bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevention of unsafe abortion: Analysis of the current situation and the task ahead
Authors: Faúndes Anibal , Zaidi Shahida
Published: May 2010

An evaluation of the current situation regarding implementation of the plans of action for the prevention of unsafe abortion shows that more than half of the countries selected for the initiative have progressed as planned or have surpassed expectations. The greatest barriers to faster progress have been insufficient resources or infrastructure and the sensitivity of the subject matter, as well as lack of a more active commitment from the societies of obstetrics and gynecology and their members. The most frequently mentioned facilitating factors were the strength of the project/FIGO leadership, the commitment of the collaborating agencies, and incorporation of the activities of the plans of action into the agenda of the Ministry of Health. The commitment of the societies of obstetrics and gynecology and a good relationship between these societies and their Ministry of Health were also mentioned as being important facilitating factors. On the operational side, the monitoring visits and the regional workshops were seen as facilitators by over three‐quarters and two‐thirds of the countries, respectively. FIGO is committed to continue providing technical and political support to the societies involved in this initiative, promoting strategies to overcome the barriers while taking full advantage of the facilitating factors.
Fluorodeoxyglucose positron emission tomography of mild cognitive impairment with clinical follow‐up at 3 years
Authors: Pardo José V. , Lee Joel T. , Kuskowski Michael A. , Munch Kristin R. , Carlis John V. , Sheikh Sohail A. , Surerus Christa , Lewis Scott M. , McCarten J. Riley , Fink Howard , McPherson Susan , Shah Hemant H. , Rottunda Susan , Dysken Maurice W.
Published: May 2010

Background

Alzheimer's disease (AD) is the most common dementing illness. Development of effective treatments directed at AD requires an early diagnosis. Mild cognitive impairment (MCI) often heralds AD. Thus, characterizing MCI is fundamental to the early diagnosis of AD.

Methods

19 MCI patients referred from a memory loss clinic and 27 healthy subjects, all followed up for 3 years. Metabolism scans (MCI minus controls) were compared voxel‐wise after anatomic normalization and were examined both visually and with a computerized classifier.

Results

Agreement between raters as to whether the individual scans were normal or abnormal was high. Agreement between raters of the eventual clinical diagnosis and baseline metabolic pattern was poor. A computerized classifier was unsuccessful at classifying MCI from normal; however, its performance improved when using only prototypic AD‐like MCI scans, indicating the classifier worked well when shared patterns existed in the data. Outcomes on follow‐up were nine of 19 AD, five of 19 remained MCI, and five of 19 developed dementias other than AD. Both MCI cases of early Lewy body dementia (LBD) showed an AD‐like metabolic pattern.

Conclusions

Visual inspection proved reliable in determining normal from abnormal scans, but it proved unreliable at predicting diagnosis on follow‐up. Computerized classification of MCI by using an AD‐like metabolic template (such as derived from the averaged MCI images) showed potential to identify patients who will develop AD. However, the metabolic pattern in early LBD did not differ from that in AD.
The Alzheimer's Disease Neuroimaging Initiative positron emission tomography core
Authors: Jagust William J. , Bandy Dan , Chen Kewei , Foster Norman L. , Landau Susan M. , Mathis Chester A. , Price Julie C. , Reiman Eric M. , Skovronsky Daniel , Koeppe Robert A. ,   Alzheimer's Disease Neuroimaging Initiative
Published: May 2010

Background

This is a progress report of the Alzheimer's Disease Neuroimaging Initiative (ADNI) positron emission tomography (PET) Core.

Methods

The Core has supervised the acquisition, quality control, and analysis of longitudinal [18F]fluorodeoxyglucose PET (FDG‐PET) data in approximately half of the ADNI cohort. In an “add on” study, approximately 100 subjects also underwent scanning with [11C] Pittsburgh compound B PET for amyloid imaging. The Core developed quality control procedures and standardized image acquisition by developing an imaging protocol that has been widely adopted in academic and pharmaceutical industry studies. Data processing provides users with scans that have identical orientation and resolution characteristics despite acquisition on multiple scanner models. The Core labs have used many different approaches to characterize differences between subject groups (Alzheimer's disease, mild cognitive impairment, controls), to examine longitudinal change over time in glucose metabolism and amyloid deposition, and to assess the use of FDG‐PET as a potential outcome measure in clinical trials.

Results

ADNI data indicate that FDG‐PET increases statistical power over traditional cognitive measures, might aid subject selection, and could substantially reduce the sample size in a clinical trial. Pittsburgh compound B PET data showed expected group differences, and identified subjects with significant annual increases in amyloid load across the subject groups. The next activities of the PET core in ADNI will entail developing standardized protocols for amyloid imaging using the [18F]‐labeled amyloid imaging agent AV45, which can be delivered to virtually all ADNI sites.

Conclusions

ADNI has demonstrated the feasibility and utility of multicenter PET studies and is helping to clarify the role of biomarkers in the study of aging and dementia.
Japanese Alzheimer's Disease Neuroimaging Initiative: Present status and future
Authors: Iwatsubo Takeshi
Published: May 2010

Japanese Alzheimer's Disease Neuroimaging Initiative (J‐ADNI) was launched in 2008, aiming at conducting a longitudinal workup of a standardized neuroimaging, biomarker and clinico‐psychological surveys. The research protocol was designed to maximize compatibility with that of US‐ADNI, including structural magnetic resonance imaging analysis for the evaluation of brain atrophy, fluorodeoxyglucose and amyloid positron emission tomography, cerebrospinal fluid sampling, APOE genotyping, together with a set of clinical and psychometric tests that were prepared to achieve the highest compatibility to those used in the United States. Japanese ADNI has recruited ~357 participants (142 amnestic mild cognitive impairment, ~134 normal aged and 72 mild Alzheimer's disease (AD), as of April 15, 2010). World‐wide ADNI activities will establish the rigorous quantitative descriptions of the natural course of AD in its very early stages. The data, as well as the methodologies and infrastructures, will facilitate the clinical trials of disease‐modifying therapies for AD using surrogate biomarkers.
Autopsy consent, brain collection, and standardized neuropathologic assessment of ADNI participants: The essential role of the Neuropathology Core
Authors: Cairns Nigel J. , Taylor‐Reinwald Lisa , Morris John C. ,   Alzheimer's Disease Neuroimaging Initiative
Published: May 2010

Background

Our objectives are to facilitate autopsy consent, brain collection, and perform standardized neuropathologic assessments of all Alzheimer's Disease Neuroimaging Initiative (ADNI) participants who come to autopsy at the 58 ADNI sites in the USA and Canada.

Methods

Building on the expertise and resources of the existing Alzheimer's Disease Research Center (ADRC) at Washington University School of Medicine, St. Louis, MO, a Neuropathology Core (NPC) to serve ADNI was established with one new highly motivated research coordinator. The ADNI‐NPC coordinator provides training materials and protocols to assist clinicians at ADNI sites in obtaining voluntary consent for brain autopsy in ADNI participants. Secondly, the ADNI‐NPC maintains a central laboratory to provide uniform neuropathologic assessments using the operational criteria for the classification of AD and other pathologies defined by the National Alzheimer Coordinating Center (NACC). Thirdly, the ADNI‐NPC maintains a state‐of‐the‐art brain bank of ADNI‐derived brain tissue to promote biomarker and multi‐disciplinary clinicopathologic studies.

Results

During the initial year of funding of the ADNI Neuropathology Core, there was notable improvement in the autopsy rate to 44.4%. In the most recent year of funding (September 1st, 2008 to August 31st 2009), our autopsy rate improved to 71.5%. Although the overall numbers to date are small, these data demonstrate that the Neuropathology Core has established the administrative organization with the participating sites to harvest brains from ADNI participants who come to autopsy.

Conclusions

Within two years of operation, the Neuropathology Core has: (1) implemented a protocol to solicit permission for brain autopsy in ADNI participants at all 58 sites who die and (2) to send appropriate brain tissue from the decedents to the Neuropathology Core for a standardized, uniform, and state‐of‐the‐art neuropathologic assessment. The benefit to ADNI of the implementation of the NPC is very clear. Prior to the establishment of the NPC in September 2007, there were 6 deaths but no autopsies in ADNI participants. Subsequent to the establishment of the Core there have been 17 deaths of ADNI participants and 10 autopsies. Hence, the autopsy rate has gone from 0% to 59%. The third major accomplishment is the detection of co‐existent pathologies with AD in the autopsied cases. It is possible that these co‐morbidities may contribute to any variance in ADNI data.
War and State Formation in Ancient China and Early Modern Europe
Authors: Hui Victoria Tin-bor
Published: May 2010

The Eurocentric conventional wisdom holds that the West is unique in having a multi-state system in international relations and liberal democracy in state-society relations. At the same time, the Sinocentric perspective believes that China is destined to have authoritarian rule under a unified empire. In fact, China in the Spring and Autumn and Warring States periods (656–221 BC) was once a system of sovereign territorial states similar to Europe in the early modern period. Both cases witnessed the prevalence of war, formation of alliances, development of the centralized bureaucracy, emergence of citizenship rights, and expansion of international trade. This book, first published in 2005, examines why China and Europe shared similar processes but experienced opposite outcomes. This historical comparison of China and Europe challenges the presumption that Europe was destined to enjoy checks and balances while China was preordained to suffer under a coercive universal status.
Low levels of faecal lactobacilli in women with iron-deficiency anaemia in south India
Authors: Balamurugan Ramadass , Mary R. Regina , Chittaranjan Sucharita , Jancy Hepsiba , Shobana Devi R. , Ramakrishna Balakrishnan S.
Published: May 2010

Fe deficiency in women contributes significantly to maternal and child morbidity in India. The intestinal bacterial flora may facilitate absorption of Fe from the caecum and proximal colon. The present study investigated the possibility that intestinal microbiota of anaemic young women may differ from that of women with normal Hb levels. The microbiota was quantified by real-time PCR in faeces of eight anaemic (Hb ≤ 100 g/l) and twenty-six normohaemic (Hb ≥ 120 g/l) women aged 18–25 years. Sequences of 16S ribosomal DNA (rDNA) specific to Bifidobacterium genus, Lactobacillus acidophilus group, Bacteroides–Prevotella–Porphyromonas group, Clostridium leptum group and Eubacterium rectale were amplified and expressed (as relative difference) relative to the universally conserved bacterial 16S rDNA sequences. Dietary intakes of energy, carbohydrate, fibre and Fe were ascertained by maintenance of a diet diary for a week. Faecal lactobacilli were significantly lower in anaemic women (median 6·6 × 10− 8, relative difference compared with total bacteria) than in the reference group (2·9 × 10− 6; P = 0·001, unpaired t test with logarithmic transformation). There was no difference between the two groups with respect to any of the other bacteria that were examined. Intakes of energy, carbohydrate, fibre, Fe and milk were similar in both the groups. Fe deficiency in young women in south India was associated with low levels of lactobacilli in the faeces. The relationship between lactobacilli and Fe deficiency needs to be explored further.
La religion dans l’espace public post-séculier, une confrontation critique des perspectives de Habermas et de Gauchet
Authors: Braeckman Antoon
Published: May 2010

RÉSUMÉ : Dans sa lecture du rôle de la religion dans l’espace public, Habermas fait abstraction du pouvoir de la religion d’instituer symboliquement les communautés. Gauchet part d’une vision de la religion dans laquelle cette dimension est centrale. Je considère toutefois que Gauchet sous-estime également la mesure dans laquelle la religion a conservé ce pouvoir au sein de la société post-séculière.
La religion dans l’espace public : quelques commentaires sur les positions récentes de Habermas.
Authors: Courtois Stéphane
Published: May 2010

RÉSUMÉ : Cet article présente une évaluation d’ensemble des positions récentes de Habermas sur la place de la religion dans l’espace public. Après avoir comparé les positions respectives de Rawls et de Habermas sur cette question, en vue de mieux faire ressortir l’originalité de la contribution de Habermas, l’auteur se propose ensuite de montrer que cette dernière soulève un certain nombre de difficultés au plan théorique et pratique. Au plan théorique, il est démontré que la contribution de Habermas soulève un problème de cohérence par rapport à la conception plus générale qu’il se fait de la démocratie délibérative. Au plan pratique, le bien-fondé du rôle civique attendu des citoyens, tant religieux que laïcs, dans l’espace public ne paraît pas exempt de problèmes.
Contrasting Middle Jurassic and Early Cretaceous mafic intrusive rocks from western Liaoning, North China craton: petrogenesis and tectonic implications
Authors: ZHANG XIAOHUI , ZHANG HONGFU , JIANG NENG , WILDE SIMON A.
Published: May 2010

Zircon U–Pb dating, whole-rock major oxide, trace element and Sr–Nd isotopic data are presented for the Late Mesozoic mafic intrusive rocks from Yiwulüshan of western Liaoning along the eastern segment of the Yanshan belt, North China craton, with two episodes of magmatism documented. Middle Jurassic hornblende-rich gabbros show enrichment of large ion lithophile elements and light REE, and prominent depletion in high field strength elements, and possess moderately enriched isotopic compositions with (87Sr/86Sr)i ranging from 0.7056 to 0.7065 and ɛNd(t) from −5.0 to −7.1. These features suggest that the gabbros were derived from an amphibole-bearing harzburgitic lithospheric mantle source metasomatized recently by slab-derived fluids. By contrast, Early Cretaceous mafic dykes are gabbroic dioritic to dioritic in composition, with comparable trace element characteristics to continental crust and depleted isotopic signatures ((87Sr/86Sr)i = 0.7048–0.7055, ɛNd(t) = 0 to −3.0). They probably originated from partial melting of a relatively fertile asthenospheric mantle in the spinel stability field, with subsequent lower crustal assimilation and fractional crystallization. These two contrasting mafic intrusive suites, together with multiple Mesozoic mafic volcanic rocks from western Liaoning, documented a localized lithospheric thinning process, mainly through prolonged hydro-weakening or melt–rock interaction and triggered by gravitational collapse, possibly within an evolved post-collisional to within-plate extensional regime.
The Food of Post-Larval Fish
Authors: Lebour Marie V.
Published: May 2010

Although much investigation has been made on the food of adult fish the information as to the food of the very young is scattered and fragmentary. It is the purpose of this paper to report on the food of a number of post-larval fish which have been examined fresh from the tow-nettings through the year 1917 from Plymouth Sound within the Breakwater and outside as far as the region of the Panther and Knap Buoys (about 2 miles from the shore) and occasionally from Cawsand Bay. The food of a number of preserved post-larval fish has also been investigated which were taken in the Young Fish Trawl in 1914 and reported on by Dr. Allen (1917).
Steady and quasi-steady thin viscous flows near the edge of a solid surface
Authors: BARENBLATT G. I. , BERTSCH M. , GIACOMELLI L.
Published: May 2010

A new approach is proposed for the description of thin viscous flows near the edges of a solid surface. For a steady flow, the lubrication approximation and the no-slip condition are assumed to be valid on most of the surface, except for relatively small neighbourhoods of the edges, where a universality principle is postulated: the behaviour of the liquid in these regions is universally determined by flux, external conditions and material properties. The resulting mathematical model is formulated as an ordinary differential equation involving the height of the liquid film and the flux as unknowns, and analytical results are outlined. The form of the universal functions which describe the behaviour in the edge regions is also discussed, obtaining conditions of compatibility with lubrication theory for small fluxes. Finally, an ordinary differential equation is introduced for the description of intermediate asymptotic profiles of a liquid film which flows off a bounded solid surface.
Participation of States in the International Conference of the Red Cross and Red Crescent and assemblies of other international organizations
Authors: Casalin Deborah , Lamb Christopher
Published: May 2010

The International Conference of the Red Cross and Red Crescent (‘International Conference’) is one of the few international fora in which governments take part on an equal footing with other entities. The origins of the International Conference, and its capacity to adopt decisions that are binding on both National Red Cross and Red Crescent Societies and on governments in their dealings with National Societies as their auxiliary partners, give rise to special considerations concerning state participation. This article provides an overview of the models for participation in the assemblies of other international organizations, and how problematic cases have been dealt with in various fora. The authors then examine the participation of states and other political entities in the International Conference, as well as the controversial cases that have put the Conference to the test.
Comment on “The Prediction of Two Large Earthquakes in Greece”
Authors: Papadopoulos Gerassimos A.
Published: May 2010

Uyeda and Kamogawa [2008] reported on the VAN experimental method for short‐term earthquake prediction (VAN was named for three Greek physicists, Panayiotis Varotsos, Kessar Alexopoulos, and Konstantine Nomicos), which reportedly recorded seismic electric signals (SESs) before the Mw 6.8 earthquake on 14 February 2008. They claimed that a prediction is documented by P. A. Varotsos et al. (Seismic electric signals and 1/f “noise” in natural time, version 3, 2008; available at http://arxiv.org/abs/0711.3766v3) and in the newspaper Ethnos (10 February 2008; http://www.ethnos.gr/article.asp?catid=11424&subid2&tag=8777&pubid=444473). This claim is unjustified because the prediction was not submitted to Greece's Permanent Special Scientific Committee for the Assessment of Seismic Hazard and the Evaluation of Seismic Risk. According to Greek legislation, the committee is officially charged with analyzing and vetting earthquake hazard assessments (including predictions and ongoing seismic crises) and ultimately advising the government. Through civil protection authorities, the government handles the social, economic, and other negative consequences of impending earthquakes. But perhaps more scientifically grievous, this prediction was not documented elsewhere beforehand.
Climate change in cities due to global warming and urban effects
Authors: McCarthy Mark P. , Best Martin J. , Betts Richard A.
Published: May 2010

Urbanisation is estimated to result in 6 billion urban dwellers by 2050. Cities will be exposed to climate change from greenhouse gas induced radiative forcing, and localised effects from urbanisation such as the urban heat island. An urban land‐surface model has been included in the HadAM3 Global Climate Model. It shows that regions of high population growth coincide with regions of high urban heat island potential, most notably in the Middle East, the Indian sub‐continent, and East Africa. Climate change has the capacity to modify the climatic potential for urban heat islands, with increases of 30% in some locations, but a global average reduction of 6%. Warming and extreme heat events due to urbanisation and increased energy consumption are simulated to be as large as the impact of doubled CO2 in some regions, and climate change increases the disparity in extreme hot nights between rural and urban areas.
Inhibition of GGTase‐I and FTase disrupts cytoskeletal organization of human PC‐3 prostate cancer cells
Authors: Virtanen Sanna S. , Sandholm Jouko , Yegutkin Gennady , Väänänen Kalervo H. , Härkönen Pirkko L.
Published: May 2010

The mevalonate synthesis pathway produces intermediates for isoprenylation of small GTPases, which are involved in the regulation of actin cytoskeleton and cell motility. Here, we investigated the role of the prenylation transferases in the regulation of the cytoskeletal organization and motility of PC‐3 prostate cancer cells. This was done by using FTI‐277, GGTI‐298 or NE‐10790, the specific inhibitors of FTase (farnesyltransferase), GGTase (geranylgeranyltransferase)‐I and ‐II, respectively. Treatment of PC‐3 cells with GGTI‐298 and FTI‐277 inhibited migration and invasion in a time‐ and dose‐dependent manner. This was associated with disruption of F‐actin organization and decreased recovery of GFP–actin. Immunoblot analysis of various cytoskeleton‐associated proteins showed that the most striking change in GGTI‐298‐ and FTI‐277‐treated cells was a markedly decreased level of total and phosphorylated cofilin, whereas the level of cofilin mRNA was not decreased. The treatment of PC‐3 cells with GGTI‐298 also affected the dynamics of GFP–paxillin and decreased the levels of total and phosphorylated paxillin. The levels of phosphorylated FAK (focal adhesion kinase) and PAK (p‐21‐associated kinase)‐2 were also lowered by GGTI‐298, but levels of paxillin or FAK mRNAs were not affected. In addition, GGTI‐298 had a minor effect on the activity of MMP‐9. RNAi knockdown of GGTase‐Iβ inhibited invasion, disrupted F‐actin organization and decreased the level of cofilin in PC‐3 cells. NE‐10790 did not have any effect on PC‐3 prostate cancer cell motility or on the organization of the cytoskeleton. In conclusion, our results demonstrate the involvement of GGTase‐I‐ and FTase‐catalysed prenylation reactions in the regulation of cytoskeletal integrity and motility of prostate cancer cells and suggest them as interesting drug targets for development of inhibitors of prostate cancer metastasis.
Erythrocytes anion transport and oxidative change in β‐thalassaemias
Authors: Maria Crupi , Leonardo Romano , Pietro Romano , Mario Venza , Isabella Venza , Diana Teti
Published: May 2010

β‐Thalassaemia is characterized by a decrease in globin β‐chain synthesis and an excess in free α‐globin chains. This induces alterations in membrane lipids and proteins resulting from a reduction in spectrin/band 3 ratio, partial oxidation of band 4.1 and clustering of band 3. The membrane injury provokes hyperhaemolysis and bone marrow hyperplasia. The pathophysiology of thalassaemia is associated with iron overload that generates oxygen free radicals and oxidative tissue injury with ocular vessel alterations. The aim of this research is to investigate the influence of oxidative stress on band 3 efficiency, which is an integral membrane protein of RBCs (red blood cells). Band 3 protein, of which there are more than 1 million copies per cell, is the most abundant membrane protein in human RBCs. It mediates the anion exchange and acid–base equilibrium through the RBC membrane. Some experiments were performed on thalassaemic cells and β‐thalassaemia‐like cells and tested for sulfate uptake. To test the antioxidant effect of Mg2+, other experiments were performed using normal and pathological cells in the presence of Mg2+. The oxidant status in thalassaemic cells was verified by increased K+ efflux, by lower GSH levels and by increased G6PDH (glucose‐6‐phosphate dehydrogenase) activity. The rate constant of SO4 2− uptake decreases in thalassaemic cells as well as in β‐thalassaemia‐like cells when compared with normal cells. It increases when both cells are incubated with Mg2+. Our data show that oxidative stress plays a relevant role in band 3 function of thalassaemic cells and that antioxidant treatment with Mg2+ could reduce oxidative damage to the RBC membrane and improve the anion transport efficiency regulated by band 3 protein.
Changes in the expression pattern of mesenchymal and pluripotent markers in human adipose‐derived stem cells
Authors: Park Eulsoon , Patel Amit N.
Published: May 2010

Pluripotent marker genes encode transcription factors that suppress differentiation and allow stem cells to continue proliferation while remaining poised to develop into cells from multiple lineages. Mesenchymal marker proteins are widely used to identify and characterize multipotent stem cells that are capable of differentiation into cells of the mesenchymal lineage. We examine here the expression pattern of mesenchymal and pluripotent markers in ADSCs (human adipose‐derived stem cells) during culture. Flow cytometry indicates that a large fraction of ADSCs were positive for multiple mesenchymal markers, such as CD29, CD44 and CD90. The expression levels of these markers increase and become more uniform in cells that are cultured for long periods. Alternatively, mRNAs for several pluripotent genes, such as Nanog, Oct‐4 and Rex‐1, are detected only in cells from early passages. In addition, ADSCs cultured over long periods express several cardiac genes in response to serum deprivation and treatment with phorbol ester. Thus, these data demonstrate that ADSCs expanded in culture over multiple passages consistently express mesenchymal markers with the ability to differentiate towards the cardiac lineage.
Dressed electrostatic solitary waves in quantum dusty pair plasmas
Authors: Akbari-Moghanjoughi M.
Published: May 2010

Quantum-hydrodynamics model is applied to investigate the nonlinear propagation of electrostatic solitary excitations in a quantum dusty pair plasma. A Korteweg de Vries evolution equation is obtained using reductive perturbation technique and the higher-nonlinearity effects are derived by solving the linear inhomogeneous differential equation analytically using Kodama–Taniuti renormalizing method. The possibility of propagation of bright- and dark-type solitary excitations is examined. It is shown that a critical value of quantum diffraction parameter H exists, on either side of which, only one type of solitary propagation is possible. It is also found that unlike for the first-order amplitude component, the variation of H parameter dominantly affects the soliton amplitude in higher-order approximation. The effect of fractional quantum number density on compressive and rarefactive soliton dynamics is also discussed.
Influence of global rotation and Reynolds number on the large-scale features of a turbulent Taylor–Couette flow
Authors: Ravelet F. , Delfos R. , Westerweel J.
Published: May 2010

We experimentally study the turbulent flow between two coaxial and independently rotating cylinders. We determined the scaling of the torque with Reynolds numbers at various angular velocity ratios (Rotation numbers) and the behavior of the wall shear stress when varying the Rotation number at high Reynolds numbers. We compare the curves with particle image velocimetry analysis of the mean flow and show the peculiar role of perfect counter-rotation for the emergence of organized large scale structures in the mean part of this very turbulent flow that appear in a smooth and continuous way: the transition resembles a supercritical bifurcation of the secondary mean flow.
A seamless hybrid RANS-LES model based on transport equations for the subgrid stresses and elliptic blending
Authors: Fadai-Ghotbi Atabak , Friess Christophe , Manceau Rémi , Borée Jacques
Published: May 2010

The aim of the present work is to develop a seamless hybrid Reynolds-averaged Navier–Stokes (RANS) large-eddy simulation (LES) model based on transport equations for the subgrid stresses, using the elliptic-blending method to account for the nonlocal kinematic blocking effect of the wall. It is shown that the elliptic relaxation strategy of Durbin is valid in a RANS (steady) as well as a LES context (unsteady). In order to reproduce the complex production and redistribution mechanisms when the cutoff wavenumber is located in the productive zone of the turbulent energy spectrum, the model is based on transport equations for the subgrid-stress tensor. The partially integrated transport model (PITM) methodology offers a consistent theoretical framework for such a model, enabling to control the cutoff wavenumber κc, and thus the transition from RANS to LES, by making the Cε2 coefficient in the dissipation equation of a RANS model a function of κc. The equivalence between the PITM and the Smagorinsky model is shown when κc is in the inertial range of the energy spectrum. The extension of the underlying RANS model used in the present work, the elliptic-blending Reynolds-stress model, to the hybrid RANS-LES context, brings out some modeling issues. The different modeling possibilities are compared in a channel flow at Reτ=395. Finally, a dynamic procedure is proposed in order to adjust during the computation the dissipation rate necessary to drive the model toward the expected amount of resolved energy. The final model gives very encouraging results in comparison to the direct numerical simulation data. In particular, the turbulence anisotropy in the near-wall region is satisfactorily reproduced. The contribution of the resolved and modeled fields to the Reynolds stresses behaves as expected: the modeled part is dominant in the near-wall zones (RANS mode) and decreases toward the center of the channel, where the relative contribution of the resolved part increases. Moreover, when the mesh is modified, the amount of resolved energy changes but the total Reynolds stresses remain nearly constant.
Electron-nucleus cusp correction scheme for the relativistic zeroth-order regular approximation quantum Monte Carlo method
Authors: Nakatsuka Yutaka , Nakajima Takahito , Hirao Kimihiko
Published: May 2010

A cusp correction scheme for the relativistic zeroth-order regular approximation (ZORA) quantum Monte Carlo method is proposed by extending the nonrelativistic cusp correction scheme of Ma et al. [J. Chem. Phys. 122, 224322 (2005)]. In this scheme, molecular orbitals that appear in Slater–Jastrow type wave functions are replaced with the exponential-type correction functions within a correction radius. Analysis of the behavior of the ZORA local energy in electron-nucleus collisions reveals that the Kato’s cusp condition is not applicable to the ZORA QMC method. The divergence of the electron-nucleus Coulomb potential term in the ZORA local energy is remedied by adding a new logarithmic correction term. This method is shown to be useful for improving the numerical stability of the ZORA-QMC calculations using both Gaussian and Slater basis functions.
Molecular aniline clusters. I. The electronic ground state
Authors: Schemmel Dominik , Schütz Martin
Published: May 2010

The aniline dimer and trimer are investigated in their electronic ground state. The potential energy surface was thoroughly searched for low lying minima by applying global optimizations on a model potential, which is recalibrated on-the-fly by ab initio calculations (spin-component-scaled LMP2) at relevant configurations. The most stable structure of the dimer corresponds to a head-to-tail arrangement with both aniline monomers being nearly equivalent. DFT-SAPT calculations reveal that the interaction energy is dominated by van der Waals dispersion, which is of comparable size as for the benzene dimer, but with a much larger total interaction energy than for the latter. The global minimum of the aniline trimer corresponds to a hydrogen bonding arrangement involving three directional NH–N hydrogen bonds, with the individual monomers being clearly distinguishable. Nonadditive three-body dispersion contributions appear to play a minor role for the trimer.
Interferometer density measurements of a high-velocity plasmoid
Authors: Case A. , Messer S. , Bomgardner R. , Witherspoon F. D.
Published: May 2010

The plasmoid produced by a half-scale contoured gap coaxial plasma accelerator using ablative polyethylene capillary plasma injectors is measured using a quadrature heterodyne HeNe interferometer. The plasmoid is found to have a sharp rise in density at the leading edge, with a gradual falloff after the peak density. For this early test series, an average bulk density of 5×1014 cm−3 is observed, with densities up to 8×1014 cm−3 seen on some shots. Although plasmoid mass is only about 58 μg due to the low current and injected mass used in these tests, good shot-to-shot repeatability is attained making analysis relatively straightforward, thus providing a solid foundation for interpreting future experimental results.
Effects of oxide-shell structures on the dynamics of oxidation of Al nanoparticles
Authors: Wang Weiqiang , Clark Richard , Nakano Aiichiro , Kalia Rajiv K. , Vashishta Priya
Published: May 2010

Effects of the crystalline and amorphous structure of alumina shells on the dynamics of oxidation of an aluminum nanoparticle (ANP) are studied using multimillion-atom molecular dynamics simulations. With an amorphous shell, formation of oxidized nanocluster fragments produced by the shattering of the shell, combined with the fragmentation and dispersion of the nanoparticle, catalyzes faster oxidation reactions. Consequently, the energy release rate of an ANP with an amorphous shell is much higher than that with a crystalline shell. Analysis on the formation of oxygen-rich fragments further confirms an enhanced reaction rate with an amorphous shell.
Dielectric charging characterization on microelectromechanical switches by discharge current transient
Authors: Molinero David , Castaner Luis
Published: May 2010

The discharge current method is used to quantify the dielectric reliability of microelectromechanical switches. Two dielectrics, silicon oxide and silicon nitride, were used to extract the charge trapped, the emissivity and the dielectric relaxation time by means of a circuital model with a current source simulating the charge trap. A figure of merit is proposed to better quantify the dielectric reliability issues.
Gyrotropic band gap optical sensors
Authors: Dissanayake Neluka K. , Levy Miguel , Jalali Amir A. , Fratello V. J.
Published: May 2010

Faraday-effect-active photonic band gap structures fabricated in iron garnet films are shown to provide a platform for optical sensing based on refractive index detection. Strong near-band gap-edge polarization rotations serve as a sensitive probe to cover-index changes in birefringent magneto-optic waveguides. A wide index range from air to n=1.6 is explored. Device sensitivity is found to improve with cover index increase. Theoretical analysis of Bloch modes polarization state shows large near stop-band edge rotations and strong sensitivity to cover index. The combined effects of geometrical waveguide birefringence and Faraday rotation contribute to the strength of the sensor response.
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase is a distant IPK member with a singular inositide binding site for axial 2-OH recognition
Authors: González Beatriz , Baños-Sanz Jose Ignacio , Villate Maider , Brearley Charles Alistair , Sanz-Aparicio Julia
Published: May 2010

Inositol phosphates (InsPs) are signaling molecules with multiple roles in cells. In particular

(InsP
6
) is involved in mRNA export and editing or chromatin remodeling among other events. InsP
6
accumulates as mixed salts (phytate) in storage tissues of plants and plays a key role in their physiology. Human diets that are exclusively grain-based provide an excess of InsP
6
that, through chelation of metal ions, may have a detrimental effect on human health. Ins(1,3,4,5,6)P
5
2-kinase (InsP
5
2-kinase or Ipk1) catalyses the synthesis of InsP
6
from InsP
5
and ATP, and is the only enzyme that transfers a phosphate group to the axial 2-OH of the myo-inositide. We present the first structure for an InsP
5
2-kinase in complex with both substrates and products. This enzyme presents a singular structural region for inositide binding that encompasses almost half of the protein. The key residues in substrate binding are identified, with Asp368 being responsible for recognition of the axial 2-OH. This study sheds light on the unique molecular mechanism for the synthesis of the precursor of inositol pyrophosphates.
Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states
Authors: Miller Yifat , Ma Buyong , Nussinov Ruth
Published: May 2010

Although a key factor in Alzheimer’s disease etiology is enrichment of Zn
2+
in aggregates, and there are data suggesting that zinc promotes aggregation,
how
Zn
2+
-A
β
coordination promotes aggregation is elusive. Here we probe the structures and mechanisms through which Zn
2+
can affect amyloidosis. By covalently linking fragments (that have experiment-based coordinates) we observed that, in oligomeric Zn
2+
-A
β
42
, Zn
2+
can
simultaneously
coordinate intra- and intermolecularly, bridging two peptides. Zinc coordination significantly decreases the solvation energy for large Zn
2+
-A
β
42
oligomers and thus enhances their aggregation tendency. Zn
2+
binding does not change the β-sheet association around the C-terminal hydrophobic region; however, it shifts the relative population of the
preexisting
amyloid polymorphic ensembles. As a result, although a parallel β-sheet arrangement is still preferred, antiparallel and other less structured assemblies are stabilized, also becoming major species. Overall, Zn
2+
coordination promotes A
β
42
aggregation leading to less uniform structures. Our replica exchange molecular dynamics simulations further reproduced an experimental observation that the increasing Zn
2+
concentration could slow down the aggregation rate, even though the aggregation rates are still much higher than in Zn
2+
-free solution.
Deep levels fine structure in proton implanted p-type GaAs
Authors: Coelho A V P , Adam M C , Boudinov H
Published: May 2010

Proton irradiation related deep levels in p-type GaAs were measured by deep level transient spectroscopy (DLTS) at T < 70 K and Laplace DLTS at 42 K ⩽ T ⩽ 48 K. Besides level H0 (apparent energy E
pa = 0.06 eV and apparent hole capture cross section σpa = 1.6 × 10−16 cm2), also present in electron irradiated GaAs, three other levels were identified (E
pa = 0.1 eV, σpa = 2.5 × 10−15 cm2; E
pa = 0.085 eV, σpa = 1 × 10−14 cm2 and E
pa = 0.065 eV, σpa = 3 × 10−16 cm2). Another level (E
pa = 0.095 eV and σpa = 2 × 10−15 cm2) became evident after annealing steps at the temperature range 150 °C ⩽ T ⩽ 200 °C. All levels suffered a strong concentration reduction after annealing steps at 250 °C ⩽ T ⩽ 300 °C.
Nanocoating of ionic liquid and polypyrrole for durable electro-active paper actuators working under ambient conditions
Authors: Mahadeva Suresha K , Kim Jaehwan
Published: May 2010

This paper reports that nanocoating of polypyrrole (PPy) and ionic liquid (IL) on cellulose film improves the electromechanical performance and durability of a cellulose electro-active paper actuator. Cellulose–PPy–IL nanocomposites were fabricated by the polymerization-induced adsorption process of PPy followed by subsequent activation in IL solutions. X-ray photoelectron spectroscopy, transmission electron microscopy and secondary ion mass spectroscopy analyses validated the successful nanocoating of the PPy and IL layers on the cellulose. The results revealed that the cellulose–PPy–IL nanocomposites are suitable for durable bending actuators working under ambient conditions. Preparation, characterization and performance test of the nanocomposites are explained.
TiO
2/CdS nanocomposite films: fabrication, characterization, electronic and optical properties
Authors: Dang Tran Chien , Pham Duy Long , Le Ha Chi , Pham Van Hoi
Published: May 2010

In this work, TiO
2 nanocrystalline thin films were obtained through evaporating Ti films by electron beam deposition (EBD) followed by thermal treatment. The results show that after annealing at 300, 400 and 450 °C for 8 h, the obtained TiO
2 thin films have nanoparticle and nanorod structures of 15–30 nm diameter and 100–300 nm length. At 750 °C for 8 h, the rutile phase was formed. The incorporation of cadmium sulfide (CdS) into TiO
2 nanoparticle thin films was investigated. A CdS thin film was vacuum deposited onto the pre-deposited TiO
2 film by a thermal evaporation technique. The obtained TiO
2 and TiO
2/CdS nanocomposite films were characterized by x-ray diffraction (XRD) and a field emission scanning electron microscope (FE-SEM). The TiO
2/CdS composite film was used in a photo-electrochemical (PEC) cell as a working electrode and in a platinum electrode as a counter electrode. The electrolyte solution contains 1 M KCl and 0.1 M Na
2
S. The results show that the cell with the TiO
2/CdS composite film electrode has significantly improved photoelectric capability in comparison with that of pure TiO
2 thin films, and the best thickness of the CdS thin film deposited on the ITO/TiO
2 substrates is 70–140 nm.
Arcadia: a visualization tool for metabolic pathways
Authors: Villéger Alice C. , Pettifer Stephen R. , Kell Douglas B.
Published: May 2010

Summary: Arcadia translates text-based descriptions of biological networks (SBML files) into standardized diagrams (SBGN PD maps). Users can view the same model from different perspectives and easily alter the layout to emulate traditional textbook representations.

Availability and Implementation: Arcadia is written in C++. The source code is available (along with Mac OS and Windows binaries) under the GPL from http://arcadiapathways.sourceforge.net/

Contact:  alice.villeger@manchester.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Discover regulatory DNA elements using chromatin signatures and artificial neural network
Authors: Firpi Hiram A. , Ucar Duygu , Tan Kai
Published: May 2010

Motivation: Recent large-scale chromatin states mapping efforts have revealed characteristic chromatin modification signatures for various types of functional DNA elements. Given the important influence of chromatin states on gene regulation and the rapid accumulation of genome-wide chromatin modification data, there is a pressing need for computational methods to analyze these data in order to identify functional DNA elements. However, existing computational tools do not exploit data transformation and feature extraction as a means to achieve a more accurate prediction.

Results: We introduce a new computational framework for identifying functional DNA elements using chromatin signatures. The framework consists of a data transformation and a feature extraction step followed by a classification step using time-delay neural network. We implemented our framework in a software tool CSI-ANN (chromatin signature identification by artificial neural network). When applied to predict transcriptional enhancers in the ENCODE region, CSI-ANN achieved a 65.5% sensitivity and 66.3% positive predictive value, a 5.9% and 11.6% improvement, respectively, over the previously best approach.

Availability and Implementation: CSI-ANN is implemented in Matlab. The source code is freely available at http://www.medicine.uiowa.edu/Labs/tan/CSIANNsoft.zip

Contact:  kai-tan@uiowa.edu

Supplementary Information:  Supplementary Materials are available at Bioinformatics online.
Differential effects of magnetic pulses on the orientation of naturally migrating birds
Authors: Holland Richard A.
Published: May 2010

In migratory passerine birds, strong magnetic pulses are thought to be diagnostic of the remagnetization of iron minerals in a putative sensory system contained in the beak. Previous evidence suggests that while such a magnetic pulse affects the orientation of migratory birds in orientation cages, no effect was present when pulse-treated birds were tested in natural migration. Here we show that two migrating passerine birds treated with a strong magnetic pulse, designed to alter the magnetic sense, migrated in a direction that differed significantly from that of controls when tested in natural conditions. The orientation of treated birds was different depending on the alignment of the pulse with respect to the magnetic field. These results can aid in advancing understanding of how the putative iron-mineral-based receptors found in birds' beaks may be used to detect and signal the intensity and/or direction of the Earth's magnetic field.
Rhizobium borbori sp. nov., aniline-degrading bacteria isolated from activated sludge
Authors: Zhang Guo Xia , Ren Sui Zhou , Xu Mei Ying , Zeng Guo Qu , Luo Hui Dong , Chen Jin Lin , Tan Zhi Yuan , Sun Guo Ping
Published: May 2010

Three aniline-degrading bacteria, strains DN316T, DN316-1 and DN365, were isolated from activated sludge. According to 16S rRNA gene sequence-based phylogenetic analysis, the isolates belonged to the genusRhizobium, withRhizobium( = Agrobacterium)radiobacterLMG 140Tas the closest relative, with 96.5 % sequence similarity. Phylogenetic analysis of the representative strain DN316Tusing sequences of theglnA,thrCandrecAgenes and the 16S–23S intergenic spacer region confirmed the phylogenetic arrangement obtained from analysis of the 16S rRNA gene. DNA–DNA relatedness between DN316TandR. radiobacterLMG 140Twas 43.7 %, clearly indicating that the representative strain DN316Trepresents a novel species. Phenotypic and biochemical characterization of the isolates and insertion sequence-PCR fingerprinting patterns showed several distinctive features that differentiated them from closely related species. The major components of the cellular fatty acids were C18 : 1ω7c(57.10 %), C16 : 0(11.31 %) and C19 : 0cyclo ω8c(10.13 %). Based on our taxonomic analysis, the three isolates from activated sludge represent a novel species of the genusRhizobium, for which the nameRhizobium borborisp. nov. is proposed. The type strain is DN316T( = CICC 10378T = LMG 23925T).
Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera
Authors: Chen Ming-Hui , Sheu Shih-Yi , Chen Chaolun Allen , Wang Jih-Terng , Chen Wen-Ming
Published: May 2010

A bacterial strain, designated SW6T, was isolated from the reef-building coral Isopora palifera, collected from seawater off the coast of southern Taiwan, and characterized using a polyphasic taxonomic approach. Strain SW6T was Gram-negative, aerobic, beige coloured, rod-shaped and motile by monopolar flagella. 16S rRNA gene sequence studies showed that the strain clustered closely with Shimia marina JCM 13038T (97.9 % 16S rRNA gene sequence similarity). Strain SW6T required NaCl for growth and exhibited optimal growth at 25–30 °C and 3–4 % NaCl. The predominant cellular fatty acid was summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 64.1 %). The major respiratory quinone was ubiquinone Q-10 and the DNA G+C content was 54.9 mol%. The results of physiological and biochemical tests allowed clear phenotypic differentiation of this isolate from previously described species of the genus Shimia. It is evident from the genotypic, phenotypic and chemotaxonomic data that the new strain should be classified as a representative of a novel species in the genus Shimia. The name proposed for this taxon is Shimia isoporae sp. nov.; the type strain is SW6T ( = LMG 25377T = BCRC 80085T).