bluuebunny/crossref_metadata_2025 huggingface dataset:
Delineating the maladaptive pathways of child maltreatment: A mediated moderation analysis of the roles of self-perception and social support
Authors: Appleyard Karen , Yang Chongming , Runyan Desmond K.
Published: April 2010

The current study investigated concurrent and longitudinal mediated and mediated moderation pathways among maltreatment, self-perception (i.e., loneliness and self-esteem), social support, and internalizing and externalizing behavior problems. For both genders, early childhood maltreatment (i.e., ages 0–6) was related directly to internalizing and externalizing behavior problems at age 6, and later maltreatment (i.e., ages 6–8) was directly related to internalizing and externalizing behavior problems at age 8. Results of concurrent mediation and mediated moderation indicated that early maltreatment was significantly related to internalizing and externalizing behavior problems at age 6 indirectly both through age 6 loneliness and self-esteem for boys and through age 6 loneliness for girls. Significant moderation of the pathway from early maltreatment to self-esteem, and for boys, significant mediated moderation to emotional and behavioral problems were found, such that the mediated effect through self-esteem varied across levels of social support, though in an unexpected direction. No significant longitudinal mediation or mediated moderation was found, however, between the age 6 mediators and moderator and internalizing or externalizing problems at age 8. The roles of the hypothesized mediating and moderating mechanisms are discussed, with implications for designing intervention and prevention programs.
Testing a social ecological model for relations between political violence and child adjustment in Northern Ireland
Authors: Cummings E. Mark , Merrilees Christine E. , Schermerhorn Alice C. , Goeke-Morey Marcie C. , Shirlow Peter , Cairns Ed
Published: April 2010

Relations between political violence and child adjustment are matters of international concern. Past research demonstrates the significance of community, family, and child psychological processes in child adjustment, supporting study of interrelations between multiple social ecological factors and child adjustment in contexts of political violence. Testing a social ecological model, 300 mothers and their children (M= 12.28 years,SD= 1.77) from Catholic and Protestant working class neighborhoods in Belfast, Northern Ireland, completed measures of community discord, family relations, and children's regulatory processes (i.e., emotional security) and outcomes. Historical political violence in neighborhoods based on objective records (i.e., politically motivated deaths) were related to family members' reports of current sectarian antisocial behavior and nonsectarian antisocial behavior. Interparental conflict and parental monitoring and children's emotional security about both the community and family contributed to explanatory pathways for relations between sectarian antisocial behavior in communities and children's adjustment problems. The discussion evaluates support for social ecological models for relations between political violence and child adjustment and its implications for understanding relations in other parts of the world.
Trajectories of desistance and continuity in antisocial behavior following court adjudication among serious adolescent offenders
Authors: Mulvey Edward P. , Steinberg Laurence , Piquero Alex R. , Besana Michelle , Fagan Jeffrey , Schubert Carol , Cauffman Elizabeth
Published: April 2010

Because many serious adolescent offenders reduce their antisocial behavior after court involvement, understanding the patterns and mechanisms of the process of desistance from criminal activity is essential for developing effective interventions and legal policy. This study examined patterns of self-reported antisocial behavior over a 3-year period after court involvement in a sample of 1,119 serious male adolescent offenders. Using growth mixture models, and incorporating time at risk for offending in the community, we identified five trajectory groups, including a “persister” group (8.7% of the sample) and a “desister” group (14.6% of the sample). Case characteristics (age, ethnicity, antisocial history, deviant peers, a criminal father, substance use, psychosocial maturity) differentiated the five trajectory groups well, but did not effectively differentiate the persisting from desisting group. We show that even the most serious adolescent offenders report relatively low levels of antisocial activity after court involvement, but that distinguishing effectively between high-frequency offenders who desist and those who persist requires further consideration of potentially important dynamic factors related to this process.
Trauma and resilience in young refugees: A 9-year follow-up study
Authors: Montgomery Edith
Published: April 2010

The aim of the present study was to assess and understand the long-term trajectory of psychological problems among young Middle Eastern refugees in Denmark. Participants were 131 young refugees from the Middle East (76 girls, 55 boys; mean age = 15.3 years) from 67 families. They were assessed first on arrival in Denmark in 1992–1993 and again 8–9 years later. The high prevalence of psychological problems at arrival was considerably reduced by the time of follow-up, but it was still somewhat higher than what has been found in most community studies using the same assessment tools. Groups of children differed in showing low levels of symptoms at arrival that were stable (spared) or increased (reacting) and high levels at arrival that persisted (traumatized) or decreased (adapted). The number of types of traumatic experiences before arrival distinguished the spared and the traumatized young refugees and the number of types of stressful events after arrival the adapted and the traumatized, also after corrections for age, sex, specific traumatic events, parents' education and health, and the social situation of the young refugees. The study emphasizes the importance of environmental factors for healthy long-term adaptation after traumatic experiences related to war and other organized violence.
Sources of constructional cross‐chain volcanism in the southern Havre Trough: New insights from HFSE and REE concentration and isotope systematics
Authors: Todd E. , Gill J. B. , Wysoczanski R. J. , Handler Monica R. , Wright I. C. , Gamble J. A.
Published: April 2010

We report new compositional and isotopic data for submarine lavas erupted on the Rumble V Ridge cross chain behind the Kermadec Arc at ∼36°S and for locally subducting sediment. In order to constrain cross‐arc changes in the melt source, Havre Trough ambient mantle wedge isotope and trace element characteristics are interpreted from regional back‐arc basalts that are relatively free of slab‐derived components. They have MORB‐like trace element concentrations and are isotopically “Pacific” but define greater heterogeneity in 206Pb/204Pb and 176Hf/177Hf than previously known within the Havre Trough. In contrast with the ambient mantle, all Rumble V Ridge lavas have trace element and isotopic characteristics consistent with subduction zone contributions despite their rear‐arc setting but are less fluid‐enriched than at the Kermadec volcanic front. A broad trend in Nd‐Hf isotopic space and the correlation between 176Hf/177Hf and Hf concentration anomaly for Rumble V Ridge lavas is explained by across‐arc changes in (1) the mantle wedge component, (2) the nature of the subduction component, and (3) the mass fraction of subduction components added. Samples from the distal cross chain tend to have lower 176Hf/177Hf at similar 143Nd/144Nd compared with samples closer to the arc, suggesting that a low‐176Hf/177Hf component is preferentially removed from the mantle wedge during trenchward advection. Isotope trends suggest that locally subducting sediment is the primary slab component for Rumble V Ridge magmas, but bulk mixing of ambient mantle with sediment or slab‐derived fluids cannot account for cross‐arc trace element ratios. Instead, cross‐chain isotope and trace element characteristics are explained by the addition of 0.05%–2.0% sediment melts where trace zircon, monazite, and rutile are residual. The cross chain tracks an east to west increase in the mass fraction of a common subduction component. A particularly enriched subset of eastern basalts is interpreted as being derived from the addition of an even higher mass fraction of a different subduction component with greater apparent stability of refractory trace phases during sediment melting. An implication of this study is that both Nd and Hf can be mobile in sediment‐rich subduction zones, but the relative mobility depends on the sediment composition and depth of melting, and the absolute mobility is small.
Slip history of the 1944 Bolu‐Gerede earthquake rupture along the North Anatolian fault system: Implications for recurrence behavior of multisegment earthquakes
Authors: Kondo Hisao , Özaksoy Volkan , Yıldirim Cengiz
Published: April 2010

Recent research shows that active fault systems produce multisegment earthquakes; however, we have yet to understand the faulting behavior of various spatial patterns of segments. We conducted a three‐dimensional trenching survey to reconstruct the detailed slip history of a fault segment that ruptured as one of the multisegment ruptures along the North Anatolian fault system. The trench site, on the Gerede segment, recorded a maximum right‐lateral slip of up to 6 m that was associated with the 1944 Bolu‐Gerede earthquake (M 7.4). Fault exposures show evidence of four paleoearthquakes. Radiocarbon dates, a refined probability density distribution, and correlation with historical earthquakes place the mean repeat time at ∼330 years. Four discrete paleoslips yield a slip per event of 5.0 ± 0.8 m with a coefficient of variation of 0.2. Our research suggests that multisegment earthquakes exhibit various spatial patterns, regardless of recurrence with quasiperiodicity and characteristic slip. Coincidentally, the fault geometry exhibits extremely linear traces, suggesting simple stress accumulation and release through earthquake cycles. Furthermore, the 1944 event did not occur in a single segment, and the Gerede segment probably ruptured within a slip‐pulse‐like rupture during a multisegment earthquake. A comparable geological slip rate of ∼17 mm a−1 based on a GPS‐based strain rate supports the persistence of macroscopic asperity through recent geological time. Therefore we conclude that a segment with simple fault geometry along a strike‐slip fault system plays an important role in forecasting the timing of future multisegment earthquakes, but the spatial extent of such earthquakes needs to be explored further.
Radiative forcing of haze during a forest fire in Spain
Authors: Calvo A. I. , Pont V. , Castro A. , Mallet M. , Palencia C. , Roger J. C. , Dubuisson P. , Fraile R.
Published: April 2010

Intense fires occurred in northwestern Spain on 6 September 2000, filling a valley with smoke haze. Aerosol size distribution measurements were performed during 1 day with a thermal inversion, so the aging process of the smoke aerosol could be closely monitored. In 3.5 h, the fine aerosol increased up to 0.06 μm in the geometric median diameter of the fine mode. This aging process enhanced the scattering ability of aerosols. On the basis of several hypotheses on the data obtained, shortwave radiative forcing at surface level, at top level, and in the atmosphere was estimated: instantaneous surface forcing reached up to between −80.4 and −67.4 W/m2, top of the atmosphere (TOA) instantaneous forcing reached up to between −23.4 and +4.9 W/m2, and instantaneous atmosphere forcing reached up to between +44.2 and +85.3 W/m2. The study reveals not only the absorption of solar radiation in the atmosphere by smoke aerosols but also an aerosol‐induced case study, where TOA cooling forcing shifts to warming for specific aerosol single scattering albedo. The daily mean heating rate of the smoke haze was estimated at 5.9 ± 0.6 K/d.
Stochastic modeling in sediment dynamics: Exner equation for planar bed incipient bed load transport conditions
Authors: Ancey Christophe
Published: April 2010

Even under flow equilibrium conditions, river bed topography continuously evolves with time, producing trains of irregular bed forms. The idea has recently emerged that the variability in the bed form geometry results from some randomness in sediment flux. In this paper, we address this issue by using the Exner equation and a population exchange model derived in an earlier paper. In this model, particle entrainment and deposition are idealized as population exchanges between the stream and the bed, which makes it possible to use birth‐death Markov process theory to track the number of moving grains. The paper focuses on nascent bed forms on initially planar beds, a situation in which the coupling between the stream and bed is weak. In a steady state, the number of moving particles follows a negative binomial distribution. Although this probability distribution does not enter the family of heavy‐tailed distributions, it may give rise to large and frequent fluctuations because the standard deviation can be much larger than the mean, a feature that is not accounted for with classic probability laws (e.g., Hamamori's law) used so far for describing bed load fluctuations. In the large‐system limit, the master equation of the birth‐death Markov process can be transformed into a Fokker‐Planck equation. This transformation is used here to show that the number of moving particles can be described as an Ornstein‐Uhlenbeck process. An important consequence is that in the long term, the number of moving particles follows a Gaussian distribution. Laboratory experiments show that this approximation is correct when the mean number per unit length of stream, /L, is sufficiently large (typically two particles per centimeter in our experiments). The particle number fluctuations give rise to bed elevation fluctuations, whose spectrum falls off like ω−2 in the high‐frequency regime (with ω the angular frequency) and variance grows linearly with time. These features are in agreement with recent observations on bed form development (in particular, ripple growth).
What is the significance of pore pressure in a saturated shale layer?
Authors: Gonçalvès J. , Rousseau‐Gueutin P. , de Marsily G. , Cosenza P. , Violette S.
Published: April 2010

Electrostatic interactions, associated with negatively charged surfaces of clay minerals, produce a so‐called “disjoining pressure” when diffuse layers overlap, i.e., at low porosity. Disjoining pressure is the pressure difference between the water in the clay pore space and that in a bulk solution at the same depth. Another widely used concept in clay‐rocks is the “swelling pressure.” It corresponds in fact to the macroscopic average of the disjoining pressure. This study proposes to determine the value of the swelling pressure of a natural material by a simple volume‐averaging approach of the disjoining pressure, calculated for each clay mineral present in the material. The swelling pressure, which is dependent on the salinity of the pore fluid, is introduced into a hydrochemomechanical coupling, yielding a more general pressure diffusion equation. The results are compared to swelling pressure measurements for natural shale samples. The implications of this swelling pressure for water pressure measurements in natural formations are also discussed.
New Executive Director Selected
Authors: Grove Timothy L.
Published: April 2010

Christine W. McEntee will join AGU on 30 August as the Union's third executive director. She has been executive vice president and chief executive officer of the American Institute of Architects (AIA) since February 2006.

We are very fortunate to have McEntee join us at this stage in AGU's transformation to an inclusive, participative organization. We are also excited about her outreach expertise and ability to help AGU become an authoritative voice of Earth and space science. She is definitely up to the challenge after having successfully accomplished a similar result at AIA.
Facilitating Progress on the Quaternary History of Sea Level Change: Understanding Future Sea Level Rise: The Challenges of Dating Past Interglacials; Woods Hole, Massachusetts, 20–25 September 2009
Authors: Thompson W. G. , Andersen M. B.
Published: April 2010

Substantial uncertainty exists in projections of future sea level rise, due primarily to a lack of understanding about ice sheet dynamics. Paleo Constraints on Sea Level Rise (PALSEA) is a working group of the Past Global Changes (PAGES) project and the International Marine Global Change Studies (IMAGES) program that aims to extract information bout ice sheet response to temperature change by examining the history of sea level over the Quaternary (spanning the past ∼2.5 million years). In particular, PALSEA focuses on the past 800,000 years, particularly interglacial periods, with a range of temperatures bracketing the modern.
Does a ballast effect occur in the surface ocean?
Authors: Sanders Richard , Morris Paul J. , Poulton Alex J. , Stinchcombe Mark C. , Charalampopoulou Anastasia , Lucas Mike I. , Thomalla Sandy J.
Published: April 2010

The oceanic biological carbon pump (BCP), a large (10 GT C yr−1) component of the global carbon cycle, is dominated by the sinking (export) of particulate organic carbon (POC) from surface waters. In the deep ocean, strong correlations between downward fluxes of biominerals and POC (the so‐called ‘ballast effect’) suggest a potential causal relationship, the nature of which remains uncertain. We show that similar correlations occur in the upper ocean with high rates of export only occurring when biominerals are also exported. Exported particles are generally biomineral rich relative to the upper ocean standing stock, due either to: (1) exported material being formed from the aggregation of a biomineral rich subset of upper ocean particles; or (2) the unfractionated aggregation of the upper ocean particulate pool with respiration then selectively removing POC relative to biominerals until particles are dense enough to sink.
Is the basin‐wide warming in the North Atlantic Ocean related to atmospheric carbon dioxide and global warming?
Authors: Wang Chunzai , Dong Shenfu
Published: April 2010

A basin‐wide warming in the North Atlantic Ocean has occurred since the mid‐1990s; however, the cause of this basin‐wide warming is controversial. Some studies argued that the warming is due to global warming in association with the secular increase of the atmospheric greenhouse gas of carbon dioxide (CO2), while others suggested that it is caused by the Atlantic multidecadal oscillation (AMO) – an oscillatory mode occurring in North Atlantic sea surface temperature. Here we show that both global warming and AMO variability make a contribution to the recent basin‐wide warming in the North Atlantic and their relative contribution is approximately equal. It is further shown that after removing a linear trend and the seasonal cycle, atmospheric CO2 measured from 1958–2008 varies approximately with the AMO. On the assumption that a linear trend can be removed from the CO2 time series, then there are suggestive similarities between CO2 and AMO temperature anomalies. That is, atmospheric CO2 increases (decreases) when the AMO is in the warm (cold) phase. This would suggest that the recent basin‐wide warming of the North Atlantic might contribute to global ocean warming via its associated increase of atmospheric CO2.
Integrase illuminated
Authors: Cherepanov Peter
Published: April 2010

Antiretroviral drugs to prevent integration of the HIV viral genome into chromosomes are undergoing clinical trials, yet they have been developed with an imperfect understanding of their mechanism of action. The recent crystal structure of the major viral protein integrase from a related, little‐known retrovirus, has finally provided insight into how the drugs work and, more importantly, how to improve them.
Quantitative Analysis of [11C]AZ10419369 Binding to 5-HT1B Receptors in Human Brain
Authors: Varnäs Katarina , Nyberg Svante , Halldin Christer , Varrone Andrea , Takano Akihiro , Karlsson Per , Andersson Jan , McCarthy Dennis , Smith Mark , Pierson M Edward , Söderström Johan , Farde Lars
Published: April 2010

A novel radioligand for positron emission tomography (PET) imaging of serotonin 5-HT1B receptors, [11C]AZ10419369, has been recently described. In this study, the potential for quantitative analysis of [11C]AZ10419369 binding to central 5-HT1B receptors was evaluated in human subjects. PET measurements were performed after injection of [11C]AZ10419369 in 10 subjects. Data were analyzed with kinetic modeling and linear graphical analysis using the arterial plasma as input function, and with reference tissue models using cerebellar cortex as the reference region. Binding of [11C]AZ10419369 was highest in pallidum, ventral striatum, and occipital cortex and lowest in cerebellum. The percentage of unchanged radioligand in plasma was 97% to 99%, indicating that no significant amounts of radioactive metabolites were formed during the time of analysis. Time–activity curves of [11C]AZ10419369 could be described with both one-tissue compartment (1-TC) and two-tissue compartment (2-TC) models in the majority of subjects. The 2-TC model failed to deliver reasonable estimates of the kinetic parameters. However, stable estimates of binding potential ( BPND) were obtained by constraining K1/ k2 to the distribution volume obtained with the 1-TC model in the cerebellar cortex. BPND values estimated with reference tissue models were correlated with the corresponding values obtained with kinetic modeling. The findings support the use of reference tissue models in applied clinical studies with [11C]AZ10419369.
Scavenger Receptor Class-A Has a Central Role in Cerebral Ischemia–Reperfusion Injury
Authors: Lu Chen , Hua Fang , Liu Li , Ha Tuanzhu , Kalbfleisch John , Schweitzer John , Kelley Jim , Kao Race , Williams David , Li Chuanfu
Published: April 2010

The innate immune response is involved in the pathophysiology of cerebral ischemia–reperfusion (I/R) injury. Recent evidence suggests that scavenger receptors have a role in the induction of innate immunity. In this study, we examined the role of scavenger receptor A (SR-A) in focal cerebral I/R injury. Both SR-A−/− mice ( n=10) and age-matched wild-type (WT) mice ( n=9) were subjected to focal cerebral ischemia (60 minutes), followed by reperfusion (for 24 hours). Infarct size was determined by TTC (triphenyltetrazolium chloride) staining. The morphology of neurons in the brain sections was examined by Nissl's staining. Activation of intracellular signaling was analyzed by western blot. Cerebral infarct size in SR-A−/− mice was significantly reduced by 63.9% compared with WT mice after cerebral I/R. In SR-A−/− mice, there was less neuronal damage in the hippocampus compared with WT mice. Levels of FasL, Fas, FADD, caspase-3 activity, and terminal deoynucleotidyl transferase-mediated 2′-deoxyuridine 5′-triphosphate-biotin nick end labeling-positive apoptotic cells were significantly increased in WT mice after cerebral I/R, but not in SR-A−/− mice. Cerebral I/R increased nuclear factor-κB activation in WT mice, but not in SR-A−/− mice. These data suggest that SR-A has a central role in cerebral I/R injury and that suppression of SR-A may be a useful approach for ameliorating brain injury in stroke patients.
Obesity and Type 2 Diabetes in Rats are Associated with Altered Brain Glycogen and Amino-Acid Homeostasis
Authors: Sickmann Helle M , Waagepetersen Helle S , Schousboe Arne , Benie Andrew J , Bouman Stephan D
Published: April 2010

Obesity and type 2 diabetes have reached epidemic proportions; however, scarce information about how these metabolic syndromes influence brain energy and neurotransmitter homeostasis exist. The objective of this study was to elucidate how brain glycogen and neurotransmitter homeostasis are affected by these conditions. [1-13C]glucose was administered to Zucker obese (ZO) and Zucker diabetic fatty (ZDF) rats. Sprague–Dawley (SprD), Zucker lean (ZL), and ZDF lean rats were used as controls. Several brain regions were analyzed for glycogen levels along with 13C-labeling and content of glutamate, glutamine, GABA, aspartate, and alanine. Blood glucose concentrations and 13C enrichment were determined. 13C-labeling in glutamate was lower in ZO and ZDF rats in comparison with the controls. The molecular carbon labeling (MCL) ratio between alanine and glutamate was higher in the ZDF rats. The MCL ratios of glutamine and glutamate were decreased in the cerebellum of the ZO and the ZDF rats. Glycogen levels were also lower in this region. These results suggest that the obese and type 2 diabetic models were associated with lower brain glucose metabolism. Glucose metabolism through the TCA cycle was more decreased than glycolytic activity. Furthermore, reduced glutamate–glutamine cycling was also observed in the obese and type 2 diabetic states.
Regulation of LIM-domain-binding 1 protein expression by ubiquitination of Lys134
Authors: Howard Paul W. , Jue Shall F. , Ransom David G. , Maurer Richard A.
Published: April 2010

LDB1 (LIM-domain-binding 1) is a cofactor that participates in formation of transcriptional regulatory complexes involving transcription factors containing LIM domains as well as other factors. The amount of LDB1 protein in cells has previously been shown to be modulated by RNF12 (RING finger protein 12). RNF12 is an E3 ubiquitin ligase that can target LDB1 for poly-ubiquitination and degradation via the proteasome. We find that in HEK (human embryonic kidney)-293 cells expression of RNF12 leads to mono-ubiquitination of LDB1 and increased levels of LDB1 protein. Mutagenesis studies identified Lys134 of LDB1 as the residue that is mono-ubiquitinated by RNF12. Mutation of Lys134 of LDB1 to arginine blocks the formation of mono-ubiquitinated LDB1 and surprisingly also increases LDB1 protein expression in HEK-293 cells. This leads to a model in which Lys134 of LDB1 can be either mono-ubiquitinated, leading to stabilization, or poly-ubiquitinated, leading to degradation by the proteasome pathway. We also find that ubiquitin–LDB1 fusion proteins are stabilized in HEK-293 cells, offering further evidence that mono-ubiquitination stabilizes LDB1 in these cells. Expression in Xenopus laevis embryos of an LDB1 protein in which Lys134 is replaced with arginine leads to enhanced expression of the mutant protein as compared with the wild-type protein. These findings provide evidence that modification of Lys134 can play a major role in regulating LDB1 expression.
The arginylation-dependent association of calreticulin with stress granules is regulated by calcium
Authors: Carpio Marcos A. , López Sambrooks Cecilia , Durand Edith S. , Hallak Marta E.
Published: April 2010

Post-translational modifications of proteins are important for the regulation of cell functions; one of these modifications is post-translational arginylation. In the present study, we show that cytoplasmic CRT (calreticulin) is arginylated by ATE1 (arginyl-tRNA protein transferase). We also show that a pool of CRT undergoes retrotranslocation from the ER (endoplasmic reticulum) to the cytosol, because in CRT-knockout cells transfected with full-length CRT (that has the signal peptide), cytoplasmic CRT appears as a consequence of its expression and processing in the ER. After the cleavage of the signal peptide, an N-terminal arginylatable residue is revealed prior to retrotranslocation to the cytoplasm where arginylation takes place. SGs (stress granules) from ATE1-knockout cells do not contain CRT, indicating that CRT arginylation is required for its association to SGs. Furthermore, R-CRT (arginylated CRT) in the cytoplasm associates with SGs in cells treated with several stressors that lead to a reduction of intracellular Ca2+ levels. However, in the presence of stressors that do not affect Ca2+ levels, R-CRT is not recruited to these loci despite the fact that SGs are formed, demonstrating Ca2+-dependent R-CRT association to SGs. We conclude that post-translational arginylation of retrotranslocated CRT, together with the decrease in intracellular Ca2+, promotes the association of CRT to SGs.
Human pancreas-specific protein disulfide-isomerase (PDIp) can function as a chaperone independently of its enzymatic activity by forming stable complexes with denatured substrate proteins
Authors: Fu Xin-Miao , Zhu Bao Ting
Published: April 2010

Members of the PDI (protein disulfide-isomerase) family are critical for the correct folding of secretory proteins by catalysing disulfide bond formation as well as by serving as molecular chaperones to prevent protein aggregation. In the present paper, we report that the chaperone activity of the human pancreas-specific PDI homologue (PDIp) is independent of its enzymatic activity on the basis of the following lines of evidence. First, alkylation of PDIp by iodoacetamide fully abolishes its enzymatic activity, whereas it still retains most of its chaperone activity in preventing the aggregation of reduced insulin B chain and denatured GAPDH (glyceraldehyde-3-phosphate dehydrogenase). Secondly, mutation of the cysteine residues in PDIp's active sites completely abolishes its enzymatic activity, but does not affect its chaperone activity. Thirdly, the b-b′ fragment of PDIp, which does not contain the active sites and is devoid of enzymatic activity, still has chaperone activity. Mechanistically, we found that both the recombinant PDIp expressed in Escherichia coli and the natural PDIp present in human or monkey pancreas can form stable complexes with thermal-denatured substrate proteins independently of their enzymatic activity. The high-molecular-mass soluble complexes between PDIp and GAPDH are formed in a stoichiometric manner (subunit ratio of 1:3.5–4.5), and can dissociate after storage for a certain time. As a proof-of-concept for the biological significance of PDIp in intact cells, we demonstrated that its selective expression in E. coli confers strong protection of these cells against heat shock and oxidative-stress-induced death independently of its enzymatic activity.
Contribution of DEAH-box protein DHX16 in human pre-mRNA splicing
Authors: Gencheva Marieta , Kato Mitsuo , Newo Alain N.S. , Lin Ren-Jang
Published: April 2010

Studies of mammalian splicing factors are often focused on small nuclear ribonucleoproteins or regulatory RNA-binding proteins, such as hnRNP (heterogeneous nuclear ribonucleoprotein) and SR proteins (serine/arginine-rich proteins); however, much less is known about the contribution of DExD/H-box proteins or RNA helicases in mammalian pre-mRNA splicing. The human DEAH-box protein DHX16 [also known as DBP2 (DEAD-box protein 2)], is homologous with Caenorhabditis elegans Mog-4, Schizosaccharomyces pombe Prp8 and Saccharomyces cerevisiae Prp2. In the present study, we show that DHX16 is required for pre-mRNA splicing after the formation of a pre-catalytic spliceosome. We found that anti-DHX16 antiserum inhibited the splicing reaction in vitro and the antibody immunoprecipitated pre-mRNA, splicing intermediates and spliceosomal small nuclear RNAs. Cells that expressed DHX16 that had a mutation in the helicase domain accumulated unspliced intron-containing minigene transcripts. Nuclear extracts isolated from the dominant-negative DHX16-G724N-expressing cells formed splicing complex B, but were impaired in splicing. Adding extracts containing DHX16-G724N or DHX16-S552L mutant proteins to HeLa cell nuclear extracts resulted in reduced splicing, indicating that the mutant protein directly inhibited splicing in vitro. Therefore our results show that DHX16 is needed for human pre-mRNA splicing at a step analogous to that mediated by the S. cerevisiae spliceosomal ATPase Prp2.
Impact of in situ oxygen plasma cleaning on the resistance of Ru and Au-Ru based rf microelectromechanical system contacts in vacuum
Authors: Walker M. , Nordquist C. , Czaplewski D. , Patrizi G. , McGruer N. , Krim J.
Published: April 2010

Contact resistance measurements are reported for radio frequency microelectromechanical system switches operating in an ultrahigh vacuum system equipped with in situ oxygen plasma cleaning capabilities. Ru-based contacts were prepared by means of standard sputtering techniques, sputtering followed by postdeposition oxidation, (surface RuO2) or reactive sputtering in the presence of oxygen (bulk RuO2). In situ oxygen plasma cleaning lowered the resistance of Ru contacts by two or more orders of magnitude but not lower than Au contacts, irrespective of whether the Au contacts were cleaned. The time dependence of the resistance was fit to power law extrapolations to infer contact creep properties and resistance values at t=∞. Time-dependent creep properties of mixed Au-Ru contacts were observed to be similar to those of Au-Au contacts, while the absolute value of the resistance of such contacts was more comparable to Ru-Ru contacts. Prior to, and for short oxygen plasma exposure times, bulk RuO2 resistance values exhibited much larger variations than values measured for surface RuO2. For O2 plasma exposure times exceeding about 5 min, the bulk and surface RuO2 resistance values converged, at both t=0 and t=∞, with the t=∞ values falling within experimental error of theoretical values predicted for ideal surfaces. The data strongly support prior reports in the surface science literature of oxygen plasma induced thickening of oxide layers present on Ru surfaces. In addition, they demonstrate that vacuum alone is insufficient to remove contaminants from the contact surfaces and/or prevent such contaminants from reforming after oxygen plasma exposure.
Iron-related defect levels in SrTiO3 measured by photoelectron paramagnetic resonance spectroscopy
Authors: Dashdorj J. , Zvanut M. E. , Stanley L. J.
Published: April 2010

The optical absorption of defect centers in SrTiO3 substrates grown by the Vernuil method are investigated using photoinduced electron paramagnetic resonance (photo-EPR) at room temperature. As received samples revealed EPR signatures for Fe3+, Cr3+, Mn4+, and an iron-oxygen vacancy complex, Fe3+VO. An anneal in dry oxygen at 800 °C decreased the intensity of all of the centers except, Mn4+. More significantly, the anneal induced a new charge state of Fe, Fe5+. Photo-EPR data of the annealed samples were interpreted in terms of two defect levels, the 4+ to 5+ transition of Fe (Fe4+/5+) at 2.5 eV below the conduction band edge and the 3+ to 4+ transition of the iron-oxygen vacancy complex (Fe3+/4+VO) at 1.2 eV above the valence band edge. The former is consistent with reported defect levels and the latter provides a modified value based on measurements over a larger portion of the band gap than had been reported previously.
Crossover from a nearly constant loss to a superlinear power-law behavior in Mn-doped Bi(Mg1/2Ti1/2)O3–PbTiO3 ferroelectrics
Authors: Ke Shanming , Huang Haitao , Yu Shuhui , Zhou Limin
Published: April 2010

Mn-doped Bi(Mg1/2Ti1/2)–PbTiO3 disordered ferroelectric ceramics were studied under ac electric fields and a crossover from a nearly constant loss to a superlinear power-law behavior was observed. Our results confirmed that the nearly constant loss behavior also exists in disordered ferroelectrics. The exponent of the superlinear power-law was found to be temperature dependent. Such a behavior was related to the local movements of oxygen vacancies.
Temperature dependent properties of silicon containing diamondlike carbon films prepared by plasma source ion implantation
Authors: Hatada R. , Flege S. , Baba K. , Ensinger W. , Kleebe H.-J. , Sethmann I. , Lauterbach S.
Published: April 2010

Silicon containing diamondlike carbon (Si-DLC) films were prepared on silicon wafer substrates by a plasma source ion implantation method with negative pulses superposed on a negative dc voltage. A mixture of acetylene and tetramethylsilane gas was introduced into the discharge chamber as working gases for plasma formation. Ions produced in the plasma are accelerated toward a substrate holder because of the negative voltage applied directly to it. After deposition, the films were annealed for 0.5 h in ambient air at temperatures up to 923 K in order to evaluate the thermal stability of the Si-DLC films. The films were analyzed by x-ray photoelectron spectroscopy (XPS), high resolution transmission electron microscopy, and Raman spectroscopy. The surface morphology of the films and the film thickness were observed by atomic force microscopy and scanning electron microscopy. The mechanical and tribological properties were investigated by an indentation method and a ball-on-disk test. The results show the silicon containing DLC films were amorphous and the surface roughness of the Si containing DLC films was very smooth and no special structure was observed. Integrated intensity ratios ID/IG of Raman spectroscopy of the Si containing DLC films decreased with Si content. The Raman spectra showed that the structure of the Si-free DLC film changed to a graphitelike structure with increasing annealing temperature, whereas that of the 24 at. % Si containing DLC films did not change at the maximum temperature used in this study. A very low friction coefficient was obtained for the 13 at. % Si containing DLC film. The surface roughness and the hardness of the films changed with increasing annealing temperature. The formation of Si oxide in a near surface layer was confirmed by XPS and it prevents further oxidation of the inside of the film. Heat resistivity of DLC films can be improved by Si addition into the DLC films.
Femtosecond pump-probe studies of reduced graphene oxide thin films
Authors: Ruzicka Brian A. , Werake Lalani K. , Zhao Hui , Wang Shuai , Loh Kian Ping
Published: April 2010

The dynamics of photocarriers in reduced graphene oxide thin films is studied by using ultrafast pump-probe spectroscopy. Time dependent differential transmissions are measured with sample temperatures ranging from 9 to 300 K. At each sample temperature and probe delay, the sign of the differential transmission remains positive. A fast energy relaxation of hot carriers is observed, and is found to be independent of sample temperature. Our experiments show that the carrier dynamics in reduced graphene oxide is similar to other types of graphene, and that the differential transmission is caused by phase-state filling effects of carriers.
Opposing effects of attention and consciousness on afterimages
Authors: van Boxtel Jeroen J. A. , Tsuchiya Naotsugu , Koch Christof
Published: April 2010

The brain's ability to handle sensory information is influenced by both selective attention and consciousness. There is no consensus on the exact relationship between these two processes and whether they are distinct. So far, no experiment has simultaneously manipulated both. We carried out a full factorial 2 × 2 study of the simultaneous influences of attention and consciousness (as assayed by visibility) on perception, correcting for possible concurrent changes in attention and consciousness. We investigated the duration of afterimages for all four combinations of high versus low attention and visible versus invisible. We show that selective attention and visual consciousness have opposite effects: paying attention to the grating decreases the duration of its afterimage, whereas consciously seeing the grating increases the afterimage duration. These findings provide clear evidence for distinctive influences of selective attention and consciousness on visual perception.
Prevalence and Characteristics of Staphylococcus aureus Colonization among Healthcare Professionals in an Urban Teaching Hospital
Authors: Elie-Turenne Marie-Carmelle , Fernandes Helen , Mediavilla José R. , Rosenthal Marnie , Mathema Barun , Singh Ashima , Cohen Tiffany R. , Pawar Kimmerle A. , Shahidi Hosseinali , Kreiswirth Barry N. , Deitch Edwin A.
Published: April 2010

Objective.

To determine the prevalence of asymptomatic carriage of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) among healthcare professionals (HCPs) who experience varying degrees of exposure to ambulatory patients and to genetically characterize isolates.

Methods.

This single-center, cross-sectional study enrolled 256 staff from the intensive care units, emergency department, and prehospital services of an urban tertiary care university hospital in 2008. Occupational histories and nasal samples for S. aureus cultures were obtained. S. aureus isolates were genetically characterized with the use of spa typing and screened for mecA. MRSA isolates underwent further characterization.

Results.

S. aureus was isolated from 112 of 256 (43.8%) HCPs, including 30 of 52 (57.7%) paramedics, 51 of 124 (41.1%) nurses, 11 of 28 (39.3%) clerical workers, and 20 of 52 (38.5%) physicians. MRSA was isolated from 17 (6.6%) HCPs, including 1 (1.9%) paramedic, 13 (10.5%) nurses, 1 (3.6%) clerical worker, and 2 (3.8%) physicians. Among S. aureus isolates, 15.2% were MRSA. MRSA prevalence was 9.6% (12/125) in emergency department workers, 5.1% (4/79) in intensive care unit workers, and 1.9% (1/52) in emergency medical services workers. Compared with paramedics, who had the lowest prevalence of methicillin resistance among S. aureus isolates (1 of 30 [3.3%] isolates), nurses, who had the highest prevalence (13 of 51 [25.4%] isolates), had an odds ratio of 9.92 (95% confidence interval, 1.32-435.86; P = .02) for methicillin resistance. Analysis of 15 MRSA isolates revealed 7 USA100 strains, 6 USA300 strains, 1 USA800 strain, and 1 EMRSA-15 strain. All USA300 strains were isolated from emergency department personnel.

Conclusions.

The observed prevalence of S. aureus and MRSA colonization among HCPs exceeds previously reported prevalences in the general population. The proportion of community-associated MRSA among all MRSA in this colonized HCP cohort reflects the distribution of the USA300 community-associated strain observed increasingly among US hospitalized patients.
Staphylococcus aureusNasal Colonization and Subsequent Infection in Intensive Care Unit Patients: Does Methicillin Resistance Matter?
Authors: Honda Hitoshi , Krauss Melissa J. , Coopersmith Craig M. , Kollef Marin H. , Richmond Amy M. , Fraser Victoria J. , Warren David K.
Published: April 2010

Background.

Staphylococcus aureusis an important cause of infection in intensive care unit (ICU) patients. Colonization with methicillin-resistantS. aureus(MRSA) is a risk factor for subsequentS. aureusinfection. However, MRSA-colonized patients may have more comorbidities than methicillin-susceptibleS. aureus(MSSA)-colonized or noncolonized patients and therefore may be more susceptible to infection on that basis.

Objective.

To determine whether MRSA-colonized patients who are admitted to medical and surgical ICUs are more likely to develop anyS. aureusinfection in the ICU, compared with patients colonized with MSSA or not colonized withS. aureus,independent of predisposing patient risk factors.

Design.

Prospective cohort study.

Setting.

A 24-bed surgical ICU and a 19-bed medical ICU of a 1,252-bed, academic hospital.

Patients.

A total of 9,523 patients for whom nasal swab samples were cultured forS. aureusat ICU admission during the period from December 2002 through August 2007.

Methods.

Patients in the ICU for more than 48 hours were examined for an ICU-acquired S.aureusinfection, defined as development ofS. aureusinfection more than 48 hours after ICU admission.

Results.

S. aureuscolonization was present at admission for 1,433 (27.8%) of 5,161 patients (674 [47.0%] with MRSA and 759 [53.0%] with MSSA). An ICU-acquiredS. aureusinfection developed in 113 (2.19%) patients, of whom 75 (66.4%) had an infection due to MRSA. Risk factors associated with an ICU-acquiredS. aureusinfection included MRSA colonization at admission (adjusted hazard ratio, 4.70 [95% confidence interval, 3.07-7.21]) and MSSA colonization at admission (adjusted hazard ratio, 2.47 [95% confidence interval, 1.52-4.01]).

Conclusion.

ICU patients colonized with S.aureuswere at greater risk of developing aS. aureusinfection in the ICU. Even after adjusting for patient-specific risk factors, MRSA-colonized patients were more likely to developS. aureusinfection, compared with MSSA-colonized or noncolonized patients.
ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking
Authors: Wilkerson Matthew D. , Hayes D. Neil
Published: April 2010

Summary: Unsupervised class discovery is a highly useful technique in cancer research, where intrinsic groups sharing biological characteristics may exist but are unknown. The consensus clustering (CC) method provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset. ConsensusClusterPlus implements the CC method in R and extends it with new functionality and visualizations including item tracking, item-consensus and cluster-consensus plots. These new features provide users with detailed information that enable more specific decisions in unsupervised class discovery.

Availability: ConsensusClusterPlus is open source software, written in R, under GPL-2, and available through the Bioconductor project (http://www.bioconductor.org/).

Contact:  mwilkers@med.unc.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Phospholipids act as secondary receptor during the entry of the enveloped, double-stranded RNA bacteriophage φ6
Authors: Cvirkaitė-Krupovič Virginija , Poranen Minna M. , Bamford Dennis H.
Published: April 2010

Bacteriophage φ6 is the type member of the family Cystoviridae and infects Gram-negative Pseudomonas syringae cells. The virion consists of a protein-rich lipid envelope enclosing a nucleocapsid. The nucleocapsid covers the icosahedral polymerase complex that encloses the double-stranded RNA genome. Here, we demonstrate that nucleocapsid surface protein P8 is the single nucleocapsid component interacting with the cytoplasmic membrane. This interaction takes place between P8 and phospholipid. Based on this and previous studies, we propose a model where the periplasmic nucleocapsid interacts with the phospholipid head groups and, when the membrane voltage exceeds the threshold of 110 mV, this interaction drives the nucleocapsid through the cytoplasmic membrane, resulting in an intracellular vesicle containing the nucleocapsid.
Crystal structure of equine rhinitis A virus in complex with its sialic acid receptor
Authors: Fry Elizabeth E. , Tuthill Tobias J. , Harlos Karl , Walter Thomas S. , Rowlands David J. , Stuart David I.
Published: April 2010

Equine rhinitis A virus (ERAV) shares many features with foot-and-mouth disease virus (FMDV) and both are classified within the genus Aphthovirus of the family Picornaviridae. ERAV is used as a surrogate for FMDV research as it does not require high-level biosecurity. In contrast to FMDV, which uses integrins as cellular receptors, the receptor for ERAV has been reported to involve the sugar moiety sialic acid. This study confirmed the importance of sialic acid for cell entry by ERAV and reports the crystal structure of ERAV particles complexed with the receptor analogue 3′-sialyllactose. The receptor is attached to the rim of a capsid pit adjacent to the major immunogenic site and distinct from the sialic acid binding site used by a related picornavirus, the cardiovirus Theiler's murine encephalitis virus. The structure of the major antigenic determinant of the virus, previously identified from antibody escape mutations, is also described as the EF loop of VP1, which forms a hairpin stretching across the capsid surface close to the icosahedral fivefold axis, neighbouring the receptor-binding site, and spanning two protomeric units.