bluuebunny/crossref_metadata_2025 huggingface dataset:
Room-temperature remote-plasma sputtering of c-axis oriented zinc oxide thin films
Authors: García-Gancedo L. , Pedrós J. , Zhu Z. , Flewitt A. J. , Milne W. I. , Luo J. K. , Ford C. J. B.
Published: July 2012

Highly c-axis oriented ZnO films have been deposited at room temperature with high rates (∼50 nm·min−1) using an innovative remote plasma sputtering configuration, which allows independent control of the plasma density and the sputtering ion energy. The ZnO films deposited possess excellent crystallographic orientation, high resistivity (>109 Ω·m), and exhibit very low surface roughness. The ability to increase the sputtering ion energy without causing unwanted Ar+ bombardment onto the substrate has been shown to be crucial for the growth of films with excellent c-axis orientation without the need of substrate heating. In addition, the elimination of the Ar+ bombardment has facilitated the growth of films with very low defect density and hence very low intrinsic stress (<100 MPa for 3 μm-thick films). This is over an order of magnitude lower than films grown with a standard magnetron sputtering system.
Radiative and non-radiative effects of a substrate on localized plasmon resonance of particles
Authors: Venkatapathi Murugesan , Kumar Tiwari Abhay
Published: July 2012

Experiments have shown strong effects of some substrates on the localized plasmons of metallic nano particles but they are inconclusive on the affecting parameters. Here, we have used discrete dipole approximation in conjunction with Sommerfeld integral relations to explain the effect of the substrates as a function of the parameters of incident radiation. The radiative coupling can both quench and enhance the resonance and its dependence on the angle and polarization of incident radiation with respect to the surface is shown. Non-radiative interaction with the substrate enhances the plasmon resonance of the particles and can shift the resonances from their free-space energies significantly. The non-radiative interaction of the substrate is sensitive to the shape of particles and polarization of incident radiation with respect to substrate. Our results show that the plasmon resonances in coupled and single particles can be significantly altered from their free-space resonances and are quenched or enhanced by the choice of substrate and polarization of incident radiation.
Barrier discharges driven by sub-microsecond pulses at atmospheric pressure: Breakdown manipulation by pulse width
Authors: Hoder Tomáš , Höft Hans , Kettlitz Manfred , Weltmann Klaus-Dieter , Brandenburg Ronny
Published: July 2012

Barrier discharges at atmospheric pressure in nitrogen-oxygen mixture powered by high voltage pulses of widths between 10 μs and 200 ns were investigated. The development of the microdischarges on rising and falling slopes was recorded by streak and intensified CCD cameras simultaneously. The breakdown on the falling slope strongly depends on the pulse width. As a result of pulse width variation the starting point of ignition changes and positive and negative streamers occur simultaneously in the falling slope. The observed effect is caused by the electric field rearrangement in the gap due to the different positive ion densities related to their gap crossing times.
A finite-difference time-domain simulation of high power microwave generated plasma at atmospheric pressures
Authors: Ford Patrick J. , Beeson Sterling R. , Krompholz Hermann G. , Neuber Andreas A.
Published: July 2012

A finite-difference algorithm was developed to calculate several RF breakdown parameters, for example, the formative delay time that is observed between the initial application of a RF field to a dielectric surface and the formation of field-induced plasma interrupting the RF power flow. The analysis is focused on the surface being exposed to a background gas pressure above 50 Torr. The finite-difference algorithm provides numerical solutions to partial differential equations with high resolution in the time domain, making it suitable for simulating the time evolving interaction of microwaves with plasma; in lieu of direct particle tracking, a macroscopic electron density is used to model growth and transport. This approach is presented as an alternative to particle-in-cell methods due to its low complexity and runtime leading to more efficient analysis for a simulation of a microsecond scale pulse. The effect and development of the plasma is modeled in the simulation using scaling laws for ionization rates, momentum transfer collision rates, and diffusion coefficients, as a function of electric field, gas type and pressure. The incorporation of plasma material into the simulation involves using the Z-transform to derive a time-domain algorithm from the complex frequency-dependent permittivity of plasma. Therefore, the effect of the developing plasma on the instantaneous microwave field is calculated. Simulation results are compared with power measurements using an apparatus designed to facilitate surface flashover across a polycarbonate boundary in a controlled N2, air, or argon environment at pressures exceeding 50 Torr.
Ordered nano-scale dimple pattern formation on a titanium alloy (Ti-6Al-4V)
Authors: Wang Yue , Singh Sherdeep , Kruse Peter
Published: July 2012

Due to the many applications of nanostructured surfaces – including in biomaterials – there is a strong interest in cost- and time-efficient methods for their fabrication. Previously, our group established a simple electrochemical method generating nanoscale patterns on large areas of a number of different metal surfaces. They consist of dimples that are around 6-10 nm deep and hexagonally closed packed with a tunable periodicity of around 50 nm. Ordering requires careful tuning of the surface chemistry, which makes the translation of these findings to multi-component alloys non-obvious. Here, we demonstrate for the first time that such a pattern can also be achieved on the surface of an alloy, namely Ti-6Al-4V. This alloy is of particular interest for biomedical implants. While dimple formation on the main component metals titanium and aluminum has previously been reported (albeit under conditions that differ from each other), we now also report dimple formation on pure vanadium surfaces to occur under very different conditions. Dimple formation occurs preferentially on the (dominant) α-phase grains of the alloy. The size of dimples of the alloy material is subject to the electropolishing potential, electrolyte concentration and surface chemical composition, which gives us the opportunity to control the surface features. Since a main application of this alloy are biomedical implants, this level of control will be an important tool for accommodating cell growth.
A review of introduced cervids in Chile
Authors: Flueck Werner T. , Smith-Flueck Jo Anne M.
Published: July 2012

We review the extent of exotic deer distributions in Chile, which are encountered in all provinces, including Tierra del Fuego, except for possibly Region III; many deer are contained in at least 107 enclosures. Red deer (Cervus elaphus) by far has the largest feral population of exotic cervids in southern South America, providing source animals that can easily cross the Andes between Chile and Argentina. Red deer was introduced from Europe to the central valley of Chile in 1928. Since the 1940s, feral populations have also expanded from Argentina into Chile, by way of easily accessible, low-elevation mountain passes of the Andes, accompanied by further direct shipments from Argentina. The area occupied by 1990 was estimated at 3400 km2, whereas an analysis in 2003 estimated an area of 7700 km2. The overall area invaded by 2003 was between 37°42′S and 54°55′S, and 73°36′W and 69°50′W (Argentina and Chile combined, although non-contiguous). Ecological impact of the red deer in Chile has been described since 1981, and red deer features in the Chilean Pest Manual. A conservative rate for the red deer expansion was estimated at 1 km/year, but likely is more rapid where habitat modifications facilitate movement. The pre-Columbian northern limit of the native cervid huemul (Hippocamelus bisulcus) was 30°S, and because red deer has occupied all habitat types currently used by huemul, it could thus spread >750 km further north. To the south, all areas are suitable for red deer. Invasion patterns will depend on additional intentional introductions and enclosures on both sides of the Andes because of the omnipresent risk of escapes. Fallow, axis and roe deer (Dama dama, Axis axis, Capreolus capreolus, respectively) also have been introduced to Chile and occur in many enclosures. Fallow deer recently escaped on Chiloé Island, became established and raised concerns because of its potential impacts on several endemic species on the island. The striking lack of information on feral deer may relate to policies and laws about firearms and restricted access to hunting areas, resulting in the apparent absence of popular hunting, which, nevertheless, could be a potential tool should the invasion continue and lead to future deer overabundance.
Huemul heresies: beliefs in search of supporting data. 1. Historical and zooarcheological considerations
Authors: Flueck Werner T. , Smith-Flueck Jo Anne M.
Published: July 2012

Patagonian huemul (Hippocamelus bisulcus) was eliminated from many former ranges before arrival of early explorers who already acknowledged its rareness. Considering huemul analogous to ungulates in mountains back home, huemul was called mountain deer, which is repeatedly cited without validation and remains the orthodox interpretation. Yet other species considered analogous also use lowlands, flatlands, deserts and grasslands, and the only congeneric, H. antisensis, uses habitat with high affinity to Patagonian grasslands. Recent comparative analyses of the post-cranial morphology show that huemul cannot be associated with rock-climbing species, but falls within ranges of other cervids. Interpretations of past human utilisation rely on one study of economic anatomy and bone remains, frequently concluding that huemul was unimportant to hunter-gatherers. However, considering only bone fat and omitting easily removable fat is erroneous. Total energy of deer in autumn–winter partitions into 53% as fat and hunter-gatherers elsewhere focussed on deer during the peak fat cycle, using all easily removable fat (>1200% more energy than in bones) and consuming fat and marrow while butchering. Natives are likely to have influenced huemul distribution and density in winter ranges due to high incentives (fat) and easiness to kill. Sparse evidence is likely the result of surveys in Patagonia having been biased towards caves, leaving out transient movements and camps. Generalist cervids passed the Panama land-bridge filter to reach South America. Considering paleoclimate, Hippocamelus dispersed east of the Andes, pushed by glaciations even to north-eastern Brazil. Hippocamelus would reach and cross Andes only after deglaciations. As a mixed feeder, huemul utilised Patagonian steppe. Hunter-gatherers arrived after the last glaciation and influenced the local distribution of Hippocamelus, especially in northern and central Chile, after early adoption of an agricultural lifestyle. Introduction of horses converted native economies through adoption of an equestrian lifestyle and arrival of millions of introduced livestock, which thus affected early writings. Only few records indicate the presence of large groups of huemul far from forests, and substantial killings. Human-caused range contractions of northern ungulates affected mainly losses at low elevations and most species persisted in the marginal periphery, including high-elevation refuges. Paleoecology, zoogeography and land-use history in southern South America indicate that mountain huemul is a secondary relict created by impacts of post-Columbian colonisation. We caution against the rigid application of modern huemul habitats in interpreting past habitat use and huemul ecology, and simply considering the few extra-Andean accounts as abnormal outliers.
Huemul heresies: beliefs in search of supporting data. 2. Biological and ecological considerations
Authors: Flueck Werner T. , Smith-Flueck Jo Anne M.
Published: July 2012

Scarce information from remnant huemul (Hippocamelus bisulcus) populations in marginal habitats can lead to erroneous interpretations of the species’ natural history, such as assumptions of being a highly inflexible species. We evaluated discrepancies between historical accounts and recent interpretations regarding biological and ecological traits to better understand factors preventing recovery of highly endangered huemul. Early information supports the theory that huemul are currently living under suboptimal conditions. We find variability to be the norm for huemul, as with other cervids, in regard to antler characteristics, group size and density, sexual segregation, and social and feeding behaviours. No evidence supports competition and disease from livestock or red deer as having caused declines or preventing recovery. Instead, livestock management, particularly presence of people and dogs, creates incompatibilities. Where red deer are sympatric with huemul, red deer are outnumbered by livestock by 2100%, and being regularly inspected at slaughter, livestock provide a good proxy for diseases afflicting red deer. Inadequate antipredator responses due to evolutionary absence of cursorial predators are unsupported as several Canis species coexisted with huemul, overlapping with dogs that arrived with Paleoindians. Three populations have increased despite high predator density. Age at maturity for huemul is 1 year, with evidence that fawns may also breed. Reported twinning needs confirmation, but occurs in congeneric taruca (H. antisensis) and other Odocoilines, and huemul frequently raise fawns successfully every year; life cycle calculations should apply these parameters. Like taruca, dominance group breeding systems have been described repeatedly. Although huemul bucks were recently claimed unique by displaying territoriality year-round, data do not support such behaviour. Two sole dispersal records (8 and 15.5 km) are unlikely to represent maximum dispersal capacity and do not support barriers assumed from few kilometres of unsuitable habitat. Huemul using 500 ha could predictably disperse up to 90 km, well within the ranges of other cervids. Mistakenly assuming barriers and underestimating reproductive capacity may distract from discovering the factors affecting recolonisations. Sustained recovery may depend on re-establishing source populations on more productive habitats, guided by zooarcheological and historical data.
Parasitological survey of the Uruguayan populations of wild Pampas deer (Ozotoceros bezoarticus L. 1758)
Authors: Hernández Z. , González S.
Published: July 2012

The pampas deer (Ozotoceros bezoarticus) is one of the most endangered neotropical mammals in Uruguay. Although it has a wide geographic distribution in south-eastern South America (from 5°S to 41°S), the habitat required by this species has been greatly reduced by agriculture and urbanisation. The species decline was due to human activities, and currently two isolated populations survive. The parasitological load is a good indicator of the health of the species and the ecosystem. The objective of the present study was to survey and determine the parasitological composition of the two Uruguayan pampas deer populations. We quantified the coproparasite load, by analysing the effect of seasonality through the year, the micro-ecosystem environment, the topography and also the livestock of the paddock. The taxonomic assessment was based on adult individuals obtained from the post mortem necropsy examination in individuals found dead in the field. The genera of the endoparasites recorded through the morphological eggs, larvae and/or adults were Trichuris, Capillaria, Strongyloides, Fasciola, Paramphistomum, Moniezia, Haemonchus, Ostertagia, Trichostrongylus, Oesophagostomum and Coccidias ooquiste. Our results showed that the parasitological community in the pampas deer is strongly correlated with the environmental conditions, topology, micro-ecosystem and the land use, as well as the effect of the livestock load. Moreover, because we have diagnosed the same genera of helminths in domestic ruminants, we recommend balancing the carrying capacities of the field paddocks, and performing periodical surveys of the livestock parasite load that will be helpful in maintaining control at lower values.
Comparison of vocalisations of introduced European red deer stags (Cervus elaphus) in north-western Patagonia (Argentina) with native European populations
Authors: Hurtado A. M. , Smith-Flueck J. M. , Black-Decima P.
Published: July 2012

Polygynous deer are very vocal species, producing calls in various contexts. Male rutting calls in red deer (Cervus elaphus) have been most studied in captive and/or free-ranging European populations. The recent application of ‘source-filter theory’ has identified the independent roles of fundamental frequency (F0) and formants in the production of deer calls and demonstrated the relation between formant spacing and anatomical characteristics such as body size. The present paper describes and characterises the acoustical properties of male rutting vocalisations for a free-ranging red deer population located in the ecotone of the eastern Andean cordillera within the Nahuel Huapi National Reserve (Neuquén, Argentina), and is the first acoustic study of free-ranging red deer stags outside their historic distribution. Recordings were made of seven identified and several unidentified stags at the peak of the rut in 2007. Calculated F0 was found to be higher for these identified stags than for Scottish red deer on the island of Rhum. The analysis of formant spacing was used to calculate the length of the vocal tract (VTL) for the seven males studied; values were comparable to those found in stags from Rhum. The longest calculated VTLs within these males corresponded to those of the four stags with the largest antler racks and the only stags holding harems. Previous studies have shown that VTL correlates with body size, age and reproductive success and that these deer have the ability to lower their larynx and extend their vocal tracts to a maximum, which is probably under sexual selection. Our data fit with this explanation. The higher F0s recorded in this population may result from the influence of wapiti genes, known to be present in these deer, because wapiti have a much higher-frequency rutting call, namely, the bugle. Alternatively, they may be related to the mating strategy, which differs substantially from the northern European populations.
Periodontal disease and fluoride bone levels in two separate Iberian red deer populations
Authors: Azorit C. , Rodrigo M. J. , Tellado S. , Sánchez-Ariza M. C.
Published: July 2012

The mandibles of 209 red deer (Cervus elaphus hispanicus) from 6 months to 15 years old, shot between 2001 and 2002 in the Sierra de Andújar Natural Park (n = 173) and National Park of Doñana (n = 36) in southern Spain, were studied in order to assess spatial variations in the occurrence of periodontal disease and bone fluoride levels in two separate populations. Similarities were found in periodontal disease prevalence between the study areas (20.8% in Sierra de Andújar Natural Park and 33.3% in National Park of Doñana), and enamel defects or abnormal abrasion (7–10%, respectively). There were also variations in fluoride levels according to the area and the occurrence of periodontal disease, irrespective of age. Fluoride content was significantly lower in deer in Sierra de Andújar (250.5 ± 158.9 mg F/kg ash) than in Doñana (752.4 ± 451.0 mg F/kg ash), and the higher levels of bone fluoride occurred in mandibles showing periodontal disease in both areas (358.6 ± 201.7 and 1224.9 ± 422.34 mg F/kg, respectively). The fluoride levels were lower than expected, typical of non-polluted areas, and there was no significant influence of the occurrence of enamel defects on the bone fluoride concentration. In these areas pathologically increased attrition, enamel discolouration or enamel surface lesions seem not to be caused by fluorosis, so that special care must also be taken in using macroscopic lesions instead of fluoride determination as an indicator for monitoring the magnitude of environmental contamination. Research into the global mineral content and possible deficiencies in certain minerals such as selenium, phosphorus and calcium interacting with fluoride is necessary in order to understand the high prevalence of periodontal disease in younger animals and the higher concentrations of fluoride in mandibles with periodontal disease.
Faecal 11-ketoetiocholanolone measurement in Iberian red deer (Cervus elaphus hispanicus): validation of methodology using HPLC–MS/MS
Authors: Azorit C. , Castro J. M. , Carrasco R. , Tellado S. , Orpez R. , Moro J.
Published: July 2012

A cortisol metabolite, 11-ketoetiocholanolone (11-k), is widely used in monitoring stress in several vertebrates, and can be detected by immunoassay. However, these assays have certain limitations with respect to specificity. Also, differences in the excretion of faecal glucocorticoid metabolites (FGM) among species and even between sexes make validation necessary in each case. Therefore, our aims were, first, to develop and validate a high-pressure liquid chromatography–tandem mass spectrometry (HPLC–MS/MS) methodology for monitoring 11-k in faeces of Iberian red deer (Cervus elaphus hispanicus), and second, to investigate the capability of our method to determine variations of this FGM in a longitudinal study. Third, and finally, we assessed the correspondence between faecal 11-k concentrations and plasma cortisol. An adrenocorticotropic hormone (ACTH) test was performed on six red deer stags translocated and kept in captivity for a week and faecal samples were collected twice a day. One single blood and faecal sample from another seven stags was also collected after 2 weeks in captivity. The results of the longitudinal study showed a first peak in 11-k 36 h after the ACTH test and handling, and a second peak at 120 h of being kept indoors. Maximum concentrations of 11-k ranged from 22.71 to 375.68 ng/g. In the second stag group, 11-k concentrations of 25.09 ± 20.53 ng/g had a correlation of r2 = 0.88 with the concentration of plasma cortisol, which was 54.6 ± 55.1 ng/mL. This technique is capable of detecting changes in the concentrations of faecal 11-k. The values determined have a good correlation with the cortisol concentration in blood, and we also detected differences in different individuals’ responses to the same stressors.
Electroluminescence of Hybrid Self-Organised Fibres Incorporating CdTe Quantum Dots
Authors: Ando Masanori , Hosokawa Chie , Yang Ping , Murase Norio
Published: July 2012

We demonstrated electroluminescence from hybrid 1D glass fibres incorporating CdTe quantum dots with a thin SiO2 overlayer which contains CdS-like clusters. The self-organised fibres, prepared by refluxing precursor nanowires, exhibited red electroluminescence on Au interdigitated array electrodes at room temperature. Although fluctuation with time was observed in the electroluminescence, relatively low threshold electric field (2.6 × 106 V m–1) suggests that the CdTe quantum dots-based hybrid fibres are expected to be applied to low voltage driven electroluminescent devices.
Voltammetric Detection of Hg2+ Using Peptide-Functionalized Polymer Brushes
Authors: Schüwer Nicolas , Tercier-Waeber Mary-Lou , Danial Maarten , Klok Harm-Anton
Published: July 2012

Polymer brushes grafted by surface-initiated atom transfer radical polymerization (SI-ATRP) from the surface of Ir-based microelectrode arrays are explored as a platform for the fabrication of sensory coatings for the voltammetric detection of Hg2+. The polymer brush coatings are post-modified with a metallothionein derived peptide to enable the selective detection of Hg2+. The performance of the polymer brush modified microelectrode arrays was evaluated using both cyclic voltammetry (CV) as well as square-wave anodic stripping voltammetry (SWASV) experiments. These studies revealed that the polymer brush based coatings allowed the selective detection of Hg2+ with detection limits in the subnanomolar range.
Surface runoff and erosion after prescribed burning and the effect of different fire regimes in forests and shrublands: a review
Authors: Cawson J. G. , Sheridan G. J. , Smith H. G. , Lane P. N. J.
Published: July 2012

This paper examines the state of knowledge about the effects of prescribed burning on surface runoff and erosion at point to catchment scales in forests and shrublands. Fires can increase surface runoff and erosion by removing vegetation, changing soil hydrologic properties and providing a readily erodible layer of sediment and ash. Catchment-scale studies in prescribed-burnt areas usually report minimal impacts from the burn. However, measurements at smaller spatial scales suggest that large changes to hydrologic properties and processes do occur, and a debris-flow example from Australia demonstrates that large catchment-scale impacts are possible. It appears that existing catchment-scale studies in prescribed burns do not capture these large events as the sample size (i.e. number of studies) is too small relative to the infrequency of such events. Furthermore, numerous knowledge gaps across all spatial scales limit understanding of the processes contributing to post-prescribed burn runoff and erosion. Understanding the influence of fire regime characteristics on post-fire runoff and erosion is particularly important in the context of prescribed burning, as fire regimes can be manipulated to reduce erosion and water-quality impacts. Therefore, two directions for future research are recommended: (1) process-based studies to understand the factors controlling surface runoff and erosion, particularly in relation to aspects of the fire regime; and (2) landscape-scale surveys to quantify large erosion events.
Interferon regulatory factor 8 integrates T-cell receptor and cytokine-signaling pathways and drives effector differentiation of CD8 T cells
Authors: Miyagawa Fumi , Zhang Hong , Terunuma Atshushi , Ozato Keiko , Tagaya Yutaka , Katz Stephen I.
Published: July 2012

We recently demonstrated that differentiation of cytotoxic T cells requires cooperation between T-cell receptor (TCR)/costimulation and γc-cytokines. Here we demonstrate that the transcription factor IFN regulatory factor 8 (IRF8) is expressed in CD8 T cells by the combination of these two signals. More importantly, depletion of IRF8 in these cells abrogated the differentiation of naive CD8 T cells into effector cells in an experimental graft-vs.-host disease mouse model. We also show that IRF8 seems to not operate upstream of other critical factors such as T-bet and eomesodermin, which have been implicated in effector maturation. Collectively, our work shows that IRF8 integrates the TCR/costimulation and γc-cytokine–signaling pathways and mediates the transition of naive CD8 T cells to effector cells, thus identifying IRF8 as one of the molecular regulators of CD8 T-cell differentiation.
Synapse type-independent degradation of the endocannabinoid 2-arachidonoylglycerol after retrograde synaptic suppression
Authors: Tanimura Asami , Uchigashima Motokazu , Yamazaki Maya , Uesaka Naofumi , Mikuni Takayasu , Abe Manabu , Hashimoto Kouichi , Watanabe Masahiko , Sakimura Kenji , Kano Masanobu
Published: July 2012

The endocannabinoid 2-arachidonoylglycerol (2-AG) mediates retrograde synaptic suppression. Although the mechanisms of 2-AG production are well characterized, how 2-AG is degraded is less clearly understood. Here we found that expression of the 2-AG hydrolyzing enzyme monoacylglycerol lipase (MGL) was highly heterogeneous in the cerebellum, being rich within parallel fiber (PF) terminals, weak in Bergman glia (BG), and absent in other synaptic terminals. Despite this highly selective MGL expression pattern, 2-AG–mediated retrograde suppression was significantly prolonged at not only PF-Purkinje cell (PC) synapses but also climbing fiber-PC synapses in granule cell-specific MGL knockout (MGL-KO) mice whose cerebellar MGL expression was confined to the BG. Virus-mediated expression of MGL into the BG of global MGL-KO mice significantly shortened 2-AG–mediated retrograde suppression at PF-PC synapses. Furthermore, contribution of MGL to termination of 2-AG signaling depended on the distance from MGL-rich PFs to inhibitory synaptic terminals. Thus, 2-AG is degraded in a synapse-type independent manner by MGL present in PFs and the BG. The results of the present study strongly suggest that MGL regulates 2-AG signaling rather broadly within a certain range of neural tissue, although MGL expression is heterogeneous and limited to a subset of nerve terminals and astrocytes.
The Sin3a repressor complex is a master regulator of STAT transcriptional activity
Authors: Icardi Laura , Mori Raffaele , Gesellchen Viola , Eyckerman Sven , De Cauwer Lode , Verhelst Judith , Vercauteren Koen , Saelens Xavier , Meuleman Philip , Leroux-Roels Geert , De Bosscher Karolien , Boutros Michael , Tavernier Jan
Published: July 2012

Tyrosine phosphorylation is a hallmark for activation of STAT proteins, but their transcriptional activity also depends on other secondary modifications. Type I IFNs can activate both the ISGF3 (STAT1:STAT2:IRF9) complex and STAT3, but with cell-specific, selective triggering of only the ISGF3 transcriptional program. Following a genome-wide RNAi screen, we identified the SIN3 transcription regulator homolog A (Sin3a) as an important mediator of this STAT3-targeted transcriptional repression. Sin3a directly interacts with STAT3 and promotes its deacetylation.
SIN3A
silencing results in a prolonged nuclear retention of activated STAT3 and enhances its recruitment to the
SOCS3
promoter, concomitant with histone hyperacetylation and enhanced STAT3-dependent transcription. Conversely, Sin3a is required for ISGF3-dependent gene transcription and for an efficient IFN-mediated antiviral protection against influenza A and hepatitis C viruses. The Sin3a complex therefore acts as a context-dependent ISGF3/STAT3 transcriptional switch.
Effects of a single nucleotide polymorphism in the chicken NK-lysin gene on antimicrobial activity and cytotoxicity of cancer cells
Authors: Lee Mi Ok , Kim Eun-Hee , Jang Hyun-Jun , Park Mi Na , Woo Hee-Jong , Han Jae Yong , Womack James E.
Published: July 2012

NK-lysin is an effector protein of the innate immune system and an important component of host protection. We isolated a SNP in the NK-lysin coding sequence among different chicken breeds. This A to G substitution at the position 271 nucleotide in the ORF results in an Asn (N) to Asp (D) amino acid alteration. We synthesized two 30-aa peptides (N29N and N29D) to compare the biological activity of the helix 2-loop-helix 3 region of NK-lysin resulting from the polymorphic gene. Both peptides were found to be cytotoxic in bacteria and tumor cell cultures at micromolar concentrations. The N29N peptide, however, exhibited greater antibacterial and anticancer activity than the N29D peptide. Circular dichroism spectroscopy of the two peptides in negatively charged single unilamellar vesicles showed spectra typical of α-helical peptides. The helical profile of N29D was reduced substantially compared with that of N29N. However, no structural change was observed in neutral vesicles. ζ-Potential measurements of liposomes incubated with increasing peptide concentrations allowed surface charge neutralization with a negatively charged lipid, but not with a zwitterionic lipid. This result suggests that a difference in electrostatic interaction between lipid membranes and the helical peptides results from the polymorphic gene and is subsequently an important factor in cell lytic activity of variant NK-lysin peptides.
Non-resonant magnetic braking on JET and TEXTOR
Authors: Sun Y. , Liang Y. , Shaing K.C. , Liu Y.Q. , Koslowski H.R. , Jachmich S. , Alper B. , Alfier A. , Asunta O. , Buratti P. , Corrigan G. , Delabie E. , Giroud C. , Gryaznevich M.P. , Harting D. , Hender T. , Nardon E. , Naulin V. , Parail V. , Tala T. , Wiegmann C. , Wiesen S. , Zhang T.
Published: July 2012

The non-resonant magnetic braking effect induced by a non-axisymmetric magnetic perturbation is investigated on JET and TEXTOR. The collisionality dependence of the torque induced by the n = 1, where n is the toroidal mode number, magnetic perturbation generated by the error field correction coils on JET is observed. The observed torque is located mainly in the plasma core (normalized radius ρ < 0.4) and increases with decreasing collisionality. The neoclassical toroidal plasma viscosity (NTV) torque in the collisionless regime is modelled using the numerical solution of the bounce-averaged drift kinetic equation. The calculated collisionality dependence of the NTV torque is in good agreement with the experimental observation on JET. The reason for this collisionality dependence is that the torque in the plasma core on JET mainly comes from the flux of the trapped electrons, which are still mainly in the 1/ν regime. The strongest NTV torque on JET is also located near the plasma core. The magnitude of the NTV torque strongly depends on the plasma response, which is also discussed in this paper. There is no obvious braking effect with n = 2 magnetic perturbation generated by the dynamic ergodic divertor on TEXTOR, which is consistent with the NTV modelling.
Open field equilibrium current and cross-field passing electrons as an initiator of a closed flux surface in EC-heated toroidal plasmas
Authors: Maekawa T. , Yoshinaga T. , Uchida M. , Watanabe F. , Tanaka H.
Published: July 2012

A model for the non-inductive initiation of a closed flux surface observed in electron cyclotron (EC) heated toroidal plasmas is presented. First, a pressure-driven equilibrium toroidal current develops under a weak external vertical field so as to counter balance the pressure-ballooning and current-hoop forces. When the self-field from the current almost cancels out the external vertical field, a forward energetic part of electrons in the velocity space begins to make cross-field passing (CFP) orbits. The CFP electrons are generated by the EC heating of bulk electrons and subsequent pitch-angle scattering, which is analyzed using the Fokker–Planck equation. They provide an additional current that closes the field lines. The model is examined for experiments in the small low aspect ratio device of LATE and in the large conventional device of JT-60U with a search for appropriate modes of EC heating. Simultaneous coincidence of the model with these two experiments is obtained in terms of microwave power and driven current. The results predict that initiation of a closed flux surface requires more and more EC power as the plasma major radius increases. In particular, careful injection of high N
‖ EC waves is needed for large devices, both for initiation of a closed flux surface and for subsequent enlargement of the flux surface by the usual EC current drive onto the closed flux area.
Finite beta effects on MHD equilibria and energetic ion losses in a rippled tokamak
Authors: Bunno M. , Nakamura Y. , Suzuki Y. , Shinohara K. , Matsunaga G.
Published: July 2012

The efficiency of energetic ion confinement is reduced by ripple fields, which are mainly generated by the finite number of toroidal field coils in a tokamak reactor. Finite beta effects alter magnetic field structures and energetic ion orbits. Finite beta effects on magnetohydrodynamic (MHD) equilibria have been thoroughly researched. However, it is not known how finite beta effects affect energetic ion losses. To investigate this, the MHD equilibrium was calculated using the VMEC code. Finite beta effects on the ripple ratio were accurately investigated and it was found that the non-axisymmetric poloidal field generated by the plasma current could not be ignored. The guiding centre orbit equation was solved to clarify physical considerations of finite beta effects on the energetic ion losses. The energetic ion orbits were found to be strongly affected by the diamagnetic effect. By performing calculations for energetic ions with the same initial position, it was found that the diamagnetic effect produced two opposing effects: it reduced particle loss due to the closed |B| contour and it increased particle loss due to the high curvature of the |B| contour.
Cohomology of standard modules on partial flag varieties
Authors: Kitchen S.
Published: July 2012

Cohomological induction gives an algebraic method for constructing representations of a real reductive Lie group

G
G

from irreducible representations of reductive subgroups. Beilinson-Bernstein localization alternatively gives a geometric method for constructing Harish-Chandra modules for

G
G

from certain representations of a Cartan subgroup. The duality theorem of Hecht, Miličić, Schmid and Wolf establishes a relationship between modules cohomologically induced from minimal parabolics and the cohomology of the

D

\mathscr {D}

-modules on the complex flag variety for

G
G

determined by the Beilinson-Bernstein construction. The main results of this paper give a generalization of the duality theorem to partial flag varieties, which recovers cohomologically induced modules arising from nonminimal parabolics.
Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks
Authors: Acuña Vicente , Milreu Paulo Vieira , Cottret Ludovic , Marchetti-Spaccamela Alberto , Stougie Leen , Sagot Marie-France
Published: July 2012

Motivation: In the context of studying whole metabolic networks and their interaction with the environment, the following question arises: given a set of target metabolites T and a set of possible external source metabolites , which are the minimal subsets of that are able to produce all the metabolites in T. Such subsets are called the minimal precursor sets of T. The problem is then whether we can enumerate all of them efficiently.

Results: We propose a new characterization of precursor sets as the inputs of reaction sets called factories and an efficient algorithm to decide if a set of sources is precursor set of T. We show proofs of hardness for the problems of finding a precursor set of minimum size and of enumerating all minimal precursor sets T. We propose two new algorithms which, despite the hardness of the enumeration problem, allow to enumerate all minimal precursor sets in networks with up to 1000 reactions.

Availability: Source code and datasets used in our benchmarks are freely available for download at http://sites.google.com/site/pitufosoftware/download.

Contact:  vicente77@gmail.com, pvmilreu@gmail.com or marie-france.sagot@inria.fr
Computational prediction of N-linked glycosylation incorporating structural properties and patterns
Authors: Chuang Gwo-Yu , Boyington Jeffrey C. , Joyce M. Gordon , Zhu Jiang , Nabel Gary J. , Kwong Peter D. , Georgiev Ivelin
Published: July 2012

Motivation: N-linked glycosylation occurs predominantly at the N-X-T/S motif, where X is any amino acid except proline. Not all N-X-T/S sequons are glycosylated, and a number of web servers for predicting N-linked glycan occupancy using sequence and/or residue pattern information have been developed. None of the currently available servers, however, utilizes protein structural information for the prediction of N-glycan occupancy.

Results: Here, we describe a novel classifier algorithm, NGlycPred, for the prediction of glycan occupancy at the N-X-T/S sequons. The algorithm utilizes both structural as well as residue pattern information and was trained on a set of glycosylated protein structures using the Random Forest algorithm. The best predictor achieved a balanced accuracy of 0.687 under 10-fold cross-validation on a curated dataset of 479 N-X-T/S sequons and outperformed sequence-based predictors when evaluated on the same dataset. The incorporation of structural information, including local contact order, surface accessibility/composition and secondary structure thus improves the prediction accuracy of glycan occupancy at the N-X-T/S consensus sequon.

Availability and Implementation: NGlycPred is freely available to non-commercial users as a web-based server at http://exon.niaid.nih.gov/nglycpred/.

Contact:  ivelin.georgiev@nih.gov

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Relationship Between Fungicide Sensitivity and Control of Gummy Stem Blight of Watermelon Under Field Conditions
Authors: Thomas A. , Langston D. B. , Sanders H. F. , Stevenson K. L.
Published: July 2012

Gummy stem blight (GSB), caused by the fungus Didymella bryoniae, is the most destructive disease of watermelon and is managed primarily with fungicides. D. bryoniae has developed resistance to many fungicides that were once very effective, including azoxystrobin, boscalid, and thiophanate-methyl. Field experiments were conducted in Tifton (TN) and Reidsville (RV), GA in 2009 and 2010 to establish a relationship between frequency of resistance to a fungicide based on in vitro assays and its efficacy in the management of GSB. Frequency of resistance to boscalid, thiophanate-methyl, and azoxystrobin was >0.80 in isolates collected from nontreated plots in both locations and years. All isolates collected after six applications of boscalid, thiophanate-methyl, or azoxystrobin were resistant to the respective fungicide. All isolates collected from treated and nontreated plots were sensitive to tebuconazole and difenoconazole. GSB severity was assessed on a weekly basis from 63 days after planting. GSB severity in plots treated with boscalid, thiophanate-methyl, or azoxystrobin was not significantly different from that in the nontreated plots (39%, TN-2009; 45%, TN-2010; and 16%, RV-2010). GSB severity in tebuconazole-treated plots (27%, TN-2009; 14%, TN-2010; and 4%, RV-2010) was significantly lower than all other treatments and the nontreated control. There was a consistent negative association between frequency of fungicide resistance and disease control in the field. Thus, knowledge of the frequency of fungicide resistance in the pathogen population will be helpful in selecting the most effective fungicides for the management of GSB in watermelon fields.
First Report of Anthracnose in Chinese Hickory (Carya cathayensis) Caused by Colletotrichum gloeosporioides in China
Authors: Zhang C. Q. , Xu B. C.
Published: July 2012

Chinese hickory (Carya cathayensis) has become one of the important economic forest crops in Zhejiang and Anhui Provinces in China. In May 2009, sporadic occurrence of leaf damage by anthracnose in C. cathayensis was observed in Lin'an city, Zhejiang Province. During May 2011, nearly 50% of Chinese hickory orchards in Zhejiang Province were affected by anthracnose disease. Symptoms were extensive with lesions on stems and leaves. Under wet conditions, orange masses of conidia were produced in acervuli in the center of lesions. Infected tissue samples were surface sterilized with 1.5% sodium hypochlorite for 1.5 min, plated on 2% potato dextrose agar (PDA), and incubated at 26°C in the dark for 1 week. Developing colonies were gray and contained masses of orange conidia. Conidia were hyaline, aseptate, straight with rounded or bulbous ends, and averaged 15.3 ± 1.7 μm long and 2.5 ± 0.8 μm wide. The ribosomal internal transcribed spacers ITS1 and ITS2 were amplified with primers ITS1/ITS4 from DNA extracted from mycelium and nucleotide sequences showed 100% similarity to records for C. gloeosporioides in GenBank (Accession Nos. AY266391.1 and JQ676187.1). Uninfected leaves of C. cathayensis were sprayed either with a conidia suspension of 107 conidia per ml in distilled water as inoculum, or with distilled water only to provide an uninoculated control, wrapped in plastic bags to retain moisture, and incubated for 24 h. For each isolate, 10 leaves per tree and a total of 13 trees were inoculated. After 1 week, 11 of 13 isolates caused lesions on inoculated leaves whereas no symptoms developed on the non-inoculated controls. Cultures reisolated from lesions and cultured on PDA exhibited morphological characteristics identical to those of C. gloeosporioides (1, 2, 3), confirming Koch's postulates. Inoculation tests were repeated once. Since C. gloeosporioides was found in the main production area, it poses a threat to Chinese hickory production in China. The identification of the pathogen now allows for appropriate management measures. To our knowledge, this is the first report of anthracnose in C. cathayensis.

References: (1) K. D. Hyde et al. Fung. Diversity 39:147, 2009. (2) P. M. Kirk et al. Page 159 in: The Dictionary of the Fungi. 10th edition. CABI Bioscience, UK, 2008. (3) A. J. Palmateer et al. Plant Dis. 91:631, 2007.
Transmission Efficiency of ‘Candidatus Liberibacter solanacearum’ and Potato Zebra Chip Disease Progress in Relation to Pathogen Titer, Vector Numbers, and Feeding Sites
Authors: Rashed A. , Nash T. D. , Paetzold L. , Workneh F. , Rush C. M.
Published: July 2012

With diseases caused by vector-borne plant pathogens, acquisition and inoculation are two primary stages of the transmission, which can determine vector efficiency in spreading the pathogen. The present study was initiated to quantify acquisition and inoculation successes of ‘Candidatus Liberibacter solanacearum’, the etiological agent of zebra chip disease of potato, by its psyllid vector, Bactericera cockerelli (Hemiptera: Triozidae). Acquisition success was evaluated in relation to feeding site on the host plant as well as the acquisition access period. Inoculation success was evaluated in relation to vector number (1 and 4) on the plants. Acquisition success was influenced by the feeding site on the plant. The highest acquisition success occurred when insects had access to the whole plant. The results of the inoculation study indicated that the rate of successfully inoculated plants increased with the vector number. Plants inoculated with multiple psyllids had higher bacterial titer at the point of inoculation. Although disease incubation period was significantly shorter in plants inoculated with multiple psyllids, this effect was heterogeneous across experimental blocks, and was independent of pathogen quantity detected in the leaflets 3 days postinoculation. Disease progress was not affected by bacterial quantity injected or psyllid numbers.
Human islet amyloid polypeptide at the air–aqueous interface: a Langmuir monolayer approach
Authors: Li Shanghao , Micic Miodrag , Orbulescu Jhony , Whyte Jeffrey D. , Leblanc Roger M.
Published: July 2012

Human islet amyloid polypeptide (hIAPP) is the source of the major component of the amyloid deposits found in the islets of Langerhans of around 95 per cent type 2 diabetic patients. The formation of aggregates and mature fibrils is thought to be responsible for the dysfunction and death of the insulin-producing pancreatic β-cells. Investigation on the conformation, orientation and self-assembly of the hIAPP at time zero could be beneficial for our understanding of its stability and aggregation process. To obtain these insights, the hIAPP at time zero was studied at the air–aqueous interface using the Langmuir monolayer technique. The properties of the hIAPP Langmuir monolayer at the air–aqueous interface on a NaCl subphase with pH 2.0, 5.6 and 9.0 were examined by surface pressure- and potential-area isotherms, UV–Vis absorption, fluorescence spectroscopy and Brewster angle microscopy. The conformational and orientational changes of the hIAPP Langmuir monolayer under different surface pressures were characterized by p-polarized infrared-reflection absorption spectroscopy, and the results did not show any prominent changes of conformation or orientation. The predominant secondary structure of the hIAPP at the air–aqueous interface was α-helix conformation, with a parallel orientation to the interface during compression. These results showed that the hIAPP Langmuir monolayer at the air–aqueous interface was stable, and no aggregate or domain of the hIAPP at the air–aqueous interface was observed during the time of experiments.