the dietary fat that causes prostate cancer in an uncertainty environment. To study this relationship under the indeterminate environment, data from 30 countries are selected for the prostate cancer death rate and dietary fat level in the food. The neutrosophic correlation and regression line are fitted on the data. We note from the neutrosophic analysis that the prostate cancer death rate increases as the dietary fat level in the people increases. The neutrosophic regression coefficient also confirms this claim. From this study, we conclude that neutrosophic regression is a more effective model under uncertainty than the regression model under classical statistics. We also found a statistical correlation between dietary fat and prostate cancer risk.
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