bluuebunny/crossref_metadata_2025 huggingface dataset:
Sediment loads due to fluvial transport and debris flows during the 2005 flood events in Switzerland
Authors: Rickenmann Dieter , Koschni Anja
Published: February 2010

Severe floods in August 2005 in Switzerland were associated with enormous morphologic changes along the stream channels and with large sediment transport, including many debris flows in the headwater catchments and fluvial bedload transport along the mountain rivers. We compiled data on transported sediment volumes and estimated surface runoff volumes in the streams determined from radar‐based rainfall data and stream gauge measurements lower in the catchments. A quantitative analysis of the data shows that the transported bedload volumes are related to the flood runoff volume and the relevant channel gradient. For channel gradients flatter than about 5%, our data agree with a simplified version of the Meyer‐Peter and Müller equation but two other equations tested tend to under predict bedload volumes. For channel gradients steeper than about 5%, the observed sediment volumes transported by fluvial processes are over predicted by all bedload transport equations tested, though two of them were specifically developed for this slope range, which likely results from non‐accounted energy losses and supply limitation. For events with debris flows as the dominant sediment transfer mechanism, sediment volumes show a large variability for given flood runoff volume and channel gradient. The sediment volumes of the torrent catchments show a similar functional dependence on catchment parameters as for two empirical power law equations for the estimation of a ‘design’ event magnitude of debris flows based on data from Northern Italy but our events are associated with a much smaller coefficient. Finally, the majority of our debris‐flow data is in line with the trend defined by our fluvial transport events, indicating a continuous transition to debris‐flood and debris‐flow conditions. Copyright © 2010 John Wiley & Sons, Ltd.
Resolving barometric pressure waves in seasonal snowpack with a prototype‐embedded wireless sensor network
Authors: Lampkin D. J.
Published: February 2010

Networked micro‐sensors have the capacity to enable improvements in ground‐based data collection at resolutions that are currently unresolved. Crossbow® Environmental Motes (MEP410 models) were embedded in an accumulated snowpack in a meadow at Niwot Ridge long‐term ecological research (LTER) C1 site. Motes were mounted to a custom designed deployment structure that constitutes an adaptive sensor ‘tower’ at a maximum height of 142 with sensors deployed at depths of 122, 71 and 17 cm from the ground. Barometric pressures measured from this embedded wireless network indicate low frequency fluctuations over the study period with higher frequency components varying as a function of depth. Mean pressures measured over the analysis period were 707·82 mb (122 cm), 702·48 mb (71 cm), and 704·09 mb (17 cm). Results indicate filtering of high frequency components of pressure measured at depth with reduced amplitude and time‐lag (phase shift) modulated by changes in snowpack permeability related to density changes. Copyright © 2010 John Wiley & Sons, Ltd.
On the temporal resolution of mass balance models for soluble chemicals in soils
Authors: Pistocchi A.
Published: February 2010

A daily step model of chemical mass balance in the topsoil is presented and validated at the three experimental sites in Europe, and subsequently applied to perform two distinct numerical experiments. First, an experiment was run using hypothetic soluble chemicals with half‐lives ranging from 10−1 to 104, with a range of representative European climate and soil properties, assuming uniform constant emissions of the chemicals throughout the year. Chemical mass in soil from the daily step model calculations can be surrogated by the monthly step model consistently parameterized in terms of absolute values, patterns and inter‐monthly variability with decreasing accuracy at higher chemical half‐lives. Leaching fluxes can be also surrogated by the monthly step calculation, although with higher errors. Runoff is correct in the order of magnitude, but it shows only a weak correlation with the monthly mean of the daily model output. For leaching and runoff, the accuracy depends mainly on soil properties. Variability is well reproduced for both leaching and runoff.

The second experiment represented a pulse emission of chemicals discharged on a single day in a 12‐month period. Results from the annual average mass of chemicals in the soil, annual runoff and leaching fluxes from the daily step model were compared with the results obtained from the experiment assuming constant‐removal rates for the year. The two values are within a factor of 10 for half‐lives longer than 10 days; therefore, it is possible to emulate the daily step model with a simple constant‐removal rate model for screening‐level assessment. The experiments suggest that simpler schemes may be a practical screening‐level approximation of detailed daily step models for both continuous and pulse emissions, two cases providing extreme bounds of variation to real world emissions. Copyright © 2010 John Wiley & Sons, Ltd.
Isotopic composition (δ18O and δD) of precipitation and groundwater in a semi‐arid, mountainous area (Guadiana Menor basin, Southeast Spain)
Authors: Fernández‐Chacón F. , Benavente J. , Rubio‐Campos J. C. , Kohfahl C. , Jiménez J. , Meyer H. , Hubberten H. , Pekdeger A.
Published: February 2010

We characterize the precipitation and groundwater in a mountainous (peaks slightly above 3000 m a.s.l.), semi‐arid river basin in SE Spain in terms of the isotopes18O and2H. This basin, with an extension of about 7000 km2, is an ideal site for such a study because fronts from the Atlantic and the Mediterranean converge here. Much of the land is farmed and irrigated both by groundwater and runoff water collected in reservoirs. A total of approximately 100 water samples from precipitation and 300 from groundwater have been analysed. To sample precipitation we set up a network of 39 stations at different altitudes (800–1700 m a.s.l.), with which we were able to collect the rain and snowfall from 29 separate events between July 2005 and April 2007 and take monthly samples during the periods of maximum recharge of the aquifers. To characterize the groundwater we set up a control network of 43 points (23 springs and 20 wells) to sample every 3 months the main aquifers and both the thermal and non‐thermal groundwater. We also sampled two shallow‐water sites (a reservoir and a river). The isotope composition of the precipitation forms a local meteoric water line (LMWL) characterized by the equation δD = 7·72δ18O + 9·90, with mean values for δ18O and δD of − 10·28‰ and − 69·33‰, respectively, and 12·9‰ for thed‐excess value. To correlate the isotope composition of the rainfall water with groundwater we calculated the weighted local meteoric water line (WLMWL), characterized by the equation δD = 7·40δ18O + 7·24, which takes into account the quantity of water precipitated during each event. These values of (dδD/dδ18O)< 8 andd‐excess (δD–8δ18O)< 10 in each curve bear witness to the ‘amount effect’, an effect which is more manifest between May and September, when the ground temperature is higher. Other effects noted in the basin were those of altitude and the continental influence. The isotopic compositions of the groundwater are represented by the equation δD = 4·79δ18O − 18·64. The groundwater is richer in heavy isotopes than the rainfall, with mean values of − 8·48‰ for δ18O and − 59·27‰ for δD. The isotope enrichment processes detected include a higher rate of evaporation from detrital aquifers than from carbonate ones, the effects of recharging aquifers from irrigation return flow and/or from reservoirs' leakage and enrichment in δ18O from thermal water. Copyright © 2010 John Wiley & Sons, Ltd.
Sensitivity of streamflow from a Himalayan catchment to plausible changes in land cover and climate
Authors: Ma Xing , Xu Jianchu , van Noordwijk Meine
Published: February 2010

Global climate change will likely increase temperature and variation in precipitation in the Himalayas, modifying both supply of and demand for water. This study assesses combined impacts of land‐cover and climate changes on hydrological processes and a rainfall‐to‐streamflow buffer indicator of watershed function using the Soil Water Assessment Tool (SWAT) in Kejie watershed in the eastern Himalayas. The Hadley Centre Coupled Model Version 3 (HadCM3) was used for two Intergovernmental Panel on Climate Change (IPCC) emission scenarios (A2 and B2), for 2010–2099. Four land‐cover change scenarios increase forest, grassland, crops, or urban land use, respectively, reducing degraded land. The SWAT model predicted that downstream water resources will decrease in the short term but increase in the long term. Afforestation and expansion in cropland will probably increase actual evapotranspiration (ET) and reduce annual streamflow but will also, through increased infiltration, reduce the overland flow component of streamflow and increase groundwater release. An expansion in grassland will decrease actual ET, increase annual streamflow and groundwater release, while decreasing overland flow. Urbanization will result in increases in streamflow and overland flow and reductions in groundwater release and actual ET. Land‐cover change dominated over effects on streamflow of climate change in the short and middle terms. The predicted changes in buffer indicator for land‐use plus climate‐change scenarios reach up to 50% of the current (and future) range of inter‐annual variability. Copyright © 2010 John Wiley & Sons, Ltd.
Unstructured grid generation using LiDAR data for urban flood inundation modelling
Authors: Tsubaki Ryota , Fujita Ichiro
Published: February 2010

Inundation disasters, caused by sudden water level rise or rapid flow, occur frequently in various parts of the world. Such catastrophes strike not only in thinly populated flood plains or farmland but also in highly populated villages or urban areas. Inundation of the populated areas causes severe damage to the economy, injury, and loss of life; therefore, a proper management scheme for the disaster has to be developed. To predict and manage such adversity, an understanding of the dynamic processes of inundation flow is necessary because risk estimation is performed based on inundation flow information. In this study, we developed a comprehensive method to conduct detailed inundation flow simulations for a populated area with quite complex topographical features using LiDAR (Light Detection and Ranging) data. Detailed geospatial information including the location and shape of each building was extracted from the LiDAR data and used for the grid generation. The developed approach can distinguish buildings from vegetation and treat them differently in the flow model. With this method, a fine unstructured grid can be generated representing the complicated urban land features precisely without exhausting labour for data preparation. The accuracy of the generated grid with different grid spacing and grid type is discussed and the optimal range of grid spacing for direct representation of urban topography is investigated. The developed method is applied to the estimation of inundation flows, which occurred in the basin of the Shin‐minato River. A detailed inundation flow structure is represented by the flow model, and the flow characteristics with respect to topographic features are discussed. Copyright © 2010 John Wiley & Sons, Ltd.
Impacts of climate change and human activities on surface runoff in the Dongjiang River basin of China
Authors: Liu Dedi , Chen Xiaohong , Lian Yanqing , Lou Zhanghua
Published: February 2010

Observed rainfall and flow data from the Dongjiang River basin in humid southern China were used to investigate runoff changes during low‐flow and flooding periods and in annual flows over the past 45 years. We first applied the non‐parametric Mann–Kendall rank statistic method to analyze the change trend in precipitation, surface runoff and pan evaporation in those three periods. Findings showed that only the surface runoff in the low‐flow period increased significantly, which was due to a combination of increased precipitation and decreased pan evaporation. The Pettitt–Mann–Whitney statistical test results showed that 1973 and 1978 were the change points for the low‐flow period runoff in the Boluo sub‐catchment and in the Qilinzui sub‐catchment, respectively. Most importantly, we have developed a framework to separate the effects of climate change and human activities on the changes in surface runoff based on the back‐propagation artificial neural network (BP‐ANN) method from this research. Analyses from this study indicated that climate variabilities such as changes in precipitation and evaporation, and human activities such as reservoir operations, each accounted for about 50% of the runoff change in the low‐flow period in the study basin. Copyright © 2010 John Wiley & Sons, Ltd.
Effects of fire and vegetation cover on hydrological characteristics of a Mediterranean shrubland soil
Authors: González‐Pelayo O. , Andreu V. , Gimeno‐García E. , Campo J. , Rubio J. L.
Published: February 2010

An experimental study based on the effects of fire on soil hydrology was developed at the Experimental Station of ‘La Concordia’ (Valencia, Spain). It is located on a calcareous hillside facing SSE and composed of nine erosion plots (4 × 20 m). In summer 2003, after eight years of soil and vegetation recovery from previous fires in 1995 (with three fire treatments: T1 high‐intensity fire, T2 moderate intensity, and T3 not burnt), experimental fires of low intensity were again conducted on the plots already burnt, to study the effects of repeated fires on the soil water infiltration, soil water content and runoff.

Infiltration rates and capacities were measured by the mini‐disk infiltrometer method (MDI), assessing the effects of vegetation cover by comparing the under‐canopy microenvironment (UC) and its absence on bare soil (BS), immediately before and after the fire experiments. Soil properties like water retention capacity (SWRC) and water content (SWC) were also determined for the different fire treatments (T1, T2 and T3) and microsites (UC and BS). Hydrological parameters, such as runoff and infiltration rate, were monitored at plot scale from July 2002 to July 2004. In the post‐fire period, data displayed a 20% runoff increase and a decrease in infiltration (18%).

Differences in the steady‐state infiltration rate (SSI) and infiltration capacity (IC) were tested with the MDI on the different treatments (T1, T2 and T3), and between the UC and BS microsites of each treatment. After fire, the SSI of the UC soil declined from 16 mm h−1 to 12 mm h−1 on T1, and from 24 mm h−1 to 19 mm h−1 on T2. The IC was reduced by 2/3 in the T1 UC soil, and by half on T2 UC soil. On the BS of T1 and T2, the fire effect was minimal, and higher infiltration rates and capacities were reached. Therefore, the presence/absence of vegetation when burnt influenced the post‐burnt infiltration patterns at soil microscale. On the T3, different rates and capacities were obtained depending on the microsites (UC and BS), with higher SSI (25 mm h−1) and IC (226 mm h−1) on BS than on UC (SSI of 18 mm h−1 and IC of 136 mm h−1).

The SWRC and SWC were recovered from 1995 to 2003 (prior to the fires). The 2003 fire promoted high variability on the SWC at pF 0·1, 2 and 2·5, and the SWRC on burnt soils were reduced. To summarize, the IC and SSI post‐fire decreases were related to the lower infiltration rate at plot scale, the significant differences in the SWRC between burnt and control treatments, and the increase in the runoff yield (20%).

According to the results, the MDI was a useful tool to characterize the soil infiltration on the vegetation patches of the Mediterranean maquia, and contrary to other studies, on the UC soil, the infiltration rate and IC, when soil was dry, were lower than that obtained on BS. Once the soil gets wet, similar values were found on both microenvironments. Copyright © 2010 John Wiley & Sons, Ltd.
Polycaprolactone/hydroxyapatite composite scaffolds: Preparation, characterization, and in vitro and in vivo biological responses of human primary bone cells
Authors: Chuenjitkuntaworn Boontharika , Inrung Wipawan , Damrongsri Damrong , Mekaapiruk Kongkwan , Supaphol Pitt , Pavasant Prasit
Published: February 2010

Polycaprolactone (PCL) is a synthetic biodegradable polymer that has been approved for use as bone graft substitutes. In this study, PCL scaffolds incorporating hydroxyapatite (HAp) particles were fabricated by combined solvent casting and particulate leaching techniques. The average pore dimension was in the range of about 480–500 μm. The porosity, water absorption, and compressive modulus of the scaffold were evaluated. The responses of primary bone cells cultured on the PCL and PCL/HAp scaffolds were examined both in vitro and invivo. In comparison with the cells grown on the PCL scaffold, those cultured on the PCL/HAp counterpart positively expressed the markers of osteogenic differentiation. Cells increased the mRNA expressions of type I collagen and osteocalcin on day 10 and demonstrated a significant increase in calcium deposition. In coherence with the in vitro appearance, histomorphometric analysis in a mouse calvarial model showed a significantly greater amount of new bone formation. The results demonstrated that the prepared PCL/HAp scaffold could be a good candidate as synthetic substitute for bone tissue engineering. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
Effects of cyclic flexural fatigue on porcine bioprosthetic heart valve heterograft biomaterials
Authors: Mirnajafi Ali , Zubiate Brett , Sacks Michael S.
Published: February 2010

Although bioprosthetic heart valves (BHV) remain the primary treatment modality for adult heart valve replacement, continued problems with durability remain. Several studies have implicated flexure as a major damage mode in porcine‐derived heterograft biomaterials used in BHV fabrication. Although conventional accelerated wear testing can provide valuable insights into BHV damage phenomena, the constituent tissues are subjected to complex, time‐varying deformation modes (i.e., tension and flexure) that do not allow for the control of the amount, direction, and location of flexure. Thus, in this study, customized fatigue testing devices were developed to subject circumferentially oriented porcine BHV tissue strips to controlled cyclic flexural loading. By using this approach, we were able to study layer‐specific structural damage induced by cyclic flexural tensile and compressive stresses alone. Cycle levels of 10 × 106, 25 × 106, and 50 × 106 were used, with resulting changes in flexural stiffness and collagen structure assessed. Results indicated that flexural rigidity was markedly reduced after only 10 × 106 cycles, and progressively decayed at a lower rate with cycle number thereafter. Moreover, the against‐curvature fatigue direction induced the most damage, suggesting that the ventricularis and fibrosa layers have low resistance to cyclic flexural compressive and tensile loads, respectively. The histological analyses indicated progressive collagen fiber delamination as early as 10 × 106 cycles but otherwise no change in gross collagen orientation. Our results underscore that porcine‐derived heterograft biomaterials are very sensitive to flexural fatigue, with delamination of the tissue layers the primary underlying mechanism. This appears to be in contrast to pericardial BHV, wherein high tensile stresses are considered to be the major cause of structural failure. These findings point toward the need for the development of chemical fixation technologies that minimize flexure‐induced damage to extend porcine heterograft biomaterial durability. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
Investigation of the binding of Cr(III) complexes to bovine and human serum proteins: A proteomic approach
Authors: Tkaczyk Cathy , Huk Olga L. , Mwale Fackson , Antoniou John , Zukor David J. , Petit Alain , Tabrizian Maryam
Published: February 2010

Chromium (Cr) compounds are widely used in alloys manufacturing and forming processes. One of the main concerns in the use of cobalt‐chromium (Co‐Cr) alloy‐based implants is the long‐term fate of Co and Cr ions in the blood, organs, and urine of patients. Our previous studies have shown that Cr(III) forms complexes in different cell culture media, whereas Cr(VI) does not form any detectable structure under the same conditions. Because Cr(VI) is known to be more toxic than Cr(III), we hypothesized that the presence of serum proteins in the molecular structure of Cr(III) may be responsible for the difference in toxicity. We investigated the interaction of the Cr(III) complexes with serum proteins and their internalization by U937 macrophage‐like cells. By using a proteomic approach, we showed that in the presence of fetal bovine serum, Cr(III) complexes interacted only with albumin, whereas they interacted mainly with albumin, transferrin, and immunoglobulins (Ig) in the presence of human serum (HS). Cr(III) complexes were more easily engulfed by U937 macrophage‐like cells when they were formed with HS. To the best of our knowledge, this is the first report on the formation of Cr(III) complexes in the presence of serum proteins and the interaction of these complexes with U937 macrophage‐like cells. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
Cellular inhibition produced by dental curing lights is a heating artifact
Authors: Blay Jonathan , Price Richard B.
Published: February 2010

Dental curing lights deliver energy in the 380–520 nm wavelength range. It has been reported that irradiation in these wavelengths may have a negative effect on cell function. We examined the effect of three dental curing lights on the viability of mouse (NIH3T3, Balb/c3T3) and human (HGF‐1) fibroblastic cells, and epithelial (HT‐29) cells grown in culture. Cell inhibition was observed using the MTT assay of mitochondrial function and measures of DNA fragmentation and DNA synthesis. Analyzing the experimental method and careful measurement of the temperature adjacent to the cell monolayer during irradiation showed that damage to the cells was not due to cumulative light exposure, but instead occurred when the temperature of the culture medium rose above 42°C. We conclude that dental curing lights do not cause cell damage as a direct result of the light irradiation. Instead it is caused by the local temperature increase in the cells. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2010
Fabrication and characterization of a porous multidomain hydroxyapatite scaffold for bone tissue engineering investigations
Authors: Buckley Conor Timothy , O'Kelly Kevin Unai
Published: February 2010

Tissue‐engineering scaffold‐based strategies have suffered from limited cell depth viability when cultured in vitro, with viable cells existing within the outer periphery of the fluid–scaffold interface. This is primarily believed to be due to the lack of nutrient delivery into and waste removal from the inner regions of the scaffold construct. This work develops a hydroxyapatite trimodal porous scaffold architecture (i.e., a scaffold providing a discrete domain for cell occupancy and a separate domain for nutrient delivery) through a freeze drying process. Unidirectional channels (500 μm diameter) were incorporated through CNC machining with total combined apparent porosities of 85.1% ± 0.22%. Effective diffusion coefficients for the bimodal phase (consisting of micro‐ and meso‐pores, without channels) were also determined (7.9 × 10−10 m2 s−1). Trimodal scaffolds also demonstrated enhanced permeability values (∼18‐fold increase) compared with bimodal scaffold architectures. In vitro experiments were used to assess initial seeding efficiency and distribution as well as cell viability. The presence of unidirectional channels significantly enhanced initial cell seeding distribution throughout the scaffold depth, while maintaining relatively high seeding efficiencies (67.7% ± 2.2% for trimodal, 79.1% ± 2.1% for bimodal scaffolds). Numerical models demonstrated the effectiveness and efficacy of incorporating channels to increase the core oxygen concentration, with the accuracy of these models improved by using experimentally measured cellular oxygen consumption rates and effective diffusion coefficients. The presence of channels had a positive influence in minimizing the concentration gradients compared with bimodal scaffolds for the same cell density distributions. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2010
Liquid flow circulating within an unbaffled vessel agitated with an unsteady forward–reverse rotating impeller
Authors: Yoshida Masanori , Wakura Yuma , Yamagiwa Kazuaki , Ohkawa Akira , Tezura Shuichi
Published: February 2010

Liquid‐phase mixing is a common operation, often performed in vessels using mechanically rotating impellers. To enhance axial mixing the vessels are generally equipped with baffles; however, in industries where cleaning the vessel interior is a major concern, i.e. food and pharmaceuticals, and crystallization, where baffles can disturb particle growth, unbaffled vessels are preferred. One method of agitation in unbaffled vessels is an impeller that periodically changes either the direction or rate of rotation: so‐called unsteady rotation. For use in an enhanced agitation vessel, an agitation technology using an unsteady forward–reverse rotating impeller in an unbaffled vessel was investigated. Such unsteady agitation is expected to enhance mixing. However, knowledge of the liquid flows in such an apparatus remains elusive. Thus an aim of this work was to characterize the circulation flow in such a system. Circulation by a disk turbine impeller with six flat blades was studied through examination of tracer particle trajectories. Images showing flow patterns with the forward–reverse rotating impeller resembled those obtained with a unidirectionally rotating impeller in a baffled vessel. The pattern was characterized by a circulation loop whose pathway exits from the impeller rotational region and returns to that region past the wall and bottom of the vessel. Time‐series particle tracking velocimetry (PTV) images obtained during one forward–reverse rotation of the impeller showed that the flow near the vessel wall reduced the periodic fluctuation downstream and that a flow that was almost independent of time was induced near the vessel bottom. For the flow from the bottom to the impeller, unsteadiness was provided by proximity to the impeller. Based on the intensity distribution of the unsteady flow produced by this type of forward–reverse rotating impeller within the vessel, the unsteady flow was shown to have the potential to reach the region near the vessel wall. Copyright © 2010 Society of Chemical Industry
Altered sex hormone concentrations and gonadal mRNA expression levels of activin signaling factors in hatchling alligators from a contaminated Florida lake
Authors: Moore Brandon C. , Kohno Satomi , Cook Robert W. , Alvers Ashley L. , Hamlin Heather J. , Woodruff Teresa K. , Guillette Louis J.
Published: February 2010

Activins and estrogens participate in regulating the breakdown of ovarian germ cell nests and follicle assembly in mammals. In 1994, our group reported elevated frequencies of abnormal, multioocytic ovarian follicles in 6 month old, environmental contaminant‐exposed female alligators after gonadotropin challenge. Here, we investigated if maternal contribution of endocrine disrupting contaminants to the egg subsequently alters estrogen/inhibin/activin signaling in hatchling female offspring, putatively predisposing an increased frequency of multioocytic follicle formation. We quantified basal and exogenous gonadotropin‐stimulated concentrations of circulating plasma steroid hormones and ovarian activin signaling factor mRNA abundance in hatchling alligators from the same contaminated (Lake Apopka) and reference (Lake Woodruff) Florida lakes, as examined in 1994. Basal circulating plasma estradiol and testosterone concentrations were greater in alligators from the contaminated environment, whereas activin/inhibin βA subunit and follistatin mRNA abundances were lower than values measured in ovaries from reference lake animals. Challenged, contaminant‐exposed animals showed a more robust increase in plasma estradiol concentration following an acute follicle stimulating hormone (FSH) challenge compared with reference site alligators. Aromatase and follistatin mRNA levels increased in response to an extended FSH challenge in the reference site animals, but not in the contaminant‐exposed animals. In hatchling alligators, ovarian follicles have not yet formed; therefore, these endocrine differences are likely to affect subsequent ovarian development, including ovarian follicle assembly. J. Exp. Zool. 313A:218–230, 2010. © 2010 Wiley‐Liss, Inc.
Muscle development in the Japanese flounder, Paralichthys olivaceus, with special reference to some of the larval‐specific muscles
Authors: Uji Susumu , Kurokawa Tadahide , Suzuki Tohru
Published: February 2010

We investigated muscle development in the Japanese flounder Paralichthys olivaceus, focusing primarily on the cranial muscles, using a whole mount immunohistochemical staining method. It is well established that during the very early stages of morphogenesis, until 4 days post hatching (dph), muscles required for feeding develop. Later, between 8 and 16 dph, the muscle composition in the dorsal branchial arches changes to the adult form. We discovered the presence of larval‐specific muscles in this ontogenetic period, termed the larval branchial levators 2 and 3, located in the dorsal branchial arches. The larval branchial levators 2 and 3 disappear during the course of development, whereas the others remain as levator internus 1 and levator posterior, which have also been described in adult fish. In place of these regressed muscles, the levatores externi and levator internus 2 develop and regulate the branchial arches. In addition, we found that the levator posterior, which is thought to represent the fifth levator externus, and the levatores externi exhibit different origins. We also found that at least a part of the caudal fin musculature develops from the trunk myotome. J. Morphol. 2010. © 2010 Wiley‐Liss, Inc.
Specific fragmentation of the K‐shell excited/ionized pyridine derivatives studied by electron impact: 2‐, 3‐ and 4‐methylpyridine
Authors: Sakai Masamichi , Okada Kazumasa , Ohno Keiichi , Tabayashi Kiyohiko
Published: February 2010

Fragmentation of the pyridine ring upon K‐shell excitation/ionization has been studied with gaseous 2‐, 3‐ and 4‐methylpyridine by the electron‐impact method. Ab initio molecular orbital (MO) calculations were also carried out to explore electronic states correlating with specific fragments. Some specific fragmentation channels were identified from the ionic fragments enhanced characteristically at the N 1s edge. Yields of the C2HN+ and C5H5+/C5H6+ ions show that the fission of the NC2 and C4C5/C5C6 bonds of the ring is likely to occur after the N 1s excitation and ionization. Ab initio MO calculations for the 2‐methylpyridine molecule indicate that the dissociation channels to produce these ions are only accessible through the excited states of the parent molecular dication, which can be formed by Auger decays after the N 1s ionization. Fragment ions via hydrogen rearrangement are produced as well, but the rearrangement is not a phenomenon specific to the K‐shell excitation/ionization. Copyright © 2010 John Wiley & Sons, Ltd.
Prevalence, evolution, and features of infection with human papillomavirus: A 15‐year longitudinal study of routine screening of a women population in the north of Spain
Authors: de Oña María , Alvarez‐Argüelles Marta E. , Torrents Magdalena , Villa Laura , Rodriguez‐Feijoo Asunción , Palacio Ana , Boga Jose A. , Tamargo Angel , Melón Santiago
Published: February 2010

Determination of the prevalence of type‐specific human papillomavirus (HPV) is important for the development of new vaccines and to prevent malignancy. The objective of this study was to determine HPV infection in two areas in the north of Spain, and their evolution in the last 15 years. Between 1991 and 2007, 7,930 fresh cervical swabs were obtained from 5,554 women (37.8 ± 11.8 years old). From them, 425 have been followed‐up for an average of 3.7 ± 2.08 years after sampling (range 2–14.6), and 71 for 7.7 ± 2.2 years (range 5–14). Methods based on polymerase chain reaction (PCR) were carried out. Samples from 1,598 (28.8%) women were positive for HPV: 40.9% were under 25 years of age, 34.2% in the 25–35 year age group, 27.2% in the 36–45 year age group, and 19.6% older than 45 years (P < 0.001). HPV was found in 34.4% of the women with cytological alterations versus 23% of women without cervical changes (P < 0.0001). HPV‐16 was present in 25.8% of the women, although the study identified 26 different HPV genotypes. After 3 years of follow‐up, HPV remained or became undetectable in 87% of the cases, and in 5 years 70.3%. The prevalence of HPV is associated with younger women and women with cytological changes in the cervix. Although HPV‐16 is more prevalent, HPV types not included in available vaccines were found the most commonly. The low 3‐year (even 5‐year) cumulative incidence rate of HPV infection suggests that cervical screening every 3 (or even 5) years is safe and effective. J. Med. Virol. 82:597–604, 2010. © 2010 Wiley‐Liss, Inc.
Genetic variation of G4P[6] rotaviruses: Evidence for novel strains circulating between the hospital and community
Authors: Shim So‐Yeon , Jung Yeon‐Chang , Le Van Phan , Son Dong Woo , Ryoo Eell , Shim Jung Ok , Lim Inseok , Kim Wonyong
Published: February 2010

One hundred forty‐six fecal specimens collected between 2007 and 2008 from infants with acute gastroenteritis were screened for rotavirus by ELISA with VP6‐specific antibody. One hundred twenty‐three of the samples (84.2%) were confirmed to be positive for group A rotavirus (community‐acquired, n = 90 [73.2%] and nosocomial, n = 33 [26.8%]), and were typed subsequently using RT‐PCR and sequence analysis methods. Determination of G‐ and P‐type combinations showed that G4P[6] (78.9%) was the most common strain, followed by G3P[8] (7.3%), G1P[8] (6.5%), G2P[4] (0.8%), G2P[6] (0.8%), G1P[6] (0.8%), and G9P[8] (0.8%) strains. Of the 97 G4P[6] strains, 62 (63.8%) were responsible for community‐acquired cases and 35 (36.1%) were hospital‐acquired cases. Phylogenetic analysis of the VP7 gene from the G4P[6] strains revealed that both the community‐acquired and nosocomial strains were segregated to the human rotaviruses circulating world‐wide, including the prototype vaccinal strain, ST3, which constituted a novel sublineage in lineage 1. Owing to the recent emergence of G4P[6] rotaviruses within the hospital, as well as in the community, the findings from this study are important since they provide new information concerning the community and nosocomial spread of rotaviruses. J. Med. Virol. 82:700–706, 2010. © 2010 Wiley‐Liss, Inc.
Recurrent cytomegalovirus colitis with megacolon in an immunocompetent elderly man
Authors: Lin Yi‐Hsuan , Yeh Chi‐Ju , Chen Ying‐Jen , Chang Ming‐Chu , Su I‐Hao , Cheng Hao‐Tsai
Published: February 2010

Gastrointestinal infection with cytomegalovirus (CMV) is uncommon in immunocompetent hosts. The case of a 70‐year‐old male with CMV colitis, who has no history of chronic inflammatory bowel disease or immunodeficiency is described. Diagnosis was aided by the identification of inclusion bodies that reacted positively for CMV by immunohistochemical testing in biopsy specimens from the colonic mucosa. His hospital course was characterized by poor improvement of his symptoms after the CMV infection was treated with ganciclovir, and the occurrence of megacolon. A repeat colonoscopy with biopsy revealed a recurrence of the CMV infection. Although CMV colitis is common in immunocompromised patients, we believe this is the first case of CMV colitis with megacolon and recurrent CMV infection in an immunocompetent patient. Colitis caused by CMV colitis should be considered in elderly people with diarrhea. J. Med. Virol. 82:638–641, 2010. © 2010 Wiley‐Liss, Inc.
Circulating human group A rotavirus genotypes in Malaysia
Authors: Zuridah H. , Kirkwood C.D. , Bogdanovic‐Sakran N. , Bishop R.F. , Yap K.L.
Published: February 2010

This study examined the temporal distribution of rotavirus genotypes in Malaysia. Rotaviruses from children with diarrhea admitted to hospitals in 1996 (n = 93) and 2007 (n = 12) in two different regions of Peninsular (West) Malaysia were analyzed for their G and P genotypes using a hemi‐nested RT‐PCR assay. In the 2007 samples, the dominant strain was G9P[8]. It was identified in 42% of the samples. Different strains all possessing the G1 genotype were identified in the rest of the samples. In contrast, 81% of the samples collected in 1996 were the G1P[8] strain. No strains with G9 genotype were detected in samples collected in 1996. J. Med. Virol. 82:707–711, 2010. © 2010 Wiley‐Liss, Inc.
Evaluation of the performance of the novel PapilloCheck® HPV genotyping test by comparison with two other genotyping systems and the HC2 test
Authors: Schopp Betti , Holz Barbara , Zago Manola , Stubenrauch Frank , Petry Karl‐Ulrich , Kjaer Susanne Krüger , Iftner Thomas
Published: February 2010

The novel PapilloCheck® genotyping test was compared with SPF10 PCR LiPav1 and PGMY09/11 on hybrid capture 2 (HC2)‐pretested samples. From results of 826 cervical samples detection rates and kappa values for the tests were calculated using a HPV type consensus definition. With PapilloCheck® HPV types 53, 56, and 33 were found with a sensitivity of 100%. The lowest detection rate was observed for HPV 35 (72.2%). The SPF10 PCR LiPav1 was found to be 100% positive for HPV 18, 31, 53, 56, and 35 and lowest for HPV 59 (81%). The PGMY09/11 system detected only HPV 59 at 100% detection rate and showed lowest sensitivity for HPV 56 (40.5%). Multiple infection rates ranged from 25.8% (PGMY09/11 PCR‐LBA), over 39.5% (PapilloCheck®) to 55.9% (SPF10 PCR LiPav1). In samples with higher viral DNA load detection rates and concordance between the genotyping tests increases. The kappa values in comparison to the HPV consensus type ranged from k = 0.21 to k = 0.82 for comparing SPF10 PCR with the HPV consensus type, while values for PGMY09/11 PCR ranged from k = 0 to k = 0.96 and were best for the PapilloCheck® (k = 0.49–0.98). Detection rates for the identification of high‐grade cervical intraepithelial neoplasia (CIN2+) ranged from 93.7% (PGMY09/11 PCR) to 98.4% (PapilloCheck®, SPF10 PCR, HC2). In conclusion, this study shows that the PapilloCheck® give comparable results to established PCR methods. However, these results also show a necessity for the standardization of genotype‐specific HPV detection assays. J. Med. Virol. 82:605–615, 2010. © 2010 Wiley‐Liss, Inc.
Development and comparison of molecular assays for the rapid detection of the pandemic influenza A (H1N1) 2009 virus
Authors: Lam Wai‐Yip , Leung Ting‐Fan , Lee Nelson , Cheung Jo L.K. , Yeung Apple C.M. , Ho Yolanda I.I. , Chan Rickjason C.W. , Fung Kitty S.C. , Barr Ian G. , Hui David S.C. , Sung Joseph J.Y. , Chan Paul K.S.
Published: February 2010

Human infection with the novel pandemic influenza A (H1N1) virus was first identified in April 2009. Two months later, the World Health Organization (WHO) had raised the pandemic level to phase 6. Rapid case identification is essential for prompt patient management and public health actions. This study developed real‐time and conventional reverse transcription‐polymerase chain reaction (rRT‐PCR and cRT‐PCR) assays for pandemic H1N1 detection, and compared their sensitivities with protocols developed by WHO reference centres. Altogether, three rRT‐PCR and one cRT‐PCR targeting the matrix gene for universal detection of influenza A; three rRT‐PCR, one cRT‐PCR targeting the hemagglutinin (HA) gene for specific detection of pandemic H1N1; and one multiplex cRT‐PCR for differentiating co‐circulating seasonal H1N1, H3N2, and pandemic H1N1 were examined. The lower detection limit ranged from 1.252 to 125.2 copy equivalents. In general, rRT‐PCR assays were more sensitive than cRT‐PCR assays. All assays showed 100% sensitivity for “optimal” specimens (nasopharyngeal samples collected within 4 days after illness onset). For the other 36 samples, cRT‐PCR assays were less sensitive except that the new Protocol I‐cRT‐pdmH1 still retained 100% sensitivity. The new Protocol F‐rRT‐PCR‐pdmH1 was the only pandemic virus‐specific rRT‐PCR assay with 100% sensitivity across all specimen categories. In conclusion, rRT‐PCR assays are 10‐fold more sensitive than cRT‐PCR assays. The newly developed cRT‐PCR assay targeting the HA gene allows rapid, specific, and sensitive screening of this novel agent, which can serve as an alternative for laboratories where a real‐time PCR machine is not available. J. Med. Virol. 82:675–683, 2010. © 2010 Wiley‐Liss, Inc.
Analysis of complete genome sequences of swine hepatitis E virus and possible risk factors for transmission of HEV to humans in Korea
Authors: Song Young‐Jo , Jeong Hyun‐Jeong , Kim Yu‐Jin , Lee Sang‐Won , Lee Jung‐Bok , Park Seung‐Yong , Song Chang‐Seon , Park Hee‐Myung , Choi In‐Soo
Published: February 2010

The hepatitis E virus (HEV) is an emerging zoonotic agent, for which pigs are the most important reservoir. Complete genome sequences of two swine HEV strains, designated swKOR‐1 and swKOR‐2, were determined via RT‐PCR and RACE‐PCR. The strains contained genomes composed of 7,222‐ and 7,221‐bp excluding the poly(A) tails, respectively. The swKOR‐1 and swKOR‐2 strains were classified into subtype 3a of genotype 3 via phylogenetic analysis. These strains formed a distinctive cluster in the phylogenetic tree with human and swine HEVs isolated in the USA and human HEVs isolated in Japan. Anti‐HEV antibodies were identified via ELISA in 8 of 99 (8.1%) cats, whereas, among 115 cattle and 213 dogs, no HEV‐specific antibodies were detected. The conserved RNA‐dependent RNA polymerase (RdRp) gene of HEV could be detected via RT‐PCR in 8.7% of raw oysters collected from coastal regions in Korea. The HEV RNAs detected in oysters were identified as belonging to subtype 3a. The HEV RNAs in oysters most closely resembled that of the swKOR‐2 strain. They also showed a close genetic relationship with the swKOR‐1 strain and the swine and human HEVs isolated in the USA. This is the first report describing the detection in oysters of HEV that may have originated from genotype 3 swine HEV in Korea. Pigs and cats infected with HEV, as well as oysters contaminated with HEV, are potential risk factors for HEV transmission to humans. J. Med. Virol. 82:583–591, 2010. © 2010 Wiley‐Liss, Inc.
Human papillomavirus (HPV) prevalence and type distribution, and HPV‐associated cytological abnormalities in anal specimens from men infected with HIV who have sex with men
Authors: Damay Audrey , Fabre Jaqueline , Costes Valérie , Didelot Jean‐Michel , Didelot Marie‐Noëlle , Boulle Nathalie , Segondy Michel
Published: February 2010

Human papillomavirus (HPV) detection and typing using the PapilloCheck® test and cytological examination were carried out in anal samples collected from 67 men seropositive for human immunodeficiency virus (HIV) who have sex with men. Fifty (74.6%) patients had anal HPV infection, 46 (68.7%) had high‐risk (HR) HPV infection, and 38 (56.7%) had multiple infection involving 2–9 (median, 3) HPV types. The HPV types identified most frequently were HPV 44/55 (19.4%), HPV 53 (19.4%), HPV 16 (16.4%), HPV 39 (16.4%), and HPV 42 (14.9%). Thirty‐two of the 66 interpretable smears (48.5%) revealed cytological abnormalities: 9 (13.4%) atypical cells of undetermined significance, 20 (30.3%) low‐grade intraepithelial lesions, and 3 (4.5%) high‐grade intraepithelial lesions. Cytological abnormalities were associated significantly with HPV detection (P < 0.001), multiple HPV infection (P < 0.001), and increased number of HPV types (P < 0.001). The HPV types associated most frequently with cytological abnormalities were HPV 39 (28.1%), HPV 42 (28.1%), HPV 53 (28.1%), HPV 16 (25.0%), HPV 44/55 (25.0%), and HPV 59 (21.9%). HPV DNA detection as well as cytological abnormalities were associated neither with HIV RNA detection in plasma nor with CD4+ T‐cell count. Differences in age or in time since HIV acquisition were not observed in patients with or without cytological abnormalities. The present study confirms the high prevalence of anal HR‐HPV infection and cytological abnormalities in men infected with HIV who have sex with men. HPV testing and/or cytological analysis may be helpful in selecting the patients to be referred to proctological examination. J. Med. Virol. 82:592–596, 2010. © 2010 Wiley‐Liss, Inc.
Prevalence of hepatitis B and hepatitis C virus infections in France in 2004: Social factors are important predictors after adjusting for known risk factors
Authors: Meffre Christine , Le Strat Yann , Delarocque‐Astagneau Elisabeth , Dubois Fréderic , Antona Denise , Lemasson Jean‐Marie , Warszawski Josiane , Steinmetz Josiane , Coste Dominique , Meyer Jean‐François , Leiser Sandrine , Giordanella Jean‐Pierre , Gueguen René , Desenclos Jean‐Claude
Published: February 2010

To monitor the prevalence of hepatitis B and hepatitis C a cross‐sectional survey was conducted in 2004 among French metropolitan residents. A complex sampling design was used to enroll 14,416 adult participants aged 18–80 years. Data collected included demographic and social characteristics and risk factors. Sera were tested for anti‐HCV, HCV‐RNA, anti‐HBc and HBsAg. Data were analyzed with SUDAAN® software to provide weighted estimates for the French metropolitan resident population. The overall anti‐HCV prevalence was 0.84% (95% CI: 0.65–1.10). Among anti‐HCV positive individuals, 57.4% (95% CI: 43.2–70.5) knew their status. Factors associated independently with positive anti‐HCV were drug use (intravenous and nasal), blood transfusion before 1992, a history of tattoos, low socioeconomic status, being born in a country where anti‐HCV prevalence >2.5%, and age >29 years. The overall anti‐HBc prevalence was 7.3% (95%: 6.5–8.2). Independent risk factors for anti‐HBc were intravenous drug use, being a man who has sex with men, low socioeconomic status, a stay in a psychiatric facility or facility for the mentally disabled, <12 years of education, being born in a country where HBsAg prevalence >2%, age >29 and male sex. The HCV RNA and HBsAg prevalence were 0.53% (95% CI: 0.40–0.70) and 0.65% (95% CI: 0.45–0.93), respectively. Among HBsAg positive individuals, 44.8% (95% CI: 22.8–69.1) knew their status. Anti‐HCV prevalence was close to the 1990s estimates whereas HBsAg prevalence estimate was greater than expected. Screening of hepatitis B and C should be strengthened and should account for social vulnerability. J. Med. Virol. 82:546–555, 2010. © 2010 Wiley‐Liss, Inc.