HowtoprepareforaPhDThesis

or or
Howtoformulateagoodresearch g
project
Casey Chan MD CaseyChanMD
NationalUniversityofSingapore
PhD Program PhDProgram
1. Acceptedintoaprogram
2. Qualifying Exam * 2. QualifyingExam
3. Investigations
4. ThesisWriting
5 Defense * 5. Defense
QualifyingExam
Whatdoesthecommitteelookfor?
i i LiteratureReview
Motivationforproposedinvestigation p p g
Formulationofhypothesis
Preliminary results Preliminaryresults
Proposedinvestigations
Experimentalprotocols
Experimentalresults
Backupplan
Decision Process of Panel Members DecisionProcessofPanelMembers
1. ObjectiveandScopearewelldefined.
2. Sufficient Depth for PhD Thesis 2. SufficientDepthforPhDThesis
3. ResearchPlan
Wellformulated
RealisticandAchievable
4. Technicallycompetent
Difference between Final Year Project DifferencebetweenFinalYearProject
andaPhDThesis
FYP Professorsuggests
problem/objectives/hypothesis
PhD Professor points out what is the current PhD Professorpointsoutwhatisthecurrent
problem,newresearchdirectionand/or
unexplained new data unexplainednewdata
What is a hypothesis? Whatisahypothesis?
Tentativestatementofapossibleexplanation
ofsomeobservedphenomenon p
Tentativestatementofcausalrelationship
S i bl Statementistestable
Independentvariables(controlledbyscientist) p ( y )
Dependentvariables(observedbyscientist)
Example of hypothesis formulation Exampleofhypothesisformulation
Observation
Caucasian living in the tropics has a higher rate Caucasianlivinginthetropicshasahigherrate
ofskincancer
P ibl h h i Possiblehypothesis
1. Skincancerisrelatedtoultravioletlight g
exposure
2 Ski i l t d t li f it 2. Skincancerisrelatedtosalivaofmosquito
bites
Example of weak hypotheses Exampleofweakhypotheses
1. Ifyouwarmyeast,thenmoregaswillbe
produced p
2. Ifyouplaceslicedpotatoesinhypertonic
sucrose it will increase in size sucrose,itwillincreaseinsize
Whyaretheseweakhypothesis?
Observationsonly
N h i ti l ti Nomechanisticexplanation
Nothingtotest
Potato Slices in Sucrose Solution PotatoSlicesinSucroseSolution
Twopossibleexplanations:
1. Cellgrowth sizeandnumber
2. Osmoticswelling
Investigations Investigations
Hypothesis:
Skin cancer is related to ultraviolet light exposure Skincancerisrelatedtoultra violetlightexposure
Investigations:
1. Epidemiological
2 Animal 2. Animal
3. Cellular
Investigations Investigations
Hypothesis:
Skin cancer is caused by increased exposure to Skincanceriscausedbyincreasedexposureto
ultravioletlight
I i i Investigations:
1. Epidemiological p g
2. Animal
3. Cellular
Direct vs Indirect Dependent Variables Directvs IndirectDependentVariables
PossibleReadouts
Polyploidy yp y
Hyperchromatin
Cell shape Cellshape
Mutationrates
AK3
RunK
Endothelium
BoneCancer
P53
SkinCancer
Hypothesis Linkage HypothesisLinkage
IndirectDependentVariable
SkinCancer
P53
?
P53
Good Laboratory Practice GoodLaboratoryPractice
OrganizationandReportingStructure
Standard Operating Procedures StandardOperatingProcedures
ReviewandAudit
ContinuousImprovement
Documentation Documentation
Management of Data ManagementofData
ClearDocumentation
Audit Proof AuditProof
Labbook
Howtomanagerawdata
Laboratory Note Book LaboratoryNoteBook
Hardcoverwithglossylaminationforwaterproofing
Provisionsforidentificationofnotebookowner.
Stitchedbinding
Individuallynumberedpage.
PageswillfitA4paper.
Presentation of Information PresentationofInformation
JumpfromHeight
Measure
GroundReactionForce
Maximal Flexion Angle MaximalFlexionAngle
Jump from Height JumpfromHeight
Height vs
8 data points
Heightvs
AverageGRFand
MRF
8datapoints
AverageGRFandMFA
For
EachSubjectforeach
height
24datapoints
3subjects
3trialsforeachsubject
foreachheight
4heights
72datapoints
MeasureGRFandMFA
Better Presentation of Information BetterPresentationofInformation
JumpfromHeight
Fixed Parameters (Independent Variable) FixedParameters(IndependentVariable)
Height(h) 0.5m,1m
h
Measure (Dependent Variable) Measure(DependentVariable)
1. GroundReactionForce
2. MaximalFlexionAngle
MFA
GRF
Typical Data Presentation TypicalDataPresentation
Height GRF (N) MFA (
0
) Height GRF(N) MFA( )
0.5 200 45
1.0 300 20
Typical Graphical Presentation TypicalGraphicalPresentation
350
Magnitude
250
300
150
200
250
GRF(N)
100
150
MFA(o)
0
50
0 5 1 0
Height
0.5 1.0
Height
Better Graphical Presentation BetterGraphicalPresentation
GroundReaction MaximalFlexion
Force(N) Angle(
0
)
300
MFA
GRF
300
45
GRF
200
20
0 5 1 0
Height (m)
0 5 1 0
Height (m)
0.5 1.0
Height(m)
0.5 1.0
Height(m)
Typical 3D Graphical Plot Typical3DGraphicalPlot
MaximalFlexion
Angle (
0
) Angle( )
45
20
GroundReaction
Force(N)
200 300
Better 3D Graphical Plot Better3DGraphicalPlot
MaximalFlexion
Angle (
0
)
Size of Circles
Angle( )
SizeofCircles
reflectsHeight
45
20
GroundReaction
Force(N)
200 300
Better 3D Graphical Plot Better3DGraphicalPlot
MaximalFlexion
Angle (
0
)
Vertical Line
Angle( )
VerticalLine
proportionalto
Height
X
X
X
45
X
X
20
X
GroundReaction
Force(N)
200 300
Good Presentation Practice GoodPresentationPractice
1. ProblemwithPowerPoint
2. Fit Format to Message 2. FitFormattoMessage
3. ClearandDirectMessage
4. AvoidVisualGymnasticsandEyeCandy
Mesenchymal Stem Cell on Nanofiber Mesenchymal StemCellonNanofiber
Electrospun Nanofibers Electrospun Nanofibers
NeuralCellMorphology NeuralCellMorphology
Microfibers Nanofibers
Random
Castfilm
Aligned Aligned
The preferred growing direction of the neural cells is parallel to the fiber axis and the process is
dynamically directed over time.
YangF.et.al.Biomaterials2005;26:2603
NeuralCellsDifferentiation NeuralCellsDifferentiation
Alignment ofNanofibers Neurite length(m) Standarddeviation
Film 80 7.5
RandomMicrofibers 73.2 5.7
AlignedMicrofibers 76.6 4.1
RandomNanofibers 81.1 2.4
AlignedNanofibers 98.8 3.8 g
NeuralCellsDifferentiation NeuralCellsDifferentiation
Neurite lengthondifferentsubstrates
100
120
80
100
Film
Random Microfibers
60
RandomMicrofibers
AlignedMicrofibers
RandomNanofibers
20
40
AlignedNanofibers
0
NeuralCellsDifferentiation NeuralCellsDifferentiation
Neurite lengthondifferentsubstrates
100
60
80
Film
Random Microfibers
40
60
RandomMicrofibers
AlignedMicrofibers
RandomNanofibers
0
20
AlignedNanofibers
NeuralCellsDifferentiation NeuralCellsDifferentiation
Neurite lengthondifferentsubstrates
100
60
80
Film
40
60
Film
RandomMicrofibers
AlignedMicrofibers
0
20 RandomNanofibers
AlignedNanofibers
NeuralCellsDifferentiation NeuralCellsDifferentiation
Neurite lengthondifferentsubstrates
120
m
)
**
80
n
g
t
h

m
40
e
u
r
i
t
e

l
e
n
0
Film Random Aligned Random Aligned
n
e
Film Random Aligned Random Aligned
Microfibers
Nanofibers
Alignednanofibers promotetheneuriteoutgrowth.
Certaintypeofdifferentiationandphenotypeexpressioncanbeinfluenced
byfiberalignment.
Whyaremyslidesinblackandwhite
andhasnofancybackground?
Concept of dataink ration Conceptofdata inkration
DatainkRatio=dataink
Total ink used to print the graph Totalinkusedtoprintthegraph
Proportionofgraphicsinkdevotedtononredundant
Displayofdatainformation p y
1.0 Proportionofagraphicthatcanbeerasedwithout
thelossofdatainformation
Ed d T fft EdwardTuffte
DataInkRatio=20%
DataInkRatio=2%
DataInkRatio=40%
DataInkRatio=0%
WhatswrongwithPowerPoint
Presentation
f Hasnorespectforcontentor
message
Messageisdicedandslicedto
fithierarchicalformat
Oversimplifyissues
Columbia case emails detail a Columbiacase emailsdetaila
morecompellingcasethenthe
P P i t t ti PowerPointpresentation
submittedtomanagement
NapoleonMarchtoMoscow
Warof1812
CharlesJosephMinard
PLGAFibers PLGAFibers
Microfibers Nanofibers
Random
Aligned Aligned
Fiberdia =microns
Fiberdia =nanometers
NeuralCellMorphology NeuralCellMorphology p gy p gy
Castfilm
Microfibers Nanofibers
Random
Aligned Aligned
Nurites ExtendingalongAxisofAlignedFibers
YangF.et.al.Biomaterials2005;26:2603 2610.
NeuralCellsDifferentiation NeuralCellsDifferentiation
Neurite lengthondifferentsubstrates
120
**
80
g
t
h

m
)
40
n
e
u
r
i
t
e

l
e
n
g
0
Film Random Aligned Random Aligned Film Random Aligned Random Aligned
Microfibers
Nanofibers Film
Alignednanofibers promoteneurite outgrowth.
Good Research Project GoodResearchProject
Clearlystatedmotivation
Clearly stated hypothesis Clearlystatedhypothesis
WellDefinedResearchProtocol
I d t D d t V i bl Indepent vs DependentVariables
ClearInterpretationandPresentationof
Results