bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence and impact of occult hepatitis B infection in chronic hepatitis C patients treated with pegylated interferon and ribavirin
Authors: Levast Marion , Larrat Sylvie , Thelu Marie‐Ange , Nicod Sandrine , Plages Agnès , Cheveau Alice , Zarski Jean‐Pierre , Seigneurin Jean‐Marie , Morand Patrice , Leroy Vincent
Published: March 2010

The prevalence of occult hepatitis B, defined by absence of HBsAg and HBV DNA, ranges widely in patients with hepatitis C. This may influence the treatment of hepatitis C and the severity of liver disease. Sensitive and specific real‐time PCR techniques are available commercially and can detect more reliably low HBV DNA levels. The aim of this study was to determine the prevalence of occult hepatitis B virus infection using the COBAS Taqman assay (Roche Diagnostics, Meylan, France) in the serum and liver of HBsAg negative patients with chronic hepatitis C and to evaluate its clinical consequences on liver pathology and its impact on the response to treatment with peg‐IFNα and Ribavirin. HBV DNA detection was assessed retrospectively on 140 sera and 113 liver biopsies of HCV positive/HBsAg negative patients before treatment. A 4.4% (5/113) prevalence of occult hepatitis B was recorded in liver samples and in none of the sera. Anti‐HBc was not detected in one, three of whom were sustained virological responders to treatment, one was relapsed responder and one was non‐responder. Furthermore, in this cohort composed of 12% anti‐HBs negative/anti‐HBc positive and 20% anti‐HBs positive/anti‐HBc positive patients, anti‐HBc was not associated with pre‐therapeutic viral load, ALT serum levels, and histological activity or fibrosis. Using a commercial real‐time PCR assay, we observed a low prevalence of occult B hepatitis. This, just as anti‐HBC status, had no clinical impact in a large cohort of hepatitis C patients. It therefore does not appear useful to screen for occult hepatitis B in these patients with this test before beginning HCV treatment. J. Med. Virol. 82: 000–000, 2010. © 2010 Wiley‐Liss, Inc. J. Med. Virol. 82: 747–754, 2010. © 2010 Wiley‐Liss, Inc.
Prevalence of Epstein–Barr virus associated with nasal lymphoma in patients attending the regional hospital of Valdivia, Chile, between 1987 and 2005
Authors: Martin Carolina , Carrasco Cristian , Sotomayor Cristina , Otth Carola
Published: March 2010

Epstein–Barr virus (EBV) is a ubiquitous herpes virus with a widespread infection in the world's adult population. EBV has been associated with human malignancies, mainly the nasal type NK/T cell lymphoma. The disease is more frequent in Asian than in Western countries. However, there are few studies from Latin American countries. The aim of this study was to determine the prevalence of EBV in patients with nasal lymphomas diagnosed in the Regional Hospital of Valdivia, southern Chile, during 1987–2005. Immunohistochemistry was done on paraffin sections using anti‐CD3ε, anti‐CD20, and anti‐CD56. The presence of small ribonucleic acids (RNAs) of EBV was detected in paraffin sections by in situ hybridization using oligonucleotides targeting EBV‐encoded small RNAs. The present study revealed a prevalence of 27.7% of Hodgkin's lymphomas and 72.3% of non‐Hodgkin's lymphomas. From the latter group, there was a prevalence of 2.9% (10 cases) of nasal lymphoma. From these 10 cases, 6 (60%) were NK/T cell lymphomas, nasal type; 1 case (10%) was a T‐cell phenotype; and 3 cases (30%) were B‐cell phenotype. The prevalence was higher than reports from Western countries, but lower than the reports from Asian countries. These results agreed with previous reports suggesting that EBV is strongly associated with T lymphomas. This study contributes new epidemiological data on EBV in Chile. J. Med. Virol. 82: 825–828, 2010. © 2010 Wiley‐Liss, Inc.
Neither molecular diversity of the envelope, immunosuppression status, nor proviral load causes indeterminate HTLV western blot profiles in samples from human T‐cell lymphotropic virus type 2 (HTLV‐2)‐infected individuals
Authors: Olah Ingrid , Fukumori Ligia M.I. , Smid Jerusa , de Oliveira Augusto César Penalva , Duarte Alberto J.S. , Casseb Jorge
Published: March 2010

Although human T‐cell lymphotropic virus type 2 (HTLV‐2) is considered of low pathogenicity, serological diagnosis is important for counseling and monitoring. The confirmatory tests most used are Western blot (WB) and PCR. However, in high‐risk populations, about 50% of the indeterminate WB were HTLV‐2 positives by PCR. The insensitivity of the WB might be due to the use of recombinant proteins of strains that do not circulate in our country. Another possibility may be a high level of immunosuppression, which could lead to low production of virus, resulting in low stimulation of antibody. We found one mutation, proline to serine in the envelope region in the position 184, presented at least 1/3 of the samples, independent the indeterminate WB profile. In conclusion, we found no correlation of immune state, HTLV‐2 proviral load, or env diversity in the K55 region and WB indeterminate results. We believe that the only WB kit available in the market is probably more accurate to detect HTLV‐1 antibodies, and some improvement for HTLV‐2 detection should be done in the future, especially among high‐risk population. J. Med. Virol. 82: 837–842, 2010. © 2010 Wiley‐Liss, Inc.
Molecular detection and genetic variability of human metapneumovirus in Uruguay
Authors: Pizzorno A. , Masner M. , Médici C. , Sarachaga M.J. , Rubio I. , Mirazo S. , Frabasile S. , Arbiza J.
Published: March 2010

Human metapneumovirus (hMPV) has been described as circulating among the Uruguayan population at least since 1998 based on serologic evidence. However, no isolation attempts, molecular detection, or genetic studies have been carried out so far in the country. In the present study, molecular detection of circulating hMPV in children hospitalized with acute respiratory tract infection in Montevideo–Uruguay was carried out by reverse transcription‐polymerase chain reaction (RT‐PCR) amplification of the hMPV nucleoprotein (N) gene from 217 nasopharyngeal aspirates. Genetic variability analysis of the positive samples was performed by amplification and sequencing of both N and attachment glycoprotein (G) genes. Eighteen of the 217 samples tested positive for hMPV, with tachypnea, chest indrawing, and wheezing being the main clinical symptoms recorded. Phylogenetic analysis of N and G genes showed that Uruguayan samples clustered in genotypes described previously as A2, B1, and B2, with bootstrap values ≥98%. Sublineages A2a and A2b could also be distinguished within the samples that belong to A2. This is the first molecular report on the circulation of hMPV in Uruguay. The pattern of circulation of this virus, analyzed for both N and G genes independently, resembles the complex evolutionary pattern of respiratory syncytial virus (RSV). J. Med. Virol. 82:861–865, 2010. © 2010 Wiley‐Liss, Inc.
Induced tolerance to glutamate neurotoxicity through down‐regulation of NR2 subunits of N‐methyl‐D‐aspartate receptors in cultured rat striatal neurons
Authors: Kambe Yuki , Nakamichi Noritaka , Takarada Takeshi , Fukumori Ryo , Yoneda Yukio
Published: March 2010

We have previously shown differential vulnerabilities to glutamate (Glu) excitotoxicity mediated by the N‐methyl‐D‐aspartate (NMDA) receptor (NMDAR) between rat cortical and rat hippocampal neurons in culture. In this study, we evaluated the possible induced tolerance to NMDA neurotoxicity in cultured rat striatal neurons with prior sustained activation of NMDAR. Brief exposure to Glu or NMDA for 1 hr led to a significant decrease in cellular vitality determined 24 hr later in cultured rat striatal neurons, whereas no marked loss was seen in cellular survival after exposure to Glu or NMDA in striatal neurons previously cultured with Glu or NMDA. Sustained culture with Glu or NMDA invariably led to a significant decrease in protein levels of NR2, but not NR1, subunits without affecting their mRNA levels. Similar induced tolerance was seen to the excitotoxicity of NMDA in hippocampal neurons in a manner sensitive to an NMDAR antagonist. Prior culture with NMDA induced less effective alterations in both intracellular free Ca2+levels and mitochondrial membrane potentials after the addition of NMDA in striatal neurons. However, calpain inhibitor‐I significantly prevented the decreased NR2B and NR2C protein levels in striatal neurons cultured with NMDA. These results suggest that prior tonic activation of NMDAR would induce tolerance to the excitotoxicity mediated by NMDAR through a mechanism related to calpain‐induced down‐regulation of particular NR2 subunits in rat striatal neurons. © 2010 Wiley‐Liss, Inc.
Using QuikSCAT in the added value assessment of dynamically downscaled wind speed
Authors: Winterfeldt Jörg , Geyer Beate , Weisse Ralf
Published: March 2010

Hindcasts with reanalysis‐driven regional climate models (RCMs) are a common tool to assess weather statistics (i.e. climate) and recent changes and trends. A remote sensing‐based method to investigate the added value of surface marine RCM wind speed is introduced. The capability of the dynamical downscaling approach (with spectral nudging applied) to add value to the reanalysis wind speed forcing is assessed by the comparison with QuikSCAT Level 2B 12.5 km (L2B12) swath data in European waters for 2000–2007. Co‐location criteria are within 0.1° and 0.06° in longitudinal and latitudinal distance from RCM grid points and within 10 min. In the wind speed range, QuikSCAT L2B12 is reliably reproducing (3–20 m s−1), dynamically downscaled wind speed does not show an added value in ‘open ocean’ areas. However, in coastal areas with complex topography, the regional models show an added value, especially around Iceland and the Iberian Peninsula and in the Mediterranean, Baltic and Irish Seas, validating the findings of previous in situ data‐based studies on the added value. Strong interseasonal differences exist, in winter enhanced cyclonic and meso‐cyclonic activity increases the potential of dynamical downscaling. In winter time, the added value is more pronounced around Iceland and Greenland, south of Iceland and within the Gulf of Lyon/Mistral region. Summarizing the presented method can be easily applied for other ocean areas, making QuikSCAT a valuable tool to identify marine regions where dynamical downscaling adds value to surface marine wind speed. A detailed comparison of 10 m winds from the National Centres of Environmental Prediction (NCEP)/National Centre for Atmospheric Research (NCAR) and the newer NCEP/DOE‐II reanalyses is presented in the annex, motivating the use of the NCEP/NCAR reanalysis in the added value assessment. Copyright © 2010 Royal Meteorological Society
Comparison of satellite‐derived TOA shortwave clear‐sky fluxes to estimates from GCM simulations constrained by satellite observations of land surface characteristics
Authors: Anantharaj Valentine G. , Nair Udaysankar S. , Lawrence Peter , Chase Thomas N. , Christopher Sundar , Jones Thomas
Published: March 2010

Clear‐sky, upwelling shortwave flux at the top of the atmosphere $\left(S_{\rm {TOA}}^{\uparrow}\right)$, simulated using the atmospheric and land model components of the Community Climate System Model 3 (CCSM3), is compared to corresponding observational estimates from the Clouds and Earth's Radiant Energy System (CERES) sensor. Improvements resulting from the use of land surface albedo derived from Moderate Resolution Imaging Spectroradiometer (MODIS) to constrain the simulations are also examined. Compared to CERES observations, CCSM3 overestimates global, annual averaged $S_{\rm {TOA}}^{\uparrow}$ over both land and oceans. However, regionally, CCSM3 overestimates $S_{\rm {TOA}}^{\uparrow}$ over some land and ocean areas while underestimating it over other sites. CCSM3 underestimates $S_{\rm {TOA}}^{\uparrow}$ over the Saharan and Arabian Deserts and substantial differences exist between CERES observations and CCSM3 over agricultural areas. Over selected sites, after using ground‐based observations to remove systematic biases that exist in CCSM computation of $S_{\rm {TOA}}^{\uparrow}$, it is found that use of MODIS albedo improves the simulation of $S_{\rm {TOA}}^{\uparrow}$. Inability of coarse resolution CCSM3 simulation to resolve spatial heterogeneity of snowfall over high altitude sites such as the Tibetan Plateau causes overestimation of $S_{\rm {TOA}}^{\uparrow}$ in these areas. Discrepancies also exist in the simulation of $S_{\rm {TOA}}^{\uparrow}$ over ocean areas as CCSM3 does not account for the effect of wind speed on ocean surface albedo. This study shows that the radiative energy budget at the TOA is improved through the use of MODIS albedo in Global Climate Models. Copyright © 2010 Royal Meteorological Society
Climatology of tropospheric ozone and water vapour over Chennai: a study based on MOZAIC measurements over India
Authors: Sahu L. K. , Lal S. , Thouret Valérie , Smit Herman G.
Published: March 2010

Climatology of tropospheric ozone (O3) and water vapour (H2O) over a metro city of Chennai in southern India has been presented based on the Measurements of OZone and water vapour by Airbus In‐service AirCraft (MOZAIC) data during 1996–2001. The seasonal trends in mixing ratio of O3 are discussed in view of annual changes in the transport pattern, rainfall, and its relationship with ambient H2O. The vertical distributions of both O3 and H2O show large seasonal variations. The observed high mixing ratios of O3 in winter and spring months can be attributed to long‐range transport of pollutants by the northwesterly winds associated with winter monsoon circulation. The lowest mixing ratio of 15 ppbv of O3 from July to September coincides with the summer monsoon circulation over Indian subcontinent. The surface level mixing ratio of O3 was observed to be below 30 ppbv throughout the year. On the other hand, monthly rainfall and vertical distributions of H2O show just opposite seasonal variations to that of O3 mixing ratio. Chennai is a coastal city; therefore, the seasonal change in surface wind flow causes large variability in H2O concentrations of 6–30 g/kg in the lower troposphere. More or less similar annual patterns of mixing ratios of O3 and H2O are repeated during different years of 1996–1998, except for some small‐scale differences. High level of O3 mixing ratio, particularly during the early winter months of year 1997, seems unusual as we do not see such trends for other year of measurements over Chennai. The case studies of profiles of O3, relative humidity (RH), and temperature in view of long‐range transport over Chennai during the different seasons have been also discussed. Significant enhancements in tropospheric O3 were observed over Chennai due to transport of air from forest fire regions of Indonesia during October 1997. Copyright © 2010 Royal Meteorological Society
Interannual variations of early summer monsoon rainfall over South China under different PDO backgrounds
Authors: Mao Jiangyu , Chan Johnny C. L. , Wu Guoxiong
Published: March 2010

The interannual variations of the early summer South China monsoon rainfall (SCMR) in relation to different Pacific Decadal Oscillation (PDO) backgrounds are examined using station rainfall data and the European Centre for Medium‐range Weather Forecasts (ECMWF) 40‐year reanalysis (ERA‐40) data. The objective of this study is to investigate the atmospheric circulation patterns responsible for such variations, thereby understanding the interdecadal modulation and the cause for the extreme wet and dry SCMR.

The interannual SCMR variance shows an interdecadal change before and after the late 1970s, with significant differences in sea‐surface temperature (SST) and atmospheric circulation anomalies between the negative (1958–1976) and positive (1980–1998) PDO epochs. The dominant atmospheric teleconnection patterns associated with extreme wet and dry SCMR are remarkably different in these two epochs. During 1958–1976, an anomalous wet (dry) SCMR is characterized by a significantly anomalous anticyclone (cyclone) over the South China Sea (SCS) and western Pacific in the lower troposphere in the form of a meridional wave‐like coupling along the coast of western North Pacific in the early summer, and preceded by a monopole circulation anomaly over the Ural Mountain in the preceding winter. During 1980–1998, however, an anomalous wet (dry) SCMR features a relatively weak anomalous anticyclone (cyclone) over the SCS in the low level without a significantly meridional juxtaposition of anomalous circulations in the early summer, and it follows a remarkable coherent long wave train pattern in middle‐high latitudes in the preceding winter. Such interdecadal differences in anomalous circulation structures suggest that the relative roles of internal atmospheric variability and external forcing may be different from different epochs. But for both epochs, the circulation anomaly over the Ural Mountain shows a highly negative correlation with anomalous SCMR, suggesting that the winter circulation anomaly around the Ural Mountain is of great significance for improving the seasonal prediction of SCMR. Copyright © 2010 Royal Meteorological Society
Thermal decomposition of cyclic organic peroxides in pure solvents and binary solvent mixtures
Authors: Iglesias Mariángeles , Barreto Gastón P. , Eyler Gladys N. , Cañizo Adriana I.
Published: March 2010

The thermal decomposition reaction of acetone cyclic triperoxide, acetone cyclic diperoxide, 4‐heptanone cyclic diperoxide, and pinacolone cyclic diperoxide ca. 0.02 M was studied in pure solvents (acetone and 1‐propanol) and in binary mixtures of acetone/1‐propanol at 150°C. The kinetics of each system was explored by gas chromatography (GC) at different solvent compositions. The reactions showed a behavior accordingly with a pseudo‐first‐order kinetic law up to at least 90% peroxide decomposition. The main organic products derived from these thermolysis reactions were detected by GC analysis. Among them, the corresponding ketones, methane, ethane, and propane were the main identified products. The rates of decomposition of pinacolone diperoxide in the pure solvents were practically independent of the solvent characteristics, so it was of no interest to analyze its kinetic behavior in binary solvent mixtures. In acetone/1‐propanol mixtures, the solvation effect on the cyclic peroxides derived from 4‐heptanone and acetone molecules was slightly dominated by specific interactions between 1‐propanol and a diradical‐activated complex initially formed. This species was preferentially solvated by 1‐propanol instead of acetone. Specific interactions between the O atoms from the peroxidic bond and the H from the OH in 1‐propanol can be taken into account. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 347–353, 2010
Mechanisms by which the antitumor compound di‐n‐butyl‐di‐(4‐chlorobenzohydroxamato)tin(IV) induces apoptosis and the mitochondrial‐mediated signaling pathway in human cancer SGC‐7901 cells
Authors: Li Yunlan , Liu Jinjie , Li Qingshan
Published: March 2010

The mechanisms by which the strong antitumor diorganotin(IV) compound di‐n‐butyl‐di‐(4‐chlorobenzohydroxamato)tin(IV) (DBDCT) induces apoptosis of SGC‐7901 cells were first investigated. Inhibition of proliferation of four cancer cell lines compared with normal human hepatic L‐O2 cells, cancer cell apoptosis, and expression of related mRNA and protein were detected using the methyl thiazolyl tetrazolium (MTT), flow cytometry, reverse transcription polymerase chain reaction (RT‐PCR), Western blot, and DNA ladder assays, and electron microscopy and immunocytochemistry. DBDCT decreased cancer cell proliferation rates in a dose‐ and time‐dependent manner and changed the cycle distribution of SGC‐7901 cells; the proportion of cells in G0–G1 phase was increased, whereas the numbers in S and G2–M phases were decreased. Blockade of the cell cycle was perhaps associated with increased levels of p21, p27, p53 and the decreased level of proliferating cell nuclear antigen (PCNA). Apoptosis was characterized by DNA fragmentation, chromosomal condensation, apoptotic bodies, sub‐G1 peaks, and an increased apoptotic rate, as shown using the annexin V‐FITC method. Pretreatment of cells with N‐acetylcysteine and caspase‐9 inhibitor could reduce growth inhibition and DBDCT‐induced apoptosis. The results showed that DBDCT‐mediated cell‐cycle arrest might occur through the induction of p21 in a p53‐dependent manner and that DBDCT induction of the mitochondrial apoptotic signaling pathway is perhaps mediated by increasing Bax/Bcl‐2 ratios, which result in the loss of ΔΨm, release of cytochrome c into the cytoplasm, activation of caspase‐3 and ‐9, and increased reactive oxygen species (ROS) generation. Mol. Carcinog. © 2010 Wiley‐Liss, Inc.
Properties of a mean residual life function arising from renewal theory
Authors: Unnikrishnan Nair N. , Sankaran P.G.
Published: March 2010

The present article discusses the properties of the mean residual life function in a renewal process. We examine the relationship this function has with the failure rate function and the conventional mean, variance and coefficient of variation of residual life. We also discuss some monotonicity properties of the mean residual life function. A partial order based on the renewal mean residual function is introduced along with its interrelationship with some existing stochastic orders. © 2010 Wiley Periodicals, Inc. Naval Research Logistics, 2010
Isotopic evidence for Middle Horizon to 16th century camelid herding in the Osmore Valley, Peru
Authors: Thornton E. K. , Defrance S. D. , Krigbaum J. , Williams P. R.
Published: March 2010

Archaeological and zooarchaeological data indicate that camelid pastoralism was a subsistence and economic mainstay of Middle Horizon and more recent cultures in the Osmore region of southern Peru. However, it is not known whether camelids were primarily herded in highland puna pastures or near lower elevation sites in the middle valley or along the coast. This research examines the elevation of archaeological camelid herding in the Osmore Valley using stable isotope analysis. Stable carbon (δ13C) and nitrogen (δ15N) isotope ratios were measured on 28 archaeological camelid bone samples from the Middle Horizon sites of Cerro Baúl and Cerro Mejía, the Late Intermediate site of Yaral and the late pre‐Hispanic to Colonial period site of Torata Alta. Twenty‐three archaeological camelids have δ13C and δ15N values similar to five modern camelids maintained in highland puna pastures. In contrast, three camelids from the high status Wari site of Cerro Baúl, and two from Yaral have unexpectedly high δ13C and/or δ15N values outside the expected range for camelids pastured in highland puna habitats. The results may be explained by differences in foddering practices, altitudinal herding range or climatic conditions. Strontium isotope ratios (87Sr/86Sr) were also assessed to infer pasture elevation using the camelid remains from Cerro Baúl (n = 11). One individual in this sub‐sample exhibits a non‐local 87Sr/86Sr value indicative of an origin in the highland puna region east or south of Lake Titicaca. It was not possible to further distinguish between camelids herded in lower to middle elevation habitats outside the Lake Titicaca basin using 87Sr/86Sr values. This study suggests that multiple isotope proxies may be used to identify animals primarily pastured in lowland coastal versus highland puna (> 4000 masl (meters above sea level)) habitats, but are less useful at distinguishing between animals pastured in lower to middle elevation settings. Copyright © 2010 John Wiley & Sons, Ltd.
Immunoproteomic analyses of outer membrane proteins ofMannheimia haemolyticaand identification of potential vaccine candidates
Authors: Ayalew Sahlu , Confer Anthony W. , Hartson Steven D. , Shrestha Binu
Published: March 2010

Immunoproteomic analyses were used to characterize the outer membrane proteome ofMannheimia haemolytica, formerlyPasteurella haemolytica, serotype 1, and determine potential vaccine candidate proteins. 2‐DE ofM. haemolyticaouter membranes was followed by immunoblot analyses using naïve and convalescent bovine sera. Proteins were identified using MALDI‐TOF and LC‐MS/MS. Spectral data was used to mineM. haemolyticaprotein database and 132 immunoreactive proteins were identified. Bioinformatic analysis using PSORTb, SubLoc, LipoP, BOMP, MCMBB, and TMB‐Hunt/BBTM to predict subcellular localization of immunoreactive proteins and β‐barrels narrowed the list down to 55 candidates. Functional characterization of 55 proteins predicted 16 (29%) are involved in cell structure, 13 (23.6%) in transport/virulence, ten (18.2%) as unknown, six (10.9%) in general metabolism, four (7.27%) in cell process, two (3.64%) in translation, and one (1.8%) each in DNA replication, regulation, transcription, and virulence. Prediction of β‐barrel formation was between 11 and 31 immunoreactive proteins depending on the bioinformatic tool employed. Some of these proteins have potentials to be developed into stand‐alone vaccines or components of vaccines. Of those proteins, several have already been characterized. Finally, although characteristics of many ofM. haemolyticaimmunoreactive proteins identified in this study were obtained from published data and predictions using bioinformatics tools, five proteins previously listed in the publishedM. haemolyticasequence as unidentified were found to have correlates with functional proteins in other bacterial species.
Analysis of oligomeric protein complexes in the chloroplast sub‐proteome of nucleic acid‐binding proteins from mustard reveals potential redox regulators of plastid gene expression
Authors: Schröter Yvonne , Steiner Sebastian , Matthäi Kevin , Pfannschmidt Thomas
Published: March 2010

Photosynthetic light quality acclimation in plants involves redox‐controlled changes in plastid gene expression. To study proteins potentially involved in this regulation, we isolated low‐abundant chloroplast nucleic acid‐binding proteins from the crucifere mustard (Sinapis alba) and investigated if photosynthetic redox signals affect their composition and/or oligomeric structure. We purified chloroplasts from plants subjected to light quality shifts and applied organelle lysates to heparin‐Sepharose chromatography followed by 2‐D blue native PAGE. We studied accumulation and structure of oligomeric protein complexes and applied MS/MS to identify them. We found ten oligomeric protein complexes of higher order and eleven smaller protein complexes or spots including plastid‐encoded RNA polymerase (PEP), plastid transcriptionally active chromosome proteins, RNA‐binding proteins, ribosomal subunits and chaperones. A translation elongation factor was found to be the only protein displaying major differences in its amounts in response to the growth lights. Furthermore, we found a novel thioredoxin as a subunit of the PEP, a 2‐Cys‐peroxiredoxin complex and a (soluble) ferredoxin:NADP‐oxido‐reductase, which represent potential redox regulator of plastid gene expression. A T‐DNA knock‐out line of the thioredoxin from Arabidopsis exhibits a yellowish‐pale phenotype, demonstrating that this novel PEP subunit is essential for proper plastid development.
Equalizer technology – Equal rights for disparate beads
Authors: Keidel Eva‐Maria , Ribitsch Doris , Lottspeich Friedrich
Published: March 2010

One major limitation in proteomics is the detection and analysis of low‐abundant proteins, i.e. in plasma. Several years ago, a technique to selectively enrich the relative concentration of low‐abundant proteins was introduced by Boschetti and co‐workers. It is based on a specific and saturable interaction of proteins to a high diversity of binding sites, realized by a hexapeptide library coupled to beads. This technology was commercialized as Equalizer beads or ProteoMiner. However, during application of ProteoMiner beads to plasma samples unexpected results questioned the proposed mode of action. Therefore, ProteoMiner beads were compared with chromatographic beads exhibiting completely different surface chemistry. Sepabeads FP‐OD400 octadecyl, FP‐DA400 diethylamine, FP‐BU400 butyl, FP‐HG400 hydroxyl and EXE056 epoxy were used. The results show that ProteoMiner or the different Sepabeads behave surprisingly similarly in the separation of complex protein mixtures. ProteoMiner beads interact with protein mixtures according to a general hydrophobic binding mechanism, where diversity in surface ligands plays only a negligible role.
Integrating titania enrichment, iTRAQ labeling, and Orbitrap CID‐HCD for global identification and quantitative analysis of phosphopeptides
Authors: Wu Jiang , Warren Peter , Shakey Quazi , Sousa Eric , Hill Andrew , Ryan Terence E. , He Tao
Published: March 2010

Recent advances in MS instrumentation and progresses in phosphopeptide enrichment, in conjunction with more powerful data analysis tools, have facilitated unbiased characterization of thousands of site‐specific phosphorylation events. Combined with stable isotope labeling by amino acids in cell culture metabolic labeling, these techniques have made it possible to quantitatively evaluate phosphorylation changes in various physiological states in stable cell lines. However, quantitative phosphoproteomics in primary cells and tissues remains a major technical challenge due to the lack of adequate techniques for accurate quantification. Here, we describe an integrated strategy allowing for large scale quantitative profiling of phosphopeptides in complex biological mixtures. In this technique, the mixture of proteolytic peptides was subjected to phosphopeptide enrichment using a titania affinity column, and the purified phosphopeptides were subsequently labeled with iTRAQ reagents. After further fractionation by strong‐cation exchange, the peptides were analyzed by LC‐MS/MS on an Orbitrap mass spectrometer, which collects CID and high‐energy collisional dissociation (HCD) spectra sequentially for peptide identification and quantitation. We demonstrate that direct phosphopeptide enrichment of protein digests by titania affinity chromatography substantially improves the efficiency and reproducibility of phosphopeptide proteomic analysis and is compatible with downstream iTRAQ labeling. Conditions were optimized for HCD normalized collision energy to balance the overall peptide identification and quantitation using the relative abundances of iTRAQ reporter ions. Using this approach, we were able to identify 3557 distinct phosphopeptides from HeLa cell lysates, of which 2709 were also quantified from HCD scans.
SILAC analysis of oxidative stress‐mediated proteins in human pneumocytes: New role for treacle
Authors: Duan Xunbao , Kelsen Steve G. , Clarkson Allen B. , Ji Rong , Merali Salim
Published: March 2010

To better understand lung oxidant stress responses, we examined A549 lung cells exposed to H2O2 using “stable isotope labeling by amino acids.” We identified 466 cytosolic and 387 nuclear proteins; H2O2 exposure produced ≥twofold differences in 31, all were downregulations. None were previously reported as oxidant stress response proteins, although they share common functions. One of the responders, treacle, was linked to p53, an important oxidative stress response. The Treacher Collins–Franceschetti syndrome can result from treacle mutation and insufficiency was suggested to cause increased p53 leading to the syndrome. However, results here indicate p53 and treacle responses to H2O2 are independent: treacle remains suppressed after p53 recovery; the threshold for treacle reduction is well above that for p53 induction; and treacle suppression by short interfering RNA does not modify the p53 response. Evidence of treacle antioxidant activity include reduction being driven by proteasome degradation independently of mRNA, typical for oxidant‐absorbing proteins, and increased sensitivity to H2O2 consequent to short interfering RNA suppression. Data here show a link between oxidative stress and treacle reduction, demonstrate that treacle does not control p53, provide evidence of a treacle oxidant defense role, support the hypothesis that oxidant stress plays a role in the Treacher Collins–Franceschetti syndrome, and raise the possibility that treacle plays an anti‐oxidant role in lungs.
The ability of triplet nitrenes to abstract hydrogen atoms
Authors: Sankaranarayanan Jagadis , Rajam Sridhar , Hadad Christopher M. , Gudmundsdottir Anna D.
Published: March 2010

The enthalpies for H‐atom abstraction reactions by triplet imidogen as well as ethyl, alkoxycarbonyl, acyl, phenyl, and vinyl nitrenes were calculated using density functional theory calculations. These calculations show that H‐atom abstraction reactions are only feasible for triplet imidogen, alkoxycarbonyl, and acyl nitrenes in solution. The calculated charges on the N‐atoms (QNPA) in the nitrene correlate with the magnitude of the transition state barrier for the H‐atom abstraction reactions from methanol as a model reactant. Electron‐withdrawing substituents on these nitrenes make them less stable but do not affect the transition state barrier significantly. Thus, as the electron deficiency of the N‐atom in the nitrenes is increased, the H‐atom abstraction reaction becomes more feasible. Copyright © 2010 John Wiley & Sons, Ltd.
How a usual carbamate can become an unusual intermediate: a new chemical pathway to form glycinate in the interstellar medium
Authors: Bossa Jean‐Baptiste , Borget Fabien , Duvernay Fabrice , Theulé Patrice , Chiavassa Thierry
Published: March 2010

Experiments on the thermal reactivity of carbon dioxide (CO2) and methylamine (CH3NH2) are reported and show methylammonium methylcarbamate (CH3NHCOO− CH3NH) and methylcarbamic acid (CH3NHCOOH) are formed at low temperature in solid environment. The VUV (λ > 120 nm) irradiation of carbamate induces the formation of methylammonium glycinate (MAG). Calculations have been performed to give an insight on the pathway for the formation of the methylcarbamic acid (MCA). These calculations show that the methylamine environment play an important role in the barrier and a cooperative effect of the methylamine molecules has to be taken into account. The implication on the interstellar reactivity is also discussed because this pathway to form glycinate can occur in interstellar ices. Copyright © 2010 John Wiley & Sons, Ltd.
What research evidence is there for the use of art therapy in the management of symptoms in adults with cancer? A systematic review
Authors: Wood Michele J. M. , Molassiotis Alexander , Payne Sheila
Published: March 2010

Objective: Common psychosocial difficulties experienced by cancer patients are fatigue, depression, anxiety, and existential and relational concerns. Art therapy is one intervention being developed to address these difficulties. The purpose of this research was to assess and synthesize the available research evidence for the use of art therapy in the management of symptoms in adults with cancer.

Methods: A literature search of electronic databases, ‘grey’ literature, hand searching of key journals, and personal contacts was undertaken. Keywords searched were ‘art therapy’ and ‘cancer’ or ‘neoplasm’. The inclusion criteria were: research studies of any design; adult cancer population; and art therapy intervention. There were no language or date restrictions. Data extraction occurred and quality appraisal was undertaken. Data were analyzed using narrative synthesis.

Results: Fourteen papers reporting 12 studies met the inclusion criteria. Symptoms investigated spanned emotional, physical, social and global functioning, and existential/spiritual concerns. Measures used were questionnaires, in‐depth interviews, patients' artwork, therapists' narratives of sessions, and stress markers in salivary samples. No overall effect size was determined owing to heterogeneity of studies. Narrative synthesis of the studies shows art therapy is used at all stages of the cancer trajectory, most frequently by women, the most common cancer site in participants being breast.

Conclusion: Art therapy is a psychotherapeutic approach that is being used by adults with cancer to manage a spectrum of treatment‐related symptoms and facilitate the process of psychological readjustment to the loss, change, and uncertainty characteristic of cancer survivorship. Research in this area is still in its infancy. Copyright © 2010 John Wiley & Sons, Ltd.
Melanoma knowledge, perception, and awareness in ethnic minorities in Chicago: recommendations regarding education
Authors: Robinson June K. , Joshi Komal M. , Ortiz Sara , Kundu Roopal V.
Published: March 2010

Objectives: To assess the level of melanoma awareness and risk perception among ethnic minorities and to identify ways to enhance the relevance of melanoma educational materials for ethnic minorities.

 Methods: Twelve focus groups composed of participants from a single ethnicity [African‐American (n=40), Hispanic (n=40), and Asian (n=40)], participated in a 2 h discussion on melanoma and skin cancer and commented on an educational brochure by the American Cancer Society and reacted to photographs of melanoma on ethnic skin. Participants also evaluated the ability to sunburn and tan and the skin cancer risk of images of celebrities before and after the discussion. Additionally, participants assessed the skin tone of celebrities as very fair, fair, olive, light brown, dark brown, and very dark. The audiotape recordings of the 12 focus groups were transcribed and analyzed with the Non‐numerical Unstructured Data Indexing Searching and Theorizing software for common themes.

 Results: The common themes were (1) lack of relevance of skin cancer to ethnic people, (2) understanding of skin cancer risk terminology is based on personal experience and what is acquired from the media, and (3) sources of health information for ethnic minorities are fragmented and physicians are not the primary source of information. Celebrity images representing the six skin tones were selected.

 Conclusions: Relevance of melanoma education to ethnic people may be improved by using ‘melanoma skin cancer’, photographs of early melanoma in people with dark skin, and providing guidance on how to inspect hands and feet for suspicious moles. Copyright © 2010 John Wiley & Sons, Ltd.
A Global Model for the Identification of the Dominant Reactions for Atomic Oxygen in He/O2 Atmospheric‐Pressure Plasmas
Authors: Park Gan Young , Hong Yong Jun , Lee Hyun Woo , Sim Jae Yoon , Lee Jae Koo
Published: March 2010

Atmospheric pressure plasmas have attracted great interests and been widely used in biomedical applications such as sterilization, coagulation, wound healing, and cancer cells treatment. The reactive oxygen species (ROS) generated in atmospheric pressure plasmas have been believed to play a crucial role in these biomedical applications. The experimental measurement of the atomic oxygen density showed that the highest density was measured at an admixture of 0.5% of O2. The similar trend of the atomic oxygen density varying the concentration of O2 was reproduced through a global model of He/O2 in atmospheric pressure plasmas. The evolution of the dominant production and loss reactions for the atomic oxygen was analyzed. With increase in the concentration of O2, the atomic oxygen was produced mainly by the dissociation of O2 and lost through the recombinations with themselves and oxygen molecules.

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Serum biomarkers which correlate with failure to respond to immunotherapy and tumor progression in a murine colorectal cancer model
Authors: Vafadar‐Isfahani Baharak , Laversin Stephanie Anne‐Sophie , Ahmad Murrium , Ball Graham , Coveney Clare , Lemetre Christophe , Kathleen Miles Amanda , van Schalkwyk Gerhard , Rees Robert , Matharoo‐Ball Balwir
Published: March 2010

Purpose: To advance our understanding of mechanisms involved in tumor progression/regression, a CT26 colorectal mouse model treated intra‐tumorally with DISC‐herpes simplex virus as immunotherapy was used in the discovery and validation phases to investigate and ultimately identify biomarkers correlating with the failure to respond to immunotherapy.

Experimental design: For the discovery phase, serum protein/peptide profiles of a retrospective sample collection (total n=70) were analyzed using MALDI‐TOF‐MS combined with artificial neural networks. Following identification of the key predictive peptides using ESI‐MS/MS, validation of the identified proteins was carried out on serum and tissues collected in an independent sample set (total n=60).

Results: Artificial neural network analysis resulted in four discriminatory peaks with an accuracy of 86%, sensitivity of 90% and specificity of 81% between the progressor/regressor groups. Three of the identified discriminatory markers were upregulated and demonstrated a positive correlation with tumor progression following DISC‐herpes simplex virus therapy. Immunovalidation studies corroborated the MALDI‐TOF‐MS findings. Immunohistochemistry revealed that serum amyloid A‐1 and serum amyloid P produced in the liver localized intracellularly in CT26 tumor tissue.

Conclusions: MALDI‐TOF‐MS and BI analysis of the serum proteome of tumor‐bearer mice undergoing immunotherapy, identified biomarkers associating with “failure to respond” and biological arrays confirmed these findings.
Increasing protein stability: Importance of ΔCp and the denatured state
Authors: Fu Hailong , Grimsley Gerald , Scholtz J. Martin , Pace C. Nick
Published: March 2010

Increasing the conformational stability of proteins is an important goal for both basic research and industrial applications. In vitro selection has been used successfully to increase protein stability, but more often site‐directed mutagenesis is used to optimize the various forces that contribute to protein stability. In previous studies, we showed that improving electrostatic interactions on the protein surface and improving the β‐turn sequences were good general strategies for increasing protein stability, and used them to increase the stability of RNase Sa. By incorporating seven of these mutations in RNase Sa, we increased the stability by 5.3 kcal/mol. Adding one more mutation, D79F, gave a total increase in stability of 7.7 kcal/mol, and a melting temperature 28°C higher than the wild‐type enzyme. Surprisingly, the D79F mutation lowers the change in heat capacity for folding, ΔCp, by 0.6 kcal/mol/K. This suggests that this mutation stabilizes structure in the denatured state ensemble. We made other mutants that give some insight into the structure present in the denatured state. Finally, the thermodynamics of folding of these stabilized variants of RNase Sa are compared with those observed for proteins from thermophiles.
Process safety management lessons learned from a petroleum refinery spent caustic tank explosion
Authors: Bloch Kenneth P. , Wurst Dawn M.
Published: March 2010

A spent caustic tank exploded in a major Midwestern USA refinery on August 14, 2007. The explosion occurred while the operators were transferring spent caustic into the atmospheric‐relief, cone roof storage tank that had been in service since 1956. Fortunately, there were no injuries or fatalities. Property damage was, however, sufficient to interrupt the spent caustic disposal process. Unit operation was restored by commissioning an alternative, inherently safe spent caustic storage system.

An investigation was launched to determine the explosion's cause. This article details the investigation's conclusions and corrective actions. It describes how a 2005 Hazard and Operability action item's intended purpose to reduce the risk for a PSM failure was defeated by equipment design errors, an unauthorized procedure deviation, and a series of management system failures. Lessons learned are communicated for organizations to avoid repeating similar mistakes. © 2010 American Institute of Chemical Engineers Process Saf Prog, 2010
Process safety management—What is your goal?
Authors: Collins Robert L.
Published: March 2010

In this article, the basic elements of process safety management (PSM) and how they are supposed to work together to support the underlying principles of PSM and achieve the goal of zero process‐related incidents are discussed. In doing this, the reader will see how easy it can be to lose sight of this overall objective by focusing only on compliance with the regulations. It is possible to be in 100% compliance with the rules and regulations yet still have a poor quality program, as demonstrated by a failure to achieve the overall objective of PSM.

In demonstrating this, the author discusses the basic elements of PSM and how they are intended to work together to support the underlying principles of PSM. This article shows the inter‐relationships and importance of PSM program elements. In doing this, the author will show how it can be easy to lose sight of the overall objective (i.e., zero process‐related incidents) by focusing on compliance with the regulations.

The use of leading and lagging metrics to measure and improve the PSM program is introduced and discussed. The importance of creating and using leading metrics that measure both the quantity and quality of each PSM program element is explained. The creation and use of the leading metrics that evaluate performance in a nonsubjective manner can provide uniformity across the organization or an industry. Use of the right leading metrics can drive performance towards the overall objective of zero process‐related incidents. © 2010 American Institute of Chemical Engineers Process Saf Prog, 2010
Ultrasonic attenuation estimation of the pregnant cervix: a preliminary report
Authors: McFarlin B. L. , Bigelow T. A. , Laybed Y. , O'Brien W. D. , OELZE M. L. , Abramowicz J. S.
Published: March 2010

Objective

Estimates of ultrasonic attenuation (the loss of energy as an ultrasonic wave propagates through tissue) have been used to evaluate the structure and function of tissues in health and disease. The purpose of this research was to develop a method to estimate ultrasonic cervical attenuation during human pregnancy using a clinical ultrasound system.

Methods

Forty women underwent a cervical scan once during pregnancy with the Zonare® z.one clinical ultrasound system using a 4–9‐MHz endovaginal transducer. This ultrasound system provides access to radiofrequency (RF) image data for processing and analysis. In addition, a scan of a tissue‐mimicking phantom with a known attenuation coefficient was acquired and used as a reference. The same settings and transducer used in the clinical scan were used in the reference scan. Digital data of the beam‐formed image were saved in Digital Imaging and Communications in Medicine (DICOM) format on a flash drive and converted to RF data on a personal computer using a Matlab® program supplied by Zonare. Attenuation estimates were obtained using an algorithm that was independently validated using tissue‐mimicking ultrasonic phantoms.

Results

RF data were acquired and analyzed to estimate attenuation of the human pregnant cervix. Regression analysis revealed that attenuation was: a predictor of the interval from ultrasound examination to delivery (β = 0.43, P = 0.01); not a predictor of gestational age at time of examination (β = − 0.23, P = 0.15); and not a predictor of cervical length (β = 0.077, P = 0.65).

Conclusions

Ultrasonic attenuation estimates have the potential to be an early and objective non‐invasive method to detect interval between examination and delivery. We hypothesize that a larger sample size and a longitudinal study design will be needed to detect gestational age‐associated changes in cervical attenuation. Copyright © 2010 ISUOG. Published by John Wiley & Sons, Ltd.