bluuebunny/crossref_metadata_2025 huggingface dataset:
Error Estimates for 1D Asymptotic Models in Coaxial Cables with Non-Homogeneous Cross-Section
Authors: Imperiale Sébastien , Joly Patrick
Published: November 2012

This paper is the first contribution towards the rigorous justification of asymptotic 1D models for the time-domain simulation of the propagation of electromagnetic waves in coaxial cables. Our general objective is to derive error estimates between the “exact” solution of the full 3D model and the “approximate” solution of the 1D model known as the Telegraphist’s equation.
On the Fully Implicit Solution of a Phase-Field Model for Binary Alloy Solidification in Three Dimensions
Authors: Goodyer Christopher E. , Jimack Peter K. , Mullis Andrew M. , Dong Hongbiao , Xie Yu
Published: November 2012

A fully implicit numerical method, based upon a combination of adaptively refined hierarchical meshes and geometric multigrid, is presented for the simulation of binary alloy solidification in three space dimensions. The computational techniques are presented for a particular mathematical model, based upon the phase-field approach, however their applicability is of greater generality than for the specific phase-field model used here. In particular, an implicit second order time discretization is combined with the use of second order spatial differences to yield a large nonlinear system of algebraic equations as each time step. It is demonstrated that these equations may be solved reliably and efficiently through the use of a nonlinear multigrid scheme for locally refined grids. In effect this paper presents an extension of earlier research in two space dimensions (J. Comput. Phys., 225 (2007), pp. 1271-1287) to fully three-dimensional problems. This extension is validated against earlier two-dimensional results and against some of the limited results available in three dimensions, obtained using an explicit scheme. The efficiency of the implicit approach and the multigrid solver are then demonstrated and some sample computational results for the simulation of the growth of dendrite structures are presented.
Stability of Symmetric Solitary Wave Solutions of a Forced Korteweg-de Vries Equation and the Polynomial Chaos
Authors: Kim Hongjoong , Moon Kyoung-Sook
Published: November 2012

In this paper, we consider the numerical stability of gravity-capillary waves generated by a localized pressure in water of finite depth based on the forced Korteweg-de Vries (FKdV) framework and the polynomial chaos. The stability studies are focused on the symmetric solitary wave for the subcritical flow with the Bond number greater than one third. When its steady symmetric solitary-wave-like solutions are randomly perturbed, the evolutions of some waves show stability in time regardless of the randomness while other waves produce unstable fluctuations. By representing the perturbation with a random variable, the governing FKdV equation is interpreted as a stochastic equation. The polynomial chaos expansion of the random solution has been used for the study of stability in two ways. First it allows us to identify the stable solution of the stochastic governing equation. Secondly it is used to construct upper and lower bounding surfaces for unstable solutions, which encompass the fluctuations of waves.
Development of a new data-processing method for SKYNET sky radiometer observations
Authors: Hashimoto M. , Nakajima T. , Dubovik O. , Campanelli M. , Che H. , Khatri P. , Takamura T. , Pandithurai G.
Published: November 2012

Abstract. In order to reduce uncertainty in the estimation of Direct Aerosol Radiative Forcing (DARF), it is important to improve the estimation of the single scattering albedo (SSA). In this study, we propose a new data processing method to improve SSA retrievals for the SKYNET sky radiometer network, which is one of the growing number of networks of sun-sky photometers, such as NASA AERONET and others. There are several reports that SSA values from SKYNET have a bias compared to those from AERONET, which is regarded to be the most accurate due to its rigorous calibration routines and data quality and cloud screening algorithms. We investigated possible causes of errors in SSA that might explain the known biases through sensitivity experiments using a numerical model, and also using real data at the SKYNET sites at Pune (18.616° N/73.800° E) in India and Beijing (39.586° N/116.229° E) in China. Sensitivity experiments showed that an uncertainty of the order of ±0.03 in the SSA value can be caused by a possible error in the ground surface albedo or solid view angle assumed for each observation site. Another candidate for possible error in the SSA was found in cirrus contamination generated by imperfect cloud screening in the SKYNET data processing. Therefore, we developed a new data quality control method to get rid of low quality or cloud contamination data, and we applied this method to the real observation data at the Pune site in SKYNET. After applying this method to the observation data, we were able to screen out a large amount of cirrus-contaminated data and to reduce the deviation in the SSA value from that of AERONET. We then estimated DARF using data screened by our new method. The result showed that the method significantly reduced the difference of 5 W m−2 that existed between the SKYNET and AERONET values of DARF before screening. The present study also suggests the necessity of preparing suitable a priori information on the distribution of coarse particles ranging in radius between 10 μm and 30 μm for the analysis of heavily dust-laden atmospheric cases.
Using data assimilation to investigate the causes of Southern Hemisphere high latitude cooling from 10 to 8 ka BP
Authors: Mathiot P. , Goosse H. , Crosta X. , Stenni B. , Braida M. , Renssen H. , VanMeerbeek C. , Masson-Delmotte V. , Mairesse A. , Dubinkina S.
Published: November 2012

Abstract. Paleoclimate records show an atmospheric and oceanic cooling in the high latitudes of the Southern Hemisphere from 10 to 8 ka BP. In order to study the causes of this cooling, simulations covering the early Holocene period have been performed with the climate model of intermediate complexity LOVECLIM constrained to follow the signal recorded in climate proxies using a data assimilation method based on a particle filtering. The selected proxies represent oceanic and atmospheric surface temperature in the Southern Hemisphere derived from terrestrial, marine and glaciological records. Using our modeling framework, two mechanisms potentially explaining the 10–8 ka BP cooling pattern are investigated. The first hypothesis is a change in atmospheric circulation. The state obtained by data assimilation displays a modification of the meridional atmospheric circulation around Antarctica, producing a 0.6 °C drop in atmospheric temperatures over Antarctica from 10 to 8 ka BP without congruent cooling of the atmospheric and sea-surface temperature in the Southern Ocean. The second hypothesis is a cooling of the sea surface temperature in the Southern Ocean, simulated here as the response to a higher West Antarctic Ice Sheet melting rate. Using data assimilation, we constrain the fresh water flux to increase by 100 mSv from 10 to 8 ka BP. This perturbation leads to an oceanic cooling of 0.5 °C and a strengthening of Southern Hemisphere westerlies (+6%). However, the observed cooling in Antarctic and the Southern Ocean proxy records can only be reconciled with the combination of a modified atmospheric circulation and an enhanced freshwater flux.
Assessment of the potential forecasting skill of a global hydrological model in reproducing the occurrence of monthly flow extremes
Authors: Candogan Yossef N. , van Beek L. P. H. , Kwadijk J. C. J. , Bierkens M. F. P.
Published: November 2012

Abstract. As an initial step in assessing the prospect of using global hydrological models (GHMs) for hydrological forecasting, this study investigates the skill of the GHM PCR-GLOBWB in reproducing the occurrence of past extremes in monthly discharge on a global scale. Global terrestrial hydrology from 1958 until 2001 is simulated by forcing PCR-GLOBWB with daily meteorological data obtained by downscaling the CRU dataset to daily fields using the ERA-40 reanalysis. Simulated discharge values are compared with observed monthly streamflow records for a selection of 20 large river basins that represent all continents and a wide range of climatic zones. We assess model skill in three ways all of which contribute different information on the potential forecasting skill of a GHM. First, the general skill of the model in reproducing hydrographs is evaluated. Second, model skill in reproducing significantly higher and lower flows than the monthly normals is assessed in terms of skill scores used for forecasts of categorical events. Third, model skill in reproducing flood and drought events is assessed by constructing binary contingency tables for floods and droughts for each basin. The skill is then compared to that of a simple estimation of discharge from the water balance (P−E). The results show that the model has skill in all three types of assessments. After bias correction the model skill in simulating hydrographs is improved considerably. For most basins it is higher than that of the climatology. The skill is highest in reproducing monthly anomalies. The model also has skill in reproducing floods and droughts, with a markedly higher skill in floods. The model skill far exceeds that of the water balance estimate. We conclude that the prospect for using PCR-GLOBWB for monthly and seasonal forecasting of the occurrence of hydrological extremes is positive. We argue that this conclusion applies equally to other similar GHMs and LSMs, which may show sufficient skill to forecast the occurrence of monthly flow extremes.
Brief communication "Historical glacier length changes in West Greenland"
Authors: Leclercq P. W. , Weidick A. , Paul F. , Bolch T. , Citterio M. , Oerlemans J.
Published: November 2012

Abstract. Past glacier fluctuations provide insight into glacier dynamics, climate change, and the contribution of glaciers to sea-level rise. Here, the length fluctuations since the 19th century of 18 local glaciers in West and South Greenland are presented, extending and updating the study by Weidick (1968). The studied glaciers all showed an overall retreat with an average of 1.2 ± 0.2 km over the 20th century, indicating a general rise of the equilibrium line along the west coast of Greenland during the last century. Furthermore, the average rate of retreat was largest in the first half of the 20th century.
Sea ice thickness, freeboard, and snow depth products from Operation IceBridge airborne data
Authors: Kurtz N. T. , Farrell S. L. , Studinger M. , Galin N. , Harbeck J. P. , Lindsay R. , Onana V. D. , Panzer B. , Sonntag J. G.
Published: November 2012

Abstract. The study of sea ice using airborne remote sensing platforms provides unique capabilities to measure a wide variety of sea ice properties. These measurements are useful for a variety of topics including model evaluation and improvement, assessment of satellite retrievals, and incorporation into climate data records for analysis of interannual variability and long-term trends in sea ice properties. In this paper we describe methods for the retrieval of sea ice thickness, freeboard, and snow depth using data from a multi-sensor suite of instruments on NASA's Operation IceBridge airborne campaign. We assess the consistency of the results through comparison with independent data sets which demonstrate that the IceBridge products are capable of providing a reliable record of snow depth and sea ice thickness. We explore the impact of inter-campaign instrument changes and associated algorithm adaptations as well as the applicability of the adapted algorithms to the ongoing IceBridge mission. The uncertainties associated with the retrieval methods are determined and placed in the context of their impact on the retrieved sea ice thickness. Lastly, we present results for the 2009 and 2010 IceBridge campaigns which are currently available in product form via the National Snow and Ice Data Center.
Effect of Topical Pressure-Lowering Medication on Prevention of Intraocular Pressure Spikes after Intravitreal Injection
Authors: Chehab Hussam El , Le Corre Anne , Agard Emilie , Ract-Madoux Guillaume , Coste Olivier , Dot Corinne
Published: November 2012

Purpose

The aim of this study was to evaluate pressure increases after intravitreal injections (IVI) and the interest in using prophylactic pressure-lowering medications.

Methods

This was a prospective study of 250 anti–vascular endothelial growth factor IVI (ranibizumab) divided into 5 groups of 50 IVI (group 1: no intraocular pressure [IOP]–lowering medication; group 2: apraclonidine 1%; group 3: acetazolamide; group 4: fixed association brimonidine + timolol; group 5: fixed association dorzolamide + timolol). The IOP was measured before, immediately after (T1), 15 minutes after (T15), and 45 minutes after (T45) the IVI using a tonometer. The data were analyzed by analysis of variance followed by a Bonferroni as post hoc test if necessary.

Results

The mean IOP peak in group 1 was 46.4±10 mmHg at T1, 21.7±10.2 mmHg at T15, and 15.4±8.6 mmHg at T45. It was not correlated with axial length (r=0.04, p=0.81) or lens status (phakic vs pseudophakic: p=0.88). A mild but significant correlation was found with age (r=0.36, p=0.006). Topical medications produced a significant reduction of IOP at every time point, of around 9 mmHg at T1. The reduction in IOP obtained with acetazolamide was not significant at T1 (-1.6 mmHg, p=0.12), but became significant at T15 and T45 (p=0.011 and p=0.015).

Conclusions

Intraocular pressure spike was high but transient. Topical medications, however, produced a significant reduction in IOP spike as well as in the duration of the increased pressure. It would be advisable to prevent this IOP spike, especially when procedures are repeated, notably in patients with glaucoma.
Development of a real-time general medicine 30-day readmissions notification system
Authors: Bae Jonathan , Owens Thomas , Ferranti Jeffrey M. , Gilbert William , Stashko Ilona , Willis Elizabeth , Barros Tanya , Horvath Monica M.
Published: November 2012

Hospital readmissions present a costly problem for healthcare systems. Engaging care providers in reviewing readmissions may reveal opportunities for reducing readmissions and improving quality. We developed a real-time alerting method that e-mails providers when a discharged patient returns for care (emergency department [ED] or hospital admission) within 30 days. We analyzed the content of alerts to consider frequency of presentation and demographic characteristics of readmitted patients. From 3/15/2011 to 8/31/2011, 1544 alerts (943 ED returns; 601 inpatient readmissions) were generated, representing 621 unique patients (average return time: 12.8±8.5 days). Forty-eight faculty received alerts; 88.8% of alerts were sent to the correct discharging provider. Real-time alerting allows providers to re-engage with readmitted patients and offers a means for evaluating performance. Such systems may also elucidate reasons for readmission by detailing practice patterns and populations at risk for readmission as well as help to design targeted interventions to reduce hospital returns.
Ethnobotanical review of wild edible plants of Slovakia
Authors: Łuczaj Łukasz
Published: November 2012

This paper is an ethnobotanical review of wild edible plants gathered for consumption from the 19th century to the present day, within the present borders of Slovakia. Twenty-four sources (mainly ethnographic) documenting the culinary use of wild plants were analysed. The use of 106 species (over 3% of the Slovak flora) has been recorded. Nowadays most of them are no longer used, or used rarely, apart from a few species of wild fruits. The most frequently used plants include the fruits of Rubus idaeus, Fragaria spp., Rubus subgenus Rubus, Vaccinium myrtillus, V. vitis-idaea, Fagus sylvatica, Corylus avellana, Prunus spinosa, Pyrus spp., Malus spp., Crataegus spp. and the leaves of Urtica dioica, Rumex acetosa, Chenopodiaceae species, Cardamine amara, Glechoma spp., Taraxacum spp. and Oxalis acetosella. The most commonly used wild food taxa are nearly identical to those used in Poland, and the same negative association of wild vegetables with famine exists in Slovakia, resulting in their near complete disappearance from the present-day diet.
Transitive phrasal verbs in acquisition and use: A view from construction grammar
Authors: Hampe Beate
Published: November 2012

Author/s

Beate HampeErfurt University, Germany

 

ABSTRACT

This paper surveys a number of aspects involved in viewing transitive phrasal verbs as verb-particle constructions in the construction-grammar sense of the term. The two word-order templates Verb-Object-Particle and Verb-Particle-Object, as fully schematic and semantically and pragmatically distinct constructions (Gries 2003), are discussed as members of different construction networks, viz. transitive vs. caused-motion constructions, with a focus on the latter. Moreover, the word-order constructions are distinguished from specific phrasal verbs as “formal idioms”. It is argued that the notion of “allostruction” (Cappelle 2006) can be fruitfully applied only at the intermediate level of the latter.The first results of a corpus study using data from CHILDES (parts of Manchester, Fletcher), the ICE-GB and parts of the BNC are reported to support the claim that early instances of transitive phrasal verbs exhibiting the word-order Verb-Object-Particle function as precursors (Diessel 2004) to full-blown, lexically and syntactically more complex realisations of the caused-motion construction. In a more explorative and thus also preliminary way, three hierarchical configurational frequency analyses are employed to trace the constellations of selected features of transitive phrasal verbs across different age groups.
Variability in L2 acquisition of formulaic sequences: A study of linguistic factors in the use and learning of phrasal verbs by non-native speakers
Authors: Alejo-González Rafael
Published: November 2012

Author/s

Rafael Alejo-GonzálezUniversidad de Extremadura, Spain

 

ABSTRACT

In this paper, the acquisition of phrasal verbs (PVs) by L2 learners is explored from the perspective provided by a usage-based approach to language. This involves looking at low scope or item-specific schemas, which in this article are identified as the actual particles, prepositions and PVs used by the learners, together with the more abstract syntactic or semantic schemas that emerge from their use. Given the labour intensive work required by this type of analysis, the focus is placed on the use of verb-out constructions made by L2 learners of the PVs as reflected in a corpus of learner language, i.e. the Spanish, Italian, Swedish, Dutch, Russian and Bulgarian subsections of the ICLE (1,287,517 words). More concretely, I analyse L2 use of out-PVs at different grain levels and provide an account of the factors influencing the acquisition of these linguistic units. The results obtained from the analysis show 1) that out is underused by learners, at the lowest level of constituency, the level of the word and its collocates and that this may be due its low cue answer contingency (it is a short form with many meanings); 2) that out-PVs, as other formulaic sequences, shows a pattern of overuse of a small number of frequent verbs and underuse of the rest; 3) that, at a morpho-syntactic level, out-PVs used by L2 learners are typically frozen with little variability in both the tenses and the syntactic patterns chosen; and 4) that at the semantic level, more prototypical and frequent meanings in the text type analysed, not necessarily literal uses, are used with greater frequency by NNS. All in all, the usage-based approach adopted has allowed us to reveal the complexity of factors involved in explaining the difficulty L2 learners have in acquiring phrasal verbs.
Macmillan Phrasal Verbs Plus
Authors: Ishii Yasutake
Published: November 2012

Reviewed by Yasutake IshiiSeijo University, Tokyo, Japan

 

1. INTRODUCTION

“Phrasal verb” is a term that refers to those units of verbs and particles, i.e. prepositions and adverbs, that have more or less different meanings from those of the verbs alone. Phrasal verbs are extremely significant in the English language. According to Biber et al. (1999: 408-409, 415), more than 2,000 phrasal verbs, items consisting of a verb (and a complement) followed by an adverb in their definition, and over 5,000 prepositional verbs, items consisting of a verb followed by a preposition in their definition, are used in every one million words in fiction and conversations.Macmillan Phrasal Verbs Plus is a specialized dictionary of English phrasal verbs (“PVs”, henceforth) and other structurally similar phrases of verbs and particles. This dictionary is “specially designed to help learners of English deal confidently with phrasal verbs” (page vi). In this review, we will concentrate on three aspects of this dictionary: the coverage of its entry items, the effectiveness and uniqueness of the characteristic features adopted in this dictionary, and a problematic strategy found in the macrostructure of headword PV items. By considering these aspects, we will be able to see whether it is really an effective learning tool for learners.
Temporal changes and regional differences in treatment uptake of hepatitis C therapy in EuroSIDA
Authors: Grint D , Peters L , Vogel M , Beniowski M , Pradier C , Battegay M , Jevtovic D , Soriano V , Lundgren J , Rockstroh J , Kirk O , Mocroft A
Published: November 2012

Up to 30% of European HIV‐positive patients tested for hepatitis C virus (HCV) are seropositive. All co‐infected patients with chronic HCV and ≥F2 fibrosis should be considered for HCV therapy given their increased risk of death from liver disease. Despite this the extent to which co‐infected patients initiate HCV treatment is not well described. The aims of this study were to determine the rate of HCV treatment uptake among co‐infected patients and to estimate the effect of treatment on all‐cause and liver‐related death. EuroSIDA patients positive for HCV antibody and HCV‐RNA were included in the study. Baseline was defined as the date of recruitment or HCV seroconversion, whichever occurred later. Poisson regression was used to identify temporal changes and regional differences in HCV treatment uptake (use of at least interferon‐α [peg‐IFN]± ribavirin) and to study the association between HCV treatment and progression to all‐cause and liver‐related death. 1947 patients were included, with a median follow‐up time of 107 months (IQR: 57–156). Overall 456 (23.4%) of HIV/HCV co‐infected patients have received HCV therapy so far. The incidence of HCV treatment rose from 0.29 (95% CI: 0.13–0.45) per 100 person‐years follow‐up in 1998 to 5.26 (95% CI: 3.87–65) in 2007, before falling to 3.73 (95% CI: 2.40–5.06) in 2009. There were considerable regional differences (Figure). In a multivariable model treatment incidence increased 11.0% (95% CI: 4.0–18.4; p=0.0016) per 2 calendar years. Patients with CD4 cell counts greater than 350 cell/mm3 (incidence rate ratio [IRR]: 1.75 [1.37–2.23; p < 0.0001]), HIV‐RNA less than 500 copies/ml (IRR: 1.58 [1.18–2.12; p=0.0023]), with HCV genotype 3 (IRR: 1.55 [1.21–1.98; p=0.0006]) compared to genotype 1) and those from south (IRR: 1.99 (1.45–2.72; p<0.0001) and east central Europe (IRR: 1.61 [1.11–2.34; p=0.011]) compared to west Europe, were more likely to initiate treatment. In a multivariable model treatment for HCV was not significantly associated with all‐cause death (355 deaths, IRR: 0.81 [95% CI: 0.54–1.19; p=0.28]) or liver‐related death (95 deaths, IRR: 1.0 [95% CI: 0.50–2.02; p=0.99]). The incidence of treatment for HCV among co‐infected patients increased from 1998 until 2007 and was common in those with higher CD4 cell counts and lower HIV‐RNA, consistent with HCV treatment guidelines. HCV treatment was not associated with all‐cause or liver‐related death in this population.

image
CD4 count and viral load specific rates of AIDS, non‐AIDS and deaths according to current antiretroviral use
Authors: Mocroft A , Phillips A , Gatell J , Horban A , Ledergerber B , Zilmer K , Jevtovic D , Maltez F , Kirk O , Lundgren J
Published: November 2012

Background

CD4 and viral loads are used in clinical trials as surrogate endpoints for assessing efficacy of newly available antiretrovirals. If antiretrovirals act through other pathways or negatively affect the risk of disease this would not be identified prior to licensing. The aims of this study were to investigate the CD4 and viral load specific rates of fatal and non‐fatal AIDS and non‐AIDS events according to current antiretrovirals.

Methods

Poisson regression was used to compare overall events (fatal or non‐fatal AIDS, non‐AIDS or death), AIDS events (fatal and non‐fatal) or non‐AIDS events (fatal or non‐fatal) for specific nucleoside pairs and third drugs used with>1000 person‐years of follow‐up (PYFU) after January 1st 2001.

Results

9801 patients were included. The median baseline date was January 2004 (interquartile range [IQR] January 2001–February 2007), age was 40.4 (IQR 34.6–47.3 years), and time since starting cART was 3.3 (IQR 0.9–5.1 years). At baseline, the median nadir CD4 was 162 (IQR 71–257/mm3), baseline CD4 was 390 (IQR 249–571/mm3), viral load was 1.9 (IQR 1.7–3.3 log10copies/ml) and 2961 (30.2%) had a prior AIDS diagnosis and 6.4 years) prior to baseline. During 42372.5 PYFU, 1203 (437 AIDS and 766 non‐AIDS) events occurred. The overall event rate was 2.8 per 100 PYFU (95% confidence interval [CI] 2.7–3.0), of AIDS events was 1.0 (95% CI 0.9–1.1) and of non‐AIDS events was 1.8 (95% CI 1.7–1.9). Of the AIDS events, 53 (12.1%)were fatal as were 239 (31.2%) of the non‐AIDS events. After adjustment, there was weak evidence of a difference in the overall events rates between nucleoside pairs (global p‐value=0.084), and third drugs (global p‐value=0.031). Compared to zidovudine/lamivudine, patients taking abacavir/lamivudine (adjusted incidence rate ratio [aIRR] 1.22; 95% CI 0.99–1.49) and abacavir plus one other nucleoside (aIRR 1.51; 95% CI 1.14–2.02) had an increased incidence of overall events. Comparing the third drugs, those taking unboosted atazanavir had an increased incidence of overall events compared to those taking efavirenz (aIRR 1.46; 95% CI 1.09–1.95)(Figure).

image

Conclusions

There was little evidence of substantial differences between antiretrovirals in the incidence of fatal and non‐fatal AIDS and non‐AIDS events for a given CD4 or viral load, suggesting there are unlikely to be major unidentified adverse effects of specific antiretrovirals, although confounding by indication cannot be ruled out.
Importance of minor variants and their detection (ultra‐deep sequencing) in the management of HIV infection
Authors: Paredes R
Published: November 2012

Sanger genotypic drug resistance assays currently used for routine HIV management often miss low‐frequency drug‐resistant HIV variants, potentially posing patients at risk of antiretroviral treatment failure. Next‐generation sequencing (NGS) technologies allow detection of such minority variants down to approximately 0.5%–1% frequency. They also facilitate interrogating “other” HIV genomic regions like Gag or the RT connection domain, which modulate HIV resistance and are not usually addressed in routine care. Due to the capacity and scalability of NGS platforms, it is even feasible to envision full HIV genome sequencing to inform treatment design at relatively low cost and workload. Although the equipment for NGS remains rather expensive and accurate analysis of NGS still requires comprehensive bioinformatics support, even these barriers are being reduced. The steadfast evolution of NGS platforms is dramatically reducing the cost of genotyping. Open‐source and commercial bioinformatic solutions are automatizing and streamlining analyses and NGS drug resistance data interpretation to the extent that lab technicians without bioinformatics knowledge will soon be able to generate reliable estimates of drug resistance from NGS data on their own. However, despite such impressive advances, the main question remains open: do we need NGS for HIV management? In this presentation, we will review the evidence supporting (or not) NGS for HIV clinical management. We will argue that, on one hand, detection of minority variants may further improve the outcomes of first‐line efavirenz or nevirapine‐based ART, may help design more effective salvage ART regimens, and may improve clinical outcomes to CCR5 antagonists. On the other hand, although well‐powered studies are generally lacking, detection of minority variants does not seem to modify the outcomes of first‐line ART including higher genetic barrier drugs such as second‐generation NNRTIs, protease or integrase inhibitors. We will then discuss the relationship between minority variants and ART adherence and will end by summarizing the main challenges faced by NGS to reach routine HIV clinical management.
Molecular Sieving on the Surface of a Protein Provides Protection Without Loss of Activity
Authors: Liu Mi , Tirino Pasquale , Radivojevic Milos , Phillips Daniel J. , Gibson Matthew I. , Leroux Jean‐Christophe , Gauthier Marc A.
Published: November 2012

Tethering polymers to surfaces represents the cornerstone of a wide range of applications, including the stabilization of colloids/biomolecules and the preparation of functional coatings. Unfortunately, despite the prevalence of protein‐tethered polymers in the pharmaceutical sector, the analysis of such polymer monolayers on a molecular level is difficult. In this work, simple 1H NMR spectroscopy and the catalytic properties of α‐chymotrypsin are used to analyze the conformational/permeability properties of protein‐bound monolayers of poly(oligoethyleneglycol monomethylether methacrylate) (pOEGMA), a biocompatible comb‐polymer of interest in the biomedical field. By analyzing >100 distinct conjugates of α‐chymotrypsin and pOEGMA, a detailed picture of the behavior of pOEGMA on the surface of a protein was obtained. Remarkably, control of polymer conformation and inter‐penetration produced a thus far overlooked molecular sieving effect. The application of this effect for the “smart” PEGylation of proteins is portrayed, from which insight is provided for the design of other therapeutic bioconjugates and functional coatings with selective permeability properties.
Enhancement of CO2 Adsorption and CO2/N2 Selectivity on ZIF‐8 via Postsynthetic Modification
Authors: Zhang Zhijuan , Xian Shikai , Xia Qibin , Wang Haihui , Li Zhong , Li Jing
Published: November 2012

Imidazolate framework ZIF‐8 is modified via postsynthetic method using etheylenediamine to improve its adsorption performance toward CO2. Results show that the BET surface area of the modified ZIF‐8 (ED‐ZIF‐8) increases by 39%, and its adsorption capacity of CO2 per surface area is almost two times of that on ZIF‐8 at 298 K and 25 bar. H2O uptake on the ED‐ZIF‐8 become obviously lower compared to the ZIF‐8. The ED‐ZIF‐8 selectivity for CO2/N2 adsorption gets significantly improved, and is up to 23 and 13.9 separately at 0.1 and 0.5 bar, being almost twice of those of the ZIF‐8. The isosteric heat of CO2 adsorption (Qst) on the ED‐ZIF‐8 becomes higher, while Qst of N2 gets slightly lower compared to those on the ZIF‐8 Furthermore, it suggests that the postsynthetic modification of the ZIF‐8 not only improves its adsorption capacity of CO2 greatly, but also enhances its adsorption selectivity for CO2/N2/H2O significantly. ©2013 American Institute of Chemical Engineers AIChE J, 59: 2195–2206, 2013
On The Lower Lewis Basicity of Siloxanes Compared to Ethers
Authors: Passmore Jack , Rautiainen J. Mikko
Published: November 2012

1,3‐Dimethyldisiloxane, O(SiH2Me)2, diethyl ether, OEt2, and their metal complexes (Li+,Ag+) have been used as model systems to uncover the reasons underlying the lower Lewis basicity of siloxanes compared to analogous ethers. Bonding in the metal complexes has been analyzed with quantum theory of atoms in molecules as well as natural bond orbital theory. The binding to Li+by O(SiH2Me)2and OEt2is largely of monopole – dipole type whereas binding of Ag+also shows small charge transfer components. The more ionic Si–O bonds in O(SiH2Me)2compared to C–O bonds in OEt2lead to more negative charge on the oxygen atom of O(SiH2Me)2but the electrostatic attraction between metal cations and OEt2is calculated to be slightly stronger by interacting quantum atoms energy decomposition analysis. The lower electrostatic attraction by O(SiH2Me)2is due to repulsion between positively charged silicon atoms and the metal cations that compensate for the stronger attraction from the oxygen atom relative to OEt2. The total interaction of metal cations with O(SiH2Me)2was calculated to be almost as strong as that with OEt2and the lower stability of O(SiH2Me)2complexes and the lower Lewis basicity of O(SiH2Me)2is attributed to changes in the bonding and polarization of the ligands in the presence of metal cations. The polarization of O–Si bonds in O(SiH2Me)2raises the energy of the molecule more than does the polarization O–C bonds in OEt2. Despite the lower stability of O(SiH2Me)2metal complexes, solid state reaction enthalpies arising from a volume‐based thermodynamics approach suggest that they could be stabilized with a sufficiently large anion such as [Al(ORF)4]–.
Regioselective Preparation of 3‐Alkoxy‐4,5‐difluoroanilines by SNAr
Authors: Van Brandt Sven , Rombouts Frederik J. R. , Martínez‐Lamenca Carolina , Leenaerts Jos , Rauws Tom R. M. , Trabanco Andrés A.
Published: November 2012

A simple and scalable procedure to introduce alcohols selectively at the 3‐position of 3,4,5‐trifluoroaniline is described. The procedure uses powdered NaOH as base and catalytic 15‐crown‐5 in refluxing toluene with a Dean–Stark trap. A short exploration of other nucleophiles and fluoroaryl electrophiles is also described.
Investigation of Impactors on Cell Degradation Inside Planar SOFC Stacks
Authors: Guan W. B. , Jin L. , Ma X. , Wang W. G.
Published: November 2012

The impactors on cell degradation inside planar SOFC stacks were investigated using both coated and uncoated Fe–16Cr alloys as the interconnects under stable operating conditions at 750 °C and thermal cycling conditions from 750 to 200 °C. It was found that cell degradation inside the stack is primarily dependent on the interfacial contact between the cathode current‐collecting layer and the interconnect. Additionally, cell degradation is found to be independent of the high‐temperature oxidation and Cr vaporization of the interconnects during stack operation, as the stacks are well sealed. The coating on the interconnect can further improve the contact between the cell cathode and the interconnect when the latter is properly embedded into the current‐collecting layer.
Activation of canonical wnt pathway promotes differentiation of mouse bone marrow‐derived MSCs into type II alveolar epithelial cells, confers resistance to oxidative stress, and promotes their migration to injured lung tissue in vitro
Authors: Liu Ai‐ran , Liu Le , Chen Song , Yang Yi , Zhao Hong‐jie , Liu Ling , Guo Feng‐mei , Lu Xiao‐min , Qiu Hai‐bo
Published: November 2012

The differentiation of mesenchymal stem cells (MSCs) into type II alveolar epithelial (AT II) cells in vivo and in vitro, is critical for reepithelization and recovery in acute lung injury (ALI), but the mechanisms responsible for differentiation are unclear. In the present study, we investigated the role of the canonical wnt pathway in the differentiation of mouse bone marrow‐derived MSCs (mMSCs) into AT II cells. Using a modified co‐culture system with murine lung epithelial‐12 (MLE‐12) cells and small airway growth media (SAGM) to efficiently drive mMSCs differentiation, we found that GSK 3β and β‐catenin in the canonical wnt pathway were up‐regulated during differentiation. The levels of surfactant protein (SP) C, SPB, and SPD, the specific markers of AT II cells, correspondingly increased in mMSCs when Wnt3a or LiCl was added to the co‐culture system to activate wnt/β‐catenin signaling. The expression of these factors was depressed to some extent by inhibiting the pathway with the addition of DKK 1. The differentiation rate of mMSCs also depends on their abilities to accumulate and survive in inflammatory tissue. Our results suggested that the activation of wnt/β‐catenin signaling promoted mMSCs migration towards ALI mouse‐derived lung tissue in a Transwell assay, and ameliorated the cell death and the reduction of Bcl‐2/Bax induced by H2O2, which simultaneously caused reduced GSK 3β and β‐catenin in mMSCs. These data supports a potential mechanism for the differentiation of mMSCs into AT II cells involving canonical wnt pathway activation, which may be significant to their application in ALI. J. Cell. Physiol. 228: 1270–1283, 2013. © 2012 Wiley Periodicals, Inc.
Prevalence of human parechoviruses in central nervous system infections in children: A retrospective study in Shanghai, China
Authors: Zhong Huaqing , Lin Yong , Su Liyun , Cao Lingfeng , Xu Menghua , Xu Jin
Published: November 2012

Human parechoviruses (HPeV) are associated with central nervous system (CNS) infections and sepsis‐like illnesses. However, data from China are not available. The aim of this study was to determine the prevalence, age, and seasonal distributions and genotypes of HPeV infections in children with CNS related disease in Shanghai, China. Of 776 cerebrospinal fluid (CSF) samples collected from children with CNS‐related diseases under the age of 16 years during the years 2008–2011, 68 (9%) were identified to be HPeV positive. The annual prevalence varied remarkably: 1% (2/153) in 2008, 7% (12/177) in 2009, 15% (23/153) in 2010, and 11% (31/293) in 2011. The virus was detected in all age groups of children ranging from 2 days to 13 years and the median age was 14 months. Of the 31 positive samples that were genotyped successfully, 28 were HPeV1 and 3 were HPeV3. This study provided data on the molecular epidemiology of HPeV infections in CNS‐related diseases in Shanghai, China and suggest that the screening for HPeV by PCR should be included in the routine viral testing of CSF. J. Med. Virol. 85:320–326, 2013. © 2012 Wiley Periodicals, Inc.
Prevalence and molecular epidemiology of human coronavirus HKU1 in patients with acute respiratory illness
Authors: Lee Wan‐Ji , Chung Yoon‐Seok , Yoon Hee Sook , Kang Chun , Kim Kisoon
Published: November 2012

In 2005, human coronavirus HKU1 (HCoV‐HKU1) was isolated and identified from a 71‐year‐old man with pneumonia in Hong Kong. To identify and classify genotypes of HCoV‐HKU1 in Korea, a sensitive, specific, and quantitative real‐time polymerase chain reaction (PCR) assay was developed and analyzed the sequences of HCoV‐HKU1 isolated in Korea. A total of 1,985 respiratory specimens taken from patients with acute respiratory illness were tested for HCoV‐HKU1 from January 2007 to May 2008. The major clinical symptoms associated with HCoV‐HKU1 infection were examined statistically and sequence variations of the RNA‐dependent RNA polymerase (RdRp), spike, and nucleocapsid genes were also analyzed. Fifty cases (2.5%) HCoV‐HKU1 were identified by real‐time PCR and viral loads ranged from 6.7 × 104 to 1.6 × 109 copies/ml. The clinical symptoms of HCoV‐HKU1 infection included rhinorrhea (72%), cough (64%), nasal congestion (56%), fever (32%), sputum (30%), sore throat (18%), chills (16%), postnasal discharge (14%), and tonsillar hypertrophy (10%). There was a seasonal distribution of HCoV‐HKU1 infection, peaking in winter and spring. Both genotypes A and B were detected but no recombination between them was found. This is the first report on the identification and genotyping of HCoV‐HKU1 as a causative agent of acute respiratory illness in Korea. The data suggest that at least two genotypes, A and B, of HCoV‐HKU1 with scattered silent mutations were circulating in Korea from 2007 to 2008. J. Med. Virol. 85:309–314, 2013. © 2012 Wiley Periodicals, Inc.
Constraining Holocene sea‐surface conditions in the south‐western Black Sea using dinoflagellate cysts
Authors: Bradley L. R. , Marret F. , Mudie P. J. , Aksu A. E. , Hiscott R. N.
Published: November 2012

This paper presents two dinoflagellate cyst records from the south‐western shelf of the Black Sea. A new site, MAR05‐13, from the Sakarya shelf is described and placed into context with site MAR02‐45, ∼250 km distant on the Thracian shelf. The records provide a centennial resolution of surface water conditions in the Holocene. Analysis of the data suggests that the surface salinity of the south‐western shelf increased in a gradual and progressive manner. In the period ∼11 000–9000 cal a BP the assemblages suggest surface‐water salinities between 7–13 psu. The initial arrival of euryhaline species, ∼8100 cal a BP, is linked to the reconnection of the Black Sea and Marmara Sea. The suggested surface water changes related to the reconnection took approximately 1000 years. Following this initial change in assemblages, a further increase in the number of euryhaline species is noted between 5000 and 4000 cal a BP. This is linked to the establishment of more saline surface‐water conditions, close to present‐day values. The record for MAR05‐13 highlights the complexity of the changes in cyst assemblages during the mid‐Holocene. Copyright © 2012 John Wiley & Sons, Ltd.
Mucosal melanoma of the head and neck: 32‐year experience in a tertiary referral hospital
Authors: Chan Richie Chiu‐Lung , Chan Jimmy Yu Wai , Wei William Ignace
Published: November 2012

Introduction:

Primary mucosal melanomas of the head and neck (HNMM), albeit being rare, are rapidly lethal. Here we report the experience of patients with HNMM treated in our institution over a 32‐year period.

Objectives/Hypothesis:

We aim to review our experience in managing HNMM patients over a 32‐year period.

Study Design:

Retrospective study.

Methods:

Thirty‐five patients diagnosed with HNMM from 1978 to 2009 were retrospectively reviewed, with an emphasis on predictors on survival outcome.

Results:

Twenty‐four patients received curative resection, 6 of them followed by adjuvant radiotherapy. Neck dissections were performed in 8 patients. Four patients received radiotherapy as primary treatment. Seven patients were treated conservatively.

The overall mean and median survivals were 50 and 26 months, respectively. The median survival of stage I, II, and III diseases in our group of patients were 39, 10, and 16 months, respectively. The 1‐year and 5‐year overall survival rates were 65.7% and 22.9%, respectively.

Age above 60 (p = 0.007), nodal involvement (p = 0.047;) and stage at presentation (p = 0.046) were shown to be associated with worse overall survival. Sites of tumour did not seem to impact on survival. On multivariate analysis, only age (below or above 60) was found to be statistically significant [RR 4.79 (1.65–13.9), p = 0.004].

Conclusions:

Oral cavity melanomas are more likely to have nodal involvement at presentation. Prognosis of HNMM remains grave. Current evidence still supports surgery as the best chance of cure. Role of adjuvant radiotherapy is controversial and does not appear to improve overall survival. Similarly, role of neck dissection is ill‐defined. Laryngoscope, 2012
The anatomical relationship between the eustachian tube and petrous internal carotid artery
Authors: Ozturk Kayhan , Snyderman Carl H. , Gardner Paul A. , Fernandez‐Miranda Juan C.
Published: November 2012

Objectives/Hypothesis:

The aim of the present study was to investigate the relationship between the eustachian tube (ET) and petrous internal carotid artery (ICA) in whole‐mount human temporal bone specimens.

Study Design:

Descriptive study.

Methods:

Histologically prepared serial sections of 10 adult temporal bones were included in the study. Five specific landmarks were selected to evaluate relationships between the petrous segment of the ICA and the ET. The selected distances were measured using computer software (Metamorph 7.5.2.0; Molecular Devices, LLC, Sunnyvale, CA).

Results:

The ET and the ICA get close posteriorly, and the bony part of the ET and the ICA generally share the same wall.

Conclusions:

The junctional part of the ET may be a safe landmark to identify and protect the ICA during endoscopic endonasal surgery of the cranial base. Knowledge of the anatomical relationships of the ET and petrous part of the ICA, as well as their relationship with other surgical and radiological landmarks, would be useful to surgeons. Laryngoscope, 2012
Detection of human papillomavirus in sinonasal papillomas: Systematic review and meta‐analysis
Authors: Syrjänen Kari , Syrjänen Stina
Published: November 2012

Objectives/Hypothesis:

To perform a systematic review and formal meta‐analysis of the literature reporting on HPV detection in sinonasal papillomas. Since first reported in 1983, the etiological role for human papillomavirus (HPV) in sinonasal papillomas has been subject to increasing interest.

Study Design:

A systematic review, with meta‐analysis and formal meta‐regression.

Methods:

Literature was searched through April 2012. The effect size was calculated as event rates (95% confidence interval [CI]), with homogeneity testing using Cochran's Q and I2 statistics. Meta‐regression was used to test the impact of study‐level covariates (HPV detection method, geographic origin, papilloma type) on effect size, and potential publication bias was estimated using funnel plot symmetry.

Results:

Seventy‐six studies were eligible covering 1,956 sinonasal papillomas from different geographic regions. Altogether, 760 (38.8%) cases tested HPV‐positive; effect size 0.421 (95% CI 0.359‐0.485, random effects model). The summary HPV prevalence was highest (65.3%) in exophytic papillomas (EP), followed by inverted papillomas (37.8%) and cylindrical cell papillomas (22.5%). In meta‐analysis stratified by 1) HPV detection technique, 2) geographic study origin, and 3) papilloma type, the between‐study heterogeneity was significant only for the papilloma types (P = .001). In meta‐regression, HPV detection method (P = .102), geographic origin (P = .149), or histological type (P = .240) were not significant study‐level covariates. Some evidence for publication bias was found only for studies on EP. In sensitivity analysis, all meta‐analytic results were robust to all one‐by‐one study removals.

Conclusions:

Variability in HPV detection rates in sinonasal papillomas is explained by their histological types (not by HPV detection method or geographic origin of study), but none of the three were significant study‐level covariates in formal meta‐regression. Laryngoscope, 2013
Fat confounds the observed apparent diffusion coefficient in patients with hepatic steatosis
Authors: Hansmann Jan , Hernando Diego , Reeder Scott B.
Published: November 2012

Purpose: Triglyceride signal contained in peaks near the water peak remains unsuppressed by conventional fat suppression techniques used in diffusion‐weighted imaging. In this work, we investigated the dependence of the apparent diffusion coefficient (ADC) on liver fat content and whether it is confounded by fat signal. Methods: 43 patients underwent liver diffusion‐weighted imaging (b = 0, 500 s/mm2) and single‐voxel MR‐spectroscopy. Proton density fat‐fraction (PDFF; range 0.23–34.5%) was measured from MR‐spectroscopy. A theoretical model was developed to account for the effects of fat on observed ADC, and used to correct the ADC. Linear correlation analysis was performed to assess the relationship between PDFF and ADC before and after correction. Results: Linear correlation analysis showed an inverse dependence between observed ADC and PDFF before correction (r2 = 0.132; P = 0.017), and no dependence after correction (r2 = 0.033; P = 0.24). Conclusion: The observed decrease in ADC in patients with fatty liver is, at least in part, artifactual due to residual fat signal near the water peak. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.