bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of oncogenic human papillomavirus RNA and DNA tests with liquid‐based cytology in primary cervical cancer screening: The FASE study
Authors: Monsonego Joseph , Hudgens Michael G. , Zerat Laurent , Zerat Jean‐Claude , Syrjänen Kari , Halfon Philippe , Ruiz Fabrice , Smith Jennifer S. 
Published: October 2010

AbstractThe APTIMA® HPV Assay (AHPV) allows detection of 14 high‐risk human papillomavirus (HPV) RNA types in cervical specimens. Until present, the assay has been compared to HPV DNA tests only in triage settings. Herein, we compare AHPV with a DNA assay (Hybrid Capture® 2; HC2) and liquid‐based cytology (LBC; using PreservCyt® ThinPrep liquid Pap) in a screening setting (French APTIMA screening evaluation [FASE] study). Women (N = 5,006) aged 20–65 were screened by gynecologists in 17 private practices in Paris, France. One cervical specimen was collected and tested with LBC, AHPV and HC2 assays. Women were referred to colposcopy if they were ASC‐US+ in LBC or HPV positive in either HPV assay. To control for verification bias, a random group (14%) with normal LBC and dually HPV negative tests underwent colposcopy. Data from 4,429 women were analyzed. Sensitivity, specificity and predictive values were calculated for the three tests. AHPV and HC2 were highly sensitive for CIN2+ (92.0% and 96.7%) and CIN3+ (95.7% and 95.3%) detection and much more sensitive than LBC (69.1% for CIN2+ and 73.3% for CIN3+). Specificity of AHPV was higher than that of HC2, but similar to that of LBC (p < 0.001). Combining LBC with either HPV test slightly increased sensitivity but compromised specificity. AHPV assay is both specific and sensitive for the detection of high‐grade precancerous lesions and may be considered as an option for routine cervical cancer screening for women over 20 years of age.
A simple, flexible estimator for count and other ordered discrete data
Authors: Mroz Thomas A. 
Published: October 2010

SUMMARYThis paper examines a flexible way to model empirically discrete data outcomes using ‘hazard rate’ decompositions. It presents a general data‐generating mechanism based on potential outcomes to describe why the approach should work for almost any discrete distribution. Monte Carlo evidence indicates that these models estimate well the impacts of covariates on expected counts when the data follow a Poisson distribution. With data from more complex processes, these estimators continue to perform well. Since most economic count outcomes arise from occurrence‐dependent behavioral processes, using flexibly estimated distributions should reduce the dependence of results on convenient but invalid assumptions. Copyright © 2010 John Wiley & Sons, Ltd.
Extremely localized nonorthogonal orbitals by the pairing theorem
Authors: Zoboki T. , Mayer I. 
Published: October 2010

AbstractUsing the concepts of Löwdin pairing theorem, a method is developed to calculate extremely localized, but nonorthogonal, sets of molecular orbitals and their strictly localized counterparts. The method is very suitable to study to what extent a given model of bonding in a given molecule can be considered adequate from the point of view of the actual LCAO‐MO (Hartree Fock or DFT) wave function and is expected to be useful for doing local approximations of electron correlation. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010.
The first branching point in porphyrin biosynthesis: A systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen‐III decarboxylase
Authors: Bushnell Eric A. C. , Erdtman Edvin , Llano Jorge , Eriksson Leif A. , Gauld James W. 
Published: October 2010

AbstractIn humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen‐III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen‐III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate‐limiting step was found to be the initial proton transfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various active site residues as well as several other functional groups. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.
The opsin shift and mechanism of spectral tuning in rhodopsin
Authors: Rajamani Ramkumar , Lin Yen‐Lin , Gao Jiali 
Published: October 2010

AbstractMolecular dynamics simulations and combined quantum mechanical and molecular mechanical calculations have been performed to investigate the mechanism of the opsin shift and spectral tuning in rhodopsin. A red shift of −980 cm−1 was estimated in the transfer of the chromophore from methanol solution environment to the protonated Schiff base (PSB)‐binding site of the opsin. The conformational change from a 6‐s‐cis‐all‐trans configuration in solution to the 6‐s‐cis‐11‐cis conformer contributes additional −200 cm−1, and the remaining effects were attributed to dispersion interactions with the aromatic residues in the binding site. An opsin shift of 2100 cm−1 was obtained, in reasonable accord with experiment (2730 cm−1). Dynamics simulations revealed that the 6‐s‐cis bond can occupy two main conformations for the β‐ionone ring, resulting in a weighted average dihedral angle of about −50°, which may be compared with the experimental estimate of −28° from solid‐state NMR and Raman data. We investigated a series of four single mutations, including E113D, A292S, T118A, and A269T, which are located near the PSB, along the polyene chain of retinal and close to the ionone ring. The computational results on absorption energy shift provided insights into the mechanism of spectral tuning, which involves all means of electronic structural effects, including the stabilization or destabilization of either the ground or the electronically excited state of the retinal PSB. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.
Theoretical study on phosphorescence efficiency and color tuning from orange to blue‐green of Ir(III) complexes based on substituted 2‐phenylimidazo[1,2‐a]pyridine ligand
Authors: Li Xiao‐Na , Wu Zhi‐Jian , Li Xi‐Yan , Zhang Hong‐Jie , Liu Xiao‐Juan 
Published: October 2010

AbstractThe geometrical structures, phosphorescence quantum yields, and electroluminescence (EL) efficiency of six iridium(III) complexes containing 2‐phenylimidazo[1,2‐a]pyridine ligand are investigated by density functional theory (DFT), which show a wide color tuning of photoluminescence from orange (λem = 550 nm) to blue‐green (λem = 490 nm). The calculated results shed some light on the reasons of the remarkably manipulated excited‐state and EL properties through substitution effect. The Mulliken charge calculation reveals that attached CF3 groups on phenyl and imidazo[1,2‐a]pyridine (impy) moieties (4) can make both of them as electron‐deficient region, which will lead to the contraction of the whole coordination sphere and strengthen the metal–ligand interaction. While attaching two CF3 groups on phenyl ring can make it more electron‐deficient, which will induce electron transferring from acac and impy fragment to phenyl ring, and also result in the contracted structure. The largest metal‐to‐ligand charge transfer (3MLCT) character and the smaller S1–T1 energy gap (ΔES1−T1) value increase the emission quantum yields of 4 and 6 than other complexes. For EL efficiency, because of the similar highest occupied molecular orbital (HOMO) levels of 4 and 6 to that of holes injection material poly(N‐vinylcarbazole) (PVK) and the larger dipole moments, majority hole will be accumulated on the HOMO of 4 and 6. Combination with the lower lowest unoccupied molecular orbital energy levels compared with PVK, the recombination zones of 4 and 6 can be well confined within emitting material layer (EML) and lead to the higher EL efficiency. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.
Carotid plaque assessment using fast 3D isotropic resolution black‐blood MRI
Authors: Balu Niranjan , Yarnykh Vasily L. , Chu Baocheng , Wang Jinnan , Hatsukami Thomas , Yuan Chun 
Published: October 2010

AbstractBlack‐blood MRI is a promising tool for carotid atherosclerotic plaque burden assessment and compositional analysis. However, current sequences are limited by large slice thickness. Accuracy of measurement can be improved by moving to isotropic imaging but can be challenging for patient compliance due to long scan times. We present a fast isotropic high spatial resolution (0.7 × 0.7 × 0.7 mm3) three‐dimensional black‐blood sequence (3D‐MERGE) covering the entire cervical carotid arteries within 2 min thus ensuring patient compliance and diagnostic image quality. The sequence is optimized for vessel wall imaging of the carotid bifurcation based on its signal properties. The optimized sequence is validated on patients with significant carotid plaque. Quantitative plaque morphology measurements and signal‐to‐noise ratio measures show that 3D‐MERGE provides good blood suppression and comparable plaque burden measurements to existing MRI protocols. 3D‐MERGE is a promising new tool for fast and accurate plaque burden assessment in patients with atherosclerotic plaque. Magn Reson Med, 2011. © 2010 Wiley‐Liss, Inc.
Detecting blood–brain barrier disruption within minimal hemorrhage following transcranial focused ultrasound: A correlation study with contrast‐enhanced MRI
Authors: Weng Jun‐Cheng , Wu Sheng‐Kai , Lin Win‐Li , Tseng Wen‐Yih I. 
Published: October 2010

AbstractFocused ultrasound combined with an intravascular ultrasound contrast agent can induce transient disruption of the blood–brain barrier, and the blood–brain barrier disruption can be detected by contrast‐enhanced MRI. There is, however, no study investigating the ability of various MR methods to detect focused ultrasound–induced blood–brain barrier disruption within minimal hemorrhage. Sonication was applied to 15 rat brains with four different doses of ultrasound contrast agent (0, 10, 30, or 50 μL/kg), and contrast‐enhanced T1‐weighted spin echo, gradient echo images, and longitudinal relaxation rate mapping along with effective transverse relaxation time–weighted and susceptibility‐weighted images were acquired. Volume‐of‐interest–based and threshold‐based analyses were performed to quantify the contrast enhancement, which was then correlated with the ultrasound contrast agent dose and with the amount of Evans blue extravasation. Both effective transverse relaxation time–weighted and susceptibility‐weighted images did not detect histology‐proved intracranial hemorrhage at 10 μL/kg, but MRI failed to detect mild intracranial hemorrhage at 30 μL/kg. All tested sequences showed detectable contrast enhancement increasing with ultrasound contrast agent dose. In correlating with Evans blue extravasation, the gradient echo sequence was slightly better than the spin echo sequence and was comparable to longitudinal relaxation rate mapping. In conclusion, both gradient echo and spin echo sequences were all reliable in indicating the degree of focused ultrasound–induced blood–brain barrier disruption within minimal hemorrhage. Magn Reson Med, 2011. © 2010 Wiley‐Liss, Inc.
The experiences of pregnancy in women with SSA/Ro52 autoantibodies
Authors: Tingström Joanna , Barimani Mia , Sonesson Sven‐Erik , Wahren‐Herlenius Marie , Henriksson Elisabet Welin 
Published: October 2010

AbstractObjective: Congenital heart block may develop in the foetus during pregnancy in SSA/Ro52 autoantibody‐positive women. The aim of this study was to investigate how women with SSA/Ro52 autoantibodies experience their pregnancy in terms of the risk of developing foetal heart block, and in undergoing serial ultrasound Doppler echocardiography to detect early signs of congenital heart block.Methods: Data were collected through individual semi‐structured interviews with SSA/Ro52‐positive women post‐pregnancy (n = 14). The interviews were audio‐taped, transcribed verbatim and analysed according to qualitative content analysis.Results: Three categories emerged from the responses: information, emotional response and support. The information received prior to and during early pregnancy was focused on the need for attending a specialized antenatal clinic, and information on the risk for congenital heart block was scarce or missing. During gestational weeks 18–24, when the ultrasound/Doppler examinations were performed, all women described increased stress. However, the interaction with the caregivers made the women feel more safe and secure. Several women also said that they did not emotionally acknowledge the pregnancy until after gestational week 24. None had been offered psychological support.Conclusion: There is a need for structured information and organized programmes for the surveillance of women who are SSA/Ro52 positive during their pregnancy. Further, offering psychological support to the women and their families to manage the stress and to facilitate the early attachment to the child should be considered. Copyright © 2010 John Wiley & Sons, Ltd.
Structure and DNA‐binding activity of the Pyrococcus furiosus SMC protein hinge domain
Authors: Griese Julia J. , Hopfner Karl‐Peter 
Published: October 2010

AbstractStructural Maintenance of Chromosomes (SMC) proteins are essential for a wide range of processes including chromosome structure and dynamics, gene regulation, and DNA repair. While bacteria and archaea have one SMC protein that forms a homodimer, eukaryotes possess three distinct SMC complexes, consisting of heterodimeric pairs of six different SMC proteins. SMC holocomplexes additionally contain several specific regulatory subunits. The bacterial SMC complex is required for chromosome condensation and segregation. In eukaryotes, this function is carried out by the condensin (SMC2–SMC4) complex. SMC proteins consist of N‐terminal and C‐terminal domains that fold back onto each other to create an ATPase “head” domain, connected to a central “hinge” domain via a long coiled‐coil region. The hinge domain mediates dimerization of SMC proteins and binds DNA. This activity implicates a direct involvement of the hinge domain in the action of SMC proteins on DNA. We studied the SMC hinge domain from the thermophilic archaeon Pyrococcus furiosus. Its crystal structure shows that the SMC hinge domain fold is largely conserved between archaea and bacteria as well as eukarya. Like the eukaryotic condensin hinge domain, the P. furiosus SMC hinge domain preferentially binds single‐stranded DNA (ssDNA), but its affinity for DNA is weaker than that of its eukaryotic counterpart, and point mutations reveal that its DNA‐binding surface is more confined. The ssDNA‐binding activity of its hinge domain might play a role in the DNA‐loading process of the prokaryotic SMC complex during replication. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Distinct interfacial biclique patterns between ssDNA‐binding proteins and those with dsDNAs
Authors: Zeng Tao , Li Jinyan , Liu Juan 
Published: October 2010

AbstractWe introduce a new motif called interfacial biclique pattern to study the difference between double‐stranded DNA‐binding proteins (DSBs, most of them also known to play the role as transcriptional factors) and single‐stranded DNA‐binding proteins (SSBs) which are found to involve in many applications recently. An interfacial biclique pattern in a protein‐DNA complex usually consists of a group of residues and a group of nucleotides such that every residue has a contact to all of the bases. The proposal of this idea is based on a biological redundancy mechanism that: a site mutation has little influence on the other residues to recognize the target nucleotides and vice versa. The distribution of the residues on the interfacial motifs is investigated to identify distinct stable preferred residues, stable un‐preferred residues and unstable preferred residues between SSBs and DSBs. We also examine residue co‐occurrence and residue‐base association rules in the interfacial motifs to uncover the different choices of residue combinations by SSBs and DSBs that have contacts with one or more bases. We found that DSBs and SSBs have their own right residues at the right places for the binding preference and association with nucleotides. Some of our results can be supported by literature work. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Compact conformations of α‐synuclein induced by alcohols and copper
Authors: Natalello Antonino , Benetti Federico , Doglia Silvia Maria , Legname Giuseppe , Grandori Rita 
Published: October 2010

AbstractThe intrinsically disordered protein α‐synuclein aggregates into amyloid fibrils, a process known to be implicated in several neurodegenerative states. Partially folded forms of the protein are thought to trigger the aggregation process. Here, α‐synuclein conformers are characterized by analysis of the charge‐state distributions observed in electrospray‐ionization mass spectrometry under negative‐ion mode. It is found that, even at neutral pH, a small fraction of the molecular population is in a compact conformation. Several distinct partially folded forms are then identified under conditions that promote α‐synuclein aggregation, such as solutions of simple and fluorinated alcohols. Specific intermediates accumulate at increasing concentrations of ethanol, hexafluoro‐2‐propanol, and trifluoroethanol. Finally, extensive folding induced by Cu2+ binding is revealed by titrations in the presence of Cu2+–glycine. The data confirm the existence of a single, high‐affinity binding site for Cu2+. Because accumulation of this partially folded form correlates with enhancement of fibrillation kinetics, it is likely to represent an amyloidogenic intermediate in α‐synuclein conformational transitions. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Hybrid organic–inorganic materials for integrated optoelectronic devices
Authors: Wehlus T. , Körner T. , Nowy S. , Frischeisen J. , Karl H. , Stritzker B. , Brütting W. 
Published: October 2010

AbstractA device containing a microcavity organic light‐emitting diode (OLED) and a magnetooptically active bismuth iron garnet (BIG) Bi3Fe5O12 waveguide combines a planar source for polarized light generation with the material exhibiting the highest known Faraday rotation at room temperature. To build such a device an optimization of garnets and OLEDs has to be done. For a good functionality of the device it is essential to maximize the light coupled from the OLED into the waveguide and to seperate s‐ and p‐polarized emitted light. To optimize the OLED emisson numerical simulations have been performed where material and thickness of the metal anode, as well as the thickness of the hole and the electron conducting layers were varied. The stacks with the best separation of s‐ and p‐polarized light and the highest coupling into the waveguide were determined, fabricated, and characterized regarding their electrical and optical properties. OLEDs have to be deposited on plane surfaces for exhibiting low leakage currents and thus being functional. In order to get plane and crack free BIG surfaces the garnet growth and surface formation were examined on various gadolinium gallium garnet (GGG) Gd3 Ga5 O12 and buffered non‐garnet substrates. GGG substrates with different cuts and lattice constants were characterized as well as yttrium iron garnet (YIG) Y3Fe5O12 and GGG buffered sapphire, silicon, and fused silica substrates. The garnet had to be structured to fabricate a planar waveguide. Therefore laser structuring and plasma etching techniques were utilized. The structured garnets were characterized regarding the wall roughness. The optical constants of YIG and BIG were determined from films deposited on silicon using ellipsometric measurements. The combination of microcavity OLED and garnet waveguide resulted in an integrated magnetooptical modulator whose functionality has been proven by applying an external magnetic field and measuring the rotation of the polarized light.
Geochemical implications of gabbro from the slow-spreading Northern Central Indian Ocean Ridge, Indian Ocean
Authors: RAY DWIJESH , MISRA SAUMITRA , BANERJEE RANADIP , WEIS DOMINIQUE 
Published: October 2010

AbstractGabbro samples (c. < 0.4 Ma old) dredged from close to the ‘Vityaz Megamullion’ on the slow-spreading Northern Central Indian Ridge (NCIR, 18–22 mm yr−1) include mostly olivine gabbro and Fe–Ti oxide gabbro. The cumulate olivine gabbro shows ophitic to subophitic texture with early formed plagioclase crystals in mutual contact with each other, and a narrow range of compositions of olivine (Fo80–81), clinopyroxene (magnesium number: 85–87) and plagioclase (An67–70). This olivine gabbro could be geochemically cogenetic with the evolved oxide gabbro. These gabbro samples are geochemically distinct from the CIR gabbro occurring along the Vema, Argo and Marie Celeste transform faults and can further be discriminated from the associated NCIR basalts by their clinopyroxene (augite in gabbro, and diopsidic in basalts) and olivine (gabbro: Fo80–81, basalts: Fo82–88) compositions. Our major oxide, trace element and REE geochemistry analyses suggest that the gabbro and the NCIR basalts are also not cogenetic and had experienced different trends of geochemical evolution. The clinopyroxenes of the present NCIR gabbros are geochemically similar to primitive melt that is in equilibrium with mantle peridotite, and do not show any poikilitic texture with resorbed plagioclase; these results negate the possibility of these gabbros being a pre-existing cumulate that has been brought up to the shallower oceanic crust and interacted with the NCIR basalt. The Sr, Pb and Nd isotopic data of the gabbro substantially differ from those of the NCIR basalts and suggest significant contamination of the depleted mantle source of the gabbro, most likely by the Indian Ocean pelagic sediments. The Pb-isotope data suggest that the proportion of pelagic sediment that mixed in the depleted mantle source of the NCIR gabbro is much higher than the level of contamination observed for the Indian Ocean MORBs.