FORMAT FOR

THESES and DISSERTATIONS

The Institute of Environmental Sciences

Boğaziçi University

2017Version 2.2

List of Contributors

The following people have contributed to the development of this format document for the preparation of theses and dissertations completed at The Institute of Environmental Sciences.

Miray BekböletFerhan ÇeçenRaşit BilginBurak DemirelBerat Z. Haznedaroğlu

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IMPORTANT NOTICE: PLAGIARISM CONTROL WITH TURNITIN®

The first step before the format control for theses and dissertations submitted to the Institute of Environmental Sciences includes a plagiarism control/check with the online service Turnitin1 as required by The Council of Higher Education (YÖK) regulations. This check will be done by the Institute.

1 http://www.library.boun.edu.tr/turnitin.php

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TABLE OF CONTENTS

1. INTRODUCTION 6

2. GENERAL INSTRUCTIONS 7

3. FORMAT 8

3.1. Character Fonts 8

3.2. Spacing 8

3.3. Centering 8

3.4. Margins 8

3.5. Pagination 8

3.6. Paragraphs 9

3.7. Headings 10

3.7.1. Main Headings 10

3.7.2. Second Headings 10

3.7.3. First Sub-headings 10

3.7.4. Second Sub-headings 10

3.7.5. Third Sub-headings 11

3.7.6. Fourth Sub-headings 11

3.8. Footnotes 11

3.9. Bibliographical Materials 11

3.10. Specially Designated Expressions 12

3.11. Specimen Calculations 12

3.12. Units and Symbols 12

3.13. Tables, Figures, Charts and Illustrations 13

4. ARRANGEMENT 15

4.1. Title Page 14

4.2. Approval Page 14

4.3. Dedication 14

4.4. Acknowledgements 14

4.5. Abstract 16

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4.6. Table of Contents, List of Figures, List of Tables, List of

Symbols/Abbreviations 16

4.7. Additional Suggestions for the Text 16

4.8. Appendices 17

5. PREPARATION OF THE FINAL COPIES 18

5.1. Typesetting 18

5.2. Paper Quality 18

5.3 Printer Quality 18

5.4. Submission of Theses and Dissertations for the Examining

Committee 18

5.5 Submission of Theses and Dissertations for Format Control 18

6. PUBLICATION OF THESES AND DISSERTATIONS 19

6.1. Use of Copyrighted Material 19

6.2. Publications 19

APPENDIX A: SAMPLE PAGES 20

Title Page for M.Sc. Degree 21

Title Page for Ph.D. Degree 22

Approval Page 23

Abstract (within the thesis/dissertation) 24

Abstract and “Özet” (separate) 25

Abstract for the YÖK Documentation Center (separate) 26

Table of Contents 27

List of Tables 28

List of Figures 29

List of Symbols/Abbreviations 30

References 31

Sample Pages for Normal Text Arrangement (headings, paragraphs etc.) 36

Sample Page for Figures and Tables 38

APPENDIX A: FORMAT OF COMPACT DISCS CONTAINING SOFTWARE 39

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1. INTRODUCTION

The procedures and rules set forth in the following pages are for the guidance of graduate students preparing their M.S. Theses and Ph.D. Dissertations at the Institute of Environmental Sciences, Boğaziçi University. The material presented in this format should be considered as a complete manual for the writing of theses and dissertations. Other helpful information can be found in other publications. The student should consult those relevant to his/her field of study. As to the specific requirements, those listed herein should be followed. There are several books on thesis/dissertation preparation. Three of them are available in the University library:

Author: Beaud, Michel. Title: Tez yazma sanatı: Bir yüksek lisans tezi, doktora tezi, bitirme tezi veya herhangi bir üniversite çalışmasını nasıl hazırlayıp kaleme alabilirsiniz? Çev. Ayşe Meral. Imprint İstanbul, Söylem Yayınları, 2001.

General Collection LB2369.B3319 2001

Author: Watson, George. Title: Writing a thesis: A guide to long essays and dissertations.Imprint London, Longman, 1987.

General Collection LB2369.W34 1987

Author: Eco, Umberto. Title: How to write a thesis. Cambridge, Massachusetts, MIT Press, 2015. General collection LB2369.E2813 2015

Some matters of form are local and concern the weight of paper used, the title page, the table of contents, and the like. These requirements are stated in Sections 3 and 4.

Every thesis/dissertation must show correctness and clarity of expression. The responsibility for such correctness and clarity rests primarily upon the candidate, but every thesis/dissertation will be scrutinized for these qualities by the student's advisor and the Examining Committee.

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2. GENERAL INSTRUCTIONS

The following rules and statements are presented more as answers to frequently asked questions, rather than an alphabetically indexed coverage of every contingency. If for good reason a student must seek exception to the practices listed here, he/she should consult his/her advisor.

An M.S. thesis or Ph.D. dissertation should be submitted to candidate's advisor for review by the candidate. Please refer to ‘Madde 31, 43, 44; Boğaziçi Üniversitesi Lisansüstü Eğitim ve Öğretim Yönetmeliği’ for guidelines and time frames. After the approval by the advisor, copies of the thesis or dissertation should be submitted to the members of Examining Committee (Jury). It is advised that the thesis/dissertation is proofread by a person whose native language is English.

The oral examination is scheduled by the candidate's advisor in accordance with the rules and regulations of the University. When the thesis or dissertation is approved by the Examining Committee, an electronic copy should be submitted to editors for format checking and control (Please note that editorial control can take two weeks or more depending on the formatting issues). Please consult with the Institute Secretarial Office for the names of the current editors. After the format review, the editors will provide a written approval document to the student. Next, the thesis/dissertation should be printed and bound. The title page of the final copy must be signed by all members of the Examining Committee. Subsequently, a single hard-bound copy of the thesis/dissertation and the approval document from the editors should be submitted to the Executive Committee. If the thesis/dissertation is approved, the candidate will submit three hard-bound copies and two digital copies on compact disks (CD) to the Institute. The Institute will deliver one hard-bound copy and one CD copy to the Boğaziçi University Library, and will keep two hard-bound copies and one CD copy.

The Institute of Environmental Sciences requires four additional copies of a short abstract (two in English and two in Turkish), not exceeding 250 words in length (page 25). One CD containing the abstract (English and Turkish) and five keywords (English and Turkish) prepared according to the format as shown on page 25 should also be submitted to the Institute Secretarial Office. YÖK requires all candidates to fill the YÖK Thesis Data Form, which is available in this booklet, on page 26. Two signed copies of this form should also be submitted to the Institute Secretarial Office.

This format for Theses and Dissertations will come into effect on the 18 th of September 2017.

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3. FORMAT

3.1. Character Fonts. Throughout the entire thesis/dissertation, use Times New Roman as the default character font. The main headings should be in 14 point and bold. The font size must be 12 point in the text including formulas, equations, table headings, and figure captions. At least 8 point should be used within figure and table components (such as axis titles, data legends, etc).

3.2. Spacing. The main text body should have 1.5 line spacing, except footnotes where single line spacing should be used. In addition, under the “PAGE LAYOUT” menu of Microsoft Word and under the “Spacing” option, the “Before” and “After” values has to be 0 pt.

3.3. Centering. Wherever titles and headings need to be centered, the center point of the title or heading should be 112 mm from the left edge of the paper or 98 mm from the right edge of the A4 size paper. 3.4. Margins. Margins of pages should conform to the following specifications: Left margin – 2.5 cm from the edge of paper. Right margin – 1.5 cm from the edge of paper. Top margin – 2.5 cm from the edge of paper. Bottom margin – 1.5 cm from the edge of paper.

The above margins should be observed on all charts, graphs, tables, figures, and drawings. Folded papers will not be accepted unless there is absolutely no other way for the material to be presented.

3.5. Pagination. Each page in the thesis/dissertation should have a page number. Only one side of the paper should be used. The following format should be used exclusively:

The preliminary section, including the title page, approval page, dedication (if any), acknowledgements, abstract, özet, table of contents, list of figures, list of tables, and list of symbols and abbreviations should be numbered using lower case Roman Numerals, i.e., i, ii, iii, etc. The title page counts as Page i, but the number does not appear on the page. The sequence of the preliminary section is as follows and should be numbered consecutively depending on the content. An example of the numbering scheme is given on the following page:

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Title Page………………………………………. Page i, number does not appearApproval Page…………………………………. Page iiDedication (if preferred) ………………………. Do not put page number if you add

a dedication pageAcknowledgements……………………………. Page iii, iv as necessaryAbstract………………………………………... Page v or vi as necessaryÖzet……………………………………………. Page vi, vii, as necessaryTable of Contents……………………………… Page viii, ix, as necessaryList of Figures…………………………………. Page x, xi, as necessaryList of Tables…………………………………... Page xii, xiii, as necessaryList of Symbols/Abbreviations………………… Page xiv, xv, as necessary

For the remainder of the thesis/dissertation, Arabic numbers (1, 2, 3, etc.) are used. Page numbers are to be placed 1.5 cm from both the top and right hand margins on the pages. This should also apply in the case of illustrations, tables, figures, appendices, references, etc. The numbering in the main text body of the thesis/dissertation should begin with Page 1 and run consecutively to the last page.

3.6. Paragraphs: Paragraph indentations must be uniformly 0.8 cm long. For this formatting, use the

“Page Layout” menu of Microsoft Word and under the “Spacing” options, the “Before” and “After” values should be 0 pt. Under the “Paragraph” options, the “Special” option should be adjusted by “First Line” at 0.8 cm.

A new paragraph must be separated from the preceding paragraphs by two enters (2xCR), which corresponds to one line space.

A new paragraph must not begin at the bottom of a page if there is not sufficient space for at least two lines. This corresponds to (2xCR).

If a heading starts near the end of a page, there should be at least two lines of text below this heading. Otherwise, it is recommended to move this heading to the next page.

Series of paragraph items which are to be listed without headings under any of the regular headings may, for clarity, be designated as follows: (A), (B), (C) or with special bullets such as . If needed, these series of paragraphs can be further extended as (A.1), (A.2), etc. A period must not follow the parenthesis.

Series of items listed in the interior of a paragraph may be designated as follows: (a), (b), (c). In such a case, each item must begin with a lower-case letter and must end

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with a semicolon, unless it is a complete sentence. No period is necessary between the parenthesis and the first sentence.

Special attention should be given to complete the whole page with text, tables and figures, etc.

3.7. Headings The headings should contain enough information such that the insertion of a heading is justified. Ideally, there should be some unifying sentences between the headings. Examples to all kinds of headings are given on pages 32 and 33.

3.7.1. Main Headings – Should be given in Arabic numerals (1., 2., 3., etc.).

Must begin a new page and be centered. Omit period at the end of the heading. Main headings must be typed in bold face and must be in capital 14 point letters.

Main headings should reflect content of the text that follows. Main headings are not to be identified as chapters.

The numbers of the headings should be followed by a period and two spaces. Must precede the following text material or second heading by (3xCR).

3.7.2. Second Headings – Should be given in Arabic numerals (2.1., 2.2., 2.3., etc.).

Must be centered and be typed in capital, bold and lower case 12 point letters. The first letter of each word except conjunctions, prepositions, and articles must be a capital letter. Omit period at the end of heading.

The number designation of the heading should be followed by a period and two spaces.

Second headings must be (2xCR) below of preceding text and (2xCR) above of succeeding text, but need not begin a new page.

3.7.3. First sub–headings – Should be given in Arabic numerals (2.2.1., 2.2.2., 2.2.3., etc.).

Must be typed on separate lines beginning at the left margin line of the text, but need not begin a new page.

The first letter of each word except conjunctions, prepositions, and articles must be a capital letter. Omit period at the end of heading.

The number designation of the heading should be followed by a period and two spaces. Omit period at the end of the heading.

Must be separated from the preceding and succeeding text by (2xCR) spacing.

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3.7.4. Second sub–headings – Second sub–headings should be avoided if possible (2.2.2.1., 2.2.2.2., 2.2.2.3., etc.).

Must begin at the left margin and be typed in lower case letters except the first letter of the first word and proper nouns (sentence case). The text should continue on the same line.

Must be followed by a period at the end of the heading and must be underlined. The number designation should be followed by a period and two spaces. Must be separated from the preceding text by (2xCR).

3.7.5. Third sub-headings

Headings such as 2.2.2.1.1. should never be inserted. A heading at this level should be treated like a paragraph and have no number. It must be typed on separate lines beginning at the left margin line of the text and it should be in italics and underlined.

Must be separated from the preceding text by (2xCR).

3.7.6. Fourth sub-headings

If a heading is needed below the third sub-heading, it should also have no number. It must be typed on separate lines beginning at the left margin line of the text and it should be in italics but not underlined.

Must be separated from the preceding text by (2xCR).

3.8. Footnotes (Footnotes should be used only if they are absolutely necessary)

Footnote references should be indicated in the text by an Arabic number placed superior to the text and immediately following the word, phrase or sentence which the footnote concerns.

Footnotes should be sequential for each page and for the entire thesis/dissertation. Footnotes should be placed at the bottom of the page on which they are indicated. The

first line of the footnote should be indented from the margin line of the main text by 0.8 cm.

Footnotes should be single-spaced and 10 points. Footnotes should not be italicized in the text.

3.9. Bibliographical Materials

As already noted in the Introduction of this manual, theses/dissertations should follow the format used in scholarly publications of the student's field of research. Rules of

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form vary from one field to another, and it is important that the student learns the editorial usage of his/her own field. It is generally important that he/she follows such usage consistently throughout his/her thesis/dissertation.

References should be given in alphabetical order. In any case, the rules shown on pages 31-35 should be followed. The listing of references in this case should be by the surname of the first author. References should not be given in numerical order.

The references should be typed in same font and size as the main text. If any information on a website is cited, as much information should be given about

the reference as possible. These include but not limited to institution name (ex: U.S. Environmental Protection Agency), source title or author name (ex: Wikipedia), URL link, content title, and the date of access.

For citing papers accepted but not printed or published yet, document object identifier (DOI) number should be provided. Examples are given on page 32.

The general rule is that every kind of reference should be easily accessible by the reader, references without source information as described above should never be cited.

If necessary, a list of “References not cited” should be given.

3.10. Specially Designated Expressions

Specially designated expressions usually mean equations, formulas, etc. Specially designated expressions should be indented to the left margin of the page and

should be set below the preceding text and before the succeeding text by (2xCR). The expressions should be identified by an Arabic number in parenthesis placed

opposite to the expression, and indented to the right margin of the page. They should be numbered in each chapter in the order of their appearance together with the chapter number, e.g. (6.2), (6.3), (6.4), etc. The style used in in-text formulae expressions should be the same as that of displayed formulae. In the same chapter, all equations and formulas are treated at the same level and they should be numbered in the order of appearance in the text.

3.11. Specimen Calculation

In theses/dissertations involving experimental work, a specimen calculation should be included exemplifying how a routine calculation was made. The units should be clearly shown in this calculation. These specimen calculations may be inserted into the main text or in the appendices, as appropriate.

3.12. Units and Symbols

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A list of symbols with SI units should be provided. The style of using SI unit symbols should be consistent throughout the text. For example, either the kg/m3 or kg m-3 style should be preferred. In special cases units other than SI may be used. The most important criterion here is consistency throughout the text.

For more information, you may consult the website related to SI base units, derived units, and supplementary units: http://physics.nist.gov/cuu/Units/units.html

In describing wastewater treatment processes, candidates should consult “Notation for use in description of wastewater treatment processes”, Water Research 21, 135-139 (1987).

For chemical nomenclature, candidates should consult IUPAC websites such as http://www.chem.qmul.ac.uk/iupac/ or other similar websites.

Authors should follow the rules of the Commission on New Minerals and Mineral Names of the International Mineralogical Association (IMA) in all matters concerning mineral names and nomenclature (https://www.ima-mineralogy.org/Minlist.htm).

For microbial nomenclature (such as species names and taxonomical representations), candidates should refer to websites such as https://www.ncbi.nlm.nih.gov/pubmed/3555972

For genetic nomenclature (such as gene names, markers, alleles), candidates should refer to web sites such as http://www.informatics.jax.org/mgihome/nomen/gene.shtml

3.13. Tables, Figures, Charts and Illustrations

In general, all of these are special matters usually of a technical sort, and the proper form must be understood and followed after a candidate has received instructions from his/her advisor.

The designation of each table or figure in the text should have only the first letter in capital (i.e, such as “Table 4.5” or Figure 3.8”). They should be numbered from the beginning in the order of appearance in the text, such as Table 4.1, Table 4.2 or Figure 4.1, Figure 4.2, etc.

The tables and figures, as well as the captions, should be centered. The captions should be as normal text, i.e., only the first letter should be capitalized. A period must be used at the end of the Table or Figure number, followed by single space. Another period must be placed at the end of the heading (Example: Table 3.1. The relative frequency of each haplotypes.)

Captions which are too long can be justified. In the same chapter, the captions should be at a distance of (1xCR) from the table or

figure. When tables and figures are presented in appendices, they should be designated as Table A.1., A.2. or Figure B.1., B.2. etc. in the order of their appearance.

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In figures and tables, too much crowding should be avoided. The numbers in the figures and tables should be at least 8 points. The most important point is consistency throughout the text. In tables, single line spacing should be used.

If the size of a table and figure exceeds the page margins, this item may be inserted in the landscape form. The page number on landscape formatted pages should be same as the rest of the manuscript (i.e., the page number should be on top right corner when printed).

All floating items such as graphs, charts, photographs and illustrations should be considered and designated as a figure or table, whichever is appropriate.

To ensure satisfactory reproduction on black and white print, adequate contrast should be provided for graphs and charts to distinguish data points, especially for colored versions.

For footnotes associated with tables, the text should be aligned with the bottom left corner of the table, not italicized, and be exactly 8 points. Footnotes should not be used in figures (all required explanations must be provided in figure caption).

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4. ARRANGEMENT

4.1. Title Page. An example for the title page of a thesis and dissertation can be found on pages 20 and 21, respectively. The thesis/dissertation title should be (4XCR) from the top of the page, and (6XCR) from the subsiding text. The title should be capitalized, centered, and 14 points in size. Boğaziçi University and the Year below should be centered and placed at the bottom of the title page (see example template document for details). When preparing the thesis/dissertation, the candidate must list his/her prior degree(s) showing the major, the degree granting institution and the date, in chronological order. This page will not bear a number.

4.2. Approval Page. This page follows the Title Page. The thesis/dissertation title should be (4XCR) from the top of the page, centered, capitalized, and 14 points in size. “APPROVED BY” should be (10XCR, not counting the title) from the top of the page and aligned to the left margin. The names of the members of the Examining Committee will be listed starting (2XCR) from “APPROVED BY” and aligned 4.5 cm from the left margin. The names of the examining committee should follow each other in alphabetical order based on last names except the Thesis/Dissertation Advisor's, whose name will be at the top of the list. If there is a co-advisor, his/her name should be listed below the advisor. The academic titles of the members should be placed as abbreviations (Prof. Dr., Assoc. Prof. Dr., and Asst. Prof. Dr.) in front of the names. Next to each name, a dotted space should be placed 11.5 cm from left margin, and 1 cm from right margin for the signature of each examiner. The “DATE OF APPROVAL: XY/XY/XYWZ” should be provided at the bottom of the page, and be aligned to the left margin, and reflect the date the thesis/dissertation was approved by the Examining Committee. Leave two spaces after the colon and before the approval date.

4.3. Dedication Page. Occasionally, authors would like to dedicate their thesis/dissertation to their family members, friends or some scientists in their area of research, etc. The dedication sentence(s) should be placed at the bottom of page, all aligned to the right hand side of the page and italicized. The dedication page should follow right after the Approval Page. Please refer to the example format page for details.

4.4. Acknowledgements. The candidate may desire to include a page with a brief note of an acknowledgement of help received from particular people or organizations. The “Acknowledgements” page must immediately precede the Abstract and must be brief.

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If the research has been supported by Boğaziçi University Research Fund or any other fund, this should be mentioned in the acknowledgements section, along with the project number.

4.5. Abstract. It is suggested that the abstract cover the following points: statement of the problem, procedure or method, results and conclusions. Headings, tabular material, chemical formulas, footnotes, and references should be excluded in the abstract. Primarily, the abstract should give the information that will enable a scholar to tell whether he/she wishes to read the complete work. Abstracts should fit into one page and should not exceed 250 words. Abstracts should be a single paragraph body.

4.6. Table of Contents, List of Figures, List of Tables, and List of Symbols/Abbreviations. If figures and tables are present in the text, a separate “List of Figures” (and/or “List of Tables”) must be included after the Table of Contents. These lists should include page numbers. Similarly, a “List of Symbols” (or “List of Symbols/Abbreviations”, as appropriate) should be included. Formatting of these sections are included in the template document, please pay attention to the comments and notes provided.

4.7. Additional Suggestions for the Text

Periods and commas go inside the quotation marks; semicolons and colons go outside. For sentences ending with parentheses (such as citations, etc.), periods must be used

after closing the parentheses – Ex: Oxidation of this compound has been studied elsewhere (Smith and Powers, 2009).

The word “data” is plural and requires a plural verb. Numbers from one to nine, inclusive, should be spelled out, for numbers 10 and above,

use numerals. Numbers should be spelled out when they begin a sentence. Spell out per cent in the usual text format as two words without a period, but you are

allowed to use % sign if followed by a number. There should be a space between % sign and the number.

Be sure that tenses throughout the text are consistent. Italics should be used for words from other languages. However, commonly used

words, phrases and abbreviations such as "in situ", "e.g.", "et al." and "etc." should not be italicized.

Italics should also be used for organism names in Latin, as shown in the references section.

Depending on thesis/dissertation context, the main text should be organized in parts such as Introduction, Background (Theory or any appropriate term), Statement of the Problem, Materials and Methods, Results and Discussion, etc. In theses/dissertations

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including no experimental work, this order may be changed with the consent of the advisor.

Avoid the insertion of excessive literature or other studies which are not directly related to the thesis/dissertation.

In some theses/dissertations, the format may be adjusted such that the thesis/dissertation is divided into independent chapters each containing Introduction, Theoretical (or any appropriate term), Materials and Methods, Results and Discussion, References, etc. parts. For doing this, the students should get the approval of their advisor.

In some theses/dissertations, the format may be adjusted such that the thesis/dissertation is divided into independent chapters each containing a journal publication. The publication should include volume, issue and page number or it should be in press. For doing this, one should get the approval of the advisor.

For headings placed at the end of pages, there should be at least two lines of subsequent text, otherwise, they should start at the beginning of next page.

If tables or figures placed after presiding text are moved to the next page due to size limitations, the text following tables or figures should be moved to previous page in order not to leave blank space.

Abbreviations should be written in full and in parenthesis only for the first time in the text. Abbreviations should not be used in main and sub-headings throughout the text.

4.8. AppendicesExamples of appendix material include data sheets, questionnaire samples, flowcharts, illustrations, maps, software listings, charts, etc. Each appendix should have a descriptive title just like chapter headings, and should be formatted as main headings. If more than one appendix is needed, each should be labeled alphabetically (Ex: APPENDIX A, APPENDIX B, etc.).

The developed computer programs should be given in a separate CD: the format and contents of this CD are explained in Appendix B of this booklet.

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5. PREPARATION OF THE FINAL COPIES

5.1. Typesetting. Use of a professional typesetting program, such as MS-Word is recommended.

5.2. Paper Quality. The original copy should be typed on 75 or 80 g/m2 white paper. All copies should also be printed on the same grade of paper. The size of paper should be A4.

5.3. Printer Quality. Only Laser-Jet outputs are acceptable.

5.4. Submission of Theses/Dissertations for the Examining Committee Theses/Dissertations submitted to the Examining Committee should not be in a loose

form but in a booklet form. This does not necessarily mean that the thesis/dissertation should be bound in the official dark blue hard cover, a version of the thesis/dissertation bound in spiral will be adequate.

5.5. Submission of Theses/Dissertations for Format Control Prior to thesis and dissertation format checking by the editors, a plagiarism

control/check is mandatory by YÖK regulations. This check will be done by the Institute by using the online service Turnitin (available through the BOUN Library).

Once the plagiarism control/check is completed and all revisions are made, the theses/dissertations should be submitted to the editors for format control in MS-Word form.

Candidates should plan for at least two weeks of format control. Depending on the extent of revisions requested, this duration can be prolonged.

Once all revisions are accepted by the editors, an approval form will be provided to the candidate.

Upon final approval by the editors and the completion of signatures by the Examining Committee, thesis/dissertation should be bound in hard cover, in the color required by the Institute (dark blue).

Regarding the cover of the bound copy, the surname of the candidate, the type of degree obtained and the year should be printed in the above order on the spine of the cover. When the thesis/dissertation is placed front cover up, the spine should read from left to right.

An example for the hard cover title page is presented on page 38. Please follow the example carefully for the form and spacing. At the bottom of the example page where year is shown, use the year only, in which the requirements for the degree in question were satisfied.

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6. PUBLICATION OF THESES AND DISSERTATIONS

6.1. Use of Copyrighted Material

Candidates must assume full responsibility for use of any copyrighted material in their theses/dissertations. Written permission of the copyright owner must be obtained when such material is used. Copyright granting permission for including such material should be kept on file by the candidate for later reference in case questions arise.

6.2. Publications

Theses, or extracts from them, may be published only upon release for publication by the major advisor and provided that proper credit is given to Boğaziçi University. No thesis/dissertation may be published as such before it has been approved by the major advisor. All theses/ dissertations are the property of the University.

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APPENDIX A: SAMPLE PAGES

Title Page for M.S. Degree 21

Title Page for Ph.D. Degree 22

Approval Page 23

Abstract (within the thesis/dissertation) 24

Example of Abstract (within the thesis/dissertation) 25

Abstract for the YÖK Documentation center (separate) 26

Table of Contents 27

List of Tables 28

List of Figures 29

List of Symbols/Abbreviations 30

References 31

Sample page for a text arrangement (headings, paragraphs, etc.) 36

Sample page for Figures and Tables 38

Sample page for Thesis/Dissertation 39

Cover Page 40

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Example of Title Page for M.Sc. Degree

EVALUATION OF MULTIMEDIA FATE OF ORGANOPHOSPHORUS

INSECTICIDES: A LEVEL II FUGACITY MODEL

by

Ayse Baylan

B.Sc. in Chemistry, Boğaziçi University, 1997

Submitted to the Institute of Environmental Sciences

in partial fulfillment of the requirements for the degree of

Master of Science

in

Environmental Sciences

Boğaziçi University

Year

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Example of Title Page for Ph.D. Degree

STATISTICAL ANALYSES OF AIR POLLUTION AND METEOROLOGICAL

DATA IN ISTANBUL

by

Orhan Yenigün

B.Sc. in Chemical Engineering, Middle East Technical University, 1993

M.Sc. in Environmental Engineering, Boğaziçi University, 1995

Submitted to the Institute of Environmental Sciences

in partial fulfillment of the requirements for the degree of

Doctor of Philosophy

Boğaziçi UniversityYear

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Example of Page of Approval

TITLE OF THESIS OR DISSERTATION (all caps)

APPROVED BY:

Title, Name2 . . . . . . . . . . . . . . .

Thesis/Dissertation Advisor

Title, Name . . . . . . . . . . . . . . .

Thesis/Dissertation Co-Advisor

Title, Name . . . . . . . . . . . . . . .

Title, Name . . . . . . . . . . . . . . .

Title, Name . . . . . . . . . . . . . . .

DATE OF APPROVAL: Day/Month/Year

2 The surnames of the members of the Examining committee will be listed one below the other in alphabetical order with respect to the academic title (i.e. Prof. Dr., Assoc. Prof. Dr., Assist Prof. Dr., Dr.) except the Thesis/Dissertation Advisor's and Co-advisor’s, whose names will be at the top of the list. Beside each name, space for the signature of each examiner should be left.

23

Example of Abstract within the thesis/dissertation

EVALUATION OF BOD ANALYSES AND DIFFERENT BOD METHODS IN THE CASE OF LANDFILL LEACHATE

For the disposal of solid wastes, landfills are the most economical and

environmentally acceptable method throughout the world. However, one of the most

important aspects of concern during landfilling of solid wastes is the generation of

leachates. Leachates contain a variety of chemical constituents generated from the

solubilization of the compounds collected in the landfill. The measurement of BOD is not

easy due to the variable characteristics of leachate such as high ammonia, chloride

concentrations, heavy metals and hazardous substances. BOD measurement can be carried

out by two major methods: The dilution method and manometric method. These methods

have both advantages and disadvantages and they may yield different results although the

same procedure is followed. In this thesis/dissertation these two methods were used and

compared with each other under various seeding and dilution conditions. Besides, the

inhibitory effects of high chloride and nitrogen concentrations on both BOD methods were

investigated in the case of leachate. In this study, the manometric method was found to be

more sensitive to the inhibitors than the dilution method. The results were compared with a

standard glucose-glutamic acid solution of known BOD5 and reaction rate constants were

assessed in the case of both methods.

24

Example of Abstract to be submitted separately for M.Sc. DegreeTITLE OF THESIS (all caps)

(2 spaces)

Name of Degree Candidate

(1 space)

(Name of Program) M.S. Thesis, Year

(1 space)

Thesis Advisor: Name of Advisor

(3 spaces)

Keywords: (At most 5 keywords to be selected from Citation Index)

(2 spaces)

Text of Abstract (One A4 page, maximum) (1.5 line spacing)

______________________________________________________________Example of Abstract to be submitted separately for Ph.D. Degree

TITLE OF DISSERTATION (all caps)

(2 spaces)

Name of Degree Candidate

(1 space)

(Name of Program) Ph.D. Thesis, Year

(1 space)

Thesis Advisor: Name of Advisor

(3 spaces)

Keywords: (At most 5 keywords to be selected from Citation Index)

(2 spaces)

Text of Abstract (One A4 page, maximum) (1.5 line spacing)

25

YÖK tarafından istenilen Tez Veri Giriş Formu YÖK web sitesine girilerek doldurulacak ve basıldıktan sonra imzalanarak teslim edilecektir.

İlgili formun bulunduğu adres:

https://tez.yok.gov.tr/UlusalTezMerkezi/giris.jsp

26

Example of Table of ContentsTABLE OF CONTENTS

ACKNOWLEDGEMENTS.................................................................................... iii

ABSTRACT............................................................................................................iv

ÖZET...................................................................................................................... v

TABLE OF CONTENTS........................................................................................vi

LIST OF FIGURES................................................................................................ viii

LIST OF TABLES.................................................................................................. ix

LIST OF SYMBOLS/ABBREVIATIONS.............................................................x

1. INTRODUCTION............................................................................................. 1

1.1. General Characteristics of Birds, Investigated Along With Their

Phylogenetic Relationships........................................................................2

1.2. Turkish Bird Fauna.................................................................................... 3

1.3. Conservation of Birds................................................................................ 4

1.4. General Characteristics of Bird Haemosporidians.....................................5

1.5. Life Cycle of Leucocytozoidae Species.....................................................7

1.5.1. The Hosts Used in the Different Stages………….……………….7

1.5.1.1 Animal Hosts………………………………………….... 7

1.6. Host-Switching.......................................................................................... 8

1.7. Objective of the Thesis.............................................................................. 9

2. LITERATURE REVIEW.................................................................................. 10

3. MATERIALS AND METHODS.......................................................................14

3.1. Collection of Blood Samples..................................................................... 14

3.2. DNA Extraction......................................................................................... 15

3.3. PCR Screening........................................................................................... 15

4. RESULTS.......................................................................................................... 20

4.1. Identification of Samples and Results of PCR Screening..........................20

4.2. Results of Phylogenetic Analysis...............................................................22

5. DISCUSSION.................................................................................................... 38

6. CONCLUSION..................................................................................................42

REFERENCES....................................................................................................... 43

APPENDIX A: INFORMATION ON THE SAMPLES OF THE STUDY…..... 51

27

Example of List of FiguresLIST OF FIGURES

Figure 1.1. Taxonomy of cetaceans……………………………………………... 1

Figure 1.2. Global distribution map of Phocoena phocoena..................................9

Figure 2.1. The range map of Phocoena phocoena used in the Sea of Marmara

and Black Sea in Turkey…………………………………………….. 14

Figure 2.2. A close-up map of Phocoena phocoena sampled in the Sea of

Marmara and Western Black Sea in Turkey…………………………. 15

Figure 3.1. Haplotype network for the Phocoena phocoena sequences………….19

Figure 3.2. Phylogenetic relationships of 32 haplotypes of

Phocoena phocoena………………………………………………….22

28

Example of List of TablesLIST OF TABLES

Table 3.1. Haplotype numbers of different regions……………………………… 20

Table 3.2. The descriptive statistics of Phocoena phocoena……………………. 25

Table 3.3. Corrected (Dxy) and uncorrected P - distance values between

populations…………………………………………………………….28

Table 3.4. Фst values of the population calculated by using pairwise

differences method……………………………………………………29

29

Example of List of Symbols/Abbreviations

LIST OF SYMBOLS/ABBREVIATIONS3

A Hamaker Constant

ADE Advective-Diffusive Equation

AFM Atomic Force Microscopy

AgNP Silver Nanoparticle

CBFT Clean-Bed Filtration Theory

DDL Diffuse Double Layer

DLS Dynamic Light Scattering

DLVO Derjaguin and Landau, Verwey and Overbeek

EOR Enhanced Oil Recovery

Ƙ Debye length

kB Boltzmann Constant

ρ Density

ψo Potential of the Surface

NOM Natural Organic Mater

nZVI Nanozerovalent Iron

PAA-EG Poly (Acrylic Acid)-Ethylene Glycol

QD Quantum Dot

R Radius

TEM Transmission Electron Microscopy

UV-vis Ultraviolet-visible Spectroscopy

XRD X-ray Diffraction

α Attachment coefficient

γ Reduced Surface Potential

εο Dielectric Constant

η Collector Efficiency

3 First Latin, then Greek Letters, both in alphabetical order.

30

Example of ReferencesREFERENCES

References should be given in alphabetical order. The following rules should be followed.

Journal Article:

Frimmel, F.H., 1998. Impact of light on the properties of aquatic natural organic matter.

Environment International, 24, 559-571.

Hull, C.S., Reckhow, D.A., 1993. Removal of DOX precursors in municipal wastewater

treatment plants. Water Research, 27, 419-425.

Rounds, S.A., Tiffany, B.A., Pankow, J.F., 1999. Description of gas/particle sorption

kinetics with an interparticle diffusion model: Desorption experiments. Environmental

Science and Technology, 27, 366-377.

Same authors and same year:

Tay, T.-H., Liu, Q.-S., Liu, Y., 2002a. Aerobic granulation in sequential sludge blanket

reactor. Water Science and Technology, 46, 4-5, 13-18.

Tay, T.-H., Liu, Q.-S., Liu, Y., 2002b. Hydraulic selection pressure-induced nitrifying

granulation in sequencing batch reactors. Applied Microbiology and Biotechnology, 59,

332-337.

Same first author, different co-authors and different years:

Vodacek, A., Hoge, F., Swift, R.N., Yungel, J.K., Peltzer, E.T., Blough, N.V., 1995. The

use of in situ and airborne fluorescence measurements to determine UV absorption

coefficients and DOC concentration in surface waters. Limnology and Oceanography, 40,

411-415.

Vodacek, A., Blough, N.V., deGrandpre, D., Peltzer, E.T., Nelson, R.K., 1997. Seasonal

variation of CDOM in the Middle Atlantic Bight: Terrestrial inputs and photooxidation.

Limnology and Oceanography, 42, 674-686.

31

Same first author, different co-authors and same year:

Vodacek, A., Blough, N.V., deGrandpre, D., Peltzer, E.T., Nelson, R.K., 1997. Seasonal

variation of CDOM in the Middle Atlantic Bight: Terrestrial inputs and photooxidation.

Limnology and Oceanography, 42, 674-686.

Vodacek, A., Hoge, F., Swift, R.N., Yungel, J.K., Peltzer, E.T., Blough, N.V., 1997. The

use of in situ and airborne fluorescence measurements to determine UV absorption

coefficients and DOC concentration in surface waters. Limnology and Oceanography, 40,

411-415.

Citing early-view articles with digital object identifier (DOI):

Smith, A., Jones, B., 2004. Seasonal variation of CDOM in the Middle Atlantic. Worm

Journal, doi:10.1111/j.1234-4321.2004.01234.x 

Book:

Belter, P.A., Cussler, E.L., Wei-Shou, H., 1988. Bioseparations: Downstream Processing

for Biotechnology, 77-98, John Wiley and Sons, Inc., U.S.A.

Breed, R.S., Murray E.G.D., Smith N.R. (Eds), 1957. Bergley's Manual of Determinative

Bacteriology, Seventh Ed., Williams and Wilkins Company, U.S.A.

Banerjee, P.K., Butterfield, R. (Eds), 1980. Development of Boundary Element

Methods - I, Applied Science Publishers, London, UK.

Article in a Book:

Beal, P.T., 1979. Application of Cell Biology to an Understanding of Biological Water. In:

Drost-Hansen W., Clegg J. S. (Eds.), Cell Associated Water, 271-291, Academic Press,

New York, U.S.A.

M.Sc. Thesis:

32

Berk, H., 1986. Heavy Metal Toxicity on Blue Green Alga, M.Sc. Thesis, Boğaziçi

University, Turkey.

Ph.D. Thesis:

Akmehmet, I., 1990. Heterogeneous Photocatalytic Oxidation of Organic Compounds by

TiO2, Ph.D. Thesis, Boğaziçi University, Turkey.

Liu, W.K., 1981. Development of Finite Element Procedures for Fluid-Structure

Interaction, Ph.D. Dissertation, California Institute of Technology, U.S.A.

Conference Paper:

Persson, G.A., 1987. Acid Rain-A Threat to Europe’s Environment, Proceedings of the

International Symposium on Environmental Management: Environment’ 87, 1169-1182,

Istanbul, 5-7 June 1987, Turkey.

Report:

Nett, A. L. and Trucker, J. D., 1998. A Comparison of Pollutant Transport Models PT1

and PT2, RSRE Memorandum No. 4157, RSRE Malvern, U.S.A.

AWWA Membrane Technology Research Committee, Committee Report, 1992.

Membrane Processes in Potable Water Treatment. Journal of American Water Works

Association, 84, 59-67, U.S.A.

U.S.EPA, 1993. Perox-pure Chemical Oxidation Technology, Peroxidation Systems,

Inc.: Applications Analysis Report. Office of Research and Development, SITE Program.

Washington, DC. EPA/540/AR-93/501. July, U.S.A.

Ataman, Y., Çaycı, G., Baran, A., Kütük, C., Özaytekin, H., Dengiz, O., 1999. A research

on reclamation of physical properties of Yeniçağa-Bolu peat in Turkey as plant growing

medium. Project No. TOGTAG-1700. Scientific and Technical Research Council of

Turkey.

33

Article in Internet:

Miller, D., 1996. Prolog: An Introduction to the Language and its Logic,

http://www.cis.upenn.edu/~dale/lProlog/index.html . Date accessed July 2001.

U.S. Environmental Protection Agency Envirofacts Data Warehouse Home Page.

http://www.epa.gov/enviro/index-java.html. Date accessed June 2001.

Selective examples of citations:

APHA, AWWA, WEF, 1995. Standard Methods for the Examination of Water and

Wastewater, 16th Edition, Washington, D.C., U.S.A.

Conlon, M., Khraisheh, M., 2002. Bioadsorption process for the removal of color from

textile effluent. GB Patent WO 0242228, U.K.

EC Directive 91/271/EEC, 1991. Concerning Urban Wastewater Treatment.

ISO/TC 147, 2001. Water quality-On line sensors/analyzing equipment for water.

Specifications and performance tests. Draft International Standard ISO/DIS 15839.

International Organization for Standardization, Geneva, Switzerland.

Van Vooren, L., Willems, P., Ottoy, J.-P., Vansteenkiste, G.C., Verstraete, W., 1996.

Automatic buffer capacity based sensor for effluent quality monitoring. Water Science and

Technology, 33, 1, 81-87.

deClercq, J., Devisscher, M., Bonen, I., Vanrolleghem, P.A., Defrancq, J., 2002. A new

one-dimensional clarifier model verification using full scale experimental data. In:

Proceedings 3rd IWA World Water Congress April 7-12, Melbourne, Australia.

diPinto, A.C., Limoni, W., Passino, R., Rozzi, A., Tomei, M.C., 1990. Anaerobic process

control by automated bicarbonate monitoring. In: Instrumentation, Control and Automation

of Water and Wastewater Treatment and Transport Systems. Briggs, R. (Ed) Pergamon

Press, London, U.K., 51-58.

34

McCarty, P.L., 1964. Anaeorobic waste treatment fundamentals. Part two. Environmental

requirements and control. Public Works, 95, 123-126.

Mac Craith, B., Gratten, K.T.V., Connely, D., Briggs, R., Boyle, R., Avis, M., 1993. Cross

comparison of techniques for the monitoring of total organic carbon (TOC) in water

resources and supplies. Water Science and Technology, 28, 11-12, 457-463.

WPCF, 1980. Sludge Thickening. Manual of Practice No. FD.1. Water Pollution Control

Federation, Washington, D.C., U.S.A.

McTavish, H., Fuchs, J.A., Hooper, A.B., 1993. Sequence of the gene coding for ammonia

monooxygenase in Nitrosomonas europaea. Journal of Bacteriology, 175, 2436-2442.

Türkiye Çevre Vakfı, 1995. Türkiye’nin Çevre Sorunları. TÇV Yayınları, Ankara,

Türkiye.*

Metcalf and Eddy, 1991. Wastewater Engineering, Treatment, Disposal and Reuse.

McGraw Hill, New York, U.S.A.

Ataman, C., 2002. Personal communication. Director of MEKA Wastewater Treatment

Plant, İstanbul, Turkey.

*Reports/Documents… published in Turkish will be cited as Türkiye.

35

Sample pages for normal text arrangement4. MATERIALS AND METHODS

4.1. Preparation Step for the Enrichment of Nitrifiers

A mixed liquor was taken from the aeration tank recycle line of the Istanbul Pasakoy

Advanced Biological Sewage Treatment Plant and enriched for nitrifiers in a 16 L batch

reactor for 4 months. A synthetic feed stock solution consisting of 37.75 g/L (NH4)2SO4,

97.8 g/L NaHCO3 and a synthetic mineral stock solution consisting of 2 g/L MgSO4.7H2O,

0.103 g/L CaCO3 were prepared. The culture was daily fed based on ----- .

4.2. Experimental Procedure

4.2.1. Oxygen Uptake Rate Experiments

In the first phase of experiments, the TCE range was studied which caused inhibition

of nitrification. For this purpose, oxygen uptake rate (OUR) experiments were carried out

in eight sets in 300 mL capped glass bottles. In each set of experiment, the stock enriched

nitrifier culture was rinsed and diluted by deionized water to a VSS concentration of 100-

150 mg/L and aerated till saturation ---

4.2.2. Inhibitory effect of TCE

Based on preliminary OUR experiments, 6 sets of batch experiments were performed

in the selected TCE concentration range of 50-4500 ppb. The aim was to investigate the

inhibitory effect of TCE on ammonium oxidation and cometabolic degradation rate of TCE

in the presence of ammonium. --------------------

4.2.2.1. Inhibitory effect of TCE on ammonium oxidation. At a constant initial ammonium

concentration of 40 mg/L NH4-N, the specific ammonium utilization rate (qNH4-N) was

evaluated with respect to the initial TCE concentration. --------------------------

Cometabolic degradation of TCE. At a constant initial ammonium concentration of 40

mg/L NH4+-N, the specific cometabolic degradation rate of TCE (qTCE) was assessed with

respect to the initial TCE concentration (Figure 5).

36

Further examples of second sub-headings and others:

3.1.1.1. Analytical Methods. All analyses were performed in accordance with those

outlined in Standard Methods (APHA, AWWA, WPCF, 1998).

Gas chromatography. The extracts were analyzed by Hewlett Packard 5890 Gas

Chromatograph equipped with a J&W prosteel megabore column (0.53 mm ID, 30 m

length) and an electron capture detector (ECD). The chromatograph was operated

isothermally at 1000C oven, 2500C injection port and 2500C detector temperatures -----

VSS analyses. These were performed using the Method 2540E presented in Standard

Methods (APHA, AWWA, WPCF, 1995). Liquid samples for TCE analysis were extracted

into n-pentane by EPA Method 502.1.

Nitrogen analyses. All forms of nitrogen were analyzed as outlined by the following

methods……...

Ammonium. NH4+-N concentrations were analyzed using the Nessler Method with Hach

DR/2000 spectrophotometer.

Nitrate Nitrogen. These were performed with standard …kits provided

by----------------------------------and according to the method---------------

37

Example of Figure

0.000001 0.00001 0.0001 0.0011.00E-09

1.00E-08

1.00E-07

1.00E-06

1.00E-05

Tracer BrinePower (Brine)

Velocity, m/s

Dis

pers

ion

Coe

ffici

ent,

m2/

s

Figure 2.1. Apparent dispersion coefficients from tracer and brine displacement

experiments as a function of groundwater velocity in the sand column.

Examples of Tables

Table 2.1. Summary of results of waste activated sludge polymer conditioning.

Blending Time,min

Cell Lysis,%

Critical PolymerDose, mg/L

CST at CriticalPolymer Dose, s

0.0 0 100 10.0 0.5 0 50 9.8 1.0 0 50 8.8 2.0 0 60 9.9 5.0 7 80 10.7 20.0 22 80 9.8

Table 3.1. Characteristics of several pulp bleaching wastewaters generated from different

stages of pulp production.

Sample Wastewatertype

pH CODmg L-1

Cl-

mg L-1TKN

mg L-1Total Pmg L-1

1 combined effluent 6.05 1866 1099 523 0.72 combined effluent 5.75 845 1064 n.m 0.863 combined effluent 6.83 1600 729 469 n.m4 combined effluent 3.49 567 890 21.8 n.m5 combined effluent 4.07 927 880 30 n.m6a C/E-H stage 7.62 1675 1611 0 n.m6b mixed* 2.56 909 1112 0 n.m

*Wastewaters from C/E-H and D-E/D stages were present in approximately 1:1 ratio.

n.m: not measured.

38

APPENDIX A: FORMAT OF CDs CONTAINING COMPUTER SOFTWARE

Listings of software should be given in a diskette specified by the Institute. The diskette should contain files containing the source code, one or more sample input and corresponding output separately. Other than these there must be another file named "READ.ME". In this ASCII text file, the following sections must appear.

Files in the Disk. In this section, the names of the files together with their contents must be listed.

Hardware Requirements. In this section, the equipment, graphics card, numeric coprocessor, mouse, disk capacity, RAM capacity etc. necessary to run the software must be noted.

Software Requirements. In this section, the operating system, the compiler, linker, and the libraries etc. necessary to compile and link the software must be listed. Please note that no copyrighted material file (compiler, library etc.) must be put on the disk without obtaining the necessary license from the copyright owner.

39