bluuebunny/crossref_metadata_2025 huggingface dataset:
Short-Term Outcome Following Referral to a Psychiatric Emergency Service
Authors: Spooren Daniel , van Heeringen Kees , Jannes Constantin
Published: August 2007

The study described here is part of an evaluation of a pilot project concerning the implementation of three psychiatric crisis units in general hospitals in Belgium. The purpose was to evaluate the short-term outcome of a multidisciplinary crisis intervention for psychiatric patients referred to the emergency department. Patients were assessed with the General Health Questionnaire (GHQ-28) at the time of referral to the emergency department and again 1 month later. Patients referred for a psychiatric crisis intervention were compared with patients receiving short-term psychiatric inpatient treatment in another hospital. Patients referred to the emergency department showed a considerable degree of psychiatric disturbance. The General Health Questionnaire appeared to be a good measure for assessment of the “state” aspect of a psychiatric disturbance. The state of distress was significantly reduced one month after referral in both treatment conditions. Nevertheless, an important proportion of patients remained in a state of considerable distress. The results indicate that a short hospital-based crisis intervention approach is comparable with more traditional acute inpatient treatment. However, in the case of more severely distressed patients it may be insufficient. Several limitations of this study are also discussed (risk of overestimation of improvement, influence of time or pre-existing differences).
Restricting Access to Methods of Suicide
Authors: Hawton Keith
Published: August 2007

Abstract. Restriction of access to means for suicidal behavior, especially dangerous methods, is a key element in most national suicide prevention strategies. In this paper the rationale for this is discussed, including the fact that suicidal impulses are often brief, that availability of a method may influence both the occurrence and outcome of a suicidal act, and that if a favored means becomes less available it does not always result in substitution by another method. Examples of evidence for the effectiveness of restricting availability of suicidal methods on subsequent suicidal behavior are presented, plus the supporting findings from studies of long-term survivors of serious suicide attempts in which only a minority have gone on to die in subsequent suicide attempts. Finally, factors likely to determine the effectiveness of modifying access to means for suicide are considered, together with the main elements that need to be addressed in evaluation.
Restrictions in Availability of Drugs Used for Suicide
Authors: Nordentoft Merete
Published: August 2007

Abstract. Availability of drugs with high lethality has been hypothesized to increase the risk of self-poisoning suicides. A literature search concerning deliberate self-poisoning and the effect of restricting access to drugs was conducted, and the effect of restrictions in availability of barbiturates, tricyclic antidepressants, dextropropoxyphene, and weak analgesics was reviewed. The correlations between method-specific and overall suicide rates and sales figures for barbiturates, dextropropoxyphene, weak analgesics, and tricyclic antidepressants were reviewed. It is concluded that restriction in availability of drugs with high case fatality should be a part of suicide prevention strategies.
Gun-Control Legislation and the Impact on Suicide
Authors: Leenaars Antoon A.
Published: August 2007

Abstract. Gun control is the prototypical example of controlling the environment for the means of suicide, an effective public health approach to suicide prevention. Canada's Criminal Law Amendment Act of 1977 (Bill C-51) provides an excellent opportunity to illustrate the effects of legislative gun-control laws and the impact on suicide. The research in Canada supports the significant effect of C-51 in reducing suicides and firearm suicides, even if one controls for socioeconomic factors, although not equally for all ages. The young, a high-risk group, show the most significant decrease, without significant substitution of other methods (displacement). Studies on gun-control laws from New Zealand, the United States, and Australia support the Canadian findings. It is concluded that, although not equally applicable in all countries, gun control may well have significant applications in reducing suicide worldwide.
Interaction between coronal mass ejections and the solar wind
Authors: Jones R. A. , Breen A. R. , Fallows R. A. , Canals A. , Bisi M. M. , Lawrence G.
Published: August 2007

Observations suggest that the interplanetary extensions of coronal mass ejections (iCMEs) may be accelerated or decelerated in their passage through the solar wind. Interplanetary scintillation measurements (IPS) can detect the passage of iCMEs beyond the field of view of the Large‐Angle and Spectrometric Coronagraph coronagraphs and can provide information on their velocities. The European Incoherent Scatter Radar and the Multi Element Radio Linked Interferometer Network systems, with a field of view covering 10–120 solar radii, can provide information on iCMEs in the inner regions of the solar wind. IPS observations can also provide solar wind velocity measurements ahead of the iCME, and using this information, we consider the velocity profile of a number of clearly defined iCMEs and the relationship between iCME velocities and that of the background solar wind. The results provide additional confirmation that iCMEs converge toward the velocity of the solar wind ahead of the event and that most of the resulting acceleration or deceleration occurs in the innermost regions of the solar wind.
Estimation of aerosol single scattering albedo from solar direct spectral radiance and total broadband irradiances measured in China
Authors: Zhao Fengsheng , Li Zhanqing
Published: August 2007

Aerosol single scattering albedo (ωo) is a primary factor dictating aerosol radiative effect. Ground‐based remote sensing of ωo has been employed most widely using spectral sky radiance measurements made from a scanning Sun photometer. Reliable results can be achieved for high aerosol loadings and for solar zenith angle >50°. This study presents an alternative method using spectral direct radiance measurements or aerosol optical depths together with total sky irradiance to retrieve ωo. The method does not require sky radiance data that can only be acquired by the expensive scanning Sun photometer. The method is evaluated using extensive measurements by a suite of instruments deployed in northern China under the East Asian Study of Tropospheric Aerosols: An International Regional Experiment (EAST‐AIRE) project. The sensitivities of the retrieval to various uncertain factors were first examined by means of radiative transfer simulations. It was found the retrieval is most sensitive to cloud screening, total irradiance and the Angstrom Exponent (AE), but only weakly depends on surface albedo and the fine structure of aerosol size distribution. Using 1 year of rigorously screened clear‐sky measurements made at the Xianghe site, the retrieved ωo values were found to agree with those retrieved from the Cimel Sun photometer by the AERONET method to within ∼0.03 (RMS), and ∼0.003 (mean bias). As part of the differences originate from different sky views seen by the Sun photometers and pyranometer under comparison, a further test was conducted by using total sky irradiances simulated with the retrieved aerosol properties from the AERONET. The resulting estimates of ωo agree to within 0.01–0.02 (RMS differences) and 0.002–0.003 (mean bias). These values are better measure of the true retrieval uncertainties, as they are free from any data mismatch. The characteristics of ωo retrievals were discussed.
Hydration state of the Martian surface as seen by Mars Express OMEGA: 1. Analysis of the 3 μm hydration feature
Authors: Jouglet D. , Poulet F. , Milliken R. E. , Mustard J. F. , Bibring J.‐P. , Langevin Y. , Gondet B. , Gomez C.
Published: August 2007

Global mapping by the visible/near‐infrared OMEGA spectrometer gives the first opportunity to study in detail the characteristics of the 3 μm hydration absorption on the surface of Mars. This feature is caused by bending and stretching vibrations of adsorbed or structural H2O and/or OH‐ bound to minerals. A specific data reduction scheme has been developed to remove the contribution of thermally emitted radiance from OMEGA spectra. With the derived albedo spectra, variations in strength and shape of the 3 μm feature can be accurately assessed. Calibration issues are discussed and data only within the nominal calibration level of the instrument are analyzed, which corresponds to a surface coverage of ∼30%. All OMEGA spectra exhibit the presence of this absorption feature, which can be explained by the presence of adsorbed water as well as by alteration rinds or coatings resulting from weathering. Strong variations of the band strength are observed. Correlations between hydration, albedo, and elevation are examined. Terrains enriched in phyllosilicates, sulfates, or hydroxides exhibit an increased hydration signature as well as a weaker combination overtone H2O absorption at ∼1.9 μm. Careful analysis also reveals seasonal variations in surface hydration, with soils in the northern midlatitudes decreasing in hydration between northern spring and summer. This hydration change is best explained by the presence of winter frost followed by equilibration of frost‐free soil with the atmosphere and by increased surface temperatures reducing the adsorptive capacity of the regolith.
Searching for microbial life remotely: Satellite‐to‐rover habitat mapping in the Atacama Desert, Chile
Authors: Warren‐Rhodes K. , Weinstein S. , Dohm J. , Piatek J. , Minkley E. , Hock A. , Cockell C. , Pane D. , Ernst L. A. , Fisher G. , Emani S. , Waggoner A. S. , Cabrol N. A. , Wettergreen D. S. , Apostolopoulos D. , Coppin P. , Grin E. , Diaz Chong , Moersch J. , Oril G. G. , Smith T. , Stubbs K. , Thomas G. , Wagner M. , Wyatt M.
Published: August 2007

The Atacama Desert, one of the most arid landscapes on Earth, serves as an analog for the dry conditions on Mars and as a test bed in the search for life on other planets. During the Life in the Atacama (LITA) 2004 field experiment, satellite imagery and ground‐based rover data were used in concert with a ‘follow‐the‐water’ exploration strategy to target regions of biological interest in two (1 coastal, 1 inland) desert study sites. Within these regions, environments were located, studied and mapped with spectroscopic and fluorescence imaging (FI) for habitats and microbial life. Habitats included aqueous sedimentary deposits (e.g., evaporites), igneous materials (e.g., basalt, ash deposits), rock outcrops, drainage channels and basins, and alluvial fans. Positive biological signatures (chlorophyll, DNA, protein) were detected at 81% of the 21 locales surveyed with the FI during the long‐range, autonomous traverses totaling 30 km. FI sensitivity in detecting microbial life in extreme deserts explains the high percentage of positives despite the low actual abundance of heterotrophic soil bacteria in coastal (<1–104 CFU/g‐soil) and interior (<1–102 CFU/g‐soil) desert soils. Remote habitat, microbial and climate observations agreed well with ground‐truth, indicating a drier and less microbially rich interior compared to the relatively wetter and abundant biology of the coastal site where rover sensors detected the presence of fog and abundant surface lichens. LITA project results underscore the importance of an explicit focus by all engineering and science disciplines on microbially relevant scales (mm to nm), and highlight the success of satellite‐based and ‘follow‐the‐water’ strategies for locating diverse habitats of biological promise and detecting the microbial hotspots within them.
Superoxide radical assays and applications in Mars‐like Atacama soils
Authors: Georgiou Christos D. , Papapostolou Ioannis , Sun Henry , McKay Christopher P.
Published: August 2007

Soils on Mars are thought to accumulate superoxide radicals, as they are formed continually by UV radiation hits on basalt minerals. Yet, beyond electron paramagnetic resonance (EPR) spectroscopy, no other methods exist that detect and quantify superoxide radicals in soils. This study describes two such assays that are based on the reaction of superoxide radical with hydroethidine and oxidized cytochrome c. They are unique in being able to test unambiguously for the presence of superoxide in a soil matrix with a high level of accuracy. Applications with soils from the Atacama Desert showed that the sensitivity of the assays is equal to or greater than that of EPR spectroscopy.
Interpretation of macroscale variables in Darcy's law
Authors: Nordbotten J. M. , Celia M. A. , Dahle H. K. , Hassanizadeh S. M.
Published: August 2007

The pursuit of a theoretical foundation of Darcy's law based on volume averaging of equations at the scale of flow in pores has a long history. While theories are well established for homogeneous systems, more complex systems exhibit inconsistencies in the resulting equations. The difficulties often lie in the treatment of surface integral terms arising from the classical averaging theorems used to transform averages of derivatives into derivatives of averages. In this work we extend the intrinsic phase average as a macroscale variable to a family of more general macroscale variables, which take into account systematic dependencies of averaging volume size on the macroscale. Comparison to Darcy's law gives new insight into the relationship between variables at the microscale and macroscale.
Data management of river water quality data: A semi‐automatic procedure for data validation
Authors: Clement L. , Thas O. , Ottoy J. P. , Vanrolleghem P. A.
Published: August 2007

Monitoring networks typically generate large amounts of data. Before the data can be added to the database, they have to be validated. In this paper, a semi‐automatic procedure is presented to validate river water quality data. On the basis of historical data, additive models are established to predict new observations and to construct prediction intervals (PI's). A new observation is accepted if it is located in the interval. The coverage of the prediction intervals and its power to detect anomalous data are assessed in a simulation study. The method is illustrated on two case studies in which the method detected abnormal nitrate concentrations in the water body provoked by a dry summer which was followed by an extreme winter period. The case studies also show that similar to classical multivariate outlier detection tools, the semi‐automatic procedure allows the detection of suspicious observations lying at the edges as well as observations lying at the center of the univariate distribution of the observations, but, without having to impose linear relationships typically associated with these classical methods.
Theoretical expression for the autoconversion rate of the cloud droplet number concentration
Authors: Liu Yangang , Daum Peter H. , McGraw Robert L. , Miller Mark A. , Niu Shengjie
Published: August 2007

Accurate parameterization of the autoconversion rate of the cloud droplet concentration (number autoconversion rate in cm−3 s−1) is critical for evaluating aerosol indirect effects using climate models; however, existing parameterizations are empirical at best. A theoretical expression is presented in this contribution that analytically relates the number autoconversion rate to the liquid water content, droplet concentration and relative dispersion of the cloud droplet size distribution. The analytical expression is theoretically derived by generalizing the analytical formulation previously developed for the autoconversion rate of the cloud liquid water content (mass autoconversion rate in g cm−3 s−1). Further examination of the theoretical number and mass autoconversion rates reveals that the former is not linearly proportional to the latter as commonly assumed in existing parameterizations. The formulation forms a solid theoretical basis for developing multi‐moment representation of the autoconversion process in atmospheric models in general.
Substorm plasma sheet ion pressure profiles
Authors: Wing Simon , Gjerloev Jesper W. , Johnson Jay R. , Hoffman R. A.
Published: August 2007

The plasma sheet pressure, temperature, and density profiles inferred from DMSP observations are used to investigate substorm growth, expansion, early‐recovery, and late‐recovery phases. During the growth phase, the pressure peaks at the inner edge of the plasma sheet. The premidnight pressure peak is associated with the temperature peak, while the postmidnight peak is associated with the density enhancement. After the substorm onset, the pressure at the inner edge diminishes. Instead, the pressure peaks at premidnight from X = −10 to −40 RE, which can be associated with temperature enhancement. During the early and late recovery phases, the pressure peaks at postmidnight, which is associated with a cold, dense ion population, possibly resulting from ion outflow and the substorm current systems. In the near‐Earth region, the entropy decreases after substorm onset, but the specific entropy appears to be roughly conserved.
Inferring fault characteristics using fold geometry constrained by Airborne Laser Swath Mapping at Raplee Ridge, Utah
Authors: Mynatt I. , Hilley G. E. , Pollard D. D.
Published: August 2007

We used Airborne Laser Swath Mapping (ALSM) data to define the geometry of strata in Raplee Ridge in southeastern Utah that were likely deformed by slip on an underlying fault. The fold geometry was used to infer the fault geometry and loading responsible for the folding using the Boundary Element Model, Poly3D. Monte Carlo Markov‐Chain (MCMC) methods created probability density functions (pdfs) that reveal the most likely fault geometry and loading conditions and their uncertainties. Despite the restrictive assumptions of Poly3D, in which body deformations occur from slip on displacement discontinuities in a homogeneous linear‐elastic half‐space, the strata deflections are matched remarkably well, and the resulting inferences of fault geometry and stress field appear reasonable. We propose that similar methods may be used with models that include more complicated rheologies and heterogeneous and anisotropic material properties to estimate fault geometries and loading conditions where only deflection of strata record these parameters.
Adjustment for proxy number and coherence in a large‐scale temperature reconstruction
Authors: Frank David , Esper Jan , Cook Edward R.
Published: August 2007

Proxy records may display fluctuations in climate variability that are artifacts of changing replication and interseries correlation of constituent time‐series and also from methodological considerations. These biases obscure the understanding of past climatic variability, including estimation of extremes, differentiation between natural and anthropogenic forcing, and climate model validation. Herein, we evaluate as a case‐study, the Esper et al. (2002) extra‐tropical millennial‐length temperature reconstruction that shows increasing variability back in time. We provide adjustments considering biases at both the site and hemispheric scales. The variance adjusted record shows greatest differences before 1200 when sample replication is quite low. A reduced amplitude of peak warmth during Medieval Times by about 0.4°C (0.2°C) at annual (40‐year) timescales slightly re‐draws the longer‐term evolution of past temperatures. Many other regional and large‐scale reconstructions appear to contain variance‐related biases.
Large‐scale longitudinal variation in ionospheric height and equatorial spread F occurrences observed by ionosondes
Authors: Saito S. , Maruyama T.
Published: August 2007

Variations in ionospheric height associated with the prereversal enhancement (PRE) at two equatorial ionosonde stations separated by 6.34° in longitude were studied for the first time. The stations used were in Chumphon (10.7°N, 99.4°E, 3.3 Mag. Lat.), Thailand and Bac Lieu (9.3°N, 105.7°E, 1.6 Mag. Lat.), Vietnam. Variations in the virtual height of the bottomside of the F region (h′F) at 2.5 MHz observed at these two stations were analyzed for a period in March and April 2006. When the equatorial spread F (ESF) was not observed, h′F variations at the two stations were very similar, with a local time shift corresponding to the longitude separation. However, when ESF was observed, they were often significantly different. Our results show that h′F enhancement, which could be interpreted as being due to the eastward electric field enhancement, is quite localized in longitude when ESF occurs.
Double‐diffusive convection in groundwater wells
Authors: Love Andrew J. , Simmons Craig T. , Nield D. A.
Published: August 2007

Double‐diffusive convection caused by variations in solute concentration and temperature within a fluid body has previously been studied in connection with oceanic mixing processes, astrophysics, metallurgy, geology, and vadose zone hydrology but has not previously been studied in connection with thermohaline transport in a groundwater well. This paper considers whether double‐diffusive convection induced by salinity and/or temperature variations is a plausible mechanism for heat and solute transport in a groundwater well. This is examined theoretically using Rayleigh number stability “onset” criteria for fluid in a cylinder that considers the cylindrical well geometry and geothermal/solute boundary conditions. Theoretical results suggest that both monotonic and oscillatory double‐diffusive convection are plausible transport phenomena in groundwater wells. These analyses have important implications for hydrogeology because they provide another theoretically plausible mechanism by which heat and solute may mix in a well. This previously unaccounted for thermohaline mixing phenomenon may therefore be critical in the interpretation of well hydrogeologic and hydrochemical data.
Dendrimers and their applications in immunoassays and clinical diagnostics
Authors: Singh Pratap
Published: August 2007

Unlike other synthetic polymeric materials, Starburst® (Dendritic Nanotechnologies Inc., Mount Pleasant, MI, U.S.A.) dendrimers are a unique class of nanoscopic synthetic macromolecules. They allow controlled architecture, low polydispersity and defined molecular mass. These molecules contain a very large number of reactive terminal functional groups that have been utilized to covalently couple a large variety of molecules, including proteins. The unique properties associated with these dendrimer‐coupled protein complexes have been exploited in the development of sensitive immunoassays for a variety of clinically significant biochemical markers. In addition, dendrimer‐coupled antibody reagents have been utilized in the Stratus® CS system, an automated clinical analyser available commercially since 1998. The present review provides an overview of the synthesis and properties of these dendrimers, preparation of dendrimer‐coupled protein reagents and their applications in development of immunoassays.
Rac1 and RhoA GTPases have antagonistic functions during N‐cadherin‐dependent cell—cell contact formation in C2C12 myoblasts
Authors: Comunale Franck , Causeret Marie , Favard Cyril , Cau Julien , Taulet Nicolas , Charrasse Sophie , Gauthier‐Rouvière Cécile
Published: August 2007

Background information. N‐cadherin, a member of the Ca2+‐dependent cell—cell adhesion molecule family, plays an essential role in the induction of the skeletal muscle differentiation programme. However, the molecular mechanisms which govern the formation of N‐cadherin‐dependent cell—cell contacts in myoblasts remain unexplored.

Results. In the present study, we show that N‐cadherin‐dependent cell contact formation in myoblasts is defined by two stages. In the first phase, N‐cadherin is highly mobile in the lamellipodia extensions between the contacting cells. The second stage corresponds to the formation of mature N‐cadherin‐dependent cell contacts, characterized by the immobilization of a pool of N‐cadherin which appears to be clustered in the interdigitated membrane structures that are also membrane attachment sites for F‐actin filaments. We also demonstrated that the formation of N‐cadherin‐dependent cell—cell contacts requires a co‐ordinated and sequential activity of Rac1 and RhoA. Rac1 is involved in the first stage and facilitates N‐cadherin‐dependent cell—cell contact formation, but it is not absolutely required. Conversely, RhoA is necessary for N‐cadherin‐dependent cell contact formation, since, via ROCK (Rho‐associated kinase) signalling and myosin 2 activation, it allows the stabilization of N‐cadherin at the cell—cell contact sites.

Conclusions. We have shown that Rac1 and RhoA have opposite effects on N‐cadherin‐dependent cell—cell contact formation in C2C12 myoblasts and act sequentially to allow its formation.
A dinoflagellate CDK5‐like cyclin‐dependent kinase
Authors: Bertomeu Thierry , Rivoal Jean , Morse David
Published: August 2007

Background information. Mitosis during the dinoflagellate cell cycle is unusual in that the nuclear envelope remains intact and segregation of the permanently condensed chromosomes uses a cytoplasmic mitotic spindle. To examine regulation of the dinoflagellate cell cycle in the context of these unusual nuclear features, it is necessary to isolate and characterize cell cycle regulators such as CDK (cyclin‐dependent kinase).

Results. We report the characterization of a CDK from the dinoflagellate Lingulodinium polyedrum. This CDK reacts with an anti‐PSTAIRE antibody and was identified by protein microsequencing after partial purification. The protein microsequence shows homology toward the Pho85/CDK5 clade of CDKs. Neither the amount nor the phosphorylation state changed over the course of the cell cycle, in agreement with results reported for CDK5 family members in other systems.

Conclusions. We conclude we have probably isolated a dinoflagellate CDK5‐like protein. The data reported here support the identification of this protein as a CDK5 homologue, and suggest that dinoflagellates may contain several CDK families.
Firing of transcription and compartmentalization of splicing factors in tomato radicle nuclei during germination1
Authors: Echeverría Olga , Vázquez‐Nin Gerardo , Juárez‐Chavero Silvia , de la Espina Susana Moreno Díaz
Published: August 2007

Background information. Germination is a well‐characterized process in which embryo cells of seeds experience a programmed transition from quiescence to proliferation. For this reason they constitute a very good system to analyse nuclear evolution from a dehydrated practically inactive state until the steady state of proliferation. We analysed the temporal and spatial organization of transcription and splicing factors in nuclei of tomato radicle cells during germination. To address this issue we performed in situ immunodetection of several markers of these processes: the Z‐DNA stretches forming behind the active RNA polymerases, the splicing proteins U2B″ and Sm, and the trimethyl guanosin cap of small nuclear RNA. The concomitant structural changes of the different nuclear compartments were studied in meristematic nuclei by electron microscopy and high‐resolution cytochemistry for DNA and ribonucleoproteins.

Results. In quiescent cells practically no Z‐DNA stretches were detected and splicing components localized mainly to one or two Cajal bodies associated to the nucleolus. In early germination, a massive de‐condensation of chromatin and nucleolar Z‐DNA conformation stretches were first detected, followed by the relocation of scarce splicing components to the small interchromatin spaces. Nucleoplasmic Z‐DNA stretches were not detected until 4 h of imbibition and were accompanied by an important increase of splicing components in this nuclear domain. Soon after the post‐germination stage, transcription and splicing topology and nuclear organization in meristematic nuclei resemble those in steady state growing tomato roots.

Conclusions. Our results demonstrate that, in tomato, dormant nuclei splicing factors are stored in nucleolar Cajal bodies. In early germination, RNA polymerase I transcription is first activated, whereas mRNA transcription is fired later and is accompanied by a massive de‐condensation of chromatin and accumulation of splicing factors in the interchromatin domains. Nucleoplasmic Cajal bodies appear later in germination.
Halting a cellular production line: responses to ribosomal pausing during translation
Authors: Buchan J. Ross , Stansfield Ian
Published: August 2007

Cellular protein synthesis is a complex polymerization process carried out by multiple ribosomes translating individual mRNAs. The process must be responsive to rapidly changing conditions in the cell that could cause ribosomal pausing and queuing. In some circumstances, pausing of a bacterial ribosome can trigger translational abandonment via the process of trans‐translation, mediated by tmRNA (transfer—messenger RNA) and endonucleases. Together, these factors release the ribosome from the mRNA and target the incomplete polypeptide for destruction. In eukaryotes, ribosomal pausing can initiate an analogous process carried out by the Dom34p and Hbs1p proteins, which trigger endonucleolytic attack of the mRNA, a process termed mRNA no‐go decay. However, ribosomal pausing can also be employed for regulatory purposes, and controlled translational delays are used to help co‐translational folding of the nascent polypeptide on the ribosome, as well as a tactic to delay translation of a protein while its encoding mRNA is being localized within the cell. However, other responses to pausing trigger ribosomal frameshift events. Recent discoveries are thus revealing a wide variety of mechanisms used to respond to translational pausing and thus regulate the flow of ribosomal traffic on the mRNA population.
High frequency dynamics and structural relaxation process in liquid ammonia
Authors: Giura P. , Angelini R. , Datchi F. , Ruocco G. , Sette F.
Published: August 2007

The dynamic structure factor S(Q,ω) of liquid ammonia has been measured by inelastic x-ray scattering in the terahertz frequency region as a function of the temperature in the range of 220–298K at a pressure P=85bars. The data have been analyzed using the generalized hydrodynamic formalism with a three term memory function to take into account the thermal, the structural, (α) and the microscopic (μ) relaxation processes affecting the dynamics of the liquid. This allows to extract the temperature dependence of the structural relaxation time (τα) and strength (Δα). The former quantity follows an Arrhenius behavior with an activation energy Ea=2.6±0.2kcal∕mol, while the latter is temperature independent suggesting that there are no changes in the interparticle potential and arrangement with T. The obtained results, compared with those already existing in liquid water and liquid hydrogen fluoride, suggest the strong influence of the connectivity of the molecular network on the structural relaxation.
Integration of vacuum potential energy into ideal magnetohydrodynamic stability calculations for flux-core-spheromak configurations
Authors: Alladio F. , Mancuso A. , Micozzi P. , Rogier F.
Published: August 2007

In the calculation of the ideal magnetohydrodynamic free-boundary stability of magnetoplasma equilibria, the integration of the perturbed magnetic energy in the vacuum region that can exist between the plasma edge and nearby conducting shells is extended to axisymmetric configurations composed in part by closed and in part by open field lines. Examples of such equilibria are flux-core-spheromaks and spherical tori with a plasma central column, where a magnetic separatrix divides a spherical torus—with closed field lines—from a central screw pinch discharge—with open field lines that end on the sustaining electrodes. These configurations pose two problems: their plasma-vacuum interface is composed of multiple flux surfaces (i.e., they enclose different values of toroidal and poloidal flux) and their plasma extends up to the symmetry axis. A Green’s function method based on two-dimensional finite elements is used to solve both problems, and an application to the experimental results of the Tokyo University Spherical Torus No. 3 flux-core-spheromak experiment [N. Amemiya, A. Morita, and M. Katsurai, J. Phys. Soc. Jpn. 63, 1552 (1993)] is illustrated.
Electronic circular dichroism of disulphide bridge: Ab initio quantum-chemical calculations
Authors: Skomorowski Wojciech , Pecul Magdalena , Sałek Paweł , Helgaker Trygve
Published: August 2007

Electronic circular dichroism (ECD) parameters of the disulphide chromophore have been calculated for dihydrogen disulphide, dimethyl disulphide, and cystine using density-functional theory, coupled-cluster theory, and multiconfigurational self-consistent field theory. The objective is twofold: first, to examine the performance of the Coulomb-attenuated CAM-B3LYP functional for the calculation of ECD spectra; second, to investigate the dependence of the ECD parameters on the conformation around the disulphide bridge. The CAM-B3LYP functional improves considerably on the B3LYP functional, giving results comparable to CCSD theory and to MCSCF theory in an extended active space. The conformational dependence of the ECD parameters does not change much upon substitution, which is promising for the application of ECD in structural investigations of proteins containing disulphide bridges.
Xe
129
chemical shift by the perturbational relativistic method: Xenon fluorides
Authors: Lantto Perttu , Vaara Juha
Published: August 2007

Xe 129 nuclear shielding tensor is calculated at the leading-order, one-electron Breit-Pauli perturbation theory (BPPT) level for the xenon fluorides XeF+, XeF2, XeF3+, and XeF4 that cover the large nuclear magnetic resonance chemical shift range of this nucleus. BPPT is found to improve the shift range and relative shifts as compared to the nonrelativistic (NR) theory. While the full BPPT expansion consists of 16 relativistic terms, 5 of them are responsible for the entire chemical shift and shielding anisotropy. The remaining terms are practically isotropic, corelike contributions that are significant for the absolute shielding constant but cancel for the relative chemical shifts. The five principal terms are due to the spin-orbit-modified wave function allowing the Fermi contact and spin-dipole hyperfine interactions to be coupled to the orbital Zeeman interaction, as well as three distinct scalar relativistic modifications of the NR paramagnetic shielding: wave function change due to mass-velocity and Darwin interactions and the relativistic modification of the orbital hyperfine interaction. A very good agreement with the experimental shifts is obtained for XeF2 and the particularly challenging XeF+ species when both the NR and the five main relativistic terms are calculated at electron-correlated ab initio levels of theory. The performance of density-functional theory (DFT) with different pure and hybrid exchange-correlation functionals (with increasing exact exchange admixture) is tested against the ab initio data for each individual contribution. It is shown that DFT has difficulties in the description of paramagnetic shielding, already and especially in the NR contribution, which causes a large discrepancy of DFT results with experiment for xenon fluorides. In contrast, the DFT errors for the relativistic terms cancel out to the extent that a fairly good approximation of the total relativistic shift and anisotropy contributions may be obtained. A combination of high-level ab initio NR calculation with hybrid DFT estimates of the five main BPPT terms is proposed for reasonable estimates of xenon chemical shift in molecules. For the difficult cases such as the present XeF+ and XeF3+ cations, correlated ab initio calculations are unavoidable throughout. None of the other currently available relativistic methods, either at the fully relativistic or a variationally stable quasirelativistic levels of theory, surpasses the quality of the present approach for Xe shifts in these systems.
Self-consistent field tight-binding model for neutral and (multi-) charged carbon clusters
Authors: Montagnon Laurent , Spiegelman Fernand
Published: August 2007

A semiempirical model for carbon clusters modeling is presented, along with structural and dynamical applications. The model is a tight-binding scheme with additional one- and two-center distance-dependent electrostatic interactions treated self-consistently. This approach, which explicitly accounts for charge relaxation, allows us to treat neutral and (multi-) charged clusters not only at equilibrium but also in dissociative regions. The equilibrium properties, geometries, harmonic spectra, and relative stabilities of the stable isomers of neutral and singly charged clusters in the range n=1–14, for C20 and C60, are found to reproduce the results of ab initio calculations. The model is also shown to be successful in describing the stability and fragmentation energies of dictations in the range n=2–10 and allows the determination of their Coulomb barriers, as examplified for the smallest sizes (C22+,C32+,C42+). We also present time-dependent mean-field and linear response optical spectra for the C8 and C60 clusters and discuss their relevance with respect to existing calculations.
On the use of the Kolmogorov-Landau approach in deriving various correlation functions in two-dimensional incompressible turbulence
Authors: Chakraborty Sagar
Published: August 2007

We look at various correlation functions, which include those that involve both the velocity and the vorticity fields, in two-dimensional (2D) isotropic homogeneous decaying turbulence. We adopt the more intuitive approach due to Kolmogorov (and subsequently Landau in his text on fluid dynamics) and show that how the 2D turbulence results, obtainable using other methods, may be established in a simpler way. Also, some experimentally verifiable correlation functions in the dissipation range have been derived for the same system. The paper also showcases the inability of the Kolmogorov-Landau approach to get the “one-eighth law” in the enstrophy cascade region. As discussed in the paper, this may raise the spectre of logarithmic corrections once again in 2D turbulence.
Effects of parallel ion motion on zonal flow generation in ion-temperature-gradient mode turbulence
Authors: Anderson J. , Li J. , Kishimoto Y.
Published: August 2007

The role of parallel ion motion for zonal flow generation in ion-temperature-gradient (ITG) mode turbulence is investigated with focus on the effects of acoustic modes and toroidicity on the zonal flow. One possible reason for the weak suppression of ITG turbulence by zonal flows found in experiments in the Columbia Linear Machine [Phys. Plasmas 13, 055905 (2006)] might be due to the small toroidicity (ϵn=2Ln∕R) in the experiment. The zonal flow is often directly dependent on the ITG mode and the coupling of zonal flow to acoustic modes and hence is directly affected by any change of the relevant parameters. The model consists of the continuity, temperature, and parallel ion momentum equations for the ITG turbulence. The zonal flow time evolution is described by a Hasegawa-Mima-like equation, and a fifth-order zonal flow dispersion relation is derived. The results are interpreted in terms of quality of zonal flows, i.e., the ratio of growth rate and real frequency (Q=ΩIM∕ΩRE). It is found that the quality of the zonal flow rapidly decreases with decreasing toroidicity.
Water diffusion through a membrane protein channel: A first passage time approach
Authors: van Hijkoop Vincent J. , Dammers Anton J. , Malek Kourosh , Coppens Marc-Olivier
Published: August 2007

Water diffusion through OmpF, a porin in the outer membrane of Escherichia coli, is studied by molecular dynamics simulation. A first passage time approach allows characterizing the diffusive properties of a well-defined region of this channel. A carbon nanotube, which is considerably more homogeneous, serves as a model to validate the methodology. Here we find, in addition to the expected regular behavior, a gradient of the diffusion coefficient at the channel ends, witness of the transition from confinement in the channel to bulk behavior in the connected reservoirs. Moreover, we observe the effect of a kinetic boundary layer, which is the counterpart of the initial ballistic regime in a mean square displacement analysis. The overall diffusive behavior of water in OmpF shows remarkable similarity with that in a homogeneous channel. However, a small fraction of the water molecules appears to be trapped by the protein wall for considerable lengths of time. The distribution of trapping times exhibits a broad power law distribution ψ(τ)∼τ−2.4, up to τ=10ns, a bound set by the length of the simulation run. We discuss the effect of this distribution on the dynamic properties of water in OmpF in terms of incomplete sampling of phase space.
Targeted excited state algorithms
Authors: Dorando Jonathan J. , Hachmann Johannes , Chan Garnet Kin-Lic
Published: August 2007

To overcome the limitations of the traditional state-averaging approaches in excited state calculations, where one solves and represents all states between the ground state and excited state of interest, we have investigated a number of new excited state algorithms. Building on the work of van der Vorst and Sleijpen [SIAM J. Matrix Anal. Appl. 17, 401 (1996)], we have implemented harmonic Davidson and state-averaged harmonic Davidson algorithms within the context of the density matrix renormalization group (DMRG). We have assessed their accuracy and stability of convergence in complete-active-space DMRG calculations on the low-lying excited states in the acenes ranging from naphthalene to pentacene. We find that both algorithms offer increased accuracy over the traditional state-averaged Davidson approach, and, in particular, the state-averaged harmonic Davidson algorithm offers an optimal combination of accuracy and stability in convergence.
20
dB
-enhanced coupling to slot photonic crystal waveguide using multimode interference coupler
Authors: Chen Xiaonan , Jiang Wei , Chen Jiaqi , Gu Lanlan , Chen Ray T.
Published: August 2007

The authors experimentally demonstrate a slot photonic crystal structure for guiding light in a sub-100-nm-wide low-index region. A multimode interference-based coupling structure is introduced to couple light into such a narrow slot photonic crystal waveguide. A coupler of 1.26μm long enhances the coupling efficiency by 20dB for the quasi-transverse-electric mode over 35nm optical bandwidth centered at 1562nm. The measured transmission spectra are in good agreement with the simulated band diagram.
Effects of clustering on the properties of defects in neutron irradiated silicon
Authors: Fleming R. M. , Seager C. H. , Lang D. V. , Cooper P. J. , Bielejec E. , Campbell J. M.
Published: August 2007

We have exposed silicon bipolar transistors to fast neutrons and characterized the properties of the resulting defects using capacitance-based spectroscopy of the n-type collector. We have performed low-temperature electron capture measurement of the divacancy (=/−) and vacancy-oxygen (−/0) defects after the samples were annealed from 350–500 K. We show from a simple rate equation analysis that one can define an unambiguous test for cluster-induced reductions of defect level occupation due to slow capture. This allows easy identification of deep level transient spectroscopy (DLTS) levels where the capture is inhibited due to band bending. Our measurements show extremely long, temperature-dependent capture times for the doubly charged state of the divacancy. We have modeled the capture dynamics as a function of annealing using a simple electrostatic band-bending approach coupled with a realistic simulation of the cluster size and shape distribution as estimated from computer simulation of the damage cascades. We find that our simulation of neutron damage combined with electrostatic modeling of the capture data, with only a limited number of adjustable parameters, fits the measured data very well. Our annealing studies indicate, however, that isolated divacancies (those with visible DLTS signals from two acceptor states) comprise only about 30% of the charge in the defect cluster.
Multiple modes of instability in a box heated from the side in low-Prandtl-number fluids
Authors: Henry D. , BenHadid H.
Published: August 2007

The existence of multiple modes of instability in Rayleigh-Bénard or Marangoni-Bénard situations has been known for many years. This existence is shown for the first time for low-Prandtl-number flows in three-dimensional cavities heated from the side. For such a situation, the study of the flow transitions has long remained a challenge, as these transitions occur in already very intense flows. The study is possible here thanks to performing numerical methods, and the ten first instability modes are determined for a wide range of aspect ratios and Prandtl number values. The most striking feature of our results is the very frequent change of leading mode when aspect ratios or Prandtl number are changed, which indicates different flow structures triggered at the transitions, either steady or oscillatory and breaking some of the symmetries of the problem.
Using pn junction depletion regions to position epitaxial nanowires
Authors: Quitoriano Nathaniel J. , Kamins Theodore I.
Published: August 2007

Si nanowires were grown horizontally using the vapor-liquid-solid method from vertical {111} surfaces etched into a (110) Si substrate. The nanowires were catalyzed by negatively charged, citrate-stabilized, Au nanoparticles. The negative charge on the nanoparticles was used to position them along a positively charged depletion region formed by a pn junction. By positioning the nanoparticle catalysts, the epitaxial Si nanowires catalyzed by the nanoparticles were also positioned along this junction. The structure that best positioned the nanowires was highly doped n-type material on a lightly doped p-type substrate. Enhanced positioning of the nanowires was accomplished using a reverse bias across the pn junction.
Relieving Sn whisker growth driven by oxidation on Cu leadframe by annealing and reflowing treatments
Authors: Wei C. C. , Liu P. C. , Chen Chih , Lee Jeffrey C.B. , Wang I Ping
Published: August 2007

Owing to environmental concern, Pb-free solders are replacing eutectic tin lead in electronic packaging industry. Thus, whisker growth becomes a serious reliability issue for Sn finishes. In this study, the mechanism of whisker growth from Sn finish on Cu leadframe was investigated under the temperature/humidity storage test. It is found that oxidation of the Sn finish was the driving force behind the whisker growth. Thermal treatments including annealing at 220 °C and reflowing at 260 °C were employed to mitigate the whisker growth. It is found that both heat treatments can significantly reduce the whisker growth rate. It is speculated that the heat treatments can relieve the residual stress in the Sn finishes and can modify their grain structure, resulting in a slower oxidation rate. Thus, they can slow down the grow rate of Sn whiskers. In addition, reflowing treatment can change the columnar grain structure of the Sn film to the equiaxed grain structure in some of its regions, resulting in a lower grain boundary diffusion rate of Sn. Therefore, the reflowed sample had the lowest growth rate of Sn whiskers.
Adsorption of polar molecules on krypton clusters
Authors: Rosso A. , Pokapanich W. , Öhrwall G. , Svensson S. , Björneholm O. , Tchaplyguine M.
Published: August 2007

The formation process of binary clusters has been studied using synchrotron based core level photoelectron spectroscopy. Free neutral krypton clusters have been produced by adiabatic expansion and doped with chloromethane molecules using the pickup technique. The comparison between the integrated intensities, linewidths, and level shifts of the cluster features of pure krypton and of chloromethane-krypton clusters has been used to obtain information about the cluster geometry. We have shown that most of the chloromethane molecules remain on the surface of the clusters.