bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of water clusters upon UV‐excitation leading to ionization: Nonempirical study
Authors: Novakovskaya Yulia V. 
Published: May 2007

AbstractNonempirical direct molecular dynamics of neutral and cationic water clusters involving four to six molecules is studied to shed light on the character of the ionization of water clusters. Potential energy and forces are calculated in the second‐order of the Møller‐Plesset perturbation theory with a 6–31++G(1d, 1p) basis set. Upon vertical ionization of a water cluster, H3O+ and OH fragments appear. The process needs no less than 40 fs, and in some cases, up to 100 or 150 fs. The resulting configuration of the cluster (neglecting its generally larger volume) is close to that obtained in the geometry optimization run. Vibrational excitation of a neutral cluster with a total energy about half its adiabatic ionization potential may promote the appearance of structures similar to that of the stable cation at certain moments in time. In particular, a configuration in which only one water molecule separates H3O+ and OH− fragments forms much faster than upon vertical electron detachment from a stable neutral cluster, in nearly 18 fs. Such structure reorganization is noticeably impeded by the rotational–vibrational excitation of the whole cluster, especially when hydrogen bonds are substantially distorted. The effect of distorting motions becomes very pronounced after 20 fs. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
THEMATICS analysis for functional ion channels
Authors: Shehadi Ihsan A. 
Published: May 2007

AbstractIon channels, as a group of integral membrane proteins, span the cell membrane forming ion‐conducting pores that allow ions to traverse the hydrophobic lipid environment rapidly and selectively. The structure of the Streptomyces lividians (KcsA) and Mycobacterium tuberculosis ion channel (Mscl) potassium ion channel have provided the impetus and has helped further the understanding of the structural and functional studies of these channels. The KcsA adapts the voltage‐gated mechanism for opening and closing of the channel. While Mcsl represents the mechanosensitive model of the channels. However, the mechanism of the opening and closing of these channels are not fully understood. Electrostatic methods (THEMATICS) are used to locate the site where closing and opening of the channels are controlled. Two clusters of amino acid residues are identified in each of the previously mentioned active models where net charges play an important role in controlling the mechanism of the opening and closure of the ion channels. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Neural networks to approach potential energy surfaces: Application to a molecular dynamics simulation
Authors: Latino Diogo A. R. S. , Freitas Filomena F. M. , Aires‐De‐Sousa João , Silva Fernandes Fernando M. S. 
Published: May 2007

AbstractPotential energy surfaces (PES) are crucial to the study of reactive and nonreactive chemical systems by Monte Carlo (MC) or molecular dynamics (MD) simulations. Ideally, PES should have the accuracy provided by ab initio calculations and be set up as fast as possible. Recently, neural networks (NNs) turned out as a suitable approach for estimating PES from ab initio/DFT energy datasets. However, the accuracy of the properties determined by MC and MD simulation methods from NNs surfaces has not yet, to our knowledge, been systematically analyzed in terms of the minimum number of energy points required for training and the usage of different NN‐types. The goal of this work is to train NNs for reproducing PES represented by well‐known analytical potential functions, and then to assess the accuracy of the method by comparing the simulation results obtained from NNs and analytical PES. Ensembles of feed‐forward neural networks (EnsFFNNs) and associative neural networks (ASNNs) are used to estimate the full energy surface. Training sets with different number of points, from 15 differently parameterized Lennard–Jones (LJ) potentials, are used and argon is taken to test the network. MD simulations have been performed using the tabular potential energies, predicted by NNs, for working out thermal, structural, and dynamic properties which are compared with the values obtained from the analytical function. Our results show that, at least for LJ‐type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Core‐ionized and core‐excited states of macromolecules
Authors: Loos Pierre‐François , Assfeld Xavier 
Published: May 2007

AbstractWe report the calculation of core‐ionized states of small organic compounds and macromolecular systems in the framework of a new method based on the local self‐consistent field (LSCF). This new theoretical scheme avoids the variational collapse of the empty core orbital (CO) of the core‐excited states and ensures the orthogonality between the ground state and the excited states. Compared to experimental data and other theoretical methods, accurate carbon 1s ionization energies using the Boys‐Foster (BF) localization criterion for the determination of the CO and the PBE0/6‐311++G**//B3LYP/6‐311++G** level of theory was obtained to calculate both the ground and excited states. The macromolecular systems, a sequence of 15 alanine amino acids in both α‐helix and β‐sheet conformations, are computed using hybrid quantum mechanics/molecular mechanics (QM/MM) method within the LSCF/MM framework. The results show a weak impact of the MM surrounding in the alanine polypeptides cases compared with that of previous studies based on electrically charged residue, such as glutamate in the crambin protein. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Phase Separation of Binary Blends in Polymer Nanoparticles
Authors: Kietzke Thomas , Neher Dieter , Kumke Michael , Ghazy Omayma , Ziener Ulrich , Landfester Katharina 
Published: May 2007

AbstractPolymer blends in nanoparticles have been studied by transmission electron microscopy (TEM) and photoluminescence (PL) spectroscopy. The TEM studies show that blend particles formed from two immiscible polymers by the miniemulsion process exhibit biphasic morphologies. The fact that no core–shell type but Janus‐like structures were found indicates that the surface free energies between both polymers and the solution–water interface (including the surfactant molecules) are similar; therefore, the blend morphology and composition of the individual phases are mainly determined by the interaction between the two polymer components. Both the TEM studies and the PL experiments provide strong evidence that phase separation in these particles strictly follows the Flory–Huggins theory. This highlights the applicability of the nanoparticle approach to fabricate blend systems with well‐controllable properties and to study structure–property relationships under well‐defined conditions.
NF‐κB responds to mechanical strains in osteoblast‐like cells, and lighter strains create an NF‐κB response more readily
Authors: Liu Jun , Zou Ling , Zheng Yi , Zhao Zhihe , Li Yu , Yang Pu , Luo Songjiao 
Published: May 2007

AbstractThis study was to examine the early responses of nuclear factor kappa B (NF‐κB) to mechanical strains in MG‐63. MG‐63 cells were subjected to cyclic uniaxial compressive or tensile strain, produced by a four‐point bending system, at 1000 μstrain or 4000 μstrain for 5 min, 15 min, 30 min and 1 h, respectively. Control cells received the same treatment with no mechanical stress loading. Expression of NF‐κB (p60) was measured by Western blotting. NF‐κB responded rapidly to mechanical stimuli in MG‐63 cells. NF‐κB was activated by cyclic uniaxial stretch at 1000 μstrain while it was restrained under a compressive strain environment at 1000 μstrain (P < 0.001). The effects reversed for tension and compression at 4000 μstrain (P < 0.001). Furthermore, strains at 1000 μstrain affected NF‐κB expression much easier than those at 4000 μstrain. This indicates that there may be different responding mechanisms or mechanotransduction pathways for different mechanical stimuli.
Maternal and neonatal outcomes of hospital vaginal deliveries in Tibet
Authors: Miller S. , Tudor C. , Nyima  , Thorsten V.R. , Sonam  , Droyoung  , Craig S. , Le P. , Wright L.L. , Varner M.W. 
Published: May 2007

AbstractIntroduction: To determine the outcomes of vaginal deliveries in three study hospitals in Lhasa, Tibet Autonomous Region (TAR), People's Republic of China (PRC), at high altitude (3650 m). Methods: Prospective observational study of 1121 vaginal deliveries. Results: Pre‐eclampsia/gestational hypertension (PE/GH) was the most common maternal complication 18.9% (n = 212), followed by postpartum hemorrhage (blood loss ≥ 500 ml) 13.4%. There were no maternal deaths. Neonatal complications included: low birth weight (10.2%), small for gestational age (13.7%), pre‐term delivery (4.1%) and low Apgar (3.7%). There were 11 stillbirths (9.8/1000 live births) and 19 early neonatal deaths (17/1000 live births). Conclusion: This is the largest study of maternal and newborn outcomes in Tibet. It provides information on the outcomes of institutional vaginal births among women delivering infants at high altitude. There was a higher incidence of PE/GH and low birth weight; rates of PPH were not increased compared to those at lower altitudes.
Sedimentology, stratigraphy, and glacier dynamics, western scottish Highlands
Authors: Golledge Nicholas R. 
Published: May 2007

AbstractGlacial sediments of the western Scottish Highlands are comprehensively described and characterized here for the first time, enabling the first glacial stratigraphy for the area to be proposed. This classification is based on the results of extensive geological mapping and field investigation of sedimentary sequences and their structures, X-ray diffraction and particle size distribution analyses, and comparison with deposits formed in contemporary glaciated environments. These new data are subsequently appraised in terms of their implications for late Pleistocene glacier evolution and dynamics. Together, the data suggest that much of the landscape is palimpsest, and can be attributed to the Weichselian (Late Devensian) glaciation. Subsequent glacier advance during the Younger Dryas did little to modify the area, suggesting that ice flow was dominated by sliding on a meltwater-lubricated rigid bed, with deformation of basal sediments playing a more limited role. Final deglaciation was marked by a significant increase in basal meltwater flux, reflecting the warming climate and increasing precipitation. These new palaeoglaciological and palaeoenvironmental insights advance our understanding of former glacier dynamics in the western Scottish Highlands, improve our knowledge of Pleistocene landscape evolution of this area, and enable comparisons to be made with sedimentary sequences elsewhere.
CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
Authors: Jakobsson Mattias , Rosenberg Noah A. 
Published: May 2007

Abstract
Motivation: Clustering of individuals into populations on the basis of multilocus genotypes is informative in a variety of settings. In population-genetic clustering algorithms, such as BAPS, STRUCTURE and TESS, individual multilocus genotypes are partitioned over a set of clusters, often using unsupervised approaches that involve stochastic simulation. As a result, replicate cluster analyses of the same data may produce several distinct solutions for estimated cluster membership coefficients, even though the same initial conditions were used. Major differences among clustering solutions have two main sources: (1) ‘label switching’ of clusters across replicates, caused by the arbitrary way in which clusters in an unsupervised analysis are labeled, and (2) ‘genuine multimodality,’ truly distinct solutions across replicates.
Results: To facilitate the interpretation of population-genetic clustering results, we describe three algorithms for aligning multiple replicate analyses of the same data set. We have implemented these algorithms in the computer program CLUMPP (CLUster Matching and Permutation Program). We illustrate the use of CLUMPP by aligning the cluster membership coefficients from 100 replicate cluster analyses of 600 chickens from 20 different breeds.
Availability: CLUMPP is freely available at http://rosenberglab.bioinformatics.med.umich.edu/clumpp.html
Contact: mjakob@umich.edu
Transtensional fault‐termination basins: an important basin type illustrated by the Pliocene San Jose Island basin and related basins in the southern Gulf of California, Mexico
Authors: Umhoefer Paul J. , Schwennicke Tobias , Del Margo Maya T. , Ruiz‐Geraldo Gabriela , Ingle James C. , McIntosh William 
Published: May 2007

ABSTRACTTranstensional basins are sparsely described in the literature compared with other basin types. The oblique‐divergent plate boundary in the southern Gulf of California has many transtensional basins: we have studied those on San Jose island and two other transtensional basins in the region. One major type of transtensional basin common in the southern Gulf of California region is a fault‐termination basin formed where normal faults splay off of strike‐slip faults. These basins suggest a model for transtensional fault‐termination basins that includes traits that show a hybrid nature between classic rift and strike‐slip (pull‐apart) basins. The traits include combinations of oblique, strike‐slip and normal faults with common steps and bends, buttress unconformities between the fault steps and beyond the ends of faults, a common facies pattern of terrestrial strata changing upward and away from the faults into marine strata, small fault blocks within the basin that result in complex lateral facies relations, common Gilbert deltas, dramatic termination of the margin of the basin by means of fault reorganization and boundary faults dying and an overall short basin history (few million years). Similar transtensional fault‐termination basins are present in Death Valley and other parts of the Eastern California shear zone of the western United States, northern Aegean Sea and along ancient strike‐slip faults.
Ethnic differences in TSH but not in free T4 concentrations or TPO antibodies during pregnancy
Authors: Benhadi N. , Wiersinga W. M. , Reitsma J. B. , Vrijkotte T. G. M. , Van Der Wal M. F. , Bonsel G. J. 
Published: May 2007

SummaryObjective  To describe the TSH, free T4 and thyroid peroxidase antibody (TPO‐Ab) concentrations during pregnancy among four ethnic groups and to determine reference values for these parameters during normal pregnancy.Methods  Cross‐sectional study of a cohort of 3270 pregnant women living in the city of Amsterdam. Blood samples were drawn at first booking in the first or second trimester. TSH, free T4 and TPO‐Ab concentrations were determined. Four ethnic groups were studied: Dutch, Surinam, Turkish and Moroccan.Results  Plasma TSH increased and free T4 decreased from the first to the second trimester of pregnancy for all the ethnic groups. Ethnic differences were observed in TSH concentrations, with Dutch females having the highest TSH levels compared to the other three ethnic groups. The median TSH difference was 0·16 mU/l between the Dutch and Moroccan women, 0·15 mU/l between the Dutch and Surinam women and 0·10 mU/l between the Dutch and Turkish women. These could not be explained by differences in age, parity and current smoking status. No differences were seen in free T4 concentrations between the four ethnic groups. The prevalence of TPO‐Ab was comparable across the ethnic groups (about 6% in each); the concentration of TPO‐Ab was also comparable among the ethnic groups. The Dutch women had a higher lower‐limit (2·5 percentile) of the TSH reference range than the Surinam, Turkish and Moroccan women, ranging from 0·14 mU/l for the Surinam and Moroccan to 0·27 mU/l for the Dutch women.Conclusion  The increase in TSH and decrease in free T4 values during pregnancy correspond to previous reported studies. Pregnant Dutch women had consistently higher TSH values than the ethnic group, but corresponding free T4 levels and TPO‐Ab did not differ between these ethnic groups.
Phenotypic variability in 17β‐hydroxysteroid dehydrogenase‐3 deficiency and diagnostic pitfalls
Authors: Lee Yung Seng , Kirk Jeremy M. W. , Stanhope Richard G. , Johnston Derek I. , Harland Sharon , Auchus Richard J. , Andersson Stefan , Hughes Ieuan A. 
Published: May 2007

SummaryObjective  17β‐hydroxysteroid dehydrogenase type 3 isoenzyme (17β‐HSD3) is required to produce testosterone for male sex differentiation. Mutations in the HSD17B3 gene cause 17βHSD3 deficiency and result in XY sex reversal of varying degree. We report the phenotypes of 14 subjects with 17βHSD3 deficiency in relation to sex of rearing, androgen production, and HSD17B3 mutations.Design  Cases were identified through the Cambridge Disorders of Sex Development Database where detailed clinical information was recorded, results of hCG stimulation tests were available, and HSD17B3 mutation was identified.Results  Fourteen subjects from seven pedigrees (four consanguineous) had the following seven mutations: A56T, N130S, E215D, S232L, C268Y, V205E, and a novel mutation M197K. XY sex reversal was classified as complete in 10 infants at birth. Inguinal masses suggestive of androgen insensitivity syndrome (AIS) occurred in five infants. Contrasexual virilization reminiscent of 5α‐reductase deficiency occurred in four subjects at puberty. The median (range) testosterone : androstenedione (T/A) ratio after a short hCG stimulation test was 0·32 (0·12–3·4). The S232L mutation identified in three affected family members caused isolated, severe hypospadias in one member who was raised male; virilization occurred despite in vitro studies showing an inactive mutant enzyme. Ratios of T/A in this pedigree were more than 0·8.Conclusion  XY sex reversal is sufficiently variable in 17βHSD3 deficiency to cause problems in accurate diagnosis, particularly in distinguishing it from AIS. It should be considered in undervirilized male infants with normal Wolffian duct structures, absent Müllerian ducts, and normal adrenal steroid biosynthesis; or when an assigned female subject virilizes at puberty. Elevated hCG‐stimulated T/A ratio may occur, and sex of rearing may not be concordant within affected families with the same HSD17B3 mutation. The T/A ratio, mutation analysis and functional analysis of the mutant enzyme taken in isolation, respectively, may not conclusively establish a diagnosis of 17βHSD3 deficiency in undervirilized male subjects; the reasons for these discrepancies remain unknown.
Asymptomatic bilateral adrenal pheochromocytoma in a patient with a germline V804M mutation in the RET proto‐oncogene
Authors: Recasens M. , Oriola J. , Fernández‐Real J. M. , Roig J. , Rodríguez‐Hermosa J. I. , Font J. A. , Galofre P. , López‐Bermejo A. , Ricart W. 
Published: May 2007

SummaryA diagnosis of bilateral pheochromocytoma warrants exclusion of hereditary pheochromocytoma.Objective  To describe the first case of a bilateral pheochromocytoma associated with V804M mutation in the RET proto‐oncogene.Patients  The index case was a 54‐year‐old man with bilateral adrenal masses discovered during a CT scan performed for other reasons.Measurements  Genetic analysis included exons 8–11 and 13–17 in the RET proto‐oncogene, all four exons and flanking intronic regions in the SDHD gene, all eight exons and flanking intronic regions in the SDHB, and all three exons in the VHL gene.Results  Investigations revealed elevated urinary metanephrines (32·3 µmol/day), and laparoscopic bilateral adrenalectomy confirmed bilateral pheochromocytomas.A heterozygous V804M mutation in exon 14 of the RET was found in the index case and in four relatives. Total thyroidectomy, performed in four of five affected members in this kindred, disclosed a medullary thyroid carcinoma in the index case and in a 50‐year‐old woman, and nodular C‐cell hyperplasia in the other two subjects.Conclusions  This clinical case suggests that individuals carrying the germline V804M mutation should be screened annually for the presence of pheochromocytoma.
Cortisol levels and measures of body composition in middle‐aged and older men
Authors: Travison Thomas G. , O'Donnell Amy B. , Araujo Andre B. , Matsumoto Alvin M. , McKinlay John B. 
Published: May 2007

SummaryIntroduction  Similarities in the symptomatic expressions of excess adiposity and hypercortisolaemic conditions suggest that elevated glucocorticoid exposure may influence the pathogenesis of obesity. Circulating cortisol levels are not typically elevated in obese subjects, but data from large prospective samples are rare. We undertook an analysis to determine both cross‐sectional and longitudinal associations between body composition and serum cortisol concentrations in a randomly chosen group of 999 community‐dwelling men, aged 40–79 years.Methods  Data were obtained from the two follow‐up waves of the Massachusetts Male Ageing Study (T2: 1995–97; T3: 2002–04). Partial correlation and multivariate regression analyses were used to estimate cross‐sectional (T2) and longitudinal associations between serum cortisol concentrations and a range of measures of subjects’ body composition, including weight, body mass index (BMI), waist circumference (WC), waist‐to‐hip girth ratio (WHR), and percentage body fat (measured by bioelectrical impedance at T3); similar analyses were conducted to assess the association between change (T2 to T3) in serum cortisol and simultaneous change in body composition parameters.Results  We observed weak negative associations between cortisol concentrations and all body composition parameters, with the exception of percentage body fat. Longitudinal results demonstrated similar relationships but associations were of lesser magnitude. T2 cortisol concentrations were not associated with change in body composition over time, whereas T2 body size was positively associated with longitudinal changes in cortisol concentrations, providing limited evidence that weight change drives changes in cortisol concentrations, rather than vice versa. Results were unchanged when age and other covariate effects were controlled.Conclusions  Circulating cortisol concentrations are somewhat lower in obese than in nonobese community‐dwelling men. There is some evidence that excess adiposity presages increases in cortisol concentrations, rather than the reverse. However, this observation should be greeted with caution, as age‐related weight loss – and not gain – was associated with simultaneous increases in serum cortisol concentrations.