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1.

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(Dirac)
1998 24 SCI

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4. idea
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ideapaper

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Title: Be short, accurate, and unambiguous; Give your paper a distinct personality; Begin
with the subject of the study.
Introduction: What is known; What is unknown; Why we did this study?
Methods: Participants, subjects; Measurements; Outcomes and explanatory variables;
Statistical methods.
Results: Sample characteristics; Univariate analyses; Bivariate analyses; Multivariate
analyses.
Tables and figures: No more than six tables or figures; Use Table 1 for sample
characteristics (no P values); Put most important findings in a figure.
Discussion: State what you found; Outline the strengths and limitations of the study;
Discuss the relevance to current literature; Outline your implications with a clear "So
what?" and "Where now?"


References: All citations must be accurate; Include only the most important, most
rigorous, and most recent literature; Quote only published journal articles or books; Never
quote "second hand"; Cite only 20-35 references.
Formatting: Include the title, author, page numbers, etc. in headers and footers; Start
each section on a new page; Format titles and subtitles consistently; Comply with
"Instructions to authors".

1. Introduction
A.
HoweverHowever, little information(little

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attention/little work/little data/little research)(or few studies/few investigations/few

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question will be resolved (fall away) with our proposed method (approach).
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aspects of this problem have to be addressed. The first question involvesThe second
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this study has examined only

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determine this from this dataOur results are lack of

Not withstanding its limitation, this study does suggest

However, these problems could be solved if we considerDespite its preliminary
character, this study can clearly indicate

3. Others
A.
Abbreviation(1) AppendixAbbreviation
(2)Abbreviation
B.
credits.negative
Their results are wrong, very questionable, have no commensence, etc.
Their studies may be more reasonable if they hadconsidered this

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PubMed
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paperpaper

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lxj35288

http://emuch.net/bbs/viewthread.php?tid=490458&fpage=1

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ElsevierSpringer

1 Google Google
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2 title Google
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title ,,
Publication PDF , ftp
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Dear Professor
I am in Institute of , Chinese Academy of Sciences. I am writing to request
your assistance. I search one of your papers:

but I can not read full-text content, would you mind sending your papers by E-mail? Thank
you for your assistance.
Best wishes !(or best regards)

, E-mail
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0.3

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[]
ceramic
http://emuch.net/bbs/viewthread.php?tid=499419&fpage=1

01

SCI 6 1 IF 16

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APSACersSIEEE

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lxj35288
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20

Dr. George StellDr. Harold Friedman

Dr.
Carol HallGopen

Dr. Martin KarplusKarplus

yqzhou@iupui.edu
http://sparks.informatics.iupui.edu

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1.

Samples for the 2-dimensional projection of kinetic trajectories are shown in Figure 7. The
coil states are loosely gathered while the native states can form a black cluster with extremely high
density in the 2-dimensional projection plane.
The coil states

Kinetic trajectories are projected onto xx and yy variables in Figure 7. This figure shows two
populated states. One corresponds to loosely gathered coil states while the other is the native state
with a higher density.

Figuretwo statescoil states

The accuracy of the model structures is given by TM-score. In case of a perfect match to the
experimental structure, TM-score would be 1.
TM-score a perfect match to
experimental structure
The accuracy of the model structures is measured by TM-score, which is equal to 1 if there is
a perfect match to the experimental structure.

2.

[1]
The smallest URFs (URFA6L), a 207-nucleotide (nt) reading frame overlapping out of phase
the NH2-terminal portion of the adenosinetrip hosphatase (ATPase) subinit 6 gene has been
identified as the animal equivalent of the recently discovered yeast H+-ATPase subunit 8 gene.

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[1]
The smallest of the URFs is URFA6L, a 207-nucleotide (nt) reading frame overlapping out of
phase the NH2-terminal portion of the adenosinetriphosphatase (ATPase) subinit 6 Gene; it has
been identified as the animal equivalent of the recently discovered yeast H+-ATPase subunit 8
gene.

3.
[1]
URFA6L has been identified as the animal equivalent of the recently discovered yeast
H+-ATPase subunit 8 gene.
Recently discovered yeast H+-ATPase subunit 8 gene has a corresponding animal equivalent
gene URFA6L.

[1]
The enthalpy of hydrogen bond formation between the nucleoside bases 2-deoxyguanosine
(dG) and 2-deoxycytidine (dC) has been determined by direct measurement.
direct measurement
[1]
We have directly measured the enthalpy of hydrogen bond formation between the nucleoside
bases 2-deoxyguanosine (dG) and 2-deoxycytidine (dC).

[1]
The enthalpy of hydrogen bond formation between the nucleoside bases 2-deoxyguanosine
(dG) and 2-deoxycytidine (dC) has been determined by direct measurement. dG and dC were
derivatized at the 5 and 3 hydroxyls with triisopropylsilyl groups to obtain solubility of the
nucleosides in non-aqueous solvents and to prevent the ribose hydroxyls from forming hydrogen
bonds. From isoperibolic titration measurements, the enthalpy of dC:dG base pair formation is
-6.650.32 kcal/mol.
(enthalpy)
[1]
We have directly measured the enthalpy of hydrogen bond formation between the nucleoside
bases 2-deoxyguanosine (dG) and 2-deoxycytidine (dC). dG and dC were derivatized at the 5 and
3 hydroxyls with triisopropylsilyl groups; these groups serve both to solubilize the nucleosides in
non-aqueous solvents and to prevent the ribose hydroxyls from forming hydrogen bonds. The
enthalpy of dC:dG base pair formation is -6.650.32 kcal/mol according to isoperibolic titration
measurements,
1 dGdC
2

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[1]
Large earthquakes along a given fault segment do not occur at random intervals because it
takes time to accumulate the strain energy for the rupture. The rates at which tectonic plates move
and accumulate strain at their boundaries are approximately uniform. Therefore, in first
approximation, one may expect that large ruptures of the same fault segment will occur at
approximately constant time intervals. If subsequent main shocks have different amounts of slip
across the fault, then the recurrence time may vary, and the basic idea of periodic main shocks
must be modified.
Rate Of Strain Accumulation)

[1]
Large earthquakes along a given fault segment do not occur at random intervals because it
takes time to accumulate the strain energy for the rupture. The rates of strain accumulation at the
boundaries of tectonic plates are approximately uniform. Therefore, nearly constant time intervals
(at first approximation) would be expected between large ruptures of the same fault segment.
[However?], the recurrence time may vary; the basic idea of periodic main shocks may need to be
modified if subsequent main shocks have different amounts of slip across the fault.

1 2
1: [1]
2: [1]

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)[2]

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X Y

1).

2). ()

3).

4). ()

5).

6).

()()

()

()
()
RobustRobust

1)2)

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(
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Steric restrictions in protein folding: an alpha-helix cannot be followed by

a contiguous beta-strand Interpreting the folding kinetics of
helical proteins Native proteins are surface-molten solids:
Application of the Lindemann criterion for the solid versus liquid state
Native proteins are surface-molten solids

(
)

[3]
Assessing secondary structure assignments of protein structures by using pairwise
sequence-alignment benchmarks
The secondary structure of a protein refers to the local conformation of its polypeptide
backbone. Knowing secondary structures of proteins is essential for their structure
classification,understanding folding dynamics and mechanisms, and discovering conserved
structural/functional motifs. Secondary structure information is also useful for sequence and
multiple sequence alignment, structure alignment, and sequence to structure alignment (or
threading). As a result, predicting secondary structures from protein sequences continues to be an

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active field of research fifty six years after Pauling and Corey first predicted -helix andthat the
most common regular patterns of protein backbones are the -sheet.the Prediction and
application of protein secondary structures rely on prior assignment of the secondary-structure
elements from a given protein structure by human or computational methods.


Many computational methods have been developed to automate the assignment of secondary
structures. Examples are DSSP,STRIDE, DEFINE, P-SEA, KAKSI,P-CURVE, XTLSSTR,
SECSTR, SEGNO, and VoTAP. These methods are based on either the hydrogen-bond pattern,
geometric features, expert knowledge or their combinations. However, they often disagree on their
assignments. For example, disagreement among DSSP, P-CURVE, and DEFINE can be as large as
25%. More beta sheet is assigned by XTLSSTR and more pi-helix by SECSTR than by DSSP. The
discrepancy among different methods is caused by non-ideal configurations of helices and sheets.
As a result, defining the boundaries between helix, sheet, and coil is problematical and a
significant source of discrepancies between different methods.
Inconsistent assignment of secondary structures by different methods highlights the need for a
criterion or a benchmark of standard assignments that could be used to assess and compare
assignment methods. One possibility is to use the secondary structures assigned by the authors
who solved the protein structures. STRIDE, in fact, has been optimized to achieve the highest
agreement with the authors annotations. However, it is not clear what is the criterion used for
manual or automatic assignment of secondary structures by different authors. Another possibility
is to treat the consensus prediction by several methods as the gold standard. However, there is no
obvious reason why each method should weight equally in assigning secondary structures and
which method should be used in consensus. Other used criteria include helix-capping propensity,
the deviation from ideal helical and sheet configurations, and structural accuracy produced by
sequence-to-structure alignment guided by secondary structure assignment.
In this paper, we propose to use sequence-alignment benchmarks for assessing secondary
structure assignments. These benchmarks are produced by 3D-structure alignment of structurally
homologous proteins. Instead of assessing the accuracy of secondary-structure assignment directly,
which is not yet feasible, we compare the two assignments of secondary structures in structurally
aligned positions. We assume that the best method should assign the same secondary-structure
element to the highest fraction of structurally aligned positions. Certainly, structurally aligned
positions do not always have the same secondary structures. Moreover, different
structure-alignment methods do not always produce the same result. Nevertheless, this criterion
provides a means to locate a secondary-structure assignment method that is most consistent with
tertiary structure alignment. We suggest that this approach provides an objective evaluation of
secondary structure assignment methods.

)
)

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)[4]
One question about the complex homopolymer phase diagram presented here is whether it is
caused by the discontinuous feature of the square-well potential. We cannot give a direct answer
because the DMD simulation is required to obtain well-converged results for the thermodynamics.
However, the critical phenomena predicted for a fluid composed of particles interacting with a
square-well potential are as realistic as those predicted for a fluid composed of particles
interacting with a LJ potential. Also an analogous complex phase diagram is found in simulations
of LJ clusters. The present results for square-well homopolymers may well be found in more
realistic homopolymer models and even in real polymers.

)[3]
How to make an objective assignment of secondary structures based on a protein structure is
an unsolved problem. Defining the boundaries between helix, sheet, and coil structures is arbitrary,
and commonly accepted standard assignments do not exist. Here, we propose a criterion that
assesses secondary-structure assignment based on the similarity of the secondary structures
assigned to structurally aligned residues in sequence-alignment benchmarks. This criterion is used
to rank six secondary-structure assignment methods: STRIDE, DSSP, SECSTR, KAKSI, P-SEA,
and SEGNO with three established sequence-alignment benchmarks (PREFAB, SABmark and
SALIGN). STRIDE and KAKSI achieve comparable success rates in assigning the same
secondary structure elements to structurally aligned residues in the three benchmarks. Their
success rates are between 1-4% higher than those of the other four methods. The consensus of
STRIDE, KAKSI, SECSTR, and P-SEA, called SKSP, improves assignments over the best single
method in each benchmark by an additional 1%. These results support the usefulness of the
sequence alignment benchmarks as the benchmarks for secondary structure assignment.

1.

2.

3.
)
4.

5.

6.
7.

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8.

9.

10.

11.

Exciting
Remarkable Exciting
Remarkable

The Science of Scientific Writing by G. D. Gopen and J. A. Swan,
American Scientist, 78, 550-558, 1990. Gopen 1995
Martin Karplus()George Stell (
), Harold L. Friedman () Carol Hall ()

[1] G. D. Gopen and J. A. Swan, American Scientist, 78, 550-558 (1990)

[2] H. Zhou and Y. Zhou, Bioinformatics 21, 3615--3621 (2005).
[3] W. Zhang, K. Dunker, and Y. Zhou, Proteins, in press (2007).
[4] Y. Zhou, C. K. Hall, and M. Karplus, Phys. Rev. Lett. 77 , 2822 (1996).

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Fengyunhon

http://www.soudoc.com/bbs/read.php?tid-8489311.html
YOU AND YOUR RESEARCH - RICHARD HAMMING

run-of-mill

Shannon

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Los Alamos Los

Alamos National Laboratory 1943

Feynman1965 Fermi
TellerOppenheimer1902-1967,
Hans Bethe,1906-2005,, 1967

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Bode
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The particular thing you do is luck,but that

you do something is not

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12 14

local maximum

local maximum 12 14 -

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Bill Pfann
zone melting

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John Pierce
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!
-

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disgustingly young

May
Brattain,, 1956
Arnold ArnoldAuditorium

Shannoninformation
theoryingot
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ingot
sterilize you

superbonly good

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Grace HopperGrace Murray Hopper

, COBOL

-
JohnTukey
1973
10
John Tukey
John Bode
John Tukey

Bode compound interest

Bod
e

99% 1%

didn
t have so much to show for itit must be applied sensibly

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there
it is!

,andtheres the answer.

-you keep your thoughts on the

problem

Alan Chynoweth

Shockley1956
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en Mckay

Dave McCall

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John Tukey

AT&T

Los Alamos
Berkeley

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people who work with the door open or the door close

10

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digital computer
Hamming

Hammings method of Integrating Differential Equiations

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IBM

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loaned

BSTJThe Bell System TechnicalJournal.

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John Tukey
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Murray Hill
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Not that you shouldnt occasionally!


Murray Hill

Barney Oliver, SETI HP

IEEEInstitute of Electrical and ElectronicsEngineers
IEEE
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a
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10
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what was a defect became an asset

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Hamming

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criticalmass

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John Pierce


Ed Gilbert

Hamming
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HammingHamming windowTukey
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17 340


20

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Hamming

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