The lecture aimed to provide students with an understanding of scientific papers and the publication process. It explained that papers are written to report new results to the scientific community and establish priority. The process involves peer review, where editors and unpaid reviewers provide quality checks of submissions. Finally, papers are written for a community of peers and include different sections like introduction, results, discussion and materials and methods.

1. Ge#ng
the
Measure
of
Scien3fic
Papers
Prof
Stephen
Curry
12
February
2013
1

2. SOLE 2013
The lecture on primary
literature interpretation was
completely useless especially
so close before exams; it
Warning: seemed completely irrelevant
to us and was not at all
interesting, it appeared to be
purely a method of self-
gratification for Curry, to "show
off" his successes in the field.
2

3. What
is
this
lecture
for?
• The
scien3fic
literature
is…
• …unavoidable,
daun3ng,
hard
to
read
(some3mes)
• What
do
you
need
to
know?
• How
it
is
produced
• How
to
read
it
(a
few
3ps)
• Papers
aren't
solely
wriJen
to
be
read…
3

4. Star3ng
point:
What
is
a
scien3fic
paper
for?
• To
report
the
new
results
to
the
scien3fic
community
• formal
version
of
record
• To
establish
'priority'
• To
avoid
perishing…
4

5. Where
did
journals
come
from?
• 17th
Century
innova3on
-­‐
replaced
leJers
• Now
published
by
learned
socie3es
and
private
companies
(e.g.
Elsevier,
Springer,
Wiley,
NPG)
• There
are
1,000's
of
them
6
March
1665
5
5
January
1665 See
h0p://en.wikipedia.org/wiki/Scien=fic_journal

6. How
are
papers
wriJen?
• Different
types:
• Primary
research
ar3cles
—
submiJed
when
you're
ready
• Review
ar3cles
—
oYen
requested;
synthesis
of
the
literature
• When:
• When
you
have
enough
informa3on?
• An
interes'ng
result
supported
by
addi3onal
experiments:
e.g.
structure
and
func3on
• What
about
nega3ve
results?
• How:
• Who
is
the
audience
-­‐
small
community
of
peers;
who
else?
• Style
of
wri3ng:
1st
or
3rd
person?
• Figures
—
always
tricky
to
get
right
6

7. Figures
are
hard
to
make
and
read
Zunszain
et
al.
(2010)
7 J
Mol
Biol
395,
375–389

8. Submission
to
the
journal
• Choice
of
journal?
• Review
process:
editors
and
peer-­‐reviewers
• Peer
reviewers
• unpaid,
usually
anonymous;
• author
can
ask
for
some
people
to
be
barred
from
reviewing
• a
quality
check
(but
not
foolproof)
• Outcomes
of
the
review:
• reject,
minor
revision,
major
revision,
accept
Re:
JVI03151-­‐12
Structures
of
the
Compact
Helical
Core
Domains
of
Feline
Calicivirus
and
Murine
Norovirus
VPg
proteins
Dear
Stephen,
Thank
you
for
submiWng
your
manuscript
to
Journal
of
Virology.
Below
you
will
find
the
comments
of
two
reviewers
who,
as
you
will
see,
liked
the
work
very
much
but
had
comments
about
the
func=onal
data
and
their
interpreta=on.
8 Revisions
are
requested…

9. Costs
of
Publica3on
• Author
pays
—
from
a
grant
(and
is
not
remunerated
for
wri3ng)
• Page
charges,
colour
figures
e.g.
J.
Virol.
-­‐
pages
$67-­‐$125
each;
colour
figs
$375
• Open
access:
addi3onal
charges
($0-­‐$5000)
-­‐
see
later
9

10. The
published
paper:
who
did
what?
• Significance
of
author
posi3on
in
list
(first
and
last
author)
• Signposts
for
further
reading...
10 hJp://www.plosone.org/ar3cle/info%3Adoi%2F10.1371%2Fjournal.pone.0038723

11. The
published
paper:
read
the
abstract
first
(closely)
Abstract
Murine
noroviruses
have
emerged
as
a
valuable
tool
for
inves3ga3ng
the
molecular
basis
of
infec3on
and
pathogenesis
of
the
closely
related
human
noroviruses,
which
are
the
major
cause
of
non-­‐bacterial
gastroenteri3s.
The
replica3on
of
noroviruses
relies
on
the
proteoly3c
processing
of
a
large
polyprotein
precursor
into
six
non-­‐structural
proteins
(NS1–2,
NS3,
NS4,
NS5,
NS6pro,
NS7pol)
by
the
virally-­‐encoded
NS6
protease.
We
report
here
the
crystal
structure
of
MNV
NS6pro,
which
has
been
determined
to
a
resolu3on
of
1.6
Å.
Adven33ously,
the
crystal
contacts
are
mediated
in
part
by
the
binding
of
the
C-­‐terminus
of
NS6pro
within
the
pep3de-­‐binding
cleY
of
a
neighbouring
molecule.
This
inser3on
occurs
for
both
molecules
in
the
asymmetric
unit
of
the
crystal
in
a
manner
that
is
consistent
with
physiologically-­‐relevant
binding,
thereby
providing
two
independent
views
of
a
protease-­‐pep'de
complex.
Since
the
NS6pro
C-­‐terminus
is
formed
in
vivo
by
NS6pro
processing,
these
crystal
contacts
replicate
the
protease-­‐product
complex
that
is
formed
immediately
following
cleavage
of
the
pep'de
bond
at
the
NS6-­‐NS7
junc'on.
The
observed
mode
of
binding
of
the
C-­‐terminal
product
pep3de
yields
new
insights
into
the
structural
basis
of
NS6pro
specificity.
11 hJp://www.plosone.org/ar3cle/info%3Adoi%2F10.1371%2Fjournal.pone.0038723

12. Read
the
"News
&
Views"
(or
equivalent)
12 hJp://www.nature.com/nature/current_issue.html

13. The
published
paper:
read
as
it
suits
you
Introduc'on
• Why
is
this
problem
important?
• What
other
work
has
been
done
on
this
problem?
Results
• What
experiments
did
we
do?
• What
did
we
find?
Discussion
• Why
what
we
found
is
interes3ng/significant
Materials
and
Methods
• Enough
informa3on
for
others
to
repeat
the
study
(maybe)
Supplementary
Informa'on
• Addi3onal
material
that
wasn't
interes3ng
enough
to
put
in
13 the
body
of
the
paper
(internet
infla3on…)

14. Just
because
it's
published
doesn't
mean
it's
an
easy
read
NLK
Is
a
Novel
Therapeu'c
Target
for
PTEN
Deficient
Tumour
Cells
PTEN
(Phosphatase
and
tensin
homolog)
is
a
tumour
suppressor
gene
commonly
defec=ve
in
human
cancer,
and
is
thus
a
poten=ally
important
therapeu=c
target.
Targe=ng
tumour
suppressor
loss-­‐of-­‐func=on
is
possible
by
exploi=ng
the
gene=c
concept
of
synthe=c
lethality
(SL).
By
combining
the
use
of
isogenic
models
of
PTEN
deficiency
with
high-­‐
throughput
RNA
interference
(RNAi)
screening,
we
have
iden=fied
Nemo-­‐Like
Kinase
(NLK)
inhibi=on
as
being
synthe=cally
lethal
with
PTEN
deficiency.
This
synthe=c
lethality
is
likely
mediated
by
the
transcrip=on
factor
FOXO1
(Forkhead
box
O1),
an
NLK
substrate,
as
the
selec=vity
of
NLK
gene
silencing
for
PTEN
deficient
cells
can
be
reversed
by
FOXO1
knockdown.
In
addi=on,
we
provide
evidence
that
PTEN
defec=ve
cells
targeted
by
NLK
gene
deple=on
undergo
senescence,
sugges=ng
that
NLK
func=on
is
cri=cal
for
the
con=nued
prolifera=on
of
PTEN
deficient
cells.
Taken
together,
these
data
provide
new
insight
into
the
poten=al
of
targe=ng
of
NLK
to
treat
a
range
of
tumourigenic
condi=ons
characterised
by
PTEN
deficiency.
PLoS
ONE
7(10):
e47249
14 To
be
fair,
it
is
hard
to
write
clearly
about
complex
ideas…

15. The
published
paper:
how
good
is
it?
• Published
but
is
it
true?
• Try
not
to
be
in3midated
—
your
are
allowed
to
cri3cise
• Reviewers/authors
may
have
missed
something
• Mistakes
should
be
reported
15 hJp://www.plosone.org/ar3cle/info%3Adoi%2F10.1371%2Fjournal.pone.0038723

16. Fraud:
some
'mistakes'
are
deliberate
Why?
16
See
also
hJp://www.science-­‐fraud.org

17. Fraud:
how
common
is
it?
Science
339,
386–389
(2013)
Ferric
Fang
• A
small
minority
• On
the
increase?
Arturo
Casadevall
17 See
also:
h0p://retrac=onwatch.wordpress.com

18. What
else
is
a
paper
for?
To
advance
your
career
-­‐
'publish
or
perish'
• Promo3on
• Lecturer,
Senior
Lecturer,
Reader,
Professor
• Grant
applica3ons
• ~20%
success
rate
in
the
UK
• Research
Excellence
Framework
(REF
2014)
• Assessment
of
research
in
UK
universi3es
• Dept
submits
4
papers
for
every
member
of
staff
• A
key
determinant
of
future
income
from
govt
The
hierarchy
of
journals
—
where
to
publish?
•
The
impact
factor
18 See
also:
Lawrence,
P.
The
Heart
of
Research
is
Sick.
Lab
Times
24–31
(2011).

19. Impact
factors:
a
measure
of
journals,
not
papers
For
each
journal,
impact
factor
=
Number
of
cita=ons
to
papers
in
past
2
yrs
Total
number
of
papers
published
in
past
2
yrs
Mean
value
of
IF
is
dominated
by
small
number
of
very
highly
cited
papers.
Typically
only
15%
of
papers
have
more
cita=ons
than
average.
IF
is
a
poor
measure
of
average/likely
performance
From
Wikipedia
19 h0p://occamstypewriter.org/scurry/2012/08/13/sick-­‐of-­‐impact-­‐factors/

20. Inside
the
College
database
of
staff
publica3ons
20

21. 21

22. Open
Access
22

23. Where
are
scientific
journals
going?
The
Web
changes
everything:
Expectations
of
information
accessibility
Faster
publication
&
exchange
Scalability:
text
and
data
mining
237

24. Policy
developments
in
the
UK
-­‐
2012
Dame
Janet
Finch:
“The
principle
that
the
results
of
research
that
has
been
publicly
funded
should
be
freely
accessible
in
the
public
domain
is
a
compelling
one,
and
fundamentally
unanswerable.”
Rt
Hon
David
WilleWs
MP:
The
"funding
model
is
surely
going
to
have
to
change
even
beyond
the
welcome
transi3on
to
open
access…
that’s
already
underway.
To
try
to
preserve
the
old
model
is
the
wrong
baWle
to
fight."
24

25. UK
policy
from
April
2013
• All
publicly-­‐funded
research
must
be
open
access
• Gold
OA
-­‐
immediately
available
in
OA
journal
(costs
$0-­‐$5000)
• Green
OA
-­‐
author's
version
of
manuscript
made
available
aYer
6
months
($0)
Big
debate...
(needs
another
lecture)
• For
now,
UK
will
pay
OA
fees
and
journal
subscrip3ons…
• UK:
only
6%
of
world's
research
• For
policy
to
succeed,
need
the
whole
world
to
go
for
OA
• But
nobody
knows
how…
h0p://www.economist.com/node/21559317
h0p://occamstypewriter.org/scurry/2012/09/05/key-­‐ques=ons-­‐for-­‐open-­‐access-­‐policy-­‐in-­‐the-­‐uk/
25

26. Just
publish?
Interes3ng
3mes...
26

27. Ques3ons?
27