bluuebunny/crossref_metadata_2025 huggingface dataset:
Psychiatric aspects of chronic palliative care: Waiting for death
Authors: Sirois François
Published: March 2012

This article emphasizes the shifting paradigm of palliative care from cancer patients to vital organ failure in chronic diseases. It offers a view about a type of palliative care for patients reaching the pre-terminal phase of a chronic illness. Unlike cancer patients, time is not as sharply delineated and physical pain is not a major factor, but psychological distress is often a major component of the clinical condition. Starting from the perspective of a psychiatric consultant on medical and surgical wards, I present short clinical vignettes to introduce a discussion about psychological manifestations in patients with chronic vital organ failure. The objective is to help patients find meaning to the last stage of their life. To that effect, four key sensitive areas are presented for clinicians to assess end-of-life coping: pressure on character organization, the management of hope, mourning problems, and ill health as a screen for psychological distress.
Methane exchange between marshland and the atmosphere over China during 1949–2008
Authors: Xu Xiaofeng , Tian Hanqin
Published: March 2012

We used a process‐based ecosystem model to examine methane (CH4) fluxes in the marshland across China as a result of multifactor global changes during 1949–2008. Our simulated results show a significant declining rate of 18.7 Gg Ca−1 (1Gg = 109 g) (with a 95% confidence boundary of 17.6 ∼ 19.8 Gg C a−1) at national scale, but substantially varying from the maximum annual CH4 emission of 2.4 Tg C a−1 (1Tg = 1012 g) (with a 95% confident boundary of 1.8 ∼ 3.4 Tg C a−1) in 1952 to the minimum annual CH4 emission of 1.3 Tg C a−1 (with a 95% confident boundary of 1.0 ∼ 1.9 Tg C a−1) in 2003. The marshland loss made the largest contribution to the CH4 emission reduction with an cumulative effect of 37.9 Tg C (with a 95% confident boundary of 28.0 ∼ 54.1 Tg C) for the past 60 years. Ozone pollution reduced CH4 emission, while elevated atmospheric CO2, nitrogen deposition, climate change, and multiple‐factor interaction, cumulatively stimulated CH4emission. Climate variability predominately controlled the inter‐annual variations in CH4 emissions. A substantial spatial variation in CH4 emission was observed across China's marshland. At regional scale, the Northeast, followed by Northwest and Southeast, made the greatest contribution, while North and Southwest made minor contributions to the national CH4 emission. This study suggests that it is necessary to consider multiple global change factors when estimating regional CH4 fluxes in natural wetlands.
Contribution of winter soil respiration to annual soil CO2 emission in a Mollisol under different tillage practices in northeast China
Authors: Shi Xiuhuan , Zhang Xiaoping , Yang Xueming , Drury Craig F. , McLaughlin Neil B. , Liang Aizhen , Fan Ruqin , Jia Shuxia
Published: March 2012

Winter soil CO2 emission is a very important component of the annual carbon budgets, however, almost no information on winter CO2 emission is available from the cropland soil in northeast China. In this study, soil CO2flux was measured for a 2‐year period from an ongoing tillage trial on Black soil in northeast China to quantify seasonal patterns in soil CO2 flux rate and wintertime contribution to annual soil respiration. Average soil CO2 flux rates in the winter (November to March) were between 0.64 to 1.22 g CO2 m−2 d−1, in the non‐growing season (October and April) were 2.09–3.56 g CO2 m−2 d−1, whereas in the growing season (May to September) they were between 10.9 to 12.7 g CO2 m−2 d−1, with no significant differences among tillage treatments. Total winter, non‐growing and growing season soil CO2 emissions were 0.28–0.45 Mg C ha−1, 0.36–0.53 Mg C ha−1, and 4.52–5.55 Mg C ha−1, respectively, among tillage treatments. The contributions of winter soil respiration to annual soil CO2emission ranged from 5.1 to 7.1%, and the non‐growing season emission ranged from 11.4 to 15.2% among tillage treatments. Our results indicate that in northeast China, cropland Black soil continuously emits CO2throughout the non‐growing season, and the wintertime soil respiration plays a significant role in annual soil carbon budgets. Hence winter soil CO2 emission must be taken into consideration when the role of the soil ecosystem is assessed as either a sink or source of CO2 to the atmosphere.
Modeling solar zenith angle effects on the polar wind
Authors: Glocer A. , Kitamura N. , Toth G. , Gombosi T.
Published: March 2012

We use the Polar Wind Outflow Model (PWOM) to study the geomagnetically quiet conditions in the polar cap during solar maximum. The PWOM solves the gyrotropic transport equations for O+, H+, and He+ along several magnetic field lines in the polar region in order to reconstruct the full 3D solution. We directly compare our simulation results to the data based empirical model of Kitamura et al. (2011) of electron density which is based on 63 months of Akebono satellite observations. The modeled ion and electron temperatures are also compared with a statistical compilation of quiet time data obtained by the EISCAT Svalbard Radar (ESR) and Intercosmos Satellites. The data and model agree reasonably well, albeit with some differences. This study shows that photoelectrons play an important role in explaining the differences between sunlit and dark results of electron density, ion composition, as well as ion and electron temperatures of the quiet time polar wind solution. Moreover, these results provide an initial validation of the PWOM's ability to model the quiet time “background” solution.
Summertime formaldehyde observations in New York City: Ambient levels, sources and its contribution to HOx radicals
Authors: Lin Yu Chi , Schwab James J. , Demerjian Kenneth L. , Bae Min‐Suk , Chen Wei‐Nai , Sun Yele , Zhang Qi , Hung Hui‐Ming , Perry Jacqueline
Published: March 2012

Measurements of ambient formaldehyde (HCHO), related gases and particulate matter were carried out from the SUNY Albany mobile platform at the Queens College site in New York City (NYC) from 15 July to 3 August 2009. Ambient HCHO was measured using a quantum cascade laser (QCL) trace gas detector. HCHO concentrations ranged from 0.4 to 7.5 ppb with a mean value of 2.2 ± 1.1 ppb. Daily HCHO peaks were nearly always found between 1100 EST (Eastern Standard Time) and noontime throughout the sampling period. HCHO correlated strongly with NOx and black carbon during the traffic rush hours, but around noontime HCHO correlated much better with total oxidants (Ox = O3 + NO2). Using the diurnal pattern of HCHO/BC ratios, we estimated that 70% of HCHO present between 1200 EST to 1500 EST was produced by photochemical reactions. Sources of photochemically produced HCHO were calculated using measured concentrations of hydrocarbons, their reaction kinetics with OH radicals, and HCHO yields. These calculations indicated that isoprene oxidation was the dominant source of HCHO for this period at this site, responsible for 44%, followed by methane (25%) and propene (18%). To assess the impact of HCHO as a radical source, the HOx production rates from HCHO, HONO, O3 photolysis, and alkenes +O3 were calculated as well. Daily averaged HOx production rates from HONO, HCHO, O3 photolysis and alkenes +O3 were 8.6 × 106, 2.3 × 106, 1.7 × 106, 2.1 × 105 molecules cm−3 s−1, respectively, contributing 67, 18, 13 and 2% to the overall daily HOx radical budget from these precursors.
PM2.5 source apportionment in the southeastern U.S.: Spatial and seasonal variations during 2001–2005
Authors: Chen Yingjun , Zheng Mei , Edgerton Eric S. , Ke Lin , Sheng Guoying , Fu Jiamo
Published: March 2012

The seasonal and spatial variations of source contributions of 112 composite fine particulate matter (PM2.5) samples collected in the Southeastern Aerosol Research and Characterization Study (SEARCH) monitoring network during 2001–2005 using molecular marker‐based chemical mass balance (CMB‐MM) model were determined. The lowest PM2.5 concentration occurs in January with higher values in warm months (maxima in July at four inland sites versus October at the coastal sites). Sulfate shows a similar pattern and plays a primary role in PM2.5 seasonality. Carbonaceous material (organic matter plus EC) exhibits less seasonality, but more spatial variations between the inland and coastal sites. Compared with the data at coastal sites, source attributions of diesel exhaust, gasoline exhaust, other organic matter (other OM), secondary sulfate, nitrate, and ammonium in PM2.5 mass at inland sites are higher. The difference in source attributions of wood combustion, meat cooking, vegetative detritus, and road dust among the eight sites is not significant. Contributions of eight primary sources to fine OC are wood burning (17 ± 19%), diesel exhaust (9 ± 4%), gasoline exhaust (5 ± 7%), meat cooking (5 ± 5%), road dust (2 ± 3%), vegetative detritus (2 ± 2%), cigarette smoke (2 ± 2% at four urban sites), and coke production (2 ± 1% only at BHM). Primary and secondary sources explain 82–100% of measured PM2.5 mass at the eight sites, including secondary ionic species (SO42−, NH4+, and NO3−; 41.4 ± 5.7%), identified OM (24.9 ± 11.3%), “other OM” (unexplained OM, 23.3 ± 10.3%), and “other mass” (11.4 ± 9.6%). Vehicle exhaust from both diesel and gasoline contributes the lowest fraction to PM2.5 mass in July and higher fractions at BHM and JST than other sites. Wood combustion, in contrast, contributes significantly to a larger fraction in winter than in summer. Road dust shows relatively high levels in July and April across the eight sites, while minor sources such as meat cooking and other sources (e.g., vegetative detritus, coke production, and cigarette smoke) show relatively small seasonal and spatial variations in the SEARCH monitoring network.
Development of a physically based PDSI and its application for assessing the vegetation response to drought in northern China
Authors: Xu Jing , Ren Li‐Liang , Ruan Xiao‐Hong , Liu Xiao‐Fan , Yuan Fei
Published: March 2012

A physically based Palmer Drought Severity Index (PB‐PDSI) was developed by replacing the two‐stage bucket water balance model in the original PDSI with the distributed hydrological model. The PB‐PDSI was tested and compared with Liu's PDSI, which is applied commonly in China. The results indicate that the monthly water balance computation of the PB‐PDSI is a more realistic approximation when utilizing remote sensing data that characterize the land surface and incorporating the two‐source PET (Potential EvapoTranspiration) method, the hybrid runoff model and a flow routing module on the basis of daily hydrologic simulation. The impact of the vegetation cover change on drought was also reflected appropriately by the PB‐PDSI. The spatial distribution of the PDSI over the whole basin by the PB‐PDSI allows for the exploration of the relationship between vegetation vigor and moisture availability. Pearson correlation analysis indicated that the NDVI (Normalized Difference Vegetation Index) is highly and positively correlated to the PB‐PDSI during the first half of the plant growing season and that the two are weakly correlated or uncorrelated during plant senescence. This result implies that the vegetation response to water availability depends on the plant growth stage. June was shown to be the “moisture‐sensitive period” for the vegetation in the Laohahe River catchment. When the seasonality effects are incorporated, an accurate estimation of the relationship between the NDVI and PB‐PDSI can be derived using the regression model with dummy variables. This suggests that the PB‐PDSI has the potential to elucidate the interaction mechanism between drought and the changing environment.
Volcanic ash over Scandinavia originating from the Grímsvötn eruptions in May 2011
Authors: Tesche M. , Glantz P. , Johansson C. , Norman M. , Hiebsch A. , Ansmann A. , Althausen D. , Engelmann R. , Seifert P.
Published: March 2012

A volcanic ash plume that originated from the eruptions of Iceland's Grímsvötn volcano in May 2011 was observed over the Nordic countries using a combination of satellite observations and ground‐based measurements. The dispersion of the plume was investigated using London VAAC ash forecasts and MODIS observations. Hourly PM10 concentrations at air quality monitoring stations in the southern parts of Norway, Sweden, and Finland exceeded 100 μg/m3 for several hours. The FLEXPART dispersion model has been used to confirm the Icelandic origin of the sampled air masses. Column‐integrated quantities from a Sun photometer and vertical profiles from a Raman lidar were used to estimate the ash concentration within an elevated layer over Stockholm. A lofted layer with an optical thickness of 0.3 at 532 nm passed Stockholm in the morning hours of 25 May 2011. Considering a realistic range of coarse‐mode fractions and specific ash extinctions from the literature, an estimated range of maximum ash mass concentration of 150–340 μg/m3 was derived from the lidar measurements at an altitude of 2.8 km. The lower estimate of the lidar‐derived ash mass concentrations within the planetary boundary layer was found to be in good agreement with surface observations of PM10.
Paleoseismology of the Mejillones Fault, northern Chile: Insights from cosmogenic10Be and optically stimulated luminescence determinations
Authors: Cortés A. J. , González L. Gabriel , Binnie S. A. , Robinson R. , Freeman S. P. H. T. , Vargas E. G.
Published: March 2012

We have undertaken the first paleoseismological study on an upper plate fault in Chile. The selected structure was the Mejillones Fault, which is marked by a conspicuous fault‐scarp. Using cosmogenic10Be and OSL dating and detailed sedimentary logging of trenches, we have constrained the abandonment of two alluvial surfaces by fault activity at ca. 35 ka and ca.14 ka. Based on stratigraphic observation we characterized the fault evolution in four intervals over the last ca. 35 ka. During the first three intervals the fault had a steady slip rate of 0.61 ± 0.26 m/ka. The fourth interval is delineated by the last vertical fault slip and the accumulation of un‐deformed hillslope deposits after ca. 3.3 ka and has a slip rate of 0.22 ± 0.06 m/ka. The younger surface abandonment was caused by two Mw ∼ 7 paleoearthquakes with a recurrence interval of 5.0 ± 3.5 ka. The third interval is characterized by the interaction of hillslope deposits and aseismic slip and/or centimeter scale seismic slip events. At ca. 3.5 ka, a last large (Mw ∼ 6.6) earthquake took place. The recurrence intervals of large (Mw > 8.5) subduction earthquakes do not appear to be the same as the recurrence intervals of the Mw ∼ 7 events on the upper plate Mejillones Fault.
Flow‐plant interactions in open‐channel flows: A comparative analysis of five freshwater plant species
Authors: Siniscalchi Fabio , Nikora Vladimir I.
Published: March 2012

The paper reports a laboratory study of drag forces exerted on aquatic vegetation and their coupling with flow turbulence. The experiments were conducted in a 12.5 m long and 0.30 m wide flume, using five different freshwater plant species (Ranunculus penicillatus, Fontinalis antipyretica, Myriophyllum alterniflorum, Glyceria fluitans, and Callitriche stagnalis). Velocity components and drag forces were measured using two acoustic Doppler velocimeters (ADV) and a specially designed drag measurement device. Drag fluctuations exerted on the plants appeared to be closely related to the ambient turbulence, especially to large‐scale turbulent structures. The enhanced turbulent energy downstream from the plants was associated with wake generation, with its magnitude controlled by plant morphology reconfiguration. Frequency spectra of drag fluctuations reveal a frequency range where they follow a power law that can be parameterized using plant and flow properties. The rescaled spectral functions are shown to match the collected data reasonably well. In addition, drag‐velocity cross‐correlation analyses enabled the estimation of the location of the resultant drag force, which can be interpreted as an integral measure of plant adaptation to the flow. The results revealed different degrees of adaptation of the plants to flowing water, withFontinalis and Glyceria showing the best hydrodynamic performances, i.e., lower levels of turbulence and drag generation.
Bayesian model averaging using particle filtering and Gaussian mixture modeling: Theory, concepts, and simulation experiments
Authors: Rings Joerg , Vrugt Jasper A. , Schoups Gerrit , Huisman Johan A. , Vereecken Harry
Published: March 2012

Bayesian model averaging (BMA) is a standard method for combining predictive distributions from different models. In recent years, this method has enjoyed widespread application and use in many fields of study to improve the spread‐skill relationship of forecast ensembles. The BMA predictive probability density function (pdf) of any quantity of interest is a weighted average of pdfs centered around the individual (possibly bias‐corrected) forecasts, where the weights are equal to posterior probabilities of the models generating the forecasts, and reflect the individual models skill over a training (calibration) period. The original BMA approach presented by Raftery et al. (2005) assumes that the conditional pdf of each individual model is adequately described with a rather standard Gaussian or Gamma statistical distribution, possibly with a heteroscedastic variance. Here we analyze the advantages of using BMA with a flexible representation of the conditional pdf. A joint particle filtering and Gaussian mixture modeling framework is presented to derive analytically, as closely and consistently as possible, the evolving forecast density (conditional pdf) of each constituent ensemble member. The median forecasts and evolving conditional pdfs of the constituent models are subsequently combined using BMA to derive one overall predictive distribution. This paper introduces the theory and concepts of this new ensemble postprocessing method, and demonstrates its usefulness and applicability by numerical simulation of the rainfall‐runoff transformation using discharge data from three different catchments in the contiguous United States. The revised BMA method receives significantly lower‐prediction errors than the original default BMA method (due to filtering) with predictive uncertainty intervals that are substantially smaller but still statistically coherent (due to the use of a time‐variant conditional pdf).
Slow slip events in Costa Rica detected by continuous GPS observations, 2002–2011
Authors: Jiang Yan , Wdowinski Shimon , Dixon Timothy H. , Hackl Matthias , Protti Marino , Gonzalez Victor
Published: March 2012

A network of continuously recording GPS stations has operated in the Nicoya Peninsula of northern Costa Rica since 2002. We processed all available data from this network for the period of 2002–2011 to investigate the occurrence of Slow Slip Events (SSE) on the subduction interface between the Cocos and Caribbean plates. In order to overcome signal masking by high levels of tropospheric noise, we developed a new technique that facilitates detection of transient events in the presence of noise. We identified five significant SSEs during the 2002–2011 period, with event middle times in 2003, 2005, 2007, 2009 and 2011, with an average recurrence interval of 21 ± 6 months. Time series analysis shows that transient deformation imparts a signature similar to random walk. Removal of the SSEs and regional common mode errors from the time series reduced velocity uncertainty by nearly an order of magnitude. Limited available data for the 2003, 2005 and 2011 events preclude detailed characterization of these events. However, good spatiotemporal coverage of the 2007 and 2009 events suggest that both events had irregular duration and distribution. In the 2007 event, slow slip started in the northwest coastal area and migrated southeastward over a period of ∼1 month. The 2009 event had a significantly longer event duration and larger surface displacement. Stations in the northwest area observed two separate SSEs in 2008.6 and 2009.4, correlating well with the tremor episodes offshore, indicating a shallow SSE slip patch with shorter recurrence interval. Significant differences between the 2009 and 2007 events lead us to question the simple recurrence interval model for the SSE in Nicoya.
Greenland ice core evidence for spatial and temporal variability of the Atlantic Multidecadal Oscillation
Authors: Chylek Petr , Folland Chris , Frankcombe Leela , Dijkstra Henk , Lesins Glen , Dubey Manvendra
Published: March 2012

The Greenland δ18O ice core record is used as a proxy for Greenland surface air temperatures and to interpret Atlantic Multidecadal Oscillation (AMO) variability. An analysis of annual δ18O data from six Arctic ice cores (five from Greenland and one from Canada's Ellesmere Island) suggests a significant AMO spatial and temporal variability within a recent period of 660 years. A dominant AMO periodicity near 20 years is clearly observed in the southern (Dye3 site) and the central (GISP2, Crete and Milcent) regions of Greenland. This 20‐year variability is, however, significantly reduced in the northern (Camp Century and Agassiz Ice Cap) region, likely due to a larger distance from the Atlantic Ocean, and a much lower snow accumulation. A longer time scale AMO component of 45–65 years, which has been seen clearly in the 20th century SST data, is detected only in central Greenland ice cores. We find a significant difference between the AMO cycles during the Little Ice Age (LIA) and the Medieval Warm Period (MWP). The LIA was dominated by a ∼20 year AMO cycle with no other decadal or multidecadal scale variability above the noise level. However, during the preceding MWP the 20 year cycle was replaced by a longer scale cycle centered near a period of 43 years with a further 11.5 year periodicity. An analysis of two coupled atmosphere‐ocean general circulation models control runs (UK Met Office HadCM3 and NOAA GFDL CM2.1) agree with the shorter and longer time‐scales of Atlantic Meridional Overturning Circulation (AMOC) and temperature fluctuations with periodicities close to those observed. However, the geographic variability of these periodicities indicated by ice core data is not captured in model simulations.
Spatial variations in earthquake source characteristics within the 2011 Mw = 9.0 Tohoku, Japan rupture zone
Authors: Bilek Susan L. , DeShon Heather R. , Engdahl E. Robert
Published: March 2012

The great Mw = 9.0 2011 Tohoku earthquake appears to have complex rupture characteristics, with slower rupture velocity during the early portion of the rupture and spatial variations in the radiation frequency content. These spatial and temporal variations suggest that the subduction zone fault has spatially varying friction conditions that led to differences in the 2011 rupture characteristics, conditions that might also affect other earthquakes within the rupture zone. We find spatial variations for source parameters of 90 relocated earthquakes between 1992 and 2011 along northern Japan, with longer durations observed in shallow near trench events relative to shorter duration deeper events. A majority of these events do not lie within the high slip zone of 2011, however, and occur instead in the region of the 1896 tsunami earthquake to the north. We also find correlation between the longest duration event locations and low seismic velocities based on recent tomography models.
Changes in coral microbial communities in response to a natural pH gradient
Authors: Meron Dalit , Rodolfo-Metalpa Riccardo , Cunning Ross , Baker Andrew C , Fine Maoz , Banin Ehud
Published: March 2012

Surface seawater pH is currently 0.1 units lower than pre-industrial values and is projected to decrease by up to 0.4 units by the end of the century. This acidification has the potential to cause significant perturbations to the physiology of ocean organisms, particularly those such as corals that build their skeletons/shells from calcium carbonate. Reduced ocean pH could also have an impact on the coral microbial community, and thus may affect coral physiology and health. Most of the studies to date have examined the impact of ocean acidification on corals and/or associated microbiota under controlled laboratory conditions. Here we report the first study that examines the changes in coral microbial communities in response to a natural pH gradient (mean pHT 7.3–8.1) caused by volcanic CO2 vents off Ischia, Gulf of Naples, Italy. Two Mediterranean coral species, Balanophyllia europaea and Cladocora caespitosa, were examined. The microbial community diversity and the physiological parameters of the endosymbiotic dinoflagellates (Symbiodinium spp.) were monitored. We found that pH did not have a significant impact on the composition of associated microbial communities in both coral species. In contrast to some earlier studies, we found that corals present at the lower pH sites exhibited only minor physiological changes and no microbial pathogens were detected. Together, these results provide new insights into the impact of ocean acidification on the coral holobiont.
AMPK and GCN2–ATF4 signal the repression of mitochondria in colon cancer cells
Authors: Martínez-Reyes Inmaculada , Sánchez-Aragó María , Cuezva José M.
Published: March 2012

Reprogramming of energetic metabolism is a phenotypic trait of cancer in which mitochondrial dysfunction represents a key event in tumour progression. In the present study, we show that the acquisition of the tumour-promoting phenotype in colon cancer HCT116 cells treated with oligomycin to inhibit ATP synthase is exerted by repression of the synthesis of nuclear-encoded mitochondrial proteins in a process that is regulated at the level of translation. Remarkably, the synthesis of glycolytic proteins is not affected in this situation. Changes in translational control of mitochondrial proteins are signalled by the activation of AMPK (AMP-activated protein kinase) and the GCN2 (general control non-derepressible 2) kinase, leading also to the activation of autophagy. Changes in the bioenergetic function of mitochondria are mimicked by the activation of AMPK and the silencing of ATF4 (activating transcription factor 4). These findings emphasize the relevance of translational control for normal mitochondrial function and for the progression of cancer. Moreover, they demonstrate that glycolysis and oxidative phosphorylation are controlled at different levels of gene expression, offering the cell a mechanistic safeguard strategy for metabolic adaptation under stressful conditions.
Kinetic analysis of FTO (fat mass and obesity-associated) reveals that it is unlikely to function as a sensor for 2-oxoglutarate
Authors: Ma Marcella , Harding Heather P. , O'Rahilly Stephen , Ron David , Yeo Giles S. H.
Published: March 2012

Genomewide-association studies have revealed that SNPs (single nucleotide polymorphisms) in FTO (fat mass and obesity-associated) are robustly associated with BMI (body mass index) and obesity. FTO is an Fe(II) 2-OG (2-oxoglutarate)-dependent dioxygenase that can demethylate 3-meT (3-methylthymine) in single-stranded DNA, as well as 3-meU (3-methyluracil) and N6-methyl adenosine in RNA. In the present paper we describe the development of an RNase-cleavage assay measuring the demethylation activity of FTO on 3-meU. RNase A cleaves at the 3′-end of pyrimidines, including uracil, and a methyl group at position three of uracil inhibits cleavage. An oligonucleotide probe was designed consisting of a DNA stem, an RNA loop containing a single 3-meU as the only RNase A-cleavage site, a fluorescent reporter on one end and a quencher at the other end. FTO demethylation of the unique 3-meU enables RNase A cleavage, releasing the quencher and enabling a fluorescent signal. In the presence of excess RNase A, FTO activity is limiting to the development of fluorescent signal, which can be read continuously and is able to discriminate between wild-type and the catalytically dead R316Q FTO. 2-OG is a co-substrate of FTO and, as a metabolite in the citric acid cycle, is a marker of intracellular nutritional status. The assay described in the present paper was used to measure, for the first time, the Km of FTO for 2-OG. The Km of 2.88 μM is up to 10-fold lower than the estimated intracellular concentrations of 2-OG, rendering it unlikely that FTO functions as a sensor for 2-OG levels.
Ubiquitin–proteasome system inhibitors and AMPK regulation in hepatic cold ischaemia and reperfusion injury: possible mechanisms
Authors: Padrissa-Altés Susagna , Zaouali Mohamed Amine , Bartrons Ramon , Roselló-Catafau Joan
Published: March 2012

In the present Hypothesis article, we summarize and present data from the literature that support our hypothesis on the potential mechanisms by which UPS (ubiquitin–proteasome system) inhibitors reduce I/R (ischaemia/reperfusion) injury in the liver. I/R is the main cause of primary liver failure and, consequently, minimizing the detrimental effects of this process could increase the number of suitable transplantation grafts and also enhance the survival rate of patients after liver transplantation. A potential strategy to reduce I/R injury is the use of UPS inhibitors either as additives to preservation solutions or as drugs administered to patients. However, there is still controversy over whether the use of UPS inhibitors is beneficial or deleterious with regard to liver injury. From our experience and the few studies that have investigated the role of UPS in hepatic I/R, we believe that the use of UPS inhibitors is a potential strategy to reduce I/R injury in liver transplantation and graft preservation. We hypothesize that one of the main mechanisms of action of UPS inhibitors may be the up-regulation of AMPK (AMP-activated protein kinase) activity and the consequent down-regulation of mTOR (mammalian target of rapamycin), which may finally influence autophagy and preserve the energy state of the cell.
2-Methoxy-5-amino-N-hydroxybenzamide, a derivative of mesalamine, inhibits colon cancer cell growth through cyclo-oxygenase-2-dependent and -independent mechanisms
Authors: Stolfi Carmine , Franzè Eleonora , Monteleone Ivan , Caruso Roberta , Franceschilli Luana , Sileri Pierpaolo , Sica Giuseppe S. , Gaspari Achille L. , Del Vecchio Blanco Giovanna , Pallone Francesco , Monteleone Giovanni
Published: March 2012

COX-2 (cyclo-oxygenase-2) and PGE2 (prostaglandin E2) play a key role in sustaining CRC (colorectal cancer) cell growth and survival. Indeed, the use of agents targeting the COX-2/PGE2 axis has been associated with a reduction in the development of CRC in both humans and murine models of colon carcinogenesis. In the present study, we investigated whether 2-methoxy-5-amino-N-hydroxybenzamide (herein termed 2-14), a derivative of mesalamine that inhibits CRC cell growth both in vitro and in vivo, negatively regulates COX-2/PGE2 expression in CRC cells and assessed whether the 2-14-mediated anti-neoplastic effect is strictly dependent on the inhibition of this pathway. Our results show that 2-14 blocks the growth and enhances the death of HT-115, a CRC cell line overexpressing COX-2, and that these effects associate with inhibition of COX-2 but not COX-1. 2-14 also down-regulates TNFα (tumour necrosis factor α)-induced COX-2 in HT-29 cells as well as COX-2/PGE2 expression in ex vivo cultures of human CRC explants. Similarly, 2-14 reduces COX-2, but not COX-1, in tumoural areas developing in a mouse model of CAC (colitis-associated colon cancer). Finally, we show that 2-14 exhibits in vitro and in vivo anti-mitogenic effects in DLD-1, a COX-deficient CRC cell line. Taken together, these results suggest that 2-14 inhibits CRC cell growth through COX-2-dependent and -independent mechanisms.
The geometric factor of electrostatic plasma analyzers: A case study from the Fast Plasma Investigation for the Magnetospheric Multiscale mission
Authors: Collinson Glyn A. , Dorelli John C. , Avanov Levon A. , Lewis Gethyn R. , Moore Thomas E. , Pollock Craig , Kataria Dhiren O. , Bedington Robert , Arridge Chris S. , Chornay Dennis J. , Gliese Ulrik , Mariano Al , Barrie Alexander C. , Tucker Corey , Owen Christopher J. , Walsh Andrew P. , Shappirio Mark D. , Adrian Mark L.
Published: March 2012

We report our findings comparing the geometric factor (\documentclass[12pt]{minimal}\begin{document}$\mathbb {GF}$\end{document}GF) as determined from simulations and laboratory measurements of the new Dual Electron Spectrometer (DES) being developed at NASA Goddard Space Flight Center as part of the Fast Plasma Investigation on NASA’s Magnetospheric Multiscale mission. Particle simulations are increasingly playing an essential role in the design and calibration of electrostatic analyzers, facilitating the identification and mitigation of the many sources of systematic error present in laboratory calibration. While equations for laboratory measurement of the \documentclass[12pt]{minimal}\begin{document}$\mathbb {GF}$\end{document}GF have been described in the literature, these are not directly applicable to simulation since the two are carried out under substantially different assumptions and conditions, making direct comparison very challenging. Starting from first principles, we derive generalized expressions for the determination of the \documentclass[12pt]{minimal}\begin{document}$\mathbb {GF}$\end{document}GF in simulation and laboratory, and discuss how we have estimated errors in both cases. Finally, we apply these equations to the new DES instrument and show that the results agree within errors. Thus we show that the techniques presented here will produce consistent results between laboratory and simulation, and present the first description of the performance of the new DES instrument in the literature.
Spin flip probability of electron in a uniform magnetic field
Authors: Hammond Richard T.
Published: March 2012

The probability that an electromagnetic wave can flip the spin of an electron is calculated. It is assumed that the electron resides in a uniform magnetic field and interacts with an incoming electromagnetic pulse. The scattering matrix is constructed and the time needed to flip the spin is calculated.
Higher symmetries of the conformal powers of the Laplacian on conformally flat manifolds
Authors: Gover A. Rod , Šilhan Josef
Published: March 2012

On locally conformally flat manifolds, we describe a construction which maps generalised conformal Killing tensors to differential operators which may act on any conformally weighted tensor bundle; the operators in the range have the property that they are symmetries of any natural conformally invariant differential operator between such bundles. These are used to construct all symmetries of the conformally invariant powers of the Laplacian (often called the GJMS operators) on manifolds of dimension at least 3. In particular, this yields all symmetries of the powers of the Laplacian Δk, \documentclass[12pt]{minimal}\begin{document}$k\in \mathbb {Z}>0$\end{document}k∈Z>0, on Euclidean space \documentclass[12pt]{minimal}\begin{document}$\mathbb {E}^n$\end{document}En. The algebra formed by the symmetry operators is described explicitly.
Observable quasi-bound states of the H2 molecule
Authors: Selg Matti
Published: March 2012

Characteristic parameters (energetic positions, widths, etc.) of the 23 spectroscopically observed (or potentially observable) quasi-bound energy levels for the ground state H2 molecule are determined with high accuracy. The recent advances concerning nonadiabatic, relativistic, and quantum electrodynamical corrections have been taken into consideration. Theoretical approach is based on the careful investigation of the energy dependences of the real stationary scattering-state wave functions (their phase shifts and amplitudes). These energy dependences can be very accurately fitted to simple analytic formulas resulting from the quantum scattering theory. General criteria for the assignment of quasi-bound states are discussed and a new criterion is proposed, which excludes too broad and ambiguous resonances. To implement the proposed approach, a special high-precision computational method was used, which is described in full detail.
Injector for scattering measurements on fully solvated biospecies
Authors: Weierstall U. , Spence J. C. H. , Doak R. B.
Published: March 2012

We describe a liquid jet injector system developed to deliver fully solvated microscopic target species into a probe beam under either vacuum or ambient conditions. The injector was designed specifically for x-ray scattering studies of biological nanospecies using x-ray free electron lasers and third generation synchrotrons, but is of interest to any application in which microscopic samples must be delivered in a fully solvated state and with microscopic precision. By utilizing a gas dynamic virtual nozzle (GDVN) to generate a sample-containing liquid jet of diameter ranging from 300 nm to 20 μm, the injector avoids the clogging problems associated in this size range with conventional Rayleigh jets. A differential pumping system incorporated into the injector shields the experimental chamber from the gas load of the GDVN, making the injector compatible with high vacuum systems. The injector houses a fiber-optically coupled pump laser to illuminate the jet for pump-probe experiments and a hermetically sealed microscope to observe the liquid jet for diagnostics and alignment during operation. This injector system has now been used during several experimental runs at the Linac Coherent Light Source. Recent refinements in GDVN design are also presented.
A spherical crystal imager for OMEGA EP
Authors: Stoeckl C. , Fiksel G. , Guy D. , Mileham C. , Nilson P. M. , Sangster T. C. , Shoup M. J. , Theobald W.
Published: March 2012

A narrowband x ray imager for the Cu Kα line at ∼8 keV using a spherically bent quartz crystal has been implemented on the OMEGA EP laser at the University of Rochester. The quartz crystal is cut along the 2131 (211) planes for a 2d spacing of 0.3082 nm, resulting in a Bragg angle of 88.7°, very close to normal incidence. An optical system is used to remotely align the spherical crystal without breaking the vacuum of the target chamber. The images show a high signal-to-background ratio of typically >100:1 with laser energies ≥1 kJ at a 10-ps pulse duration and a spatial resolution of less than 10 μm.
Photoelectron spectra and structures of three cyclic dipeptides: PhePhe, TyrPro, and HisGly
Authors: Wickrama Arachchilage Anoja P. , Wang Feng , Feyer Vitaliy , Plekan Oksana , Prince Kevin C.
Published: March 2012

We have investigated the electronic structure of three cyclic dipeptides: cyclo(Histidyl-Glycyl) (cHisGly), cyclo(Tyrosyl-Prolyl) (cTyrPro), and cyclo(Phenylalanyl-Phenylalanyl) (cPhePhe) in the vapor phase, by means of photoemission spectroscopy and theoretical modeling. The last compound was evaporated from the solid linear dipeptide, but cyclised, losing water to form cPhePhe in the gas phase. The results are compared with our previous studies of three other cyclopeptides. Experimental valence and core level spectra have been interpreted in the light of calculations to identify the basic chemical properties associated with the central diketopiperazine ring, and with the additional functional groups. The valence spectra are generally characterized by a restricted set of outer valence orbitals separated by a gap from most other valence orbitals. The theoretically simulated core and valence spectra of all three cyclic dipeptides agree reasonably well with the experimental spectra. The central ring and the side chains act as independent chromophores whose spectra do not influence one another, except for prolyl dipeptides, where the pyrrole ring is fused with the central ring. In this case, significant changes in the valence and core level spectra were observed, and explained by stronger hybridization of the valence orbitals.
Heat capacity and thermal expansion of gadolinium tetraboride at low temperatures
Authors: Novikov V. V. , Mitroshenkov N. V. , Morozov A. V. , Matovnikov A. V. , Avdashchenko D. V.
Published: March 2012

Temperature dependences of heat capacity and lattice parameters of gadolinium tetraboride (GdB4) at the temperatures of 2–300 K have been studied experimentally. In the course of the experiment, the anomalies of these properties caused by the processes of transition into the antiferromagnetic state at TN = 41.87 K were revealed. Temperature changes of electronic and lattice, the magnetic contribution to GdB4 heat capacity, as well as the Schottky contribution were singled out and analyzed. Residual entropy of the Gd3+ magnetic subsystem caused by frustration was found to be Rln3.2. Temperature variations of linear and volumetric thermal expansion coefficients were calculated. It was established that processes of magnetic ordering in GdB4 give rise to a negative spontaneous magnetostriction and are not accompanied by the distortion of the crystalline lattice.
Fabrication of submicron devices on the (011) cleave surface of a cleaved-edge-overgrowth GaAs/AlGaAs crystal
Authors: Chang A. M. , Zhang Hao , Pfeiffer L. N. , West K. W.
Published: March 2012

We describe the fabrication of submicron devices on the (011) cleave surface of a GaAs heterostructure crystal, in which this surface is extremely narrow. Special purpose devices are produced, which take advantage of the unique characteristics of cleaved-edge-overgrowth. The successful fabrication relies on understanding the surface tension of the electron beam polymethyl methacrylate resist, the workable degree of variation in resist thickness, and on gluing the crystal onto a backing substrate to increase structural strength. We demonstrate functional gate-controlled quantum point contact constrictions placed 9 μm from one edge of the cleave surface.
Hydration strongly affects the molecular and electronic structure of membrane phospholipids
Authors: Mashaghi Alireza , Partovi-Azar P. , Jadidi Tayebeh , Nafari Nasser , Maass Philipp , Tabar M. Reza Rahimi , Bonn Mischa , Bakker Huib J.
Published: March 2012

We investigate the structure and electronic properties of phosphatidylcholine (PC) under different degrees of hydration at the single-molecule and monolayer type level by linear scaling ab initio calculations. Upon hydration, the phospholipid undergoes drastic long-range conformational rearrangements which lead to a sickle-like ground-state shape. The structural unit of the tilted gel-phase PC appears to be a water-bridged PC dimer. We find that hydration dramatically alters the surface potential, dipole and quadrupole moments of the lipids and consequently guides the interactions of the lipids with other molecules and the communication between cells.
A wireless handheld probe with spectrally constrained evolution strategies for diffuse optical imaging of tissue
Authors: Flexman M. L. , Kim H. K. , Stoll R. , Khalil M. A. , Fong C. J. , Hielscher A. H.
Published: March 2012

We present a low-cost, portable, wireless diffuse optical imaging device. The handheld device is fast, portable, and can be applied to a wide range of both static and dynamic imaging applications including breast cancer, functional brain imaging, and peripheral artery disease. The continuous-wave probe has four near-infrared wavelengths and uses digital detection techniques to perform measurements at 2.3 Hz. Using a multispectral evolution algorithm for chromophore reconstruction, we can measure absolute oxygenated and deoxygenated hemoglobin concentration as well as scattering in tissue. Performance of the device is demonstrated using a series of liquid phantoms comprised of Intralipid®, ink, and dye.
Improvements of the thermoelectric properties of PbTe via simultaneous doping with indium and iodine
Authors: Guch Mykhailo , Raj Sankar Cheriyedath , Salvador James R. , Meisner Gregory P. , Kleinke Holger
Published: March 2012

The thermoelectric properties of n-type InxPb1−xTe1−yIy (with x = 0.005, 0.01, 0.015; y = 0.001, 0.002, 0.004, 0.006) were investigated at elevated temperatures up to 655 K. This co-doping significantly affected the Seebeck coefficient and electrical conductivity of all samples within the measured temperature regime except for the sample with the largest concentration of In, wherein the effects of I-doping are comparatively minor. For a given concentration of In, the sample with the largest amount of iodine possesses the highest electrical conductivity, which is consistent within all three sets of samples in our present study. Thermal conductivity values are generally lower than those of undoped PbTe. An increasing iodine concentration at fixed In content was found to gradually increase the dimensionless figure-of-merit, ZT, an effect most significantly observed when x = 0.01.
Energy transfer and energy level decay processes in Tm3+-doped tellurite glass
Authors: Gomes Laércio , Lousteau Joris , Milanese Daniel , Scarpignato Gerardo C. , Jackson Stuart D.
Published: March 2012

The primary excited state decay and energy transfer processes in singly Tm3+-doped TeO2:ZnO:Bi2O3:GeO2 (TZBG) glass relating to the 3F4 → 3H6 ∼1.85 μm laser transition have been investigated in detail using time-resolved fluorescence spectroscopy. Selective laser excitation of the 3H4 manifold at 794 nm, the 3H5 manifold at 1220 nm, and 3F4 manifold at 1760 nm has established that the 3H5 manifold is entirely quenched by multiphonon relaxation in tellurite glass. The luminescence from the 3H4 manifold with an emission peak at 1465 nm suffers strong suppression due to cross relaxation that populates the 3F4 level with a near quadratic dependence on the Tm3+ concentration. The 3F4 lifetime becomes longer as the Tm3+ concentration increases due to energy migration and decreases to 2.92 ms when [Tm3+] = 4 mol. % as a result of quasi-resonant energy transfer to free OH− radicals present in the glass at concentrations between 1 × 1018 cm−3 and 2 × 1018 cm−3. Judd-Ofelt theory in conjunction with absorption measurements were used to obtain the radiative lifetimes and branching ratios of the energy levels located below 25 000 cm−1. The spectroscopic parameters, the cross relaxation and Tm3+(3F4) → OH− energy transfer rates were used in a numerical model for laser transitions emitting at 2335 nm and 1865 nm.
Tunable silica shell and its modification on photoluminescent properties of Y2O3:Eu3+@SiO2 nanocomposites
Authors: Liu Tong , Xu Wen , Bai Xue , Song Hongwei
Published: March 2012

The core-shell rare earth (RE) doped nanophosphors are attracting current interests owing to their potential application in bio-images. Understanding the modification of core-shell structure on photoluminescent (PL) properties of RE ions is important in obtaining efficient nanophosphors. In this paper, Y2O3:Eu3+@SiO2 composites with fixed cubic Y2O3:Eu3+ core (∼80 nm) and controllable thickness of silica shell (∼3−21 nm) were synthesized via a modified Stöber method and characterized by x-ray diffraction patterns, transmission electronic microscope images, and Fourier-transform infrared absorption spectra. The dependences of PL properties of Y2O3:Eu3+ on the thickness of the silica shell and excitation power density were systemically studied under charge transfer excitation (254 nm) and 7FJ-5D2 inner-shell excitation (460-486 nm). It is interesting to observe that under 7FJ-5D2 excitation the intensity ratio of 5D0-7F2/5D0-7FJ (J ≠ 2) for Eu3+ increases considerably with the increase of shell thickness and decreases with the increasing excitation power density, which confirms the variation of long-scale radiative energy transfer (RET) among Eu3+ ions and redistribution of 5D0-7FJ(J = 0−4) transitions. And more, the radiative decay time of 5D0-7FJ as a function of shell thickness demonstrates an optimum, which are assigned to the co-impacts of effective refractive index (neff) and RET among Eu3+ ions.