bluuebunny/crossref_metadata_2025 huggingface dataset:
Symmetry‐restrained molecular dynamics simulations improve homology models of potassium channels
Authors: Anishkin Andriy , Milac Adina L. , Guy H. Robert
Published: September 2009

Most crystallized homo‐oligomeric ion channels are highly symmetric, which dramatically decreases conformational space and facilitates building homology models (HMs). However, in molecular dynamics (MD) simulations channels deviate from ideal symmetry and accumulate thermal defects, which complicate the refinement of HMs using MD. In this work we evaluate the ability of symmetry constrained MD simulations to improve HMs accuracy, using an approach conceptually similar to Critical Assessment of techniques for protein Structure Prediction (CASP) competition: build HMs of channels with known structure and evaluate the efficiency of proposed methods in improving HMs accuracy (measured as deviation from experimental structure). Results indicate that unrestrained MD does not improve the accuracy of HMs, instantaneous symmetrization improves accuracy but not stability of HMs during subsequent unrestrained MD, while gradually imposing symmetry constraints improves both accuracy (by 5–50%) and stability of HMs. Moreover, accuracy and stability are strongly correlated, making stability a reliable criterion in predicting the accuracy of new HMs. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case
Authors: Boechi Leonardo , Mañez Pau Arroyo , Luque F. Javier , Marti Marcelo A. , Estrin Dario A.
Published: September 2009

Truncated hemoglobins (trHbs) are heme proteins present in bacteria, unicellular eukaryotes, and higher plants. Their tertiary structure consists in a 2‐over‐2 helical sandwich, which display typically an inner tunnel/cavity system for ligand migration and/or storage. The microorganism Bacillus subtilis contains a peculiar trHb, which does not show an evident tunnel/cavity system connecting the protein active site with the solvent, and exhibits anyway a very high oxygen association rate. Moreover, resonant Raman results of CO bound protein, showed that a complex hydrogen bond network exists in the distal cavity, making it difficult to assign unambiguously the residues involved in the stabilization of the bound ligand. To understand these experimental results with atomistic detail, we performed classical molecular dynamics simulations of the oxy, carboxy, and deoxy proteins. The free energy profiles for ligand migration suggest that there is a key residue, GlnE11, that presents an alternate conformation, in which a wide ligand migration tunnel is formed, consistently with the kinetic data. This tunnel is topologically related to the one found in group I trHbs. On the other hand, the results for the CO and O2 bound protein show that GlnE11 is directly involved in the stabilization of the cordinated ligand, playing a similar role as TyrB10 and TrpG8 in other trHbs. Our results not only reconcile the structural data with the kinetic information, but also provide additional insight into the general behaviour of trHbs. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Improving the analysis of NMR spectra tracking pH‐induced conformational changes: Removing artefacts of the electric field on the NMR chemical shift
Authors: Kukić Predrag , Farrell Damien , Søndergaard Chresten R. , Bjarnadottir Una , Bradley John , Pollastri Gianluca , Nielsen Jens Erik
Published: September 2009

pH‐induced chemical shift perturbations (CSPs) can be used to study pH‐dependent conformational transitions in proteins. Recently, an elegant principal component analysis (PCA) algorithm was developed and used to study the pH‐dependent structural transitions in bovine β‐lactoglobulin (βLG) by analyzing its NMR pH‐titration spectra. Here, we augment this analysis method by filtering out changes in the NMR chemical shift that stem from effects that are electrostatic in nature. Specifically, we examine how many CSPs can be explained by purely electrostatic effects arising from titrational events in βLG. The results show that around 20% of the amide nuclei CSPs in βLG originate exclusively from “through‐space” electric field effects. A PCA of NMR data where electric field artefacts have been removed gives a different picture of the pH‐dependent structural transitions in βLG. The method implemented here is well suited to be applied on a whole range of proteins, which experience at least one pH‐dependent conformational change. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Multi‐scale characterization of the energy landscape of proteins with application to the C3D/Efb‐C complex
Authors: Haspel Nurit , Geisbrecht Brian V. , Lambris John , Kavraki Lydia
Published: September 2009

We present a novel multi‐level methodology to explore and characterize the low energy landscape and the thermodynamics of proteins. Traditional conformational search methods typically explore only a small portion of the conformational space of proteins and are hard to apply to large proteins due to the large amount of calculations required. In our multi‐scale approach, we first provide an initial characterization of the equilibrium state ensemble of a protein using an efficient computational conformational sampling method. We then enrich the obtained ensemble by performing short Molecular Dynamics (MD) simulations on selected conformations from the ensembles as starting points. To facilitate the analysis of the results, we project the resulting conformations on a low‐dimensional landscape to efficiently focus on important interactions and examine low energy regions. This methodology provides a more extensive sampling of the low energy landscape than an MD simulation starting from a single crystal structure as it explores multiple trajectories of the protein. This enables us to obtain a broader view of the dynamics of proteins and it can help in understanding complex binding, improving docking results and more. In this work, we apply the methodology to provide an extensive characterization of the bound complexes of the C3d fragment of human Complement component C3 and one of its powerful bacterial inhibitors, the inhibitory domain of Staphylococcus aureus extra‐cellular fibrinogen‐binding domain (Efb‐C) and two of its mutants. We characterize several important interactions along the binding interface and define low free energy regions in the three complexes. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Neuroprotective effects of Brazilian green propolis and its main constituents against oxygen‐glucose deprivation Stress, with a gene‐expression analysis
Authors: Nakajima Yoshimi , Shimazawa Masamitsu , Mishima Satoshi , Hara Hideaki
Published: September 2009

Our purpose was to investigate the neuroprotective effects (and the underlying mechanism) exerted by water extract of Brazilian green propolis (WEP) and its main constituents against the neuronal damage induced by oxygen‐glucose deprivation (OGD)/reoxygenation in retinal ganglion cells (RGC‐5, a rat ganglion cell‐line transformed using E1A virus). Cell damage was induced by OGD 4 h plus reoxygenation 18 h exposure. In RGC‐5, and also in PC12 (rat pheochromocytoma, neuronal cells), WEP and some of its main constituents attenuated the cell damage. At the end of the period of OGD/reoxygenation, RNA was extracted and DNA microarray analysis was performed to examine the gene‐expression profile in RGC‐5. Expression of casein kinase 2 (CK2) was down‐regulated and that of Bcl‐2‐related ovarian killer protein (Bok) was up‐regulated following OGD stress, results that were confirmed by quantitative reverse transcriptase‐PCR (qRT‐PCR). These effects were normalized by WEP. Our findings indicate that WEP has neuroprotective effects against OGD/reoxygenation‐induced cell damage and that certain constituents of WEP (caffeoylquinic acid derivatives, artepillin C, and p‐coumaric acid) may be partly responsible for its neuroprotective effects. Furthermore, the protective mechanism may involve normalization of the expressions of antioxidant‐ and apoptosis‐related genes (such as CK2 and Bok, respectively). Copyright © 2009 John Wiley & Sons, Ltd.
The effect of latent cooling processes in tropical cyclone simulations
Authors: Frisius Thomas , Hasselbeck Thomas
Published: September 2009

In order to estimate the role of latent cooling processes for tropical cyclones, we have performed sensitivity simulations with both the axisymmetric cloud‐resolving model HURMOD and the fully three‐dimensional COSMO model of the German Weather Service. As an idealised initial state, a convectively unstable vortex with superimposed entropy anomalies has been assumed. While growth rate and maximum wind speeds become unnaturally large in simulations without latent cooling processes, the presence of these processes proves to be necessary to maintain convection outside the eyewall and turns out to be responsible for a delayed development of the tropical cyclone. The latter result is in accordance with the findings of Gray, based on observations. Furthermore, intensity fluctuations of the mature tropical cyclone only occur in HURMOD when latent cooling processes are simulated.

An analysis of CAPE, CIN and DCAPE reveals that convection outside the eyewall explains these intensity fluctuations by mixing low‐entropy air into the boundary layer, while without latent cooling processes significant convective inhibition due to drying by absence of evaporation and cyclone‐scale subsidence suppresses vertical mixing. HURMOD does not exhibit a threshold amplitude but a sea‐surface temperature threshold for tropical cyclogenesis, while the latter only occurs with latent cooling processes. However, a threshold depending on the initial vortex amplitude, together with a stronger response to latent cooling processes, is found in the COSMO model simulations. This seems to be caused by non‐axisymmetric disturbances which may circumvent cyclogenesis for a small initial vortex amplitude. Copyright © 2009 Royal Meteorological Society
Theoretical studies on ionization potential of aluminum clusters
Authors: Phung Thi Viet Bac , Hashimoto Taihei , Nishikawa Kyoshi , Nagao Hidemi
Published: September 2009

The ionization potentials (IPs) of aluminum Al (clustersN) are investigated using density functional calculations based on the plane‐wave basis set and the projector‐augmented wave method. We discuss the size dependence of the IP in relation to the electron affinity, the chemical hardness of both the small‐sized and large cuboctahedral AlN containing up to 923 atoms and compare the computational results with other models of Wood and Perdew based on the jellium model. We show that the IP and electron affinity of large clusters in this size region can be extrapolated to the value of the work function for the bulk aluminum. Expressions of the higher‐order IP of metallic clusters are derived by the extension of the Perdew model. We discuss the IP of a collective system of metallic clusters as a simple model of clusters on a thin film in the framework of the Perdew model. The critical size of superconductivity of aluminium cluster is discussed by using the present results of the average energy‐level spacing. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Molecular simulation of the water meniscus in dip‐pen nanolithography
Authors: Kim Hyojeong , Saha Leton C. , Saha Joyanta K. , Jang Joonkyung
Published: September 2009

We report a molecular dynamics simulation of the nanometer water meniscus formed in dip‐pen nanolithography (DPN). When an atomic force microscope tip is in contact with a surface, the meniscus is significantly asymmetric around the tip axis. The meniscus as a whole can move away from the tip axis due to surface diffusion. The structure of the meniscus fluctuates and its periphery has a finite thickness as large as 25% of its width. We simulated the transport of nonpolar hydrophobic molecules through a water meniscus. Molecules move on the surface of, not dissolving into the interior of, the meniscus. As a result, an annular pattern forms in DPN. Even if the meniscus is cylindrically symmetric, the molecular flow from the tip and the subsequent pattern growth on the surface are anisotropic at the nanosecond timescale. SCANNING 32: 2–8, 2010. © 2009 Wiley Periodicals, Inc.
Toward the Development of “Nano‐QSARs”: Advances and Challenges
Authors: Puzyn Tomasz , Leszczynska Danuta , Leszczynski Jerzy
Published: September 2009

The most significant achievements and challenges relating to an application of quantitative structure–activity relationship (QSAR) approach in the risk assessment of nanometer‐sized materials are highlighted. Recent advances are discussed in the context of “classical” QSAR methodology. The possible ways for the structural characterization of compounds existing at the nanoscale (at least one dimension of 100 nm or less) are briefly reviewed. The applicability of the existing toxicological data for developing QSAR models is evaluated. Finally, the existing models are presented. The need to develop new interpretative descriptors for the nanosystems is also highlighted. It is suggested that, due to high variability in the molecular structures and different mechanisms of toxicity, individual classes of nanoparticles should be modeled separately.

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Microfabricated Devices for Enhanced Bioadhesive Drug Delivery: Attachment to and Small‐Molecule Release Through a Cell Monolayer Under Flow
Authors: Ainslie Kristy M. , Lowe Rachel D. , Beaudette Tristan T. , Petty Lamar , Bachelder Eric M. , Desai Tejal A.
Published: September 2009

The development of a novel microfabricated device for oral drug delivery that overcomes many of the common barriers present in the gastrointestinal tract is reported. Specifically, the attachment of targeting ligands, subsequent device binding, and small molecule release from the microdevices in flow are investigated. A diffusion chamber that permits the simultaneous study of particle binding and small‐molecule release under physiologically relevant shear conditions is developed. It is observed that once the particles bind to the cell surface, they remain attached. A small fraction of the devices detach in flow; however, most of these devices readily reattach to the cell layer in a new location. This steady‐state density of microdevices is most likely the result of larger order microdevice clusters releasing their loose interactions with nearby microdevices, shifting slightly downstream, and subsequently reattaching to the cell monolayer. The release of a model small molecule from microdevices over time is roughly linear and approximately ten times greater than that observed with the small molecule alone. Overall, the preparation and characterization of an oral drug‐delivery microdevice system capable of both targeting and asymmetric release in flow is reported.
Nanomolding of PEG‐Based Hydrogels with Sub‐10‐nm Resolution
Authors: Diez Mar , Mela Petra , Seshan Venkatash , Möller Martin , Lensen Marga C.
Published: September 2009

A simple, soft nanolithographic method is used to fabricate sub‐10‐nm structures on star polyethylene glycol‐based hydrogels and perfluoropolyether‐based materials. Very small features, for example, gold nanoparticles of size ≈8 nm with an interparticle distance of ≈100 nm, are successfully reproduced from a hard silicon master into both elastomers. Scanning force microscopy is used to investigate the replicas, and the original hexagonal pattern of the nanoparticles is clearly recognized. In addition, both replicas are usable as secondary, soft molds yielding positive copies of the primary, hard master. The results presented here show similar replication capabilities for both elastomers despite the markedly different properties of the precursors. Moreover, the hydrogel material can be easily peeled off from both soft and silicon masters without the need for surface treatment. The procedure allows nanopatterning of a biocompatible material over large areas, which is a useful tool to investigate cellular responses to defined nanotopography.
Droplet‐Based Microfluidic Synthesis of Anisotropic Metal Nanocrystals
Authors: Duraiswamy Suhanya , Khan Saif A.
Published: September 2009

A droplet‐based microfluidic method for the preparation of anisotropic gold nanocrystal dispersions is presented. Gold nanoparticle seeds and growth reagents are dispensed into monodisperse picoliter droplets within a microchannel. Confinement within small droplets prevents contact between the growing nanocrystals and the microchannel walls. The critical factors in translating macroscale flask‐based methods to a flow‐based microfluidic method are highlighted and approaches are demonstrated to flexibly fine tune nanoparticle shapes into three broad classes: spheres/spheroids, rods, and extended sharp‐edged structures, thus varying the optical resonances in the visible–near‐infrared (NIR) spectral range.
Structural Trends in Coordination Polymers Containing Perfluorinated Dicarboxylates and 4,4′‐Bipyridine
Authors: Hulvey Zeric , Ayala Elizabeth , Cheetham Anthony K.
Published: September 2009

A new family of coordination polymers has been synthesized using cobalt or zinc, 4,4′‐bipyridine (4,4′‐bpy), and the perfluorinated dicarboxylates tetrafluoroterephthalate (tftpa), tetrafluorophthalate (tfpha), tetrafluoroisophthalate (tfipa), and tetrafluorosuccinate (tfsuc). These materials form under similar conditions and all display similar octahedral metal coordination environments despite significant differences in their structures. The compounds M(4,4′‐bpy)(tftpa)(H2O)2 (M = Co, Zn) (1) and M(4,4′‐bpy)(tfpha)(H2O)2 (M = Co, Zn) (2) are two‐dimensional layered structures, whereas Co(4,4′‐bpy)(tfsuc)(H2O)2 (3) and M(4,4′‐bpy)(tfipa)(H2O)2 (M = Co, Zn) (4) display three‐dimensional connectivity built up from two types of interconnected chains.
National Selection and Recruitment in Urology: 2009
Authors: Bolton J.F. , Lemberger R.J. , Neligan P. , Eardley I.
Published: September 2009

In 2009, recruitment into higher urological training changed dramatically to a process of national selection.

This article describes the process used, presents feedback from the assessors and candidates involved, and discusses possible improvements for future rounds.
Ultrasound and pain in children: A review
Authors: Mossetti Valeria , Ivani Giorgio
Published: September 2009

Ultrasound guidance has been demonstrated to improve block characteristics in children including shorter block performance time, higher success rates, shorter onset time, longer block duration, less volume of local anesthetic agents and visibility of neuraxial structures.

Clinical studies in children suggest that ultrasound guidance has some advantages over more traditional nerve stimulation‐based techniques for regional block. However, the advantage of ultrasound guidance on safety over traditional has not been adequately demonstrated in children except ilio‐inguinal blocks.

There are only a limited number of randomized control trails in children comparing ultrasound guided peripheral nerve block with other techniques. Available evidence in children demonstrates that ultrasound guided peripheral nerve blocks improve the quality, onset, duration and success rate of nerve blocks and help to lower the local anesthetic volume needed to perform blocks.
Cesarean delivery outcomes from the WHO global survey on maternal and perinatal health in Africa
Authors: Shah Archana , Fawole Bukola , M'Imunya James Machoki , Amokrane Faouzi , Nafiou Idi , Wolomby Jean‐José , Mugerwa Kidza , Neves Isilda , Nguti Rosemary , Kublickas Marius , Mathai Matthews
Published: September 2009

Objective

To assess the association between cesarean delivery rates and pregnancy outcomes in African health facilities.

Methods

Data were obtained from all births over 2–3 months in 131 facilities. Outcomes included maternal deaths, severe maternal morbidity, fresh stillbirths, and neonatal deaths and morbidity.

Results

Median cesarean delivery rate was 8.8% among 83 439 births. Cesarean deliveries were performed in only 95 (73%) facilities. Facility‐specific cesarean delivery rates were influenced by previous cesarean, pre‐eclampsia, induced labor, referral status, and higher health facility classification scores. Pre‐eclampsia increased the risks of maternal death, fresh stillbirths, and severe neonatal morbidity. Adjusted emergency cesarean delivery rate was associated with more fresh stillbirths, neonatal deaths, and severe neonatal morbidity—probably related to prolonged labor, asphyxia, and sepsis. Adjusted elective cesarean delivery rate was associated with fewer perinatal deaths.

Conclusion

Use of cesarean delivery is limited in the African health facilities surveyed. Emergency cesareans, when performed, are often too late to reduce perinatal deaths.
Association between habitual coffee consumption and normal or increased estimated glomerular filtration rate in apparently healthy adults
Authors: Nakajima Kei , Hirose Kazuki , Ebata Midori , Morita Kumiko , Munakata Hiromi
Published: September 2009

Habitual coffee consumption is associated with the prevention of type 2 diabetes, which often accompanies diabetic nephropathy. However, the relationship between coffee consumption and kidney function is unclear. Therefore, we investigated the associations between habitual coffee consumption and kidney function and damage assessed by the estimated glomerular filtration rate (eGFR) and proteinuria using dipstick urinalysis, respectively, in a cross-sectional study of 342 apparently healthy adults. Habitual coffee consumption was defined as drinking one or more cups of coffee per d. eGFR in coffee consumers (n182; 80·1 (sd15·0) ml/min per 1·73 m2) was significantly higher than that in non-coffee consumers (n160; 76·9 (sd12·6) ml/min per 1·73 m2) (P < 0·05). Multivariate logistic analysis showed that, compared with non-coffee consumption, coffee consumption was significantly associated with normal or increased eGFR (NIGFR) ( ≥ 90 ml/min per 1·73 m2), but not proteinuria, which was not attenuated, even after adjustment for age, sex, smoking, tea consumption and other cardiovascular risks (OR 2·91; 95 % CI 1·51, 5·61;P = 0·001). When we took into account eGFR measured 1 year before in a subgroup of the subjects (n262), coffee consumption (n142) had a significant relationship with eGFR, which was consistently higher with a difference of 4·0 ml/min per 1·73 m2compared with non-coffee consumption (P = 0·01; two-way repeated ANOVA). Similar associations were observed in both sexes when data were reanalysed according to sex. In conclusion, our findings suggest that habitual coffee consumption is associated with NIGFR independently of clinical confounders. Further studies are needed to confirm this association and to explore whether the effect of coffee consumption on eGFR is beneficial for the kidney.
Vitamin D supplementation reduces insulin resistance in South Asian women living in New Zealand who are insulin resistant and vitamin D deficient – a randomised, placebo-controlled trial
Authors: von Hurst Pamela R. , Stonehouse Welma , Coad Jane
Published: September 2009

Low serum 25-hydroxyvitamin D (25(OH)D) has been shown to correlate with increased risk of type 2 diabetes. Small, observational studies suggest an action for vitamin D in improving insulin sensitivity and/or insulin secretion. The objective of the present study was to investigate the effect of improved vitamin D status on insulin resistance (IR), utilising randomised, controlled, double-blind intervention administering 100 μg (4000 IU) vitamin D3(n42) or placebo (n39) daily for 6 months to South Asian women, aged 23–68 years, living in Auckland, New Zealand. Subjects were insulin resistant – homeostasis model assessment 1 (HOMA1)>1·93 and had serum 25(OH)D concentration < 50 nmol/l. Exclusion criteria included diabetes medication and vitamin D supplementation >25 μg (1000 IU)/d. The HOMA2 computer model was used to calculate outcomes. Median (25th, 75th percentiles) serum 25(OH)D3increased significantly from 21 (11, 40) to 75 (55, 84) nmol/l with supplementation. Significant improvements were seen in insulin sensitivity and IR (P = 0·003 and 0·02, respectively), and fasting insulin decreased (P = 0·02) with supplementation compared with placebo. There was no change in C-peptide with supplementation. IR was most improved when endpoint serum 25(OH)D reached ≥ 80 nmol/l. Secondary outcome variables (lipid profile and high sensitivity C-reactive protein) were not affected by supplementation. In conclusion, improving vitamin D status in insulin resistant women resulted in improved IR and sensitivity, but no change in insulin secretion. Optimal vitamin D concentrations for reducing IR were shown to be 80–119 nmol/l, providing further evidence for an increase in the recommended adequate levels. Registered Trial No. ACTRN12607000642482.
Glycaemic index and glycaemic load values of a selection of popular foods consumed in Hong Kong
Authors: Lok Kris Y. , Chan Ruth , Chan Dicken , Li Liz , Leung Grace , Woo Jean , Lightowler Helen J. , Henry C. Jeya K.
Published: September 2009

The objective of the present paper is to provide glycaemic index (GI) and glycaemic load (GL) values for a variety of foods that are commonly consumed in Hong Kong and expand on the international GI table of Chinese foods. Fasted healthy subjects were given 50 g of available carbohydrate servings of a glucose reference, which was tested twice, and test foods of various brands of noodles (n5), instant cereals (n3) and breads (n2), which were tested once, on separate occasions. For each test food, tests were repeated in ten healthy subjects. Capillary blood glucose was measured via finger-prick samples in fasting subjects ( − 5, 0 min) and at 15, 30, 45, 60, 90 and 120 min after the consumption of each test food. The GI of each test food was calculated geometrically by expressing the incremental area under the blood glucose response curve (IAUC) of each test food as a percentage of each subject's average IAUC for the reference food. GL was calculated as the product of the test food's GI and the amount of available carbohydrate in a reference serving size. The majority of GI values of foods tested were medium (a GI value of 56–69) to high (a GI value of 70 or more) and compared well with previously published values. More importantly, our dataset provides GI values of ten foods previously untested and presents values for foods commonly consumed in Hong Kong.
Low calcium:phosphorus ratio in habitual diets affects serum parathyroid hormone concentration and calcium metabolism in healthy women with adequate calcium intake
Authors: Kemi Virpi E. , Kärkkäinen Merja U. M. , Rita Hannu J. , Laaksonen Marika M. L. , Outila Terhi A. , Lamberg-Allardt Christel J. E.
Published: September 2009

Excessive dietary P intake alone can be deleterious to bone through increased parathyroid hormone (PTH) secretion, but adverse effects on bone increase when dietary Ca intake is low. In many countries, P intake is abundant, whereas Ca intake fails to meet recommendations; an optimal dietary Ca:P ratio is therefore difficult to achieve. Our objective was to investigate how habitual dietary Ca:P ratio affects serum PTH (S-PTH) concentration and other Ca metabolism markers in a population with generally adequate Ca intake. In this cross-sectional analysis of 147 healthy women aged 31–43 years, fasting blood samples and three separate 24-h urinary samples were collected. Participants kept a 4-d food record and were divided into quartiles according to their dietary Ca:P ratios. The 1st quartile with Ca:P molar ratio ≤ 0·50 differed significantly from the 2nd (Ca:P molar ratio 0·51–0·57), 3rd (Ca:P molar ratio 0·58–0·64) and 4th (Ca:P molar ratio ≥ 0·65) quartiles by interfering with Ca metabolism. In the 1st quartile, mean S-PTH concentration (P = 0·021) and mean urinary Ca (U-Ca) excretion were higher (P = 0·051) than in all other quartiles. These findings suggest that in habitual diets low Ca:P ratios may interfere with homoeostasis of Ca metabolism and increase bone resorption, as indicated by higher S-PTH and U-Ca levels. Because low habitual dietary Ca:P ratios are common in Western diets, more attention should be focused on decreasing excessively high dietary P intake and increasing Ca intake to the recommended level.
Development of larvalContracaecum rudolphiiHartwich, 1964 (Ascaridida: Anisakidae) in experimentally infected goldfish (Carassius auratusL., 1758)
Authors: Dziekońska-Rynko J. , Rokicki J. , Gomułka P.
Published: September 2009

Laboratory-bred goldfish were experimentally infected withContracaecum rudolphii, either directly (with nematode larvae) or indirectly via infected zooplankton. Intensity and prevalence of infection were markedly higher in fish exposed to the infected zooplankton than in goldfish exposed to nematode larvae. When transmitted to fish via the zooplankton, larvae developed much faster and, after 8 weeks, became firmly encysted in the intestine wall. The digestive tract of larvae isolated from the intestine wall showed a well-developed ventriculus, ventricular appendix and intestinal caecum. The mouth was surrounded by three lips. When free-living larvae induced infection, they rapidly penetrated the intestine wall and migrated to internal organs (e.g. liver). The primordial lips of those larvae were poorly visible, the ventricular appendix was short, and the intestinal caecum was absent. During the 10-week experiment, no encysted larvae were found in fish infected with free-living larvae.
The Uses of Books in a Late Mughal Takiyya: Persianate Knowledge Between Person and Paper
Authors: GREEN NILE
Published: September 2009

This paper addresses several questions that appear preliminary to understanding the circulation of knowledge in early modern India (circa1500 to 1800): What work did writing do? What was the relationship between writing and speaking? And what can our answers to these questions tell us about cultural formulations of ‘knowledge’ in this period? After addressing these questions on ‘modes’ of circulation, this paper turns to the more practical issue of ‘means’ of circulation, looking at the intersection between religious and bureaucratic patterns of the production and consumption of books in the absence of printing in Indian languages. Overall, the paper argues for early modernity as a period of tension and transition between ‘anthropocentric’ and ‘bibliocentric’ attitudes towards the location and thence circulation of knowledge in a Persianate context. The issues are exemplified by reference to the various and, at times, perplexing uses of books in an imperial dervish lodge ortakiyya.
Letters Home: Banaras pandits and the Maratha regions in early modern India
Authors: O'HANLON ROSALIND
Published: September 2009

Maratha Brahman families migrated to Banaras in increasing numbers from the early sixteenth century. They dominated the intellectual life of the city and established an important presence at the Mughal and other north Indian courts. They retained close links with Brahmans back in the Maratha regions, where pressures of social change and competition for rural resources led to acrimonious disputes concerning ritual entitlement and precedence in the rural social order. Parties on either side appealed to Banaras for resolution of the disputes, raising serious questions about the nature of Brahman community and identity. Banaras pandit communities struggled to contain these disputes, even as the symbols of their own authority came under attack from the Mughal emperor Aurangzeb. By the early eighteenth century, the emergence of the Maratha state created new models of Brahman authority and community, and new patterns for the resolution of such disputes.
Case-control study on Puumala virus infection: smoking is a risk factor
Authors: VAPALAHTI K. , VIRTALA A.-M. , VAHERI A. , VAPALAHTI O.
Published: September 2009

Puumala hantavirus (PUUV) is apparently transmitted to humans by inhalation of aerosolized secretions of carrier rodents (bank voles). The means of transmission and the associated risk factors are poorly defined. An epidemiological study during the peak of an epidemic season in Finland was conducted based on 282 acute clinical PUUV infections and 204 controls without PUUV infection or immunity. The main risk factors adjusted by age, sex and living environment were cigarette smoking [odds ratio (OR) 3·6, 95% confidence interval (CI) 2·1–5·9,P<0·0001] and buildings with holes allowing rodents to enter (OR 3·3, 95% CI 2·0–5·6); these results were similar in two subsets. Further, use of rodent traps (OR3·5, 95% CI 2·2–5·7) and handling firewood (OR 2·7, 95% CI 1·6–4·4) were associated with a risk. The risk attributed to smoking also remained high using simulated population controls with average smoking habits. The results suggest that hantavirus transmission occurs by inhalation mainly indoors and is dependent on the condition of the respiratory tract.
Epidemiology of group B streptococcus in Korean pregnant women
Authors: LEE B. K. , SONG Y. R. , KIM M. Y. , YANG J. H. , SHIN J. H. , SEO Y. S. , OH K. Y. , YOON H. R. , PAI S. Y. , FOXMAN B. , KI M.
Published: September 2009

Between January 2006 and May 2008, 2624 pregnant S. Korean women between 35–37 weeks gestation were screened for group B streptococcus (GBS). Resistance to antimicrobials was tested by disk diffusion and serotype determined using co-agglutination assays and microarray methods. Overall, 8% of pregnant women were colonized. Serotype III was the predominant serotype (43·8%), followed by serotypes V (20·3%), Ia (12·1%), and Ib (9·5%). GBS was frequently resistant to clindamycin (54·0%) and erythromycin (25·6%); 3·7% were resistant to cefazolin. More than three-quarters of serotype V were resistant to clindamycin or erythromycin or both, and 71% of serotype III were resistant to clindamycin but only 12% were resistant to erythromycin. GBS prevalence exceeded earlier reports by one-third. This is the first report of cefazolin resistance in Korea. These results underscore the need to establish screening measures and chemoprophylaxis guidelines regarding GBS infections in Korea.
Modelling the impact of one-dosevs. two-dose vaccination regimens on the epidemiology of varicella zoster virus in Australia
Authors: GAO Z. , GIDDING H. F. , WOOD J. G. , MacINTYRE C. R.
Published: September 2009

We examined the impact of one-dosevs. two-dose vaccination strategies on the epidemiology of varicella zoster virus (VZV) in Australia, using a mathematical model. Strategies were assessed in terms of varicella (natural and breakthrough) and zoster incidence, morbidity, average age of infection and vaccine effectiveness (VE). Our modelling results suggest that compared to a one-dose vaccination strategy (Australia's current vaccination schedule), a two-dose strategy is expected to not only produce less natural varicella cases (5%vs. 13% of pre-vaccination state, respectively) but also considerably fewer breakthrough varicella cases (only 11·4% of one-dose strategy). Therefore a two-dose infant vaccination programme would be a better long-term strategy for Australia.
Tense and verb raising in advanced L2 French
Authors: HERSCHENSOHN JULIA , ARTEAGA DEBORAH
Published: September 2009

Two UG approaches to L2A propose different views of parameter resetting, depending on the capacity of interlanguage grammars to gain new values for uninterpretable functional features. Representational Deficit/Interpretability (e.g. Hawkins, 2003) maintains that parameter settings are limited to L1 values, whereas Full Access (e.g. Prévost & White, 2000) claims L2 parameter values may be gained; both assume initial transfer of L1 morphosyntactic settings. We examine verb morphosyntax of three advanced anglophone learners of L2 French, beginning with a description of the theoretical issues. We next report the study: the subjects, data collection and results. The final section discusses the data in terms of the two approaches, concluding that the results generally support FA over RD/I.
Second-person pronoun use in French language discussion fora
Authors: WILLIAMS LAWRENCE , VAN COMPERNOLLE RÉMI A.
Published: September 2009

This article examines the use of second-person pronouns in on-line French language discussion fora, with specific focus onDoctissimoandMeilleur du chef, two fora from which approximately 400,000 words were collected for this corpus. Two hundred discussion threads (i.e., series of linked postings), with a minimum of fifteen postings (i.e., messages) and a maximum of twenty per thread, were analysed in three different ways in order to determine whethertu,vous-singular, or neither could be considered the default address pronoun. The results of the analysis suggest that whiletuis clearly preferred in many cases, its use has not become systematic.
Sarcoglycanopathies: molecular pathogenesis and therapeutic prospects
Authors: Sandonà Dorianna , Betto Romeo
Published: September 2009

Sarcoglycanopathies are a group of autosomal recessive muscle-wasting disorders caused by genetic defects in one of four cell membrane glycoproteins, α-, β-, γ- or δ-sarcoglycan. These four sarcoglycans form a subcomplex that is closely linked to the major dystrophin-associated protein complex, which is essential for membrane integrity during muscle contraction and provides a scaffold for important signalling molecules. Proper assembly, trafficking and targeting of the sarcoglycan complex is of vital importance, and mutations that severely perturb tetramer formation and localisation result in sarcoglycanopathy. Gene defects in one sarcoglycan cause the absence or reduced concentration of the other subunits. Most genetic defects generate mutated proteins that are degraded through the cell's quality control system; however, in many cases, conformational modifications do not affect the function of the protein, yet it is recognised as misfolded and prematurely degraded. Recent evidence shows that misfolded sarcoglycans could be rescued to the cell membrane by assisting their maturation along the ER secretory pathway. This review summarises the etiopathogenesis of sarcoglycanopathies and highlights the quality control machinery as a potential pharmacological target for therapy of these genetic disorders.
Late Cenozoic evolution of the central Longmen Shan, eastern Tibet: Insight from (U‐Th)/He thermochronometry
Authors: Godard V. , Pik R. , Lavé J. , Cattin R. , Tibari B. , de Sigoyer J. , Pubellier M. , Zhu J.
Published: September 2009

This article presents (U‐Th)/He thermochronological data from the Longmen Shan belt, eastern Tibet. Located between the Songpan‐Garze terrane and the Yangtze craton, this mountain range is one of the steepest margins of the Tibetan Plateau and an important area for the comprehension of the mechanisms that control the dynamics of such plateau borders in terms of spatial distribution of deformation or timing of topographic building. We describe several age‐elevation transects and perform forward modeling of our data to derive quantitative information on the exhumation of the range. A major phase of exhumation started at 8–11 Ma, with an average rate of ∼0.65 mm a−1. Comparison of zircon and apatite ages indicates that the eastern part of the range may have experienced a significant decrease in exhumation since 2–3 Ma. We use the distribution of finite exhumation across the major faults of the area to quantify their dip‐slip throw rate over the last 10 Ma. The Beichuan Fault, which was activated during the 2008 Sichuan earthquake, is the major active structure of the Longmen Shan since the late Miocene, with an average thrusting slip rate between 0.4 and 1 mm a−1. Conversely, over the same time period, only minor dip‐slip activity occurred on the Wenchuan Fault Zone. This distribution in space and time of exhumation and deformation is discussed and compared to the different proposed models for the geodynamical evolution of the eastern Tibetan margin. It also provides an important long‐term perspective to put in context the destructive 2008 Sichuan earthquake that struck the central Longmen Shan.
Satellite assessment of land surface evapotranspiration for the pan‐Arctic domain
Authors: Mu Qiaozhen , Jones Lucas A. , Kimball John S. , McDonald Kyle C. , Running Steven W.
Published: September 2009

Regional evapotranspiration (ET), including water loss from plant transpiration and soil evaporation, is essential to understanding interactions between land‐atmosphere surface energy and water balances. Vapor pressure deficit (VPD) and surface air temperature are key variables for stomatal conductance and ET estimation. We developed an algorithm to estimate ET using the Penman‐Monteith approach driven by Moderate Resolution Imaging Spectroradiometer (MODIS)‐derived vegetation data and daily surface meteorological inputs including incoming solar radiation, air temperature, and VPD. The model was applied using alternate daily meteorological inputs, including (1) site level weather station observations, (2) VPD and air temperature derived from the Advanced Microwave Scanning Radiometer (AMSR‐E) on the EOS Aqua satellite, and (3) Global Modeling and Assimilation Office (GMAO) reanalysis meteorology‐based surface air temperature, humidity, and solar radiation data. Model performance was assessed across a North American latitudinal transect of six eddy covariance flux towers representing northern temperate grassland, boreal forest, and tundra biomes. Model results derived from the three meteorology data sets agree well with observed tower fluxes (r > 0.7; P < 0.003; root mean square error of latent heat flux <30 W m−2) and capture spatial patterns and seasonal variability in ET. The MODIS‐AMSR‐E–derived ET results also show similar accuracy to ET results derived from GMAO, while ET estimation error was generally more a function of algorithm parameterization than differences in meteorology drivers. Our results indicate significant potential for regional mapping and monitoring daily land surface ET using synergistic information from satellite optical IR and microwave remote sensing.
Characterization of soil moisture responses on a hillslope to sequential rainfall events during late autumn and spring
Authors: Kim Sanghyun
Published: September 2009

In this study, the results of intensive soil moisture monitoring and analysis are reported in order to highlight the seasonal differences in hydrological processes on a hillslope scale. A soil monitoring system for a steep hillslope was designed and installed to monitor the temporal features of soil moisture with respect to the terrain attributes. Comparison of soil moisture analyses for two different periods, one during late autumn and the other during late spring, yielded different soil moisture characteristics, even though both seasons were subject to similar rainfall and saturation conditions. Comparative analyses indicated that soil moisture response patterns can be characterized and classified into three different zones. A substantial portion of the rainfall contributed to recharge of the water storage in autumn, while soil moisture responses were less variable during spring. Infiltration patterns between the two seasons were significantly different, hence the different distribution of soil moisture and hydrological responses. Vertical flux and recharge were the requirements for lateral redistribution of soil moisture in the study area. The seasonal impact of the vegetation, such as transpiration, fine root density, and interception, is apparent on the soil moisture distribution on the hillslope scale as well as runoff features in the mountainous forest catchment.
Empirical analysis of the planform curvature‐migration relation of meandering rivers
Authors: Güneralp İnci , Rhoads Bruce L.
Published: September 2009

Meandering rivers are among the most dynamic Earth surface systems, exhibiting progressive change in channel location as they migrate across their floodplains over time. Theoretical models of meandering have defined the influence of planform curvature on meandering in the form of a spatial convolution function that expresses migration at any point along the channel as a weighted aggregate of local, upstream, and, most recently, downstream curvature. This study evaluates empirically the spatial planform curvature‐migration relation of meandering rivers using data obtained from natural meandering rivers with varying degrees of planform complexity and compares the empirical results with the assumed relationships embodied in the theoretical meander migration models. The study is based on a framework that views a meandering river as a dynamical input‐output system where the migration process is characterized by a spatial filter through which planform curvature produces migration. Discrete signal processing is used to derive the spatial planform curvature‐migration relation for each study reach and to analyze the characteristics of this relation via transfer function models. The results demonstrate that the spatial structure of the planform curvature effect on migration rates depends on the complexity of the planform geometry. A first‐order difference equation, in which the planform curvature effect is characterized as an exponential decay, can satisfactorily describe the migration process of a planform containing simple bends, but a high‐order difference equation, which includes oscillatory terms superimposed on exponential decay, is necessary to capture the development of complex meander forms. The findings support recent theoretical studies that suggest that high‐order terms are required in spatial convolution models to generate complex bend geometries.
Net radiative effect of dust aerosols from satellite measurements over Sahara
Authors: Yang Eun‐Su , Gupta Pawan , Christopher Sundar A.
Published: September 2009

The clear‐sky aerosol top of atmosphere shortwave (SW) and longwave (LW) radiative effects over the Saharan desert (15–30°N, 10°W–30°E) are investigated based entirely on the satellite observations of aerosol optical thickness (AOT), surface albedo, surface temperature, surface emissivity, atmospheric water vapor content, and SW/LW fluxes. The Ozone Monitoring Instrument (OMI) on Aura and the Multi‐angle SpectroRadiometer (MISR) on Terra satellite are used to estimate AOT at 558 nm (EAOT) for June to September, 2005–2006 when the predominant aerosol type is dust. We then use these EAOT values in conjunction with broadband measurements from the Clouds and the Earth's Radiant Energy System (CERES) to calculate the top‐of‐atmosphere SW and LW flux radiative effect due to these aerosols. The difference in SW flux between desert surface and dust aerosols is found to be negligible due to the high surface reflectance over the Sahara desert. The instantaneous area‐averaged LW radiative effect is calculated as +11.4 Wm−2 with radiative efficiencies ranging from +11 to +26 Wm−2/AOT. The results indicate that net radiative effect of dust over the Sahara desert is dominated by the longwave effect in contrast to oceans where the shortwave effect dominates.
An empirical seasonal prediction model of the east Asian summer monsoon using ENSO and NAO
Authors: Wu Zhiwei , Wang Bin , Li Jianping , Jin Fei‐Fei
Published: September 2009

How to predict the year‐to‐year variation of the east Asian summer monsoon (EASM) is one of the most challenging and important tasks in climate prediction. It has been recognized that the EASM variations are intimately but not exclusively linked to the development and decay of El Niño or La Niña. Here we present observed evidence and numerical experiment results to show that anomalous North Atlantic Oscillation (NAO) in spring (April–May) can induce a tripole sea surface temperature pattern in the North Atlantic that persists into ensuing summer and excite downstream development of subpolar teleconnections across the northern Eurasia, which raises (or lowers) the pressure over the Ural Mountain and the Okhotsk Sea. The latter strengthens (or weakens) the east Asian subtropical front (Meiyu‐Baiu‐Changma), leading to a strong (or weak) EASM. An empirical model is established to predict the EASM strength by combination of the El Niño–Southern Oscillation (ENSO) and spring NAO. Hindcast is performed for the 1979–2006 period, which shows a hindcast prediction skill that is comparable to the 14 state‐of‐the‐art multimodel ensemble hindcast. Since all these predictors can be readily monitored in real time, this empirical model provides a real time forecast tool.