bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solubilization of C60 by micellization with a thermoresponsive block copolymer in water: Characterization, singlet oxygen generation, and DNA photocleavage
Authors: Yusa Shin‐Ichi , Awa Shigeki , Ito Masanori , Kawase Takeshi , Takada Tadao , Nakashima Kenichi , Liu Dian , Yamago Shigeru , Morishima Yotaro 
Published: April 2011

AbstractWater‐soluble diblock copolymer, poly(N‐isopropylacrylamide)‐block‐poly(N‐vinyl‐2‐pyrroridone) (PNIPAMm‐b‐PNVPn), was found to associate with fullerene (C60), and thus C60 can be solubilized in water. The 63C60/PNIPAMm‐b‐PNVPn micelle formed a core‐shell micelle‐like aggregate comprising a C60/PNVP hydrophobic core and a thermoresponsive PNIPAM shell. The C60‐containing polymer micelle formation and its thermoresponsive behavior were characterized using light scattering and 1H NMR techniques. The hydrodynamic radius (Rh) of the C60‐bound polymer micelle increased with increasing temperature, which was ascribed to the hydrophobic association between dehydrated PNIPAM shells above lower critical solution temperature (LCST). 1H NMR data suggest that the motion of the PNIPAM block is restricted above LCST due to the dehydration of the PNIPAM shell in water. The generation of singlet oxygen by photosensitization by the C60‐bound polymer micelle was confirmed from photooxidation of 9,10‐anthracenedipropionic acid. Furthermore, DNA was found to be cleaved by visible light irradiation in the presence of the C60‐bound polymer micelle. Therefore, there may be a hope for a pharmaceutical application of the C60‐bound polymer micelle to cancer photodynamic therapy. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.
Statistical analysis of protein structures suggests that buried ionizable residues in proteins are hydrogen bonded or form salt bridges
Authors: Bush Jeffrey , Makhatadze George I. 
Published: April 2011

AbstractIt is well known that nonpolar residues are largely buried in the interior of proteins, whereas polar and ionizable residues tend to be more localized on the protein surface where they are solvent exposed. Such a distribution of residues between surface and interior is well understood from a thermodynamic point: nonpolar side chains are excluded from the contact with the solvent water, whereas polar and ionizable groups have favorable interactions with the water and thus are preferred at the protein surface. However, there is an increasing amount of information suggesting that polar and ionizable residues do occur in the protein core, including at positions that have no known functional importance. This is inconsistent with the observations that dehydration of polar and in particular ionizable groups is very energetically unfavorable. To resolve this, we performed a detailed analysis of the distribution of fractional burial of polar and ionizable residues using a large set of ˜2600 nonhomologous protein structures. We show that when ionizable residues are fully buried, the vast majority of them form hydrogen bonds and/or salt bridges with other polar/ionizable groups. This observation resolves an apparent contradiction: the energetic penalty of dehydration of polar/ionizable groups is paid off by favorable energy of hydrogen bonding and/or salt bridge formation in the protein interior. Our conclusion agrees well with the previous findings based on the continuum models for electrostatic interactions in proteins. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Protein–protein interactions: Analysis of a false positive GST pulldown result
Authors: Wissmueller Sandra , Font Josep , Liew Chu Wai , Cram Edward , Schroeder Thilo , Turner Jeremy , Crossley Merlin , Mackay Joel P. , Matthews Jacqueline M. 
Published: April 2011

AbstractOne of the most common ways to demonstrate a direct protein–protein interaction in vitro is the glutathione‐S‐transferse (GST)‐pulldown. Here we report the detailed characterization of a putative interaction between two transcription factor proteins, GATA‐1 and Krüppel‐like factor 3 (KLF3/BKLF) that show robust interactions in GST‐pulldown experiments. Attempts to map the interaction interface of GATA‐1 on KLF3 using a mutagenic screening approach did not yield a contiguous binding face on KLF3, suggesting that the interaction might be non‐specific. NMR experiments showed that the proteins do not interact at protein concentrations of 50–100 μM. Rather, the GST tag can cause part of KLF3 to misfold. In addition to misfolding, the fact that both proteins are DNA‐binding domains appears to introduce binding artifacts (possibly nucleic acid bridging) that cannot be resolved by the addition of nucleases or ethidium bromide (EtBr). This study emphasizes the need for caution in relying on GST‐pulldown results and related methods, without convincing confirmation from different approaches. Proteins 2011; © 2011 Wiley‐Liss, Inc.
A machine learning approach for the prediction of protein surface loop flexibility
Authors: Hwang Howook , Vreven Thom , Whitfield Troy W. , Wiehe Kevin , Weng Zhiping 
Published: April 2011

AbstractProteins often undergo conformational changes when binding to each other. A major fraction of backbone conformational changes involves motion on the protein surface, particularly in loops. Accounting for the motion of protein surface loops represents a challenge for protein–protein docking algorithms. A first step in addressing this challenge is to distinguish protein surface loops that are likely to undergo backbone conformational changes upon protein–protein binding (mobile loops) from those that are not (stationary loops). In this study, we developed a machine learning strategy based on support vector machines (SVMs). Our SVM uses three features of loop residues in the unbound protein structures—Ramachandran angles, crystallographic B‐factors, and relative accessible surface area—to distinguish mobile loops from stationary ones. This method yields an average prediction accuracy of 75.3% compared with a random prediction accuracy of 50%, and an average of 0.79 area under the receiver operating characteristic (ROC) curve using cross‐validation. Testing the method on an independent dataset, we obtained a prediction accuracy of 70.5%. Finally, we applied the method to 11 complexes that involve members from the Ras superfamily and achieved prediction accuracy of 92.8% for the Ras superfamily proteins and 74.4% for their binding partners. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Efficient mapping of ligand migration channel networks in dynamic proteins
Authors: Lin Tu‐Liang , Song Guang 
Published: April 2011

AbstractFor many proteins such as myoglobin, the binding site lies in the interior, and there is no obvious route from the exterior to the binding site in the average structure. Although computer simulations for a limited number of proteins have found some transiently open channels, it is not clear if there exist more channels elsewhere or how the channels are regulated. A systematic approach that can map out the whole ligand migration channel network is lacking. Ligand migration in a dynamic protein resembles closely a well‐studied problem in robotics, namely, the navigation of a mobile robot in a dynamic environment. In this work, we present a novel robotic motion planning inspired approach that can map the ligand migration channel network in a dynamic protein. The method combines an efficient spatial mapping of protein inner space with a temporal exploration of protein structural heterogeneity, which is represented by a structure ensemble. The spatial mapping of each conformation in the ensemble produces a partial map of protein inner cavities and their inter‐connectivity. These maps are then merged to form a super map that contains all the channels that open dynamically. Results on the pathways in myoglobin for gaseous ligands demonstrate the efficiency of our approach in mapping the ligand migration channel networks. The results, obtained in a significantly less amount of time than trajectory‐based approaches, are in agreement with previous simulation results. Additionally, the method clearly illustrates how and what conformational changes open or close a channel. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Optical monitoring of nonequilibrium carrier diffusion in single crystalline CVD and HPHT diamonds under high optical excitation
Authors: Ščajev P. , Malinauskas T. , Lubys L. , Ivakin E. , Nesladek M. , Haenen K. , Jarašiūnas K. 
Published: April 2011

AbstractWe report on a novel approach for the contactless, all‐optical study of ambipolar carrier diffusion in single‐crystalline diamond layers. Using interband two‐photon and single photon absorption (at 351 nm and 213 nm), we created a spatially‐modulated free‐carrier light‐induced transient grating and monitored the in‐plane carrier diffusion in a wide range of injected carrier densities (1015cm–3 to 1018cm–3) and temperatures (80 K to 800 K). A drastic decrease of the ambipolar diffusion coefficient from ∼50 cm2/s at low injections to 6–10 cm2/s at high ones was observed at room temperature and even stronger at lower temperatures. The modelling based on bandgap renormalization and electron–hole scattering provided a fit to the injection‐dependent diffusivity. The determined low‐injection ambipolar mobility data for CVD layer were found in a good agreement with electrical time‐of‐flight measurements. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Intravascular catheter navigation using path planning and virtual visual feedback for oral cancer treatment
Authors: Wang Junchen , Ohya Takashi , Liao Hongen , Sakuma Ichiro , Wang Tianmiao , Tohnai Iwai , Iwai Toshinori 
Published: April 2011

AbstractBackgroundIt is tedious and difficult to position a flexible catheter in a target vessel branch within complicated‐shaped vessels owing to the lack of real‐time visual feedback. Digital subtraction angiography and fluoroscopic guidance are currently used for catheter placement.MethodsThe proposed method employs an electromagnetic (EM) tracking system to track a sensor‐attached catheter. Vessel centerlines are extracted from the CT angiography image, based on which a navigational information tree is built to facilitate catheter manipulation. A virtual endoscopy technique is adopted to generate virtual intravascular video as visual feedback. Unscented Kalman filtering based image registration is performed to align the EM tracker frame with the anatomical atlas and to envision the target registration error.ResultsPreliminary experimental results showed the feasibility and effectiveness of the new method, with navigation accuracy of 1.80 ± 0.85 mm.ConclusionsThe proposed method can provide continuous virtual visual feedback to facilitate catheter placement and has the potential for clinical use, with significant reduction in X‐ray radiation exposure and doses of contrast agents. Copyright © 2011 John Wiley & Sons, Ltd.
An approach for testing pointcut descriptors in AspectJ
Authors: Delamare Romain , Baudry Benoit , Ghosh Sudipto , Gupta Shashank , Le Traon Yves 
Published: April 2011

AbstractAspect‐oriented programming (AOP) promises better software quality through enhanced modularity. Crosscutting concerns are encapsulated in separate units called aspects and are introduced at specific points in the base program at compile time or runtime. However, aspect‐oriented mechanisms also introduce new risks for reliability that must be tackled by specific testing techniques in order to fully benefit from the use of AOP. This paper focuses on the pointcut descriptor (PCD) that declares the set of points in the base program's execution where the crosscutting concern must be woven. A fault in the PCD can have a ripple effect and result in many different faults. New behavior may be added in unexpected places, or places where new behavior should be added may be missed. When implementing aspect‐oriented programs with AspectJ, JUnit is most commonly used to test the program. However, JUnit does not offer any mechanism to look for faults specifically located in the PCD. As a consequence, these faults can be detected only through complex test scenarios and side effects that are difficult to trigger and observe. This paper proposes to monitor the execution of advices in an aspect‐oriented program and use this information to build test cases that target faults in PCDs. The AdviceTracer tool has been developed to automatically monitor and store all information related to advice executions. It also offers a set of operations that can be used to check the presence or absence of advices at specific points in the execution. These operations improve the definition of an oracle for PCD test cases. An empirical study is performed to compare JUnit and AdviceTracer for testing PCDs in terms of the complexity of test cases and their ability to detect faults. The study is performed on a Healthwatcher system that has 93 classes and 19 PCDs. It reveals that test cases that use AdviceTracer to test PCDs are easier to write (shorter test cases and written in less time than with JUnit) and detect more faults. Copyright © 2011 John Wiley & Sons, Ltd.
Evolution and personal religious belief: Christian university biology‐related majors' search for reconciliation
Authors: Winslow Mark W. , Staver John R. , Scharmann Lawrence C. 
Published: April 2011

AbstractThe goal of this study was to explore Christian biology‐related majors' perceptions of conflicts between evolution and their religious beliefs. This naturalistic study utilized a case study design of 15 undergraduate biology‐related majors at or recent biology‐related graduates from a mid‐western Christian university. The broad sources of data were interviews, course documents, and observations. Outcomes indicate that most participants were raised to believe in creationism, but came to accept evolution through evaluating evidence for evolution, negotiating the literalness of Genesis, recognizing evolution as a non‐salvation issue, and observing professors as Christian role models who accept evolution. This study lends heuristic insight to researchers and educators seeking to understand the complex processes by which Christian biology‐related majors approach learning about evolution. © 2011 Wiley Periodicals, Inc. J Res Sci Teach 48: 1026–1049, 2011
Laser-induced fluorescence spectroscopy of
and absolute density calibration by Rayleigh scattering in capacitively coupled rf discharges
Authors: Nemschokmichal S , Bernhardt F , Krames B , Meichsner J 
Published: April 2011

Laser-induced fluorescence spectroscopy (LIF) was applied to measure absolute densities of the first metastable
state in capacitively coupled rf discharges at 13.56 MHz. The metastable state was transferred to the B
3Πg, v = 3 state with a dye laser at 687.44 nm and the fluorescence of the transition to the
state was observed at 762 nm. The time-depending LIF signal was investigated and the effective lifetime of the B
3Πg, v = 3 state was determined by eliminating the delay due to the photomultiplier circuit. The absolute density calibration was done by comparison with Rayleigh scattering at the laser wavelength of 687 nm. Therewith, axial density profiles were measured and their dependence on pressure and power was investigated. The metastable densities vary between 1012 and 1013 cm−3 for pressures from 40 to 1000 Pa. Furthermore, small amounts of oxygen (0.5–2%) were added and the influence on the metastable density is discussed.
A NAIVE BAYES SOURCE CLASSIFIER FOR X-RAY SOURCES
Authors: Broos Patrick S. , Getman Konstantin V. , Povich Matthew S. , Townsley Leisa K. , Feigelson Eric D. , Garmire Gordon P. 
Published: April 2011

ABSTRACT
The Chandra Carina Complex Project (CCCP) provides a sensitive
X-ray survey of a nearby starburst region over >1 deg2 in extent.
Thousands of faint X-ray sources are found, many concentrated into rich young
stellar clusters. However, significant contamination from unrelated Galactic and
extragalactic sources is present in the X-ray catalog. We describe the use of a
naive Bayes classifier to assign membership probabilities to individual sources,
based on source location, X-ray properties, and visual/infrared properties. For
the particular membership decision rule adopted, 75% of CCCP sources are
classified as members, 11% are classified as contaminants, and 14% remain
unclassified. The resulting sample of stars likely to be Carina members is used
in several other studies, which appear in this special issue devoted to the
CCCP.
GLOBAL X-RAY PROPERTIES OF THE O AND B STARS IN
CARINA
Authors: Nazé Y. , Broos P. S. , Oskinova L. , Townsley L. K. , Cohen D. , Corcoran M. F. , Evans N. R. , Gagné M. , Moffat A. F. J. , Pittard J. M. , Rauw G. , ud-Doula A. , Walborn N. R. 
Published: April 2011

ABSTRACT
The key empirical property of the X-ray emission from O stars is a strong
correlation between the bolometric and X-ray luminosities. In the framework of
the Chandra Carina Complex Project, 129 O and B stars have been
detected as X-ray sources; 78 of those, all with spectral type earlier than B3,
have enough counts for at least a rough X-ray spectral characterization. This
leads to an estimate of the
L
X–L
BOL ratio for an
exceptional number of 60 O stars belonging to the same region and triples the
number of Carina massive stars studied spectroscopically in X-rays. The derived
log(L
X/L
BOL) is
−7.26 for single objects, with a dispersion of only 0.21 dex. Using the
properties of hot massive stars listed in the literature, we compare the X-ray
luminosities of different types of objects. In the case of O stars, the
L
X–L
BOL ratios are
similar for bright and faint objects, as well as for stars of different
luminosity classes or spectral types. Binaries appear only slightly harder and
slightly more luminous in X-rays than single objects; the differences are not
formally significant (at the 1% level), except for the
L
X–L
BOL ratio in the
medium (1.0–2.5 keV) energy band. Weak-wind objects have similar X-ray
luminosities but they display slightly softer spectra compared with “normal” O
stars with the same bolometric luminosity. Discarding three overluminous
objects, we find a very shallow trend of harder emission in brighter objects.
The properties of the few B stars bright enough to yield some spectral
information appear to be different overall (constant X-ray luminosities, harder
spectra), hinting that another mechanism for producing X-rays, besides wind
shocks, might be at work. However, it must be stressed that the earliest and
X-ray brightest among these few detected objects are similar to the latest O
stars, suggesting a possibly smooth transition between the two processes.
X-RAY STAR CLUSTERS IN THE CARINA COMPLEX
Authors: Feigelson Eric D. , Getman Konstantin V. , Townsley Leisa K. , Broos Patrick S. , Povich Matthew S. , Garmire Gordon P. , King Robert R. , Montmerle Thierry , Preibisch Thomas , Smith Nathan , Stassun Keivan G. , Wang Junfeng , Wolk Scott , Zinnecker Hans 
Published: April 2011

ABSTRACT
The distribution of young stars found in the Chandra Carina
Complex Project (CCCP) is examined for clustering structure. X-ray surveys are
advantageous for identifying young stellar populations compared to optical and
infrared surveys in suffering less contamination from nebular emission and
Galactic field stars. The analysis is based on smoothed maps of a spatially
complete subsample of ∼3000 brighter X-ray sources classified as Carina members
and ∼10,000 stars from the full CCCP sample. The principal known clusters are
recovered, and some additional smaller groups are identified. No rich embedded
clusters are present, although a number of sparse groups are found. The CCCP
reveals considerable complexity in clustering properties. The Trumpler 14 and 15
clusters have rich stellar populations in unimodal, centrally concentrated
structures several parsecs across. Non-spherical internal structure is seen, and
large-scale low surface density distributions surround these rich clusters.
Trumpler 16, in contrast, is comprised of several smaller clusters within a
circular boundary. Collinder 228 is a third type of cluster which extends over
tens of parsecs with many sparse compact groups likely arising from triggered
star formation processes. A widely dispersed, but highly populous, distribution
of X-ray stars across the ∼50 pc CCCP mosaic supports a model of past
generations of star formation in the region. Collinder 234, a group of massive
stars without an associated cluster of pre-main-sequence stars, may be part of
this dispersed population.
2-adic properties of modular functions associated to Fermat curves
Authors: Kazalicki Matija 
Published: April 2011

For an odd integer

N
N

, we study the action of Atkin’s

U
(
2
)

U(2)

-operator on the modular function

x
(
τ
)

x(\tau )

associated to the Fermat curve:

X
N

+

Y
N

=
1

X^N+Y^N=1

. The function

x
(
τ
)

x(\tau )

is modular for the Fermat group

Φ
(
N
)

\Phi (N)

, generically a noncongruence subgroup. If

x
(
τ
)
=

q

−
1

+

∑

i
=
1

∞

a
(
i
N
−
1
)

q

i
N
−
1

x(\tau )=q^{-1}+\sum _{i=1}^\infty a(iN-1)q^{iN-1}

, we essentially prove that

lim

n
→
0

a
(
n
)
=
0

\lim _{n \rightarrow 0}a(n)=0

in the

2
2

-adic topology.
Inspiratory Oxygen Fraction and Postoperative Complications in Obese Patients
Authors: Stæhr Anne K. , Meyhoff Christian S. , Rasmussen Lars S. 
Published: April 2011

Background
Obese patients are at a high risk of postoperative complication, including surgical site infection (SSI). Our aim was to evaluate the effect of a high inspiratory oxygen fraction (80%) on SSI and pulmonary complications in obese patients undergoing laparotomy.

Methods
This study was a planned analysis of the obese patients (body mass index ≥ 30 kg/m²) recruited in the Danish multicenter, patient- and observer-blinded, PROXI Trial of 1,400 patients undergoing acute or elective laparotomy. Patients were randomized to receive either 80% or 30% oxygen during and for 2 h after surgery. The primary outcome was SSI within 14 days. Secondary outcomes were atelectasis, pneumonia, and respiratory failure.

Results
Two hundred thirteen patients had a body mass index ≥ 30 kg/m². The median (5-95% range) body mass index was 34 kg/m² (30-44) and 33 kg/m² (30-41) in patients allocated to the 80% and 30% oxygen group. SSI occurred in 32 of 102 (31%) versus 29 of 111 (26%) patients given 80% and 30% oxygen, respectively (odds ratio, 1.29; 95% CI, 0.71-2.34; P = 0.40). In addition, the incidence of pulmonary complications was not significantly different, with atelectasis occurring in 9% versus 6%, pneumonia in 6% versus 5%, and respiratory failure in 8% versus 5% in patients given 80% and 30% oxygen, respectively.

Conclusion
Administration of 80% oxygen, compared with 30% oxygen, did not reduce the frequency of SSI in obese patients. Moreover, no significant association was found between oxygen fraction and the risk of pulmonary complications.