bluuebunny/crossref_metadata_2025 huggingface dataset:
The influence of wildfire extent and severity on streamwater chemistry, sediment and temperature following the Hayman Fire, Colorado
Authors: Rhoades Charles C. , Entwistle Deborah , Butler Dana
Published: May 2011

The 2002 Hayman Fire was the largest fire in recent Colorado history (558 km2). The extent of high severity combustion and possible effects on Denver’s water supply focussed public attention on the effects of wildfire on water quality. We monitored stream chemistry, temperature and sediment before the fire and at monthly intervals for 5 years after the fire. The proportional extent of a basin that was burned or that burned at high severity was closely related to post-fire streamwater nitrate and turbidity. Basins that burned at high severity on >45% of their area had twice the streamwater nitrate and four times the turbidity as basins burned to a lower extent; these analytes remained elevated through 5 years post-fire. In those basins, the highest post-fire streamwater nitrate concentrations (23% of USA drinking water standards) were measured during spring, the peak discharge period. Summer streamwater was 4.0°C higher in burned streams on average compared with unburned streams; these persistent post-fire stream temperature increases are probably sufficient to alter aquatic habitat suitability. Owing to the slow pace of tree colonisation and forest regrowth, recovery of the watersheds burned by the Hayman Fire will continue for decades.
Physical, chemical and hydrological properties of Ponderosa pine ash
Authors: Gabet Emmanuel J. , Bookter Andy
Published: May 2011

In this study, ash is analysed as a geological material; in particular, we focus on ash produced by the burning of Ponderosa pine, a conifer that is widespread throughout mountainous landscapes of western North America. One set of ash samples used in the analyses was collected from a wildfire site and another set was created in the laboratory. We found that the median particle size of the ash was in the fine sand to silt range with at least 25–50% of the particle size distribution in the appropriate range for maintaining debris flow behaviour. Measurements of the infiltration capacity of ash found values similar to fine sands, indicating that a layer of ash can reduce the infiltration capacity of coarse soils. The elemental composition of ashes analysed through inductively coupled plasma emission spectrometry was dominated by Ca, K, Mg, P, Mn, Fe and Al. X-ray diffraction analysis revealed the presence of calcite, quartz and feldspars in ashes created from a variety of fuels; fuel type and combustion temperature were found to have a dominant control on ash mineralogy. The results suggest that the elemental and mineral composition of ash could be used to identify dominant fuel sources and combustion temperatures.
Numerical modelling of the aerial drop of firefighting agents by fixed-wing aircraft. Part I: model development
Authors: Amorim J. H.
Published: May 2011

The efficiency of the aerial drop of firefighting agents (water and retardants) is extremely dependent on pilot skills in dealing with complex atmospheric conditions, mostly because on-board systems for computer-assisted drops have not yet been used operationally. Hence, numerical modelling tools can be of primary importance for the optimisation of firefighting operations and in the testing of new chemical products. The current work addresses the development of the operational Aerial Drop Model. This numerical tool allows a near real-time simulation of aerial drops with fixed-wing aircraft, while covering the fundamental stages of the process. It copes with a wide range of product viscosities, from water to highly thickened long-term retardants. The Aerial Drop Model simulates the continuous stripping of droplets from the liquid jet by the action of Rayleigh–Taylor and Kelvin–Helmholtz instabilities applying the linear stability theory. The subsequent secondary breakup and deformation of the formed droplets due to aerodynamic forces is based on experimental correlations defined in terms of the dimensionless Weber number. Droplet trajectories are computed by applying a Lagrangian approach, in which a dynamical drag module accounts for the effect of deformation. This operational tool provides an improved understanding of the behaviour and effectiveness of aerially delivered firefighting liquids.
Numerical modelling of the aerial drop of firefighting agents by fixed-wing aircraft. Part II: model validation
Authors: Amorim J. H.
Published: May 2011

The validation of the Aerial Drop Model consisted of the comparison of computed ground patterns with experimental data from a set of real-scale drop tests using water and a wide range of fire retardant viscosities. Results were analysed in terms of pattern length and area. A total of 78% of the computed line lengths per coverage level were within a 10% error, with an average normalised mean squared error of 0.01 and a Pearson correlation coefficient above 0.9. In all cases, nearly 90% of the results were within a factor of 2 of observations. The accuracy of the simulations showed no strong relation with the viscosity, although better results were obtained in the range from 700 to 1100 cP. In general, the model produced a good representation of the spatial distribution of the agent for various coverage levels and its accuracy was, in fact, within the statistical uncertainty of the cup-and-grid sampling method. The good performance obtained demonstrates that this tool, for the tested range of drop conditions, fulfils the requirements for use in the optimisation of firefighting operations, as a complementary method to real-scale drop testing, and in firefighter training activities.
Fire ignition patterns affect production of charcoal in southern forests
Authors: Carvalho Eric Oliveira , Kobziar Leda N. , Putz Francis E.
Published: May 2011

Although charcoal represents a relatively minor portion of available biomass burned in wildfires and prescribed burns, its recalcitrant properties confer residence times ranging from centuries to millennia, with significance for carbon sequestration in frequently burned forests. Here, we determined whether charcoal formation differed between the two most common prescribed fire spread patterns in southern forests: head (with the wind) and backing (against the wind). Pine wood samples were distributed randomly within a mesic flatwoods burn unit in north-central Florida, and subjected either to a head fire (n = 34) or a backing fire (n = 34). Backing fires formed more than twice as much charcoal as head fires (1.53 v. 0.38% of available biomass), presumably because of differences in residence times, oxygen availability and fire intensity between the two fire spread patterns. These results suggest that the contribution of charcoal to ecosystem carbon sequestration is greater when flatwoods forests are burned against the prevailing wind direction, and that further investigation of these trends is warranted.
Neuroanatomical dissociation for taxonomic and thematic knowledge in the human brain
Authors: Schwartz Myrna F. , Kimberg Daniel Y. , Walker Grant M. , Brecher Adelyn , Faseyitan Olufunsho K. , Dell Gary S. , Mirman Daniel , Coslett H. Branch
Published: May 2011

It is thought that semantic memory represents taxonomic information differently from thematic information. This study investigated the neural basis for the taxonomic-thematic distinction in a unique way. We gathered picture-naming errors from 86 individuals with poststroke language impairment (aphasia). Error rates were determined separately for taxonomic errors (“pear” in response to apple) and thematic errors (“worm” in response to apple), and their shared variance was regressed out of each measure. With the segmented lesions normalized to a common template, we carried out voxel-based lesion-symptom mapping on each error type separately. We found that taxonomic errors localized to the left anterior temporal lobe and thematic errors localized to the left temporoparietal junction. This is an indication that the contribution of these regions to semantic memory cleaves along taxonomic-thematic lines. Our findings show that a distinction long recognized in the psychological sciences is grounded in the structure and function of the human brain.
Chemical reporters for fluorescent detection and identification of O-GlcNAc-modified proteins reveal glycosylation of the ubiquitin ligase NEDD4-1
Authors: Zaro Balyn W. , Yang Yu-Ying , Hang Howard C. , Pratt Matthew R.
Published: May 2011

The dynamic modification of nuclear and cytoplasmic proteins by the monosaccharide
N
-acetyl-glucosamine (GlcNAc) continues to emerge as an important regulator of many biological processes. Herein we describe the development of an alkynyl-modified GlcNAc analog (GlcNAlk) as a new chemical reporter of O-GlcNAc modification in living cells. This strategy is based on metabolic incorporation of reactive functionality into the GlcNAc biosynthetic pathway. When combined with the Cu(I)-catalyzed [3 + 2] azide-alkyne cycloaddition, this chemical reporter allowed for the robust in-gel fluorescent visualization of O-GlcNAc and affinity enrichment and identification of O-GlcNAc-modified proteins. Using in-gel fluorescence detection, we characterized the metabolic fates of GlcNAlk and the previously reported azido analog, GlcNAz. We confirmed previous results that GlcNAz can be metabolically interconverted to GalNAz, whereas GlcNAlk does not, thereby yielding a more specific metabolic reporter of O-GlcNAc modification. We also used GlcNAlk, in combination with a biotin affinity tag, to identify 374 proteins, 279 of which were not previously reported, and we subsequently confirmed the enrichment of three previously uncharacterized proteins. Finally we confirmed the O-GlcNAc modification of the ubiquitin ligase NEDD4-1, the first reported glycosylation of this protein.
Magnetic anisotropy and spin-spiral wave in V, Cr and Mn atomic chains on Cu(0 0 1) surface: first principles calculations
Authors: Tung J C , Wang Y K , Guo G Y
Published: May 2011

Recent ab intio studies of the magnetic properties of all 3d transition metal (TM) freestanding atomic chains have predicted that these nanowires could have a giant magnetic anisotropy energy (MAE) and might support a spin-spiral structure, thereby suggesting that these nanowires would have technological applications in, e.g. high-density magnetic data storage. In order to investigate how the substrates may affect the magnetic properties of the nanowires, here we systematically study V, Cr and Mn linear atomic chains on a Cu(0 0 1) surface based on the density functional theory with the generalized gradient approximation. We find that V, Cr and Mn linear chains on the Cu(0 0 1) surface still have a stable or metastable ferromagnetic state. However, the ferromagnetic state is unstable against the formation of a noncollinear spin-spiral structure in the Mn linear chains and also the V linear chain on the atop sites on the Cu(0 0 1) surface, due to the frustrated magnetic interactions in these systems. Nonetheless, the presence of the Cu(0 0 1) substrate does destabilize the spin-spiral state already present in the freestanding V linear chain and stabilizes the ferromagnetic state in the V linear chain on the hollow sites on Cu(0 0 1). When spin–orbit coupling (SOC) is included, the spin magnetic moments remain almost unchanged due to the weakness of SOC in 3d TM chains. Furthermore, both the orbital magnetic moments and MAEs for V, Cr and Mn are small, in comparison with both the corresponding freestanding nanowires and also the Fe, Co and Ni linear chains on the Cu(0 0 1) surface.
Engineered one-dimensional magneto-photonic crystals for wavelength division multiplexing systems
Authors: Hamidi S M , Tehranchi M M , Shasti M
Published: May 2011

We have investigated the behaviour of an engineered one-dimensional magneto-photonic crystal with a (TiO2/SiO2)6/Bi : YIG/(SiO2/TiO2)6 structure for use in wavelength division multiplexing. The magnetic defect layer was fabricated using the pulsed laser deposition technique between two dielectric mirrors. The optical and magneto-optical properties of the sample were studied in detail so as to corroborate, or otherwise, the hypotheses formulated to achieve sufficient Faraday rotation of the media originating in the localized peak of light. Results indicate that this magneto-photonic crystal can be considered as a candidate for a multichannel isolator in wavelength division multiplexing systems. Also, the low-temperature behaviour of this sample indicates five order of magnitude enhancements in the magneto-optical Faraday rotation.
Plasma propagation of a 13.56 MHz asymmetric surface barrier discharge in atmospheric pressure air
Authors: Dedrick J , Boswell R W , Audier P , Rabat H , Hong D , Charles C
Published: May 2011

The propagation of an rf asymmetric surface barrier discharge in atmospheric pressure air has been investigated. Measurements of the pulse-modulated 13.56 MHz voltage and current together with ICCD images of the plasma were recorded to study the visible plasma structure with respect to the rf pulses, time within the pulses and the rf waveforms. When exposing images over full rf pulses, which comprise over 150 oscillations of the applied voltage, clearly defined filamentary structures are observed indicating a strong memory effect. The discharge intensity decreases exponentially with distance from the electrode edge, and the average propagation length increases linearly with the applied voltage. Similar to some lower frequency asymmetric surface dielectric barrier discharges, two distinct breakdown events occur during one period of the voltage waveform. The number of filaments is found to be the same for both breakdown events, and collective effects are observed in both discharges.
Plasma parameters of a small surface-wave discharge at atmospheric pressure obtained by line-ratio method
Authors: Kiss'ovski Zh , Ivanov A , Iordanova S , Koleva I
Published: May 2011

Plasma parameters of a small surface-wave discharge in argon gas at atmospheric pressure are obtained by optical emission spectroscopy applying the line-ratio method. The microwave discharge is maintained at a frequency of 2.45 GHz in a ceramic tube with an inner diameter of 1 mm and a length of 11 mm. The discharge is ignited at power levels below 10 W. Emission spectra of the argon plasma are measured in the wavelength range 645–825 nm at different gas flows and forward microwave powers. The electron temperature and the plasma density are determined simultaneously through a ‘cross-point’ method using two line-intensity ratios and their values are T
e ≅ 1.6 eV and n
e = (3.6–4.5) × 1014 cm−3, respectively. The results show a stronger dependence of the plasma parameters on the gas flow rather than on the input power in the case of plasma columns longer than the tube length.
A global model for the afterglow of pure argon and of argon with negatively charged dust particles
Authors: Denysenko I , Stefanović I , Sikimić B , Winter J , Azarenkov N A , Sadeghi N
Published: May 2011

Zero-dimensional, space-averaged global models of argon dust-free and dusty afterglow plasmas are developed, which describe the time behaviour of electron n
e(t) and Ar* metastable n
m(t) densities. The theoretical description is based on the assumption that the free electron density is smaller than the dust charge density. In pure argon, fairly good agreement with the experimentally measured densities and their decay times in the afterglow is obtained when the electron energy loss term to the chamber walls is included in the electron energy balance equation. In dusty plasma afterglow, the agreement between theory and experiment is less satisfactory. The calculated metastable density is 3 times smaller than the measured one and the electron decay is much faster in the late afterglows. The difference should probably arise from the assumption that the electron energy distribution function is Maxwellian. Different sources of secondary electrons in the dusty plasma afterglow are analysed. Comparison of the model with experimental results of argon dusty plasma suggests that the metastable pooling could be the source of the experimentally observed electron density increase in the early afterglow but electron generation from metastable–dust interactions cannot be fully discarded.
Direct observation of local resistance switching in WO3 films
Authors: Dong C Y , Shi L , Shang D S , Chen W , Wang J , Shen B G , Sun J R
Published: May 2011

Local resistance switching in WO3 films has been studied based on the conducting atomic force microscope technique. Special attention was paid to the formation/reproducibility of local conduction regions on the metal–oxide interface for repeated setting–resetting operations and the effects of microscopic inhomogeneity. It is found that most of the conducting spots prefer to stay where they were once formed. However, only a minority of them (∼30%) are repeatable in resistance values for the writing–erasing cycling. According to the resistance switching behaviours, five kinds of locations can be classified in total, and they are inactive regions, weak transition regions, weak to stable transition regions, stable transition regions and irregular transition regions. A further analysis shows the preferential locations of conduction spots at protuberant grains.
Extended wide band gap amorphous aluminium-doped zinc oxide thin films grown at liquid nitrogen temperature
Authors: Chou H , Yang M S , Wu C P , Tsao Y C , Chen B J , Liao T F , Sun S J , Chiou J W
Published: May 2011

Amorphous aluminium-doped zinc oxide (AZO) thin films are grown by standard RF sputtering at low temperatures on glass substrates. Due to poor thermal conductivity and thermal energy generated by the sputter gun, controlling the substrate surface temperature is the key to controlling the growth of amorphous and nanocrystalline films. The ratio of grains and amorphous part of the films can be controlled by selective growth conditions. During a transmission electron microscope (TEM) inspection process, the amorphous films react immediately and strongly with an electron beam and transform to a mixture of amorphous and nanocrystalline phases. The films having a mixture of amorphous and nanocrystalline phases, either as-grown or after transformation by irradiation of the electron beam, are stable in the TEM inspection, indicating that the low interface energy stabilizes the mixture phase. The optical band gap increases with the content of amorphous phase and is 4.3 eV for pure amorphous AZO films.
Raman scattering study of iodine intercalated bundles of single-wall carbon nanotubes
Authors: Nguyen Van Minh , Kim Sung-Jin , Yang In-Sang
Published: May 2011

We present the results of Raman and field emission studies of the structural and physical features of iodine intercalated bundles of single-walled carbon nanotubes (SWNTs). The periodicity of hexagonally closest-packed pristine nanotubes was destroyed by the intercalation of iodine molecules in interstitial sites of carbon nanotube bundles. The Raman spectra obtained using a 647.1 nm line of Kr-ion laser indicate that I
2 intercalation does affect the electronic state of metallic SWNTs of small diameters of ∼1.26 nm changing into the insulating state. The turn-on electric fields obtained from the I–V measurements for iodine intercalated SWNTs and pristine SWNTs were 2.43 and 3.41 V μm
−1, respectively, and iodine intercalated SWNTs show higher field emission than pristine SWNTs do.
Electrical conductivity and electromagnetic interference shielding characteristics of multiwalled carbon nanotube filled polyurethane composite films
Authors: Hoang Anh Son
Published: May 2011

Multiwalled carbon nanotubes (MWCNTs) were homogeneously dispersed in a pure polyurethane resin by grinding in a planetary ball mill. The structure and surface morphology of the MWCNTs and MWCNT/polyurethane composites were studied by filed emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM) methods. The electrical conductivity at room temperature and electromagnetic interference (EMI) shielding effectiveness (SE) of the composite films with different MWCNT loadings were investigated and the measurement of EMI SE was carried out in a frequency range of 8–12 GHz (X-band). The experimental results show that with a low MWCNT concentration the composite films could achieve a high conductivity and their EMI SE has a strong dependence on MWCNT content. For the composite films with 22 wt% of MWCNTs, the EMI SE attained an average value of 20 dB, so that the shielding effect reduced the penetrating power to 1%.
Synthesis and characterization of zinc-organic frameworks with 1,4-benzenedicarboxylic acid and azobenzene-4,4′-dicarboxylic acid
Authors: Nguyen Van Hung , Nguyen Ngoc Phuong Thuy , Nguyen Thi Tuyet Nhung , Le Thi Thanh Thuy , Le Van Nghiem , Nguyen Quoc Chinh , Ton That Quang , Nguyen Thai Hoang , Nguyen Thi Phuong Thoa
Published: May 2011

The solvothermal reactions of 1,4-bezenedicarboxylic acid (H
2
BDC) or azobenzene-4,4′-dicarboxylic acid (H
2
ABD) with zinc ions/clusters lead to the formation of four crystalline materials. All of these compounds were characterized by x-ray diffraction, optical microscopy, thermo-gravimetric analysis and nitrogen adsorption. Block-shaped crystals (BZ1) with various shapes and sizes were obtained at H
2
BDC:Zn mole ratio of 1:1 and H
2
BDC concentration of 0.1 M. At more dilute H
2
BDC concentration of 0.01 M and H
2
BDC:Zn mole ratio of 1 : 4, the reaction product was cubic crystals (BZ2) with a size of 250 μm. In the H
2
ABD system, flat-plate-like crystals (AZ1) were obtained at H
2
ABD:Zn mole ratio of 1 : 1 and H
2
ABD concentration of 0.01 M. Meanwhile, thick-block-like crystals (AZ2) were formed at the same H
2
ABD:Zn mole ratio but at 0.004 M H
2
ABD. The Langmuir surface area (S

Lang
) of the materials was remarkable, enhanced by diluting the reaction solution. For the compounds synthesized in N
,
N′-dimethylformamide (DMF), S

Lang
increased from 304.6 m
2 
g
−1 for BZ1 to 2631 m
2 
g
−1 for BZ2 and from 475.8 m
2 
g
−1 for AZ1 to 3428 m
2 
g
−1 for AZ2. Meanwhile, BZ2 synthesized in N
,
N′-diethylformamide (BZ2/DEF) got the highest S

Lang
of 4330 m
2 
g
−1. Both AZ2 and BZ2 materials were stable up to 400 °C.
On the Hasse principle for certain quartic hypersurfaces
Authors: Quan Nguyen
Published: May 2011

We prove that there are infinitely many non-isomorphic quartic curves which are counter-examples to the Hasse principle explained by the Brauer-Manin obstruction. Further, these quartic curves have no points defined over number fields of odd degree. As a consequence, we show that there are infinitely many quartic hypersurfaces of arbitrary dimension violating the Hasse principle.
Covariant derivatives of the Berezin transform
Authors: Engliš Miroslav , Otáhalová Renata
Published: May 2011

Improving upon recent results of Coburn, Xia, Li, Engliš and Zhang, Bommier-Hato, and others, we give estimates for higher-order covariant derivatives of the Berezin transform of bounded linear operators on a reproducing kernel Hilbert space of holomorphic functions. The answer turns out to involve the curvature of the Bergman-type metric associated to the reproducing kernel.
Circulating MicroRNA Is a Biomarker of Pediatric Crohn Disease
Authors: Zahm Adam M , Thayu Meena , Hand Nicholas J , Horner Amber , Leonard Mary B , Friedman Joshua R
Published: May 2011

Objective:

The gold standard for the diagnosis and evaluation of Crohn disease (CD) is endoscopy/colonoscopy, although this is invasive, costly, and associated with risks to the patient. Recently, circulating microRNAs (miRNAs) have emerged as promising noninvasive biomarkers. Here, we examined the utility of serum miRNAs as biomarkers of CD in children.

Patients and Methods:

Studies were conducted using sera samples from patients with pediatric CD, healthy controls, and a comparison group of patients with pediatric celiac disease. Serum miRNA levels were explored initially using a microfluidic quantitative reverse transcription‐polymerase chain reaction array platform. Findings were subsequently validated using quantitative reverse transcription‐polymerase chain reaction in larger validation sample sets. The diagnostic utility of CD‐associated serum miRNA was examined using receiver operating characteristic analysis.

Results:

A survey of miRNA levels in the sera of control and patients with CD detected significant elevation of 24 miRNAs, 11 of which were chosen for further validation. All of the candidate biomarker miRNAs were confirmed in an independent CD sample set (n = 46). To explore the specificity of the CD‐associated miRNAs, they were measured in the sera of patients with celiac disease (n = 12); none were changed compared with healthy controls. Receiver operating characteristic analyses revealed that serum miRNAs have promising diagnostic utility, with sensitivities for CD above 80%. Significant decreases in serum miRNAs were observed in 24 incident patients with pediatric CD after 6 months of treatment.

Conclusions:

The present study identifies 11 CD‐associated serum miRNA with encouraging diagnostic potential. Our findings suggest serum miRNAs may prove useful as noninvasive biomarkers in CD.
Peter Hague Nye. 16 September 1921 — 13 February 2009
Authors: Greenland D. J. , Tinker P. B. , Kirk G. J. D.
Published: May 2011

Peter Nye was at the forefront of research in plant and soil sciences for over 40 years. He began his career in West Africa in the 1950s, where he did seminal work on the soils under shifting cultivation systems of agriculture. He spent the rest of his career in Oxford, where he pioneered research on the complexities of the plant root–soil interface and mathematical modelling of plant and soil processes.
Postglacial migration supplements climate in determining plant species ranges in Europe
Authors: Normand Signe , Ricklefs Robert E. , Skov Flemming , Bladt Jesper , Tackenberg Oliver , Svenning Jens-Christian
Published: May 2011

The influence of dispersal limitation on species ranges remains controversial. Considering the dramatic impacts of the last glaciation in Europe, species might not have tracked climate changes through time and, as a consequence, their present-day ranges might be in disequilibrium with current climate. For 1016 European plant species, we assessed the relative importance of current climate and limited postglacial migration in determining species ranges using regression modelling and explanatory variables representing climate, and a novel species-specific hind-casting-based measure of accessibility to postglacial colonization. Climate was important for all species, while postglacial colonization also constrained the ranges of more than 50 per cent of the species. On average, climate explained five times more variation in species ranges than accessibility, but accessibility was the strongest determinant for one-sixth of the species. Accessibility was particularly important for species with limited long-distance dispersal ability, with southern glacial ranges, seed plants compared with ferns, and small-range species in southern Europe. In addition, accessibility explained one-third of the variation in species' disequilibrium with climate as measured by the realized/potential range size ratio computed with niche modelling. In conclusion, we show that although climate is the dominant broad-scale determinant of European plant species ranges, constrained dispersal plays an important supplementary role.
A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses
Authors: Koelle Katia , Ratmann Oliver , Rasmussen David A. , Pasour Virginia , Mattingly Jonathan
Published: May 2011

Antigenically variable RNA viruses are significant contributors to the burden of infectious disease worldwide. One reason for their ubiquity is their ability to escape herd immunity through rapid antigenic evolution and thereby to reinfect previously infected hosts. However, the ways in which these viruses evolve antigenically are highly diverse. Some have only limited diversity in the long-run, with every emergence of a new antigenic variant coupled with a replacement of the older variant. Other viruses rapidly accumulate antigenic diversity over time. Others still exhibit dynamics that can be considered evolutionary intermediates between these two extremes. Here, we present a theoretical framework that aims to understand these differences in evolutionary patterns by considering a virus's epidemiological dynamics in a given host population. Our framework, based on a dimensionless number, probabilistically anticipates patterns of viral antigenic diversification and thereby quantifies a virus's evolutionary potential. It is therefore similar in spirit to the basic reproduction number, the well-known dimensionless number which quantifies a pathogen's reproductive potential. We further outline how our theoretical framework can be applied to empirical viral systems, using influenza A/H3N2 as a case study. We end with predictions of our framework and work that remains to be done to further integrate viral evolutionary dynamics with disease ecology.
Volumetric imaging of shark tail hydrodynamics reveals a three-dimensional dual-ring vortex wake structure
Authors: Flammang Brooke E. , Lauder George V. , Troolin Daniel R. , Strand Tyson
Published: May 2011

Understanding how moving organisms generate locomotor forces is fundamental to the analysis of aerodynamic and hydrodynamic flow patterns that are generated during body and appendage oscillation. In the past, this has been accomplished using two-dimensional planar techniques that require reconstruction of three-dimensional flow patterns. We have applied a new, fully three-dimensional, volumetric imaging technique that allows instantaneous capture of wake flow patterns, to a classic problem in functional vertebrate biology: the function of the asymmetrical (heterocercal) tail of swimming sharks to capture the vorticity field within the volume swept by the tail. These data were used to test a previous three-dimensional reconstruction of the shark vortex wake estimated from two-dimensional flow analyses, and show that the volumetric approach reveals a different vortex wake not previously reconstructed from two-dimensional slices. The hydrodynamic wake consists of one set of dual-linked vortex rings produced per half tail beat. In addition, we use a simple passive shark-tail model under robotic control to show that the three-dimensional wake flows of the robotic tail differ from the active tail motion of a live shark, suggesting that active control of kinematics and tail stiffness plays a substantial role in the production of wake vortical patterns.
Phloem-Specific Expression of Yang Cycle Genes and Identification of Novel Yang Cycle Enzymes inPlantagoandArabidopsis
Authors: Pommerrenig Benjamin , Feussner Kirstin , Zierer Wolfgang , Rabinovych Valentyna , Klebl Franz , Feussner Ivo , Sauer Norbert
Published: May 2011

The 5-methylthioadenosine (MTA) or Yang cycle is a set of reactions that recycle MTA to Met. In plants, MTA is a byproduct of polyamine, ethylene, and nicotianamine biosynthesis. Vascular transcriptome analyses revealed phloem-specific expression of the Yang cycle gene 5-METHYLTHIORIBOSE KINASE1 (MTK1) in Plantago major and Arabidopsis  thaliana. As Arabidopsis has only a single MTK gene, we hypothesized that the expression of other Yang cycle genes might also be vascular specific. Reporter gene studies and quantitative analyses of mRNA levels for all Yang cycle genes confirmed this hypothesis for Arabidopsis and Plantago. This includes the Yang cycle genes 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE1 and DEHYDRATASE-ENOLASE-PHOSPHATASE-COMPLEX1. We show that these two enzymes are sufficient for the conversion of methylthioribose-1-phosphate to 1,2-dihydroxy-3-keto-5-methylthiopentene. In bacteria, fungi, and animals, the same conversion is catalyzed in three to four separate enzymatic steps. Furthermore, comparative analyses of vascular and nonvascular metabolites identified Met, S-adenosyl Met, and MTA preferentially or almost exclusively in the vascular tissue. Our data represent a comprehensive characterization of the Yang cycle in higher plants and demonstrate that the Yang cycle works primarily in the vasculature. Finally, expression analyses of polyamine biosynthetic genes suggest that the Yang cycle in leaves recycles MTA derived primarily from polyamine biosynthesis.
Two-Phase Resolution of Polyploidy in theArabidopsisMetabolic Network Gives Rise to Relative and Absolute Dosage Constraints
Authors: Bekaert Michaël , Edger Patrick P. , Pires J. Chris , Conant Gavin C.
Published: May 2011

The abundance of detected ancient polyploids in extant genomes raises questions regarding evolution after whole-genome duplication (WGD). For instance, what rules govern the preservation or loss of the duplicated genes created by WGD? We explore this question by contrasting two possible preservation forces: selection on relative and absolute gene dosages. Constraints on the relative dosages of central network genes represent an important force for maintaining duplicates (the dosage balance hypothesis). However, preservation may also result from selection on the absolute abundance of certain gene products. The metabolic network of the model plant Arabidopsis thaliana is a powerful system for comparing these hypotheses. We analyzed the surviving WGD-produced duplicate genes in this network, finding evidence that the surviving duplicates from the most recent WGD (WGD-α) are clustered in the network, as predicted by the dosage balance hypothesis. A flux balance analysis suggests an association between the survival of duplicates from a more ancient WGD (WGD-β) and reactions with high metabolic flux. We argue for an interplay of relative and absolute dosage constraints, such that the relative constraints imposed by the recent WGD are still being resolved by evolution, while they have been essentially fully resolved for the ancient event.
Induction of antitumor immunity using dendritic cells electroporated with Polo‐like kinase 1 (Plk1) mRNA in murine tumor models
Authors: Park Jung‐Sun , Sohn Hyun‐Jung , Park Gyeong‐Sin , Chung Yeun‐Jun , Kim Tai‐Gyu
Published: May 2011

Polo‐like kinase 1 (Plk1), a serine–threonine kinase, plays a key role in the regulation of the cell cycle. Elevated Plk1 expression in various cancers is correlated with poor prognosis and poor patient survival rates. Several Plk1 inhibitors are currently being developed as potential treatments for cancer. In the present study, we investigated whether dendritic cells (DC) electroporated with mouse Plk1RNA (mPlk1RNA/DC) can induce Plk1‐specific immune responses and exert antitumor effects in various murine tumor models. Overexpression of Plk1 protein was confirmed in several mouse and human tumor cell lines and various cancer tissues. Furthermore, Plk1‐specific CD4+ and CD8+ T cells were induced by vaccination with mPlk1RNA/DC and the cytotoxic activity of the T cells was demonstrated against several Plk1‐expressing tumor cell lines. Vaccination with mPlk1RNA/DC inhibited the growth of MC‐38 and B16F10 tumors in C57BL/6 mice and the growth of CT26 tumors in BALB/c mice. Depletion of CD8+ T cells reversed the inhibition of tumor growth by mPlk1RNA/DC vaccination. Homologous human Plk1RNA‐electroporated DC also inhibited tumor growth in MC‐38 tumor‐bearing mice. In addition, Plk1‐specific cytotoxic T lymphocytes from PBMC of healthy donors could be induced using autologous monocyte‐derived DC electroporated with RNA encoding the whole gene of human Plk1. Taken together, the results of the present study suggest that Plk1 could be a universal tumor antigen recognized by cytotoxic T lymphocytes for cancer immunotherapy. (Cancer Sci 2011; 102: 1448–1454)
The effects of age and gender on the pharmacokinetics and pharmacodynamics in healthy subjects of the plasminogen activator, lanoteplase
Authors: Vachharajani Nimish N. , Raymond Ralph H. , Shyu Wen‐Chyi , Stouffer Bruce C. , Boulton David W.
Published: May 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• The pharmacokinetics and pharmacodynamics of the plasminogen activator lanoteplase have not been extensively characterized in specific populations and the need for dose adjustment on the basis of age and/or gender has not been established.

WHAT THIS STUDY ADDS

• This paper is the first report of lanoteplase administered to healthy subjects in order to address its clinical use in these important specific populations. The results support the use of the same doses of lanoteplase in males and females and young and elderly patients.

AIMS To investigate the influence of age and gender on the intravenous pharmacokinetics and pharmacodynamics of the plasminogen activator, lanoteplase.

METHODS Forty healthy subjects (10 each of young males, elderly males, young females and elderly females) received a single bolus 10 kU kg−1 intravenous dose of lanoteplase. Plasma from blood serially collected for 24 h post‐dose was analyzed for lanoteplase (antigen), fibrinogen, plasminogen and α2‐antiplasmin concentrations, plasma plasminogen activation activity (PPAA) and rapid plasminogen activator inhibitor (PAI‐1).

RESULTS Lanoteplase mean total systemic clearance (CLt) values ranged from 1.9 to 2.8 l h−1 and mean steady‐state volume of distribution (Vss) values ranged from 12.3 to 15.6 l. Age‐by‐gender interactions were observed for lanoteplase CLt (P= 0.04), but no differences were observed for Vss or elimination half‐life. Elderly females had a 27% lower mean CLt than young females (95% CI for the difference 0.17, 1.27 l h−1) and 32% lower CLt than elderly males (95% CI for the difference 0.15, 1.65 l h−1). PPAA AUC/dose values did not show an age‐by‐gender interaction. Haemostasis parameters indicated only a slight degree of systemic plasminogen activation.

CONCLUSIONS Elderly females had a lower mean lanoteplase CLt than elderly males and young females. However, no difference was observed between young and elderly females for the AUC/dose of PPAA. In addition, there were no age‐related or gender‐related differences observed in the other pharmacodynamic parameters measured.
Selective serotonin re‐uptake inhibiting antidepressants and the risk of overanticoagulation during acenocoumarol maintenance treatment
Authors: Teichert Martina , Visser Loes E. , Uitterlinden Andrė G. , Hofman Albert , Buhre Peter J. , Straus Sabine , De Smet Peter A. G. M. , Stricker Bruno HCh
Published: May 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Coumarin anticoagulants and selective serotonin re‐uptake inhibitors (SSRIs) have been reported to cause bleeding. Combination of these drug groups might enhance this risk. Case reports showed an increase of prothrombin time for the combination of warfarin with fluvoxamine and fluoxetine. This has not yet been confirmed by population based studies.

WHAT THIS STUDY ADDS

• Fluvoxamine and venlafaxine increased prothrombin time in users of acenocoumarol above a critical value which is associated with an increased bleeding risk. The other SSRIs had no influence on acenocoumarol effectiveness, however numbers of drug users were low. The combination of fluvoxamine and venlafaxine with acenocoumarol should be monitored by measurements of the international normalized ratio to avoid overanticoagulation.

AIM The aim of this study was to investigate the effects of co‐medication with selective serotonin re‐uptake inhibitors (SSRIs) on overanticoagulation during acenocoumarol maintenance treatment.

METHODS All subjects from The Rotterdam Study who received acenocoumarol maintenance treatment between April 1 1991 and September 9 2009 were followed for the event of an international normalized ratio (INR) ≥6, until death, end of treatment or end of the study period. With the Andersen‐Gill extension of the Cox proportional hazards model, risks for repeated events of overanticoagulation in relation to concomitant SSRI use were calculated.

RESULTS The risk for overanticoagulation during acenocoumarol maintenance treatment was increased in combination with fluvoxamine (HR 2.63, 95% CI 1.49, 4.66) and venlafaxine (HR 2.19, 95% CI 1.21, 3.99). There was no increase in risk for the other SSRIs, but numbers of exposed cases were low for all SSRIs except paroxetine.

CONCLUSION Fluvoxamine and venlafaxine were associated with a more than double risk of INR values ≥6 in acenocoumarol treated subjects.
Recent advances in the understanding and management of MYH9‐related inherited thrombocytopenias
Authors: Balduini Carlo L. , Pecci Alessandro , Savoia Anna
Published: May 2011

MYH9‐related disease (MYH9‐RD) is one of the most frequent forms of inherited thrombocytopenia. It is transmitted in an autosomal dominant fashion and derives from mutations of MYH9, the gene for the heavy chain of non‐muscle myosin IIA. Patients present with congenital macrothrombocytopenia with mild bleeding tendency and may develop kidney dysfunction, deafness and cataracts later in life. The term MYH9‐RD encompasses four autosomal‐dominant thrombocytopenias that were previously described as distinct disorders, namely May‐Hegglin Anomaly, Sebastian, Fechtner and Epstein syndromes. Thrombocytopenia is usually mild and derives from complex defects of megakaryocyte maturation and platelet formation. It is easily diagnosed, in that the presence of giant platelets in peripheral blood raises the suspicion of MYH9‐RD and a simple immunofluorescence test on blood films confirms the diagnostic hypothesis. However, genotype/phenotype correlations have been recognized and mutation screening is therefore required to define the risk of acquiring extra‐haematological defects. Results of a small clinical study suggested that a non‐peptide thrombopoietin mimetic might greatly benefit both thrombocytopenia and bleeding tendency of MYH9‐RD patients.
Climate change and disease: bleaching of a chemically defended seaweed
Authors: CAMPBELL ALEXANDRA H. , HARDER TILMANN , NIELSEN SHAUN , KJELLEBERG STAFFAN , STEINBERG PETER D.
Published: May 2011

Disease is emerging as an important impact of global climate change, due to the effects of environmental change on host organisms and their pathogens. Climate‐mediated disease can have severe consequences in natural systems, particularly when ecosystem engineers, such as habitat‐formers or top predators are affected, as any impacts can cascade throughout entire food webs. In temperate marine ecosystems, seaweeds are the dominant habitat‐formers on rocky reefs. We investigated a putative bleaching disease affectingDelisea pulchra, a chemically defended seaweed that occurs within a global warming ‘hot‐spot’ and assessed how patterns of this phenomenon were influenced by ocean temperature, solar radiation, algal chemical defences and microbial pathogens. Warmer waters were consistently and positively correlated with higher frequencies of bleaching in seaweed populations, but patterns of bleaching were not consistently influenced by light levels. Bleached thalli had low levels of antibacterial chemical defences relative to healthy conspecifics and this was observed across entire thalli of partially bleached algae. Microbial communities associated with bleached algae were distinct from those on the surfaces of healthy seaweeds. Direct testing of the importance of algal chemical defences, done here for the first time in the field, demonstrated that they protected the seaweed from bleaching. Treatment of algal thalli with antibiotics reduced the severity of bleaching in experimental algae, especially at high water temperatures. These results indicate that bleaching inD. pulchrais the result of temperature‐mediated bacterial infections and highlight the potential for warming to influence disease dynamics by stressing hosts. Understanding the complex ways in which global change may affect important organisms such as habitat‐forming seaweeds, is essential for the management and conservation of natural resources.
Central nervous system bleeding in patients with rare bleeding disorders
Authors: SIBONI S. M. , ZANON E. , SOTTILOTTA G. , CONSONNI D. , CASTAMAN G. , MIKOVIC D. , BIONDO F. , TAGLIAFERRI A. , IORIO A. , MANNUCCI P. M. , PEYVANDI F.
Published: May 2011

Summary.  Central nervous system (CNS) bleeding is one of the most severe and debilitating manifestations occurring in patients with rare bleeding disorders (RBDs). The aim of this study was to retrospectively collect data on patients affected with RBDs who had CNS bleeding, to establish incidence of recurrence, death rate, neurological sequences, most frequent location, type of bleeding and efficacy of treatments. Results pertained to 36 CNS bleeding episodes in 24 patients with severe deficiency except one with moderate factor VII (FVII) deficiency. Six patients (25%) experienced a recurrence and two had more than one recurrence. Seven patients (29%) had an early onset of CNS bleeding before the first 2 years of life, others (71%) later in life. In 76% of cases, CNS bleeding was spontaneous. CNS bleeding was intracerebral in 19 cases (53%), extracerebral in 10 (28%) and both intracerebral and extracerebral in two cases (6%). Neurosurgery was performed in 11 cases, in association with replacement therapy in seven cases. Seizures were noted in four patients. Residual psychomotor abnormalities were seen in two patients. No death was recorded. To prevent recurrence, 17/24 patients (71%) were put on secondary prophylaxis. In conclusion, recurrence of CNS bleeding was confirmed to be relatively frequent in patients with severe FV, FX, FVII and FXIII deficiencies. Most patients were managed with replacement therapy alone, surgery being reserved for those with worsening neurological conditions. Our results indicate that some RBDs require early prophylactic treatment to prevent CNS bleeding. Optimal dosage and frequency of treatment need further evaluation.
Recovery of aroma compounds from Zhenjiang aromatic vinegar by supercritical fluid extraction
Authors: Lu Zhen‐Ming , Xu Wei , Yu Ning‐Hua , Zhou Tu , Li Guo‐Quan , Shi Jing‐Song , Xu Zheng‐Hong
Published: May 2011

Zhenjiang aromatic vinegar, which is produced from sticky rice through solid‐state fermentation, is highly prized as one of the four famous China‐style vinegars, owing to its unique flavour. In this study, a method of supercritical fluid extraction (SFE) was used for the first time to recover aroma compounds from Zhenjiang aromatic vinegar. For this purpose, the optimal conditions for the extraction of aroma compounds by SFE were determined as follows: CO2 flow rate, 25 L h−1; extraction time, 2 h; extraction pressure, 35 MPa; and extraction temperature, 323 K. Using headspace solid‐phase microextraction‐gas chromatography–mass spectrometry (HS‐SPME‐GC‐MS) analysis, a total of 49 and 44 aroma compounds were identified in Zhenjiang aromatic vinegar and its SFE extract, respectively. Acetic acid, ethyl acetate, furfural, phenethyl alcohol, tetramethyl‐pyrazine, 3‐hydroxybutanone and benzaldehyde were the main aroma compounds in the vinegar and its SFE extract. SFE is a fast and sensitive method to recovery aroma compounds from the vinegar.
Comparison of digestion and solid sampling techniques for the determination of Pb and Cu in blackpepper
Authors: Baysal Asli , Akman Suleyman
Published: May 2011

Copper and lead in blackpepper samples were determined by graphite furnace atomic absorption spectrometry using microwave‐assisted digestion and direct solid sampling technique. At first, the samples were dissolved by microwave‐assisted digestion method and directly pipetted into the graphite furnace for digestion technique. Secondly, the powdered samples were directly analysed by solid sampling technique. The experimental parameters were optimised for the two techniques. The two of the methods were applied for determination of copper and lead in pepper samples obtained commercially from markets in Istanbul, Turkey and results were statistically evaluated and compared. The limits of detections for microwave digestion and solid sampling techniques were 0.3 and 0.4 ng g−1, for lead, and 5.1 and 11.3 ng g−1, for copper, respectively. The advantages and disadvantages of the two sampling methods were discussed.