Statistical analysis of a lung cancer spectral histopathology (SHP) data set

Analyst

Volumn 140, Issue 7, 2015, Pages 2449-2464

  Mu, Xinying ^a,b   Kon, Mark ^a,b   Ergin, Ayşegül ^b   Remiszewski, Stan ^b   Akalin, Ali ^c   Thompson, Clay M ^b,d   Diem, Max ^b,e  

^a USA   (United States)

^b Cireca Theranostics   (United States)

^c UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^d Creative Creek LLC   (United States)

^e NORTHEASTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTIFICIAL INTELLIGENCE; HUMAN; INFRARED SPECTROPHOTOMETRY; LUNG NEOPLASMS; PATHOLOGY; STATISTICAL ANALYSIS;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; DATA INTERPRETATION, STATISTICAL; HUMANS; LUNG NEOPLASMS; SPECTROPHOTOMETRY, INFRARED;

EID: 84925339096     PISSN: 00032654     EISSN: 13645528     Source Type: Journal    
DOI: 10.1039/c4an01832j     Document Type: Article

References (36)

1. M. Diem, et al., Molecular pathology via Infrared and Raman spectral imaging, in Ex-vivo and in vivo Optical Pathology, ed., M. Schmitt, and, J. Popp, Wiley-VCH, 2013
2. M. Diem et al., Applications of Infrared and Raman Micro-spectroscopy of Cells in Medical Diagnostics: Present Status and Future Promises Spectroscopy - Biomedical Applications 2012 27 5-6 463 496
3. M. Diem, Introduction to Modern Vibrational Spectroscopy, Wiley-Interscience, New York, 1993
4. Y. Wang et al., Differentiation in MALDI-TOF MS and FTIR spectra between two closely related species Acidovorax oryzae and Acidovorax citrulli BMC Microbiol. 2012 12 182 189
5. M. Wenning et al., Identification and differentiation of food-related bacteria: A comparison of FTIR spectroscopy and MALDI-TOF mass spectrometry J. Microbiol. Methods 2014 103 44 52
6. M. Diem, et al., IR Spectroscopic Imaging: from Cells to Tissue, in Spectrochemical Analysis using Infrared Multichannel Detectors, ed., R. Bhargava, and, I. W. Levin, Blackwell Publishing, Sheffield (UK), 2005, pp. 189-203
7. M. Diem et al., A decade of vibrational micro-spectroscopy of human cells and tissue (1994-2004) Analyst 2004 129 10 880 885
8. P. Lasch et al., Imaging of colorectal adenocarcinoma using FT-IR microspectroscopy and cluster analysis Biochim. Biophys. Acta 2004 1688 2 176 186
9. P. Bassan et al., Automated high-throughput assessment of prostate biopsy tissue using infrared spectroscopic chemical imaging Proc. SPIE-Int. Soc. Opt. Eng. 2014 9041 1 10
10. R. Bhargava, D. C. Fernandez, M. D. Schaeberle and I. W. Levin, FTIR Imaging of Biological Tissue for Histopathological Analysis, in PittCon, New Orleans, 2002
11. F. N. Pounder and R. Bhargava, Toward Automated breast Histopathology Using Mid-IR Spectroscopic Imaging, in Vibrational Spectroscopic Imaging for Biomedical Appications, ed., G. Srinivasa, McGraw Hill, New York, 2010
12. E. Ly et al., Combination of FTIR spectral imaging and chemometrics for tumour detection from paraffin-embedded biopsies Analyst 2008 133 197 205
13. B. Bird et al., Detection of Breast Micro-Metastases in Axillary Lymph Nodes by Infrared Micro-Spectral Imaging Analyst 2009 134 1067 1076
14. M. J. Hackett et al., Chemical alterations to murine brain tissue induced by formalin fixation: implications for biospectroscopic imaging and mapping studies of disease pathogenesis Analyst 2011 136 2941 2952
15. S. E. Holton M. J. Walsh R. Bhargava Subcellular localization of early biochemical transformations in cancer-activated fibroblasts using infrared spectroscopic imaging Analyst 2011 136 2953 2958
16. C. Krafft et al., Analysis of human brain tissue, brain tumors and tumor cells by infrared spectroscopic mapping Analyst 2004 129 10 921 925
17. A. Akalin et al., Classification of Malignant and Benign Tumors of the Lung by Infrared Spectral Histopathology (SHP) Lab. Invest. 2015
18. B. Bird et al., Infrared Spectral Histopathology (SHP): A Novel Diagnostic Tool for the Accurate Classification of Lung Cancers Lab. Invest. 2012 92 1358 1373
19. foliobio.com. Deparaffin Protocol. Available from: http://foliobio.com/media/pdf/Deparaffin%20protocol.pdf
20. M. Miljković et al., Spectral Cytopathology: new aspects of data collection, manipulation and confounding effects Analyst 2013 138 3975 3982
21. M. Diem et al., Molecular pathology via Infrared and Raman spectral imaging J. Biophotonics 2013 6 11-12 855 886
22. P. Bassan et al., The inherent problem of transflection-mode infrared spectroscopic microscopy and the ramifications for biomedical single point and imaging applications Analyst 2013 138 144 157
23. T. P. Wrobel et al., Electric field standing wave effects in FT-IR transflection spectra of biological sections: Simulated models of experimental variability Vib. Spectrosc. 2013 69 84 92
24. M. Miljković B. Bird M. Diem Dispersive line shape effects in infrared spectroscopy Analyst 2012 137 3954 3964
25. A. Ergin et al., A method for the comparison of multi-platform spectral histopathology (SHP) data sets Analyst 2015 DOI: 10.1039/c4an1879f
26. S. Remiszewski, et al., A multi-centre, multi-platform spectral histopathology (SHP) study for lung cancer diagnostics and prognostics, Spec2014, Cracow, Poland, 2014, Poster 186.
27. M. M. Rahman D. N. Davis Addressing the Class Imbalance Problem in Medical Datasets Intern. J. machine Learning Computing 2013 3 2 224 228
28. A. Statnikov, et al., A Gentle Introduction to Support Vector Machines in Biomedicine, Volume 1: Theory and Methods, World Scientific Publishing, Hackensack, NJ, 2011, pp. 1-181
29. X. Zhang et al., Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data BMC Bioinformatics 2006 7 1 197
30. Y.-J. Lee and O. L. Mangasarian, RSVM: Reduced Support Vector Machines, Proceedings of the 2001 SIAM International Conference on Data Mining, 2001
31. K.-M. Lin C.-J. Lin A study on reduced support vector machines IEEE Trans. Neural Netw. 2003 14 1449 1459
32. C. Beleites et al., Sample size planning for classification models Anal. Chim. Acta 2013 760 25 33
33. M. Diem, et al., Infrared and Raman Spectroscopy and Spectral Imaging of Individual Cells, in Infrared and Raman Spectroscopic Imaging, ed., R. Salzer, and, H. W. Siesler, Wiley - VCH Publishing, Weinheim, Germany, 2014, pp. 181-223
34. P. Lasch, et al., Antemortem Identification of Transmissible Spongiform Encephalopathy (TSE) from Serum by Mid-infrared Spectroscopy, in Vibrational Spectroscopy for Medical Diagnosis, ed., M. Diem, P. R. Griffiths, and, J. M. Chalmers, Chichester, UK, 2008, pp. 97-122
35. D. Kurouski et al., Is Supramolecular Filament Chirality the Underlying Cause of Major Morphology Differences in Amyloid Fibrils? J. Am. Chem. Soc. 2014 136 2302 2312
36. W. D. Travis et al., International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society International Multidisciplinary Classification of Lung Adenocarcinoma J. Thorac. Oncol. 2011 6 2 244 285