bluuebunny/crossref_metadata_2025 huggingface dataset:
How effective is CALL in ELT?
Authors: Kettemann Bernhard
Published: December 2008

Recently the NCET (National Council for Educational Technology) published a survey of the results of various studies on the evaluation and effectiveness of computer assisted teaching in Great Britain.1 This survey lists several positive effects of computer assisted teaching in a wide variety of educational applications. These range from increased motivation and eagerness to learn by disturbed or handicapped children to an increase in the performance of good learners by e.g. training analytic and divergent thinking.
LOCKEAN PROPERTY AND LITERARY WORKS
Authors: Peterson Jonathan
Published: December 2008

This paper develops a Lockean account of literary property. Seana Shiffrin has recently argued, on the basis of an egalitarian interpretation of Locke's theory of property, that the Lockean view does not justify property rights in intellectual works. I argue that Shiffrin fails to take an important strand of Locke's view into account, namely, the view that makers have rights to what they have made. If this aspect of Locke's view is given its proper place, a plausible Lockean account of property in literary works can be developed. This account of literary property places us in a better position to appreciate both the strengths and weaknesses of the Lockean theory of intellectual property.
The Obesity Epidemic: What does it mean to the PeriAnesthesia Practitioner?
Authors: Menard Kathleen J.
Published: December 2008

Alexander and Liston coined the term ‘Obesogenic society – where people are addicted to fast foods and supermarkets and a sedentary lifestyle promoted by television and cars’ [Alexander and Liston, 2006, p. 1167]. It is an undeniable fact that the United States has an overweight and obesity problem, the prevalence has doubled since 1960, the latest statistics from the Center for Disease Control and Prevention (CDC) report obesity (body mass index (BMI)⩾30) in adult men (33.3%) and adult women (35.3%) and more than 66% of adult Americans are considered overweight [CDC (Department of Health and Human Services), 2008]. Extreme obesity has increased from 0.8% to 4.9% [Bellaret al, 2008]. Visit the CDC website athttp://www.cdc.gov/nccdphp/dnpa/obesity/trend/maps/index.htmfor a very graphic slide show of the ‘fatting of America.’

The Weight Control Information Network classifies obesity as a chronic illness with an annual $117 billion cost (Weight-control Information Network (National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) of the National Institutes of Health (NIH)), 2007). In 2003, obesity was the second leading cause of preventable death in the United States [Garza, 2003]; it is now on the way to surpassing smoking [Abir and Bell, 2004]. But it is not just a problem in the United States; it is becoming a worldwide problem. What does this obesity epidemic mean to the PeriAnesthesia practitioner?
Lesekompetenz und Lesemotivation
Authors: McElvany Nele , Kortenbruck Marthe , Becker Michael
Published: December 2008

Die vorliegende Studie beschäftigt sich mit der Entwicklung der Lesekompetenz und der intrinsischen Lesemotivation in den Klassenstufen 3 bis 6 sowie den Zusammenhängen zwischen Kompetenz, Motivation und Leseverhalten. Hintergrund sind der Mangel an längsschnittlichen Analysen der Entwicklung der Konstrukte in dieser Altersgruppe in Deutschland, die unzureichende empirische Überprüfung theoretischer Wirkungsannahmen (zsf. Möller & Schiefele, 2004 ) und die berichteten Defizite in der Lesemotivation älterer Schüler (u. a. Artelt, Stanat, Schneider & Schiefele, 2001 ). Die empirische Überprüfung erfolgt anhand der längsschnittlichen Daten des Berliner Leselängsschnitts der Klassenstufen 3 bis 6 mit Hilfe von Wachstumskurvenmodellen und autoregressiven Cross-lag Panel-Modellen. Die Ergebnisse bestätigen die erwartete gegenläufige Entwicklung von ansteigender Kompetenz und sich verringernder Motivation im Untersuchungszeitraum. Die Pfadanalysen weisen auf die wechselseitigen Einflüsse der drei Konstrukte im Quer- und Längsschnitt sowie auf einen indirekten Effekt der frühen Lesemotivation auf spätere Lesekompetenz vermittelt über das Leseverhalten hin. Die Lesekompetenz wird von der Motivation und dem Leseverhalten insgesamt jedoch in vergleichsweise geringem Umfang vorhergesagt, während umgekehrt beide Konstrukte auch von der Kompetenz beeinflusst werden. Implikationen für zukünftige Forschung und pädagogische Praxis werden diskutiert.
Mid‐depth internal wave energy off the Iberian Peninsula estimated from seismic reflection data
Authors: Krahmann G. , Brandt P. , Klaeschen D. , Reston T.
Published: December 2008

Energy levels of internal waves are estimated from seismic reflection data. Three legacy seismic sections from 1993 and 1997 obtained off the Iberian Peninsula have been analyzed for acoustic reflections within the water column. The reflections are aligned continuously for up to several kilometers over large parts of the sections and in the depth interval from 200 to 2000 m. Depth variations of these reflections are thought to be caused by the background internal wave field. From the variations we derive horizontal wave number spectra of normalized internal wave displacement. The general slope of the power density spectra is remarkably consistent for all sections and agrees well with model spectra for internal waves. Significant differences within the sections can be found when sufficiently large subsections are averaged. The spatial variation of the energy level indicates increasing internal wave activity with shallower water depths as well as near a subsurface eddy.
Water flux components and soil water‐atmospheric controls in a temperate pine forest growing in a well‐drained sandy soil
Authors: McLaren Joshua D. , Arain M. Altaf , Khomik Myroslava , Peichl Matthias , Brodeur Jason
Published: December 2008

The influences of soil water supply and atmospheric demand on transpiration were studied to gain insight into the physical mechanisms limiting forest water use within the broader context of total canopy water loss to the atmosphere. Evaporation from forests (E) can be partitioned in to four main source components: canopy transpiration (Ec), understorey transpiration (Eu), evaporation from the soil (Es), and the evaporation of intercepted water (EI). Ec and EI usually make up most of E. Ec estimated from sap flow measurements and modeled EI estimates were compared with eddy covariance measured values of E to quantify the components of the above canopy water flux to the atmosphere, in a temperate pine forest ecosystem established on a well‐drained sandy plain at Turkey Point in southern Ontario, Canada. Daily values of E averaged 2.4 mm d−1 and reached maximums of 4 mm d−1 while daily values of Ec averaged 1.2 mm d−1 over the growing season. The evaporation of intercepted water (EI) was generally between 2 and 3 mm per event. EI accounted for 34% and Ec accounted for 47% (31 to 67% range on a monthly basis), together accounting for 81% of E during the growing season. Ec increased linearly with vapor pressure deficit (VPD) until a transition point was reached, after which mid‐day Ec rates remained more or less constant. For analysis purposes, data were segregated by early morning VPD (or VPDin) in an attempt to characterize the atmosphere at the beginning of the daily transpiration cycle. This technique revealed that shifts in the timing and magnitude of Ec rates masked the response of Ec to changes in soil water content. Analysis also suggested that while increasing VPDs may limit maximum transpiration rates, daily total transpiration is a conservative quantity. This study improves the understanding of the physical mechanisms limiting water loss in forested ecosystems growing on water‐stressed soils by investigating the effects of VPD and soil water content on Ec.
Private management and public finance in the Italian water industry: A marriage of convenience?
Authors: Massarutto Antonio , Paccagnan Vania , Linares Elisabetta
Published: December 2008

In many countries, reforms of water and sanitation utilities have favored private sector participation. The drivers of this trend are the need to improve efficiency, professional capabilities of service operations, and willingness to relieve public budgets of the heavy burden of investment. Scant attention has been devoted to the great impact this strategy can have on water bills because of the higher cost of capital that is implicit, given the economic risk that the private sector is required to accept. Since it is a capital‐intensive industry with a long economic life of its assets, the water industry is particularly vulnerable to the cost of capital. This creates the case for publicly‐supported financial schemes in order to keep this cost as low as possible and guarantee long‐run viability as well as affordability. The Italian water industry is an excellent case study to investigate the importance of this situation: in the last 15 years, a far‐reaching reform has been introduced with the aim of substituting a financing model, based entirely on public spending, with one delegating financial responsibilities to operators through full‐cost recovery. Our simulations show that delegating all responsibilities and risks to the private sector can lead to unsustainable price increases once replacement of existing assets are required. The solution is not to give up full‐cost recovery, but rather to search for risk allocation patterns that are more coherent with the risk profile of the water industry and help keeping the cost of capital low.
Behavior of current sheets at directional magnetic discontinuities in the solar wind at 0.72 AU
Authors: Zhang T. L. , Russell C. T. , Zambelli W. , Vörös Z. , Wang C. , Cao J. B. , Jian L. K. , Strangeway R. J. , Balikhin M. , Baumjohann W. , Delva M. , Volwerk M. , Glassmeier K.‐H.
Published: December 2008

Venus Express interplanetary magnetic field measurements have been examined for magnetic “holes,” accompanied by magnetic field directional changes. We examine both the thickness of the current sheet and the depth of the magnetic field depression. We find the thickness of the current sheet is not correlated with the depth of the field depression. The depth of the magnetic holes is related to directional angle change. Since total pressure should balance across these discontinuities, there must be enhanced plasma pressure within the magnetic holes. The dependence of the depth of the hole (i.e., size of the plasma pressure enhancement) on the directional changes suggests that the heating of the plasma associated with the hole formation may be provided by annihilation of the magnetic energy in the current sheet, via slow reconnection.
Inverse cascade feature in current disruption
Authors: Lui A. T. Y. , Yoon P. H. , Mok Chinook , Ryu Chang‐Mo
Published: December 2008

We investigate the origin of waves leading to current disruption and dipolarization observed by a THEMIS satellite at XGSM ∼ −8 RE in the magnetotail near a substorm expansion onset on 29 January 2008. Continuous wavelet transform of the magnetic activity associated with current disruption shows a clear inverse cascade feature of waves starting at frequencies slightly below the ion cyclotron frequency to waves at low frequencies that correspond to the time scale of dipolarization. There was no other low‐frequency wave associated with the time scale of dipolarization. On the basis of this inverse cascade feature, we provide a preliminary theoretical analysis to propose that the initial excited waves causing eventual dipolarization in this event may originate from the drift‐driven electromagnetic ion cyclotron instability, which is an electromagnetic version of the Weibel instability, or an ordinary mode instability similarly driven by the cross‐field ion drift.
Damage patterns, stress rotations and pore fluid pressures in strike‐slip fault zones
Authors: Healy David
Published: December 2008

Active faults unfavorably oriented with respect to the regional maximum compressive stress have been labeled as “weak.” The seismic hazards posed by these faults make understanding this apparent weakness a priority. Stress rotations in these fault zones, together with an increase in mean stress, could enable high pore fluid pressures to weaken a fault zone. Such a model requires a foundation in the physics and mechanics of damage. This paper presents a new model for stress rotations in fault zones by combining the Effective Medium Theory with anisotropic poroelasticity. This approach enables the quantitative characterization of crack damage and the prediction of progressive changes in the elastic properties of rocks across the fault zone. The processes of fault growth and wear will lead to distinct patterns of crack damage, with different effects on the elastic properties. Elevated pore fluid pressures have long been known to change the effective normal and shear stresses of anisotropic rocks, and this work incorporates these effects into a multilayer fault zone model. It is shown that high pore fluid pressures in the anisotropic rocks of the core zone can generate large stress rotations (i.e., more fault‐parallel), and increases in mean stress, sufficient to weaken the fault. Stress rotations in the damage zones of unfavorably oriented faults tend to be away from the fault (i.e., more fault‐normal) for likely combinations of damage patterns and pore fluid pressure.
Ice‐Tethered Profiler observations of the double‐diffusive staircase in the Canada Basin thermocline
Authors: Timmermans M.‐L. , Toole J. , Krishfield R. , Winsor P.
Published: December 2008

Six Ice‐Tethered Profilers (ITP), deployed in the central Canada Basin of the Arctic Ocean between 2004 and 2007, have provided detailed potential temperature and salinity measurements of a double‐diffusive staircase at about 200–300 m depth. Individual layers in the staircase are of order 1 m in vertical height but appear to extend horizontally for hundreds of kilometers, with along‐layer gradients of temperature and salinity tightly related. On the basis of laboratory‐derived double‐diffusive flux laws, estimated vertical heat fluxes through the staircase are in the range 0.05–0.3 W m−2, only about one tenth of the estimated mean surface mixed layer heat flux to the sea ice. It is thus concluded that the vertical transport of heat from the Atlantic Water in the central basin is unlikely to have a significant impact to the Canada Basin ocean surface heat budget. Icebreaker conductivity‐temperature‐depth data from the Beaufort Gyre Freshwater Experiment show that the staircase is absent at the basin periphery. Turbulent mixing that presumably disrupts the staircase might drive greater flux from the Atlantic Water at the basin boundaries and possibly dominate the regionally averaged heat flux.
Multistatistics metric evaluation of ocean general circulation model sea surface temperature: Application to 0.08° Pacific Hybrid Coordinate Ocean Model simulations
Authors: Kara A. B. , Metzger E. J. , Hurlburt H. E. , Wallcraft A. J. , Chassignet E. P.
Published: December 2008

This study is a multimetric statistical evaluation of interannual and climatological mean sea surface temperature (SST) over the Pacific Ocean (north of 20°S) simulated by an ocean model. The evaluation procedure is outlined using daily and monthly SSTs from eddy‐resolving (0.08°) Hybrid Coordinate Ocean Model (HYCOM). Satellite‐based products and buoy measurements are used for model‐data comparisons. Three are three principal findings. (1) Using monthly mean climatological atmospheric forcing with the addition of a 6‐hourly wind component can yield realistic simulations of monthly mean climatological SST in comparison with observations and interannually forced simulations. (2) Nondimensional skill score can be a very useful metric for validating SST from an ocean model in a large region, such as the Pacific Ocean, where the amplitude of the SST seasonal cycle has large spatial variations. The use of skill score is extensively discussed along with its advantages over other traditional metrics. Interannual model‐data comparisons (1993–2003) using satellite‐based SST give basin‐averaged yearly mean skill score values ranging from 0.35 to 0.58 for HYCOM. (3) A comparison of HYCOM to 804 yearlong daily buoy SST time series spanning 1990–2003 gives a median root mean square value of 0.83°C. Relatively small SST biases and high skill values are essential prerequisites for SST assimilation using an ocean model as a first guess and for SST forecasting. The validation procedures presented in this paper include a variety of statistical metrics and use a comprehensive observational buoy data set. Such procedures can be applied to any global‐ or basin‐scale ocean general circulation model that predicts SST.
Tsunami forecast analysis for the May 2006 Tonga tsunami
Authors: Tang L. , Titov V. V. , Wei Y. , Mofjeld H. O. , Spillane M. , Arcas D. , Bernard E. N. , Chamberlin C. , Gica E. , Newman J.
Published: December 2008

This study applies tsunami forecast models developed for NOAA's Tsunami Warning and Forecast System to investigate the May 2006 Tonga Tsunami. Inversion of the Deep‐ocean Assessment and Reporting of Tsunamis (DART) measurements estimates a tsunami magnitude equivalent to an earthquake moment magnitude of 8.0. The DART‐constrained modeling forecasts show good agreement with observations at eight coastal tide stations in Hawaii, U.S. West Coast, and Alaska, including first arrival times, wave periods, wave amplitudes, and decay during the day following the earthquake. The forecast system correctly reproduces the reflected waves from North America and the scattered waves by the bottom topography in the South Pacific, which arrived in the Hawaiian Islands 16 and 18.5 h after the earthquake, respectively. Wavelet analysis of the tsunami waves suggests that harbor and local shelf resonances may be predominantly responsible for the late occurrence of the maximum wave observed in some coastal areas. These results suggest expanding the operational use of the real‐time forecast models and demonstrate the applicability of the forecast results for “all‐clear” evaluations, search and rescue operations, as well as event and postevent planning. This research highlights the value of high‐resolution inundation models in real‐time forecasts during a long‐duration hazard for coastal communities. It also provides a rigorous and successful test of the performance and accuracy of the forecast models when run in real‐time mode.
Comparison of lower stratospheric tropical mean vertical velocities
Authors: Schoeberl M. R. , Douglass A. R. , Stolarski R. S. , Pawson S. , Strahan S. E. , Read W.
Published: December 2008

We have analyzed 13 years (1993–2005) of tropical stratospheric water vapor data from the Halogen Occultation Experiment and over 3 years of data (October 2004 through November 2007) from the Aura Microwave Limb Sounder. By correlating the phase lag of the water vapor “tape recorder” signal between levels we estimate the time mean vertical velocity. Our estimated vertical velocity compares well with calculations from the Goddard Earth Observing System (GEOS) chemistry‐climate model (CCM) and from the GEOS data assimilation system. Between 18 and 26 km both the GEOS CCM simulations and water vapor observations agree that the vertical velocity is below 0.04 cm/s, with a minimum near 20 km of 0.03 cm/s. Vertical velocities deduced from water vapor observations are higher than those from the GEOS CCM in the region 16–18 km (0.04 cm/s) and above 26–30 km (up to 0.07 cm/s). These estimates are close to earlier estimates from a shorter water vapor record and radiative transfer models. No evidence is found for velocities as high as 0.15 cm/s as was recently estimated from aircraft CO2 measurements in the upper troposphere/lower stratosphere. Further diagnosis of the aircraft CO2 data and model simulations of CO2 show that while the CO2 data give an apparent upward transport velocity of ∼0.06 cm/s, about half of this is due to vertical and horizontal eddy transport. Accounting for the eddy terms gives a CO2‐based estimate of the vertical velocity of ∼0.03 cm/s, in much closer agreement with that estimated from water vapor.
Aerosol and cloud interaction observed from high spectral resolution lidar data
Authors: Su Wenying , Schuster Gregory L. , Loeb Norman G. , Rogers Raymond R. , Ferrare Richard A. , Hostetler Chris A. , Hair Johnathan W. , Obland Michael D.
Published: December 2008

Recent studies utilizing satellite retrievals have shown a strong correlation between aerosol optical depth (AOD) and cloud cover. However, these retrievals from passive sensors are subject to many limitations, including cloud adjacency (or three‐dimensional) effects, possible cloud contamination, uncertainty in the AOD retrieval. Some of these limitations do not exist in High Spectral Resolution Lidar (HSRL) observations; for instance, HSRL observations are not affected by cloud adjacency effects, are less prone to cloud contamination, and offer accurate aerosol property measurements (backscatter coefficient, extinction coefficient, lidar ratio, backscatter Angstrom exponent, and aerosol optical depth) at a fine spatial resolution (<100 m) in the vicinity of clouds. Hence the HSRL provides an important data set for studying aerosol and cloud interaction. In this study, we statistically analyze aircraft‐based HSRL profiles according to their distance from the nearest cloud, assuring that all profile comparisons are subject to the same large‐scale meteorological conditions. Our results indicate that AODs from HSRL are about 8–17% higher in the proximity of clouds (∼100 m) than far away from clouds (4.5 km), which is much smaller than the reported cloud three‐dimensional effect on AOD retrievals. The backscatter and extinction coefficients also systematically increase in the vicinity of clouds, which can be explained by aerosol swelling in the high relative humidity (RH) environment and/or aerosol growth through in‐cloud processing (albeit not conclusively). On the other hand, we do not observe a systematic trend in lidar ratio; we hypothesize that this is caused by the opposite effects of aerosol swelling and aerosol in‐cloud processing on the lidar ratio. Finally, the observed backscatter Angstrom exponent (BAE) does not show a consistent trend because of the complicated relationship between BAE and RH. We demonstrate that BAE should not be used as a surrogate for Angstrom exponent, especially at high RH.
TLR9 traffics through the Golgi complex to localize to endolysosomes and respond to CpG DNA
Authors: Chockalingam Annapoorani , Brooks James C , Cameron Jody L , Blum Lisa K , Leifer Cynthia A
Published: December 2008

Toll‐like receptor 9 (TLR9) promiscuously binds self‐ and microbial DNA, but only microbial DNA elicits an inflammatory response. How TLR9 discriminates between self‐ and foreign DNA is unclear, but inappropriate localization of TLR9 permits response to self‐DNA, suggesting that TLR9 localization and trafficking are critical components. The molecular mechanisms controlling the movement of TLR9 may provide new insight into the recognition of DNA in normal and in pathological conditions such as autoimmune systemic lupus erythematosus. We have shown earlier that TLR9 is retained in the endoplasmic reticulum (ER) and it moves to endolysosomes to recognize CpG DNA. Other studies have suggested that TLR9 bypasses the Golgi complex to access endolysosomes. Here, we show that TLR9 translocates from ER to endolysosomes through the Golgi complex and that Golgi export is required for optimal TLR9 signaling. In all, 6–13% of TLR9 constitutively exits the ER, moves through the Golgi complex and resides in lysosomal‐associated membrane protein‐1‐positive vesicles. TLR9 bound to CpG DNA had glycan modifications indicative of Golgi processing confirming that TLR9 travels through the Golgi complex to access CpG DNA in endolysosomes. Together, these data support a model where TLR9 uses traditional secretory pathways and does not bypass the Golgi complex.
A three-dimensional resistor network model for the linear magnetoresistance of Ag2+δSe and Ag2+δTe bulks
Authors: Xu Jie , Zhang Duanming , Yang Fengxia , Li Zhihua , Pan Yuan
Published: December 2008

A network model for the linear magnetoresistance (MR) of the Ag2+δSe and Ag2+δTe bulks is proposed. The bulk sample is considered as a two-phase (the metal phase and the semiconductor phase) composite and dispersed into a three-dimensional resistor network. The network is constructed from six-terminal resistor units and the mobility of carriers within the network has a modified Gaussian distribution, i.e., a Gaussian distribution with two constraint conditions. The modified Gaussian distribution is related with the mobility of carriers in the two phases and the volume fraction of the metal phase. The model predicts that the MR increases linearly with the increasing magnetic fields and does not show the saturation at high field. Moreover, the temperature dependence of the MR predicted by the model is discussed. A good agreement is found between the theoretical MR predictions and the available experimental data.
Structural and electronic properties of pentacene-fullerene heterojunctions
Authors: Salzmann Ingo , Duhm Steffen , Opitz Ricarda , Johnson Robert L. , Rabe Jürgen P. , Koch Norbert
Published: December 2008

In this study the performance differences of layered and bulk-heterojunction based organic solar cells composed of the prototypical p- and n-type organic semiconductors pentacene (PEN) and fullerene (C60) are correlated with the physical properties of the heterostructures. The electronic structure of layered and codeposited thin PEN and C60 films on the conducting polymer substrate poly(ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) was investigated with ultraviolet photoelectron spectroscopy. Layered structures of C60 on PEN precovered PEDOT:PSS exhibited an offset of the highest occupied molecular orbital (HOMO) levels of 1.45 eV. In contrast, codeposited films of PEN and C60 showed a reduced HOMO-level offset of 0.85 eV, which increased to 1.45 eV by precoverage of the substrate with a thin PEN layer. In this case, the PEN-HOMO level was Fermi-level pinned at 0.35 eV binding energy and charge transfer between PEN and PEDOT:PSS decreased the vacuum level by 0.75 eV. In addition, the morphology and crystal structure of the respective systems have been investigated by atomic force microscopy (AFM), x-ray diffraction (XRD) and Fourier-transform infrared spectroscopy, which indicated pronounced phase separation of PEN and C60 in the codeposited films. XRD revealed crystalline growth of PEN in all investigated cases forming crystallites that exceeded the nominal film thickness by an order of magnitude, whereas C60 was crystalline only if grown on the PEN precovered substrates. AFM investigations allowed to correlate morphology and structure revealing micro- and nanophase separation between PEN and C60.
Low temperature photoluminescence from dilute bismides
Authors: Kini R. N. , Mascarenhas A. , France R. , Ptak A. J.
Published: December 2008

We report on photoluminescence measurements of GaAs(1−x)Bix thin films containing dilute concentration (x≤0.045%) of isoelectronic impurity Bi. At a temperature of 4 K, we observed a sharp emission line at ∼1.510 eV and a series of undulations in an energy range of ∼20 meV below it. We attribute the sharp line at ∼1.510 eV to the recombination of excitons bound to a complex formed by unintentionally incorporated acceptor or donor atoms in the samples. Undulations observed below the sharp line at 1.510 eV are assigned to the vibronic levels of the acceptors, generated by the dynamic Jahn–Teller effect due to the coupling between the holes bound to Bi and acceptors. The sharp line at ∼1.510 eV and the undulation peaks show a redshift with increasing Bi concentration due to the decrease in band gap as a result of the strong perturbation to the GaAs band structure induced by isoelectronic Bi impurities. No spectral evidence for isolated Bi forming a bound state in GaAs was seen and similar to the case of Bi in GaP, no Bi–Bi pair states were observed.
Dry etching characteristics of amorphous As2S3 film in CHF3 plasma
Authors: Choi Duk-Yong , Madden Steve , Rode Andrei , Wang Rongping , Luther-Davies Barry
Published: December 2008

The authors describe the dry etching characteristics of amorphous As2S3 films in CHF3 plasma and the development of an optimized fabrication process for compact waveguides. The observed etching behavior is due to the relative densities of fluorine atoms, polymer precursors, and ions in the plasma which are controlled by the process parameters. In particular, the flow rate of the CHF3 gas has a significant influence on the etched profile and surface roughness as well as the etch rate of the As2S3. The profile evolves from isotropic to vertical with the flow rate due to passivation by increasing polymer deposition on the sidewalls. Such passivation also helps achieve smooth sidewalls because it inhibits differential etching between the phases in the inherently phase-separated As2S3 film, which otherwise results in a grainy and rough etched surface. At the highest flow rate, however, excessive polymer deposition occurs and this results in positive-sloped sidewall and grassy etched surface due to micromasking.
An evaluation of genetic analyses, skull morphology and visual appearance for assessing dingo purity: implications for dingo conservation
Authors: Elledge Amanda E. , Allen Lee R. , Carlsson Britt-Louise , Wilton Alan N. , Leung Luke K.-P.
Published: December 2008

The introgression of domestic dog genes into dingo populations threatens the genetic integrity of ‘pure’ dingoes. However, dingo conservation efforts are hampered by difficulties in distinguishing between dingoes and hybrids in the field. This study evaluates consistency in the status of hybridisation (i.e. dingo, hybrid or dog) assigned by genetic analyses, skull morphology and visual assessments. Of the 56 south-east Queensland animals sampled, 39 (69.6%) were assigned the same status by all three methods, 10 (17.9%) by genetic and skull methods, four (7.1%) by genetic and visual methods; and two (3.6%) by skull and visual methods. Pair-wise comparisons identified a significant relationship between genetic and skull methods, but not between either of these and visual methods. Results from surveying 13 experienced wild dog managers showed that hybrids were more easily identified by visual characters than were dingoes. A more reliable visual assessment can be developed through determining the relationship between (1) genetics and phenotype by sampling wild dog populations and (2) the expression of visual characteristics from different proportions and breeds of domestic dog genes by breeding trials. Culling obvious hybrids based on visual characteristics, such as sable and patchy coat colours, should slow the process of hybridisation.
The use of hollow-bearing trees by vertebrate fauna in wet and dry Eucalyptus obliqua forest, Tasmania
Authors: Koch Amelia , Munks Sarah , Driscoll Don
Published: December 2008

The loss of hollow-bearing trees in production forest areas can have large impacts on animal populations that rely on them for shelter. This study facilitates the selection of appropriate trees for retention by examining the proportion and type of trees that were used by vertebrate fauna in mature wet and dry Eucalyptus obliqua forest in Tasmania. Felled trees were searched for hollows and secondary evidence of use by fauna. Classification Trees and Bayesian logistic regression modelling were used to examine the site and tree attributes that best explained the use of a tree by fauna. We did two separate analyses: one using attributes expected to be causally related to hollow use, and a second using attributes that might be correlated with hollow use and could be easily assessed in standing trees. In all, 28% of hollow-bearing trees examined showed evidence of use, which is at the lower end of the scale found in other areas of Australia. The variables most strongly related to the use of a tree were hollow abundance, tree size and senescence. Random Forest modelling indicated that the likelihood of a hollow being used increased with hollow size, particularly hollow depth. Counting the number of hollows in standing trees was the best way to identify a tree that is likely to be used by fauna and this was particularly important for younger and healthier trees. It was recommended that trees to be retained should contain at least one large hollow. It was estimated that 8–15 trees per hectare were used by hollow-using fauna in mature wet and dry E. obliqua forest in Tasmania.
Synergistic effects of climate-related variables suggest future physiological impairment in a top oceanic predator
Authors: Rosa Rui , Seibel Brad A.
Published: December 2008

By the end of this century, anthropogenic carbon dioxide (CO2) emissions are expected to decrease the surface ocean pH by as much as 0.3 unit. At the same time, the ocean is expected to warm with an associated expansion of the oxygen minimum layer (OML). Thus, there is a growing demand to understand the response of the marine biota to these global changes. We show that ocean acidification will substantially depress metabolic rates (31%) and activity levels (45%) in the jumbo squid,Dosidicus gigas, a top predator in the Eastern Pacific. This effect is exacerbated by high temperature. Reduced aerobic and locomotory scope in warm, high-CO2surface waters will presumably impair predator–prey interactions with cascading consequences for growth, reproduction, and survival. Moreover, as the OML shoals, squids will have to retreat to these shallower, less hospitable, waters at night to feed and repay any oxygen debt that accumulates during their diel vertical migration into the OML. Thus, we demonstrate that, in the absence of adaptation or horizontal migration, the synergism between ocean acidification, global warming, and expanding hypoxia will compress the habitable depth range of the species. These interactions may ultimately define the long-term fate of this commercially and ecologically important predator.
An essential role for the antiviral endoribonuclease, RNase-L, in antibacterial immunity
Authors: Li Xiao-Ling , Ezelle Heather J. , Kang Tae-Jin , Zhang Lei , Shirey Kari Ann , Harro Janette , Hasday Jeffrey D. , Mohapatra Saroj K. , Crasta Oswald R. , Vogel Stefanie N. , Cross Alan S. , Hassel Bret A.
Published: December 2008

Type I IFNs were discovered as the primary antiviral cytokines and are now known to serve critical functions in host defense against bacterial pathogens. Accordingly, established mediators of IFN antiviral activity may mediate previously unrecognized antibacterial functions. RNase-L is the terminal component of an RNA decay pathway that is an important mediator of IFN-induced antiviral activity. Here, we identify a role for RNase-L in the host antibacterial response. RNase-L
−/−
mice exhibited a dramatic increase in mortality after challenge with
Bacillus anthracis
and
Escherichia coli
; this increased susceptibility was due to a compromised immune response resulting in increased bacterial load. Investigation of the mechanisms of RNase-L antibacterial activity indicated that RNase-L is required for the optimal induction of proinflammatory cytokines that play essential roles in host defense from bacterial pathogens. RNase-L also regulated the expression of the endolysosomal protease, cathepsin-E, and endosome-associated activities, that function to eliminate internalized bacteria and may contribute to RNase-L antimicrobial action. Our results reveal a unique role for RNase-L in the antibacterial response that is mediated through multiple mechanisms. As a regulator of fundamental components of the innate immune response, RNase-L represents a viable therapeutic target to augment host defense against diverse microbial pathogens.
Single virus detection from the reactive shift of a whispering-gallery mode
Authors: Vollmer F. , Arnold S. , Keng D.
Published: December 2008

We report the label-free, real-time optical detection of Influenza A virus particles. Binding of single virions is observed from discrete changes in the resonance frequency/wavelength of a whispering-gallery mode excited in a microspherical cavity. We find that the magnitude of the discrete wavelength-shift signal can be sufficiently enhanced by reducing the microsphere size. A reactive sensing mechanism with inverse dependence on mode volume is confirmed in experiments with virus-sized polystyrene nanoparticles. By comparing the electromagnetic theory for this reactive effect with experiments, the size and mass (≈5.2 × 10
−16
g) of a bound virion are determined directly from the optimal resonance shift.
Engineered biosynthesis of bacterial aromatic polyketides in
Escherichia coli
Authors: Zhang Wenjun , Li Yanran , Tang Yi
Published: December 2008

Bacterial aromatic polyketides are important therapeutic compounds including front line antibiotics and anticancer drugs. It is one of the last remaining major classes of natural products of which the biosynthesis has not been reconstituted in the genetically superior host
Escherichia coli
. Here, we demonstrate the engineered biosynthesis of bacterial aromatic polyketides in
E. coli
by using a dissected and reassembled fungal polyketide synthase (PKS). The minimal PKS of the megasynthase PKS4 from
Gibberella fujikuroi
was extracted by using two approaches. The first approach yielded a stand-alone Ketosynthase (KS)_malonyl-CoA:ACP transferase (MAT) didomain and an acyl-carrier protein (ACP) domain, whereas the second approach yielded a compact PKS (PKS_WJ) that consists of KS, MAT, and ACP on a single polypeptide. Both minimal PKSs produced nonfungal polyketides cyclized via different regioselectivity, whereas the fungal-specific C2-C7 cyclization mode was not observed. The kinetic properties of the two minimal PKSs were characterized to confirm both PKSs can synthesize polyketides with similar efficiency as the parent PKS4 megasynthase. Both minimal PKSs interacted effectively with exogenous polyketide cyclases as demonstrated by the synthesis of predominantly PK8 3 or NonaSEK4 6 in the presence of a C9-C14 or a C7-C12 cyclase, respectively. When PKS_WJ and downstream tailoring enzymes were expressed in
E. coli
, the expected nonaketide anthraquinone SEK26 was recovered in good titer. High-cell density fermentation was performed to demonstrate the scale-up potential of the in vivo platform for the biosynthesis of bacterial polyketides. Using engineered fungal PKSs can therefore be a general approach toward the heterologous biosynthesis of bacterial aromatic polyketides in
E. coli
.
Cross-modal individual recognition in domestic horses (
Equus caballus
)
Authors: Proops Leanne , McComb Karen , Reby David
Published: December 2008

Individual recognition is considered a complex process and, although it is believed to be widespread across animal taxa, the cognitive mechanisms underlying this ability are poorly understood. An essential feature of individual recognition in humans is that it is cross-modal, allowing the matching of current sensory cues to identity with stored information about that specific individual from other modalities. Here, we use a cross-modal expectancy violation paradigm to provide a clear and systematic demonstration of cross-modal individual recognition in a nonhuman animal: the domestic horse. Subjects watched a herd member being led past them before the individual went of view, and a call from that or a different associate was played from a loudspeaker positioned close to the point of disappearance. When horses were shown one associate and then the call of a different associate was played, they responded more quickly and looked significantly longer in the direction of the call than when the call matched the herd member just seen, an indication that the incongruent combination violated their expectations. Thus, horses appear to possess a cross-modal representation of known individuals containing unique auditory and visual/olfactory information. Our paradigm could provide a powerful way to study individual recognition across a wide range of species.
NPY
genes and AGC kinases define two key steps in auxin-mediated organogenesis in
Arabidopsis
Authors: Cheng Youfa , Qin Genji , Dai Xinhua , Zhao Yunde
Published: December 2008

Auxin is an essential regulator of plant organogenesis. Most key genes in auxin biosynthesis, transport, and signaling belong to gene families, making it difficult to conduct genetic analysis of auxin action in plant development. Herein we report the functional analysis of several members of 2 gene families (
NPY
/
ENP
/
MAB4
genes and AGC kinases) in auxin-mediated organogenesis and their relationships with the
YUC
family of flavin monooxygenases that are essential for auxin biosynthesis. We show that 5
NPY
genes (
NPY1
to
NPY5
) and 4 AGC kinases (
PID
,
PID2
,
WAG1
, and
WAG2
) have distinct, yet overlapping, expression patterns. Disruption of
NPY1
does not cause obvious defects in organogenesis, but
npy1 npy3 npy5
triple mutants failed to make flower primordia, a phenotype that is also observed when AGC kinase
PID
is compromised. Inactivation of
YUC1
and
YUC4
in
npy1
background also phenocopies
npy1 npy3 npy5
and
pid
. Simultaneous disruption of
PID
and its 3 closest homologs (
PID2
,
WAG1
, and
WAG2
) completely abolishes the formation of cotyledons, which phenocopies
npy1 pid
double mutants and
yuc1 yuc4 pid
triple mutants. Our results demonstrate that
NPY
genes and
AGC
kinases define 2 key steps in a pathway that controls YUC-mediated organogenesis in
Arabidopsis
.
Role of root UV-B sensing in
Arabidopsis
early seedling development
Authors: Tong Hongyun , Leasure Colin D. , Hou Xuewen , Yuen Gigi , Briggs Winslow , He Zheng-Hui
Published: December 2008

All sun-exposed organisms are affected by UV-B [(UVB) 280–320 nm], an integral part of sunlight. UVB can cause stresses or act as a developmental signal depending on its fluence levels. In plants, the mechanism by which high-fluence-rate UVB causes damages and activates DNA-repair systems has been extensively studied. However, little is known about how nondamaging low-fluence-rate UVB is perceived to regulate plant morphogenesis and development. Here, we report the identification of an
Arabidopsis
mutant,
root UVB sensitive 1
(
rus1
), whose primary root is hypersensitive to very low-fluence-rate (VLF) UVB. Under standard growth-chamber fluorescent white light,
rus1
displays stunted root growth and fails to form postembryonic leaves. Experiments with different monochromatic light sources showed that
rus1
phenotypes can be rescued if the seedlings are allowed to grow in light conditions with minimum UVB. We determined that roots, not other organs, perceive the UVB signal. Genetic and molecular analyses confirmed that the root light-sensitive phenotypes are independent of all other known plant photoreceptors. Three
rus1
alleles have been identified and characterized. A map-based approach was used to identify the
RUS1
locus.
RUS1
encodes a protein that contains DUF647 (domain of unknown function 647), a domain highly conserved in eukaryotes. Our results demonstrate a root VLF UVB-sensing mechanism that is involved in
Arabidopsis
early seedling morphogenesis and development.
Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics
Authors: Cho Samuel S. , Levy Yaakov , Wolynes Peter G.
Published: December 2008

Energy landscape theory requires that the protein-folding mechanism is generally globally directed or funneled toward the native state. The collective nature of transition state ensembles further suggests that sufficient averaging of the native interactions can occur so that the knowledge of the native topology may suffice for predicting the mechanism. Nevertheless, while simple homogeneously weighted native topology-based models predict the folding mechanisms for many proteins, for other proteins knowledge of the native topology, by itself, seems not to suffice in determining the folding mechanism. Simulations of proteins with differing topologies reveal that the failure of homogeneously weighted topology-based models can, however, be completely understood within the framework of a funneled energy landscape and can be quantified by comparing the fluctuation of entropy cost for forming contacts to the expected fluctuations in contact energy. To be precise, we find the transition state ensembles of proteins with all-α topologies, which are more uniform in the specific entropy cost of contact formation, have transition state ensembles that are more readily perturbed by differences in energetic weights than are the transition state ensembles of proteins with significant amounts of β-structure, where the specific entropy costs of contact formation are more widely distributed. This behavior is consistent with a random-field Ising model analogy that follows from the free energy functional approach to folding.
Reduction of CCR5 with low-dose rapamycin enhances the antiviral activity of vicriviroc against both sensitive and drug-resistant HIV-1
Authors: Heredia Alonso , Latinovic Olga , Gallo Robert C. , Melikyan Gregory , Reitz Marv , Le Nhut , Redfield Robert R.
Published: December 2008

Vicriviroc (VCV) is a chemokine (C-C motif) receptor 5 (CCR5) antagonist with potent anti-HIV activity that currently is being evaluated in phase III clinical trials. In the present study, donor CCR5 density (CCR5 receptors/CD4 lymphocytes) inversely correlated with VCV antiviral activity (Spearman's correlation test;r= 0.746,P= 0.0034). Low doses of the transplant drug rapamycin (RAPA) reduced CCR5 density and enhanced VCV antiviral activity. In drug interaction studies, the RAPA/VCV combination had considerable antiviral synergy (combination indexes of 0.1–0.04) in both multicycle and single-cycle infection of lymphocytes. The synergy between RAPA and VCV translated into dose reduction indexes of 8- to 41-fold reductions for RAPA and 19- to 658-fold reductions for VCV. RAPA enhanced VCV antiviral activity against both B and non-B clade isolates, potently suppressing clade G viruses with reported reduced sensitivities to VCV and to the licensed CCR5 antagonist maraviroc. Importantly, RAPA reduction of CCR5 density in lymphocytes sensitized VCV-resistant strains to VCV, inhibiting virus production by ∼ 90%. We further demonstrated the role of CCR5 density on VCV activity against resistant virus in donor lymphocytes and in cell lines expressing varying CCR5 densities. Together, these results suggest that low doses of RAPA may increase the durability of VCV-containing regimens in patients by enhancing VCV viral suppression, by allowing the use of lower doses of VCV with reduced potential for toxicity, and by controlling emerging VCV-resistant variants.