bluuebunny/crossref_metadata_2025 huggingface dataset:
Effekte des Stepping Stones Elterngruppentrainings für Familien mit behinderten Kindern
Authors: Hampel Olaf Alexander , Hasmann Sandra Elisabeth , Schaadt Anna-Katharina , Holl Reinhard , Petermann Franz , Hasmann Reiner
Published: February 2010

Stepping Stones Triple P wurde als verhaltenstherapeutisch orientiertes Elterngruppentraining bereits in Australien erfolgreich evaluiert. Im Rahmen einer Multicenterstudie in verschiedenen Sozialpädiatrischen Zentren (SPZ) und weiterer Versorgungseinrichtungen wurde Stepping Stones Triple P als Elterngruppentraining eingeführt und auf seine Wirksamkeit im deutschen Sprachraum überprüft. Unsere Daten zeigen eine signifikante Reduktion dysfunktionalen Erziehungsverhaltens, elterlicher Belastungen und kindlicher Verhaltensprobleme. Die vorliegende Analyse zeigt, dass ungünstige psychosoziale Belastungen den Therapieerfolg stark reduzieren. Gute bzw. eingeschränkte elterlicher Mitarbeit beeinflussen dagegen den Therapieerfolg nur leicht.
Geodetic imaging of plate motions, slip rates, and partitioning of deformation in Japan
Authors: Loveless John P. , Meade Brendan J.
Published: February 2010

Interseismic deformation in Japan results from the combined effects of tectonic processes including rotation of crustal blocks and the earthquake cycle process of elastic strain accumulation about upper plate faults and subduction zone interfaces. We use spherical linear block theory constrained by geodetic observations from densely spaced Global Positioning System (GPS) stations to estimate plate motions, fault slip rates, and spatially variable interplate coupling on the Japan‐Kuril, Sagami, and Nankai subduction zones. The reference model developed in this paper consists of 20 blocks, produces a mean residual velocity magnitude of 1.84 mm/yr at 950 stations, and accounts for 96% of the observed interseismic deformation signal. We estimate fault slip rates in excess of 15 mm/yr along the Niigata‐Kobe Tectonic Zone and Itoigawa‐Shizuoka Tectonic Line through central Japan, confirming their hypothesized roles as major tectonic boundaries. Oblique convergence across the Nankai Trough is partitioned, with 3/4 of the ∼30 mm/yr of trench‐parallel motion accommodated by strike‐slip motion on the subduction interface and the remaining 1/4 accommodated by right‐lateral slip on the Median Tectonic Line. In contrast, our models suggest negligible slip partitioning in eastern Hokkaido, where oblique slip on the Japan‐Kuril subduction interface accommodates all of the trench‐parallel component of relative plate motion. Inferred spatial variations in the rake and magnitude of slip deficit on subduction zone interfaces reflect the influences of megathrust geometry and earthquake cycle processes such as enhanced elastic strain accumulation about seismic asperities and coseismic sense fault motion indicative of silent slip events or afterslip following large earthquakes.
Predicting the potential for lightning activity in Mediterranean storms based on the Weather Research and Forecasting (WRF) model dynamic and microphysical fields
Authors: Yair Yoav , Lynn Barry , Price Colin , Kotroni Vassiliki , Lagouvardos Konstantinos , Morin Efrat , Mugnai Alberto , Llasat Maria del Carmen
Published: February 2010

A new parameter is introduced: the lightning potential index (LPI), which is a measure of the potential for charge generation and separation that leads to lightning flashes in convective thunderstorms. The LPI is calculated within the charge separation region of clouds between 0°C and −20°C, where the noninductive mechanism involving collisions of ice and graupel particles in the presence of supercooled water is most effective. As shown in several case studies using the Weather Research and Forecasting (WRF) model with explicit microphysics, the LPI is highly correlated with observed lightning. It is suggested that the LPI may be a useful parameter for predicting lightning as well as a tool for improving weather forecasting of convective storms and heavy rainfall.
Physically based model of downstream fining in bedrock streams with lateral input
Authors: Chatanantavet Phairot , Lajeunesse Eric , Parker Gary , Malverti Luce , Meunier Patrick
Published: February 2010

Bed load particles in bedrock streams receiving lateral input from hillslopes may or may not show a clear, monotonic pattern of size reduction in the downstream direction. Both abrasion and selective sorting may play important roles in generating downstream fining. The objective of this study is to develop a physically based model of downstream fining in bedrock streams with lateral input based on both processes. A surface‐based gravel transport relation for the size mixture is employed to account for the effect of selective sorting (differential transport). While the model produces silt and sand by abrasion, it is also assumed to loosely capture particle fracturing via a lumped abrasion coefficient embodied in Sternberg's law. The model is here tested against field data from Vieux Habitants River in Guadeloupe Island, which is located in the Caribbean Sea. The river shows clear downstream fining, and this pattern is captured reasonably well by the model. The model results indicate that abrasion (including fracturing) is solely responsible for the downstream fining pattern for most of the study reach of the Vieux Habitants River. Sensitivity analysis of the model has also been performed. The model results suggest that, in general, selective sorting by differential transport can play a role in downstream fining only in cases of streams with relatively fine gravel sizes and lower slopes. The results also indicate that abrasion (including fracturing) and selective sorting can be equally important for downstream fining in bedrock rivers. The results also suggest that future work should explicitly consider fracturing (comminution) separately from abrasion (wear) rather than lumping them in a Sternberg‐type coefficient.
An investigation of the association between steady magnetospheric convection and CIR stream interfaces
Authors: Kissinger J. , McPherron R. L. , Angelopoulos V. , Hsu T.‐S. , McFadden J. P.
Published: February 2010

It has been postulated that steady magnetospheric convection (SMC), a mode of response of the Earth's magnetosphere to solar wind driving, is caused by balanced day and night side reconnection. We investigate this possibility with a statistical study of return flows in the magnetotail during SMC using the THEMIS mission. Between December 2007 to April 2009, 153 events were identified. We find flows greater than 100 km/s throughout the magnetotail but no distinct pattern of flow channels. SMC occurrence is compared with that of stream interfaces (SI) at the center of corotating interaction regions. “Frequent” SMCs are observed ±1 day around the SI, and “infrequent” 3 to 1.5 days before the SI. The typical solar wind parameters in the frequent interval are higher than expected from previous studies. We found that rectified solar wind electric field steadiness predicts that SMC will occur when this is smaller than average.
From solar radiation measurements to optical properties: 1998–2008 trends in Japan
Authors: Kudo Rei , Uchiyama Akihiro , Yamazaki Akihiro , Sakami Tomonori , Kobayashi Eriko
Published: February 2010

Trends from April 1998 to March 2008 in surface global irradiance, aerosol surface direct radiative forcing, and aerosol optical properties (optical thickness, single scattering albedo, and asymmetry factor) were investigated based on measurements of the surface solar radiation under clear skies at Tsukuba, Japan. The optical properties were estimated by optimizing the external mixture of four assumed aerosols (water soluble, soot, sea salt, and dust) to the surface direct and diffuse irradiances in visible and near infrared regions. The surface global irradiance was increased by an increase of single scattering albedo, not by a decrease of optical thickness. Furthermore, the increasing trend of single scattering albedo may be related to the reduced emission of black carbon in East Asia.
Improving the consistency of ocean color data: A step toward climate data records
Authors: Gregg Watson W. , Casey Nancy W.
Published: February 2010

Two ocean color missions, SeaWiFS and MODIS, overlap in time and are processed with consistent methods. Global annual median chlorophyll from SeaWiFS and MODIS differ by 12.2%. These discrepancies exceed the maximum observed interannual variability globally and in every major oceanographic basin. Estimates of trends are affected as well. For 1998–2007 the SeaWiFS global trend is −2.6% (not statistically significant). Substitution of MODIS for SeaWiFS in 2003–2007 produces a −18% significant trend. A new approach that incorporates in situ data improves the consistency of the two sensor data sets. The global difference is −0.6% and the 10‐year trend of SeaWiFS and MODIS agrees with standalone SeaWiFS (−3.3%, not significant). In oceanographic basins where sampling biases are small the differences are less than the maximum observed interannual variability. The approach improves the consistency of multiple successive ocean color missions and represents a step toward scientifically reliable Climate Data Records.
Observations of ice nucleation by ambient aerosol in the homogeneous freezing regime
Authors: Richardson Mathews S. , DeMott Paul J. , Kreidenweis Sonia M. , Petters Markus D. , Carrico Christian M.
Published: February 2010

We measured the freezing activation curves for ambient particles as a function of relative humidity with respect to water over the temperature range of −40° to −50°C using a continuous flow diffusion chamber, and compared the observations with those for ammonium sulfate particles and predictions from a parametric representation of homogeneous freezing of solution particles as a function of water activity and temperature. Since it has been proposed that the rate of homogeneous freezing depends on solution water activity, we made separate measurements of the hygroscopicity (κ) of the ambient aerosol. Observed κ ranged from 0.1 to 0.2, lower than that of ammonium sulfate (0.6) and representative of a continental aerosol. As predicted for this difference in κ, there was no significant difference between the homogeneous freezing conditions of size‐selected ammonium sulfate and the apparent homogeneous freezing conditions of same‐sized ambient aerosol. Further, the parameterization predicted freezing fraction‐relative humidity relationships for non size‐selected ambient aerosol that differed by only 0.5 to 1.5% relative humidity from observed relations at the tested temperatures, well within experimental uncertainty. Our findings confirm that the tested ambient aerosols, with hygroscopicities typical of continental regions, freeze homogeneously as expected based on present understanding for single component solution drops in the laboratory. Results also confirm that freezing is more sensitive to particle size than to composition, for particles containing at least a few percent by volume of hygroscopic species.
Retrieving electric resistivity data from self‐potential measurements by cross‐correlation
Authors: Slob Evert , Snieder Roel , Revil André
Published: February 2010

We show that the two‐point cross‐correlation of self‐potential field recordings is equal to the electric resistivity between the two points. This holds under the condition that spatially and temporally uncorrelated noise sources exist throughout the volume. These sources should have a known amplitude spectrum and their correlated strengths should be proportional to the dissipative medium property function. Natural fluctuations, such as thermal noise, may occur that satisfy the necessary conditions. When these fluctuations are random deviations from a state of thermal equilibrium, the fluctuation‐dissipation theorem can be used to describe these sources. Other types of sources may exist, such as the ones creating the self‐potential field through coupling with fluctuations in pressure, temperature and chemical potential gradients.
Phytoplankton and light limitation in the Southern Ocean: Learning from high‐nutrient, high‐chlorophyll areas
Authors: Venables Hugh , Moore C. Mark
Published: February 2010

Most of the Southern Ocean is a high‐nutrient, low‐chlorophyll (HNLC) area. There are exceptions to this situation downstream of some of the islands, where iron from the islands or surrounding shallow plateau fertilizes the mixed layer and causes a phytoplankton bloom in spring and summer. The main locations where this occurs are downstream of the South Georgia, Crozet, and Kerguelen islands. Data on mixed layer depths from Argo float profiles together with Sea‐viewing Wide Field‐of‐view Sensor chlorophyll a (chl a) and photosynthetically available radiation from these high‐nutrient, high‐chlorophyll (HNHC) areas are combined to study the effects of mixed layer‐averaged light availability on phytoplankton concentrations in areas where iron limitation has been lifted. The results of this analysis are then transferred to HNLC areas to assess the potential importance of light limitation through the year. We conclude that light limitation does not significantly constrain the annual integrated standing stock of chl a in the HNLC Southern Ocean.
Atmospheric chemistry of an Antarctic volcanic plume
Authors: Oppenheimer Clive , Kyle Philip , Eisele Fred , Crawford Jim , Huey Greg , Tanner David , Kim Saewung , Mauldin Lee , Blake Don , Beyersdorf Andreas , Buhr Martin , Davis Doug
Published: February 2010

We report measurements of the atmospheric plume emitted by Erebus volcano, Antarctica, renowned for its persistent lava lake. The observations were made in December 2005 both at source, with an infrared spectrometer sited on the crater rim, and up to 56 km downwind, using a Twin Otter aircraft; with the two different measurement platforms, plume ages were sampled ranging from <1 min to as long as 9 h. Three species (CO, carbonyl sulfide (OCS), and SO2) were measured from both air and ground. While CO and OCS were conserved in the plume, consistent with their long atmospheric lifetimes, the downwind measurements indicate a SO2/CO ratio about 20% of that observed at the crater rim, suggesting rapid chemical conversion of SO2. The aircraft measurements also identify volcanogenic H2SO4, HNO3 and, recognized for the first time in a volcanic plume, HO2NO2. We did not find NOx in the downwind plume despite previous detection of NO2 above the crater. This suggests that near‐source NOx was quickly oxidized to HNO3 and HO2NO2, and probably NO32−(aq), possibly in tandem with the conversion of SO2 to sulfate. These fast processes may have been facilitated by “cloud processing” in the dense plume immediately downwind from the crater. A further striking observation was O3 depletion of up to ∼35% in parts of the downwind plume. This is likely to be due to the presence of reactive halogens (BrO and ClO) formed through heterogeneous processes in the young plume. Our analysis adds to the growing evidence for the tropospheric reactivity of volcanic plumes and shows that Erebus volcano has a significant impact on Antarctic atmospheric chemistry, at least locally in the Southern Ross Sea area.
Comparison of CHAMP and TIME‐GCM nonmigrating tidal signals in the thermospheric zonal wind
Authors: Häusler K. , Lühr H. , Hagan M. E. , Maute A. , Roble R. G.
Published: February 2010

Four years (2002–2005) of continuous accelerometer measurements taken onboard the CHAMP satellite (orbit altitude ∼400 km) offer a unique opportunity to investigate the thermospheric zonal wind on a global scale. Recently, we were able to relate the longitudinal wave‐4 structure in the zonal wind at equatorial latitudes to the influence of nonmigrating tides and in particular to the eastward propagating diurnal tide with zonal wave number 3 (DE3). The DE3 tide is primarily excited by latent heat release in the tropical troposphere in deep convective clouds. In order to investigate the mechanisms that couple the tidal signals to the upper thermosphere, we undertook a comparison with the thermosphere‐ionosphere‐mesosphere‐electrodynamics general circulation model (TIME‐GCM) developed at the National Center for Atmospheric Research (NCAR). We ran the model for a day in March, June, September, and December and applied the same processing steps to the model output as was done for the CHAMP tidal analysis. The main results of the comparison can be summarized as follows: (1) TIME‐GCM simulations do not correctly reproduce the observed intra‐annual variations of DE3 and the eastward propagating diurnal tide with zonal wave number 2 (DE2). (2) Simulations of DE3 for June are more successful. Both TIME‐GCM and CHAMP show an increase in DE3 amplitudes with decreasing solar flux level. (3) The amplitudes of the simulated westward propagating diurnal tide with zonal wave number 2 (DW2) and the standing diurnal tide (D0) increase with increasing solar flux in June. The predicted dependence of DW2 and DO on solar flux is also observed by CHAMP.
Markov‐switching model for nonstationary runoff conditioned on El Niño information
Authors: Gelati E. , Madsen H. , Rosbjerg D.
Published: February 2010

We define a Markov‐modulated autoregressive model with exogenous input (MARX) to generate runoff scenarios using climatic information. Runoff parameterization is assumed to be conditioned on a hidden climate state following a Markov chain, where state transition probabilities are functions of the climatic input. MARX allows stochastic modeling of nonstationary runoff, as runoff anomalies are described by a mixture of autoregressive models with exogenous input, each one corresponding to a climate state. We apply MARX to inflow time series of the Daule Peripa reservoir (Ecuador). El Niño‐Southern Oscillation (ENSO) information is used to condition runoff parameterization. Among the investigated ENSO indexes, the NINO 1+2 sea surface temperature anomalies and the trans‐Niño index perform best as predictors. In the perspective of reservoir optimization at various time scales, MARX produces realistic long‐term scenarios and short‐term forecasts, especially when intense El Niño events occur. Low predictive ability is found for negative runoff anomalies, as no climatic index correlating properly with negative inflow anomalies has yet been identified.
MHC Restriction of V-V Interactions in Serum IgG
Authors: Leung Earnest , Hoffmann Geoffrey
Published: February 2010

According to Jerne’s idiotypic network hypothesis, the adaptive immune system is regulated by interactions between the variable regions of antibodies, B cells, and T cells. The symmetrical immune network theory is based on Jerne’s hypothesis, and provides a basis for understanding many of the phenomena of adaptive immunity. The theory includes the postulate that the repertoire of serum IgG molecules is regulated by T cells, with the result that IgG molecules express V region determinants that mimic V region determinants present on suppressor T cells. In this paper we describe rapid binding between purified murine serum IgG of H-2b and H-2d mice and serum IgG from the same strain and from MHC-matched mice, but not between serum IgG preparations of mice with different MHC genes. We interpret this surprising finding in terms of a model in which IgG molecules are selected to have both anti-anti-self MHC and anti-anti-anti-self MHC specificity.
New neutron source aims to be top in energy and environmental stewardship
Authors: Feder Toni
Published: February 2010

From windmills to green roofs, the European Spallation Source may be setting a trend for major scientific facilities.
Slow antihydrogen
Authors: Gabrielse Gerald
Published: February 2010

The quest to precisely compare cold antihydrogen and hydrogen atoms should enable physicists to test our understanding of one of reality’s fundamental symmetries.
Origin and Nature of Transmission Modes of Anomalous Effects of meta-Substituents on the 13C Chemical Shift of the Carboxyl Carbon (δCO) of Benzoic Acid
Authors: Sen Gupta Susanta K. , Prasad Rajendra
Published: February 2010

Studies of substituent effects on NMR chemical shifts are of great benefit in determining fine details of electron distribution in molecules. Interestingly, NMR substituent effects are often different and even opposite to those associated with chemical reactivity. Among molecules exhibiting anomalous (reverse) substituent effects is benzoic acid, the standard model for studying substituent effects. The substituent effect on the 13C chemical shift of its carboxyl carbon (δ CO) is just the opposite of that on its acid strength or reactivity. To develop insights into the origin of the anomalous effect of a substituent on δ CO, occupancies of natural atomic orbitals at the carboxyl and ring carbons of a set of 10 meta-substituted benzoic acids have been calculated at the density functional theory level using the B3LYP function with split valance 6–311G++** basis set. Statistical correlations obtained for the 13C chemical shifts, δ CO and δ C-ring of these benzoic acids with the natural atomic orbital occupancies calculated for respective carbon atoms on one hand and with Taft’s inductive and resonance parameters (σ I and σ R BA ) of the substituents on the other hand have been critically analyzed. The findings have established firmly that a meta-substituent’s anomalous effect on δ CO is caused by the substituent-induced changes in the total occupancy of only the p z natural atomic orbitals at the carboxyl carbon. The study has demonstrated further that the transmission of the anomalous effect can be successfully interpreted by a 5.5:–2.5:1 combination of the localized, extended, and resonance-induced π-polarization effects.
Crystal Structures, Topological Analyses, and Magnetic Properties of Manganese-Dihydroxyterephthalate Complexes
Authors: Gao Qiang , Jiang Fei-Long , Wu Ming-Yan , Huang You-Gui , Wei Wei , Zhang Qing-Fu , Hong Mao-Chun
Published: February 2010

Two manganese(ii)-dihydroxyterephthalate complexes were obtained under solvothermal conditions: [Mn(H2dhtp)(H2O)2]
n
(1) and [Mn2(dhtp)(H2O)2]
n
(2) (H4dhtp = 2,5-dihydroxyterephthalate). The 3D framework of complex 1 is constructed by H2dhtp ligands joined to 1D carboxylate-bridged Mn(ii) chains, which features a (4,4)-connected PtS net. Complex 2 contains a novel inorganic honeycomb Mn(ii)–O layer, which is further connected into a 3D (4,8)-connected flu net by dhtp ligands. Magnetic measurements of 1 and 2 were performed in the range of 2–300 K and the results indicate that antiferromagnetic coupling exits in the manganese(ii) centres of both complexes.
Synthesis, Structure, and Selective Cytotoxicity of Organometallic Cp*RuII O-Alkyl-N-phenylcarbamate Sandwich Complexes
Authors: Loughrey Bradley T. , Williams Michael L. , Carruthers Thomas J. , Parsons Peter G. , Healy Peter C.
Published: February 2010

Tetraphenylborate salts of the η6-arene Cp*RuII O-alkyl-N-phenyl carbamate organometallic sandwich complexes, [Cp*Ru(PhNHCO2R)]BPh4 for R = Me (1), Et (2), and n-Pr (3), have been prepared by a facile one-pot reaction between ruthenium trichloride, pentamethylcyclopentadiene, and phenylisocyanate in refluxing alcohol solutions, and have been characterized by Fourier-transform IR and NMR spectroscopy, electrospray mass spectrometry, and single-crystal X-ray structure determinations. In vitro cytotoxicity studies show the complexes to be potent growth inhibitors for a range of tumour cell lines, while expressing significantly lower levels of toxicity towards a normal human fibroblast cell line.
Towards 'Computer-on-a-Particle' Devices: Optoelectronic 1:2 Demultiplexer Based on Nanostructured Cadmium Sulfide
Authors: Podborska Agnieszka , Szaciłowski Konrad
Published: February 2010

Nanocrystalline sulfur-doped cadmium sulfide (CdS) prepared by microwave synthesis was investigated. Photoelectrochemical and optical characteristics of sulfur-doped CdS exhibit the photoelectrochemical photocurrent switching effect. Depending on the wavelength and applied bias, the anodic and/or cathodic photocurrent was observed. The unusual behaviour of nanocrystalline CdS allowed the construction of a combinatorial logic system from this material.
A Unimolecular Half-Subtractor Based on Effective Photoinduced Electron Transfer and Intramolecular Charge Transfer Processes of 1,8-Naphthalimide Derivative
Authors: Leng Bing , Tian He
Published: February 2010

We report a unimolecular system as a combinatorial logic half-subtractor based on a naphthalimide derivative. Chemical inputs (OH– and H+) can significantly change the absorption and fluorescence characteristics through modulating intramolecular charge transfer and photoinduced electron transfer process upon protonation or deprotonation of the molecule. An XOR gate is obtained following the absorbance variations at 485 nm, and an INHIBIT gate is induced when the output signal is monitored at 535 nm in the fluorescence spectra. Large differences in output signals allow unequivocal assignment of logic-0 and logic-1 of both logic gates, which may function in parallel to implement the half-subtractor.
Inheritance and formation of smectite in a texture contrast soil in the Pilliga State Forests, New South Wales
Authors: Walsh Peter G. , Humphreys Geoff S.
Published: February 2010

Smectite genesis is generally considered to require an alkaline environment, for in acid environments it is reportedly unstable. This study shows that smectite is forming in an acid, texture-contrast soil in the Pilliga State Forests in north-western New South Wales. Three modes of smectite genesis in the study soil are presented. The first mode involves direct inheritance from the underlying parent rock. The second and third modes involve precipitation of smectite from solution and its deposition from suspension, respectively. While the bulk of the smectite in the study soil is inherited from the transformation of labile primary minerals and rock fragments in the parent rock, restricted drainage coupled with a parent material capable of supplying the elemental constituents of smectite are also important factors in its genesis.
The antiapoptotic DeltaNp73 is degraded in a c-Jun–dependent manner upon genotoxic stress through the antizyme-mediated pathway
Authors: Dulloo Iqbal , Gopalan Ganesan , Melino Gerry , Sabapathy Kanaga
Published: February 2010

p73, the structural and functional homologue of p53, exists as two major forms: the transactivation-proficient, proapoptotic TAp73 or the transactivation-deficient, antiapoptotic DNp73. Expectedly, expression of both these major forms has to be coordinated precisely to achieve the desired cellular outcome. Genotoxic insults resulting in cell death lead to the stabilization of TAp73, mainly through posttranslational modifications, and the concomitant degradation of DNp73, through poorly understood mechanisms. We have therefore investigated the possible mechanisms of stress-induced DNp73 degradation and show here that c-Jun, the AP-1 family member activated by stress signals and involved in stabilizing TAp73, promotes DNp73 degradation. Genotoxic stress-mediated DNp73 degradation was found to occur in a c-Jun–dependent manner through a ubiquitin-independent but proteasome-dependent mechanism. Absence or down-regulation of c-Jun expression abrogated the reduction of DNp73 levels upon stress insults, whereas overexpression of c-Jun led to its degradation. c-Jun controlled DNp73 degradation through the nonclassical, polyamine-induced antizyme (Az) pathway by regulating the latter’s processing during stress response. Consistently, expression of c-Jun or Az, or addition of polyamines, promoted DNp73 degradation, whereas silencing Az expression or inhibiting Az activity in cells exposed to stress reduced c-Jun–dependent DNp73 degradation. Moreover, Az was able to bind to DNp73. These data together demonstrate the existence of a c-Jun–dependent mechanism regulating the abundance of the antiapoptotic DNp73 in response to genotoxic stress.
The mouse ortholog of NEIL3 is a functional DNA glycosylase in vitro and in vivo
Authors: Liu Minmin , Bandaru Viswanath , Bond Jeffrey P. , Jaruga Pawel , Zhao Xiaobei , Christov Plamen P. , Burrows Cynthia J. , Rizzo Carmelo J. , Dizdaroglu Miral , Wallace Susan S.
Published: February 2010

To protect cells from oxidative DNA damage and mutagenesis, organisms possess multiple glycosylases to recognize the damaged bases and to initiate the Base Excision Repair pathway. Three DNA glycosylases have been identified in mammals that are homologous to the
Escherichia coli
Fpg and Nei proteins, Neil1, Neil2, and Neil3. Neil1 and Neil2 in human and mouse have been well characterized while the properties of the Neil3 protein remain to be elucidated. In this study, we report the characterization of
Mus musculus
(house mouse) Neil3 (MmuNeil3) as an active DNA glycosylase both in vitro and in vivo. In duplex DNA, MmuNeil3 recognizes the oxidized purines, spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino- 5-formamidopyrimidine (FapyA), but not 8-oxo-7,8-dihydroguanine (8-oxoG). Interestingly, MmuNeil3 prefers lesions in single-stranded DNA and in bubble structures. In contrast to other members of the family that use the N-terminal proline as the nucleophile, MmuNeil3 forms a Schiff base intermediate via its N-terminal valine. We expressed the glycosylase domain of MmuNeil3 (MmuNeil3Δ324) in an
Escherichia coli
triple mutant lacking Fpg, Nei, and MutY glycosylase activities and showed that MmuNeil3 greatly reduced both the spontaneous mutation frequency and the level of FapyG in the DNA, suggesting that Neil3 plays a role in repairing FapyG in vivo.
Stimulated coherent anti-Stokes Raman spectroscopy (CARS) resonances originate from double-slit interference of two-photon Stokes pathways
Authors: Rahav Saar , Mukamel Shaul
Published: February 2010

Coherent anti-Stokes Raman spectroscopy (CARS) uses vibrational resonances to study nuclear wavepacket motions and is widely used in cell imaging and other applications. The resonances usually lie on top of a parametric component that involves no change in the molecular state and creates an undesirable background which reduces the sensitivity of the technique. Here, by examining the process from the perspective of the molecule, rather than the field, we are able to separate the two components and recast each resonance as a modulus square of a transition amplitude which contains an interference between two Stokes pathways, each involving a different pair of field modes. We further propose that dissipative signals obtained by measuring the total absorption of all field modes in a convenient collinear pulse geometry can eliminate the parametric component and retain the purely resonant contributions. Specific vibrational resonances may then be readily detected using pulse shapers through derivatives with respect to pulse parameters.
Kadison–Singer algebras, II: General case
Authors: Ge Liming , Yuan Wei
Published: February 2010

A new class of operator algebras, Kadison–Singer (KS-) algebras, is introduced. These highly noncommutative, non self-adjoint algebras generalize triangular matrix algebras. They are determined by certain minimally generating lattices of projections in the von Neumann algebras corresponding to the commutant of the diagonals of the KS-algebras. It is shown that these lattices and their reduced forms are often homeomorphic to classical manifolds such as the sphere.
Initiation of DNA replication after fertilization is regulated by p90Rsk at pre-RC/pre-IC transition in starfish eggs
Authors: Tachibana Kazunori , Mori Masashi , Matsuhira Takashi , Karino Tomotake , Inagaki Takuro , Nagayama Ai , Nishiyama Atsuya , Hara Masatoshi , Kishimoto Takeo
Published: February 2010

Initiation of DNA replication in eukaryotic cells is controlled through an ordered assembly of protein complexes at replication origins. The molecules involved in this process are well conserved but diversely regulated. Typically, initiation of DNA replication is regulated in response to developmental events in multicellular organisms. Here, we elucidate the regulation of the first S phase of the embryonic cell cycle after fertilization. Unless fertilization occurs, the Mos-MAPK-p90Rsk pathway causes the G1-phase arrest after completion of meiosis in starfish eggs. Fertilization shuts down this pathway, leading to the first S phase with no requirement of new protein synthesis. However, how and in which stage the initiation complex for DNA replication is arrested by p90Rsk remains unclear. We find that in G1-arrested eggs, chromatin is loaded with the Mcm complex to form the prereplicative complex (pre-RC). Inactivation of p90Rsk is necessary and sufficient for further loading of Cdc45 onto chromatin to form the preinitiation complex (pre-IC) and the subsequent initiation of DNA replication. However, cyclin A-, B-, and E-Cdk's activity and Cdc7 accumulation are dispensable for these processes. These observations define the stage of G1 arrest in unfertilized eggs at transition point from pre-RC to pre-IC, and reveal a unique role of p90Rsk for a negative regulator of this transition. Thus, initiation of DNA replication in the meiosis-to-mitosis transition is regulated at the pre-RC stage as like in the G1 checkpoint, but in a manner different from the checkpoint.
Irrelevant Conjunction: Statement and Solution of a New Paradox
Authors: Crupi Vincenzo , Tentori Katya
Published: February 2010

The so-called problem of irrelevant conjunction has been seen as a serious challenge for theories of confirmation. It involves the consequences of conjoining irrelevant statements to a hypothesis that is confirmed by some piece of evidence. Following Hawthorne and Fitelson, we reconstruct the problem with reference to Bayesian confirmation theory. Then we extend it to the case of conjoining irrelevant statements to a hypothesis that isdisconfirmed by some piece of evidence. As a consequence, we obtain and formally present a novel and more troublesome problem of irrelevant conjunction. We conclude by indicating a possible solution based on a measure-sensitive approach and by critically discussing a major alternative way to address the problem.
Epistemic Values and the Argument from Inductive Risk
Authors: Steel Daniel
Published: February 2010

Critics of the ideal of value-free science often assume that they must reject the distinction between epistemic and nonepistemic values. I argue that this assumption is mistaken and that the distinction can be used to clarify and defend the argument from inductive risk, which challenges the value-free ideal. I develop the idea that the characteristic feature of epistemic values is that they promote, either intrinsically or extrinsically, the attainment of truths. This proposal is shown to answer common objections to the distinction and provide a principled basis for separating legitimate from illegitimate influences of nonepistemic values in scientific inference.
Levels of Explanation Reconceived
Authors: Potochnik Angela
Published: February 2010

A common argument against explanatory reductionism is that higher-level explanations are sometimes or always preferable because they are more general than reductive explanations. Here I challenge two basic assumptions that are needed for that argument to succeed. It cannot be assumed that higher-level explanations are more general than their lower-level alternatives or that higher-level explanations are general in the right way to be explanatory. I suggest a novel form of pluralism regarding levels of explanation, according to which explanations at different levels are preferable in different circumstances because they offer different types of generality, which are appropriate in different circumstances of explanation.
The Principle of the Identity of Indiscernibles and Quantum Mechanics
Authors: Ladyman James , Bigaj Tomasz
Published: February 2010

It is argued that recent discussion of the principle of the identity of indiscernibles (PII) and quantum mechanics has lost sight of the broader philosophical motivation and significance of PII and that the ‘received view' of the status of PII in the light of quantum mechanics survives recent criticisms of it by Muller, Saunders, and Seevinck.
The power of protein interaction networks for associating genes with diseases
Authors: Navlakha Saket , Kingsford Carl
Published: February 2010

Motivation: Understanding the association between genetic diseases and their causal genes is an important problem concerning human health. With the recent influx of high-throughput data describing interactions between gene products, scientists have been provided a new avenue through which these associations can be inferred. Despite the recent interest in this problem, however, there is little understanding of the relative benefits and drawbacks underlying the proposed techniques.

Results: We assessed the utility of physical protein interactions for determining gene–disease associations by examining the performance of seven recently developed computational methods (plus several of their variants). We found that random-walk approaches individually outperform clustering and neighborhood approaches, although most methods make predictions not made by any other method. We show how combining these methods into a consensus method yields Pareto optimal performance. We also quantified how a diffuse topological distribution of disease-related proteins negatively affects prediction quality and are thus able to identify diseases especially amenable to network-based predictions and others for which additional information sources are absolutely required.

Availability: The predictions made by each algorithm considered are available online at http://www.cbcb.umd.edu/DiseaseNet

Contact:  carlk@cs.umd.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
SPICi: a fast clustering algorithm for large biological networks
Authors: Jiang Peng , Singh Mona
Published: February 2010

Motivation: Clustering algorithms play an important role in the analysis of biological networks, and can be used to uncover functional modules and obtain hints about cellular organization. While most available clustering algorithms work well on biological networks of moderate size, such as the yeast protein physical interaction network, they either fail or are too slow in practice for larger networks, such as functional networks for higher eukaryotes. Since an increasing number of larger biological networks are being determined, the limitations of current clustering approaches curtail the types of biological network analyses that can be performed.

Results: We present a fast local network clustering algorithm SPICi. SPICi runs in time O(V log V+E) and space O(E), where V and E are the number of vertices and edges in the network, respectively. We evaluate SPICi's performance on several existing protein interaction networks of varying size, and compare SPICi to nine previous approaches for clustering biological networks. We show that SPICi is typically several orders of magnitude faster than previous approaches and is the only one that can successfully cluster all test networks within very short time. We demonstrate that SPICi has state-of-the-art performance with respect to the quality of the clusters it uncovers, as judged by its ability to recapitulate protein complexes and functional modules. Finally, we demonstrate the power of our fast network clustering algorithm by applying SPICi across hundreds of large context-specific human networks, and identifying modules specific for single conditions.

Availability: Source code is available under the GNU Public License at http://compbio.cs.princeton.edu/spici

Contact:  mona@cs.princeton.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes
Authors: Muffato Matthieu , Louis Alexandra , Poisnel Charles-Edouard , Crollius Hugues Roest
Published: February 2010

Summary: Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to infer evolutionary events remain restricted to two or three genomes at a time, thus limiting the breadth and the nature of the question that can be investigated. Here we present Genomicus, a new synteny browser that can represent and compare unlimited numbers of genomes in a broad phylogenetic view. In addition, Genomicus includes reconstructed ancestral gene organization, thus greatly facilitating the interpretation of the data.

Availability: Genomicus is freely available for online use at http://www.dyogen.ens.fr/genomicus while data can be downloaded at ftp://ftp.biologie.ens.fr/pub/dyogen/genomicus

Contact:  hrc@biologie.ens.fr
ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules
Authors: Loriot Sébastien , Cazals Frédéric , Bernauer Julie
Published: February 2010

Summary: The ever increasing number of structural biological data calls for robust and efficient software for analysis. Easy Structural Biology Template Library (ESBTL) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric constructions and analyses. The parser and data model provided by this ready-to-use include-only library allows adequate treatment of usually discarded information (insertion code, atom occupancy, etc.) while still being able to detect badly formatted files. The template-based structure allows rapid design of new computational structural biology applications and is fully compatible with the new remediated PDB archive format. It also allows the code to be easy-to-use while being versatile enough to allow advanced user developments.

Availability: ESBTL is freely available under the GNU General Public License from http://esbtl.sf.net. The web site provides the source code, examples, code snippets and documentation.

Contact:  julie.bernauer@inria.fr
N‐terminal pro‐brain natriuretic peptide from fresh urine for the biochemical detection of heart failure and left ventricular dysfunction
Authors: Jungbauer Carsten G. , Buchner Stefan , Birner Christoph , Resch Markus , Heinicke Norbert , Debl Kurt , Buesing Monika , Biermeier Daniela , Schmitz Gerd , Riegger Günter , Luchner Andreas
Published: February 2010

Aims

Plasma N‐terminal pro‐brain natriuretic peptide (NT‐proBNP) is a strong biochemical marker of heart failure and left ventricular dysfunction (LVD). Due to renal arterio‐venous clearance of NT‐proBNP and the correlation of plasma concentrations with renal function, we hypothesized that NT‐proBNP may have potential as a urinary marker. The objective of this study was to assess urinary concentrations of NT‐proBNP and to identify the predictive value of urinary NT‐proBNP for detecting LVD and heart failure.

Methods and results

N‐terminal pro‐brain natriuretic peptide (Elecsys proBNP®, Roche) was assessed simultaneously in fresh spot urine and plasma from 191 individuals. In patients with heart failure (n = 149), urinary and plasma NT‐proBNP concentrations were positively correlated (r = 0.79, P < 0.001), but urinary NT‐proBNP was significantly lower than plasma NT‐proBNP (42 ± 25 vs. 1389 ± 325 pg/mL, P < 0.001). Upon receiver operating curve analysis, urinary NT‐proBNP detected LV dysfunction (ejection fraction <40%) with a sensitivity of 91% and a specificity of 98% at a cutpoint of 22 pg/mL [area under the curves (AUC) 0.98]. At the same cutpoint, symptomatic heart failure (NYHA‐class > 2) was detected with a sensitivity of 97% and specificity of 98% (AUC 0.99) and clinical signs of fluid retention were detected with a sensitivity and specificity of 98% each (AUC 0.99).

Conclusion

N‐terminal pro‐brain natriuretic peptide concentrations were markedly lower in the urine than in the plasma. However, urinary NT‐proBNP levels increased stepwise with the severity of heart failure and LVD, and therefore yielded satisfactory predictive values for the detection of significant LVD and symptomatic heart failure. Measurement of urinary NT‐proBNP is a novel, promising, and simple method for the biochemical detection of heart failure.
Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays
Authors: Lee Charlie Wah Heng , Koh Chee Wee , Chan Yang Sun , Aw Pauline Poh Kim , Loh Kuan Hon , Han Bing Ling , Thien Pei Ling , Nai Geraldine Yi Wen , Hibberd Martin L. , Wong Christopher W. , Sung Wing-Kin
Published: February 2010

In April 2009, a new influenza A (H1N1 2009) virus emerged that rapidly spread around the world. While current variants of this virus have caused widespread disease, particularly in vulnerable groups, there remains the possibility that future variants may cause increased virulence, drug resistance or vaccine escape. Early detection of these virus variants may offer the chance for increased containment and potentially prevention of the virus spread. We have developed and field-tested a resequencing kit that is capable of interrogating all eight segments of the 2009 influenza A(H1N1) virus genome and its variants, with added focus on critical regions such as drug-binding sites, structural components and mutation hotspots. The accompanying base-calling software (EvolSTAR) introduces novel methods that utilize neighbourhood hybridization intensity profiles and substitution bias of probes on the microarray for mutation confirmation and recovery of ambiguous base queries. Our results demonstrate that EvolSTAR is highly accurate and has a much improved call rate. The high throughput and short turn-around time from sample to sequence and analysis results (30 h for 24 samples) makes this kit an efficient large-scale evolutionary biosurveillance tool.
Fractional rate of change of swim-bladder volume is reliably related to absolute depth during vertical displacements in teleost fish
Authors: Taylor Graham K. , Holbrook Robert Iain , de Perera Theresa Burt
Published: February 2010

Fish must orient in three dimensions as they navigate through space, but it is unknown whether they are assisted by a sense of depth. In principle, depth can be estimated directly from hydrostatic pressure, but although teleost fish are exquisitely sensitive to changes in pressure, they appear unable to measure absolute pressure. Teleosts sense changes in pressure via changes in the volume of their gas-filled swim-bladder, but because the amount of gas it contains is varied to regulate buoyancy, this cannot act as a long-term steady reference for inferring absolute pressure. In consequence, it is generally thought that teleosts are unable to sense depth using hydrostatic pressure. Here, we overturn this received wisdom by showing from a theoretical physical perspective that absolute depth could be estimated during fast, steady vertical displacements by combining a measurement of vertical speed with a measurement of the fractional rate of change of swim-bladder volume. This mechanism works even if the amount of gas in the swim-bladder varies, provided that this variation occurs over much longer time scales than changes in volume during displacements. There is therefore noa prioriphysical justification for assuming that teleost fish cannot sense absolute depth by using hydrostatic pressure cues.