# **Beyond Energy Efficiency in Architecture. New Challenges and Research Trajectories for Buildings and the Built Environment**

Edited by

Tiziana Poli, Andrea Giovanni Mainini, Gabriele Lobaccaro, Mitja Košir and Juan Diego Blanco Cadena Printed Edition of the Special Issue Published in *Applied Sciences*

www.mdpi.com/journal/applsci


**7. References**

Transform-Infrared and Raman Spectroscopic Mapping. Analytical Chemistry, 2008; 80(23) 9065-9072.

Multivariate Analysis for Fourier Transform Infrared Spectra of Complex Biological Systems and Processes 217

[22] Heraud P, Tobin MJ. The emergence of biospectroscopy in stem cell research. Stem Cell

[23] Kazarian SG, Chan KL. Applications of ATR-FTIR spectroscopic imaging to biomedical

[24] Holman H-YN, Martin MC, McKinney WR. Tracking chemical changes in a live cell: Biomedical applications of SR-FTIR spectromicroscopy, 2003; 17 (2-3) 139-159. [25] Tanthanuch W, Thumanu K, Lorthongpanich C, Parnpai R, Heraud P. Neural differentiation of mouse embryonic stem cells studied by FTIR spectroscopy. Journal of

[26] Caine S, Heraud P, Tobin MJ, McNaughton D, Bernard CC. The application of Fourier transform infrared microspectroscopy for the study of diseased central nervous system

[27] Nakamura T, Kelly JG, Trevisan J, Cooper LJ, Bentley AJ, Carmichael PL, Scott AD, Cotte M, Susini J, Martin-Hirsch PL, Kinoshita S, Fullwood NJ, Martin FL. Microspectroscopy of spectral biomarkers associated with human corneal stem cells.

[28] Ami D, Natalello A, Zullini A, Doglia SM. Fourier transform infrared microspectroscopy as a new tool for nematode studies. FEBS Letters, 2004; 576(3) 297-

[29] Casal HL, Mantsch HH. Polymorphic phase behaviour of phospholipid membranes studied by infrared spectroscopy. Biochimica et Biophysica Acta, 1984; 779(4) 381-401. [30] Barth A. Infrared spectroscopy of proteins. Biochimica et Biophysica Acta, 2007; 1767 (9)

[31] Banyay M, Sarkar M, Gräslund A. A library of IR bands of nucleic acids in solution.

[32] Banyay M, Gräslund A. Structural effects of cytosine methylation on DNA sugar pucker

[33] Kačuráková M, Mathlouthi M. FTIR and laser-Raman spectra of oligosaccharides in water: characterization of the glycosidic bond. Carbohydrate Research, 1996; 284 145-

[34] Wong PT, Wong RK, Caputo TA, Godwin TA, Rigas B. Infrared spectroscopy of exfoliated human cervical cells: evidence of extensive structural changes during carcinogenesis. Proceedings of the National Academy of Sciences USA, 1991; 88(24)

[35] Ami D, Neri T, Natalello A, Mereghetti P, Doglia SM, Zanoni M, Zuccotti M, Garagna S, Redi CA. Embryonic stem cell differentiation studied by FT-IR spectroscopy.

[36] Konorov SO, Schulze HG, Caron NJ, Piret JM, Blades MW, Turner RFB. Raman microspectroscopic evidence that dry-fixing preserves the temporal pattern of nonspecific differentiation in live human embryonic stem cells. Journal of Raman

studied by FTIR. Journal of Molecular Biology, 2002; 324(4) 667-676.

samples. Biochimica et Biophysica Acta, 2006; 1758(7) 858-867.

Molecular Structure, 2010; 967(1–3) 189–195.

tissue. Neuroimage, 2012; 59(4) 3624-3640.

Biophysical Chemistry, 2003; 104(2) 477-488.

Biochimica et Biophysica Acta, 2008; 1783(1) 98-106.

Spectroscopy, 2011; 42(4) 576–579.

Molecular Vision, 2010; 16 359-368.

300.

157.

10988-10992.

1073–1101.

Research, 2009; 3(1) 12-14.

Multivariate Analysis for Fourier Transform Infrared Spectra of Complex Biological Systems and Processes 217

[22] Heraud P, Tobin MJ. The emergence of biospectroscopy in stem cell research. Stem Cell Research, 2009; 3(1) 12-14.

216 Multivariate Analysis in Management, Engineering and the Sciences

of Biological Chemistry, 2010; 285(41) 31202-31207.

Biophysica Acta, 2003; 639(3) 152-158.

80(23) 9065-9072.

137(14) 3202-3215.

1176-1184.

Research, 2011; 10(4) 1437-1448.

Bioanalytical Chemistry, 2008; 391(5) 1641-1654.

424-431.

Transform-Infrared and Raman Spectroscopic Mapping. Analytical Chemistry, 2008;

[9] Diomede L, Cassata G, Fiordaliso F, Salio M, Ami D, Natalello A, Doglia SM, De Luigi A, Salmona M. Tetracycline and its analogues protect Caenorhabditis elegans from β amyloid-induced toxicity by targeting oligomers. Neurobiology of Disease, 2010; 40(2)

[10] Kuzyk A, Kastyak M, Agrawal V, Gallant M, Sivakumar G, Rak M, Del Bigio MR, Westaway D, Julian R, Gough KM. Association among amyloid plaque, lipid, and creatine in hippocampus of TgCRND8 mouse model for Alzheimer disease. The Journal

[11] Choo LP, Wetzel DL, Halliday WC, Jackson M, LeVine SM, Mantsch HH. In situ characterization of beta-amyloid in Alzheimer's diseased tissue by synchrotron Fourier transform infrared microspectroscopy. Biophysical Journal, 1996; 71(4) 1672-1679. [12] Kneipp J, Miller LM, Joncic M, Kittel M, Lasch P, Beekes M, Naumann D. In situ identification of protein structural changes in prion-infected tissue. Biochimica et

[13] Bellisola G, Sorio C. Infrared spectroscopy and microscopy in cancer research and

[14] Walsh MJ, German MJ, Singh M, Pollock HM, Hammiche A, Kyrgiou M, Stringfellow HF, Paraskevaidis E, Martin-Hirsch PL, Martin FL. IR microspectroscopy: potential

[15] Petibois C, Déléris G. Chemical mapping of tumor progression by FT-IR imaging: towards molecular histopathology. Trends in Biotechnology, 2006; 24(10) 455-462. [16] Kastyak-Ibrahim MZ, Nasse MJ, Rak M, Hirschmugl C, Del Bigio MR, Albensi BC, Gough KM. Biochemical label-free tissue imaging with subcellular-resolution synchrotron FTIR with focal plane array detector. Neuroimage, 2012; 60(1) 376-383. [17] Miller LM, Dumas P. From structure to cellular mechanism with infrared microspectroscopy. Current Opinion in Structural Biology, 2010; 20(5) 649-656. [18] Trevisan J, Angelov PP, Carmichael PL, Scott AD, Martin FL. Extracting biological information with computational analysis of Fourier-transform infrared (FTIR) biospectroscopy datasets: current practices to future perspectives. The Analyst, 2012;

[19] Kelly JG, Trevisan J, Scott AD, Carmichael PL, Pollock HM, Martin-Hirsch PL, Martin FL. Biospectroscopy to metabolically profile biomolecular structure: a multistage approach linking computational analysis with biomarkers. Journal of Proteome

[20] Wang L, Mizaikoff B. Application of multivariate data-analysis techniques to biomedical diagnostics based on mid-infrared spectroscopy. Analytical and

[21] Martin FL, German MJ, Wit E, Fearn T, Ragavan N, Pollock HM. Identifying variables responsible for clustering in discriminant analysis of data from infrared microspectroscopy of a biological sample. Journal of Computational Biology, 2007; 14(9)

applications in cervical cancer screening. Cancer Letters, 2007; 246(1-2) 1-11.

diagnosis. American Journal of Cancer Research, 2012; 2(1) 1-21.

	- [37] Zhao R, Quaroni L, Casson AG. Fourier transform infrared (FTIR) spectromicroscopic characterisation of stem-like cell populations in human esophageal normal and adenocarcinoma cell lines. The Analyst, 2010; 135(1) 53–61.

Multivariate Analysis for Fourier Transform Infrared Spectra of Complex Biological Systems and Processes 219

[56] Rezzi S, Giani I, Héberger K, Axelson DE, Moretti VM, Reniero F and Claude G. Classification of Gilthead Sea Bream (Sparus aurata) from 1H NMR Lipid Profiling Combined with Principal Component and Linear Discriminant Analysis. Journal of

[57] Skrobot LS, Castro VRE, Pereira RCC, Pasa VMD and Fortes ICP. Use of Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) in Gas Chromatographic (GC) Data in the Investigation of Gasoline Adulteration. Energy &

[58] Walsh MJ, Singh MN, Pollock HM, Cooper LJ, German MJ, Stringfellow HF, Fullwood NJ, Paraskevaidis E, Martin-Hirsch PL, Martin FL. ATR microspectroscopy with multivariate analysis segregates grades of exfoliative cervical cytology. Biochemical and

[59] Pereira RCC, Skrobot VL, Castro EVR, Fortes ICP, Pasa VMD. Determination of Gasoline Adulteration by Principal Components Analysis-Linear Discriminant Analysis

[60] Héberger K, Csomós E andLivia S. Principal Component and Linear Discriminant Analyses of Free Amino Acids and Biogenic Amines in Hungarian Wines. Journal of

[61] Indahl UG, Liland KH, Naes T. Canonical partial least squares - a unified PLS approach to classification and regression problems. Journal of Chemometrics 2009; 23 495–504. [62] Rieppo L, Rieppo J, Jurvelin JS, Saarakkala S: Fourier transform infrared spectroscopic imaging and multivariate regression for prediction of proteoglycan content of articular

[63] Hemmateenejad B, Akhond M and Samari F. A comparative study between PCR and PLS in simultaneous spectrophotometric determination of diphenylamine, aniline, and phenol: Effect of wavelength selection, Spectrochimica Acta Part A: Molecular and

[64] Krogh A. What are artificial neural networks? Nature Biotechnology, 2008; 25(2) 195-

[65] Haykin S. Neural Networks: A Comprehensive Foundation. Englewood Cliffs: Prentice

[66] Bentley AJ, Nakamura T, Hammiche A, Pollock HM, Martin FL, Kinoshita S, Fullwood NJ. Characterization of human corneal stem cells by synchrotron infrared micro-

[67] Yousef I, Bréard J, SidAhmed-Adrar N, Maâmer-Azzabi A, Marchal C, Dumas P, Le Naour F. Infrared spectral signatures of CDCP1-induced effects in colon carcinoma

[68] German MJ, Hammiche A, Ragavan N, Tobin MJ, Cooper LJ, Matanhelia SS, Hindley AC, Nicholson CM, Fullwood NJ, Pollock HM, Martin FL. Infrared spectroscopy with multivariate analysis potentially facilitates the segregation of different types of prostate

[69] Walsh MJ, Singh MN, Stringfellow HF, Pollock HM, Hammiche A, Grude O, Fullwood NJ, Pitt MA, Martin-Hirsch PL, Martin FL. FTIR Microspectroscopy Coupled with Two-

agricultural and food chemistry 2007; 55 9963-9968.

Biophysical Research Communications, 2007; 352(1) 213-219.

Applied to FTIR Spectra. Energy & Fuels 2006; 20: 1097-1102.

Agricultural and Food Chemistry 2003; 51 8055-8060.

cartilage. PloS ONE 2012, 7 e32344.

197

Hall Inc.; 1999.

Biomolecular Spectroscopy 2007; 67 958-965.

spectroscopy. Molecular Vision, 2007; 13 237-242.

cell. Biophysical Journal, 2006; 90(10) 3783-3795.

cells. The Analyst, 2011; 136(24) 5162-5168.

Fuels 2007; 21 3394-3400.

[56] Rezzi S, Giani I, Héberger K, Axelson DE, Moretti VM, Reniero F and Claude G. Classification of Gilthead Sea Bream (Sparus aurata) from 1H NMR Lipid Profiling Combined with Principal Component and Linear Discriminant Analysis. Journal of agricultural and food chemistry 2007; 55 9963-9968.

218 Multivariate Analysis in Management, Engineering and the Sciences

adenocarcinoma cell lines. The Analyst, 2010; 135(1) 53–61.

enzymes. Methods in Enzymology, 1986;130 290-311.

Chemistry, 2005; 56 429-474.

Micron, 1996; 27(5) 303-314.

Academy; 2006.

2004.

scattering biological samples. The Analyst, 2010; 135(2) 268-277.

biomedical investigations. Vibrational Spectroscopy, 2003; 32 3–21.

[37] Zhao R, Quaroni L, Casson AG. Fourier transform infrared (FTIR) spectromicroscopic characterisation of stem-like cell populations in human esophageal normal and

[38] Bassan P, Kohler A, Martens H, Lee J, Byrne HJ, Dumas P, Gazi E, Brown M, Clarke N, Gardner P. Resonant Mie scattering (RMieS) correction of infrared spectra from highly

[39] Susi H, Byler DM. Resolution-enhanced Fourier transform infrared spectroscopy of

[40] Levin IW, Bhargava R. Fourier transform infrared vibrational spectroscopic imaging: integrating microscopy and molecular recognition. Annual Review of Physical

[41] Dumas P, Miller L. The use of synchrotron infrared microspectroscopy in biological and

[42] Katon JE. Infrared Microspectroscopy. A Review of Fundamentals and Applications.

[43] Eriksson L, Johansson E, Kettaneh-Wold N, Trygg J, Wikstrom C, Wold S. Multivariate and Megavariate Data Analysis Basic Principles and Applications. San Jose: Umetrics

[44] Manly BFJ. Multivariate Statistical Methods. London: Chapman & Hall/CRC press;

[45] Hestenes MR, Stiefel E. Methods of Conjugate Gradients for Solving Linear Systems.

[46] Marquardt D. An Algorithm for Least-Squares Estimation of Nonlinear Parameters.

[47] Levenberg K. A Method for the Solution of Certain Non-Linear Problems in Least

[48] Goldberg D E. Genetic Algorithms in Search Optimization and Machine Learning.

[50] Nas T, Isaksson T, Fearn T, Davies T. Multivariate Calibration and Classification.

[51] Fisher RA. The use of multiple measurements in taxonomic problems. Annals of

[52] Fearn, T. (2002). Discriminant analysis, In: Handbook of Vibrational Spectroscopy,

[53] Fukunaga K. Introduction to Statistical Pattern Recognition. San Diego: Academic Press

[54] Bishop CM. Neural Networks for Pattern Recognition. New York: Oxford University

[55] Jonathan P, McCarthy WV, Roberts MIA. Discriminant Analysis With Singular Covariance Matrices. A Method Incorporating Cross-Validation And Efficient

Randomized Permutation Tests. Journal Of Chemometrics, 1996; 10(4) 189-213.

Journal of Research of the National Bureau of Standards 1952;49: 409-436.

SIAM Journal on Applied Mathematics 1963; 11(2) 431-441.

Squares. Quarterly of Applied Mathematics 1944; 2 164-168.

[49] Rencher A C. Methods of Multivariate Analysis. Hoboken: Wiley; 2002.

Chalmers, J.M. & Griffiths, P.R. (eds.), New York: Wiley, p2086–2093.

Boston: Addison-Wesley Longman Publishing; 1969.

Chichester: NIR Publications; 2004.

Eugenics 1936; 7 179-188.

Professional Inc.; 1990.

Press; 1995.

Class Discrimination Segregates Markers Responsible for Inter- and Intra-Category Variance in Exfoliative Cervical Cytology. Biomarker Insights, 2008; 3 179–189.

**Chapter 11**

© 2012 Chahouki, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

© 2012 Chahouki, licensee InTech. This is a paper distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

**Classification and Ordination Methods as a Tool**

Community ecologists aim at understanding the occurrence and abundance of taxa (usully species) in space and time and the goal of all studies in plant ecology, is finding spatial and temporal interactions add to the complexity of vegetation systems. Hence for this purpose, it

In this study, some important classification and ordination methods such as cluster analysis (CA), Two way Indicator Species Analysis (TWINSPAN), Polar Ordination (PO), Nonmetric Multidimensional Scaling (NMS), Principal component analysis (PCA), Detrended Correspondence Analysis (DCA), Canonical correspondence analysis (CCA), Redundancy

Ordination (or inertia) methods, like principal component and correspondence analysis,and clustering and classification methods are currently used in many ecological studies (Anderson, 1971; Gauch et aL, I982a; Orloci, 1978; Whittaker et al, 1967; Legendre &

The choice of the mathematical method of analysis is mainly determined by availability rather than an accurate knowledge of the properties and limitations of the possible different

This study aims to explain these methods as tool for analyzing of plant Communities. The use of multivariate analysis has been extended much more widely over the past 20 years. Much more is included on techniques such as Canonical Correspondence Analysis (CCA) and Non-metric Multidimensional Scaling (NMS), Principal component analysis (PCA) and another technique to include plant communication and plant-environment relationships (Kent, 2006). It is a main objective in data analysis to distinguish random from deterministic components. Therefore spatial and temporal interactions add to the complexity of

**for Analyzing of Plant Communities**

Mohammad Ali Zare Chahouki

analysis (RDA) will be explained briefly.

methods (Legendre & Legendre, 1998).

vegetation systems (Wildi, 2010).

http://dx.doi.org/10.5772/54101

**1. Introduction**

Legendre, 1998).

Additional information is available at the end of the chapter

is necessary to imply best statistical methods (Causton, 1988)