bluuebunny/crossref_metadata_2025 huggingface dataset:
Biosynthesis stimulation of nor‐secotriterpene anxiolytics in cell suspension cultures of Galphimia glaucaCav
Authors: Osuna Lidia , Tapia Nadia , Zamilpa Alejandro , Jiménez‐Ferrer Enrique , Tortoriello Jaime
Published: May 2013

Galphimia glauca produces compounds denominated galphimines (galphimine‐A, galphimine‐B and galphimine‐E). Due to their important anxiolytic activity, we initiated in vitro cultures of the species with the purpose of developing a biotechnological process for obtaining galphimines. In this work, we stimulated the biosynthesis and excretion of galphimines with two‐phase batch‐type cell suspension cultures of G. glauca. The effect of nutritional variation and the 2,4‐dichlorophenoxy acetic acid added to Murashige & Skoog(MS) culture medium was evaluated. Later, we evaluated the effect of the stimulation with calcium and methyl jasmonate (MeJ). The greatest production of galphimine‐B (3.39 × 10−5 g/L day−1) was obtained on day 40 of kinetics, and induced by a treatment containing concentrations of nitrates and phosphate that are double of those normally used in MS medium, without sucrose but with added 2,4‐dichlorophenoxy acetic acid (4 mg/L). Time of galphimine‐B biosynthesis diminished due to the effect of MeJ in combination with calcium, and induced the excretion (100%) of galphimine‐B (6.35 × 10−5 g/L day−1) into the culture medium. Thus, the use of calcium and MeJ comprises a viable alternative to stimulate the production and excretion of galphimine‐B and galphimine‐A in batch‐type cultures of G. glauca in modified MS medium. Once optimized, the production of the anxiolytic compounds can be scaled up to the industrial level.
Is it clean or contaminated soil? Using petrogenic versus biogenic GC-FID chromatogram patterns to mathematically resolve false petroleum hydrocarbon detections in clean organic soils: A crude oil–spiked peat microcosm experiment
Authors: Kelly-Hooper Francine , Farwell Andrea J. , Pike Glenna , Kennedy Jocelyn , Wang Zhendi , Grunsky Eric C. , Dixon D. George
Published: May 2013

The Canadian Council of Ministers of the Environment (CCME) reference method for the Canada-wide standard (CWS) for petroleum hydrocarbon (PHC) in soil provides chemistry analysis standards and guidelines for the management of contaminated sites. However, these methods can coextract natural biogenic organic compounds (BOCs) from organic soils, causing false exceedences of toxicity guidelines. The present 300-d microcosm experiment used CWS PHC tier 1 soil extraction and gas chromatography–flame ionization detector (GC-FID) analysis to develop a new tier 2 mathematical approach to resolving this problem. Carbon fractions F2 (C10–C16), F3 (C16–C34), and F4 (>C34) as well as subfractions F3a (C16–C22) and F3b (C22–C34) were studied in peat and sand spiked once with Federated crude oil. These carbon ranges were also studied in 14 light to heavy crude oils. The F3 range in the clean peat was dominated by F3b, whereas the crude oils had approximately equal F3a and F3b distributions. The F2 was nondetectable in the clean peat but was a significant component in crude oil. The crude oil–spiked peat had elevated F2 and F3a distributions. The BOC-adjusted PHC F3 calculation estimated the true PHC concentrations in the spiked peat. The F2:F3b ratio of less than 0.10 indicated PHC absence in the clean peat, and the ratio of greater than or equal to 0.10 indicated PHC presence in the spiked peat and sand. Validation studies are required to confirm whether this new tier 2 approach is applicable to real-case scenarios. Potential adoption of this approach could minimize unnecessary ecological disruptions of thousands of peatlands throughout Canada while also saving millions of dollars in management costs. Environ Toxicol Chem 2013;32:2197–2206. © 2013 SETAC
Bioavailability of purified subcellular metals to a marine fish
Authors: Guo Feng , Yao Jie , Wang Wen-Xiong
Published: May 2013

In the present study, the authors used a supply of naturally contaminated oysters to investigate how the subcellular metal distribution and the metal burden in prey affected the transfer of metals to a marine fish, the grunt Terapon jarbua. The oysters, Crassostrea hongkongensis, each with different contamination histories, were collected and separated into 3 subcellular fractions: 1) metal-rich granules, 2) cellular debris, and 3) a combined fraction of organelles, heat-denatured proteins, and metallothionein-like proteins, defined as the trophically available metal (TAM). These purified fractions showed a wide range of metal concentrations and were fed to the fish for a period of 7 d at a daily comparable feeding rate of 3% of fish body weight. After 7 d exposure, the newly absorbed metals were mainly distributed in the intestine and liver, indicating a significant tissue-specific trophic transfer, especially for Cd and Cu. The trophic transfer factors (TTFs) showed a sequence of cellular debris >TAM > metal-rich granules, suggesting the impact of subcellular distribution in prey on metal bioavailability. However, significant inverse relationships between the TTFs and the metal concentrations in diets were also found in the present study, especially for Cd and Zn. The subcellular metal compartmentalization might be less important than the metal concentration in prey influencing the trophic transfer. The authors' results have important implications for bioavailability and environmental assessment of dietary metals. Environ Toxicol Chem 2013;32:2109–2116. © 2013 SETAC
The influence of sea level rise and changes in fringing reef morphology on gradients in alongshore sediment transport
Authors: Grady A. E. , Moore L. J. , Storlazzi C. D. , Elias E. , Reidenbach M. A.
Published: May 2013

Climate‐change‐induced alterations to coral reef ecosystems, in combination with sea level rise, have the potential to significantly alter wave dissipation across reefs, leading to shifts in alongshore sediment transport gradients and alterations to tropical coastlines. We used Delft3D to model schematized profiles of two reef flat widths based on the south Molokai, Hawaii coast. Simulated anthropogenic modifications include incremental degradation of the reef structure as well as sea level rise. Our findings indicate that sea level rise has a greater relative effect on wave energy flux and alongshore sediment transport over a wide flat, whereas both reef degradation and sea level rise exert similar influence over a narrow flat. These results suggest reefs that vary in width alongshore are more likely to experience changes in alongshore sediment transport gradients, and therefore shifts in shoreline erosion and accretion patterns, than more uniform reef systems.
FRAMING THE WILLINGNESS‐TO‐PAY QUESTION: IMPACT ON RESPONSE PATTERNS AND MEAN WILLINGNESS TO PAY
Authors: Gyrd‐Hansen Dorte , Jensen Mette Lundsby , Kjaer Trine
Published: May 2013

In this study, respondents were randomly allocated to three variants of the payment card format and an open‐ended format in order to test for convergent validity. The aim was to test whether preferences (as measured by willingness to pay additional tax) would be affected by framing the willingness‐to‐pay question differently. Results demonstrated that valuations were highly sensitive to whether respondents were asked to express their maximum willingness to pay per month or per year. Another important finding is that the introduction of a binary response filter prior to the payment card follow‐up tends to eliminate the positive aspects of introducing a payment card and produces response patterns that are much in line with those of the open‐ended contingent valuation format. However, although a filter will impact on the distribution of willingness‐to‐pay bids and on the rate of zero and protest bids, the overall impact on the welfare estimate is minor. The outcomes of this study indicate that valuations in the stated preference literature may be, at least in part, a function of the instrument designed to obtain the valuations. Copyright © 2013 John Wiley & Sons, Ltd.
Low vitamin D serum concentration is associated with high levels of hepatitis B virus replication in chronically infected patients
Authors: Farnik Harald , Bojunga Jörg , Berger Annemarie , Allwinn Regina , Waidmann Oliver , Kronenberger Bernd , Keppler Oliver T. , Zeuzem Stefan , Sarrazin Christoph , Lange Christian M.
Published: May 2013

Vitamin D is an important immune modulator that plays an emerging role in inflammatory and metabolic liver diseases, including infection with hepatitis C virus (HCV). In contrast, the relationship between vitamin D metabolism and chronic hepatitis B (CHB) is less well characterized. Therefore, we quantified 25(OH)D3 serum levels in a cohort of 203 treatment-naïve patients with chronic hepatitis B virus (HBV) infection and tested for their association with clinical parameters of CHB. Of 203 patients, 69 (34%), 95 (47%), and 39 (19%) had severe vitamin D deficiency (25(OH)D3 <10 ng/mL), vitamin D insufficiency (25(OH)D3 ≥10 and <20 ng/mL), or adequate vitamin D serum levels (25(OH)D3 ≥20 ng/mL), respectively. In both uni- and multivariate analyses, HBV DNA viral load (log10 IU/mL) was a strong predictor of low 25(OH)D3 serum levels (

P

= 0.0007 and

P

= 0.000048, respectively) and vice versa. Mean 25(OH)D3 serum concentrations in patients with HBV DNA <2,000 versus ≥2,000 IU/mL were 17 versus 11 ng/mL, respectively (

P

< 0.00001). In addition, hepatitis B early antigen (HBeAg)-positive patients had lower 25(OH)D3 serum levels than HBeAg-negative patients (

P

= 0.0013). Finally, 25(OH)D3 and HBV DNA serum levels showed inverse seasonal fluctuations.

Conclusion

: Low 25(OH)D3 serum levels are associated with high levels of HBV replication in patients with CHB. This represents a major difference from chronic hepatitis C, where numerous previous studies have shown a lack of correlation between HCV viral load and vitamin D serum levels. Inverse seasonal fluctuations of 25(OH)D3 and HBV DNA serum levels are suggestive of a functional relationship between both variables. (Hepatology 2013;58:1270–1276)
Circulating chemokine (C-X-C Motif) receptor 5+CD4+ T cells benefit hepatitis B e antigen seroconversion through IL-21 in patients with chronic hepatitis B virus infection
Authors: Li Yongyin , Ma Shiwu , Tang Libo , Li Yun , Wang Wei , Huang Xuan , Lai Qintao , Zhang Mingxia , Sun Jian , Li Chris Kafai , Abbott William G.H. , Naoumov Nikolai V. , Zhang Yu , Hou Jinlin
Published: May 2013

Given the clinical significance of hepatitis B e antigen (HBeAg) seroconversion in chronic hepatitis B virus (HBV) infection, it is critical to elucidate the mechanisms regulating this process. In the present study, we found that the frequency of circulating chemokine (C-X-C motif) receptor 5 (CXCR5)+CD4+ T cells was higher in patients who had achieved HBeAg seroconversion in both cross-sectional (

P

< 0.001) and longitudinal (

P =

0.009) studies. These cells were able to produce a significantly higher level of intracellular interleukin 21 (IL-21) after stimulation with HBV peptides in patients with telbivudine-induced HBeAg seroconversion (

P

= 0.007). Furthermore, sorted CXCR5+CD4+ T cells from HBeAg seroconverters boosted a higher frequency of antibody against hepatitis B e antigen (anti-HBe)-secreting B cells in coculture assay (

P

= 0.011). Of note, the increase in frequency of anti-HBe-secreting B cells was abrogated by soluble recombinant IL-21 receptor-Fc chimera (

P

= 0.027), whereas exogenous recombinant IL-21 enhanced this effect (

P

= 0.043). Additionally, circulating CXCR5+CD4+ T cells shared similar phenotypic markers, and were positively correlated in frequency with, splenic follicular T helper cells.

Conclusion

: Circulating CXCR5+CD4+ T cells, by producing IL-21, may have a significant role in facilitating HBeAg seroconversion in patients with chronic HBV infection. (Hepatology 2013;58:1277–1286)
The small molecule, genistein, increases hepcidin expression in human hepatocytes
Authors: Zhen Aileen W. , Nguyen Nancy H. , Gibert Yann , Motola Shmulik , Buckett Peter , Wessling-Resnick Marianne , Fraenkel Ernest , Fraenkel Paula G.
Published: May 2013

Hepcidin, a peptide hormone that decreases intestinal iron absorption and macrophage iron release, is a potential drug target for patients with iron overload syndromes because its levels are inappropriately low in these individuals. Endogenous stimulants of

Hepcidin

transcription include bone morphogenic protein 6 (BMP6) and interleukin-6 (IL-6) by effects on mothers against decapentaplegic homolog (Smad)4 or signal transducer and activator of transcription (Stat)3, respectively. We conducted a small-scale chemical screen in zebrafish embryos to identify small molecules that modulate

hepcidin

expression. We found that treatment with the isoflavone, genistein, from 28-52 hours postfertilization in zebrafish embryos enhanced

Hepcidin

transcript levels, as assessed by whole-mount

in situ

hybridization and quantitative real-time reverse-transcriptase polymerase chain reaction. Genistein's stimulatory effect was conserved in human hepatocytes: Genistein treatment of HepG2 cells increased both

Hepcidin

transcript levels and promoter activity. We found that genistein's effect on

Hepcidin

expression did not depend on estrogen receptor signaling or increased cellular iron uptake, but was impaired by mutation of either BMP response elements or the Stat3-binding site in the

Hepcidin

promoter. RNA sequencing of transcripts from genistein-treated hepatocytes indicated that genistein up-regulated 68% of the transcripts that were up-regulated by BMP6; however, genistein raised levels of several transcripts involved in Stat3 signaling that were not up-regulated by BMP6. Chromatin immunoprecipitation and ELISA experiments revealed that genistein enhanced Stat3 binding to the

Hepcidin

promoter and increased phosphorylation of Stat3 in HepG2 cells.

Conclusion

: Genistein is the first small-molecule experimental drug that stimulates

Hepcidin

expression

in vivo

and

in vitro

. These experiments demonstrate the feasibility of identifying and characterizing small molecules that increase

Hepcidin

expression. Genistein and other candidate molecules may subsequently be developed into new therapies for iron overload syndromes. (Hepatology 2013;58:1315–1325)
Advanced glycation endproducts induce fibrogenic activity in nonalcoholic steatohepatitis by modulating TNF-α-converting enzyme activity in mice
Authors: Jiang Joy X. , Chen Xiangling , Fukada Hiroo , Serizawa Nobuko , Devaraj Sridevi , Török Natalie J.
Published: May 2013

Advanced glycation endproducts (AGEs) accumulate in patients with diabetes, yet the link between AGEs and inflammatory and fibrogenic activity in nonalcoholic steatohepatitis (NASH) has not been explored. Tumor necrosis factor alpha (TNF-α)-converting enzyme (TACE) is at the center of inflammatory processes. Because the main natural regulator of TACE activity is the tissue inhibitor of metalloproteinase 3 (Timp3), we hypothesized that AGEs induce TACE through nicotinamide adenine dinucleotide phosphate reduced oxidase 2 (NOX2); and the down-regulation of Sirtuin 1 (Sirt1)/Timp3 pathways mediate fibrogenic activity in NASH. The role of NOX2, Sirt1, Timp3, and TACE was evaluated in choline-deficient L-amino acid defined (CDAA) or Western diet (WD)-fed wild-type (WT) and NOX2−/− mice. To restore Timp3, mice were injected with adenovirus (Ad)-Timp3. Sirt1 and Timp3 expressions were studied in livers from NASH patients, and we found that their levels were significantly lower than in healthy controls. In WT mice on the CDAA or WD, Sirt1 and Timp3 expressions were lower, whereas production of reactive oxidative species and TACE activity significantly increased with an increase in active TNF-α production as well as induction of fibrogenic transcripts. Ad-Timp3 injection resulted in a significant decline in TACE activity, procollagen α1 (I), alpha smooth muscle actin (α-SMA) and transforming growth factor beta (TGF-β) expression. NOX2−/− mice on the CDAA or WD had no significant change in Sirt1, Timp3, and TACE activity or the fibrosis markers assessed.

In vitro

, AGE exposure decreased Sirt1 and Timp3 in hepatic stellate cells by a NOX2-dependent pathway, and TACE was induced after exposure to AGEs.

Conclusion

: TACE activation is central to the pathogenesis of NASH and is mediated by AGEs through NOX2 induction and down-regulation of Sirt1/Timp3 pathways. (Hepatology 2013;58:1339–1348)
Importance of cardiometabolic risk factors in the association between nonalcoholic fatty liver disease and arterial stiffness in adolescents
Authors: Huang Rae-Chi , Beilin Lawrence J. , Ayonrinde Oyekoya , Mori Trevor A. , Olynyk John K. , Burrows Sally , Hands Beth , Adams Leon A.
Published: May 2013

Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide and is regarded as the hepatic manifestation of the metabolic syndrome. In adults, NAFLD is a determinant of arterial stiffness and cardiovascular risk, independent of the metabolic syndrome. Our aim was to ascertain if NAFLD is associated with arterial stiffness, independent of cardiometabolic factors in a population-based cohort of adolescents. The 17-year-olds (n = 964) from an Australian birth cohort had measures of anthropometry, blood pressure, fasting insulin, glucose, lipids, and NAFLD by ultrasound. Two-step cluster analysis identified youth at high metabolic risk. Measures of arterial stiffness (pulse wave velocity [PWV] and augmentation index corrected for heart rate [AI@75]) were obtained using applanation tonometry. The overall prevalence of NAFLD was 13.3%. The “high risk” metabolic cluster at age 17 years included 16% males and 19% females. Compared to “low risk,” the “high risk” cluster participants had greater waist circumference, triglycerides, insulin, systolic blood pressure, and lower high-density lipoprotein (HDL) cholesterol (all

P

< 0.0001). Those who had NAFLD but were not in the “high risk” metabolic cluster did not have increased PWV or AI@75. However, males and females who had NAFLD in the presence of the metabolic cluster had greater PWV (b = 0.20, 95% confidence interval [CI] 0.01 to 0.38,

P

= 0.037). Males who had NAFLD in the presence of the metabolic cluster had greater AI@75 (b = 6.3, 95% CI 1.9 to 10.7,

P

= 0.005).

Conclusion

: NAFLD is only associated with increased arterial stiffness in the presence of the “high risk” metabolic cluster. This suggests that arterial stiffness related to the presence of NAFLD is predicated on the presence of an adverse metabolic profile in adolescents. (Hepatology 2013;58:1306–1314)
The Dimensions of Expatriate Adjustment
Authors: Haslberger Arno , Brewster Chris , Hippler Thomas
Published: May 2013

A narrow and partial theoretical base has limited current concepts of expatriate adjustment and the research based upon them. This conceptual article explores one of the less theorized aspects of expatriate adjustment: the fact that it has multiple dimensions. We conceive of adjustment as a person‐environment relationship that takes place in the three dimensions of cognitions, feelings, and behaviors. Combining these elements takes us one step closer to a comprehensive and more realistic understanding of the nature of expatriate adjustment. We include suggestions for future research that follow from our reconceptualization.
The Association of Meaningfulness, Well‐Being, and Engagement with Absenteeism: A Moderated Mediation Model
Authors: Soane Emma , Shantz Amanda , Alfes Kerstin , Truss Catherine , Rees Chris , Gatenby Mark
Published: May 2013

We theorized that absence from work is a resource‐based process that is related to perceived meaningfulness of work, well‐being, and engagement. Broaden‐and‐build theory (Fredrickson, 1998, 2001) and engagement theory (Bakker, Schaufeli, Leiter, & Taris, 2008; Kahn, 1990) were used to develop a framework for explaining absence. Results of a study of 625 employees and human resource records of subsequent absenteeism data for a three‐month period supported our hypotheses that meaningful work increases engagement with work, and that engagement is associated with low levels of absenteeism. Furthermore, data showed that engagement fully mediated the relationship between meaningfulness and absence, and that well‐being strengthened the relationship between meaningfulness and engagement. The results have implications for understanding the role of individual‐level resources in the workplace, and how meaningfulness, well‐being, and engagement influence absence.
Tournament Compensation Systems, Employee Heterogeneity, and Firm Performance
Authors: Backes‐Gellner Uschi , Pull Kerstin
Published: May 2013

Tournament compensation systems are widely used in practice and have been extensively analyzed theoretically. However, one major problem has hardly been studied in a company context so far: Although it is theoretically well understood that tournament compensation systems are only effective when employees are homogeneous, it has rarely been analyzed what companies can do when they are confronted with employee heterogeneity. In our article, we derive hypotheses on the performance effects of tournament compensation systems in a context of employee heterogeneity based on tournament and expectancy theory. Using personnel records from incentive travel contests, we are able to show that performance is lower in a situation with employee heterogeneity, but that in heterogeneous tournaments, incentives may still work for a subgroup of employees whom we term the “threshold group.” In addition, we also show how companies manage to design the information disclosure systems necessary to install effective “handicapping” or “league‐building” systems in order to increase the effort‐performance expectancy.
Radially anisotropic structure beneath the Shikoku Basin from broadband surface wave analysis of ocean bottom seismometer records
Authors: Takeo A. , Nishida K. , Isse T. , Kawakatsu H. , Shiobara H. , Sugioka H. , Kanazawa T.
Published: May 2013

We have analyzed broadband surface wave data from ocean bottom seismometers deployed in the Shikoku Basin in the northeastern Philippine Sea to determine the radially anisotropic uppermost mantle structure beneath this oceanic basin. We first applied noise correlation method to continuous microseismic records to obtain phase velocities for fundamental‐mode and first higher‐mode Rayleigh waves and fundamental‐mode Love waves at periods of 7–29 s. At longer periods, we applied an array analysis method to teleseismic surface waves to obtain phase velocities of fundamental‐mode Rayleigh and Love waves at periods of 29–117 s. Using these broadband phase velocity measurements, we have determined the one‐dimensional radially anisotropic structure from the crust to the low velocity zone (LVZ) beneath the Shikoku Basin without assuming a priori structure in the uppermost mantle. The final structural model (SB‐RA10) has a high‐velocity lid from the Moho to a depth of ∼40 km, with an LVZ at greater depths. S wave velocities decrease by 6%–10% at a depth range of ∼40–70 km. This large decrease in velocity suggests that there is either a large difference in grain size between these layers or indicates the presence of partial melt or water in the LVZ. Furthermore, strong radial anisotropy of 4%–5% (VSH>VSV) is observed in the uppermost mantle, which may be stronger in the LVZ.
Influence of viscosity pressure dependence on deep lithospheric tectonics during continental collision
Authors: Gray R. , Pysklywec R. N.
Published: May 2013

Previous geodynamic models of continental collision show that the behavior of the continental lithosphere is strongly influenced by its rheology. We build on previous work by quantitatively investigating with numerical experiments the influence of the pressure dependence of viscosity on the process of tectonic deformation during collision. The models demonstrate how the inclusion of viscosity pressure dependence can quite substantially alter the style of continental mantle lithosphere deformation. At low activation volumes, high convergence rates, and low to moderate initial Moho temperatures, the subduction style of mantle lithosphere deformation is dominant. Increasing the activation volume of mantle material allows the subduction style of deformation to occur at all convergence rates studied in the experiments, at the expense of the subduction‐drip and ablative‐drip styles of deformation. At low activation volumes, high convergence rates, and high initial Moho temperatures, the distributed pure shear style of deformation occurs. With these same conditions, increasing the activation volume of mantle material produces an ablative subduction style of mantle lithosphere deformation. At low activation volumes, low convergence rate, and moderate to high initial Moho temperatures, the mantle lithosphere prefers a convective removal style of deformation; increasing the activation volume here yields an ablative‐drip and distributed pure shear styles of deformation. The results demonstrate that inclusion of the pressure dependence of viscosity—quite often neglected in lithosphere‐scale geodynamic models—can be significant in modulating deformation of the deforming lithosphere.
Regulation of p14ARF expression by HPV‐18 E6 variants
Authors: Vazquez‐Vega Salvador , Sanchez‐Suarez Lilia Patricia , Andrade‐Cruz Rafael , Castellanos‐Juarez Emilio , Contreras‐Paredes Adriana , Lizano‐Soberon Marcela , Garcia‐Carranca Alejandro , Benitez Bribiesca Luis
Published: May 2013

A common causative agent for uterine cervical cancer is the human papillomavirus type 18 (HPV‐18) which has three phylogenic variants: Asian‐Amerindian, European, and African. Each variant shows significant molecular differences in the E6 gene. E6 oncoprotein is a negative regulator of tumor suppressor protein p53, hence, this oncoprotein indirectly regulates the expression of tumor‐suppressor p14ARF. p14ARF and p16INK4A genes are overexpressed in—and have been proposed as markers for—HPV‐related cervical cancer. In order to dissect the role of E6 on the regulation of p14ARF expression, separating it from that of other intervening factors, transfection of E6 variants to MCF‐7 cells was performed, assessing cDNA transcript levels by RT‐PCR, whereas p14ARF and p53 expression were evaluated by immunocytochemistry and Western blot. E6 transfected cells differentially expressed transcripts of two molecular forms: E6 and E6*. The ratio of these two forms varied with the transfected E6 variant. With the Asian‐Amerindian variant, the ratio was E6 > E6*, whereas with the European and the African the ratio was E6* > E6. As expected with the E6* construct, E6* transcripts were solely observed. In addition, when E6 > E6* and p53 expression was low, p14ARF was high and when E6* > E6 and p53 expression was high, p14ARF was low. In conclusion, each E6 variant distinctively affects p53 levels and consequently p14ARF expression, finding that could be related with the differences in oncogenic effect of infection with the diverse high‐risk HPV variants. J. Med. Virol. 85:1215–1221, 2013. © 2013 Wiley Periodicals, Inc.
Hepatitis C genotype distribution and homology among geographically disparate injecting drug users in Afghanistan
Authors: Sanders‐Buell Eric , Rutvisuttinunt Wiriya , Todd Catherine S. , Nasir Abdul , Bradfield Andrea , Lei Esther , Poltavee Kultida , Savadsuk Hathairat , Kim Jerome H. , Scott Paul T. , de Souza Mark , Tovanabutra Sodsai
Published: May 2013

Hepatitis C virus (HCV) prevalence is high among injecting drug users in Afghanistan, but transmission dynamics are poorly understood. Samples from HCV‐infected injecting drug users were sequenced to determine circulating genotypes and potential transmission linkages. Serum samples were obtained from injecting drug user participants in Hirat, Jalalabad, and Mazar‐i‐Sharif between 2006 and 2008 with reactive anti‐HCV rapid tests. Specimens with detected HCV viremia were amplified and underwent sequence analysis. Of 113 samples evaluated, 25 samples (35.2%) were only typeable in NS5B, nine samples (12.7%) were only typeable in CE1, and 37 samples (52.1%) were genotyped in both regions. Of those with typeable HCV, all were Afghan males with a mean age of 31.1 (standard deviation [SD] ± 8.0) years and mean duration of injecting of 3.9 (SD ± 4.3) years. Most reported residence outside Afghanistan in the last decade (90.1%) and prior incarceration (76.8%). HCV genotypes detected were: 1a, (35.2%, n = 25), 3a (62.0%, n = 44), and 1b (2.8%, n = 2). Cluster formation was detected in NS5B and CE1 and were generally from within the same city. All participants within clusters reported being a refugee in Iran compared to 93.5% of those outside clusters. Only 22.2% (4/11) of those within clusters had been refugees in Pakistan and these four individuals had also been refugees in Iran. Predominance of genotype 3a and the association between HCV viremia and having been a refugee in Iran potentially reflects migration between Afghanistan and Iran among IDUs from Mazar‐i‐Sharif and Hirat and carry implications for harm reduction programs for this migratory population. J. Med. Virol. 85:1170–1179, 2013. © 2013 Wiley Periodicals, Inc.
Simple and rapid human papillomavirus genotyping method by restriction fragment length polymorphism analysis with two restriction enzymes
Authors: Chen Linghan , Watanabe Ken , Haruyama Takahiro , Kobayashi Nobuyuki
Published: May 2013

Cervical cancer, the third most common cancer that affects women worldwide, is caused by the human papillomavirus (HPV) and is treatable when detected at an early stage. To date, more than 100 different HPV types have been described, and the development of simple, low‐cost, and accurate methods to distinguish HPV genotypes is highly warranted. In this study, an HPV genotyping assay based on polymerase chain reaction (PCR) was evaluated. This method involved the use of MY09/11 primers followed by restriction fragment length polymorphism (RFLP) analysis with the restriction enzymes HpyCH4V and NlaIII. Cervical specimens preserved using CytoRich Blue fluid were collected from 1,134 female volunteers for HPV detection, and 1,111 valid samples were amplified using PCR. The PCR method was sensitive enough to detect 25 copies of HPV18, and three copies of HPV16. Out of 202 PCR‐positive samples, HPV genotypes were determined in 189 samples (93.6%) by this RFLP method. Results were then evaluated further by capillary sequencing method. Concordant results between the two tests were as high as 96.0%. Thirteen samples, which tested negative with RFLP, were verified as non‐specific amplifications with PCR. In conclusion, this PCR‐RFLP method using restriction enzymes HpyCH4V and NlaIII is simple, non‐labor intensive, and is applicable for the inexpensive determination of HPV genotypes in clinical samples. J. Med. Virol. 85:1229–1234, 2013. © 2013 Wiley Periodicals, Inc.
Development of duplex real‐time RT‐PCR based on Taqman technology for detecting simultaneously the genome of pan‐enterovirus and enterovirus 71
Authors: Hwang Seoyeon , Kang Byunghak , Hong Jiyoung , Kim Ahyoun , Kim Hyejin , Kim Kisang , Cheon Doo‐Sung
Published: May 2013

Human enterovirus (EV) 71 is the main etiological agent of hand, foot, and mouth disease (HFMD). It is associated with neurological complications, and caused fatalities during recent outbreaks in the Asia–Pacific region. Infections caused by EV71 could lead to many complications, ranging from brainstem encephalitis to pulmonary oedema, resulting in high mortality. In this study, a duplex real‐time RT‐PCR assay was developed in order to simultaneously detect pan‐EV and EV71. EV71‐specific primers and probes were designed based on the highly conserved VP1 region of EV71. Five EV71 strains were detected as positive, and no positive fluorescence signal was observed in the duplex real‐time RT‐PCR for other viral RNA, which showed 100% specificity for the selected panel, and no cross‐reactions were observed in this duplex real‐time RT‐PCR. The EV71‐specific duplex real‐time RT‐PCR was more sensitive than conventional RT‐PCR, and detected viral titers that were 10‐fold lower than those measured by the latter. Of the 381 HFMD clinical specimens, 196 (51.4%) cases were pan‐EV‐positive, of which 170 (86.7%) were EV71‐positive when tested by pan‐EV and EV71‐specific duplex real‐time RT‐PCR. EV71‐specific duplex real‐time RT‐PCR offers a rapid and sensitive method to detect EV71 from clinical specimens, and will allow quarantine measures to be taken more effectively during outbreaks. J. Med. Virol. 85:1274–1279, 2013. © 2013 Wiley Periodicals, Inc.
Detection and molecular characterisation of noroviruses in hospitalised children in Malawi, 1997–2007
Authors: Trainor Eamonn , Lopman Ben , Iturriza‐Gomara Miren , Dove Winifred , Ngwira Bagrey , Nakagomi Osamu , Nakagomi Toyoko , Parashar Umesh , Cunliffe Nigel
Published: May 2013

Despite the increasing recognition of noroviruses as major pathogens associated with community‐acquired diarrhoea in children, there are few studies from Africa. Long‐term surveillance studies of rotavirus gastroenteritis in Malawian children have provided an opportunity to undertake a study of the importance and epidemiological features of norovirus infection in this population. Faecal specimens were collected from children <5 years of age admitted to hospital with acute diarrhoea, as well as from a comparison group of diarrhoea‐free children, in Blantyre, Malawi between 1997 and 2007. Norovirus was detected using real‐time PCR and strains genotyped by nucleotide sequence analysis. Norovirus was detected in 220/1,941 (11.3%) faecal specimens, comprising genogroup GI (1.8%), GII (9.4%) and mixed GI/GII (0.1%). The median age of children with norovirus was 6 months (range, 0–48 months). Norovirus was detected throughout the year, with peaks at the end of the rainy season (March) and towards the end of the dry season (August–November). Norovirus GII.4 was the most commonly detected genotype accounting for 70% of strains characterised, followed by GII.2 (6%), GII.6 (4%) and GII.12 (4%). Sub typing of GII.4 noroviruses demonstrated local circulation of strains prior to their subsequent detection in association with global epidemics of gastroenteritis. The prevalence of norovirus in children without diarrhoea was similar to the level in cases. This largest study to date of norovirus infection in African children indicates the potential role of paediatric surveillance in predicting the emergence of norovirus strains with global epidemic potential. J. Med. Virol. 85:1299–1306, 2013. © 2013 Wiley Periodicals, Inc.
Prospective evaluation of E6/E7 mRNA detection by the NucliSENS Easy Q HPV assay in a stepwise protocol
Authors: Padalko Elizaveta , Van Renterghem Lieve , Bamelis Mieke , De Mey Anja , Sturtewagen Yolande , Vastenavond Hilde , Weyers Steven , Praet Marleen
Published: May 2013

The objective of the study was to evaluate prospectively the added value of E6/E7 mRNA detection in a stepwise protocol. A total of 1,422 samples were collected over a period of 17 months. The samples were referred for human papillomavirus (HPV) genotyping if they showed cytological evidence of atypical squamous cells of undetermined significance, low‐ or high‐grade squamous intraepithelial lesion. If one or more of HPV types 16, 18, 31, 33, or 45 were present, mRNA was analyzed by the NucliSENS EasyQ HPV assay. The genotypical distribution of high‐risk HPV was very heterogeneous; HPV 16, 18, 31, 33, and 45 represented 20.2%, 3.4%, 10.8%, 3.4%, and 3.8% of HPV‐positive samples, respectively. Follow‐up data were available for 35 patients. Although over the half (51.4%) of follow‐up samples showing HPV DNA/mRNA consensus evolved to cervical intraepithelial neoplastic lesions, 25.7% showed no progression to neoplasia despite mRNA positivity. However, the major concern was the group (14.3%) that showed progression to cervical intraepithelial neoplasia despite mRNA negativity: all but one of these cases had a high‐risk HPV genotype other than the five included in the NucliSENS EasyQ HPV assay. Markedly, 66.7% of the discordant samples between colposcopy and histology that underestimated the degree of cervical dysplasia were found in this group. Close monitoring of high‐risk HPV DNA‐positive/mRNA‐negative cases remains necessary, which leads to questions about the added value of the evaluated protocol. J. Med. Virol. 85:1242–1249, 2013. © 2013 Wiley Periodicals, Inc.
Kinetics of relapse after pegylated interferon and ribavirin therapy for chronic hepatitis C
Authors: Brochot Etienne , Riachi Ghassan , Plantier Jean‐Christophe , Guillemard Catherine , Vabret Astrid , Mathurin Philippe , Nguyen‐Khac Eric , Duverlie Gilles ,   for the G4 group
Published: May 2013

To optimize standard treatment of chronic hepatitis C in responder patients who have achieved undetectable viral load, a prospective study was conducted to determine the factors and kinetics of virologic relapse. Responder patients were monitored 2, 4, 8, 12, 16, and 24 weeks after the end of treatment with pegylated interferon and ribavirin. Forty‐seven of the 154 patients (30.5%) relapsed. Relapse was significantly associated with absence of rapid virologic response (RVR), retreatment, higher baseline viral load, older age, and lower weight‐based dose of pegylated interferon. Relapse was more frequent in patients failing to achieve a RVR after receiving pegylated interferon alpha 2a < 2.5 µg/week or alpha 2b < 1.5 µg/week (P = 0.002). Among patients infected with hepatitis C virus (HCV) genotype 1 with non‐CC IL‐28B polymorphism (rs12979860), viral decay during treatment was lower in relapsers (P = 0.003 at week 4). Relapse was detected at weeks 2, 4, 8, and 12 after the end of treatment for 5, 8, 10, and 6 patients infected with HCV genotype 1, respectively. Positive predictive values for sustained virologic response were 70.9%, 80.2%, 91.9%, and 98.8% at weeks 2, 4, 8, and 12, respectively. Only one patient relapsed beyond 24 weeks. Closer follow‐up and treatment adaptation in patients failing to achieve RVR may decrease the relapse rate in slower responders and heavier patients. Monitoring viral load as early as 1 month after the end of treatment could be useful to assess virologic response. J. Med. Virol. 85:1191–1198, 2013. © 2013 Wiley Periodicals, Inc.
Genetic variation in NOS2A is associated with a sustained virological response to peginterferon plus ribavirin therapy for chronic hepatitis C in Taiwanese Chinese
Authors: Lim Yun‐Ping , Peng Cheng‐Yuan , Liao Wen‐Ling , Hung Dong‐Zong , Tien Ni , Chen Cing‐Yu , Chang Shih‐Yu , Chang Ching‐Yao , Tsai Fuu‐Jen , Wan Lei
Published: May 2013

This study aimed to evaluate whether genetic polymorphisms of the inducible nitric oxide synthase (iNOS) gene NOS2A could be associated with a sustained virological response (SVR) among patients infected with hepatitis C virus genotypes 1 and 2 (HCV‐1 and HCV‐2) who were treated with peginterferon plus ribavirin (PEG‐IFNα‐RBV). We analyzed the associations between SVR to PEG‐IFNα‐RBV therapy and two single nucleotide polymorphisms (SNPs) in NOS2A. This study included Taiwanese Chinese patients infected with either HCV‐1 (n = 265) or HCV‐2 (n = 195) with or without a SVR. Among the NOS2A SNPs examined, the combination of genotypes A/A and A/G of rs2248814 was inversely correlated with SVR in patients infected with HCV‐1 (P = 0.0048), particularly in males (P = 0.0281). This effect was not observed in patients infected with HCV‐2. The AC NOS2A haplotype comprising two SNPs (rs2248814 and rs2072324) was found to be associated with SVR, and its presence may decrease the chances for a successful outcome of treatment of patients infected with HCV‐1 (P = 0.0053). HCV‐1 infected patients who carried the A‐C diplotype will have a lower success rate of achieving a SVR (P = 0.0117). In addition, a multivariate logistic regression model for predicting a SVR revealed that the presence of the A‐C diplotype interactively affected the outcome of PEG‐IFNα‐RBV treatment. The presence of NOS2A SNPs and the association with SVR showed that NOS2A polymorphisms may influence the therapeutic outcomes of patients infected with HCV‐1 under standard of care treatment. J. Med. Virol. 85:1206–1214, 2013. © 2013 Wiley Periodicals, Inc.
Hepatitis B virus reverse transcriptase mutations in treatment Naïve chronic hepatitis B patients
Authors: Singla Bhupesh , Chakraborti Anuradha , Sharma Bal Krishan , Kapil Shweta , Chawla Yogesh K. , Arora Sunil K. , Das Ashim , Dhiman Radha K. , Duseja Ajay
Published: May 2013

Mutations in the reverse transcriptase (RT) region of the hepatitis B virus (HBV) genome lead to decreased susceptibility to nucleos(t)ide analogs approved for treatment of HBV infection. The aim of this study was to detect and analyze pre‐existing HBV RT mutations in treatment naïve patients with chronic hepatitis B. Seventy one chronic HBV treatment naïve patients were enrolled from January 2009 to June 2011. HBV RT sequence analysis was done by using direct bidirectional sequencing of semi‐nested PCR products. HBV genotypes were determined by multiplex PCR. Genotype D was found in 64 patients (90.1%) followed by genotype C and A which were present in 5 (7.0%) and 2 (2.8%) patients respectively. The results of the RT sequence analysis showed mutations in 34 (47.9%) patients. The rtH248N mutation was the most common mutation, accounting for 47.1% patients. Other common mutations included rtD263E/S, rtM129L, rtF122L/V/I, rtS135Y/H, rtQ149K, rtL91I, rtH126R, rtC256S/G, rtY257W, rtS259T and rtE271D, which were present in 26.5% (9/34), 29.4% (10/34), 20.6% (7/34), 20.6% (7/34), 20.6% (7/34), 17.6% (6/34), 14.7% (5/34), 14.7% (5/34), 11.8% (4/34), 11.8% (4/34) and 11.8% (4/34) patients respectively. The known primary drug resistance mutations were found in 3 (8.8%) patients. The present study shows the presence of RT amino acid substitutions in treatment‐naïve patients with chronic hepatitis B, which may decrease susceptibility to available oral antiviral drugs. On the basis of the finding of this study, genotypic testing is recommended before the start of therapy in naïve patients, so that suitable antiviral drugs can be prescribed. J. Med. Virol. 85:1155–1162, 2013. © 2013 Wiley Periodicals, Inc.
pH‐sensing nanostar probe using surface‐enhanced Raman scattering (SERS): theoretical and experimental studies
Authors: Liu Yang , Yuan Hsiangkuo , Fales Andrew M. , Vo‐Dinh Tuan
Published: May 2013

Local pH environment has been considered to be a potential biomarker for tumor diagnosis because solid tumors contain highly acidic environments. A pH‐sensing nanoprobe based on surface‐enhanced Raman scattering (SERS) using nanostars under near‐infrared excitation has been developed for potential biomedical applications. To theoretically investigate the effect of protonation state on SERS spectra of p‐mercaptobenzoic acid (pMBA), we used the density functional theory (DFT) with the B3LYP functional to calculate Raman vibrational spectra of pMBA‐Au/Ag complex in both protonated and deprotonated states. Vibrational spectral bands were assigned with DFT calculation and used to investigate SERS spectral changes observed from experiment when varying pH value between five and nine. The SERS peak position of pMBA at ~1580 cm−1 was identified to be a novel pH‐sensing index, which has small but noticeable downshift with pH increase. This phenomenon is confirmed and well‐explained with theoretical simulation. The study demonstrates that SERS is a sensitive tool to monitor minor structural changes due to local pH environment, and DFT calculations can be used to investigate Raman spectra changes associated with minor differences in molecular structure. Copyright © 2013 John Wiley & Sons, Ltd.
Raman spectroscopy utilizing Fisher‐based feature selection combined with Support Vector Machines for the characterization of breast cell lines
Authors: Fenn Michael B. , Pappu Vijay , Georgeiv Pando G. , Pardalos Panos M.
Published: May 2013

Raman spectroscopy has the potential to significantly aid in the research and diagnosis of cancer. The information dense, complex spectra generate massive datasets in which subtle correlations may provide critical clues for biological analysis and pathological classification. Therefore, implementing advanced data mining techniques is imperative for complete, rapid and accurate spectral processing. Numerous recent studies have employed various data methods to Raman spectra for classification and biochemical analysis. Although, as Raman datasets from biological specimens are often characterized by high dimensionality and low sample numbers, many of these classification models are subject to overfitting. Furthermore, attempts to reduce dimensionality result in transformed feature spaces making the biological evaluation of significant and discriminative spectral features problematic. We have developed a novel data mining framework optimized for Raman datasets, called Fisher‐based Feature Selection Support Vector Machines (FFS‐SVM). This framework provides simultaneous supervised classification and user‐defined Fisher criterion‐based feature selection, reducing overfitting and directly yielding significant wavenumbers from the original feature space. Herein, we investigate five cancerous and non‐cancerous breast cell lines using Raman microspectroscopy and our unique FFS‐SVM framework. Our framework classification performance is then compared to several other frequently employed classification methods on four classification tasks. The four tasks were constructed by an unsupervised clustering method yielding the four different categories of cell line groupings (e.g. cancer vs non‐cancer) studied. FFS‐SVM achieves both high classification accuracies and the extraction of biologically significant features. The top ten most discriminative features are discussed in terms of cell‐type specific biological relevance. Our framework provides comprehensive cellular level characterization and could potentially lead to the discovery of cancer biomarker‐type information, which we have informally termed ‘Raman‐based spectral biomarkers’. The FFS‐SVM framework along with Raman spectroscopy will be used in future studies to investigate in‐situ dynamic biological phenomena. Copyright © 2013 John Wiley & Sons, Ltd.
Verification of marine forecasts using an objective area forecast verification system
Authors: Sharpe Michael A.
Published: May 2013

Many meteorological service providers issue forecasts that contain short summary statements. These forecasts attempt to capture all the expected conditions during a forecast period. The area forecast verification system has been developed to verify these forecasts when they are issued in pre‐determined geographical areas. This system verifies forecasts by comparing them with gridded nowcast model analysis fields. Results are presented for the wind speed component of the shipping forecast and the inshore waters forecast. Both of these products are issued by the UK Met Office on behalf of the Maritime and Coastguard Agency. Like most summary forecasts these products contain hand written text. This text is carefully interpreted into a series of invariant sub‐periods. These sub‐periods are then compared to the nowcast model analysis fields. During each forecast sub‐period all available hourly nowcast model analyses are accumulated to create an observation distribution within that sub‐period. Verification is performed using a contingency table approach which is specifically designed to reflect the distribution formed by the observations within each sub‐period of the forecast. Various performance measures are calculated including the Gerrity skill score – which is weighted according to the priorities of the customer. Shipping forecasts issued during the 12 month period ending on 31 August 2011 had a proportion correct to within ± 1 Beaufort Force of 0.886 and a Gerrity skill score of 0.823. Inshore waters forecasts issued during this period had a proportion correct to within ± 1 Beaufort Force of 0.940 and a Gerrity skill score of 0.848. Analysis indicates that both forecasts tend to exaggerate the wind speeds and often neglect to include the lower Beaufort Force categories. © 2013 British Crown copyright, the Met Office. Published by John Wiley & Sons Ltd.