bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of hillslope topography on runoff response in a small catchment in the Fudoji Experimental Watershed, central Japan
Authors: Fujimoto Masamitsu , Ohte Nobuhito , Tani Makoto
Published: January 2011

We investigated the role of different hillslope units with different topographic characteristics on runoff generation processes based on field observations at two types of hillslopes (0·1 ha): a valley‐head (a convergent hillslope) and a side slope (a planar hillslope), as well as at three small catchments having two types of slopes with different drainage areas ranging from 1·9 to 49·7 ha in the Tanakami Mountains, central Japan. We found that the contribution of the hillslope unit type to small catchment runoff varied with the magnitude of rainfall. When the total amount of rainfall for a single storm event was < 35 mm, runoff in the small catchment was predominantly generated from the side slope. As the amount of rainfall increased (>35 mm), the valley‐head also began to contribute to the catchment runoff, adding to runoff from the side slope. Although the direct runoff from the valley‐head was greater than that from the side slope, the contribution from the side slope was quantitatively greater than that from the valley‐head due to the proportionally larger area occupied by the side slope in the small catchment. The storm runoff responses of the small catchments reflected the change in the runoff components of each hillslope unit as the amount of rainfall increased and rainfall patterns changed. However, similar runoff responses were found for the small catchments with different areas. The similarity of the runoff responses is attributable to overlay effects of different hillslope units and the similar composition ratios of the valley‐head and side slope in the catchments. This study suggests that the relative roles of the valley‐head and side slope are important in runoff generation and solute transport as the catchment size increases from a hillslope/headwater to a small catchment. Copyright © 2011 John Wiley & Sons, Ltd.
Development of a three‐dimensional watershed modelling system for water cycle in the middle part of the Heihe rivershed, in the west of China
Authors: Zhou Jian , Hu Bill X. , Cheng Guodong , Wang Genxu , Li Xin
Published: January 2011

A three‐dimensional numerical modelling system is developed to study transformation processes of water resources in alluvial fan and river basin along the middle reaches of the Heihe River Basin, Northwest China, an arid and semi‐arid region. Integrating land utilization, remote sensing and geographic information systems, we have developed a numerical modelling system that can be used to quantify the effects of land use and anthropogenic activities on the groundwater system as well as to investigate the interaction between surface water and groundwater. Various hydraulic measurements are used to identify and calibrate the hydraulic boundary conditions and spatial distributions of hydraulic parameters. In the modelling study, various water exchanges and human effects on the watershed system are considered. These include water exchange between surface water and groundwater, groundwater pumping, lateral water recharges from mountain areas, land utilization, and infiltration and evaporation in the irrigation and non‐irrigation areas. The modelling system provides a quantitative method to describe spatial and temporal distributions and transformations between various water resources, and it has application to other watersheds in arid and semi‐arid areas. Copyright © 2011 John Wiley & Sons, Ltd.
On the Panday and Huyakorn surface–subsurface hydrology test case: analysis of internal flow dynamics
Authors: Gaukroger Amy M. , Werner Adrian D.
Published: January 2011

A number of previous studies using models of integrated surface‐subsurface hydrology have adopted the Panday and Huyakorn (P&H) tilted V‐catchment test case (Panday S, Huyakorn PS. 2004. A fully coupled spatially distributed model for evaluating surface/subsurface flow. Advances in Water Resources 27: 361–382) to show inter‐code comparability. The P&H test case is used to evaluate models that simulate a broad range of hydrological processes, and yet only the catchment outflow hydrograph has been presented as verification of the consistency between codes. Therefore, a more comprehensive evaluation of the surface‐subsurface hydrology of the P&H case is needed. This study explores the internal catchment functioning of the P&H case, using the popular catchment simulator MODHMS. The processes leading to streamflow generation in the model are illustrated, including separation of overland flow (OLF) and groundwater discharge to the stream. The results identify non‐physical flow processes due to the problem set‐up, and modifications to the P&H case are suggested that include changes to stream roughness and incision of the stream channel to overcome these shortcomings. A modified P&H case produced more plausible transfers between OLF and the stream, and an increased groundwater discharge to the stream (6·5% of streamflow in the modified case compared to 0·5% in the original case). Despite changes to internal flow processes, near‐identical outflow hydrographs were obtained, showing the importance of considering and comparing internal flow processes when using surface‐subsurface hydrology test cases to evaluate integrated hydrological simulators. Copyright © 2011 John Wiley & Sons, Ltd.
A complementary relationship evaporation model referring to the Granger model and the advection–aridity model
Authors: Han Songjun , Hu Heping , Yang Dawen , Tian Fuqiang
Published: January 2011

A complementary relationship evaporation model has been proposed and verified based on evaluations of the advection–aridity model and the Granger's complementary relationship model (Granger model) in dimensionless forms. Normalized by Penman potential evaporation, the Granger model and the advection–aridity model have been transformed into similar dimensionless forms. Evaporation ratio (ratio of actual evaporation to Penman potential evaporation) has been expressed as a function of dimensionless variable based on radiation and atmospheric conditions. Similar dimensionless variables for the different functions have been used in the two models. By referring to the dimensionless variable from the advection–aridity model and the function from the Granger model, a new model to estimate actual evaporation was proposed. The performance of the new model has been validated by the observed data from four sites under different land covers. The new model is an enhanced Granger model with better evaporation prediction over the aforementioned different land covers. It also offers more stable optimized parameters in a grassland site than the Granger model. The new model somewhat approximates the advection–aridity model under neither too wet nor too dry conditions, but without its system bias. Copyright © 2011 John Wiley & Sons, Ltd.
Quantifying the effects of climate variability and human activities on runoff from the Laohahe basin in northern China using three different methods
Authors: Jiang Shanhu , Ren Liliang , Yong Bin , Singh V. P. , Yang Xiaoli , Yuan Fei
Published: January 2011

Much attention has recently been focused on the effects that climate variability and human activities have had on runoff. In this study, these effects are quantified using three methods, namely, multi‐regression, hydrologic sensitivity analysis, and hydrologic model simulation. A conceptual framework is defined to separate the effects. As an example, the change in annual runoff from the semiarid Laohahe basin (18 112 km2) in northern China was investigated. Non‐parametric Mann‐Kendall test, Pettitt test, and precipitation‐runoff double cumulative curve method were adopted to identify the trends and change‐points in the annual runoff from 1964 to 2008 by first dividing the long‐term runoff series into a natural period (1964–1979) and a human‐induced period (1980–2008). Then the three quantifying methods were calibrated and calculated, and they provided consistent estimates of the percentage change in mean annual runoff for the human‐induced period. In 1980–2008, human activities were the main factors that reduced runoff with contributions of 89–93%, while the reduction percentages due to changes in precipitation and potential evapotranspiration only ranged from 7 to 11%. For the various effects at different durations, human activities were the main reasons runoff decreased during the two drier periods of 1980–1989 and 2000–2008. Increased runoff during the wetter period of 1990–1999 is mainly attributed to climate variability. This study quantitatively separates the effects of climate variability and human activities on runoff, which can serve as a reference for regional water resources assessment and management. Copyright © 2011 John Wiley & Sons, Ltd.
Polarizable protein packing
Authors: Ng Albert H. , Snow Christopher D.
Published: January 2011

To incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third‐order provides a fair approximation to the full energy while maintaining tractability. We represent the polarizable packing problem for protein G as a hypergraph and solve for optimal rotamers with the FASTER combinatorial optimization algorithm. These approximate energy models can be improved to high accuracy [root mean square deviation (rmsd) < 1 kJ mol−1] via ridge regression. The resulting trained approximations are used to efficiently identify new, low‐energy solutions. The approach is general and should allow combinatorial optimization of other many‐body problems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Theoretical mechanistic study on the reaction of CN radical with HNCN
Authors: Wu Nan‐Nan , He Chao‐Zheng , Duan Xue‐Mei , Liu Jing‐Yao
Published: January 2011

The mechanism for the reaction of the cyanogen radical (CN) with the cyanomidyl radical (HNCN) has been investigated theoretically. The electronic structure information of the singlet and triplet potential energy surfaces (PESs) is obtained at the B3LYP/6‐311+G(3df,2p) level, and the single‐point energies are refined at the CCSD(T)/6‐311+G(3df,2p) level as well as by multilevel MCG3‐MPWB method. The calculations show that the C atom of CN additions to middle‐ and end‐N atoms of HNCN are two barrierless association processes leading to the energy‐rich intermediates IM1 HN(CN)CN and IM2 HNCNCN, respectively, on the singlet PES. The higher barriers of the subsequent isomerization and dissociation channels from IM1 and IM2 indicate that these two intermediates, which have considerably thermodynamic and kinetic stability, are the dominant product at high pressure. While at low pressure, the most favorable product is P2H + NCNCN, which will be formed from both IM1 and IM2 via direct dissociation processes by the H‐N bond rupture, and the secondary feasible product is P4HCN +1NCN, while P5HCCN + N2and P6HCNC + N2are the least competitive products. On the triplet PES, P14NCNC + HN may be a comparable competitive product at high temperature. In addition, the comparison between the mechanisms of the CN + HNCN and OH + HNCN reactions is made. The present results will enrich our understanding of the chemistry of the HNCN radical in combustion processes and interstellar space. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Post traumatic myositis ossificans: Sonographic findings
Authors: Abate Michele , Salini Vincenzo , Rimondi Eugenio , Errani Costantino , Alberghini Marco , Mercuri Mario , Pelotti Patrizia
Published: January 2011

Purpose.

The aim of this paper is to describe the sonographic (US) features of post traumatic myositis ossificans (PTMO).

Methods.

Fifteen patients with histopathological diagnosis of PTMO were included. The following US parameters were evaluated: presence of a mass, calcifications, power Doppler signals, and relationship with adjacent structures.

Results.

Five patients (33.3%) were diagnosed as early PTMO and 10 (66.6%) as mature PTMO. In both early and mature PTMO, US showed an oval hypoechoic mass, without infiltrative borders, located in a muscular belly. In the early phase, a center of less echogenicity was observed, associated with an outer sheet‐like hyperechoic peripheral rim, while, in the mature phase, peripheral calcification created more reflections and distal acoustic shadowing was observed.

Conclusions.

US is highly sensitive in the detection of PTMO, helps differentiate between PTMO and malignant soft tissue tumors, and can be used for follow‐up of the lesions. © 2011 Wiley Periodicals, Inc. J Clin Ultrasound, 2011;
Studying disulfide bond rearrangement by MALDI‐RTOF PSD and MALDI‐TOF/RTOF high‐energy CID (20 keV) experiments of peptides derived from ammodytoxins
Authors: Brgles Marija , Kurtović Tihana , Halassy Beata , Allmaier Günter , Marchetti‐Deschmann Martina
Published: January 2011

Ammodytoxins (Atxs) are presynaptically neurotoxic phospholipases present in Vipera ammodytes ammodytes snake venom. Atxs show a high sequence homology and contain 14 cysteines which form seven biologically relevant disulfide bridges—connecting non‐neighboring cysteines. Formic acid cleavage was performed to confirm protein sequences by MALDI RTOF MS and resulted in 95.6% sequence coverage exhibiting only few formylations. Cysteine‐containing peptides showed adjacent signals 2 and/or 4 Da lower (according to the number of cysteines present in the peptide) than the theoretical molecular weight indicating disulfide bridge rearrangement. Post‐source decay (PSD) and high‐energy collision‐induced dissociation (CID) at 20 keV experiments showed fragmentation pattern unique for the reduced, thiol group containing and the oxidized, disulfide bridge harboring peptides. Besides typical low‐energy fragment ions observed during PSD experiments (a‐, b‐, y‐type ions), additional high‐energy fragment ions (c‐, x‐, w‐, d‐type and internal fragments) of significant intensity were generated during fragmentation at 20 keV. In the case of charge directing N‐ and C‐termini, x‐ and w‐type ions were also observed during PSD. Good and up to complete sequence coverage was achieved for all studied peptides from Atxs in the case of high‐energy CID, whereas PSD lacked information particularly for larger peptides. Copyright © 2011 John Wiley & Sons, Ltd.
Effects of the net charge on abundance and stability of supramolecular surfactant aggregates in gas phase
Authors: Bongiorno David , Ceraulo Leopoldo , Giorgi Gianluca , Indelicato Serena , Ferrugia Mirella , Ruggirello Angela , Liveri Vincenzo Turco
Published: January 2011

Self‐assembling of amphiphilic molecules under electrospray ionization (ESI) conditions is characterized by quite unexpected phenomenology. The noticeable differences with respect to the condensed phase are attributable to the absence of the surfactant‐solvent interactions, the presence of net charge in the aggregates, and the strong deviation from equilibrium conditions. Aiming to investigate the effects of the net charge on abundance and stability of supramolecular surfactant aggregates, positively and negatively charged aggregates of sodium bis(2‐ethylhexyl)sulfosuccinate (AOT) and sodium methane sulfonate (MetS), butane sulfonate (ButS) and octane sulfonate (OctS) have been studied by ESI mass spectrometry, energy resolved mass spectrometry and density functional theory calculations. The negatively charged aggregates are found to be less stable than their positive counterparts. The results are consistent with a self‐assembling pattern dominated by electrostatic interactions involving the counterions and head groups of the investigated amphiphilic compounds while the alkyl chains point outwards, protecting the aggregates from unlimited growth processes. Copyright © 2011 John Wiley & Sons, Ltd.
Simultaneous determination of raltegravir and raltegravir glucuronide in human plasma by liquid chromatography–tandem mass spectrometric method
Authors: Wang Ling‐Zhi , Lee Lawrence Soon‐U , Thuya Win‐Lwin , Soon Gaik Hong , Kong Li‐Ren , Nye Pei‐Ling , Deoon Lee Edmund Jon , Flexner Charles , Goh Boon‐Cher
Published: January 2011

Raltegravir is a highly efficacious inhibitor of HIV integrase. Large pharmacokinetic variability has been reported in clinical trials and this could be due to glucuronidation of raltegravir, the only reported metabolism pathway. In order to precisely evaluate and monitor the raltegravir and raltegravir glucuronide simultaneously, a novel, sensitive and robust liquid chromatography‐tandem mass spectrometric method was developed and validated for simultaneous determination of raltegravir and raltegravir glucuronide in human plasma. A simple protein precipitation with acetonitrile was utilized for plasma sample preparation prior to analysis. Baseline chromatographic separation was achieved on a ZORBAX Eclipse XDB‐C8 using gradient elution mode. The run time was 9 min at a constant flow rate of 0.4 ml/min. The mass spectrometer was operated under a positive electrospray ionization condition. Excellent linearity (r2 ≥ 0.9997) was achieved for raltegravir and raltegravir glucuronide in the range of 2–2000 nmol/l. The average recovery of raltegravir and raltegravir glucuronide was 105.8% and 102.2%, respectively. The precision (coefficient of variation) was 1.6–6.6% for raltegravir and 2.1–6.9 for raltegravir glucuronide, respectively. The accuracy was 98.6–106.1% for raltegravir and 96.3–100.3% for raltegravir glucuronide. The plasma samples were tested to be stable after nine freeze–thaw cycles and exposure to room temperature for 24 h. This well‐validated assay was applied for the quantification of raltegravir and raltegravir glucuronide in plasma samples within 24 h after a single oral dose of 400 mg raltegravir in six healthy subjects. Copyright © 2011 John Wiley & Sons, Ltd.
Alternative CHCA‐based matrices for the analysis of low molecular weight compounds by UV‐MALDI‐tandem mass spectrometry
Authors: Porta Tiffany , Grivet Chantal , Knochenmuss Richard , Varesio Emmanuel , Hopfgartner Gérard
Published: January 2011

Analysis of low molecular weight compounds (LMWC) in complex matrices by vacuum matrix‐assisted laser desorption/ionization (MALDI) often suffers from matrix interferences, which can severely degrade limits of quantitation. It is, therefore, useful to have available a range of suitable matrices, which exhibit complementary regions of interference. Two newly synthesized α‐cyanocinnamic acid derivatives are reported here; (E)‐2‐cyano‐3‐(naphthalen‐2‐yl)acrylic acid (NpCCA) and (2E)‐3‐(anthracen‐9‐yl)‐2‐cyanoprop‐2enoic acid (AnCCA). Along with the commonly used α‐cyano‐4‐hydroxycinnamic acid (CHCA), and the recently developed 4‐chloro‐α‐cyanocinnamic acid (Cl‐CCA) matrices, these constitute a chemically similar series of matrices covering a range of molecular weights, and with correspondingly differing ranges of spectral interference. Their performance was compared by measuring the signal‐to‐noise ratios (S/N) of 47 analytes, mostly pharmaceuticals, with the different matrices using the selected reaction monitoring (SRM) mode on a triple quadrupole instrument equipped with a vacuum MALDI source. AnCCA, NpCCA and Cl‐CCA were found to offer better signal‐to‐noise ratios in SRM mode than CHCA, but Cl‐CCA yielded the best results for 60% of the compounds tested. To better understand the relative performance of this matrix series, the proton affinities (PAs) were measured using the kinetic method. Their relative values were: AnCCA > CHCA > NpCCA > Cl‐CCA. This ordering is consistent with the performance data. The synthesis of the new matrices is straightforward and they provide (1) tunability of matrix background interfering ions and (2) enhanced analyte response for certain classes of compounds. Copyright © 2011 John Wiley & Sons, Ltd.
Development and validation of a liquid chromatography–tandem mass spectrometry method for the quantitation of synthetic cannabinoids of the aminoalkylindole type and methanandamide in serum and its application to forensic samples
Authors: Dresen Sebastian , Kneisel Stefan , Weinmann Wolfgang , Zimmermann Ralf , Auwärter Volker
Published: January 2011

After the discovery of synthetic cannabimimetic substances in ‘Spice’‐like herbal mixtures marketed as ‘incense’ or ‘plant fertilizer’ the active compounds have been declared as controlled substances in several European countries. As expected, a monitoring of new herbal mixtures which continue to appear on the market revealed that shortly after control measures have been taken by legal authorities, other compounds were added to existing mixtures and to new products. Several compounds of the aminoalkylindole type have been detected so far in herbal mixtures but still their consumption cannot be detected by commonly used drug‐screening procedures, encouraging drug users to substitute cannabis with those products. There is a increasing demand on the part of police authorities, hospitals and psychiatrists for detection and quantification of synthetic cannabinoids in biological samples originating from psychiatric inpatients, emergency units or assessment of fitness to drive. Therefore, a liquid chromatography–tandem mass spectrometry method after liquid–liquid extraction for the quantitation of JWH‐015, JWH‐018, JWH‐073, JWH‐081, JWH 200, JWH‐250, WIN 55,212‐2 and methanandamide and the detection of JWH‐019 and JWH‐020 in human serum has been developed and fully validated according to guidelines for forensic toxicological analyses. The method was successfully applied to 101 serum samples from 80 subjects provided by hospitals, detoxification and therapy centers, forensic psychiatric centers and police authorities. Fifty‐seven samples or 56.4% were found positive for at least one aminoalkylindole. JWH‐019, JWH‐020, JWH‐200, WIN 55,212‐2 and methanandamide were not detected in any of the analyzed samples. Copyright © 2011 John Wiley & Sons, Ltd.
Prevalence of HBV infection among different HIV‐risk groups in Hai Phong, Vietnam
Authors: Nguyen Cuong Hung , Ishizaki Azumi , Chung Phan Thi Thu , Hoang Huyen Thi , Nguyen Trung Vu , Tanimoto Tomoaki , Lihana Raphael , Matsushita Kaori , Bi Xiuqiong , Van Pham Thuc , Ichimura Hiroshi
Published: January 2011

Hepatitis B virus (HBV) infection in Hai Phong, northern Vietnam, was characterized by analyzing the prevalence and genotype distribution of HBV as well as co‐infection with human immunodeficiency virus type 1 (HIV‐1) among five different risk groups for HIV infection. Plasma samples were collected from intravenous drug users (n = 760, anti‐HIV‐1 antibody positive rate: 35.9%), female sex workers (FSWs; n = 91, 23.1%), seafarers (n = 94, 0%), pregnant women (n = 200, 0.5%), and blood donors (n = 210, 2.9%) in 2007 [Ishizaki et al. (2009): AIDS Res Hum Retroviruses 25:175–182]. Samples were screened for the hepatitis B surface antigen (HBsAg) and anti‐HBs antibody and analyzed genetically. The cumulative HBV incidence rate (HBsAg + anti‐HBs) was 53.2% (10.7 + 42.5%) in intravenous drug users, 51.6% (11.0 + 40.6%) in FSWs, 54.3% (9.6 + 44.7%) in seafarers, 50.5% (12.5 + 38.0%) in pregnant women, and 51.0% (18.1 + 32.9%) in blood donors; there was no significant difference among these groups. Of 163 HBsAg‐positive samples, 113 could be analyzed genetically. Phylogenetic analysis, based on the preS1 region, revealed genotype B4 was most prevalent (90/113; 79.6%), followed by C1 (17.7%), I1 (1.8%), and B2 (0.9%). There was no significant difference in HBV genotype distribution among different HIV infection‐risk groups. The prevalence of HBsAg was 10.3% (31/301) in HIV‐1‐infected individuals and 12.5% (132/1,054) in non‐HIV‐1‐infected individuals, which was not significant. In addition, no significant difference in HBV genotype distribution was observed between HBV/HIV‐1 co‐infected and HBV mono‐infected groups. These results suggest that, although HBV and HIV‐1 share modes of transmission, major transmission routes of HBV have been different from those of HIV‐1 in Hai Phong, Vietnam. J. Med. Virol. 83:399–404, 2011. © 2011 Wiley‐Liss, Inc.
Target epitopes of HTLV‐1 recognized by class I MHC‐restricted cytotoxic T lymphocytes in patients with myelopathy and spastic paraparesis and infected patients with autoimmune disorders
Authors: Kozako Tomohiro , Akimoto Masaki , Toji Shingo , White Yohann , Suzuki Susumu , Arima Takehiro , Suruga Yukio , Matsushita Kakushi , Shimeno Hiroshi , Soeda Shinji , Kubota Ryuji , Izumo Shuji , Uozumi Kimiharu , Arima Naomichi
Published: January 2011

Human T‐cell lymphotropic virus type I (HTLV‐1) causes adult T‐cell leukemia/lymphoma and HTLV‐1‐associated myelopathy/tropical spastic paraparesis (HAM/TSP). The different patterns of clinical diseases are thought to be linked to immunogenetic host factors. A variety of autoimmune diseases, such as Sjögren's syndrome, have been reported in persons infected with HTLV‐1, although the precise relationship between these disorders and HTLV‐1 infection remains unknown. There is no report on the repertoire of HTLV‐1‐specific CD8+ T‐cells in HAM/TSP patients or carriers with autoimmune diseases, both characterized by an abnormal immune state. In this study, to characterize HTLV‐1‐specific CD8+ T‐cells in asymptomatic HTLV‐1 carriers, HAM/TSP patients and carriers with autoimmune diseases, we examined the frequency and diversity of HTLV‐1‐specific CD8+ T‐cells using HTLV‐1 tetramers. HTLV‐1 Env‐specific CD8+ T‐cells were significantly more frequent in HAM/TSP and carriers with autoimmune diseases compared with asymptomatic HTLV‐1 carriers, while the frequency of HTLV‐1 Tax‐specific CD8+ T‐cells was not significantly different among them. CD8+ cells binding to HTLV‐1 Tax tetramers in carriers with autoimmune diseases were significantly reduced compared with HAM/TSP patients. This study demonstrates the importance of CD8+ T‐cells recognizing HTLV‐1 Env‐tetramers in HAM/TSP patients and carriers with autoimmune diseases, thereby suggesting that the diversity, frequency and repertoire of HTLV‐1 Env‐specific CD8+ T‐cell clones may be related to the hyperimmune response in HAM/TSP and carriers with autoimmune diseases, although different immunological mechanisms may mediate the hyperimmunity in these conditions. J. Med. Virol. 83:501–509, 2011. © 2011 Wiley‐Liss, Inc.
KSHV DNA viremia correlates with low CD4+ cell count in Italian Males at the time of diagnosis of HIV infection
Authors: Parisi Saverio G. , Boldrin Caterina , Andreis Samantha , Ferretto Roberto , Fuser Rodolfo , Malena Marina , Manfrin Vinicio , Panese Sandro , Scaggiante Renzo , Dori Luca , Sarmati Loredana , Biasolo Maria A. , Nicastri Emanuele , Andreoni Massimo , Cruciani Mario , Palù Giorgio
Published: January 2011

To evaluate the relevance and the virological and immunological markers of Kaposi sarcoma herpesvirus 8 (KSHV) viremia in Italian male patients at the time of diagnosis of infection with HIV‐1, 481 men infected with HIV were recruited consecutively. The presence of KSHV DNA was evaluated in peripheral blood mononuclear cells (PBMCs) and in plasma and correlated with demographic and viro‐immunological parameters. Seventy‐four patients had KSHV DNA detected in PBMCs. By univariate analysis, the presence of KSHV DNA was associated significantly with unprotected homosexual relationships (P = 0.003) and it was significantly higher in patients with CD4+ cell <350 (P = 0.025). By multivariate analysis, homosexual relationships were associated independently with KSHV DNA in PBMCs (OR: 3.25; 95% CI: 1.1–9.7; P = 0.035). Among the 74 patients with KSHV DNA detected in PBMCs, plasma samples from 60 were analyzed and 33 were positive for KSHV DNA. The CD4+ cell counts and percentages were significantly lower in patients with KSHV DNA in both PBMCs and plasma as compared to patients with only KSHV DNA in PBMCs (P = 0.006 and P = 0.019, respectively). Among the patients with KSHV DNA detected in PBMCs, all 13 patients with CD4+ cells count <200 had detectable levels of KSHV in their plasma. By multivariate analysis adjusted for the epidemiologic and virological parameters, low CD4+ cell count was the only independent variable associated with the presence of KSHV DNA in plasma (OR, 0.001; 95% CI: <0.001–0.001; P = 0.03). In HIV‐positive antiretroviral therapy‐naïve males, KSHV active replication as detected by KSHV DNA in plasma was associated significantly with low CD4+ cell count. J. Med. Virol. 83:384–390, 2011. © 2011 Wiley‐Liss, Inc.
Virological and clinical characteristics on reactivation of occult hepatitis B in patients with hematological malignancy
Authors: Sugauchi Fuminaka , Tanaka Yasuhito , Kusumoto Shigeru , Matsuura Kentaro , Sugiyama Masaya , Kurbanov Fuat , Ueda Ryuzo , Mizokami Masashi
Published: January 2011

The virological characteristics of hepatitis B virus (HBV) implicated in the reactivation of occult hepatitis B in patients who have received hematopoietic stem‐cell transplantation or chemotherapy for the hematological malignancy are not well defined. Twenty‐eight HBsAg‐negative patients who received hematopoietic stem‐cell transplantation and 138 HBsAg‐negative patients treated for malignant lymphoma with chemotherapy including rituximab were enrolled. Three of the 28 patients (10.7%) received hematopoietic stem‐cell transplantation and one of the 138 (0.72%) patients treated for malignant lymphoma with chemotherapy developed de novo HBV hepatitis. Anti‐HBc was detected in four and anti‐HBs in two patients. Genotype Bj was detected in two and C in two of they all possessed wild‐type sequences in the core promoter region. A precore stop mutation (A1896) was detected in a patient with genotype Bj who developed fulminant hepatic failure. HBV DNA was detected in pretreatment HBsAg‐negative samples in two of four patients, and the HBV genome sequence identified from sera before chemotherapy and at the time of de novo HBV hepatitis showed 100% homology. In an in vitro replication model, genotype Bj with the A1896 clone obtained from a fulminant case had a replication level much higher than clones obtained from de novo hepatitis B patients with genotype Bj or C with G1896. In conclusion, this is the first report demonstrating de novo hepatitis B from the reactivation of occult HBV infection confirmed by molecular evolutional analysis. The fulminant outcome of HBV reactivation can be associated with genotype Bj exhibiting high replication due to the A1896 mutation. J. Med. Virol. 83:412–418, 2011. © 2011 Wiley‐Liss, Inc.
A first report on the characterization of rotavirus strains in Sierra Leone
Authors: Jere K.C. , Sawyerr T. , Seheri L.M. , Peenze I. , Page N.A. , Geyer A. , Steele A.D.
Published: January 2011

In an effort to reduce the high mortalities associated with rotavirus infections, a number of African countries are considering introducing human rotavirus vaccines. The demonstrated safety and efficacy of the live‐attenuate human rotavirus vaccines in several clinical trials worldwide has accelerated such initiatives. Although the percentage‐mortality rates for Sierra Leone are top of the list for rotavirus‐associated deaths in Africa, no study has reported the prevalent strains circulating within this country. In this study, stool specimens were collected from 128 Sierra Leonean children presenting with diarrhea in 2005. Almost 37.5% (48/128) were rotavirus positive by EIA, of which 89.6% (43/48) revealed a short electropherotype, and a further 6.98% (3/48) could not be assigned a PAGE pattern. Genotyping analysis revealed G2P[4] (30.23%), G2P[6] (13.95%), G8P[6] (11.63%), G2P[8] (4.65%), G8P[4] (4.65%), and G8P[8] (2%) strains. About 11% were only assigned VP7 genotypes (G2), while 20.9% had mixed G and P types. The frequent detection of G2 rotaviruses could be of concern considering data generated from some studies that suggests lower efficacy of Rotarix® vaccine against G2 rotaviruses. This underscores the need for extensive and continuous regional strain surveillance to support rotavirus vaccines introduction and guide future vaccine development efforts. Such information will be useful before considering administration of specific rotavirus vaccine candidates in countries like Sierra Leone where little is known about circulating rotavirus strains. J. Med. Virol. 83:540–550, 2011. © 2011 Wiley‐Liss, Inc.
Sequences in the interferon sensitivity‐determining region and core region of hepatitis C virus impact pretreatment prediction of response to PEG‐interferon plus ribavirin: Data mining analysis
Authors: Kurosaki Masayuki , Sakamoto Naoya , Iwasaki Manabu , Sakamoto Minoru , Suzuki Yoshiyuki , Hiramatsu Naoki , Sugauchi Fuminaka , Tamori Akihiro , Nakagawa Mina , Izumi Namiki
Published: January 2011

The aim of the present study was to clarify the significance of viral factors for pretreatment prediction of sustained virological response to pegylated‐interferon (PEG‐IFN) plus ribavirin (RBV) therapy for chronic hepatitis C using data mining analysis. Substitutions in the IFN sensitivity‐determining region (ISDR) and at position 70 of the HCV core region (Core70) were determined in 505 patients with genotype 1b chronic hepatitis C treated with PEG‐IFN plus RBV. Data mining analysis was used to build a predictive model of sustained virological response in patients selected randomly (n = 304). The reproducibility of the model was validated in the remaining 201 patients. Substitutions in ISDR (odds ratio = 9.92, P < 0.0001) and Core70 (odds ratio = 1.92, P = 0.01) predicted sustained virological response independent of other covariates. The decision‐tree model revealed that the rate of sustained virological response was highest (83%) in patients with two or more substitutions in ISDR. The overall rate of sustained virological response was 44% in patients with a low number of substitutions in ISDR (0–1) but was 83% in selected subgroups of younger patients (<60 years), wild‐type sequence at Core70, and higher level of low‐density lipoprotein cholesterol (LDL‐C) (≥120 mg/dl). Reproducibility of the model was validated (r2 = 0.94, P < 0.001). In conclusion, substitutions in ISDR and Core70 of HCV are significant predictors of response to PEG‐IFN plus RBV therapy. A decision‐tree model that includes these viral factors as predictors could identify patients with a high probability of sustained virological response. J. Med. Virol. 83:445–452, 2011. © 2011 Wiley‐Liss, Inc.
Uncultured bacterial diversity in tropical maize (Zea mays L.) rhizosphere
Authors: Chauhan Puneet Singh , Chaudhry Vasvi , Mishra Sandhya , Nautiyal Chandra Shekhar
Published: January 2011

Structure of maize (Zea mays L.) rhizosphere bacteria was evaluated to explore the feasibility of identifying novel rhizosphere bacteria using culture‐independent method based on direct amplification and analysis of 16S rRNA gene (rRNA) sequences and especially to obtain a better understanding of bacterial community structure and diversity from maize. A total of 274 sequences were analyzed and assigned 48.00% Proteobacteria, 10.30% Actinobacteria, 9.90% Bacteroidetes, 6.60% Verrucomicrobia, 4.80% Acidobacteria, 1.80% Firmicutes, 1.50% Chloroflexi, 1.50% TM7, 1.10% Deinococcus‐Thermus, 0.70% Planctomycetes, 0.70% Gemmatimonadetes and 0.40% Cyanobacteria. Economically important phyla Actinobacteria was second most dominant group after Proteobacteria, in our clone library. It would be interesting to hypothesize that root exudates from maize rhizosphere favors growth of Actinobacteria like microbes to eliminate pathogenic bacteria and decompose plant matter, for enhanced plant and soil health. An additional 12.8% of clone library (35 operational taxonomical units (OTUs) from 43 clones) with less than 94% similarity to any GenBank sequence could not be assigned to any known phylum and may represent unidentified bacterial lineages and suggests that a large amount of the rhizobacterial diversity remains to be characterized by culturing. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Isolation and phosphate‐solubilizing ability of a fungus, Penicillium sp. from soil of an alum mine
Authors: Chai Bo , Wu Yan , Liu Pengming , Liu Biao , Gao Meiying
Published: January 2011

The use of microorganisms to solubilize elemental phosphorus from insoluble rock phosphate is a promising method to greatly reduce not only environmental pollution but also production costs. Phosphate‐solubilizing microorganisms were isolated from soils in China, and a fungus strain (PSM11‐5) from a soil sample from an alum mine, with the highest phosphate solubilization potential, was selected and identified as a Penicillium sp. Strain PSM11‐5 could grow in buffered medium with pH values between 3.0 and 8.0 and showed phosphate solubilizing activity at pH values from 5.0 to 8.0. It also exhibited a degree of tolerance to the heavy metal ions, Cd2+, Co2+, and Cr6+. PSM11‐5 could rapidly solubilize tricalcium phosphate, and a high phosphate‐solubilizing efficiency of 98% was achieved in an optimized medium. The strain could solubilize rock phosphate and aluminum phosphate with a solubilizing efficiency of approximately 74.5%, but did not solubilize iron phosphate. Solubilization of phosphate depended on acidification. Analysis of PSM11‐5 culture supernatants by capillary electrophoresis showed that tricalcium phosphate was solubilized to PO43– and Ca2+, and that the organic acid produced by the fungus was mainly gluconic acid at approximately ca. 13 g l–1. In addition, PSM11‐5 produced ca. 830 mg l–1 of citric acid when it was used to solubilize rock phosphate. These excellent properties of strain PSM11‐5 suggest that the fungus has potential for agricultural and industrial utilization. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Screening of promoters from rhizosphere metagenomic DNA using a promoter‐trap vector and flow cytometric cell sorting
Authors: Lee Se Hee , Kim Jeong Myeong , Lee Hyo Jung , Jeon Che Ok
Published: January 2011

We constructed a facilitative and efficient promoter‐trap vector, pCM‐EGFP, for capturing and analyzing functional promoters from environmental DNA. The pCM‐EGFP vector showed good chloramphenicol sensitivity and no enhanced green fluorescent protein (EGFP) gene expression. Promoter libraries were constructed for screening promoters responding to naringenin, a key molecule released from plant roots. After electroporation, E. coli transformants were incubated in LB broth containing chloramphenicol (10 μg/ml) to select against transformants with no cloned promoter. E. coli cells were sorted using flow cytometry without naringenin, and then sorted again with high fluorescence after incubation in LB broth with naringenin (1 mM) at 28 °C for 12 h. The inducible properties of approximately 400 sorted cells were evaluated, with most cells showing only strong EGFP gene expression without inducible properties. Two clones (5‐4E and 15‐3D) displayed naringenin inducibility, and both contained a promoter bounded by a TetR‐family regulator. The regulator knock‐out mutant of the 5‐4E clone lost its ability to be induced by naringenin. In conclusion, the pCM‐EGFP vector may be used as an efficient promoter‐trap vector and a combination of the vector with flow cytometric cell sorting was demonstrated to be an useful method for screening promoters responding to specific conditions or inducers. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Determination of polar impurities in biodiesels using solid‐phase extraction and gas chromatography–mass spectrometry
Authors: Yang Zeyu , Hollebone Bruce P. , Wang Zhendi , Yang Chun , Landriault Mike
Published: January 2011

This paper reports on a method for development and validation for simultaneous characterization and determination of oxygenated polar impurities – free fatty carboxylic acids (FFAs), partial glycerides (monoacylglycerides, MGs), residual glycerol and free sterols – in various biodiesels based on the combination of solid‐phase extraction (SPE), silylation and GC/MS technologies. The effects of various SPE and silylation conditions on the method recoveries were evaluated. Using this integrated SPE‐GC/MS method, 38 target polar compounds (13 FFAs, 17 glycerides and 8 sterols) in 9 biodiesels derived from 4 different feedstocks were successfully separated and quantified. It was found that the carbon chain length of FFAs was ranged from C6 to C24, with C16 and C18 being the most abundant in all biodiesels. The total FFAs concentration was consistent with the acid values (AVs) measured by standard method ASTM D974‐04. MG congeners with carbon number of 18 (mono‐C18) were most abundant in the biodiesel samples, followed by mono‐C16 and free glycerol. β‐Sitosterol and campesterol were found to be the prevailing phytosterols in all pure vegetable oil‐based biodiesels, while brassicasterol and stigmasterol was only significant in the biodiesel from canola oil and soybean oil, respectively, and abundant cholesterol was only detected in animal fat‐based biodiesels.
Exploring the elution mechanism of selenium species on liquid chromatography
Authors: Tsopelas Fotios , Tsantili‐Kakoulidou Anna , Ochsenkühn‐Petropoulou Maria
Published: January 2011

In the present work, the chromatographic behavior of eight selenium species, namely selenites (Se(IV)), selenates (Se(VI)), seleno‐DL‐methionine (Se‐Met), selenocystine (Se‐Cyst), selenocystamine (Se‐CM), selenourea (Se‐U), dimethylselenide ((CH3)2Se) and dimethyldiselenide ((CH3)2Se2), was investigated under different stationary and mobile phase conditions, in an effort to unravel secondary interferences in their underlying elution mechanism. For this purpose, two end‐capped and a polar‐embedded reversed‐phase stationary phases were employed using different mobile phase conditions. Retention factors (log kw) were compared with octanol–water distribution coefficients (log D) as well as with log kw values on two immobilized artificial membrane (IAM) columns and two immobilized artificial plasma proteins stationary phases, obtained in our previous work. The role of electrostatic interactions was confirmed by introducing the net charge of the investigated Se species as an additional term in the log kw/log D interrelation, which in most cases proved to be statistically significant. Principal component analysis of retention factors on all stationary phases and octanol–water log D values, however, showed that the elution of the investigated selenium species is mainly governed by partitioning mechanism under all different chromatographic conditions, while the pH of the mobile phase and the special column characteristics have only a minor effect.
Application of indicator systems for monitoring and assessment of desertification from national to global scales
Authors: Sommer S. , Zucca C. , Grainger A. , Cherlet M. , Zougmore R. , Sokona Y. , Hill J. , Della Peruta R. , Roehrig J. , Wang G.
Published: January 2011

This paper suggests how the United Nations Convention to Combat Desertification (UNCCD) community can progressively make use of a flexible framework of analytical approaches that have been recently developed by scientific research. This allows a standardized but flexible use of indicator sets adapted to specific objectives or desertification issues relevant for implementing the Convention. Science has made progress in understanding major issues and proximate causes of dryland degradation such that indicator sets can be accordingly selected from the wealth of existing and documented indicator systems. The selection and combination should be guided according to transparent criteria given by existing indicator frameworks adapted to desertification conceptual frameworks such as the Dryland Development Paradigm and can act as a pragmatic entry point for selecting area‐ and theme‐specific sets of indicators from existing databases. Working on different dryland sub‐types through a meaningful stratification is proposed to delimit and characterize affected areas beyond the national level. Such stratification could be achieved by combining existing land use information with additional biophysical and socio‐economic data sets, allowing indicator‐based monitoring and assessment to be embedded in a framework of specific dryland degradation issues and their impacts on key ecosystem services. Copyright © 2011 John Wiley & Sons, Ltd.
Q‐switched and modelocked all‐fiber lasers based on advanced acousto‐optic devices
Authors: Cuadrado‐Laborde C. , Díez A. , Cruz J.L. , Andrés M.V.
Published: January 2011

The interest in all‐fiber lasers is stimulated by the inherent advantages they have over bulk lasers in aspects such as heat dissipation and robustness. The performance of Q‐switched and modelocked fiber lasers can benefit enormously from the development of all‐fiber configurations. A fiber laser with strictly all‐fiber components can fulfil the requirements of mechanical stability, low maintenance, enhanced power efficiency, simplified assembly process, and low cost. In this framework, recent developments infiber acousto‐optic devices are reviewed that have demonstrated new possibilities for actively Q‐switched distributed feedback fiber lasers, modelocking lasers and doubly active Q‐switched modelocked lasers. The aim is to demonstrate the great potential of infiber devices for the active control of different types of fiber lasers.
Competition Between Viscoelasticity and Surfactant Dynamics in Flow Focusing Microfluidics
Authors: Lee Wingki , Walker Lynn M. , Anna Shelley L.
Published: January 2011

The goal of this work is to quantify the impact of viscoelasticity on a tipstreaming phenomenon observed in flow focusing microfluidic devices. Tipstreaming, or thread formation, is a phenomenon caused by surfactant transport to, from, and along, deforming interfaces that leads to long filaments in microfluidic devices. Viscoelasticity also leads to stable filaments, so possible synergies are investigated here. The ability to generate extremely long and thin filaments that will break up via interfacial instabilities will lead to the formation of droplets much smaller than the device lengthscales. Viscoelastic Boger fluids are used as the dispersed phase liquid in a flow focusing device and surfactant is added to the continuous phase liquid. We find a region of operating space in which viscoelasticity appears to couple with surfactant transport to form long threads. The phenomenon is described qualitatively and is related to fluid relaxation times.

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A Dual Colorimetric and Fluorometric Sensor for Lead Ion Based on Conjugated Polydiacetylenes
Authors: Lee Kyung Mi , Chen Xiaoqiang , Fang Wang , Kim Jong‐Man , Yoon Juyoung
Published: January 2011

A PDA based sensor, derived from a di‐(2‐picolyl) amine (DPA) substituted diacetylene monomer, displayed a selective colorimetric change and a large fluorescence enhancement in the presence of lead ions. The lead selective PDA‐based chemosensor enabled easy detection of the presence of lead in 100% aqueous solution by the naked‐eye.

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RAFT Mediated Polymerization of Methyl Methacrylate Initiated by Bergman Cyclization: Access to High Molecular Weight Narrow Polydispersity Polymers
Authors: Gerstel Peter , Barner‐Kowollik Christopher
Published: January 2011

The first RAFT mediated polymerization of methyl methacrylate initiated by diradicals derived from Bergman cyclization was performed employing 3,4‐benzocyclodec‐3‐ene‐1,5‐diyne (BCDY) as diradical source and cyanoisopropyldithiobenzoate (CPDB) as RAFT agent. The polymerization was conducted in bulk at 80 °C for 3 h. The concentration of the enediyne was kept constant at 3.0 × 10−2 mol · L−1 and the RAFT agent concentration was varied between 0.0 mol · L−1 and 2.4 × 10−1 mol · L−1. A detailed ESI‐MS analysis reveals the absence of intramolecular termination reactions (ring formation) in the RAFT mediated system, which usually makes diradicalic initiation unfavorable. The presence of polymeric chains propagating at both ends could be confirmed. The conversion of the RAFT mediated polymerization was up to more than two times higher than the RAFT free polymerization at identical conditions. Thus, polymers with narrow polydispersities (1.1 ≤ PDI ≤ 1.5) even at very high molecular weights (near 400 000 Da) were obtained within modest reaction times.

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