UNIVERSITI TEKNOLOGI MARA

[PLEASE TYPE YOUR THESIS

TITLE] CHEMOMETRICS METHOD
WITH APPLICATIONS TO
ENVIRONMENTAL AND
QUANTITATIVE STRUCTURE-
ACTIVITY RELATIONSHIP
STUDIES
[MAX 10 LINES]

MOHD ZULI BIN JAAFAR

[MAX 2 LINES]

Choose an item

July 2023
UNIVERSITI TEKNOLOGI MARA

[PLEASE TYPE YOUR THESIS

TITLE] CHEMOMETRICS METHOD
WITH APPLICATIONS TO
ENVIRONMENTAL AND
QUANTITATIVE STRUCTURE-
ACTIVITY RELATIONSHIP
STUDIES
[MAX 10 LINES]

MOHD ZULI BIN JAAFAR

[MAX 2 LINES]

Choose an item submitted in Choose an item

of the requirements for the degree of
Master of Education
(Educational Management and Leadership)

Faculty of Education

July 2023
 CONFIRMATION BY PANEL OF EXAMINERS

I certify that a Panel of Examiners has met on Enter viva date to conduct the final
examination of Mohd Zuli Bin Jaafar on Choose an item Doctors of Philosophy thesis
entitled “Chemometrics Method with Applications to Environmental and Quantitative
Structure-Activity Relationship Studies” in accordance with Universiti Teknologi
MARA Act 1976 (Akta 173). The Panel of Examiner recommends that the student be
awarded the relevant degree. The Panel of Examiners was as follows:

Ahmad Sazali Hamzah, PhD

Professor
Faculty of Applied Sciences
Universiti Teknologi MARA
(Chairman)

Mohammad Nawawi Seroji, PhD

Associate Professor
College of Engineering
Universiti Teknologi MARA
(Internal Examiner)

Mohd Zuli Jaafar, PhD

Senior Lecturer
Faculty of Applied Sciences
University of Bristol
(External Examiner)

Wan Azlan Wan Zainal Abidin, PhD

Professor
Faculty of Engineering
University of Birmingham
(External Examiner)

PROF IR DR ZUHAINA HAJI ZAKARIA

Dean
Institute of Graduates Studies
Universiti Teknologi MARA
Date: 17 July 2023

ii
 AUTHOR’S DECLARATION

I declare that the work in this Choose an item. was carried out in accordance with the
regulations of Universiti Teknologi MARA. It is original and is the results of my own
work, unless otherwise indicated or acknowledged as referenced work. This thesis has
not been submitted to any other academic institution or non-academic institution for
any degree or qualification.

I, hereby, acknowledge that I have been supplied with the Academic Rules and
Regulations for Post Graduate, Universiti Teknologi MARA, regulating the conduct of
my study and research.

Name of Student : izzan ismail

Student ID. No. : 2014202020

Programme : Master of Science (Integrated Construction Project

Management) – AP780

Faculty : Applied Sciences

Thesis Title : Chemodmetrics with Applications to Environmental

and Quantitative Structure-Activity Relationship
Studies

Signature of Student : ……………………………………………..

Date : July 2023

iii
 ABSTRACT

The lack of management data and not knowing what level of park quality local
authorities are trying to deliver is becoming a growing concern. The problem of urban
landscape cannot be solved simply by providing more parks and spending more money
on development and management. There is an urgent need for innovation, for better
understanding of the current and potential role of the park to meet the needs in modern
urban life. Thus, the adoption of a strategic approach is needed to planning and
managing that urban landscape to carry out its function and roles. This research aim is
to study the factors of park attributes that influence the development, planning and
management of successful urban park in Kuala Muda. It specifically studies on Taman
Tasik Cini as the sole representative of urban park in the context of Kuala Muda
Structure Plan 2020. This research is based on data obtained from survey questionnaire
that polled public attitudes regarding the factors of park attributes based on visitor’s
perception and Harris’s (2008), park success factors. The data was analysed to evaluate
and determine the park attributes and its level of preferences that influence the strategic
approach to the planning and management of successful urban park. The research
suggested that successful urban park as are linked to the physical and functional
qualities of the park; security and comfort; visitors’ preferences and needs of the place.
The results of the study also suggested that a holistic strategic approach is needed for
the local authority to successfully managing the urban park. It is hope that the study can
contribute to the improvement of urban park planning and management in Kuala Muda.

--please delete--
Note:
Master – minimum 200 words
PhD – minimum 250 words
Limit to one (1) page only
No Paragraph
Font: Times New Roman - 12

iv
 ACKNOWLEDGEMENT

Firstly, I wish to thank God for giving me the opportunity to embark on my PhD and
for completing this long and challenging journey successfully. My gratitude and thanks
go to my supervisor Assoc Prof Datuk.

My appreciation goes to the Captain and crewmembers of the MMC who provided the
facilities and assistance during sampling. Special thanks to my colleagues and friends
for helping me with this project.

Finally, this thesis is dedicated to the loving memory of my very dear late father and
mother for the vision and determination to educate me. This piece of victory is dedicated
to both of you. Alhamdulilah.

--please delete--
Must include all supervisors names
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v
 TABLE OF CONTENTS

Page

CONFIRMATION BY PANEL OF EXAMINERS ii

AUTHOR’S DECLARATION iii
ABSTRACT iv
ACKNOWLEDGEMENT v
TABLE OF CONTENTS vi
LIST OF TABLES ix
LIST OF FIGURES x
LIST OF PLATES xi
LIST OF SYMBOLS xii
LIST OF ABBREVIATIONS xiii
LIST OF NOMENCLATURE xiv

CHAPTER 1 INTRODUCTION 1
1.1 Research Background 1
1.2 Motivation for This Work 1
1.3 Problem Statement 1
1.4 Research Objectives 4
1.5 Research Question 4
1.6 Significance of Study 5
1.6.1 Univariate Regression 10
1.6.2 Multivariate Regression 10
1.7 Limitation 11
1.8 Assumption 12
1.9 Ethical Committee 12
1.10 Thesis Scope 12
1.11 Thesis Outline 12

CHAPTER 2 LITERATURE REVIEW 13

2.1 Introduction 13

vi
 2.1.1 Data Pre-Processing and Data Drift: The Utility of Principal
Component Analysis, Self-Organizing Maps and Class Separation
Indices 13
2.1.2 Multivariate Linear Regression 14
2.2 Environmental Studies for Data Pre-Processing and Data Drift: The Utility
of Principal Component Analysis, Self-Organizing Maps and Class
Separation Indices 15
2.2.1 Data Pre-Processing and Data Drift: The Utility of Principal
Component Analysis, Self-Organizing Maps and Class Separation
Indices 15
2.2.2 Airborne Particulate Matter Datasets 16
2.2.3 Meteorological Dataset 17
2.3 Quantitative Structure Activity Relationships Studies on the Active and
Inactive Antimalarial Compounds 18

CHAPTER 3 RESEARCH METHODOLOGY 24

3.1 Introduction 24
3.2 Data Pre-Processing for Classifcation 24
3.2.1 Individual Transformation 25
3.2.2 Row Scaling 26
3.2.3 Column Scaling 26
3.3 Exploratory Data Analysis Principal Component Analysis 27
3.4 Quantitative Structure Activity Relationships Studies on The Active and
Inactive Antibacterial Compounds 29

CHAPTER 4 RESULTS ON EXPLORATORY METHOD FOR

ANTIBACTERIAL AND ANTIFUNGAL ACIVITY 32
4.1 Introduction 32
4.2 Chemometrics 32
4.3 PCA and PLS Work. 33

CHAPTER 5 CONCLUSION 34
5.1 Introduction 34

vii
5.2 Data cleaning 34
5.3 Data Pre-Processing 34

REFERENCES 35

APPENDICES 36

AUTHOR’S PROFILE 39

viii
 LIST OF TABLES

Tables Title Page

Table 1.1 The Title for This Table is Here 2

Table 1.2 The Statistical Information of APM Dataset 2
Table 1.3 The Title for This Table is Here 3
Table 1.4 The Sample of the Table with More Than One Page Items 7
Table 2.1 The Temperature Infomation 13
Table 2.2 The Environmental Dataset Infomation 13
Table 2.3 Summary of the Meteorological Parameters 16
Table 2.4 Title for Third Table in Chapter 2 17
Table 2.5 The Statistical Information of APM Dataset 17
Table 2.6 The Sample of the Table with More Than One Page Items 20
Table 3.1 The QSAR Dataset the Sources in This Thesis for Regression
and Classification 31
Table 3.2 To change the overall look of your document, choose new
Theme elements on the Page Layout tab. the look of your
document to the original contained in your current template. 31

ix
 LIST OF FIGURES

Figures Title Page

Figure 1.1 The Spectra of Cooking Oil after One Hour Heating. 9
Figure 1.2 FTIR spectra for non-fried (a) and fried palm oils (b) 9
Figure 1.3 FT-NIR spectra for non-fried (blue) and fried (red) palm oils 11
Figure 3.1 Compressive Strength of Rice Husk Ash (RHA) Concrete of
Grade 30 25
Figure 3.2 Typical Steps Involved in QSAR Methodology 28
Figure 3.3 A Map Showing The Sampling Location in Islamabad,
Pakistan 29
Figure 3.4 A PCA Plots for Data Processing Strategy 30

x
 LIST OF PLATES

Plates Title Page

Plate 1.1 MZJ Formatting Logo 5

Plate 1.2 A Picture of Light 6
Plate 2.1 A Sample of Grass and Bamboo 2 19
Plate 2.2 A Sample of Formatting Method 23
Plate 2.3 The View of the Tuanku Syed Sirajuddin Building, UiTM from
the Dataran Tengku Fauziah 23

xi
 LIST OF SYMBOLS

Symbols

A Number of PLS or PCA components in the model and the

number of selected latent variable in the model

a Number of the PLS or PCA component

b PLS regression coefficient

b Number of blocks (b=1,2,3.....,K)

C Coarse APM block

Cp Pooled covariance matrix for the two classes

Cg Covariance matrix for class g

xii
 LIST OF ABBREVIATIONS

Abbreviations

PCA Principal Component Analysis

xiii
 LIST OF NOMENCLATURE

Nomenclatures

A Amplitude Ratio, (No Units)

C Centroid of pipe, inches

xiv
 CHAPTER 1
INTRODUCTION

1.1 Research Background

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1.2 Motivation for This Work

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1.3 Problem Statement

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To make your document look professionally produced, Word provides header, footer,
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1
 On the Insert tab, the galleries include items that are designed to
coordinate with the overall look of your document. You can use these
galleries to insert tables, headers, footers, lists, cover pages, and
other document building blocks. When you create pictures, charts,
or diagrams, they also coordinate with your current document look
You can easily change the formatting of selected

On the Insert tab, the galleries include items that are designed to
coordinate with the overall look of your document. You can use these
galleries to insert tables, headers, footers, lists, cover pages,

Table 1.1
The Title for This Table is Here
Title Title Title
To change the overall look of To change the overall look of To change the overall look of
your document your document your document

To change the overall look of To change the overall look of To change the overall look of
your document your document your document

Source: World Bank report 2016

Video provides a powerful way to help you prove your point. When you click
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also type a keyword to search online for the video that best fits your document.
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footer, cover page, and text box designs that complement each other. For example, you
can add a matching cover page, header, and sidebar. Click Insert and then choose the
elements you want from the different galleries as shown in Table 1.2.

Table 1.2
The Statistical Information of APM Dataset
Batch No of Average per month Percentage of LoD Percentage of LoD
samples (Coarse APM) (Fine APM)

1 100 8 samples 1.70% 6.48%

2 102 9 samples 9.29% 9.09%

3 176 9 samples 2.65% 4.34%

2
Table 1.3
The Title for This Table is Here
Chemical C Surface Area (m2g-1) Porosity
Composition (cm3g-1)
Neutral clay 0.68 0.68 Neutral clay 0.68 0.68
Neutral clay 0.68 0.68

Bleaching clay Bleaching clay

Bleaching clay

0.80 0.89
0.99

Note: Influence of the physical chemistry properties of an acid activated bentonite in the bleaching of olive oil.
(Pradas et.al., 1993, p. 23)

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Design and choose a new Theme, the pictures, charts, and SmartArt graphics change to
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theme as shown in (1.3). Equation (1.4) gives example on the use of word “Equation”
in front of the equation numbering whenever a sentence starts with an equation.
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format text directly by using the other controls on the Home tab.

y = mx + 3 (1.1)

y = mx + 3 (1.2)

3
 y = mx + 3 (1.3)

y = mx + 4 (1.4)

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1.4 Research Objectives

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a) To perform data pre-processing and exploratory analysis by using PCA,

SOMs and Class Separation Indices.

b) To analysis analysis Multiblock methods and regression analysis of

environmental dataset.

c) To find the trend using pattern recognition in method QSAR with the
application of SOMs and PLSDA.

d) To test model validity using data Splitting Methods for Regressions and
Classifications.

1.5 Research Question

i) Video provides a powerful way to help you prove your point.

ii) When you click Online Video, you can paste in the embed code for the
video you want to add.

4
 iii) You can also type a keyword to search online for the video that best fits
your document.

iv) To make your document look professionally produced, Word provides

header, footer, cover page, and text box designs that complement each
other.

v) For example, you can add a matching cover page, header, and sidebar.

1.6 Significance of Study

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controls offer a choice of using the look from the current theme or using a format that
you specify directly. The sample of plates shown in Plate 1.2

Plate 1.1 MZJ Formatting Logo

5
 Plate 1.2 A Picture of Light

Video provides a powerful way to help you prove your point. When you click
Online Video, you can paste in the embed code for the video you want to add. You can
also type a keyword to search online for the video that best fits your document.
To make your document look professionally produced, Word provides header,
footer, cover page, and text box designs that complement each other. For example, you
can add a matching cover page, header, and sidebar. Click Insert and then choose the
elements you want from the different galleries.
Themes and styles also help keep your document coordinated. When you click
Design and choose a new Theme, the pictures, charts, and SmartArt graphics change to
match your new theme. When you apply styles, your headings change to match the new
theme.
Save time in Word with new buttons that show up where you need them. To
change the way a picture fits in your document, click it and a button for layout options
appears next to it. When you work on a table, click where you want to add a row or a
column, and then click the plus sign.
Reading is easier, too, in the new Reading view. You can collapse parts of the
document and focus on the text you want. If you need to stop reading before you reach
the end, Word remembers where you left off - even on another device.

6
Table 1.4
The Sample of the Table with More Than One Page Items
No Molecular Abbreviation Groups Amount Description
Descriptors
1 Constitutional Con 0D 48 0D-descriptors, independent from molecular connectivity and conformations. Atom and bonds
descriptors counts, molecular weight, sum of atomic properties, etc
2 Topological Topo 2D 119 Molecular descriptors obtained from the molecular graph (usually H-depleted), i.e 2D-descriptors
descriptors conformationally independent.
3 Walk and path Wap 2D 47 Molecular descriptors obtained from the molecular graph, counting paths, walk and self returning
counts walks of different lengths.
4 Connectivity Coni 2D 33 Topological Molecular descriptors calculated from the vertex degree of the atoms in the H-
indices depleted molecular graph.
5 Information Info 2D 47 Molecular descriptors calculated as information content of molecules, based on the calculation of
indices equivalences classes from the molecular graph. Among them, the indices of neighbourhood
degree and edge multiplicity.
6 2D 2D 2D 96 Molecular descriptors calculated from the molecular graph by summing the products of atom
autocorrelations weights of the terminal atoms of all the paths of the considered path length (the lag)
7 Edge adjacency Edge 2D 107 Topological Molecular descriptors derived from the edge adjacency matrix which encodes the
indices connectivity between graph edges.
8 Burden Bur 2D 64 Molecular descriptors contained from the positive and negative eigenvalues of the adjacency
eigenvalues matrix, weighting the diagonal element with atom weight.
9 Topological Topoc 2D 21 First 10 eigenvalues (absolute values) obtained from a corrected adjacency matrix.
charge indices

7
No Molecular Abbreviation Groups Amount Description
Descriptors
10 Eigenvalue-based EiG 2D 44 Topological descriptors calculated by the eigenvalues of the square(usually symmetric) matrix
indices representing a molecular graph.
11 Randic molecular Ran 3D 41 Molecular descriptors derived from the distance distribution moments of the geometry matrix,
profiles defined as the average row sum of its entries raised at the k-th power, normalized by the factor k.
12 Geometrical Geo 3D 74 Different kinds of conformationally dependent descriptors based on the molecular geometry.
descriptors Reliable values are obtained if reliable conformations were previously calculated.
13 RDF descriptors RDF 3D 150 Molecular descriptors obtained by radial basis functions centred on different interatomic distances
(from 0.5A to 15.5A)
14 3D-MoRSE 3D 3D 160 Molecular descriptors calculated by summing atom weights by different angular scattering
descriptors function.
15 WHIM WHIM 3D 99 Molecular descriptors obtained as statistical indices of the atom projected onto the 3 principal
descriptors components obtained from weighted covariance matrices of the atomic coordinates.

8
 On the Insert tab, the galleries include items that are designed to coordinate with
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You can also format text directly by using the other controls on the Home tab. Most
To change the overall look of your document, choose new Theme elements on
the Page Layout tab. To change the looks available in the Quick Style gallery, use the
Change Current Quick Style Set command. Both the Themes gallery and the Quick
Styles gallery provide reset commands so that you can always restore the look of your
document to the original contained in your current template.

HB
0.35

0.3

0.25

0.2

0.15

0.1

0.05

-0.05
0 5000 10000 15000

Figure 1.1 The Spectra of Cooking Oil after One Hour Heating.

a) 0.06 b) 0.06
0.05 0.05

0.04 0.04

0.03
Absorbance

0.03
Absorbance

0.02
0.02

0.01
0.01

0
0

-0.01
-0.01
4000 3665 3330 2995 2660 2325 1990 1655 1320 985
-0.02
4000 3665 3330 2995 2660 2325 1990 1655 1320 985 Wavenumber(cm-1)

Wavenumber(cm-1)

Figure 1.2 FTIR spectra for non-fried (a) and fried palm oils (b)

9
1.6.1 Univariate Regression

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1.6.2 Multivariate Regression

1.6.2.1 Principal Components Regression

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1.6.2.2 Multivariate Regressions using PLS Method

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a) On the Insert tab, the galleries include items that are designed to coordinate
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10
 On the Insert tab, the galleries include items that are designed to coordinate with
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footers, lists, cover pages, and other document building blocks. When you create
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You can easily change the formatting of selected text in the document text by choosing
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directly. To change the overall look of your document, choose new Theme elements on
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Change Current Quick Style Set command. Both the Themes gallery and the Quick
Styles gallery provide reset commands so that you can always restore the look of your
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galleries include items that are designed to coordinate with the overall look of your
document.

1.7 Limitation

a) 4
b) 4

3.5 3.5

3 3

2.5 2.5
Absorbance

Absorbance

2 2

1.5 1.5

1 1

0.5 0.5

0 0

-0.5 -0.5
11100 10374 9648 8922 8196 7470 6744 6018 5292 4566 11100 10374 9648 8922 8196 7470 6744 6018 5292 4566
Wavenumber(cm-1) Wavenumber(cm-1)

Figure 1.3 FT-NIR spectra for non-fried (blue) and fried (red) palm oils

11
1.8 Assumption

1.9 Ethical Committee

1.10 Thesis Scope

1.11 Thesis Outline

12
 CHAPTER 2
LITERATURE REVIEW

2.1 Introduction

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Table 2.1
The Temperature Infomation
Variable Minimum Maximum Average Standard
deviation
Minimum temperature over 24 hours 0.0 30.0 15.33 7.06
preceding 0300 GMT (0C)
Maximum temperature over 24 hours 12.5 44.7 29.85 6.93
preceding 1200 GMT (0C)

Table 2.2
The Environmental Dataset Infomation
Variable Minimum Maximum Average Standard
deviation

Average relative humidity (%) 31.0 97.0 63.70 14.80

Average pressure (hPa) 994.37 1022.43 1009.04 6.48

Average wind speed (Knot) 0.0 9.0 0.79 1.43

Average rainfall (mm) 0.0 140.0 3.82 14.05

2.1.1 Data Pre-Processing and Data Drift: The Utility of Principal Component
Analysis, Self-Organizing Maps and Class Separation Indices

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13
footers, lists, cover pages, and other document building blocks. When you create
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sample of equation is given in (2.1). On the Insert tab, the galleries include items that
are designed to coordinate with the overall look of your document. You can use these
galleries to insert tables, headers, footers, lists, cover pages, and other document
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y = mx + 3 (2.1)

y = mx + dx + 5 (2.2)

2.1.2 Multivariate Linear Regression

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Change Current Quick Style Set command. Both the Themes gallery and the Quick
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14
2.2 Environmental Studies for Data Pre-Processing and Data Drift: The Utility
of Principal Component Analysis, Self-Organizing Maps and Class
Separation Indices

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you specify directly.

2.2.1 Data Pre-Processing and Data Drift: The Utility of Principal Component
Analysis, Self-Organizing Maps and Class Separation Indices

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sample of equation is given in (2.1). On the Insert tab, the galleries include items that
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galleries to insert tables, headers, footers, lists, cover pages, and other document
building blocks. When you create pictures, charts, or diagrams, they also coordinate
with your current document look as shown in (2.2).

y = mx + 3 (2.3)

y = mx + dx + 5 (2.4)

To change the overall look of your document, choose new Theme elements on
the Page Layout tab. To change the looks available in the Quick Style gallery, use the
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15
Table 2.3
Summary of the Meteorological Parameters
Variable Minimum Maximum Average Standard
deviation
Minimum temperature over 24
0.0 30.0 15.33 7.06
hours preceding 0300 GMT (0C)
Maximum temperature over 24
12.5 44.7 29.85 6.93
hours preceding 1200 GMT (0C)
Average relative humidity (%)
31.0 97.0 63.70 14.80

Average pressure (hPa)

994.37 1022.43 1009.04 6.48

Average wind speed (Knot)

0.0 9.0 0.79 1.43

Average rainfall (mm)

0.0 140.0 3.82 14.05

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2.2.2 Airborne Particulate Matter Datasets

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16
Styles gallery provide reset commands so that you can always restore the look of your
document to the original contained in your current template.

Table 2.4
Title for Third Table in Chapter 2
Title Title Title
To change the overall look of To change the overall look of To change the overall look of
your document your document your document

To change the overall look of To change the overall look of To change the overall look of
your document your document your document

Source: World Bank report 2016

Table 2.5
The Statistical Information of APM Dataset
Batch No of Average per month Percentage of LoD Percentage of LoD
samples (Coarse APM) (Fine APM)
1 100 8 samples 1.70% 6.48%
2 102 9 samples 9.29% 9.09%
3 176 9 samples 2.65% 4.34%

2.2.3 Meteorological Dataset

2.2.3.1 Data Pre-Processing and Data Drift

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17
 To change the looks available in the Quick Style gallery, use the Change Current
Quick Style Set command. Both the Themes gallery and the Quick Styles gallery
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2.3 Quantitative Structure Activity Relationships Studies on the Active and

Inactive Antimalarial Compounds

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18
 Plate 2.1 A Sample of Grass and Bamboo 2

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19
Table 2.6
The Sample of the Table with More Than One Page Items
No Molecular Descriptors Abbreviation Groups Amount Description
1 Constitutional descriptors Con 0D 48 0D-descriptors, independent from molecular connectivity and
conformations. Atom and bonds counts, molecular weight, sum of atomic
properties, etc
2 Topological descriptors Topo 2D 119 Molecular descriptors obtained from the molecular graph (usually H-
depleted), i.e 2D-descriptors conformationally independent.
3 Walk and path Wap 2D 47 Molecular descriptors obtained from the molecular graph, counting paths,
counts walk and self returning walks of different lengths.
4 Connectivity Coni 2D 33 Topological Molecular descriptors calculated from the vertex degree of
indices the atoms in the H-depleted molecular graph.
5 Information Info 2D 47 Molecular descriptors calculated as information content of molecules,
indices based on the calculation of equivalences classes from the molecular
graph. Among them, the indices of neighbourhood degree and edge
multiplicity.
6 2D 2D 2D 96 Molecular descriptors calculated from the molecular graph by summing
autocorrelations the products of atom weights of the terminal atoms of all the paths of the
considered path length (the lag)
7 Edge adjacency indices Edge 2D 107 Topological Molecular descriptors derived from the edge adjacency
matrix which encodes the connectivity between graph edges.
8 Burden Bur 2D 64 Molecular descriptors contained from the positive and negative
eigenvalues eigenvalues of the adjacency matrix, weighting the diagonal element with

20
No Molecular Descriptors Abbreviation Groups Amount Description
atom weight.
9 Topological Topoc 2D 21 First 10 eigenvalues (absolute values) obtained from a corrected
charge indices adjacency matrix.
10 Eigenvalue-based indices EiG 2D 44 Topological descriptors calculated by the eigenvalues of the
square(usually symmetric) matrix representing a molecular graph.
11 Randic molecular profiles Ran 3D 41 Molecular descriptors derived from the distance distribution moments of
the geometry matrix, defined as the average row sum of its entries raised
at the k-th power, normalized by the factor k.
12 Geometrical descriptors Geo 3D 74 Different kinds of conformationally dependent descriptors based on the
molecular geometry. Reliable values are obtained if reliable
conformations were previously calculated.
13 RDF descriptors RDF 3D 150 Molecular descriptors obtained by radial basis functions centred on
different interatomic distances (from 0.5A to 15.5A)
14 3D-MoRSE descriptors 3D 3D 160 Molecular descriptors calculated by summing atom weights by different
angular scattering function.
15 WHIM WHIM 3D 99 Molecular descriptors obtained as statistical indices of the atom projected
descriptors onto the 3 principal components obtained from weighted covariance
matrices of the atomic coordinates.
16 GETAWAY descriptors GATE 3D 197 Descriptors calculated from the leverage matrix obtained by the centred
atoic coordinates (molecular influences matrix,MIM). The first four
descriptors are calculated as information content and connectivity
indices. HATA and H descriptors are 3D-autocorrelation descriptors

21
No Molecular Descriptors Abbreviation Groups Amount Description
obtained from MIM; R and R+ descriptors obtained from the leverage.
Geometry matrix.
17 Functional group counts Funct Others 152 Molecular descriptors based on the counting of chemical functional
groups. They are calculated by knowing the molecular composition and
atom connectivities.
18 Atom-centred fragments Atom Others 120 Molecular descriptors, based on the counting of 120 atom-centered
fragments, as defined by Ghose-Crippen. Some fragments are undefined
by the authors. They are calculated by knowing the molecular
composition and atom connectivities.
19 Charged descriptors charged Others 14 Fourteen charge descriptors which are reliable only when charge are
estimated by quantum molecular methods

22
 On the Insert tab, the galleries include items that are designed to coordinate with
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Plate 2.2 A Sample of Formatting Method

Plate 2.3 The View of the Tuanku Syed Sirajuddin Building, UiTM from the
Dataran Tengku Fauziah

23
 CHAPTER 3
RESEARCH METHODOLOGY

3.1 Introduction

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3.2 Data Pre-Processing for Classifcation

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24
 Figure 3.1 Compressive Strength of Rice Husk Ash (RHA) Concrete of Grade 30

3.2.1 Individual Transformation

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sample for writing an equation are shown at (3.1and (3.2);

sq
xij = n xij (3.1)

xij = log 10 xij (3.2)

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Your Document.
Save time in Word with new buttons that show up where you need them. To
change the way a picture fits in your document, click it and a button for layout options
appears next to it. When you work on a table, click where you want to add a row or a
column, and then click the plus sign.

25
 Reading is easier, too, in the new Reading view. You can collapse parts of the
document and focus on the text you want. If you need to stop reading before you reach
the end, Word remembers where you left off - even on another device.

3.2.2 Row Scaling

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Galleries To Insert Tables, Headers, Footers, Lists, Cover Pages, And Other Document
Building Blocks.
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3.2.3 Column Scaling

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“You can easily change the formatting of selected text in the document text
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Home tab. You can also format text directly by using the other controls on
the Home tab. Most controls offer a choice of using the look from the current
theme or using a format that you specify directly.”

26
 To change the overall look of your document, choose new Theme elements on
the Page Layout tab. To change the looks available in the Quick Style gallery, use the
Change Current Quick Style Set command. Both the Themes gallery and the Quick
Styles gallery provide reset commands so that you can always restore the look of your
document to the original contained in your current template.
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theme or using a format that you specify directly.

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Styles gallery provide reset commands so that you can always restore the look of your
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3.3 Exploratory Data Analysis Principal Component Analysis

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27
controls offer a choice of using the look from the current theme or using a format that
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Data entry and curation

Molecular descriptor generation

Data visualization

Model development

Model evaluation

Figure 3.2 Typical Steps Involved in QSAR Methodology

28
 Nilore

Figure 3.3 A Map Showing The Sampling Location in Islamabad, Pakistan

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3.4 Quantitative Structure Activity Relationships Studies on The Active and

Inactive Antibacterial Compounds

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29
 PCA Biplots PCA Biplots PCA Biplots
0.5
2003 2003 2003
2004a 0.4 2004a 2004a
0.8 0.8
2004b 2004b 2004b
I I
2005 0.3 Ba 2005 2005
I S
0.6 2006 Cr 2006 0.6 2006
0.2
2007 BC 2007 2007
0.1 V P Br
PC 2 (28.4%)

PC 2 (18.3%)

PC 2 (28.1%)
0.4 Pb Na 0.4
Cl Zn As Rb
Ba Al 0 Sr Ba Al
Al Sc
Co Ni GaGe Se
0.2 S CuF Hg 0.2 S
-0.1
Cr Mo Cr
Mn K
P
VCl -0.2 P
VCl
0 BrSc
Co
Ni
AsMn
Ga
Cu 0 BrSc
Co
Mn
Ni
Cu
As
Ga
Ge
Se Fe Ge
Se Fe
Zn Pb
Rb
MoTi
Na
Hg
Sr
F Zn PbMo
Rb
Na
Hg
Sr
F
Ti
K -0.3 Fe Mg K
Ca
Ti Si
-0.2 BC -0.2 BC
Mg Ca Si -0.4 Mg Ca Si

-0.5
-0.4 -0.4
-0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 -0.4 -0.3 -0.2 -0.1 0 0.1 0.2 0.3 0.4 0.5 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6
PC 1 (39.4%) PC 1 (20.3%) PC 1 (39.0%)

a) Pre-process data: A1, R1 and C1 b) Pre-process data: A1, R1 and C2 c) Pre-process data: A1, R1, C3
PCA Biplots PCA Biplots PCA Biplots

2003 0.5 2003 2003

0.8 0.8
2004a 2004a 2004a
I 2004b 2004b I 2004b
0.4
Fe Ti Si
0.6 2005 Ca 2005 0.6 2005
2006 0.3 2006 2006
2007 Mn 2007 2007
0.4 Al 0.2 Al K 0.4 Al
Mg
PC 2 (29.2%)

PC 2 (18.1%)

PC 2 (29.1%)
Ba 0.1 Sc CoMo Ba
0.2 Cl 0.2
S V Cu
NiFGa S
Cr 0 Cr
Zn Ge
P
VCl Fe Cr SeHg Cl
PSc
0 Sc
Co
BrMnTi I P V
BrCo
Mn Ti Fe
Ni
Cu
Ga
As
Ge
Se -0.1 0 Ni
Ga
Cu
As
Ge
AsNa RbSr Se
Zn PbMo
Rb
NaK
Hg
F
Sr Br Zn PbMo
Rb
FNaK
Hg
Sr
Si Ba Pb
Ca -0.2 Si
-0.2 S Ca
Mg -0.2 Mg
BC
-0.3
BC BC
-0.4 -0.4
-0.4

-0.6 -0.4 -0.2 0 0.2 0.4 0.6 -0.5 -0.4 -0.3 -0.2 -0.1 0 0.1 0.2 0.3 0.4 0.5 -0.6 -0.4 -0.2 0 0.2 0.4 0.6
PC 1 (37.6%) PC 1 (20.1%) PC 1 (37.3%)

d) Pre-process data: A1, R2 and C1 e) Pre-process data: A1, R2 and C2 f) Pre-process data: A1, R2, C3
Figure 3.4 A PCA Plots for Data Processing Strategy

30
Table 3.1
The QSAR Dataset the Sources in This Thesis for Regression and Classification
No Name Dimension Classes/ Types Reference
1 Blood Brain 406 × 926 Non-penetrating (class 1), 136
Barrier compounds
Penetrating (class 2), 270 compounds
2 Antimalarial 57 × 1661 Regression
3 Skin 131 × 926 Strong skin sensitizers (Class 1), 67
compounds
Non- strong skin sensitizers(class 2), 64
compounds

Table 3.2
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31
 CHAPTER 4
RESULTS ON EXPLORATORY METHOD FOR
ANTIBACTERIAL AND ANTIFUNGAL ACIVITY

4.1 Introduction

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(Abbas et al., 2011)

a) On the Insert tab, the galleries include items that are designed to coordinate
with the overall look of your document.

b) You can use these galleries to insert tables, headers, footers, lists, cover
pages, and other document building blocks.

c) When you create pictures, charts, or diagrams, they also coordinate with
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4.2 Chemometrics

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controls offer a choice of using the look from the current theme or using a format that
you specify directly.(2010a; 2010b; 2013)

4.3 PCA and PLS Work.

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2006; Mohd Z Jaafar et al., 2011; Lazim et al., 2013; Sim et al., 2015)

33
 CHAPTER 5
CONCLUSION

Video provides a powerful way to help you prove your point. When you click
Online Video, you can paste in the embed code for the video you want to add. You can
also type a keyword to search online for the video that best fits your document.
5.1 Introduction

5.2 Data cleaning

5.3 Data Pre-Processing

34
REFERENCES

Abbas, M., Shehab, A. A.-M., Hassan, N., & Al-Samuraee, A. (2011). Effect of
temperature and deposition time on the optical properties of chemically
deposited nanostructure PbS thin films. Thin Solid Films, 519(15), 4917-4922.
Abdulgafour, H., Hassan, Z., Al-Hardan, N., & Yam, F. (2010a). Growth of high-
quality ZnO nanowires without a catalyst. Physica B: Condensed Matter,
405(19), 4216-4218.
Abdulgafour, H., Hassan, Z., Al-Hardan, N., & Yam, F. (2010b). Growth of zinc oxide
nanoflowers by thermal evaporation method. Physica B: Condensed Matter,
405(11), 2570-2572.
Abdulgafour, H., Hassan, Z., Yam, F., & Chin, C. (2013). Sensing devices based on
ZnO hexagonal tube-like nanostructures grown on p-GaN heterojunction by wet
thermal evaporation. Thin Solid Films, 540, 212-220.
Jaafar, M. Z., Hasan, M. N., & Wong, T. W. (2006). Quantitative structure-activity
relationships of peroxisome proliferator activated receptor Y agonist.

35
APPENDICES

36
 APPENDIX 1
Example of the Codes in PLS Algorithms

37
 APPENDIX 2
Table of Parameters Used in Data Processing for PLS Testing Precuders on the
Classification of Biological Activity

Type Formula Description

C1 x ij = x ij − x j Mean centring

C2 x ij − x j Standardisation
x ij =
1 I

I i =1
( x ij − x j ) 2

C3 x ij − min( x i ) Range scaling

x ij =
max( x i ) − min( x i )

38
 AUTHOR’S PROFILE

Mohd Zuli Jaafar obtained Bachelor of Science in Chemistry (Hons.) in 1996

from University Malaya, Kuala Lumpur, MSc in Chemistry (2002) from Universiti
Teknologi Malaysia and PhD in Chemometrics (2011) from the University of Bristol,
United Kingdom. His PhD thesis involves several methods in Chemometrics and
Pattern Recognition includes Data Preprocessing, Regression, Classification and
Variable Selection. Currently he is working on several scientific dataset i.e. Fourier
Transform Infrared Spectroscopy, Near Infrared, Particle-Induced X-Ray Emission and
Quantitative Structure-Activity Relationship.

List of Publication:

Sim, S.F., T.Y. Ling, S. Lau, and M.Z. Jaafar, A novel computer-aided multivariate
water quality index. Environ Monit Assess, 2015. 187(4): p. 181.
Yatim, N.N.M., Z.M. Zain, M.Z. Jaafar, Z. Md Yusof, A.R. Laili, M.H. Laili, and M.H.
Hisham. Noninvasive glucose level determination using diffuse reflectance near
infrared spectroscopy and chemometrics analysis based on in vitro sample and
human skin. in Systems, Process and Control (ICSPC), 2014 IEEE Conference
on. 2014.
Rasaruddin, N.F., M.E.N.M. Ruah, M.N. Hasan, and M.Z. Jaafar, Determination of
Iodine Value of Palm Oils Using Partial Least Squares Regression-Fourier
Transform Infrared Data. Jurnal Teknologi, 2014. 70(5).
Rasaruddin, N.F., M.N. Hasan, M.E.N.M. Ruah, S.S. Fong, and M.Z. Jaafar. Signal
processing strategies in FT-NIR and FTIR spectra of palm oils. in Signal

39
 Processing & its Applications (CSPA), 2014 IEEE 10th International
Colloquium on Signal Processing and its Application 2014. IEEE.
Waheed, S., M.Z. Jaafar, N. Siddique, A. Markwitz, and R.G. Brereton, PIXE analysis
of PM2. 5 and PM2. 5–10 for air quality assessment of Islamabad, Pakistan:
Application of chemometrics for source identification. Journal of
Environmental Science and Health, Part A, 2012. 47(13): p. 2016-2027.
Ridzuan, M.S.M., M.Z. Jaafar, and M.M. Zain. Quantitative structure-activity
relationship (QSAR) modelling of N-aryl derivatives as cholinesterase
inhibitors. in Humanities, Science and Engineering Research (SHUSER), 2012
IEEE Symposium on. 2012. IEEE.
Jaafar, M.Z., A.H. Khan, S. Adnan, A. Markwitz, N. Siddique, S. Waheed, and R.G.
Brereton, Multiblock analysis of environmental measurements: A case study of
using Proton Induced X-ray Emission and meteorology dataset obtained from
Islamabad Pakistan. Chemometrics and Intelligent Laboratory Systems, 2011.
107(1): p. 31-43.
Saim, N., R. Osman, D.R.S.A. Spian, M.Z. Jaafar, H. Juahir, M.P. Abdullah, and F. Ab
Ghani, Chemometric approach to validating faecal sterols as source tracer for
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