bluuebunny/crossref_metadata_2025 huggingface dataset:
Methicillin-resistant Staphylococcus aureus infection in combat support hospitals in three regions of Iraq
Authors: HUANG X.-Z. , CASH D. M. , CHAHINE M. A. , VAN HORN G. T. , ERWIN D. P. , McKAY J. T. , HAMILTON L. R. , JERKE K. H. , CO E.-M. A. , ALDOUS W. K. , LESHO E. P. , LINDLER L. E. , BOWDEN R. A. , NIKOLICH M. P.
Published: August 2010

Staphylococcus aureus is a leading cause of infections in deployed service members. Based on a molecular epidemiological study of 182 MRSA isolates from patients in three U.S. Army combat support hospitals in separate regions in Iraq, USA300 clone was the most predominant (80%) pulsotype. This finding suggested that strain carriage from the home country by military personnel is epidemiologically more important than local acquisition.
A recipe for disaster: outbreaks of campylobacteriosis associated with poultry liver pâté in England and Wales
Authors: LITTLE C. L. , GORMLEY F. J. , RAWAL N. , RICHARDSON J. F.
Published: August 2010

Despite the frequency of Campylobacter as the principal cause of bacterial gastroenteritis in the UK, outbreaks attributed to this pathogen are rare. One hundred and fourteen general foodborne outbreaks of campylobacteriosis were reported to the Health Protection Agency from 1992 to 2009 with most occurring in food service establishments (64%, 73/114). Poultry meat (38%, 43/114) was the most commonly reported vehicle of infection, of which poultry liver pâté, and undercooking, were strongly associated with this pathogen. Notably, the number of outbreaks of campylobacteriosis linked to consumption of poultry liver pâté in England and Wales increased significantly from 2007 (74% as opposed to 12%, P<0·00001) with a preponderance of these occurring in December. These outbreaks highlight the hazards associated with inappropriate culinary practices leading to undercooking of poultry liver pâté and suggest that improving catering practice is an important last line of defence in reducing exposure to Campylobacter-contaminated products.
Testicular structure and spermatogenesis of Amazonian freshwater cururu stingray Potamotrygon cf. histrix
Authors: Zaiden Sérgio Fonseca , Brinn Richard Phillip , Marcon Jaydione Luiz , Urbinati Elisabeth Criscuolo
Published: August 2010

The cururu stingray Potamotrygon cf. histrix, a new and endemic Amazonian freshwater species, presents appropriate characteristics for fish keeping and is exploited from its natural environment. The present study identified the testicular structure and spermatogenesis of this species. Gonads from adult male specimens were dissected, fixed and processed for histological analysis. The testes were of testicular/epigonial type. The presence of germinal papillae was observed in the upper portion of organ with primordial germ cells and Sertoli cell precursors. The testis was lobular with zonal organization and cystic gametogenesis, with the occurrence of spermatoblasts. The Sertoli cells underwent morphological modifications over the course of gamete formation. The spermatozoids had long heads and were spiraled on their own axis. Information on the reproductive biology will serve as basis for studies on the reproduction and phylogeny of this peculiar group of cartilaginous fish.
Cytochrome P450-2D6 extensive metabolizers are more vulnerable to methamphetamine-associated neurocognitive impairment: Preliminary findings
Authors: CHERNER MARIANA , BOUSMAN CHAD , EVERALL IAN , BARRON DANIEL , LETENDRE SCOTT , VAIDA FLORIN , ATKINSON J. HAMPTON , HEATON ROBERT , GRANT IGOR ,   THE HNRC GROUP
Published: August 2010

While neuropsychological deficits are evident among methamphetamine (meth) addicts, they are often unrelated to meth exposure parameters such as lifetime consumption and length of abstinence. The notion that some meth users develop neuropsychological impairments while others with similar drug exposure do not, suggests that there may be individual differences in vulnerability to the neurotoxic effects of meth. One source of differential vulnerability could come from genotypic variability in metabolic clearance of meth, dependent on the activity of cytochrome P450-2D6 (CYP2D6). We compared neuropsychological performance in 52 individuals with a history of meth dependence according with theirCYP2D6phenotype. All were free of HIV or hepatitis C infection and did not meet dependence criteria for other substances. Extensive metabolizers showed worse overall neuropsychological performance and were three times as likely to be cognitively impaired as intermediate/poor metabolizers. Groups did not differ in their demographic or meth use characteristics, nor did they evidence differences in mood disorder or other substance use. This preliminary study is the first to suggest that efficient meth metabolism is associated with worse neurocognitive outcomes in humans, and implicates the products of oxidative metabolism of meth as a possible source of brain injury. (JINS, 2010,16, 890–901.)
Democracy and Distrust
Authors: della Porta Donatella
Published: August 2010

Pierre Rosanvallon is one of the most important political theorists writing in French. Counter-Democracy: Politics in an Age of Distrust is a book about the limits of conventional understandings of democracy. Rosanvallon argues that while most theories of democracy focus on institutionalized forms of political participation (especially elections), the vitality of democracy rests equally on forms of “counter-democracy” through which citizens dissent, protest, and exert pressure from without on the democratic state. This argument is relevant to the concerns of a broad range of political scientists, most especially students of democratic theory, electoral and party politics, social movements, social capital, and “contentious politics.” The goal of this symposium is to invite a number of political scientists who work on these issues to comment on the book from their distinctive disciplinary, methodological, and theoretical perspectives.—Jeffrey C. Isaac, Editor
Response to Robert Gooding-Williams' review of Dreaming Blackness: Black Nationalism and African American Public Opinion
Authors: Price Melanye T.
Published: August 2010

In Dreaming Blackness, I had two major goals. First, I hoped to elucidate how changes in the American racial landscape have impacted African American support for black nationalism. To this end, I used a mixed methodological approach that included both statistical and qualitative analysis and allowed me to make claims based on a national cross section of African Americans and on more intimate discussions in smaller groups. Second, I wanted to ground my arguments in a robust discussion of African American political thought. This would ensure that my hypotheses and findings were resonant with a longitudinal understanding of how black nationalist ideology is characterized. Robert Gooding-Williams, with some caveats, suggests that I have accomplished these goals. I now address his two areas of concern related to evolving definitions of black nationalism and possible alternative interpretations, and I conclude by addressing our differing impressions of the future viability of this ideological option.
In the Shadow of Du Bois: Afro-Modern Political Thought in America. By Robert Gooding-Williams
Authors: Price Melanye T.
Published: August 2010

In this book, Robert Gooding-Williams uses the seminal work of W. E. B. Du Bois, The Souls of Black Folks (1903) to outline Du Bois' dominant influence in defining the boundaries of black politics. Du Bois' statement about the color line, still quoted more than a century after its publication, is just one example of the enduring impact of Souls and other works on the ways in which black politics scholars conceptualize, measure, and make prescriptions for black political progress. However, his import as a dominant voice in black political thought belies the fact that there was ideological and fervent opposition to his view concerning how blacks could overcome racial oppression. Unlike Du Bois, however, many of those opponents are less known or simply ignored by contemporary black scholars.
The Road to Somewhere: Why Health Reform Happened
Authors: Hacker Jacob S.
Published: August 2010

Why did comprehensive health care reform pass in 2010? Why did it take the form it did—a form that, while undeniably ambitious, was also more limited than many advocates wanted, than health policy precedents set abroad, and than the scale of the problems it tackled? And why was this legislation, despite its limits, the subject of such vigorous and sometimes vicious attacks? These are the questions I tackle in this essay, drawing not just on recent scholarship on American politics but also on the somewhat-improbable experience that I had as an active participant in this fierce and polarized debate. My conclusions have implications not only for how political scientists should understand what happened in 2009–10, but also for how they should understand American politics. In particular, the central puzzles raised by the health reform debate suggest why students of American politics should give public policy—what government does to shape people's lives—a more central place within their investigations. Political scientists often characterize politics as a game among undifferentiated competitors, played out largely through campaigns and elections, with policy treated mostly as an afterthought—at best, as a means of testing theories of electoral influence and legislative politics. The health care debate makes transparent the weaknesses of this approach. On a range of key matters at the core of the discipline—the role and influence of interest groups; the nature of partisan policy competition; the sources of elite polarization; the relationship between voters, activists, and elected officials; and more—the substance of public policy makes a big difference. Focusing on what government actually does has normative benefits, serving as a useful corrective to the tendency of political science to veer into discussions of matters deemed trivial by most of the world outside the academy. But more important, it has majoranalyticalpayoffs—and not merely for our understanding of the great health care debate of 2009–10.
Varieties of Obamaism: Structure, Agency, and the Obama Presidency
Authors: Jacobs Lawrence R. , King Desmond S.
Published: August 2010

President Obama's record stands out among modern presidents because of the wide range between his accomplishments and the boldness of his as-yet unfulfilled promises. Obamaism is a complex phenomenon, with multiple themes and policy ends. In this paper we examine the administration's initiatives drawing upon recent scholarship in political science to consider the political, economic and institutional constraints that Obama has faced and to assess how he has faced them. Our key theme is the importance of integrating the study of presidency and public leadership with the study of the political economy of the state. The paper argues against personalistic accounts of the Obama presidency in favor of a structured agency approach.
Reconstituting the Submerged State: The Challenges of Social Policy Reform in the Obama Era
Authors: Mettler Suzanne
Published: August 2010

President Barack Obama came into office with a social welfare policy agenda that aimed to reconstitute what can be understood as the “submerged state”: a conglomeration of existing federal policies that incentivize and subsidize activities engaged in by private actors and individuals. By attempting to restructure the political economy involved in taxation, higher education policy, and health care, Obama ventured into a policy terrain that presents immense obstacles to reform itself and to the public's perception of its success. Over time the submerged state has fostered the profitability of particular industries and induced them to increase their political capacity, which they have exercised in efforts to maintain the status quo. Yet the submerged state simultaneously eludes most ordinary citizens: they have little awareness of its policies or their upwardly redistributive effects, and few are cognizant of what is at stake in reform efforts. This article shows how, in each of the three policy areas, the contours and dynamics of the submerged state have shaped the possibilities for reform and the form it has taken, the politics surrounding it, and its prospects for success. While the Obama Administration won hard-fought legislative accomplishments in each area, political success will continue to depend on how well policy design, policy delivery and political communication reveal policy reforms to citizens, so that they better understand how reforms function and what has been achieved.
The American Labor Movement in the Age of Obama: The Challenges and Opportunities of a Racialized Political Economy
Authors: Warren Dorian T.
Published: August 2010

The relative weakness of the American labor movement has broader political consequences, particularly for the ambitions of the Obama presidency. Absent a strong countervailing political constituency like organized labor, well-organized and more powerful stakeholders like business and industry groups are able to exert undue influence in American democracy, thereby frustrating attempts at political reform. I argue that it is impossible to understand the current political situation confronting the Obama administration without an account of the underlying sources of labor weakness in the U.S. In such an account two factors loom especially large. One is the role of the state in structuring labor market institutions and the rules of the game for labor-business interactions. The second is the distinctively racialized character of the U.S. political economy, which has contributed to labor market segmentation, a unique political geography, and the racial division of the U.S. working class. In our current post-industrial, post-civil rights racial and economic order, whether and how the labor movement can overcome its historical racial fragmentation will determine its possibilities for renewal and ultimately its political strength in relation to the Obama presidency. If the labor movement remains an uneven and weak regional organization hobbled by racial fragmentation, the Obama Administration's efforts to advance its core policy agenda will lack the necessary political force to be effective.
Evolution of vertical knickpoints (waterfalls) with resistant caprock: Insights from numerical modeling
Authors: Haviv I. , Enzel Y. , Whipple K. X. , Zilberman E. , Matmon A. , Stone J. , Fifield K. L.
Published: August 2010

Vertical knickpoints (waterfalls) mark a prominent process transition zone whose governing mechanics is not represented by conventional stream power incision models. We examine the evolution of vertical knickpoints with resistant caprock utilizing numerical simulations that explicitly represent (1) face failure mechanisms, (2) flow acceleration and amplified erosion above a knickpoint lip, (3) deposition and removal of coarse debris below the knickpoint, and (4) base level lowering or tectonic uplift rates. Our model demonstrates that knickpoint retreat rate, where the subcaprock is weak or vertically jointed and base level fall rates are steady, is likely to become tied to downstream conditions and equal to the downstream incision rate divided by channel gradient. Mechanically, this coupling occurs where the subcaprock reaches a threshold height for failure in shear or buckling or where the weathering rate of the subcaprock is higher than the downstream incision wave velocity (Vi_ds). The height of the subcaprock face can influence its gravitational stability and the knickpoint lateral erosion rate and lead to a feedback between downstream incision and retreat rate. Retreat rate can be lower than Vi_ds during transients, which could be long (>106 years) and set by the weathering rate of the subcaprock or influenced by lag debris evacuation. Key variables other than discharge can be important in setting retreat rates. These include base level lowering rate, the rock strength of stratigraphic units downstream of the knickpoint, and the size and flux of sediment contributed from above the knickpoint or from the canyon walls. Two types of oversteepened reaches can form in association with a vertical knickpoint: (1) an upstream, free fall‐induced, oversteepened reach whose length is longer than the flow acceleration zone and (2) a downstream coarse debris‐induced oversteepened reach. Although the model was constructed with caprock‐type knickpoints in mind, some of its elements and insights are also relevant to homogenous substrates.
Numerical study on seasonal variations of gaseous pollutants and particulate matters in Hong Kong and Pearl River Delta Region
Authors: Kwok Roger H. F. , Fung Jimmy C. H. , Lau Alexis K. H. , Fu Joshua S.
Published: August 2010

This study presents Community Multiscale Air Quality (CMAQ) model results for Hong Kong (HK) and the Pearl River Delta region in January, April, July, and October 2004, representing winter, spring, summer, and autumn seasons. Two sets of observations/measurement data are referred to in order to evaluate model performance. The first set consists of hourly observations of criteria pollutants at HK Environmental Protection Department (HKEPD) ambient stations throughout HK, while the second set contains speciated PM measurements, sampled at 6‐day intervals, at six of the HKEPD ambient stations. Model‐observation agreement is good in PM species sulfate, organic carbon (OC), and elemental carbon (EC). The good performance for OC and EC, when compared to similar evaluation for North America and Europe, demonstrates the importance of correct speciation in an emission sector. Underprediction of NOx and NH3 suggests a desperate need of emission estimation improvement in these species. PM levels are higher in autumn and winter, lower in spring, and lowest in summer, coinciding with northeasterly winds due to continental outflow in autumn and winter, and with southwesterly monsoon in summer. The model is also able to reproduce the seasonal and spatial patterns for PM and O3. In terms of PM composition, the model agrees with the measured fractions of sulfate, OC, and EC. Additionally, CMAQ was rerun with emission sources partially removed, with results suggesting that pollution sources beyond the Pearl River Delta also contribute to the PM and sulfate levels in HK, particularly during the winter season.
A review of cloud top height and optical depth histograms from MISR, ISCCP, and MODIS
Authors: Marchand Roger , Ackerman Thomas , Smyth Mike , Rossow William B.
Published: August 2010

There are notable differences in the joint histograms of cloud top height and optical depth being produced from the Moderate Resolution Imaging Spectroradiometer (MODIS) and the Multiangle Imaging Spectro‐Radiometer (MISR) and by the International Satellite Cloud Climatology Project (ISCCP). These differences have their roots in the different retrieval approaches used by the three projects and are driven largely by responses of the retrievals to (1) stratocumulus (or more broadly low‐level clouds under temperature inversions), (2) small (subpixel) or broken low‐level clouds, and (3) multilayer clouds. Because each data set has different strengths and weakness, the combination tells us more about the observed cloud fields than any of the three by itself. In particular, the MISR stereo height retrieval provides a calibration insensitive approach to determining cloud height that is especially valuable in combination with ISCCP or MODIS because the combination provides a means to estimate the amount of multilayer cloud, where the upper cloud is optically thin. In this article we present a review of the three data sets using case studies and comparisons of annually averaged joint histograms on global and regional scales. Recommendations for using these data in climate model evaluations are provided.
An analysis of cloud cover in multiscale modeling framework global climate model simulations using 4 and 1 km horizontal grids
Authors: Marchand Roger , Ackerman Thomas
Published: August 2010

Over the past few years, a new type of global climate model (GCM) has emerged in which a two‐dimensional or small three‐dimensional cloud resolving model is embedded into each grid cell of a GCM. This approach is frequently called the multiscale modeling framework (MMF) but is also known as a cloud‐resolving convection parameterization or a superparameterization. In this article, we compare joint histograms of cloud top height and optical depth from the MMF with those being produced by the International Satellite Cloud Climatology Project (ISCCP) and from the Multiangle Imaging Spectroradiometer (MISR). While the form of the ISCCP and MISR data sets is conceptually similar, the satellite sensors and the algorithms differ, with the result that the joint histograms can differ quite significantly even when viewing exactly the same clouds. The analysis takes advantages of the strengths of each data set, as well as the differences in these data (which, for example, allow one to characterize the amount of some multilayer clouds). MMF simulation runs with three different resolutions are analyzed. One simulation is run using a 4 km horizontal grid with 26 vertical levels (on a stretched grid), a second simulation is run with a 1 km horizontal grid and the same 26 vertical levels, and a third simulation is run with a 1 km horizontal grid and 52 vertical levels. The analysis shows that the MMF reproduces the broad pattern of tropical convergence zones, subtropical belts, and midlatitude storm tracks as observed by ISCCP and MISR. However, the model has several significant shortcomings. Perhaps most seriously, it significantly underpredicts the amount of low‐level cloud in most regions. The simulation with a 1 km horizontal grid and 52 vertical layers is found to improve modestly several aspect of the MMF low‐level cloud cover. The model output is obtained using ISCCP and MISR instrument simulators and the role of horizontal resolution in the instrument simulators is examined.
Snapshot selection for groundwater model reduction using proper orthogonal decomposition
Authors: Siade Adam J. , Putti Mario , Yeh William W.‐G.
Published: August 2010

Water resources systems management often requires complex mathematical models whose use may be computationally infeasible for many advanced analyses, e.g., optimization, data assimilation, model uncertainty, etc. The computational demand of these analyses can be reduced by approximating the model with a simpler reduced model. Proper Orthogonal Decomposition (POD) is an efficient model reduction technique based on the projection of the original model onto a subspace generated by full‐model snapshots. In order to implement this method, an appropriate number of snapshots of the full model must be taken at the appropriate times such that the resulting reduced model is as accurate as possible. Since confined aquifers reach steady state in an exponential manner, we present a simple exponential function that can be used to select snapshots for these types of models. This selection method is then employed to determine the optimal snapshot set for a unit, dimensionless model. The optimal snapshot set is found by maximizing the minimum eigenvalue of the snapshot covariance matrix, a criterion similar to those used in experimental design. The resulting snapshot set can then be translated to any complex, real world model based on a simple, approximate relationship between dimensionless and real‐world times. This translation is illustrated using a basin scale model of Central Veneto, Italy. We show that this method is very easy to implement and produces an accurate reduced model that, in the case of Central Veneto, Italy, runs approximately 1,000 times faster than the full model.
Linking regional sources and pathways for submarine groundwater discharge at a reef by electrical resistivity tomography, 222Rn, and salinity measurements
Authors: Cardenas M. Bayani , Zamora Peter B. , Siringan Fernando P. , Lapus Mark R. , Rodolfo Raymond S. , Jacinto Gil S. , San Diego‐McGlone Maria Lourdes , Villanoy Cesar L. , Cabrera Olivia , Senal Maria Isabel
Published: August 2010

Submarine groundwater discharge (SGD) is an important component of the hydrologic cycle connecting terrestrial to marine environments. SGD in fringing reefs and its consequences on biogeochemistry and ecology remain mostly unexplored. The 222Rn activity and salinity of seawater indicate a substantial groundwater contribution throughout most of the 20 km2 studied tropical reef in Pangasinan, Philippines. Over 30 km of electrical resistivity profiles with a penetration depth of 12.5 m shows widespread zones within the reef that are much more resistive than porous reef rocks or sediment saturated with typical seawater. Some discrete resistive areas are located close to where seawater has 222Rn peaks and where geologic lineaments are likely located suggesting that these are preferential pathways for fresher groundwater discharging to the reef. SGD at the site could be a major ecological factor connecting the reef to the subsurface environment which in turn may lead to connections to land.
Sensitivity of 21st century stratospheric ozone to greenhouse gas scenarios
Authors: Eyring V. , Cionni I. , Lamarque J. F. , Akiyoshi H. , Bodeker G. E. , Charlton‐Perez A. J. , Frith S. M. , Gettelman A. , Kinnison D. E. , Nakamura T. , Oman L. D. , Pawson S. , Yamashita Y.
Published: August 2010

To understand how greenhouse gas (GHG) emissions may affect future stratospheric ozone, 21st century projections from four chemistry‐climate models are examined for their dependence on six different GHG scenarios. Compared to higher GHG emissions, lower emissions result in smaller increases in tropical upwelling with resultant smaller reductions in ozone in the tropical lower stratosphere and less severe stratospheric cooling with resultant smaller increases in upper stratospheric ozone globally. Increases in reactive nitrogen and hydrogen that lead to additional chemical ozone destruction mainly play a role in scenarios with higher GHG emissions. Differences among the six GHG scenarios are found to be largest over northern midlatitudes (∼20 DU by 2100) and in the Arctic (∼40 DU by 2100) with divergence mainly in the second half of the 21st century. The uncertainty in the return of stratospheric column ozone to 1980 values arising from different GHG scenarios is comparable to or less than the uncertainty that arises from model differences in the larger set of 17 CCMVal‐2 SRES A1B simulations. The results suggest that effects of GHG emissions on future stratospheric ozone should be considered in climate change mitigation policy and ozone projections should be assessed under more than a single GHG scenario.
Distribution and formation of chlorides and phyllosilicates in Terra Sirenum, Mars
Authors: Glotch Timothy D. , Bandfield Joshua L. , Tornabene Livio L. , Jensen Heidi B. , Seelos Frank P.
Published: August 2010

The Terra Sirenum region of Mars, located in the Noachian southern highlands, is mineralogically diverse, providing unique insight into ancient aqueous processes. Analyses of remote sensing data over the region indicate the presence of both Fe‐ or Mg‐rich phyllosilicates and a spectrally unique deposit interpreted to be rich in chloride salts. The stratigraphic relationships indicate that the phyllosilicates are part of the ancient highland crust and that the salts were deposited at a later time. In some instances, there is clear morphological evidence that salts were mobilized and deposited by near‐surface waters.
Rapid assembly of potent type II dehydroquinase inhibitorsvia “Click” chemistry
Authors: Tran Anh Thu , Cergol Katie M. , Britton Warwick J. , Imran Bokhari Syed Ali , Ibrahim Musadiq , Lapthorn Adrian J. , Payne Richard J.
Published: August 2010

The rapid synthesis of a library of potent type II dehydroquinase inhibitors is described. Inhibitors were prepared via a key quinate-derived ene-yne intermediate using Cu(i)-catalysed azide-alkyne cycloaddition (CuAAC) chemistry with a variety of aryl- and heteroaryl-azides.
HDHD1, which is often deleted in X-linked ichthyosis, encodes a pseudouridine-5′-phosphatase
Authors: Preumont Alice , Rzem Rim , Vertommen Didier , Van Schaftingen Emile
Published: August 2010

Pseudouridine, the fifth-most abundant nucleoside in RNA, is not metabolized in mammals, but is excreted intact in urine. The purpose of the present work was to search for an enzyme that would dephosphorylate pseudouridine 5′-phosphate, a potential intermediate in RNA degradation. We show that human erythrocytes contain a pseudouridine-5′-phosphatase displaying a Km ≤ 1 μM for its substrate. The activity of the partially purified enzyme was dependent on Mg2+, and was inhibited by Ca2+ and vanadate, suggesting that it belonged to the ‘haloacid dehalogenase’ family of phosphatases. Its low molecular mass (26 kDa) suggested that this phosphatase could correspond to the protein encoded by the HDHD1 (haloacid dehalogenase-like hydrolase domain-containing 1) gene, present next to the STS (steroid sulfatase) gene on human chromosome Xp22. Purified human recombinant HDHD1 dephosphorylated pseudouridine 5′-phosphate with a kcat of 1.6 s−1, a Km of 0.3 μM and a catalytic efficiency at least 1000-fold higher than that on which it acted on other phosphate esters, including 5′-UMP. The molecular identity of pseudouridine-5′-phosphatase was confirmed by the finding that its activity was negligible (<10% of controls) in extracts of B-cell lymphoblasts or erythrocytes from X-linked ichthyosis patients harbouring a combined deletion of the STS gene (the X-linked ichthyosis gene) and the HDHD1 gene. Furthermore, pseudouridine-5′-phosphatase activity was 1.5-fold higher in erythrocytes from women compared with men, in agreement with the HDHD1 gene undergoing only partial inactivation in females. In conclusion, HDHD1 is a phosphatase specifically involved in dephosphorylation of a modified nucleotide present in RNA.
Domain structure elucidation of human decorin glycosaminoglycans
Authors: Laremore Tatiana N. , Ly Mellisa , Zhang Zhenqing , Solakyildirim Kemal , McCallum Scott A. , Owens Richard T. , Linhardt Robert J.
Published: August 2010

The structure of the GAG (glycosaminoglycan) chain of recombinantly expressed decorin proteoglycan was examined using a combination of intact-chain analysis and domain compositional analysis. The GAG had a number-average molecular mass of 22 kDa as determined by PAGE. NMR spectroscopic analysis using two-dimensional correlation spectroscopy indicated that the ratio of glucuronic acid to iduronic acid in decorin peptidoglycan was 5 to 1. GAG domains terminated with a specific disaccharide obtained by enzymatic degradation of decorin GAG with highly specific endolytic and exolytic lyases were analysed by PAGE and further depolymerized with the enzymes. The disaccharide compositional profiles of the resulting domains were obtained using LC with mass spectrometric and photometric detection and compared with that of the polysaccharide. The information obtained through the disaccharide compositional profiling was combined with the NMR and PAGE data to construct a map of the decorin GAG sequence motifs.
RNA silencing of hydrogenase(-like) genes and investigation of their physiological roles in the green alga Chlamydomonas reinhardtii
Authors: Godman James E. , Molnár Attila , Baulcombe David C. , Balk Janneke
Published: August 2010

The genome of the green alga Chlamydomonas reinhardtii encodes two [FeFe]-hydrogenases, HydA1 and HydA2, and the hydrogenase-like protein HYD3. The unique combination of these proteins in one eukaryotic cell allows for direct comparison of their in vivo functions, which have not been established for HydA2 and HYD3. Using an artificial microRNA silencing method developed recently, the expression of HydA1, HydA2 and HYD3 was specifically down-regulated. Silencing of HydA1 resulted in 4-fold lower hydrogenase protein and activity under anaerobic conditions. In contrast, silencing of HydA2 or HYD3 did not affect hydrogen production. Cell lines with strongly (>90%) decreased HYD3 transcript levels grew more slowly than wild-type. The activity of aldehyde oxidase, a cytosolic Fe-S enzyme, was decreased in HYD3-knockdown lines, whereas Fe-S dependent activities in the chloroplast and mitochondria were unaffected. In addition, the HYD3-knockdown lines grew poorly on hypoxanthine, indicating impaired function of xanthine dehydrogenase, another cytosolic Fe-S enzyme. The expression levels of selected genes in response to hypoxia were unaltered upon HYD3 silencing. Together, our results clearly distinguish the cellular roles of HydA1 and HYD3, and indicate that HYD3, like its yeast and human homologues, has an evolutionary conserved role in the biogenesis or maintenance of cytosolic Fe-S proteins.
Down‐regulation of CREB‐binding protein expression inhibits thrombin‐induced proliferation of endothelial cells: possible relevance to PDGF‐B
Authors: Jiang Hong , Chen Jing , Wang Lang , Zhu Li‐hua , Wen Hua‐zhi
Published: August 2010

Thrombin acts as a potent mitogenic factor for ECs (endothelial cells) by the release of several growth factors, including PDGF‐B (platelet‐derived growth factor‐B). CBP (CREB‐binding protein), which functions as a transcriptional coactivator, links the changes in the extracellular stimuli with alterations in gene expression. Therefore, we hypothesized that CBP could mediate thrombin‐induced proliferation of ECs via PDGF‐B‐dependent way. Short hairpin RNA was used to down‐regulate the expression of CBP in ECs. CBP and PDGF‐B levels were analysed by real‐time RT‐PCR and Western blot. To evaluate ECs proliferation, cell cycle and DNA synthesis were analysed by flow cytometry and BrdU (bromodeoxyuridine) incorporation assay, respectively. PDGF‐B was involved in the mitogenic effect of thrombin on ECs. Down‐regulation of CBP attenuated ECs proliferation and inhibited cell cycle progression induced by thrombin. Silencing CBP expression also suppressed thrombin‐induced PDGF‐B expression in ECs. Mitogenic activity of thrombin was impaired by silencing CBP expression in ECs. This inhibitory effect was, in part, related to the inability to up‐regulate PDGF‐B expression in ECs. CBP could be regarded as a potential therapeutic target for vascular injury.
Transcriptome atlas of glutamine family amino acid metabolism‐related genes in eight regenerating liver cell types
Authors: Chang Cuifang , Xu Cunshuan
Published: August 2010

To explore glutamine family amino acid metabolism of eight liver cell types in rat liver regeneration, eight kinds of rat regenerating liver cells were isolated by using the combination of Percoll density gradient centrifugation and immunomagnetic bead methods, then Rat Genome 230 2.0 Array was used to detect the expression profiles of the genes associated with metabolism of glutamine family amino acid in rat liver regeneration and finally how these genes involved in activities of eight regenerating liver cell types were analysed by the methods of bioinformatics and systems biology. The results showed that in the priming stage of liver regeneration, hepatic stellate cells and sinusoidal endothelial cells transformed proline and glutamine into glutamate; hepatocytes, hepatic stellate cells, sinusoidal endothelial cells and dendritic cells catabolized glutamate to 2‐oxoglutarate or succinate; hepatic stellate cells and sinusoidal endothelial cells catalysed glutamate into glutamyl‐tRNA for protein synthesis; urea cycle, which degraded from arginine, was enhanced in biliary epithelia cells, sinusoidal endothelial cells and dendritic cells; synthesis of polyamines from arginine was enhanced in biliary epithelia cells, sinusoidal endothelial cells, Kupffer cells and dendritic cells; the content of NO was increased in sinusoidal endothelial cells and dendritic cells; degradation of proline was enhanced in hepatocytes and biliary epithelia cells. In the progress stage, biliary epithelia cells converted glutamine into GMP and glucosamine 6‐phosphate; oval cells converted glutamine into glucosamine 6‐phosphate; hepatic stellate cells converted glutamine into NAD; the content of NO, which degraded from arginine, was increased in biliary epithelia cells, oval cells, pit cells and dendritic cells. In the termination stage, oval cells converted proline into glutamate; glutamate degradation, which degraded from arginine, was enhanced in hepatocytes and dendritic cells; the content of NO was increased in oval cells, sinusoidal endothelial cells, pit cells and dendritic cells. The synthesis of creatine phosphate was enhanced in hepatocytes, biliary epithelia cells, pit cells and dendritic cells in both progress and termination stages. In summary, glutamine family amino acid metabolism has some differences in liver regeneration in different liver cells.
Enhanced expression of receptor for advanced glycation end-products is associated with low circulating soluble isoforms of the receptor in Type 2 diabetes
Authors: Tam Xystus H. L. , Shiu Sammy W. M. , Leng Lin , Bucala Richard , Betteridge D. John , Tan Kathryn C. B.
Published: August 2010

The sRAGE [soluble RAGE (receptor for advanced glycation end-products)] lack the transmembrane and cytoplasmic domain of the full-length receptor and can function as a decoy for RAGE ligands. Recent evidence suggests that sRAGE may be a potential biomarker of RAGE-mediated pathology. The present study aimed to examine the relationship between RAGE expression in peripheral blood monocytes and circulating sRAGE and esRAGE (endogenous sRAGE, a splice variant of sRAGE) in Type 2 diabetes. Protein expression of RAGE and esRAGE in monocyte cell lysate was determined by Western blot in 53 diabetic patients and 52 controls. Monocyte cell-surface-bound full-length RAGE expression was measured using flow cytometry. Serum sRAGE, esRAGE and AGE (advanced glycation end products) were assayed by ELISA. The mean HbA1c (glycated haemoglobin) of the diabetic patients was 9.74% and serum AGEs was increased. Monocyte full-length RAGE expression was significantly higher in diabetic patients whereas esRAGE expression was reduced, and serum AGEs concentration was an independent determinant of monocyte cell surface full-length RAGE expression. Serum levels of sRAGE [573.3 (375.7–754.3) compared with 608.1 (405.3–940.8) pg/ml, P<0.05] and esRAGE [241.8 (154.6–356.6) compared with 286.5 (202.6–390.0) pg/ml, P<0.05; values are medians (interquartile range)] were decreased. There was an inverse association between monocyte RAGE expression and log(serum sRAGE) (r=−0.34, P=0.01) but not with esRAGE. In conclusion, despite an increase in full-length RAGE expression, esRAGE expression was down-regulated in the diabetic patients, and serum sRAGE and esRAGE was also reduced. Hence increased full-length RAGE levels are not associated with a similar increase in sRAGE isoforms levels.
Polymer-assisted conformal coating of TiO2 thin films
Authors: Gillman E. S. , Costello D. , Moreno M. , Raspopin A. , Kasica R. , Chen L.
Published: August 2010

Conformal coating of nanofabricated structures with a high-index dielectric material is a common problem for a diverse set of integrated photonic and plasmonic devices such as planar waveguides, on-chip spectrometers, gratings, flat panel displays, optical sensors, and integrated optical devices. In this paper we were recently able to demonstrate an alternate method for conformally coating photonic nanostructures using a low cost, polymer-assisted deposition (PAD) process for the metal-oxide TiO2. In a PAD process a thermally curable, hybrid high refractive index polymer solution is spin-coated onto a substrate. The polymer controls the viscosity and binds the metal ions, resulting in a homogeneous distribution of the precursor in solution. When cured at elevated temperature, the hybrid polymer coating decomposes to form a metal oxide-rich film that has a high refractive index that conformally fills the voids in nanofabricated structures. The resulting films have refractive indices higher than 1.83 in the visible region and film thicknesses between 250–500 nm depending on the level of metal-oxide loading, cure temperature, and number of coatings.
Nanopatchwork cathodes: Patch-fields and field emission of nanosize parallel e-beams
Authors: Binh Vu Thien , Mouton R. , Adessi Ch. , Semet V. , Cahay M. , Fairchild S.
Published: August 2010

A numerical calculation of the patch-field distribution across nanopatchwork surfaces has been developed. Results show that the low work-function nanosize zones are intrinsically protected by an electrostatic screen, which is induced by the surrounding area having a higher work function. In presence of an applied field, during field emission, a preferential opening of the surface barrier above the nanopatches induces a field emission array of parallel e-beams whose geometrical distribution is defined by the positions of the nanopatches.
A quantum dot based bright source of entangled photon pairs operating at 53 K
Authors: Dousse A. , Suffczyński J. , Krebs O. , Beveratos A. , Lemaître A. , Sagnes I. , Bloch J. , Voisin P. , Senellart P.
Published: August 2010

The exciton and biexciton lines of a single quantum dot are deterministically coupled to the optical modes of a photonic molecule. The resonance between the quantum dot emission lines and the molecule cavity modes is reached at 53 K. The device operates as a very bright source of entangled photon pairs, with an extraction efficiency of 40% for each photon of the pair. Our measurements show that the use of Purcell effect allows to quench the exciton spin relaxation during the radiative cascade, at 53 K and at high excitation power.
Quantum-classical description of environmental effects on electronic dynamics at conical intersections
Authors: Kelly Aaron , Kapral Raymond
Published: August 2010

Quantum-classical Liouville theory is used to simulate the dynamics of systems containing conical intersections. In particular quantum dynamical effects on the electronic population transfer and coherence in a quantum subsystem that arise from the presence of an environment are studied. The environment, in turn, is partitioned into an immediate environment representing, say, local molecular vibrations, and a bath representing other degrees of freedom. Population transfer may be enhanced or suppressed, depending on the relative values of the characteristic frequencies of the immediate environment and bath. Electronic decoherence and the destruction of geometric phase effects were observed for bath frequencies that are large relative to the molecular vibrations. The dynamics at higher dimensional conical intersections was found to be very sensitive to the environmental coupling. When a single collective solvent coordinate couples directly to the electronic subsystem, the characteristic frequency of the new coordinate, relative to that of the nuclear vibrational modes, has a strong effect on the population dynamics. The results also serve as a test of the QCL dynamical scheme for future applications to more detailed molecular descriptions of condensed phase environments for conical intersection dynamics.
Tuning single GaAs quantum dots in resonance with a rubidium vapor
Authors: Akopian N. , Perinetti U. , Wang L. , Rastelli A. , Schmidt O. G. , Zwiller V.
Published: August 2010

We study single GaAs quantum dots with optical transitions that can be brought into resonance with the widely used D2 transitions of rubidium atoms. We achieve resonance by Zeeman or Stark shifting the quantum dot levels. We discuss an energy stabilization scheme based on the absorption of quantum dot photoluminescence in a rubidium vapor. This offers a scalable means to counteract slow spectral diffusion in quantum dots.
Time-dependent auxiliary density perturbation theory
Authors: Carmona-Espíndola Javier , Flores-Moreno Roberto , Köster Andreas M.
Published: August 2010

The recently developed auxiliary density perturbation theory is extended to time-dependent perturbations. As its static counterpart, it is based on auxiliary density functional theory in which the Coulomb and exchange-correlation potentials are expressed through one auxiliary function density. As in the case of static perturbations a noniterative alternative to the corresponding coupled perturbed Kohn–Sham method is formulated. The new methodology is validated by local and gradient corrected dynamical polarizability calculations. Comparison with experiment indicates that for low frequencies reliable dynamical polarizabilities are obtained. Our discussion also shows that the computational performance of time-dependent auxiliary density perturbation theory is similar to the previously described static approach. In order to demonstrate the potential of this new methodology, dynamic polarizabilities of C60, C180, and C240 are calculated.
Temperature dependent transport properties of p-Pb1−xMnxSe films
Authors: Sun Y. H. , Lin T. , Gao K. H. , Hu Z. G. , Wu H. Z. , Yang P. X. , Dai N. , Chu J. H.
Published: August 2010

Hall measurements are performed to survey electrical properties of p-Pb1−xMnxSe (x≈0.04) films grown by molecular beam epitaxy technique. It is indicated that these films are approaching the metal-insulator transition from the metallic side. Weak localization effect was observed up to about 50 K. The deduced phase-breaking time τϕ on temperature is interpreted according to the concept of the electron–electron scattering in highly disordered bulk conductors.
New Products
Authors: Mandelis Andreas
Published: August 2010

In order to supplement manufacturers’ information this Department will welcome the submission by our readers of brief communications reporting measurements on the physical properties of materials which supersede earlier data or suggest new research applications.
Accurate series solutions for gravity-driven Stokes waves
Authors: Dallaston Michael C. , McCue Scott W.
Published: August 2010

In the past, high order series expansion techniques have been used to study the nonlinear equations that govern the form of periodic Stokes waves moving steadily on the surface of an inviscid fluid. In the present study, two such series solutions are recomputed using exact arithmetic, eliminating any loss of accuracy due to accumulation of round-off error, allowing a much greater number of terms to be found with confidence. It is shown that a higher order behavior of the series generated by the solution casts doubt over arguments that rely on estimating the series’ radius of convergence. Further, the exact nature of the series is used to shed light on the unusual nature of convergence of higher order Padé approximants near the highest wave. Finally, it is concluded that, provided exact values are used in the series, these Padé approximants prove very effective in successfully predicting three turning points in both the dispersion relation and the total energy.
Effects of surface chemistry on thermal conductance at aluminum–diamond interfaces
Authors: Collins Kimberlee C. , Chen Shuo , Chen Gang
Published: August 2010

Synthetic diamond has potential as a heat spreading material in small-scale devices. Here, we report thermal conductance values at interfaces between aluminum and diamond with various surface terminations over a range of temperatures from 88 to 300 K. We find that conductance at oxygenated diamond interfaces is roughly four times higher than at hydrogen-treated diamond interfaces. Furthermore, we find that Al grain structure formation is not strongly dependent on diamond surface chemistry, which suggests that interfacial bonding influences thermal conductance. The results reported here will be useful for device design and for advancing models of interfacial heat flow.