bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular data show that Topeliopsis (Ascomycota, Thelotremataceae) is polyphyletic
Authors: MANGOLD Armin , MARTÍN María P. , KALB Klaus , LÜCKING Robert , LUMBSCH H. Thorsten
Published: February 2008

A phylogenetic study using DNA sequences of the nuclear ribosomal large subunit from 38 species is used to infer the phylogeny of species currently placed in Topeliopsis. The genus is shown to be polyphyletic; monophyly of previous and current circumscriptions of the genus are rejected using two alternative hypothesis tests. Topeliopsis meridiensis is shown to be closer to Chapsa than Topeliopsis, but additional studies are necessary to understand the circumscription of Chapsa. The new genus Melanotopelia Lumbsch & Mangold is described to accommodate T. toensbergii and T. rugosa. These species were previously regarded as aberrant in Topeliopsis because of their thin-walled ascospores and dark pigmented proper exciple. The new combination Graphis mexicana (Hale) Kalb, Lücking & Lumbsch is proposed and Graphis muscicola and Topeliopsis globosa reduced to synonymy with this species.
Personality and risk for depression in a birth cohort of 70-year-olds followed for 15 years
Authors: Duberstein P. R. , Pálsson S. P. , Waern M. , Skoog I.
Published: February 2008

Background

The association between personality traits and the first lifetime onset of clinically significant depression has not been studied in older adults.

Method

Experienced psychiatrists conducted interviews and chart reviews at baseline and throughout the 15-year follow-up period. Survival analyses were conducted on the presence/absence of a DSM-III-R mood disorder at follow-up.

Results

There were 59 cases of first lifetime episodes of depression. Analyses showed that Neuroticism [hazard ratio (HR) per one point increase in the Maudsley Personality Inventory (MPI)=1.05, 95% confidence interval (CI) 1.02–1.08] but not Extroversion (HR 1.02, 95% CI 0.97–1.06) amplified risk for mood disorder.

Conclusions

This prospective study on a randomly sampled birth cohort of older adults showed that Neuroticism confers risk for a first lifetime episode of clinically significant depression. Findings have implications for understanding the etiology of late-life depression (LLD) and could also aid in the identification and treatment of people at risk.
Psychological effects of chemical weapons: a follow-up study of First World War veterans
Authors: Jones E. , Everitt B. , Ironside S. , Palmer I. , Wessely S.
Published: February 2008

Background

Chemical weapons exercise an enduring and often powerful psychological effect. This had been recognized during the First World War when it was shown that the symptoms of stress mimicked those of mild exposure to gas. Debate about long-term effects followed the suggestion that gassing triggered latent tuberculosis.

Method

A random sample of 103 First World War servicemen awarded a war pension for the effects of gas, but without evidence of chronic respiratory pathology, were subjected to cluster analysis using 25 common symptoms. The consistency of symptom reporting was also investigated across repeated follow-ups.

Results

Cluster analysis identified four groups: one (n=56) with a range of somatic symptoms, a second (n=30) with a focus on the respiratory system, a third (n=12) with a predominance of neuropsychiatric symptoms, and a fourth (n=5) with a narrow band of symptoms related to the throat and breathing difficulties. Veterans from the neuropsychiatric cluster had multiple diagnoses including neurasthenia and disordered action of the heart, and reported many more symptoms than those in the three somatic clusters.

Conclusions

Mild or intermittent respiratory disorders in the post-war period supported beliefs about the damaging effects of gas in the three somatic clusters. By contrast, the neuropsychiatric group did not report new respiratory illnesses. For this cluster, the experience of gassing in a context of extreme danger may have been responsible for the intensity of their symptoms, which showed no sign of diminution over the 12-year follow-up.
Distributed gradient and particle swarm optimization for multi-robot motion planning
Authors: Rigatos Gerasimos G.
Published: February 2008

Two distributed stochastic search algorithms are proposed for motion planning of multi-robot systems: (i) distributed gradient, (ii) swarm intelligence theory. Distributed gradient consists of multiple stochastic search algorithms that start from different points in the solutions space and interact with each other while moving toward the goal position. Swarm intelligence theory is a derivative-free approach to the problem of multi-robot cooperation which works by searching iteratively in regions defined by each robot's best previous move and the best previous move of its neighbors. The performance of both approaches is evaluated through simulation tests.
Workspaces associated to assembly modes of the 5R planar parallel manipulator
Authors: Macho Erik , Altuzarra Oscar , Pinto Charles , Hernandez Alfonso
Published: February 2008

The aim of this paper is to show how it is possible to obtain for the 5R planar parallel manipulator the complete workspace associated with each solution of the direct kinematic problem or assembly mode. The workspaces associated with the different inverse kinematic problem solutions or working modes are joined and the robot moves from one to another without losing the control. An exhaustive analysis of the complete workspace and singular positions of the 5R planar parallel manipulator with two active joints is presented. Furthermore, application of these principles to path planning will be explained.
Paleogene deepwater mass composition of the tropical Pacific and implications for thermohaline circulation in a greenhouse world
Authors: Thomas Deborah J. , Lyle Mitchell , Moore Theodore C. , Rea David K.
Published: February 2008

The Pacific Ocean likely exerted the greatest marine influence on climate during the greenhouse interval of the Paleogene. The first step toward assessing the role of Pacific deepwater circulation in global heat transport is a comprehensive reconstruction of deepwater mass composition and circulation patterns. We present new deepwater mass Nd isotope data from ODP Leg 199 Sites 1215, 1217, 1219, and 1221 to augment the existing coverage provided by ferromanganese crust and fossil fish debris data. The new data corroborate the notion that the Pacific Ocean operated in a bimodal pattern with deepwater sources in both the Southern Ocean and North Pacific for much of the early to middle Paleogene. In addition, the data indicate that there was little to no influence of Atlantic waters on the deepwater composition of the tropical Pacific. The available deepwater Nd isotope data provide refined constraints on the geographic and depth range of influence of both a Southern Ocean and North Pacific deepwater mass. From ∼65 to ∼45 Ma, the deep tropical Pacific was the mixing location of deep waters sourced from the Southern Ocean and the North Pacific. The Southern Ocean deepwater mass extended from ∼1800 m to abyssal depths. Until 53.6 Ma it circulated northward in the western Pacific at least as far as the paleolocation of Fe‐Mn Crust CLD01 (∼5°N paleolatitude) and in the eastern portion of the Pacific as far as Site 1215 (∼10°N paleolatitude). A North Pacific deepwater mass extended from at least ∼2400 m to 2900 m water depth from ∼65 to 54 Ma, south to Shatsky Rise (paleolatitude ∼10–15°N), and possibly as far as Site 1215, 700 km to the south of Shatsky Rise Sites 1209 and 1211.
Effective elastic thickness variations along the Andean margin and their relationship to subduction geometry
Authors: Pérez‐Gussinyé M. , Lowry A. R. , Phipps Morgan J. , Tassara A.
Published: February 2008

We present a new map of the spatial variations in effective elastic thickness, Te, along the Andes estimated using Bouguer coherence. The Te variations reflect interactions between subducting slab and preexisting terrane structure. In the forearc, conductive cooling of the continent by the subducting slab exerts primary control on rigidity, resulting in Te that is highest (∼40 km) where the oceanic lithosphere is oldest and coldest (∼20°S). In the central Andes, Te is relatively low (∼20 km) along the volcanic chain and the Altiplano and Puna plateaus. We interpret this weakening to reflect a high geothermal gradient maintained by advective magmatic processes, a shallow and hot asthenosphere, and a very weak lower crust throughout this region. East of the plateaus, high Te delineates underthrusting of the Brazilian shield. Finally, north and south of the plateaus, flat subduction areas are characterized by high Te, high shear wave velocity, thick thermal lithosphere, and low heat flow, indicating that continental lithosphere there is thicker, colder, and stronger. On the basis of these relationships we suggest that variations in slab dip along the margin relate to variations in structure of the continental lithosphere. In particular, we propose that upper plate structure influences the width and viscosity of the asthenospheric wedge, which control the suction moment responsible for the subduction angle at depths ≥70–100 km. For example, when oceanic lithosphere subducts beneath thin continental lithosphere, the low‐viscosity asthenosphere allows the slab to detach from the continent and sink into the mantle at normal angles. However, when oceanic lithosphere subducts close or beneath thick and strong continental lithosphere, the asthenospheric wedge narrows and corner flow drags high‐viscosity mantle from the base of the thick (>150 km), cold continent into the wedge. Suction forces increase with both narrowing of the wedge and its increasing viscosity. We estimate the asthenospheric viscosity underneath thick, cold continents to be ≥1020 Pa s, sufficient to induce flat subduction. Later, after prolonged hydration and weakening of the continent's base, asthenospheric flow into the wedge may resume, allowing the slab to sink again into the mantle at normal angles.
Aluminous hydrous mineral δ‐AlOOH as a carrier of hydrogen into the core‐mantle boundary
Authors: Sano Asami , Ohtani Eiji , Kondo Tadashi , Hirao Naohisa , Sakai Takeshi , Sata Nagayoshi , Ohishi Yasuo , Kikegawa Takumi
Published: February 2008

In‐situ X‐ray diffraction experiments were conducted to determine the stability field of the aluminous hydrous mineral δ‐AlOOH over the entire conditions of the lower mantle. We observed δ‐AlOOH at pressures from 33 to 134 GPa at 1350–2300 K, indicating that this hydrous mineral in the sediment layer of a subducting slab could transport hydrogen into the core‐mantle boundary (CMB).
First three‐dimensional simulation of the Perkins instability in the nighttime midlatitude ionosphere
Authors: Yokoyama Tatsuhiro , Otsuka Yuichi , Ogawa Tadahiko , Yamamoto Mamoru , Hysell David L.
Published: February 2008

A three‐dimensional numerical simulation in the nighttime midlatitude ionosphere is developed for the first time and applied to the Perkins instability in the midlatitude F region. Growth of the Perkins instability is successfully reproduced under nighttime condition, and the numerical results basically agree with a linear theory and previous two‐dimensional numerical studies. Northwest‐southeast (NW‐SE) alignment of density perturbations is generated from random seeding by applying a southeastward neutral wind. The perturbations are dominant at altitudes of 200–300 km where a steep density gradient exists, which is consistent with the altitude of 630‐nm airglow emission that often shows NW‐SE alignment. Further simulation in terms of the E‐F coupling can be done in the near future.
Altitude variations of the horizontal thermospheric winds during geomagnetic storms
Authors: Wang W. , Burns A. G. , Wiltberger M. , Solomon S. C. , Killeen T. L.
Published: February 2008

It is generally assumed that viscosity smooths out vertical gradients of the horizontal thermospheric winds in the upper thermosphere, and thus observations of neutral winds at one height can be used at other altitudes in this region. In this paper we present neutral wind simulations of the May 1997 geomagnetic storm using the Coupled Magnetosphere‐Ionosphere‐Thermosphere (CMIT) model. The model results show that during quiet periods, the assumption of a shearless vertical profile of the horizontal winds is generally valid in low and middle latitudes, although vertical shears do occur in wind profiles in the upper thermosphere in some locations at higher latitudes. During disturbed periods, large variations in the vertical profiles of the upper thermospheric winds are seen globally in the model simulations. A diagnostic analysis of the forcing processes in the neutral momentum equations shows that (1) during quiet time, there are shearing forces, most noticeably the pressure gradient and ion drag, in the upper thermosphere that result in a net momentum forcing that changes with height; this induces altitude variations in the wind profiles at high latitudes and sometime even at middle latitudes. (2) During storm time, momentum advection, which is relatively weak during the quiet time, becomes a dominant force globally. Pressure gradient forces are also significantly enhanced. Ion drag, on the other hand, can be enhanced or suppressed, depending on the location of positive or negative effects. All these forces exhibit significant altitude variations that lead to a net force that is greatly enhanced and has large vertical shears. This produces globally enhanced neutral winds that vary with height. (3) Viscosity is less important than other forcing processes during both the quiet and storm periods and thus cannot prevent shears from occurring in the vertical profiles of the horizontal winds. Viscosity has an insignificant effect on vertical shears that change with height linearly. It, however, does restrict vertical shears that vary nonlinearly with height. The effectiveness of the viscosity in restricting such shears depends on its magnitude. In our simulations, viscosity is weaker than other forcing processes and thus is a relatively slow process, so it will take a few hours for viscosity to reduce such shears.
Improving the quality of marine geophysical track line data: Along‐track analysis
Authors: Chandler Michael T. , Wessel Paul
Published: February 2008

We have examined 4918 track line geophysics cruises archived at the U.S. National Geophysical Data Center (NGDC) using comprehensive error checking methods. Each cruise was checked for observation outliers, excessive gradients, metadata consistency, and general agreement with satellite altimetry‐derived gravity and predicted bathymetry grids. Thresholds for error checking were determined empirically through inspection of histograms for all geophysical values, gradients, and differences with gridded data sampled along ship tracks. Robust regression was used to detect systematic scale and offset errors found by comparing ship bathymetry and free‐air anomalies to the corresponding values from global grids. We found many recurring error types in the NGDC archive, including poor navigation, inappropriately scaled or offset data, excessive gradients, and extended offsets in depth and gravity when compared to global grids. While ∼5–10% of bathymetry and free‐air gravity records fail our conservative tests, residual magnetic errors may exceed twice this proportion. These errors hinder the effective use of the data and may lead to mistakes in interpretation. To enable the removal of gross errors without over‐writing original cruise data, we developed an errata system that concisely reports all errors encountered in a cruise. With such errata files, scientists may share cruise corrections, thereby preventing redundant processing. We have implemented these quality control methods in the modified MGD77 supplement to the Generic Mapping Tools software suite.
Estimation of net carbon exchange using eddy covariance CO2 flux observations and a stochastic model
Authors: Stauch Vanessa J. , Jarvis Andrew J. , Schulz Karsten
Published: February 2008

In this paper we use a stochastic model to estimate annual net carbon exchange (NCE) from eddy covariance data taken from various sites. The stochastic model is comprised of a signal and a noise component. The signal component is characterized using a semiparametric model relating CO2 flux to light, temperature and time fitted to the eddy covariance observations. The noise component is characterized from the resultant model residuals using empirical cumulative probability distributions. The estimates for NCE are then derived from multiple runs of the joint signal‐noise model within a Monte Carlo framework. This model‐based approach to estimating NCE is evaluated using synthetic data and found to give a reasonable partitioning of the signal and noise in these data. Building on this, we derive estimates of NCE from observed annual eddy covariance data sets for various sites. For the six sites analyzed, the noise to signal ratio for the annual NCE estimates lies between 5 and 17% highlighting the potential value of eddy covariance observations for this application.
An operational retrieval algorithm for determining aerosol optical properties in the ultraviolet
Authors: Taylor Thomas E. , L'Ecuyer Tristan S. , Slusser James R. , Stephens Graeme L. , Goering Christian D.
Published: February 2008

This paper describes a number of practical considerations concerning the optimization and operational implementation of an algorithm used to characterize the optical properties of aerosols across part of the ultraviolet (UV) spectrum. The algorithm estimates values of aerosol optical depth (AOD) and aerosol single scattering albedo (SSA) at seven wavelengths in the UV, as well as total column ozone (TOC) and wavelength‐independent asymmetry factor (g) using direct and diffuse irradiances measured with a UV multifilter rotating shadowband radiometer (UV‐MFRSR). A novel method for cloud screening the irradiance data set is introduced, as well as several improvements and optimizations to the retrieval scheme which yield a more realistic physical model for the inversion and increase the efficiency of the algorithm. Introduction of a wavelength‐dependent retrieval error budget generated from rigorous forward model analysis as well as broadened covariances on the a priori values of AOD, SSA and g and tightened covariances of TOC allows sufficient retrieval sensitivity and resolution to obtain unique solutions of aerosol optical properties as demonstrated by synthetic retrievals. Analysis of a cloud screened data set (May 2003) from Panther Junction, Texas, demonstrates that the algorithm produces realistic values of the optical properties that compare favorably with pseudo‐independent methods for AOD, TOC and calculated Ångstrom exponents. Retrieval errors of all parameters (except TOC) are shown to be negatively correlated to AOD, while the Shannon information content is positively correlated, indicating that retrieval skill improves with increasing atmospheric turbidity. When implemented operationally on more than thirty instruments in the Ultraviolet Monitoring and Research Program's (UVMRP) network, this retrieval algorithm will provide a comprehensive and internally consistent climatology of ground‐based aerosol properties in the UV spectral range that can be used for both validation of satellite measurements as well as regional aerosol and ultraviolet transmission studies.
Regulation of an inducible promoter by an HP1β–HP1γ switch
Authors: Mateescu Bogdan , Bourachot Brigitte , Rachez Christophe , Ogryzko Vasily , Muchardt Christian
Published: February 2008

The mammalian heterochromatin protein 1 (HP1) family of proteins was recently shown to be involved in transient repression of inducible promoters. One of these promoters is the HIV1 long terminal repeat, which, during viral latency, recruits a non‐processive RNA polymerase II (RNAPII) that synthesizes a short regulatory transcript. Here, we have used this promoter to examine the interplay of HP1α, HP1β and HP1γ with RNAPII. We find that, in the absence of stimulation, HP1β is present on the promoter together with the non‐processive RNAPII and functions as a negative regulator. On activation, HP1β bound to methylated H3K9 is rapidly released concurrent with histone H3 phospho‐acetylation, and is replaced by HP1γ. This isoform localizes to the promoter but also inside the coding region, together with the processive RNAPII. Our data show that HP1 recruitment–release is a sequential mechanism that is precisely regulated and highly dependent on transcription.
Toll-like receptor polymorphisms and susceptibility to human disease
Authors: Misch E. Ann , Hawn Thomas R.
Published: February 2008

Although several lines of evidence suggest that variation in human inflammation is genetically controlled, the genes which regulate these responses are largely unknown. TLRs (Toll-like receptors) mediate recognition of microbes, regulate activation of the innate immune response and influence the formation of adaptive immunity. Cellular and molecular studies over the past several years have identified a number of common TLR polymorphisms that modify the cellular immune response and production of cytokines in vitro. In addition, human genetic studies suggest that some of these polymorphisms are associated with susceptibility to a spectrum of diseases. In this review, we summarize studies of common TLR polymorphisms and how this work is beginning to illuminate the influence of human variation on inflammation and disease susceptibility.
Circulating renin–angiotensin system and catecholamines in childhood: is there a role for birthweight?
Authors: Franco Maria C. P. , Casarini Dulce E. , Carneiro-Ramos Marcela S. , Sawaya Ana L. , Barreto-Chaves Maria L. M. , Sesso Ricardo
Published: February 2008

There have been only a few reports on the sympathoadrenal and renin–angiotensin systems in children of small gestational age. The purpose of the present study was to investigate plasma levels of ACE (angiotensin-converting enzyme) activity, angiotensin and catecholamines in 8- to 13-year-old children and to determine whether there are correlations between the components of these systems with both birthweight and BP (blood pressure) levels. This clinical study included 66 children (35 boys and 31 girls) in two groups: those born at term with an appropriate birthweight [AGA (appropriate-for-gestational age) group, n=31] and those born at term but with a small birthweight for gestational age [SGA (small-for-gestational age) group, n=35]. Concentrations of angiotensin, catecholamines and ACE activity were determined in plasma. Circulating noradrenaline levels were significantly elevated in SGA girls compared with AGA girls (P=0.036). In addition, angiotensin II and ACE activity were higher in SGA boys (P=0.024 and P=0.050 respectively). There was a significant association of the circulating levels of both angiotensin II and ACE activity with BP levels in our study population. Although the underlying mechanisms that link restricted fetal growth with later cardiovascular events are not fully understood, the findings in the present study support the link between low birthweight and overactivity of both sympathoadrenal and renin–angiotensin systems into later childhood.
Protein restriction during gestation and/or lactation causes adverse transgenerational effects on biometry and glucose metabolism in F1 and F2 progenies of rats
Authors: Pinheiro Alessandra R. , Salvucci Isadora D. M. , Aguila Marcia B. , Mandarim-de-Lacerda Carlos A.
Published: February 2008

Substantial evidence suggests that poor intrauterine milieu elicited by maternal nutritional disturbance may programme susceptibility in the fetus to later development of chronic diseases, such as obesity, hypertension, cardiovascular disease and diabetes. One of the most interesting features of fetal programming is the evidence from several studies that the consequences may not be limited to the first-generation offspring and that it can be passed transgenerationally. In the present study, female rats (F0) were fed either a normal-protein diet [control diet (C); 19 g of protein/100 g of diet] or a low-protein diet [restricted diet (R); 5 g of protein/100 g of diet]. The offspring were termed according to the period and the types of diet the dams were fed, i.e. CC, RC, CR and RR (first letter indicates the diet during gestation and the second the diet during lactation). At 3 months of age, F1 females were bred to proven males, outside the experiment, to produce F2 offspring. At weaning, F2 offspring were divided by gender. RC1 offspring (with the number indicating the filial generation) were born with low birthweight, but afterwards they had catch-up growth, reaching the weight of the CC1 offspring. The increased glycaemia in RC1 offspring was associated with insulin resistance. CR1 and RR1 offspring had impaired growth with no changes in glucose metabolism. RC2 offspring had high BM (body mass) at birth, which was sustained over the whole experiment in male offspring. The F2 generation had more alteration in glucose metabolism than the F1 generation. CR2 and RC2 offspring had hyperglycaemia accompanied by hyperinsulinaemia and insulin resistance in both genders. CR2 offspring had an increase in body adiposity with hyperleptinaemia. In conclusion, low protein during gestation improves BM, fat mass and growth rate in F1 rats, but has adverse effects on glucose and leptin metabolism, resulting in insulin resistance in adult F1 and F2 offspring. Low protein during lactation has adverse effects on glucose, insulin and leptin metabolism, resulting in insulin resistance in adult F2 offspring. These findings suggest that low protein during gestation and/or lactation can be passed transgenerationally to the second generation.
Parabolic relationship between plasma triacylglycerols and LDL-cholesterol in familial combined hyperlipidaemia: the multiple-type hyperlipidaemia explained?
Authors: Brouwers Martijn C. G. J. , de Graaf Jacqueline , van Greevenbroek Marleen M. J. , Georgieva Anna M. , van der Kallen Carla J. H. , ter Avest Ewoud , Stehouwer Coen D. A. , Stalenhoef Anton F. , de Bruin Tjerk W. A.
Published: February 2008

FCHL (familial combined hyperlipidaemia) is a highly prevalent genetic lipid disorder that accounts for a substantial number of premature cardiovascular events. To date, FCHL has been complicated by the different lipid phenotypes that are present within one family and one individual patient over time. In the present study, we hypothesized that a parabolic relationship between plasma triacylglycerols (triglycerides) and LDL (low-density lipoprotein)-cholesterol can explain this so-called ‘multiple-type hyperlipidaemia’ in FCHL. Our hypothesis was tested in two well-documented FCHL cohorts [Maastricht (n=145) and Nijmegen (n=299)] that were followed over a 5-year interval. Three groups were constructed depending on plasma triacylglycerols: group A (individuals with both measurements below 1.5 mmol/l), group B (one measurement below and one measurement above 1.5 mmol/l) and group C (both measurement above 1.5 mmol/l). In both male, but not female, cohorts, a significant positive relationship between plasma triacylglycerols and LDL-cholesterol was observed in group A (P=0.02 for Maastricht cohort and P=0.001 for the Nijmegen cohort), a significant negative relationship in group C (P=0.01 for Maastricht cohort and P=0.02 for the Nijmegen cohort), and a relationship intermediate to group A and C in group B. In contrast, both apoB (apolipoprotein B) levels and the prevalence of cardiovascular disease were related with plasma triacylglycerols in a more linear fashion. In conclusion, a parabolic relationship between plasma triacylglycerols and LDL-cholesterol explains the ‘multiple-type hyperlipidaemia’ in FCHL. In addition, the linear relationship between triacylglycerols and both apoB levels and the prevalence of cardiovascular disease substantiate the use of apoB instead of LDL-cholesterol in the diagnosis of FCHL and the prediction of cardiovascular disease.
Collision efficiency factor for heteroaggregation: Extension to soft interactions
Authors: Olsen Aaron , Franks George , Biggs Simon , Jameson Graeme J.
Published: February 2008

An improved model for the collision efficiency factor of clusters of oppositely charged spheres has been developed, which accounts for repulsive and attractive interactions that occur at a finite distance from the colliding species, i.e., the so-called “soft” interactions. Trends in measured optimum dosages for rapid aggregation with increasing Debye length (a decrease at particle size ratios between 0.3 and 1 and an increase at particle size ratios less than 0.3) are explained qualitatively by employing the modified collision efficiency model. Several observations from the literature, specifically the formation of stringlike aggregates at low ionic strength and the uneven optimum dosage requirements of particles of equal size, are also explained in view of the model presented.
A momentum-conserving Franck-Condon approximation: Theory and application to the photodissociation of Li2+ in an intense laser field
Authors: Nichols Patrick , Hoffmann Mark R.
Published: February 2008

A new, computationally efficient approximation to calculating matrix elements between vibrational-electronic states that does not assume stationary nuclei is introduced. The approach emphasizes the importance of the conservation of nuclear momenta. The calculated quantities can be used wherever equivalent quantities from standard Franck-Condon treatments can be used. The new method is illustrated by a time-dependent perturbation theory description of the photodissociation of the Li2+ molecular cation in an intense laser field (I=0.9×1012W∕cm2), which was previously identified in a detailed study of the electronic structure [Khait et al., J. Chem. Phys. 122, 094111 (2005)] as likely to have unusual sensitivity to the initial vibrational state in dynamics. The current study confirms this speculation and shows this to be a specific instance of a situation in which nuclear dynamics during an electronic optical transition cannot be ignored.
Size dependent fragmentation of argon clusters in the soft x-ray ionization regime
Authors: Gisselbrecht Mathieu , Lindgren Andreas , Burmeister Florian , Tchaplyguine Maxim , Öhrwall Gunnar , Lundin Magnus , de Brito Arnaldo Naves , Svensson Svante , Björneholm Olle , Sorensen Stacey L.
Published: February 2008

Photofragmentation of argon clusters of average size ranging from 10 up to 1000 atoms is studied using soft x-ray radiation below the 2p threshold and multicoincidence mass spectroscopy technique. For small clusters (⟨N⟩=10), ionization induces fast fragmentation with neutral emission imparting a large amount of energy. While the primary dissociation takes place on a picosecond time scale, the fragments undergo slow degradation in the spectrometer on a microsecond time scale. For larger clusters (⟨N⟩⩾100) we believe that we observe the fragmentation pattern of multiply charged species on a time-scale which lasts a few hundred nanoseconds. The reason for these slower processes is the large number of neutral atoms which act as an efficient cooling bath where the excess energy (“heat”) dissipates among all degrees of freedom. Further degradation of the photoionic cluster in spectrometer then takes place on the microsecond time scale, similar to small clusters.
Time propagation of constrained coupled Gaussian wave packets
Authors: Fabčič Tomaž , Main Jörg , Wunner Günter
Published: February 2008

The dynamics of quantum systems can be approximated by the time propagation of Gaussian wave packets. Applying a time dependent variational principle, the time evolution of the parameters of the coupled Gaussian wave packets can be calculated from a set of ordinary differential equations. Unfortunately, the set of equations is ill behaved in most practical applications, depending on the number of propagated Gaussian wave packets, and methods for regularization are needed. We present a general method for regularization based on applying adequate nonholonomic inequality constraints to the evolution of the parameters, keeping the equations of motion well behaved. The power of the method is demonstrated for a nonintegrable system with two degrees of freedom.
The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase
Authors: Vall-llosera G. , Gao B. , Kivimäki A. , Coreno M. , Álvarez Ruiz J. , de Simone M. , Ågren H. , Rachlew E.
Published: February 2008

Near edge x-ray absorption fine structure spectra have been measured and interpreted by means of density functional theory for five different azabenzenes (pyridine, pyridazine, pyrimidine, pyrazine, and s-triazine) in the gas phase. The experimental and theoretical spectra at the N 1s and C 1s edges show a strong resonance assigned to the transition of the 1s electron in the respective N or C atoms to the lowest unoccupied molecular orbital with π* symmetry. As opposed to the N 1s edge, at the C 1s edge this resonance is split due to the different environments of the core hole atom in the molecule. The shift in atomic core-level energy due to a specific chemical environment is explained with the higher electronegativity of the N atom compared to the C atom. The remaining resonances below the ionization potential (IP) are assigned to transitions to valence/Rydberg orbitals with mixed π*∕σ* character. Upon N addition, a reduction of intensity is observed in the Rydberg region at both edges as compared to the intensity in the continuum. Above the IP one or more resonances are seen and ascribed here to transitions to σ* orbitals. Calculating the experimental and theoretical Δπ term values at both edges, we observe that they are almost the same within ±1eV as expected for isoelectronic bonded pairs. The term values of the π* and σ* resonances are discussed in terms of the total Z number of the atoms participating in the bond.
Size dependence of structural, electronic, elastic, and optical properties of selenium nanowires: A first-principles study
Authors: Kahaly Mousumi Upadhyay , Ghosh Prasenjit , Narasimhan Shobhana , Waghmare Umesh V.
Published: February 2008

We have studied the structural, elastic, and optical properties of selenium nanowires, as well as bulk selenium, by performing first-principles density functional theory calculations. The nanowires are structurally similar to bulk trigonal Se, in that they consist of hexagonal arrays of helices, though there is a slight structural rearrangement in response to the finite size of the nanowires. These small structural changes result in Young’s modulus decreasing slightly for progressively thinner nanowires. However, there is a significant effect on electronic structure and optical properties. The thinner the nanowire, the greater the band gap, and the greater the anisotropy in optical conductivity. The latter is due to the effects of finite size being much more marked for the case where the electric field is polarized perpendicular to the helical axis, than in the case where the polarization is parallel to c. For the case of bulk Se, we obtain good agreement with experimental data on the structure, elastic constants, and dielectric function.
Vibrational dynamics of ice in reverse micelles
Authors: Dokter Adriaan M. , Petersen Christian , Woutersen Sander , Bakker Huib J.
Published: February 2008

The ultrafast vibrational dynamics of HDO:D2O ice at 180K in anionic reverse micelles is studied by midinfrared femtosecond pump-probe spectroscopy. Solutions containing reverse micelles are cooled to low temperatures by a fast-freezing procedure. The heating dynamics of the micellar solutions is studied to characterize the micellar structure. Small reverse micelles with a water content up to approximately 150 water molecules contain an amorphous form of ice that shows remarkably different vibrational dynamics compared to bulk hexagonal ice. The micellar amorphous ice has a much longer vibrational lifetime than bulk hexagonal ice and micellar liquid water. The vibrational lifetime is observed to increase linearly from 0.7to4ps with the resonance frequency ranging from 3100to3500cm−1. From the pump dependence of the vibrational relaxation the homogeneous linewidth of the amorphous ice is determined (55±5cm−1).
Threshold photoelectron spectroscopy on inner-valence ionic states of NO
Authors: Hikosaka Y. , Aoto T. , Ito K. , Terasaka Y. , Hirayama R. , Miyoshi E.
Published: February 2008

The NO+ states lying in the ionization region of 20–40eV have been investigated by high-resolution threshold photoelectron spectroscopy and a configuration interaction calculation. Substantial agreement between the structures on the present experimental and theoretical spectra in the 21–27eV range enables us to assign the relevant inner-valence ionic states unambiguously. The dissociation products from the ion states are measured with threshold photoelectron-photoion coincidence spectroscopy, and the dissociation processes are discussed with reference to the potential energy curves calculated. Sharp peaks are observed in the ionization region of 27.5–35eV, which are allocated to ionic Rydberg states converging to NO2+.
Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper
Authors: Liu Yanxin , Chapagain Prem P. , Parra Jose L. , Gerstman Bernard S.
Published: February 2008

The highest level in the hierarchy of protein structure and folding is the formation of protein complexes through protein-protein interactions. We have made modifications to a well established computer lattice model to expand its applicability to two-protein dimerization and aggregation. Based on Brownian dynamics, we implement translation and rotation moves of two peptide chains relative to each other, in addition to the intrachain motions already present in the model. We use this two-chain model to study the folding dynamics of the yeast transcription factor GCN4 leucine zipper. The calculated heat capacity curves agree well with experimental measurements. Free energy landscapes and median first passage times for the folding process are calculated and elucidate experimentally measured characteristics such as the multistate nature of the dimerization process.
Effect of molecular structure on wetting behavior of water+amphiphile mixtures: A density functional approach
Authors: Yeh Ming-Chih , Chen Chia-Ming , Chen Li-Jen
Published: February 2008

A density functional approach is applied to investigate the effect of molecular structure on wetting behavior of water+amphiphile mixtures. The interaction-site model is employed to describe isomeric amphiphile structures. The hydrogen bonding between water and amphiphile is mimicked by energy enhancement according to specific molecular orientation. The calculations show that these systems exhibit Cahn-type criticality-related wetting transitions and pronounced adsorption behavior difference between isomeric systems. Excellent qualitative agreements with experiments are achieved.
Pressure dependence of SiO2 growth kinetics and electrical properties on SiC
Authors: Ray E. A. , Rozen John , Dhar Sarit , Feldman L. C. , Williams J. R.
Published: February 2008

Dry oxidations between 0.25 and 4 atm at 1150 °C are used to characterize the pressure dependence of the growth kinetics of SiO2 along three orientations of the 4H-SiC polytype. The growth curves are studied using the Deal-Grove model. The extracted linear and parabolic constants are found to scale linearly with the pressure up to 2 atm. However, the data indicate that the (0001) Si-face exhibits a retarded growth rate above 2 atm. It is also found that, like Si, there is a critical oxide thickness below which the linear-parabolic model cannot be applied. This value is found to be between 36 and 40 nm for SiO2 on 4H-SiC, and is apparently independent of the crystal orientation and oxidation pressure. The extracted critical thickness and its properties are similar to what is observed on Si, suggesting that the fast growth regime is dictated by the nature of the oxide. Finally, it is shown that the density of interface states (Dit) on the (0001) Si-face is not reduced by faster oxide growth rates within the monitored energy window.
Solvent migration from the C- to the N-terminus of amino acid in photoionization of phenylglycine-water complex
Authors: Kim Hyung Min , Han Kyu Young , Park Juyeon , Kim Gap-Sue , Kim Seong Keun
Published: February 2008

Photo-oxidation of amino acids is known to generate reactive protein radicals that lead to lethal disorders. We investigated photoionization of hydrated phenylglycine complexes in the gas phase and found that the excess internal energy from photoionization drives decarboxylation in competition with dehydration. We also found that, in decarboxylation, the solvent migrates a large distance from the C terminus of the neutral amino acid to the N terminus of the newly formed radical cation upon ionization, prior to the departure of the carboxyl group. It is noted that a solvent does not just act as a passive medium bound to the solute molecule but actively pursues its own course of action upon external perturbation that changes its chemical environment.
A Hadamard transform electron ionization time-of-flight mass spectrometer
Authors: Hudgens Jeffrey W. , Bergeron Denis E.
Published: February 2008

We describe the first Hadamard transform time-of-flight mass spectrometer (HT-TOFMS) that incorporates an electron (impact) ionization source. This implementation was realized in an existent TOF instrument using commercially available components and simple modifications to the ion source. In the present apparatus, a Hadamard mask is expressed by modulating the ion generation process within the ion source; thus, the present approach differs from previous designs that use external electrostatic devices to modulate a continuous ion stream. The present implementation may be operated in conventional TOF mode at 12.5kHz and in HT-TOF mode at 20–40MHz. In Hadamard mode the design can operate using any circulant simplex code, allowing the operator much flexibility for optimizing resolution and mass range and for eliminating nonstochastic fluctuations, e.g., encoding errors and signal hum. We demonstrate typical performance of the HT-TOFMS in standard and reflectron geometries using sequences of three constructions and of varied length, generating HT-TOF mass spectra of molecules that match conventional reference spectra. The auxiliary material includes an electrical schematic for the floating high-speed encoding amplifier, which is also of use in other high-speed electrostatic optics applications, and a list of 537 validated vectors comprising the first row of each circulant simplex sequence (Sn=3–8219) derived using maximal shift register (n=2m−1), quadratic residue (n=4m−3), and twin prime constructions [n=p(p+2)].
Validation of x-ray microfocus computed tomography as an imaging tool for porous structures
Authors: Kerckhofs G. , Schrooten J. , Van Cleynenbreugel T. , Lomov S. V. , Wevers M.
Published: February 2008

X-ray microfocus computed tomography (micro-CT) is recently put forward to qualitatively and quantitatively characterize the internal structure of porous materials. However, it is known that artifacts such as the partial volume effect are inherently present in micro-CT images, thus resulting in a visualization error with respect to reality. This study proposes a validation protocol that in the future can be used to quantify this error for porous structures in general by matching micro-CT tomograms to microscopic sections. One of the innovations of the protocol is the opportunity to reconstruct an interpolated micro-CT image under the same angle as the physical cutting angle of the microscopic sections. Also, a novel thresholding method is developed based on matching micro-CT and microscopic images. In this study, titanium porous structures are assessed as proof of principle. It is concluded for these structures that micro-CT visualizes 89% of the total amount of voxels (solid and pore) correctly. However, 8% represents an overestimation of the real structure and 3% are real structural features not visualized by micro-CT. When exclusively focusing on the solid fraction in both the micro-CT and microscopic images, only an overestimation of about 5% is found.
Negotiating Neoliberal Environments in British Columbia and Ontario, Canada: Restructuring of State – Voluntary Sector Relations and Disability Organizations' Struggles to Survive
Authors: Chouinard Vera , Crooks Valorie A
Published: February 2008

As the social programmes of the postwar welfare state have been dramatically cut back and transformed, many have looked to the voluntary nonprofit sector as the ‘beacon of hope’ in terms of delivering support and services to citizens in need of assistance. But at the same time as these organizations have been under mounting pressure to deliver support and services, they have also been subject to forces of change which limit their capacities to play this vital social role. In this paper, we examine how disability organizations in two Canadian provinces have been faring in increasingly harsh neoliberal environments. We look, in particular, at the ways in which these organizations are struggling to negotiate the pressures of diminished and inadequate funding, rising demand for their services, and changing regulatory relations with the state. Drawing on mail surveys of sixty-two disability organizations in the provinces of Ontario and British Columbia, we discuss the impacts that organizational survival strategies are having on clients, staff, volunteers and volunteerism, and on the operation and structure of such organizations. We show how disability organizations are experiencing significant pressures to change how they deliver services and supports to disabled people in need. These include pressures to diminish levels of service provision to clients, particularly those in greatest need, to reduce staffing levels and institute survival strategies that negatively impact working conditions, to rely even more heavily upon volunteer labour, and to modify their operations and organizations in a struggle to cope with harsh neoliberal conditions.