A pocke -sized ecipe o cooking up
a scien i ic manusc ip
C aig S. Ca lson
Michiel Pos ema
BioMediTech
Facul y o Medicine and Heal h Technology
Tampe e Uni e si y
2
ISBN 978-952-03-2768-2 (p in )
ISBN 978-952-03-2769-9 (pd )
DOI 10.5281/zenodo.7583988
The con en o his Open Access book, excluding hi d pa y con en , is dis-
ibu ed unde he e ms o he C ea i e Commons A ibu ion-NonComme cial-
NoDe i a i es 4.0 In e na ional License. To iew a copy o his licence, isi
h ps://c ea i ecommons.o g/licenses/by-nc-nd/4.0/
Ma e ial ha is no licensed unde a C ea i e Commons licence include pho-
og aphs, quo a ions, logos, and ma e ial p o ec ed by a adema k. You mus
eques pe mission om he copy igh owne o use he abo e-men ioned ma e-
ial.
Publishe : Tampe e Uni e si y, Tampe e
P in ed in Finland by PunaMus a Oy — Yliopis opaino
Typese ing sys em: L
A
T
EX2ε
Con en s
1 P epa a ion 7
1.1 Readme i s ............................ 7
1.2 Who is you audience? . . . . . . . . . . . . . . . . . . . . . . . 7
1.3 Choiceo jou nal.......................... 8
1.4 L
A
T
EXo WYSIWYG?........................ 8
1.5 Da amanagemen ......................... 9
1.6 English, Mu ican, o Sou h A ican English? . . . . . . . . . . . 9
1.7 Ac onyms, abb e ia ions (and pa en heses) . . . . . . . . . . . . 10
1.8 S a ingyou day.......................... 11
1.9 O de o w i ing .......................... 12
1.10 In o ming you coau ho s . . . . . . . . . . . . . . . . . . . . . 12
1.11Makingdecisions.......................... 13
1.12 As long as you ha e no submi ed... . . . . . . . . . . . . . . . 13
1.13 Dealing wi h w i e ’s dip . . . . . . . . . . . . . . . . . . . . . . 14
2 Ti le page 15
2.1 Ti le ................................ 15
2.2 Au ho s............................... 16
2.3 Keywo ds.............................. 18
3 Abs ac 19
3.1 Mo i a ion............................. 19
3.2 P oblem s a emen . . . . . . . . . . . . . . . . . . . . . . . . . 19
3.3 Pu pose .............................. 20
3.4 Me hodology............................ 21
3.5 Main esul ............................. 21
3.6 Discussion ............................. 21
3.7 Mainconclusion .......................... 22
3
4
4 In oduc ion 23
5 Theo y 25
6 Ma e ials and me hods 27
6.1 S a icpa ............................. 27
6.2 Dynamicpa ............................ 28
6.3 P epa a ion............................. 28
6.4 P ocedu e ............................. 29
7 Resul s 31
8 Discussion 33
8.1 In e p e a ions ........................... 33
8.2 Explana ions............................ 33
8.3 Implica ions ............................ 34
8.4 Jus i ica ions............................ 34
9 Conclusions 35
10 Acknowledgemen s 37
11 Re e ences 39
12 Appendices 41
13 Submi ing 43
13.1Las checks............................. 43
13.2 Accompanying le e . . . . . . . . . . . . . . . . . . . . . . . . 44
13.3Wai ing............................... 45
14 Dealing wi h he e dic 47
14.1 The e dic i sel . . . . . . . . . . . . . . . . . . . . . . . . . . 47
14.2 W i ing a ebu al . . . . . . . . . . . . . . . . . . . . . . . . . 48
15 A e accep ance 51
15.1 Uploading o a eposi o y . . . . . . . . . . . . . . . . . . . . . 52
15.2 Obliga ion o e iew . . . . . . . . . . . . . . . . . . . . . . . . 52
5
16 Pos -publica ion con lic s 53
16.1 Wi hd awing you pape . . . . . . . . . . . . . . . . . . . . . . 53
16.2E a a ............................... 53
16.3Plagia ism ............................. 54
17 Bibliog aphy 55
A Rebu al empla e 59
B Biog aphies 61
C One mo e hing 63

6
1
P epa a ion
1.1 Read me i s
This bookle is in ended o be ead om co e o co e , in he o de o w i ing.
I is no so much a gene al guideline as a p o en ecipe o ge you scien i ic
manusc ip accep ed by a pee - e iewed jou nal. Fo much be e ac ual guidance
on scien i ic w i ing, we ecommend he wo k o Hols & Cham.
We do no di e en ia e be ween high-impac pee - e iewed jou nals and low-
impac na ional con e ence p oceedings. The p inciple o w i ing is he same.
The ecipe wo ks o bo h.
Ou expe ience lies in science, business, and popula ised w i ing. Whe he
his ecipe wo ks in he a s, as well? Who knows? Do le us know!
1.2 Who is you audience?
Manusc ip s come in many ypes. Edi o ials, echnical no es, con e ence p o-
ceedings, ull-blown esea ch pape s, e iew pape s, book e iews, sho co e-
spondence, obi ua ies, and heses.
Fo jou nal pape s, i is o en assumed ha he audience a e scien i ic pee s.
Fo heses, i is o en assumed ha he audience a e he examine s. Bo h as-
7
8
sump ions a e w ong. You a e w i ing o you successo o e-do you wo k. You
audience is, in ac , you. Bu younge , less knowledgeable you. You audience is
you, wo o h ee yea s ago.
Unde s anding ha makes w i ing li e much easie . Wha did you know back
hen? You may p esume ha you jou nal eade s and hesis examine s ha e
ha as backg ound knowledge as well. Bu he skills and ja gon ha you picked
up du ing you p ojec a e p obably new o o he s, oo. So hose need enough
explana ion o younge you o unde s and.
1.3 Choice o jou nal
You eally need o us you supe iso o know bes which jou nal is he bes
choice o you la es scien i ic inding. Ne e heless, be wa y i you supe iso
ad ises you o s a w i ing i s , and o wo y abou he jou nal la e . Tha is
a eally bad plan. The jou nal o choice de e mines he o ma , he maximum
numbe o wo ds allowed, he maximum numbe o igu es, and mos impo an ly
he ield!
Conside a no el ul asonic de ice ha has applica ions in gela ion p ocesses.
Resea ch ou comes o his de ice may be p esen ed in a jou nal on scien i ic
ins umen s, elec ical enginee ing, biomedical enginee ing, applied acous ics, ul-
asonics, bioma e ials, polyme s, and gels.
The no el componen in you esea ch ha should be highligh ed depends
hea ily on he jou nal o choice.
Fo a hesis, a simila easoning holds. I you a e based a an elec ical
enginee ing depa men , he no el componen s ha a e o be highligh ed a e
qui e di e en om hose in a hesis om he same p ojec bu submi ed o a
depa men o medicine.
1.4 L
A
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EX o WYSIWYG?
Wha you see is wha you ge (WYSIWYG) is he gene ic e m used o MS
Wo d and simila packages. Al hough sui able o w i ing a le e , WYSIWYG a e
less sui able o w i ing longe documen s and comple ely unsui able o w i ing
books.
I you ha e a backg ound in he exac sciences, you a e p obably al eady
amilia wi h L
A
T
EX. I you a e no , i is wo h in es ing he ime o mas e he
9
a o w i ing in L
A
T
EX. I you en ision a scien i ic ca ee , you may also wan o
lea n o code in T
EX i sel .
Mos publishe s ha e empla es a ailable o downloading. The choice o use
L
A
T
EX o WYSIWYG elies on he o ma o he empla e. I a L
A
T
EX empla e is
a ailable, use i . I no , use WYSIWYG. Fo you hesis, use L
A
T
EX.
1.5 Da a managemen
W i ing a manusc ip may ake some ime. The e o e, some da a managemen
is equi ed. We ecommend o c ea e a sepa a e di ec o y pe manusc ip , wi h
subdi ec o ies ./submi 1,./li e a u e,./ igs, and ./old. Subdi ec o y
submi 1 comp ises he la es sou ce iles in ended o i s submission. Subdi ec-
o y li e a u e comp ises all a icles e e ed o in he manusc ip , p e e ably
enamed o "<yea > < i s au ho >.pd ". Subdi ec o y igs comp ises
he sou ce iles used o c ea e he igu es o he manusc ip . The ac ual ig-
u es should be loca ed in submi 1. Subdi ec o y old comp ises all p e ious aw
e sions o he manusc ip .
The sou ce ile should ha e a unique o ma ha is immedia ely ecognised
by coau ho s and ha has a e sion numbe in i . We used JJAP21 CSC00. ex
o he i s d a , i.e., e sion 00, o a pape o be submi ed o he Japanese
Jou nal o Applied Physics in 2021, whose i s au ho has he ini ials CSC.
E e y day, be o e opening he documen , copy he sou ce o old and inc ease
he e sion numbe by one. C ea e an o line backup o he whole di ec o y a
leas once a week, p e e ably on a ixed day.
You would no build a new house by copying you p e ious house on a di e en
spo and hen e u bishing i . Ye , mos s uden s hink ha copying a p e iously
submi ed pape and modi ying he ex is a sma idea.
Do no e e use a p e ious pape as a empla e. Tha is no jus a was e o
ime bu ac ually ca e ing o majo disas e . As edi o s and e iewe s, we ha e
seen many a pape wi h en i e sec ions om di e en pape s on o ally di e en
opics ha somehow made i h ough.
1.6 English, Mu ican, o Sou h A ican English?
The English language comes in se e al la ou s. The loca ion o he publishing
house de e mines whe he one should w i e a pape in he spelling p e e ed
16
cance cells and no mal blood leukocy es. In ou opinion, he sub i le i sel would
ha e been a much be e i le o his pape . The sub i le o Pe mea ion o p obe
molecules in o algina e mic obeads: e ec o sal and p ocessing could ha e been
a oided by changing he i le o E ec o sal and p ocessing on he pe mea ion
o p obe molecules in o algina e mic obeads.
A e y long and de ailed i le ells he subliminal message o he eade , ha
he pape is no o he poin . Which may be ue. The Ge man pa en Vo ich-
ung und Ve ah en zu Iden i ika ion, Sepa a ion und/ode zell ypspezi ischen
Manipula ion wenigs ens eine Zelle eines Zellsys ems sowie on Mik oo ganis-
men makes us c inge. No wonde i has no been ci ed.
The e e se some imes happens, oo. The no so leng hy i le Facili a ing
unde s anding, modeling and simula ion o in ec ious disease epidemics in he
age o COVID-19 was no clea a all. We co ec ed his law by calling ou
ollow-up pape Ex ac ing ansmission and eco e y pa ame e s o an adap i e
global sys em dynamics model o he COVID-19 pandemic, which is longe , ye
clea e .
A e y sho i le se s expec a ions high, ha his pape applies o e e y
si ua ion e en emo ely associa ed wi h he i le. Tim Leigh on’s mas e piece The
Acous ic Bubble has a pe ec i le, as i co e s e e y physical aspec o bubble
acous ics. One o ou own wo ks, The physics o nanoshelled mic obubbles, has
no go such an app op ia e i le, as he pape only ea s a speci ic ype o
dynamics, unde e y limi ed condi ions.
I a i le sounds unny, i ’s p obably unny only once. I a all. Google Schola
shows o e 300 000 esul s o he sea ch e m FISH and chips. On close
inspec ion, he scien i ic pape s and ex books conce ned a e abou a p ojec o
me hodology wi h he ac onym FISH, in ol ing an in-silico componen . We guess
ha he FISH ac onyms had been cons uc ed wi h he pu pose o publishing a
pape wi h he i le FISH and chips. Hila ious.
2.2 Au ho s
On you i le page, w i e he names o all con ibu o s in one line, clea ly ma king
he co esponding au ho . The co esponding au ho is esponsible o he whole
submission p ocess, which equi es p ecision and dedica ion. I you a e a sloppy
pe son, do no olun ee o be he co esponding au ho . And conside a di e en
line o wo k.
The o de o au ho s is e y impo an . Fo ge ing o include a coau ho

17
is emba assing enough, bu do no unde es ima e he li e-long animosi ies ha
come in o exis ence om adding a coau ho in he w ong posi ion.
Always discuss he coau ho s and hei o de wi h you supe iso . Do no in-
clude o exclude people wi hou p io consul a ion. I you coau ho s a e s uden s
hemsel es, hey may wan o in ol e hei supe iso s.
Despi e he poli ical side o his, he s anda d o de is s aigh o wa d. The
i s au ho is ypically he pe son doing he w i ing and also he one doing he
wo k owa ds an academic i le. The second au ho is closely in ol ed. Mos
uni e si ies allow second-au ho pape s o be included in a hesis. A e ha
ollows a lis o scien is s who we e somehow in ol ed in he p ojec . The las
au ho is esponsible o ha ing secu ed he p ima y unding o he p ojec .
Typically his is you supe iso . O he line manage o you supe iso . I
mul iple supe iso s a e in ol ed, hey will ell you he co ec o de . They
may choose o ha e he bes -known p o esso in his scien i ic ield in he mos
p ominen posi ion, e en i he ole o his pe son was a he limi ed.
Do no ge pe sonally in ol ed in discussions on who is and who isn’ on he
pape . I you a e good a wha you do, you will c ea e enough enemies al eady,
so he e’s no need o make su e o c ea e e en mo e. In case o doub , include.
I you a e a aid ha a coau ho is going o p esen you wo k as hei own, which
happens a lo , you should no ha e in ol ed ha coau ho in he p ojec in he
i s place.
We a e hesi an o include oo many au ho s, as we hink ha all coau ho s
should be able o explain hei speci ic scien i ic ole du ing an audi . Howe e ,
some g oups ha e he habi e en o include echnicians and adminis a i e pe -
sonnel as coau ho s. Make su e ha you amilia ise you sel wi h and adap o
he publishing cul u e o you g oup.
Wha e e he o de o he au ho s, hei spelling should be lawless. Make
su e ha you make clea wha is pa o he i s name and wha pa o he
las name. We may use capi als o emphasise he las name: Odd Helge GILJA,
Emme MC CORMACK. O we may choose o e e se las and i s names, using
commas and semicolons as sepa a o s: Poo inga, Albe T.; Shimizu, Ri-ichi u.
Exclude academic i les in he lis o au ho s. No e ha i s names only apply
o commone s. Lo d Rayleigh is conside ed a las name. Good luck asking him
o be a coau ho .
18
2.3 Keywo ds
Keywo ds would be he sea ch e ms ha you’d use o ind you own pape ,
excluding all wo ds in he i le. Choose you keywo ds wisely. They de e mine i
you pape is ound in he i s place.
Unlike he e m migh sugges , hey do no ha e o be indi idual wo ds. Sho
ph ases a e ine. These coun as one keywo d.
Conside a hesis on compa ing he no el use o magne ic esonance imaging
o dose planning in adia ion he apy o compu ed omog aphy da a. Assuming
ha “magne ic esonance imaging o dose planning in adia ion he apy” is pa
o he hesis i le, a good keywo d would be “MRI-based dose planning”. Bo h
“CT” and “CT da a” would be weak keywo ds o ob ious easons.
3
Abs ac
A decen abs ac is exac ly se en sen ences long.
3.1 Mo i a ion
The mo i a ion o you esea ch may be somewha gene al. Bu i should also
be an indica o o how ele an and imely you manusc ip is.
Conside a s udy on an algo i hm o de ec comp essible s uc u es in a e y
walls. The o e all ele ance may be ob ious, bu how o w i e ha in one
sen ence? “Hea disease is he p ima y dea h cause in he Wes e n wo ld” may
be ue. Bu unless you’ e go excep ional esea ch ou comes o p esen , ha
does no change because o you pape . A sen ence close o you p ojec is
p e e able: “As ulne able plaques may cause a hea a ack o s oke, ea ly
de ec ion o such uns able s uc u es is o majo in e es ”. Voil`a!
3.2 P oblem s a emen
The p oblem s a emen is a single sen ence connec ed o he mo i a ion ha
indica es why he e is a lack o p og ess in his impo an ield. I may e e o
19
20
a hia us in ou knowledge: “The speed o sound in mos c yo luids, howe e , is
unknown”. O a echnical issue: “Bu all commonly used anode ma e ials mel
a empe a u es g ea e han 3000 K”. The sen ence needs o be o mula ed such
ha he eade immedia ely unde s ands how sol ing he p oblem would bene i
he ield indica ed in he mo i a ion.
3.3 Pu pose
“The pu pose o his s udy was...” no necessa ily o sol e he p oblem in he
p oblem s a emen . Tha would be nice, o cou se, bu mos s udies ackle a
minu e pa o he p oblem. O only quan i y he ex en o he p oblem. I is
o ally ine o s udy i a supposed p oblem eally is a p oblem. O o s udy i he
occu ence o a p oblem can be modelled wi hou ac ually sol ing i .
“The pu pose o his s udy was o build an expe imen al se up o he ul a-
sonic ac iona ion o whole blood in low condi ions” may sound like a decen
pu pose. Bu he ac ual pu pose o he s udy was nonmechanical ac iona ion
o whole blood in low condi ions. The se up building and use o ul asonics
should ha e been pa o he nex sen ence on me hodology. The pu pose o a
s udy is p e e ably no an ac i i y. Analysing should no be a pu pose. Nei he
obse ing. No building.
Some p ojec s in es iga e a no el ool as an al e na i e o an exis ing ool.
The p oblem s a emen may men ion ha he exis ing ool has majo disad an-
ages. Then he pu pose is o demons a e he easibili y o using he no el ool
o he same applica ion. We s udied o sion heome y as a means o de e mine
acous ic p ope ies o iscoelas ic ma e ials. Al hough he pape was a nice ead,
he pu pose had been o mula ed so poo ly, ha i ook us a while o ind i back
in ou own pape .
“The pu pose o his s udy was o quan i y he in luence o skele al ic ion on
he damping o a pulsa ing an ibubble and he pulsa ion phase o an an ibubble
ela i e o he inciden sound wa e” and “The pu pose o his s udy was o
quan i y ansien and s eady-s a e beha io o black a oo ink unde sonica ion”
a e examples o well- o mula ed pu poses. Bo h ha e been modi ied om he
published pape s.
A pu pose may include a hypo hesis: “The pu pose o his s udy was o e alu-
a e he hypo hesis ha black a oo ink demons a es ansien dynamic ac i i y
in an ul asound ield.” Resea ch ques ions in a PhD p ojec a e commonly
o mula ed in he o m o a hypo hesis.
21
3.4 Me hodology
In he abs ac , you should no include de ails abou he ma e ials used. The
me hods should be quan i ied i possible. Fo example, “Six samples o a i icial
and po k skin we e a ooed, a ached o phan om ma e ial, and sonica ed wi h
a 13–6-MHz p obe, a e which he speed o sound and he e ac ion angles
o hese ma e ials we e de e mined” is a good sen ence. I does lea e many
ques ions. Wha ink was used? Wha phan om ma e ial? Wha pulse scheme?
How o en we e he expe imen s epea ed? Bu ha ’s wha he ac ual pape is
o .
A common mis ake is o add oo many de ails. O o lea e ou he ac ual
ac i i y done by he esea che : “We analyzed op ical eco dings o insoni ied
comp essible pa icles” says no hing and con ains a o bidden wo d. Make su e
ha he sen ence answe s he ques ion wha did you ac ually do you sel in his
p ojec ?
3.5 Main esul
An abs ac does no equi e you o sum up all ou comes. Jus w i e down
he mos impo an inding. Be as concise and quan i a i e as possible. You
esul s a e dead numbe s. So emo ional ou bu s s a e le ou : “The lin-
ea acous ic a enua ion coe icien o pu e black ink was measu ed o be
0.15±0.01 dB cm−1MHz−1.”
Resul s a e no good, bad, o p omising. The in e p e a ion o wha is high
and low, g ea and small should no be made in he esul s sen ence. Thus, “A
dynamic con as -enhanced eco ding showed he nonlinea signal o he agen
o much g ea e han o he con ol and much less han he comme cial agen
a a high concen a ion” is an abomina ion.
3.6 Discussion
Explain why he esul happened and wha he implica ion o his is. Fo example:
“These esul s we e explained by a 16-dB de ice compensa ion be ween he wo
in e aces, indica ing ha he sca e ing om nuclea ion was no jus aking place
in he dis al pa o he well c oss sec ion, bu o e he whole c oss sec ion” o
“As he incisions om he sonica ed blade we e isibly sha pe han hose om

22
he unsonica ed blade, and a leas as sha p as hose om he indus ially cu
pape edge, he acous ic ampli ude mus ha e in luenced he sha pness o he
blade”.
Do no in oduce new esul s. Do no men ion any u u e wo k.
3.7 Main conclusion
The las sen ence should answe whe he he goal was eached, whe he he
p oblem was sol ed, and wha he consequence is o he g ea e good in he
mo i a ion.
Now he abs ac is comple e. Bu i is s ill a d a . Th oughou he w i -
ing p ocess, check i he abs ac is s ill ep esen a i e o he s o yline o he
manusc ip . Feel ee o modi y i a will. A s ong abs ac makes a s ong
pape .
4
In oduc ion
Con a y o popula belie , in oduc ions should no be long. I he in oduc ion
exceeds he me hodology sec ion, i is mos de ini ely oo long.
The i s pa ag aph builds on o he mo i a ion and p oblem s a emen as
men ioned in he abs ac , bu now accompanied by e e ences o pee - e iewed
pape s o di e en g oups. The las sen ence o he pa ag aph should build a
b idge o he pu pose.
The second pa ag aph s a es he pu pose o he manusc ip . E en i he
backg ound is no ho oughly clea , do no pos pone men ioning he pu pose
o he pape . I he pu pose equi es addi ional backg ound in o ma ion, s ill
men ion i in gene al e ms he e, and epea i in mo e de ail la e .
The bulk o he in oduc ion is he backg ound, which is no some andom
blabbe ing abou simila esea ch, bu a e y p ecise o mula ion o he bounda ies
o you own p ojec . You p ojec deals wi h a speci ic a ea, because o he s ha e
al eady deal wi h adjacen a eas. I you know you ield and he no el y o you
esea ch, you can keep he backg ound e y concise.
T y o a oid e e ing o ma e ial no di ec ly ouching you esea ch a ea.
Fo example, conside a p ojec on he i s use o hyd ophobic pa icles in wood
pulp pe mea ion. Say ha a p io s udy has shown pe mea ion o wood pulp
wi h hyd ophilic pa icles. Then i is no needed o also e e o a di e en s udy
in es iga ing pe mea ion o blue-g een algae wi h hose hyd ophilic pa icles, as
23
24
he la e s udy is a s ep a he away han he o me . Howe e , i he blue-
g een algae s udy had been pe o med wi h hyd ophobic pa icles, ha should
be e e ed o.
This is he pa o you pape wi h mos e e ences. I you’ e go less han
eigh een e e ences he e, you ield is new (imp obable) o you didn’ do you
homewo k (mo e p obable).
The las pa ag aph o he in oduc ion is ese ed o ou lining he emainde
o he pape . I builds a b idge o he me hodology and may men ion some
o he easoning o choose a ce ain se up, ese ing he ull easoning o he
discussion sec ion. A oid u u e ense in his pa .
5
Theo y
Including a heo y sec ion is ce ainly no s anda d p ocedu e. I he e is no
no el componen in he heo e ical pa , you may wan o a oid a ull sec ion
and men ion exis ing heo y, including equa ions, in he backg ound pa o he
in oduc ion. A oid men ioning equa ions ha a e no ac ually used by you o
ob ain he esul s in his manusc ip .
Equa ions ha you do use a e s a ed in ull wi h e e y single pa ame e
explained. De i a ions may be s a ed, ypically om he poin whe e a p io pape
men ioned bounda y condi ions unde which he p o o-equa ion holds. Discussion
on he ele ance o he bounda y condi ions is ese ed o he discussion sec ion.
De i a ions o i s p inciples should be mo ed o an appendix. Bu he inal
equa ion should be included in he main pa o he pape .
Special a en ion needs o be paid o oman and i alics in pa ame e s, espe-
cially in subsc ip s. No e he di e ence be ween pa ame e mand he uni m. In
ai,ican be subs i u ed by a numbe , whils aimigh be he ini ial condi ion o a.
L
A
T
EX use s, please amilia ise you sel wi h he ma h m and ex subsc ip
commands. G eek lowe case is always slan ed, bu G eek uppe case ne e . So
ψ e sus Ψ.
25
32

8
Discussion
The discussion sec ion is e en longe han he me hodology. This is whe e mea-
su emen s become science.
The discussion sec ion is a ely di ided in o subsec ions. The i ems o be
discussed all in o he ollowing ou ca ego ies.
8.1 In e p e a ions
The in e pola ion and ex apola ion o esul s lead o he obse a ion o ends.
Such obse a ions a e no a esul in i sel , bu a subjec i e in e p e a ion o
esul s and he e o e belong in he discussion sec ion. De i a i e alues o i al
s a is ics all in his ca ego y. So do c oss-co ela ions.
8.2 Explana ions
Why did he ou comes happen? Can he esul s be explained o e u ed by
heo y? A e he e al e na i e explana ions? Can hei likelihood be es ima ed?
You a e allowed o add unce ain y he e. E en mild specula ion is no owned
upon he e. As opposed o he o he sec ions, he discussion sec ion may be
33
34
subjec i e. So long as emo ional adjec i es a e a oided.
8.3 Implica ions
Now ha we know why esul s happened, wha does his imply? Does he
inding mean ha he esea ch ques ion has been answe ed? In how a ? A e
he e po en ial applica ions o his esea ch? Is he ou come su icien o make
a d as ic change o he ield o s udy men ioned in he mo i a ion?
In addi ion, a e he indings ha we e beyond he o iginal scope o in e es
o scien i ic o o he communi ies?
This is also he oppo une momen o men ion any nega i e implica ions om
esul s, e.g., “As sca e ing om ink pa icles inside hese ecep acles was no
obse ed, he in luence o dilu ion on he ansien na u e and he quan i y o
acous ic sca e e s could no be es ablished.”
8.4 Jus i ica ions
So a we ha e comple ed he mos exci ing pa o he discussion sec ion. Bu
we’ e no he e ye . Now comes he pa ha mos s uden s ha e o w i e.
Fo e e y single sen ence o he heo y and me hodology sec ions, we may
discuss whe he he bounda y condi ions, assump ions, equa ions, de ices, con-
igu a ions, and se ings used we e ac ually jus i ied, gi en he ou comes o his
s udy.
The impo ance o his pa is o en unde es ima ed. Bu igno ing i may
lead o disas e . O he opposi e he eo : A amous g oup used an equa ion ha
only holds unde s ic adiaba ic condi ions o compu e he empe a u e inside
a collapsing ca i y. They concluded ha hey had disco e ed a way o cause
nuclea usion, ins ead o wonde ing whe he hei mic on-sized bubble in wa e
was eally ha adiaba ic.
This pa o he discussion sec ion c ea es some limi a ions o he implica-
ions. Whe e he implica ions may ha e an op imis ic sound o i , he jus i ica ion
may come ac oss as sligh ly pessimis ic.
9
Conclusions
The conclusions ake up only a ew sen ences. They a e ypically h ee s a emen s
wi hou addi ional explana ion.
The i s sen ence summa ises he mos impo an esul .
The second sen ence s a es he mos impo an implica ion.
The hi d sen ence answe s he esea ch ques ion.
You may ha e al eady encoun e ed jou nal a icles wi h page-long conclusions.
Those end o ha e pieces o easoning and e en discussion in hem. So hey a e
no eally conclusions now a e hey?
In conclusion, keep you conclusions as b ie as possible.
35
36
10
Acknowledgemen s
The acknowledgemen s a e w i en as one pa ag aph. The o de o sen ences
is s aigh o wa d. The i s sen ence s a s wi h “This esea ch has been sup-
po ed by” ollowed by all unding o ganisa ions, including g an numbe s ha
a e suppo ing you o any o you coau ho s. G an i les and o he de ails a e
le ou . The nex sen ence is a s a emen on con lic o in e es . This applies o
all au ho s who ha e ecei ed any ype o suppo om pa ies ha may bene i
om you esea ch. The nex sen ence is a s a emen o in o med consen , i
applicable. Nex , all e hical clea ance ce i ica es need o be men ioned in de ail.
I none o he abo e apply, you can use he ollowing s anda d ex :
Con lic o in e es : Au ho s s a e no con lic o in e es . In o med consen :
Au ho s s a e ha in o med consen is no applicable. E hical app o al:
Au ho s s a e ha no e hical app o al was equi ed o his esea ch as no
human o animal samples o da a we e used.
In addi ion o he p e ious s a emen s, echnical and adminis a i e suppo
om indi iduals may be men ioned, wi hou emo ional adjec i es. A oid hank-
ing spouses and dei ies.
37

38
Occasionally, scien is s a e hanked o “ aluable discussions”. Please lea e
such insul s ou . I you do no wan o include someone as a coau ho , ha is
ine, bu you don’ ha e o le he whole wo ld know ha you don’ wan hem on
you pape . Ins ead ha e he decency o add a e e ence o one o hei pape s.
11
Re e ences
I is ha d o e e ees o check i you ac ually did all expe imen s co ec ly, i you
checked you se ings e e y ime, and i you copied you numbe s co ec ly in o
you lab book and p ocessing so wa e. Ha d, bu no impossible.
Ou sec e is ha we check he e e ences ins ead. I he e a e sloppy e o s
in you e e ences, you make sloppy mis akes when measu ing and p og amming.
I you did no check he spelling o all he au ho names in you e e ences, you
canno be bo he ed o check he decla a ion o all a iables in all sub ou ines you
we e supposed o code. I you e e ences a e in di e en s yles, you a e a pe son
who changes se ings du ing expe imen s and o ge s o change hem back.
In o he wo ds, you e e ences should be lawless.
Ne e include a e e ence i you do no ha e access o he sou ce. A Pubmed
abs ac is no a sou ce.
Assume ha ci a ion ools make mis akes and check e e y e e ence you add.
Make su e ha double las names do no end up as pa o he au ho ini ials.
A oid e e ences o p oceedings and book chap e s i he e a e pee - e iewed
jou nal sou ces a ailable.
Some jou nals equi e e e ences in alphabe ical o de . I is handy o emem-
be ha in No dic alphabe s, mul iple le e s come a e Z. The ull alphabe ,
which includes Danish, No wegian, Swedish, and Finnish le e s, is A–Z, Æ, Ø,
˚
A, ¨
A, ¨
O. In his o de .
39
40
12
Appendices
Welcome o he pa o you wo k ha did no make i o he main ex . This is
no he pa ha a ac s a lo o eade ship. I is he e because you wan ed o
sha e ull de i a ions, p og amming code, and addi ional esul s wi h he eade s.
Appendices a e becoming inc easingly uncommon. The eason is ha jou nals
nowadays o e you he op ion o upload suppo ing ma e ial and mul imedia iles
wi h you manusc ip .
Consequen ly, appendices a e mos ly ound in disse a ions and heses.
We encou age you o spend he ime ha you could ha e used o w i e an
appendix on w i ing a nex pape ins ead.
41
48
The e dic mino changes does no mean ha a ew changes need o be
made. This e dic means ha i is up o he handling edi o whe he you
second submission is edis ibu ed o he e iewe s. I all sugges ions by he
e iewe s ha e been inco po a ed in o he esubmission, he handling edi o may
decide o accep wi hou u he e iew. I one o a numbe o sugges ions has
been omi ed, you esubmission is sen o he e iewe s again.
The e dic majo changes means ha he ew i ing o es uc u ing is so
subs an ial ha ano he e iew ound is equi ed. Some imes addi ional mea-
su emen s ha e o be done as pa o he sugges ed changes.
14.2 W i ing a ebu al
Now ha you know he e dic , i is ime o a ebu al.
Tha ’s igh . You a e s ill no going o edi he digi al e sion o you
manusc ip . Bu you may d aw nea e he ha d copy wi h pencil ma kings and,
by now, se e al co ee s ains.
You i s ask is o c ea e a ebu al documen , e y simila o he one on
he nex page.
Copy in, li e ally, all commen s om he e iewe s and om he edi o in he
le column. Make su e o numbe all commen s. In he igh column, only add
he ex The au ho s ag ee behind each commen , in bold.
Do no , we epea , do no answe any o he ques ions!
Then you a e going o add numbe s in he side ma gins o you manusc ip ,
each ep esen ing a e iewe commen . E.1 is he i s commen o he edi o ;
R2.5 is he i h commen o e iewe 2.
A e going h ough he sugges ed changes once, i ’s ime o modi y and add
ex in he ha dcopy, wi h pencil. Now is he ime ha you ealise why double
line spacing wasn’ such a bad idea, a e all.
A e a commen has been add essed in he ha d copy, w i e a sen ence ha
looks like his: The au ho s ag ee. The ollowing ex was added |modi ied
in sec ion n: “< ex in ed colou >”.

49
<Jou nal Name> <Re e ence Numbe >
Rebu al o he e iew o
“<A icle i le>”
by <Au ho s>.
Dea Edi o -in-Cha ge,
The au ho s a e mos g a e ul o he highly use ul commen s made! Please ind below a de ailed eply o each
commen . The changes made ha e been highligh ed in he e ised manusc ip in ed on . Tex changes ha e
been copied om he L
A
T
EX sou ce code. The e o e, in his ebu al, e e ences appea wi h di e en o ma ing
han in he manusc ip i sel . In addi ion, he o de o he ex and he e e ences has been es uc u ed. Fo he
con enience o he e iewe s, he enumbe ed e e ences ha e been added o his ebu al.
REVIEWER 1:
1. Copy each o he e iewe s commen s e ba im in o
his documen .
The au ho s ag ee. The e iewe is always igh , ac-
knowledge i and explain why you ag ee by de ailing wha
changes we e made in he manusc ip ha add esses he
commen .
2. T ea each sen ence as a sepa a e commen . The au ho s ag ee. I you made ex modi ica ions, i
is bene icial o indica e “exac ly wha ex was dele ed
emo ed and wha was added/changed in ed.”
REVIEWER 2:
1. Repea o each e iewe . The au ho s ag ee. E en i he e a e o e lapping com-
men s, epea he same changes ha we e made o show
ha you ha e add essed hei pa icula commen .
2. I he e a e ex a e e ences added, i is bene icial o
include he ull e e ence lis as pa o he ebu al le e
o sa e he e iewe om skipping o wa d and backwa d.
The au ho s ag ee. You a e ying o make hei li es as
easy as possible wi h he ebu al le e . Gi e hem e e y-
hing hey wan in his le e and hey will look a ou ably
on you esubmission.
EDITORIAL COMMENTS:
1. Don’ o ge o include any commen s om he edi o
ha may also be included.
The au ho s ag ee. You wan o gi e he edi o con-
idence ha you ha e add essed e e y hing ca e ully and
ully.
2. You should w i e he ebu al le e i s be o e you
e en hink abou ouching he newly c ea ed e sion o
you wo king manusc ip .
The au ho s ag ee. This way you will be able o ake
he ime o diges wha he e iewe s a e ac ually asking
o , and plan ou how you will make he changes in he
clea es possible way.
3. Make he upda es as soon as possible. You wan o ge
i back o he edi o (and e iewe s) while i is s ill esh
in hei memo y.
The au ho s ag ee. Again, i is a quali y o li e hack. I
hey emembe you manusc ip , hey will need less ime
o e- e iew he changes ha you ha e made.
Re e ences
[1] Include he ull e e ence lis he e, in he jou nal equi ed o ma , indica ing any new e e ences added in ed.
1
50
T ea e e y commen as s and-alone. E en i you hink ha you al eady
add essed he commen elsewhe e.
Take he e iewe s and he edi o se iously. We apply wo simple ules:
1. The e iewe is always igh .
2. Should he e iewe e e be w ong, see ule numbe 1.
T y o eally unde s and wha his means. I you e iewe hinks ha you pape
is abou 1-MHz HIFU, al hough i is abou 10-MHz LIFU, you should make i
mo e clea and mo e explici in se e al pa s o he manusc ip . I you e iewe
men ions expe imen s while you a e p esen ing simula ions, you should p obably
upda e he i le and men ion simula ed da a “ ha had no been de i ed om
expe imen s” a some poin .
We all ha e colleagues who claim ha hei pape s we e ejec ed because he
e iewe s did no unde s and any hing. Well, who’s aul is ha ? We all ha e
a couple o less o una e expe iences wi h e iewe s. Bu i his is s uc u al,
i may ha e some hing o do wi h poo w i ing by he au ho s, and less so wi h
poo judgemen o he e iewe s.
Only once he ebu al le e is comple e, and all sugges ions ha e been
inco po a ed in pencil w i ing in he ha d copy, can you edi he sou ce ile. So
in ou case he ile JJAP21 CSC30 MARKED. ex. S ike all ex o be emo ed
ou and dye all ex added ed. To his pu pose, L
A
T
EX use s should lea n o use
he commands sou and ex colo { ed}.
The supe iso -app o ed ma ked e sion is dis ibu ed o he coau ho s, ac-
companied by he p oposed ebu al. Again, a deadline o se en ull days is
app op ia e.
The day be o e submission, ano he ound o p oo eading may be equi ed,
especially i majo changes had been sugges ed.
A e p oo eading is done, copy you sou ce ile and eplace he addendum
MARKED by CLEAN. Commen ou all s uck-ou ex , and do a eplace-all o
ex colo { ed}by ex colo {black}. Bo h he ma ked and he clean
e sion need o be uploaded o he edi o ial sys em. Do no o ge o upload he
ebu al.
T ea e e y subsequen e dic as i i is he i s . C ea e a new ebu al
acco ding o he same ecipe. Ne e e e o p io ebu als o p io manusc ip s.
A ebu al always deals wi h he cu en e sion.
You may eel ha a e esubmi ing you pape , you dese e a holiday. Don’
o ge o b ing a ha dcopy o he clean e sion. And a pencil.
15
A e accep ance
Once you ecei e a le e o inal accep ance, please mo e a PDF o he clean
e sion o you accep ed manusc ip o he subdi ec o y ./o icial. We’ll
ell you why la e . Following inal accep ance, he manusc ip is mo ed ou
o he edi o ial sys em ha is handled by olun ee ing scien is s in you ield o
he ypese ing and p in ing acili y o he publishe ha is handled by low-waged
p o essionals wo king unde ex eme p essu e. You manusc ip is assigned a new
numbe . You dealings wi h he edi o ial o ice a e o e . Wha e e happens o
you pape , do no con ac he edi o ial o ice. They do no ha e access o you
pape . Plus, hey don’ wo k o he publishing house. I , o some eason, you
ha e an issue ha equi es con ac , ini ia e an enqui y h ough he helpdesk o
he publishing house, making su e ha you a e men ioning he co ec manusc ip
numbe s. Ne e call up a p in ing acili y i sel .
A some poin , always unexpec ed, ypically du ing a long aca ion, you
ecei e p oo p in s. You publishe expec s hem back wi hin 48 hou s. So, you
d op wha e e you a e wo king on. I you a e on holiday, in o m you lo ed ones
ha some hing u gen has come up. Time o ind a p in e o p in ou he p oo s
and ge one shee o A4 pape , ge you clean ha d copy ou o you b ie case, and
ind a quie spo o si and concen a e. Good ha you b ough a pencil. Fo wa d
he p oo s o you supe iso . You supe iso will show he same dedica ion in
p oo eading as you. No need o do he p oo eading wi h all coau ho s. Bu i
51
52
doesn’ hu o send he p oo s a ound. Du ing he p oo eading, you will ind
he s anges e o s and omissions. Don’ ge emo ional. Jus ma k he page and
line numbe on you emp y shee , wha i says now, and wha i should be. Pay
special a en ion o igu e cap ions, igu e numbe s in he ex , line hicknesses,
and exo ic symbols. Don’ o ge o ead he i le one las ime.
Do no make changes o he han unwan ed di e ences be ween accep ed
e sion and p oo . Adding a sen ence o imp o ed cla i y ac ually changes he
con en s o he pape , and equi es e- e iewing. So do no conside his. When
submi ing you changes, also answe all que ies o he au ho om he publishe .
E en i he answe is “no applicable”, s ill answe .
15.1 Uploading o a eposi o y
The copy igh o he p oo and he published e sions o you pape a e owned
by he publishe . Remembe hose copy igh ans e o ms you signed? Tha ’s
when i happened. Ne e heless, you do own he i s submission and he ac-
cep ed e sion. In ac , hey a e in he subdi ec o y ./o icial. Mos pub-
lishing houses allow you o sha e you i s submission, i.e., he e sion wi hou
modi ica ions ollowing e iew, wi h he es o he wo ld h ough a eposi o y.
A common eposi o y o submi ed e sions is Co nell Uni e si y’s a Xi .
Mos scien is s p e e o sha e he accep ed e sion. This is allowed as well,
bu ypically a e an emba go pe iod. The emba go pe iod is de e mined by he
publishe and may di e o jou nals o he same publishe . Typical emba go pe i-
ods a e 12 mon hs and 24 mon hs. A e he emba go, he accep ed manusc ip
can be sha ed h ough a eposi o y such as HAL open science. Some und-
ing agencies equi e you o sha e you publica ions h ough eposi o ies. You
supe iso may ha e ac ually chosen he jou nal based on i s sel -a chi ing o
open-access policy.
15.2 Obliga ion o e iew
E e y pee - e iewed manusc ip you w i e is handled by a leas one edi o and
h ee olun ee s o e iew he pape . Those e iewe s a e you pee s. They a e
o he au ho s o he same o a simila jou nal. Now ha you pape is ou he e,
you will be asked o e iew pape s you sel . And he answe is yes. You ha e a
mo al obliga ion o e iew a leas h ee pape s pe manusc ip ha you submi .
16
Pos -publica ion con lic s
16.1 Wi hd awing you pape
Don’ .
16.2 E a a
No long a e you pape is published, you migh disco e ha some easoning
was lawed. Some numbe s we e in he w ong o de . A plus in an equa ion
should ha e been a minus. A e m ha was neglec ed was no ha negligible
a e all.
Renewed insigh s do no mean ha you should send a co igendum pape o
e e y e a um.
The s anda d ule is he e: i he e o in you pape would lead o a di e -
en conclusion, a co igendum pape may be conside ed. Discuss wi h all you
coau ho s i s . The e migh be al e na i e ways o add ess he e o . One is o
men ion he e o in a ollow-up pape in he same jou nal.
I a pa ame e o a comme cial p oduc is inco ec ly copied om he p oduc
speci ica ion in o you pape , he manu ac u e may demand a co igendum pape
53

54
om you. This ype o co igendum pape is conside ed emba assing, as i is
jus caused by sloppy c a smanship.
S ill, a co igendum pape is o be p e e ed o e wi hd awing a pape . The
la e is associa ed wi h oul play, mos commonly plagia ism.
16.3 Plagia ism
I you suspec ha you wo k is being plagia ised, consul wi h he coau ho s on
how o add ess his. You may assume ha he jou nal and o he pa y will no
ake he accusa ion ligh ly. P oo p o ided by you migh no be seen as such.
And some imes coincidence eally is jus ha .
In he pas hi y yea s o wo king in science, we ha e been se e al imes on
he media ing, a ew imes on he accusing and one ime on he accused side.
In all cases, we managed o esol e he unpleasan si ua ion in a sa is ying way
o bo h sides. Ou ad ice is o hink o an elegan way o deal wi h you case,
wi hou u ning he o he pa y in o he opposi ion.
17
Bibliog aphy
Th oughou his ecipe, examples we e used om exis ing publica ions, o en
wi h a ew modi ica ions o highligh he good o exagge a e he bad. Gi en he
ac ha we a e coau ho s on all o he bad examples, i should be ob ious ha
he e’s no hing w ong wi h making mis akes.
1. Hols B, Cham J. Scien i ic Pape W i ing: A Su i al Guide. Sco s Valley:
C ea eSpace 2015.
2. Ko opoulis S, Haugse R, Muji´c M, Sulen A, Gullaksen SE, Mc Co mack
E, Gilja OH, Pos ema M, Gje sen BT. E alua ion o he e ec s o clinical
diagnos ic ul asound in combina ion wi h ul asound con as agen s on
cell s ess: single cell analysis o in acellula phospho-signaling pa hways
in blood cance cells and no mal blood leukocy es. IEEE In e na ional
Ul asonics Symposium P oceedings 2014: 1186–1190.
3. an Leusden P, den Ha og GJM, Bas A, Pos ema M, an de Linden
E, Sagis LMC. Pe mea ion o p obe molecules in o algina e mic obeads:
e ec o sal and p ocessing. Food Hyd ocolloids 2017; 73: 255–261.
4. Wal he T, Pos ema M. Vo ich ung und Ve ah en zu Iden i ika ion, Sep-
a a ion und/ode zell ypspezi ischen Manipula ion wenigs ens eine Zelle
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eines Zellsys ems sowie on Mik oo ganismen. Eu opean Pa en EP
2 634 246 A1 2013.
5. Rubin DM, Acha i S, Ca lson CS, Le s RFR, Pan anowi z A, Pos ema
M, Richa ds XL, Wigdo owi z B. Facili a ing unde s anding, modeling and
simula ion o in ec ious disease epidemics in he age o COVID-19. F on-
ie s in Public Heal h 2021; 9: 593417.
6. Ca lson CS, Rubin DM, Heikkil¨a V, Pos ema M. Ex ac ing ansmission
and eco e y pa ame e s o an adap i e global sys em dynamics model o
he COVID-19 pandemic. P oceedings o he IEEE AFRICON 2021.
7. Leigh on TG. The Acous ic Bubble. London: Academic P ess 1994.
8. Pos ema M, de Jong N, Schmi z G. The physics o nanoshelled mic obub-
bles. Biomedizinische Technik 2005; 50(S1): 748–749.
9. Smalbe ge C, Na han M, Rubin DM, Nel M, Ko opoulis S, Ca lson CS,
Pos ema M. Expe imen al se up o he ul asonic ac iona ion o lowing
whole blood in a capilla y. Cu en Di ec ions in Biomedical Enginee ing
2022; 8: 89–92.
10. Pos ema M, Ge ing C, Ande on N, Ca lson CS, Kellom¨aki M. Moni o ing
he gela ion o gellan gum wi h o sion heome y and b igh ness-mode
ul asound. Cu en Di ec ions in Biomedical Enginee ing 2022; 8: 33–36.
11. Ande on N, Ca lson CS, Aha onson V, Pos ema M. De e mining he in-
luence o endoskele on ic ion on he damping o pulsa ing an ibubbles.
Cu en Di ec ions in Biomedical Enginee ing 2022; 8: 781–784.
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You canno ha e a book ending on an odd page, so he e is a placeholde o
ensu e ha i olls o e on o an e en page.