bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated modeling of CO2 storage and leakage scenarios including transitions between super‐ and subcritical conditions, and phase change between liquid and gaseous CO2
Authors: Pruess Karsten 
Published: July 2011

AbstractStorage of CO2 in saline aquifers is intended to be at supercritical pressure and temperature conditions, but CO2 leaking from a geologic storage reservoir and migrating toward the land surface (through faults, fractures, or improperly abandoned wells) would reach subcritical conditions at depths shallower than 500–750 m. At these and shallower depths, subcritical CO2 can form two‐phase mixtures of liquid and gaseous CO2, with significant latent heat effects during boiling and condensation. Additional strongly non‐isothermal effects can arise from decompression of gas‐like subcritical CO2, the so‐called Joule–Thomson effect. Integrated modeling of CO2 storage and leakage requires the ability to model non‐isothermal flows of brine and CO2 at conditions that range from supercritical to subcritical, including three‐phase flow of aqueous phase, and both liquid and gaseous CO2. In this paper, we describe and demonstrate comprehensive simulation capabilities that can cope with all possible phase conditions in brine‐CO2 systems. Our model formulation includes:
an accurate description of thermophysical properties of aqueous and CO2‐rich phases as functions of temperature, pressure, salinity and CO2 content, including the mutual dissolution of CO2 and H2O;
transitions between super‐ and subcritical conditions, including phase change between liquid and gaseous CO2;
one‐, two‐, and three‐phase flow of brine‐CO2 mixtures, including heat flow;
non‐isothermal effects associated with phase change, mutual dissolution of CO2 and water, and (de‐) compression effects; and
the effects of dissolved NaCl, and the possibility of precipitating solid halite, with associated porosity and permeability change.
Applications to specific leakage scenarios demonstrate that the peculiar thermophysical properties of CO2 provide a potential for positive as well as negative feedbacks on leakage rates, with a combination of self‐enhancing and self‐limiting effects. Lower viscosity and density of CO2 as compared to aqueous fluids provides a potential for self‐enhancing effects during leakage, while strong cooling effects from liquid CO2 boiling into gas, and from expansion of gas rising towards the land surface, act to self‐limit discharges. Strong interference between fluid phases under three‐phase conditions (aqueous – liquid CO2 – gaseous CO2) also tends to reduce CO2 fluxes. Feedback on different space and time scales can induce non‐monotonic behavior of CO2 flow rates. © 2011 Society of Chemical Industry and John Wiley & Sons, Ltd
Utility of daily image guidance with intensity‐modulated radiotherapy for tumors of the base of skull
Authors: Chen Allen M. , Cheng Suzan , Farwell D. Gregory , Luu Quang , Donald Paul J. , Boggan James , Franklin Stephen , Purdy James A. 
Published: July 2011

AbstractBackgroundThis study was carried out to report our experience using intensity‐modulated radiotherapy (IMRT) with daily image‐guided radiotherapy (IGRT) for tumors involving the base of skull.MethodsIn all, 100 patients were prospectively treated with IMRT to a median dose of 64 Gy (range, 45–70 Gy). Daily helical megavoltage computed tomography (MVCT) scans were obtained as part of an IGRT registration protocol for patient alignment.ResultsThe 2‐year local‐regional control was 91%. A total of 3295 daily MVCT scans were obtained. The mean shift to account for interfraction motion was 1.18 ± 1.75 mm, 1.81 ± 1.34 mm, and 1.33 ± 1.19 mm for the medial–lateral (ML), superior–inferior (SI), and anterior–posterior (AP) directions, respectively. Pretreatment shifts of >3 mm occurred in 10%, 26%, and 18%, in the ML, SI, and AP directions, respectively.ConclusionsThe feasibility and efficacy of daily IGRT as a complement to IMRT for skull base were demonstrated. © 2011 Wiley Periodicals, Inc. Head Neck, 2011
An alkaline comet assay study on the antimalarial drug atovaquone in human peripheral blood lymphocytes: a study based on clinically relevant concentrations
Authors: Dinter Domagoj , Gajski Goran , Garaj‐Vrhovac Vera 
Published: July 2011

ABSTRACTAtovaquone, a hydroxynaphthoquinone, is an anti‐parasite drug, selectively targeting the mitochondrial respiratory chain of malaria parasite. It is used for both the treatment and prevention of malaria, usually in a fixed combination with proguanil. Although atovaquone has not often been associated with severe adverse reactions in the recommended dosages and has a relatively favorable side effect profile, the present study was undertaken to evaluate its cytogenotoxic potential towards human peripheral blood lymphocytes. Two different concentrations of atovaquone found in plasma when used in fixed‐dose combination with proguanile hydrochloride were used with and without S9 metabolic activation: 2950 ng ml−1 used for prophylactic treatment and 11 800 ng ml−1 used in treatment of malaria. The results showed that lymphocyte viability was not affected after the treatment, suggesting that atovaquone was not cytotoxic in the given concentrations. With the alkaline comet assay we demonstrated that in human peripheral blood lymphocytes no significant changes in comet parameters occurred after the treatment. There were no differences in tested parameters with the addition of S9 metabolic activation, indicating that atovaquone either has no metabolite or it is not toxic in the given concentrations. Since no effects were observed after the treatment, it is to be concluded that atovaquone is safe from the aspect of genototoxicity in the recommended dosages. Copyright © 2011 John Wiley & Sons, Ltd.
Current views on ljungan virus and its relationship to human diabetes
Authors: Niklasson Bo 
Published: July 2011

AbstractThe Ljungan virus (LV), a member of the Parechovirus genus and Picornaviridae family was isolated originally from its wild reservoir, the bank vole (Myodes glareolus) at the Ljungan River in central Sweden [Niklasson et al., 1999]. LV is associated with diseases such as myocarditis, encephalitis, pregnancy related diseases, and diabetes in several species of wild rodent [Niklasson et al., 2006a]. The same outcomes can be induced in mice under controlled laboratory conditions [Niklasson et al., 2006b]. Several mouse and rat animal models used to study diabetes have been found to carry LV naturally [Niklasson et al., 2007]. The role of the viruses in diabetes pathogenesis has been investigated by treating these animals with antiviral compounds [Holmberg et al., 2009].Variation in the incidence of type 1 diabetes has been found to track the fluctuations in native rodent populations in central Sweden. Increased prevalence of antibodies to LV has been detected in Swedish type 1 diabetes cases. However, LV virus has not been isolated and its viral RNA has not been detected in type 1 diabetes. J. Med. Virol. 83:1673–1673, 2011. © 2011 Wiley‐Liss, Inc.
Greater diversity of HIV DNA variants in the rectum compared to variants in the blood in patients without HAART
Authors: Avettand‐Fenoel Véronique , Hocqueloux Laurent , Müller‐Trutwin Michaela , Prazuck Thierry , Melard Adeline , Chaix Marie‐Laure , Agoute Eric , Michau Christophe , Rouzioux Christine 
Published: July 2011

AbstractThe gut‐associated lymphoid tissue represents the largest reservoir of HIV‐1. Improving knowledge of this reservoir by studying the diversity of viral population is a key step towards understanding the pathogenesis and dynamics of HIV. Obtaining samples is difficult and little information is available on gut viral quasispecies during the course of infection in humans. The aim of this study was to characterize rectal viral strains and their diversity and to investigate the relationships between the rectal tissue reservoir and viral variants in the blood. Phylogenetic analyses were performed on the env sequences for rectal HIV DNA, blood HIV DNA, and HIV RNA clones, with maximum‐likelihood and neighbor‐joining methods on seven patients. Genetic diversity was assessed. Higher diversity of HIV DNA clones was noted in the rectum compared to blood in four out of five patients without HAART. Viral diversity was present in the rectum from time of the primary infection. Similar degrees of diversity were observed in the rectum and blood during HAART. Rectal and blood HIV variants were interspersed partially or totally in the seven patients. A certain number of rectal HIV DNA clones were clustered together in six patients. These results suggest that variants in the rectum were more heterogeneous than variants in the blood from patients without HAART, probably because the activated milieu of gut‐associated lymphoid tissue may provide an improved environment for viral replication, and indicate exchange of viral populations between blood and rectal tissues, reflecting the dynamics of HIV during course of infection. J. Med. Virol. 83:1499–1507, 2011. © 2011 Wiley‐Liss, Inc.
Assessment of dried blood spot samples as a simple method for detection of hepatitis B virus markers
Authors: Villar Livia Melo , de Oliveira Jaqueline Correia , Cruz Helena Medina , Yoshida Clara Fumiko Tachibana , Lampe Elisabeth , Lewis‐Ximenez Lia Laura 
Published: July 2011

AbstractDetection of hepatitis B virus (HBV) serological markers in dried blood spot (DBS) samples by enzyme immunoassay (ELISA) has not yet been fully optimized. In this study, the ability to detect three HBV markers (HBsAg, anti‐HBc, and anti‐HBs) was evaluated in DBS samples using a modified commercial ELISA. Matched serum and DBS samples were obtained from individuals with or without a past history of HBV infection. Sera samples were tested according to the manufacturer's instructions, but for DBS testing, paper diameters, elution buffer, volume of input sample, and cut‐off values were evaluated to optimize the assay. Stability studies were done on DBS stored at for up to 180 days at different temperatures. The absorbance values that yielded the maximum sensitivity and specificity were determined based on the area under the ROC curve (AUROC) and chosen as the cut‐off value. Using this parameter, sensitivity was 90.5%, 97.6%, and 78% for anti‐HBc, HBsAg, anti‐HBs assays, respectively. Specificity was 92.6%, 96.7%, and 97.3% for anti‐HBc, HBsAg, and anti‐HBs assays, respectively. HBV markers could be detected in DBS samples until 63 days after sample collection at most temperatures, but storage at −20°C yielded more consistent results. These results indicate that modified ELISA can be used to detect HBV markers in DBS samples, particularly if the samples are stored appropriately. J. Med. Virol. 83:1522–1529, 2011. © 2011 Wiley‐Liss, Inc.
Monitoring of group C rotavirus in children with acute gastroenteritis in Brazil: An emergent epidemiological issue after rotavirus vaccine?
Authors: Luchs Adriana , Morillo Simone Guadagnucci , de Oliveira Cristina Mendes , Timenetsky Maria do Carmo Sampaio Tavares 
Published: July 2011

AbstractGroup C rotavirus (GpCRV) has a worldwide distribution; however, its epidemiology and ecology are still unclear. Evidence for a possible zoonotic role has been postulated recently for Brazilian children strains. The aim of this study was to monitor GpCRV in children ≤15 years with acute gastroenteritis during the 2007–2010 national Brazilian rotavirus surveillance, and to undertake the molecular characterization of the major VP6 capsid protein. A total of 3,019 fecal samples were first screened for Group A rotavirus (GpARV). A total of 2,205 GpARV ELISA negative samples were tested further for the presence of GpCRV by SDS–PAGE, electronic microscopy, and RT‐PCR for the VP6 gene. The genetic diversity of GpCRV was carried out by sequencing the VP6 gene. GpARV and GpCRV infections were detected in 24.6% (742/3,019) and 0.3% (8/3,019), respectively. The GpCRV detection rate increased from 0.2% (1/422) in 2007 to 1% (7/708) in 2008, and GpCRV cases were not detected in 2009 and 2010. The phylogenetic analysis indicated that the strains belonged to the human lineage, and showed a genetic relationship with the GpCRV strain from Japan isolated in 2009. None of the study sequences was related closely to animal GpCRV strains. This study provides further evidence that GpCRV is a minor cause of acute childhood gastroenteritis in Brazil, and does not suggest that GpCRV may assume epidemiological importance in the future, even after the introduction of a GpARV vaccine. In addition, the molecular analyses of the GpCRV samples in this study do not support the zoonotic hypothesis. J. Med. Virol. 83:1631–1636, 2011. © 2011 Wiley‐Liss, Inc.
A cluster of patients with recombinant B/F HIV‐1 infection: Epidemiological, clinical, and virological aspects
Authors: Rossotti Roberto , Foglieni Barbara , Molteni Chiara , Gatti Manuela , Guarnori Irene , La Russa Ennio , Prati Daniele , Orani Anna 
Published: July 2011

AbstractMigratory processes have caused changes in human immunodeficiency virus (HIV) epidemiology and non‐B subtypes are now playing an increasing role. In a cohort of 553 HIV‐infected outpatients tested to identify non‐B isolates, the largest group consisted of 13 subjects with a recombinant B/F form (prevalence 2.4%). Sequencing and phylogenetic analyses described a B/F recombinant clade with anomalous breakpoints that did not allow it to be classified as CRF12_BF. Viral load was not quantified efficiently because of a mismatch in the primers and probes used by commercial assays. An assessment of the clinical management, and epidemiological, immunological, and virological characteristics of these patients, who were receiving non‐nucleoside reverse transcriptase inhibitor (NNRTI)‐ or protease inhibitor (PI)‐based regimens, showed that the immunological and virological mismatch delayed the start of treatment by a mean of 6.8 months. Therapy was started in nine patients. Both NNRTI‐ and PI‐based regimens led to full virological suppression after a mean 36 weeks of treatment; the PI‐based regimens proved to be more effective in terms of immunological recovery (1,341 vs. 544 CD4+ cells/mm3). The spread of non‐B subtypes is increasing throughout the world but their response to treatment is still unclear. PIs and NNRTIs are effective but further tests are needed to allow the more efficient recognition of these viral strains and establish how they should be treated. J. Med. Virol. 83:1493–1498, 2011. © 2011 Wiley‐Liss, Inc.
Molecular characterization of measles virus strains causing subactute sclerosing panencephalitis in France in 1977 and 2007
Authors: Moulin Emilie , Beal Vanda , Jeantet Damien , Horvat Branka , Wild T. Fabian , Waku‐Kouomou Diane 
Published: July 2011

AbstractMeasles virus strains from two subacute sclerosing panencephalitis (SSPE) cases diagnosed in 1977 (Laine strain) and in 2007 (Hoedts strain) were studied. Phylogenetic analysis based on C‐terminal part of the nucleoprotein and the entire H gene showed that Hoedts strain, circulating in France presumably in the 1980s, belonged to genotype C2. However, Laine strain, suspected to have circulated between 1940s and 1960s, could not be assigned to any known measles virus genotypes. Sequences analysis of the Laine strain suggested that it originated from a measles virus that may have circulating at the same period as the Edmonston strain. The analysis of the whole genome of both SSPE strains revealed biased hypermutations in M, F, and H gene. Some of these mutations like the L165P found in the M protein sequence of the Laine strain, the amino acid position 94, where a mutation M94V was found in the F protein sequence of the Hoedts strain are known to play an important role in the glycoprotein interaction and to impair the ability of measles virus strain to produce cell‐free infectious viral particles.This is the first study on molecular characterization of the entire coding region of measles virus isolated from SSPE cases in France. J. Med. Virol. 83:1614–1623, 2011. © 2011 Wiley‐Liss, Inc.
Molecular analysis of hepatitis C virus infection in Bulgarian injecting drug users
Authors: Ciccozzi Massimo , Zehender Gianni , Cento Valeria , Lo Presti Alessandra , Teoharov Pavel , Pavlov Ivan , Bogdanova Violeta , Perno Carlo Federico , Ciotti Marco 
Published: July 2011

AbstractIntravenous drug users constitute a group at risk for hepatitis C virus (HCV) infection. Today, no data are available on the molecular epidemiology of HCV in Bulgaria despite the fact that in recent years the incidence of acute hepatitis C infection among Bulgarian intravenous drug users increased sixfold and about 2/3 of them developed a chronic infection. The aim of this study was to determine the circulation of hepatitis C genotypes among drug users and to study the evolution and transmission history of the virus by molecular clock and Bayesian methods, respectively. Sequencing of NS5B gene showed that the genotype 3a was the most prevalent type among intravenous drug users. In the Bayesian tree, the 3a subtypes grouped in one main clade with one small cluster well statistically supported. The root of the tree was dated back to the year 1836, and the main clade from Bulgaria was dated 1960. The effective number of infections remained constant until about years 1950s, growing exponentially from the 1960s to the 1990s, reaching a plateau in the years 2000. The not significant intermixing with isolates from other countries may suggest a segregated circulation of the epidemic between 1940s and 1980s. The plateau reached by the epidemic in the early 2000s may indicate the partial success of the new preventive policies adopted in Bulgaria. J. Med. Virol. 83:1565–1570, 2011. © 2011 Wiley‐Liss, Inc.
Improvement of the specificity of a pan‐viral microarray by using genus‐specific oligonucleotides and reduction of interference by host genomes
Authors: Kang Xiaoping , Qin Chengfeng , Li Yongqiang , Liu Hong , Lin Fang , Li Yuchang , Li Jing , Zhu Qingyu , Yang Yinhui 
Published: July 2011

AbstractRapid detection of viral pathogens is crucial for antiviral therapy. High‐density 60–70‐mer oligonucleotide microarrays have been explored for broad detection of many viruses. However, relatively low specificity and the complex analytical processes are the major limitations when pan‐viral oligonucleotide microarrays are used to detect viral pathogens. In this study, genus‐specific oligonucleotides were used as probes and modified sample preparations were carried out to improve the specificity and accuracy of the pan‐viral oligonucleotide microarray. Genus‐specific 63‐mer oligonucleotide probes were used for screening human pathogenic RNA viruses. A total of 628 oligonucleotide probes covering 32 RNA viral genera from 14 viral families were used. The number of oligonucleotide probes was decreased to simplify the analytical process of hybridization and to minimize cross‐hybridization. Host genomes were removed by DNase I/RNase T1 digestion before viral nucleic acid extraction, and non‐ribosomal hexanucleotides were used for reverse transcription to minimize interference of host genomes. Cultured viruses were used for microarray validation. The microarray was validated by cultured isolates that belonged to five viral genera. By using DNase I/RNase T1 digestion before viral nucleic acid extraction and non‐ribosomal hexanucleotides for reverse transcription, the specificity of the microarray was improved. Furthermore, the analytical process of hybridization results was simplified. The specificity of pan‐viral microarray could be improved by using genus‐specific oligonucleotides as probes and by using non‐ribosomal hexanucleotides for reverse transcription. Combined with subsequent degenerate reverse transcriptase‐polymerase chain reaction and sequencing processes, this improved genus‐specific oligonucleotides microarray provides a relatively flexible strategy for diagnosis of RNA virus diseases. J. Med. Virol. 83:1624–1630, 2011. © 2011 Wiley‐Liss, Inc.
Hepatitis B virus genotype B with G1896A and A1762T/G1764A mutations is associated with hepatitis B related acute‐on‐chronic liver failure
Authors: Xiao Lei , Zhou Bin , Gao Hongbo , Ma Shiwu , Yang Guifeng , Xu Min , Abbott William G.H. , Chen Jinjun , Sun Jian , Wang Zhanhui , Hou Jinlin 
Published: July 2011

AbstractThe existence of statistical associations between hepatitis B‐related acute‐on‐chronic liver failure and both hepatitis B virus (HBV) genotype and mutations in the basal core promoter (BCP) and precore (PC) regions needs to be confirmed. A total of 322 patients with a chronic HBV infection, including 77 with hepatitis B‐related acute‐on‐chronic liver failure, 109 with hepatocellular carcinoma (HCC) and 136 with chronic hepatitis B (CHB) were enrolled. The HBV genotype and the presence of mutations in the BCP/PC regions were determined by direct sequencing, and the frequencies were compared in the three patient groups. Overall, 198/322 (61.5%) were infected with genotype B and 124/322 (38.5%) with genotype C. Genotype B was significantly more frequent in patients with acute‐on‐chronic liver failure than CHB (92.2% vs. 60.3%, P < 0.001). As a contrast, genotype C was more common in patients with HCC than CHB (58.7% vs. 39.7%, P = 0.003). In genotype B patients, the A1762T/G1764A, A1846T, and G1896A mutations were significantly more prevalent in patients with acute‐on‐chronic liver failure than CHB (50.7% vs. 28.0%, P = 0.004; 59.2% vs. 34.1%, P = 0.002; 69.0% vs. 41.5%, P = 0.001, respectively). In multivariate analysis, the risk factors for acute‐on‐chronic liver failure were genotype B, A1762T/G1764A, and G1896A. In conclusion, CHB patients with genotype B, G1896A, and A1762T/G1764A had a higher tendency to develop liver failure than patients with genotype C. Therefore, HBV genotyping and detecting G1896A and A1762T/G1764A mutations might have important clinical implications as predictive risk factors for hepatitis B‐related acute‐on‐chronic liver failure. J. Med. Virol. 83:1544–1550, 2011. © 2011 Wiley‐Liss, Inc.
Hepatitis B virus genotype G: Prevalence and impact in patients co‐infected with human immunodeficiency virus
Authors: Dao Doan Y. , Balko Jody , Attar Nahid , Neak Enayet , Yuan He‐Jun , Lee William M. , Jain Mamta K. 
Published: July 2011

AbstractRelatively little is known about the role of hepatitis B virus (HBV) genotype G (HBV/G) in patients co‐infected with human immunodeficiency virus (HIV) and HBV. This study examined the prevalence and association of HBV/G to liver fibrosis in co‐infected patients. HBV genotypes were determined by direct sequencing of the HBV surface gene or Trugene® HBV 1.0 assay in 133 patients infected with HIV/HBV. Quantitative testing of HBV‐DNA, HBeAg, and anti‐HBe were performed using the Versant® HBV 3.0 (for DNA) and the ADVIA®Centaur assay. The non‐invasive biomarkers Fib‐4 and APRI were used to assess fibrosis stage. Genotype A was present in 103/133 (77%) of the cohort, genotype G in 18/133 (14%) with genotypes D in 8/133, (6%), F 2/133 (1.5%), and H 2/133 (1.5%). Genotype G was associated with hepatitis B e antigen‐positivity and high HBV‐DNA levels. Additionally, HBV/G (OR 8.25, 95% CI 2.3–29.6, P = 0.0012) was associated with advanced fibrosis score using Fib‐4, whereas, being black was not (OR 0.19, 95% CI 0.05–0.07, P = 0.01). HBV/G in this population exhibited a different phenotype than expected for pure G genotypes raising the question of recombination or mixed infections. The frequent finding of HBV/G in co‐infected patients and its association with more advanced fibrosis, suggests that this genotype leads to more rapid liver disease progression. Further studies are needed to understand why this genotype occurs more frequently and what impact it has on liver disease progression in patients with HBV/HIV. J. Med. Virol. 83:1551–1558, 2011. © 2011 Wiley‐Liss, Inc.