bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling entrainment of waterlogged large wood in stream channels
Authors: Buxton Todd H.
Published: October 2010

Research has led to an understanding of how floatable wood provides physical complexity and habitat in streams, but little is known about large wood that does not float because it is waterlogged, mineralized, or naturally heavier than water. To better understand the dynamics of this largely unrecognized component of streams, I derived a theoretical model for predicting entrainment of waterlogged logs, then constructed prototype logs to simulate waterlogged wood and used them to measure log friction and critical flow velocities at log entrainment in an alluvial creek. I then modeled critical velocities under the same conditions entrainment was observed. The model underpredicted critical velocities by an average of 24%, with a range of error from 8% to −69%. Sensitivity analyses indicated that reducing lift and drag coefficients improved the average error, but not the error range. Lack of unique drag coefficients for prototype logs, winnowing of bed material from around prototype logs during entrainment tests, error estimating friction for logs approaching neutral buoyancy, and the variability of flow velocity common in streams were probable causes of error. Observed critical velocities that entrained prototype logs averaged 0.70 m s−1. Critical velocities and log friction increased with branch length, bed roughness, and log density, but only friction increased with log length. Friction coefficients averaged 0.62 and increased with branch length and bed roughness. This model and existing equations for predicting movement of buoyant large wood can be used to compute budgets for logs with a range of attributes in streams.
Contrasting evolution of sea surface temperature in the Benguela upwelling system under natural and anthropogenic climate forcings
Authors: Leduc Guillaume , Herbert Caren T. , Blanz Thomas , Martinez Philippe , Schneider Ralph
Published: October 2010

We present alkenone‐derived Sea Surface Temperature (SST) records from three marine cores collected within the southern Benguela Upwelling System (BUS) spanning the last 3 ka. The SST evolution over the last 3 millennia is marked by aperiodic millennial‐scale oscillations that broadly correspond to climatic anomalies identified over the North Atlantic region. The BUS SST data further suggest cooling and warming trends opposite to the temperature evolution in the Moroccan upwelling region and in Antarctica. In contrast, the last decades are marked by a cooling of unprecedented magnitude in both the Benguela and Moroccan upwelling systems, which is not observed in the Antarctic record. These contrasted responses in Atlantic upwelling systems triggered by natural and anthropogenic forcings shed light on how different climatic mechanisms are mediated by ocean‐atmosphere interactions and transmitted to the geological records of past and present climate changes.
Mercury's weak magnetic field: A result of magnetospheric feedback?
Authors: Gómez‐Pérez Natalia , Solomon Sean C.
Published: October 2010

The internal magnetic field of Mercury is anomalously weak compared with the fields of other solar system dynamos. Here we investigate the effect that magnetospheric currents may have on the internal dynamo process. Although strong dipolar dynamos are not markedly affected by such magnetospheric currents, a dynamo in a weak‐dipole state can be stabilized in such a configuration by magnetospheric feedback. We suggest that Mercury's core dynamo was stabilized in a weak‐field state early in Mercury's history, when the solar wind was much stronger than today, and has been maintained in that state to the present by magnetospheric feedback. A prediction of this scenario is that secular variation should occur more rapidly for Mercury's internal field than would be expected for some other models for the planet's weak field.
Ripple migration and dune activity on Mars: Evidence for dynamic wind processes
Authors: Silvestro S. , Fenton L. K. , Vaz D. A. , Bridges N. T. , Ori G. G.
Published: October 2010

In this report we show evidence of widespread ripple migration over the stoss side of dark barchan dunes in Nili Patera on Mars. The measured average migration of ∼1.7 meters in less than 4 terrestrial months clearly indicates that active sand saltation is occurring in the study area. In addition, we document widespread changes in the dune base‐ground surface contact and in the slip face structures, showing that not only the ripples, but the whole dunes are actually migrating in the present‐day atmospheric setting. These results provide unequivocal evidence of recent aeolian activity and suggest that other dunes and ripples on Mars may also be active.
Longitudinal modulation of the O/N2 column density retrieved from TIMED/GUVI measurement
Authors: He Maosheng , Liu Libo , Wan Weixing , Lei Jiuhou , Zhao Biqiang
Published: October 2010

The longitudinal variation of thermospheric O/N2 column density ratio is studied, based on the TIMED/GUVI measurements collected during 2002‐2007. In October, a four‐peaked longitudinal fluctuation in O/N2 is found. The wavenumber‐4 fluctuation in equatorial O/N2 is generally stronger at lower solar activity, and maximizes in the morning of boreal summer and autumn. In boreal winter, the wavenumber‐4 component gives way to the wavenumber‐3. Such seasonal variation and solar activity dependence are consistent with those of the diurnal eastward‐propagating mode with wavenumber‐3, but the local time dependence is not. The daytime wavenumber‐4 pattern in O/N2 does not shift eastward in local time as expected if it is directly connected to the DE3. No definite explanation is found for this structure, but a consideration of various mechanisms suggests that the vertical wind effect may be the most potential candidate.
Substorm onset by new plasma intrusion: THEMIS spacecraft observations
Authors: Xing X. , Lyons L. , Nishimura Y. , Angelopoulos V. , Larson D. , Carlson C. , Bonnell J. , Auster U.
Published: October 2010

Recent observations from the 2‐D array of high‐resolution THEMIS all‐sky imagers (ASIs) during the 2008 tail season have shown that the majority of substorm onsets are preceded by equatorward extension of an auroral arc initiated at the poleward boundary of the aurora zone, and that the aurora breakup is likely triggered when this precursor arc reaches the onset region. These observations were used to suggest that substorm onset is driven by a new population of plasma having lower global entropy content than that of the preexisting plasma intruding into the inner plasma sheet. We have taken advantage of conjunctions between the location of the precursor arc observed by the THEMIS ASI and THEMIS spacecraft and identified four events where clear signatures of the proposed new plasma intrusion were observed simultaneously in both the magnetotail and ionosphere. In two of the events, the intrusion plasma was captured more than 10 min before substorm onset in the midtail plasma sheet. The intruding plasma is characterized as the reduction of the pressure and entropy parameter associated with more dipolarized magnetic field, as well as the enhancement of the duskward electric field and earthward flow. In two other events, the plasma intrusion was found within 2 min before onset in the inner plasma sheet region R ∼11 RE, which is very close to the onset locations. These observations are consistent with the proposal that intrusion of low‐entropy content plasma to the onset region may provide a trigger for substorm onset. We also found two plasma intrusion events not associated with substorm onset in the plasma sheet, which indicates that the new plasma intrusion is not a sufficient condition for substorm onset. We suggest that sufficient pressure and azimuthal pressure gradient buildup in the inner plasma sheet during growth phase should be another necessary condition.
Extreme low sea ice years in the Canadian Arctic Archipelago: 1998 versus 2007
Authors: Howell Stephen E. L. , Tivy Adrienne , Agnew Tom , Markus Thorsten , Derksen Chris
Published: October 2010

Extreme sea ice minima were observed within the Canadian Arctic Archipelago (CAA) during 1998 and 2007. The September average sea ice area was 2.90 and 2.65 standardized anomalies below the historical 1968–1996 climatology for 1998 and 2007, respectively. October sea ice area for 1998 was a staggering 4.45 standardized anomalies below the historical 1968–1996 climatology and 2007 was lower by 3.36 standardized anomalies. We examine the role of thermodynamic and dynamic forcing on CAA sea ice that was responsible for its extreme loss in 1998 and 2007. Thermodynamic forcing on the sea ice was concentrated over 1 month in 2007 facilitating rapid melt, contrasted against a long melt season in 1998. This variation was attributed to anomalously warm air temperatures in June, September, and October for 1998 compared to anomalously warm temperatures in July for 2007. Sea ice dynamics contributed to the 1998 minimum by inhibiting replenishment from the Arctic Ocean but actually facilitated replenishment in 2007 thereby preventing record low conditions. Replenishment was driven by dissimilarities in sea level pressure patterns over the CAA during these extreme years. Evidence for preconditioned thinning was apparent leading up to 2007 but not strongly apparent for 1998. Remarkably, at the onset of 1998 melt season, multi‐year ice area within the CAA was 11% more than the historical climatology and 48% more than at the start of the 2007 melt season yet an extreme minima was still reached.
Overflow dynamics and bottom water formation in the western Ross Sea: Influence of tides
Authors: Wang Q. , Danilov S. , Hellmer H. H. , Schröter J.
Published: October 2010

The tidal impact on overflow dynamics and bottom water production in the western Ross Sea is studied with the Finite Element Ocean Model, which allows embedding a mesh with 0.5 km resolution in a coarse resolution (30 km) setup without nesting. The simulated overflow properties inside and downstream of the western Ross Sea are described. The overflow exhibits pronounced variability at both daily and spring‐neap tidal time scales in the western Ross Sea. Tides increase mixing over both the outer shelf and upper slope there. Plume jets are shaped by tidal currents at a bathymetric bend west of the Drygalski Trough mouth, descending rapidly and supplying the bottom water. A fraction of shelf water remains over the shelf and propagates westward from the Ross Sea, but it does not contribute significantly to bottom water formation because of energetic mixing over the upper slope. Compared to a simulation without tidal forcing, tides (with the major K1 and O1 constituents) increase the outflow rate over the continental slope off Cape Adare by about 70%. A set of sensitivity experiments show that the rate of bottom water production is not a monotonic function of the tidal currents amplitude. Tidal forcing with intermediate strength leads to the most efficient bottom water formation.
Ecosystem carbon dioxide fluxes after disturbance in forests of North America
Authors: Amiro B. D. , Barr A. G. , Barr J. G. , Black T. A. , Bracho R. , Brown M. , Chen J. , Clark K. L. , Davis K. J. , Desai A. R. , Dore S. , Engel V. , Fuentes J. D. , Goldstein A. H. , Goulden M. L. , Kolb T. E. , Lavigne M. B. , Law B. E. , Margolis H. A. , Martin T. , McCaughey J. H. , Misson L. , Montes‐Helu M. , Noormets A. , Randerson J. T. , Starr G. , Xiao J.
Published: October 2010

Disturbances are important for renewal of North American forests. Here we summarize more than 180 site years of eddy covariance measurements of carbon dioxide flux made at forest chronosequences in North America. The disturbances included stand‐replacing fire (Alaska, Arizona, Manitoba, and Saskatchewan) and harvest (British Columbia, Florida, New Brunswick, Oregon, Quebec, Saskatchewan, and Wisconsin) events, insect infestations (gypsy moth, forest tent caterpillar, and mountain pine beetle), Hurricane Wilma, and silvicultural thinning (Arizona, California, and New Brunswick). Net ecosystem production (NEP) showed a carbon loss from all ecosystems following a stand‐replacing disturbance, becoming a carbon sink by 20 years for all ecosystems and by 10 years for most. Maximum carbon losses following disturbance (g C m−2y−1) ranged from 1270 in Florida to 200 in boreal ecosystems. Similarly, for forests less than 100 years old, maximum uptake (g C m−2y−1) was 1180 in Florida mangroves and 210 in boreal ecosystems. More temperate forests had intermediate fluxes. Boreal ecosystems were relatively time invariant after 20 years, whereas western ecosystems tended to increase in carbon gain over time. This was driven mostly by gross photosynthetic production (GPP) because total ecosystem respiration (ER) and heterotrophic respiration were relatively invariant with age. GPP/ER was as low as 0.2 immediately following stand‐replacing disturbance reaching a constant value of 1.2 after 20 years. NEP following insect defoliations and silvicultural thinning showed lesser changes than stand‐replacing events, with decreases in the year of disturbance followed by rapid recovery. NEP decreased in a mangrove ecosystem following Hurricane Wilma because of a decrease in GPP and an increase in ER.
Cathepsin C limits acute viral infection independently of NK cell and CD8+ T‐cell cytolytic function
Authors: Andoniou Christopher E , Fleming Peter , Sutton Vivien R , Trapani Joseph A , Degli‐Esposti Mariapia A
Published: October 2010

Destruction of target cells by cytotoxic T lymphocytes (CTLs) or natural killer (NK) cells requires the coordinated action of the pore forming protein perforin (Pfp) and the granzyme (Gzm) family of serine proteases. The activation of a number of serine proteases, including GzmA and B, is predominately mediated by cathepsin C (CatC). Deficiencies in CatC‐null mice were therefore expected to replicate the defects observed in GzmAB‐deficient mice. We have previously determined that GzmAB‐deficient mice exhibit increased susceptibility to murine cytomegalovirus (MCMV) infection. Here, we have compared the ability of CatC−/− mice to control MCMV infection with that of GzmAB‐deficient animals. We found that CatC−/− mice have organ‐specific defects in the ability to control MCMV replication, a phenotype that is distinct to that observed in GzmAB−/− mice. Significantly, the cytolytic function of CatC‐deficient NK cells and CTLs elicited during infection was indistinguishable from that of wild‐type cells. Hence, CatC is involved in limiting MCMV replication; however, this effect is independent of its role in promoting effector cytolytic activity. These data provide evidence for a novel and unexpected role of CatC during viral infection.
The roles of c‐rel and interleukin‐2 in tolerance: a molecular explanation of self–nonself discrimination
Authors: Liou Hsiou‐Chi , Smith Kendall A
Published: October 2010

The molecular mechanisms responsible for the exquisite discrimination between self and nonself molecules have remained enigmatic despite intense investigation. However, with the availability of adequate amounts of anergic lymphocytes produced by double transgenic mice, large numbers of immature B cells from sublethaly irradiated, hematopoietically‐synchronized mice, as well as critical gene‐deleted mice, it has been possible for the first time to uncover plausible molecular mechanisms that lead to tolerance versus immunity. The Rel family of transcription factors is expressed at different stages of lymphocyte maturation and differentiation. C‐Rel is not activated by immature lymphocytes, which undergo either anergy or apoptosis when triggered by antigen receptors, but c‐Rel is activated in mature lymphocytes. Antigen receptor triggering induces c‐Rel‐dependent survival and proliferative genetic programs. In T cells, a critical c‐Rel‐dependent gene encodes the T‐cell growth factor interleukin‐2 (IL‐2). Thus, T cells from c‐Rel gene‐deleted mice produce inadequate quantities of IL‐2, which renders them immunocompromised and unable to mount normal T‐cell proliferative and differentiative responses. In the face of absolute IL‐2 deficiency from birth, severe, multiorgan autoimmunity gradually ensues. Also, with more subtle IL‐2 deficiency, organ/tissue‐specific autoimmune disease becomes evident. Accordingly, both c‐Rel and IL‐2 appear to be key molecules for tolerance versus immunity, and doubtless will become foci for continued investigation, as well as future therapeutic targets in autoimmune diseases.
The autoimmunity of primary biliary cirrhosis and the clonal selection theory
Authors: Selmi Carlo , Mackay Ian R , Gershwin M Eric
Published: October 2010

Primary biliary cirrhosis (PBC) is a chronic cholestatic liver disease in which an immune‐mediated injury targets the small intrahepatic bile ducts. PBC is further characterized by highly specific serum antimitochondrial autoantibodies (AMAs) and autoreactive T cells, a striking female predominance, a strong genetic susceptibility and a plethora of candidate environmental factors to trigger the disease onset. For these reasons, PBC appears ideal to represent the developments of the clonal selection theory over the past decades. First, a sufficiently potent autoimmunogenic stimulus in PBC would require the coexistence of numerous pre‐existing conditions (mostly genetic, as recently illustrated by genome‐wide association studies and animal models) to perpetuate the destruction of the biliary epithelium by the immune system via the persistence of forbidden clones. Second, the proposed modifications of mitochondrial autoantigens caused by infectious agents and/or xenobiotics well illustrate the possibility that peculiar changes in the antigen structure and flexibility may contribute to tolerance breakdown. Third, the unique apoptotic features shown for cholangiocytes are the ideal setting for the development of mitochondrial autoantigen presentation to the immune system through macrophages and AMA; thus, turning the non‐traditional mitochondrial antigen into a traditional one. This article will review the current knowledge on PBC etiology and pathogenesis in light of the clonal selection theory developments.
Human Transcript Database Search Showed Existence Of Extremely Short Introns
Authors: Shimada Makoto , Haraguchi Noriko , Mayeda Akila
Published: October 2010

Since pre-mRNA splicing is processed by a spliceosome that is a huge complex consists of RNAs and as many as 200 proteins, it is considered that minimum intron size is limited by molecular size of the spliceosome. To understand splicing mechanism, we investigate human intron size distribution using annotated transcriptome database, H-InvDB. Distribution of obtained intron length shows that there is a mode at 83 nt in length with 4049 transcripts and number of introns decreases drastically in shorter than 65 nt, where numbers of transcripts in each locus also decrease. However, some introns less than 65 nt are observed, both shows high Codon Adaptation Index (CAI) and also observed orthologous transcripts in other mammals. These suggests that there is a limitation in minimum length to spliced out in general splicing mechanism of human, but also unknown mechanism may be exist to splice small intron exceeding the limitation.
SBML layout and render news
Authors: Gauges Ralph
Published: October 2010

This presentation gives a short overview on the layout and render extension to SBML and on recent software updates we did that support those two extensions.
BiNoM Cytoscape Plugin for constructing, querying and analyzing biological networks, using systems biology standards
Authors: Zinovyev Andrei
Published: October 2010

BiNoM is a Cytoscape plugin which allows to read, analyze and convert biological networks represented in various systems biology standards.
Systems Biology Ontology: Update
Authors: Juty Nick
Published: October 2010

The Systems Biology Ontology (SBO) is composed of hierarchically arranged sets of controlled vocabularies that are commonly used in mathematical modelling, providing an additional layer of semantic information. We present recent developments in SBO, including the ontology's OBO Foundry status, its relationship to SBGN, and detail some of the restructuring work that has been undertaken.
Ontologies for use in Systems Biology: SBO, KiSAO and TEDDY
Authors: Juty Nick , Le Novère Nicolas , Waltemath Dagmar , Knuepfer Christian
Published: October 2010

The use of computational modelling in the description and analysis of biological systems is at the heart of Systems Biology. Besides the information stored in a core model, there is increasingly a need to provide additional semantic information: to identify model components, to assist in biological interpretation of models, to define simulation conditions and to describe simulation results. This information deficit can be addressed through the use of ontologies. We describe here three ontologies created specifically to address the needs of the Systems Biology community in each sub-division, and illustrate their practical use with the 'Repressilator' model (Elowitz and Leibler, 2000).
Are Normal‐Weight Americans Over‐Fat?
Authors: St‐Onge Marie‐Pierre
Published: October 2010

Data from National Health and Nutrition Examination Surveys (NHANES) 1999–2004 have recently shown the percent body fat of American adults. Average American men and women have ∼28 and 40% body fat. When categorized by BMI and age, the data also show high percent body fat values, particularly in lower BMI categories. These data should make one reflect on the health status of Americans in all BMI categories and the use of these data for public health recommendations.
Determination of CO2 sensitivity of micro‐organisms in shaken bioreactors. I. Novel method based on the resistance of sterile closure
Authors: Amoabediny Ghassem , Büchs Jochen
Published: October 2010

Influence of carbon dioxide on growth and product kinetics of industrially important micro‐organisms is essential for the interpretation of a bioprocess. In this research, the CO2 effects on productivity and growth rate of micro‐organisms have been studied by using a variety of kplug. The applied method is based on a different concentration of CO2 in the headspace of ventilation flasks. The presented method is simple, inexpensive and shows similar results compared to large‐scale fermentation regarding the evolution of CO2 in a batch system. For the investigation of the proposed method, experiments employing Arxula adeninivorans LS3, Corynebacterium glutamicum (DM1730 and ATCC WT13032) and Hansenula polymorpha DSM70277 as model organisms in the ventilation flasks are performed. The fermentations in the RAMOS (respiratory activity monitoring system) device were carried out with a normal aeration rate (1 vvm) and under the same operating conditions as the ventilation flask f1. The modified unsteady‐state model was used to predict the operation conditions of a biological system in the ventilation flasks. In the present study, a novel and easy method for the quantification of CO2 sensitivity of micro‐organisms in shaken bioreactors (called ventilation flask) was achieved.
A Retrospective Study of Red Cell Maternal Antibodies by Chemiluminescence
Authors: Downing I. , Bromilow I. M. , Templeton J. G. , Fraser R. H.
Published: October 2010

Plasma samples from 109 patients with maternal IgG alloantibodies were investigated using a chemiluminescence (CL) assay, a functional test, to predict which antibodies were clinically significant. The CL assay was able to distinguish between those patients who were unaffected or mildly affected requiring only phototherapy, and those patients with moderate or severe haemolytic disease of the fetus or newborn (HDN) requiring transfusion therapy. The CL result was compared with the anti‐D quantification result, the number of IgG molecules bound per red cell and, in 80% of the cases, the monocyte monolayer assay. If mothers carrying Rh‐negative fetuses were ignored, then the CL assay correctly predicted the outcome for 93.4% of all cases (including those other than D), while the AutoAnalyzer and monocyte assay predicted correctly 92.7% (of the anti‐D patients) and 81.5%, respectively. Greater than 80% of patients with severe or moderate HDN had both IgG1+IgG3 subclasses in the maternal plasma, while those infants who were unaffected or only mildly affected had a greater chance of having IgG1 only (44%) in the maternal plasma, IgG3 only (27%) or both subclasses (29%).
Effect of Dietary Formic and Propionic Acids on Salmonella Pullorum Shedding and Mortality in Layer Chicks after Experimental Infection
Authors: Al‐Tarazi Y. H. , Alshawabkeh K.
Published: October 2010

This investigation was conducted to study the effect of dietary formic acid (FA) and propionic acid (PA) mixture on inhibitory effect of Salmonella pullorum in layer chicks. Nine equal groups of 1‐day‐old layer chicks, in addition to positive and negative controls, were fed on day 3 of age with acid‐treated feed containing mixture of both acids at concentrations, from 0.5 to 1.5%. Positive and negative controls were fed untreated feed. All groups except the negative control were challenged orally on day 3 with 104 CFU/ml/bird S. pullorum. Cloacal swabs were taken at three successive days and at 7, 14 and 21 days of challenge. After 1, 2 and 3 weeks after challenge, four chicks from each group were killed, and crop and caecal contents were examined for S. pullorum and pH. The numbers of S. pullorum re‐isolation from all treated groups, ‘except groups treated with mixture of 0.5% and 0.5%, 1% and 0.5% as well as 0.5% and 1% FA and PA’, decreased significantly (P < 0.05) compared with the positive control. The mortality rates of all treated groups except the group treated with 0.5% FA and 0.5% PA decreased significantly (P < 0.05) compared with the positive control. The treatment significantly (P < 0.05) lowered the pH of the crop and caecal contents in all groups except the group treated with 0.5% FA and 0.5% PA compared with the control. Also, the treatment significantly (P < 0.05) lowered the pH of the crop and caecal contents in all groups after 3 weeks of treatment compared with the first and second weeks. The treatments significantly (P < 0.05) lowered the frequency of S. pullorum recovery from crop and caecal contents in six groups treated with 1.5 and 0.5, 1 and 1, 1.5 and 1, 0.5 and 1.5, 1 and 1.5, 1.5% and 1.5% FA and PA, respectively.

These results indicate that addition of FA and PA mixture in a total concentration of 2% or more to the diet of newly hatched infected layer chicks significantly decreases the crop and caecal colonization by S. pullorum and significantly decreases S. pullorum faecal excretion and reduced the chick mortality rate.
Aetiology of Ovine Footrot in the Portuguese Region of Alto Alentejo
Authors: Jiménez R. , Píriz S. , Martín‐Palomino P. , Mateos E. , Vadillo S.
Published: October 2010

In this work, we found it appropriate to carry out a study directed towards isolating and identifying the entailed microorganisms which trigger off footrot in sheep, placing special emphasis on the serotipification of the different Dichelobacter nodosus species. With this goal in mind four flocks from the Portuguese region of ‘Alto Alentejo’ were selected, all of them had one common feature: their main health problem was ovine footrot. We also set out to determine the elastolitic capacity of isolated strict‐anaerobic bacteria, in order to be able to clarify the direct involvement of these microorganisms in the outbreak of this infectious process.
Sequence and Analysis of Genomic Segment A and B of Very Virulent Infectious Bursal Disease Virus Isolated from China
Authors: Sun J.‐H. , Lu P. , Yan Y.‐X. , Hua X.‐G. , Jiang J. , Zhao Y.
Published: October 2010

A very virulent infectious bursal disease virus (vvIBDV) field strain, named SH95, was identified and characterized from flocks with vaccination failure in Shanghai. The use of random primer and a reverse transcriptase lacking RNase‐H activity produced full‐length cDNA copies of the viral genomic A and B segments of SH95. The 3259 base pairs (bp) of segment A and 2827 bp of segment B were amplified by long and accurate PCR in a single step, then successfully cloned and sequenced. There were five to 27 amino acid substitutions compared with other IBDV strains within the segment A polyprotein (of these, three are unique) and about nine to 38 amino acid substitutions within VP1 (of which, four are unique). The comparison of sequences encoding the polyprotein showed that vvIBDV SH95 was most closely related to Asiatic vvIBDVs, which formed a closely related group clearly distinguishable from other classical strains of IBDV. Phylogenetic analysis suggested that vvIBDV SH95 and some other Asiatic vvIBDVs were derived from similar origin. But the topology tree performed on segment B was quite different from that performed on segment A, indicating that a genetic reassortment had played an important role in the emergence of vvIBDV SH95.
Otitis in Cattle, an Aetiological Review
Authors: Duarte E. R. , Hamdan J. S.
Published: October 2010

Otitis externa in cattle has a significant impact in tropical and subtropical regions, and the aetiological agents are predominantly rhabditiform nematodes and mites of the genusRaillietia. Its prevalence is higher in mature and Zebu cattle. In advanced clinical cases there can be irreversible and fatal neural lesions. Ear infection in calves has been associated with concurrent respiratory diseases and mixed infection. The principal reported agents of otitis in calves are bacteria such asActinomycesspp.,Corynebacterium pseudotuberculosis,Escherichia coli,Haemophilus somnus,Pasteurella multocida,Mannheimia haemolytica,Pseudomonasspp.,Streptococcusspp. andMycoplasma bovis. The control and treatment of bovine otitis is not standardized and there is little evidence‐based support for the diverse treatments available in the literature.
Campylobacterspp. in Irish Feedlot Cattle: A Longitudinal Study Involving Pre‐harvest and Harvest Phases of the Food Chain
Authors: Minihan D. , Whyte P. , O'Mahony M. , Fanning S. , McGill K. , Collins J. D.
Published: October 2010

The aim of this study was to investigate faecal shedding and transmission ofCampylobacterspp. in cohorts of cattle within a feedlot, to assess subsequent contamination of carcasses with this pathogen and to identify risk factors associated with faecal shedding ofCampylobacterspp. A cohort of 133 heifers housed in four adjacent pens was examined over a five and a half month period, from entering the feedlot to slaughter. A parallel investigation of individual rectal faecal samples and pen environmental samples were taken at monthly intervals from November to February. The entire outer and inner surfaces of a carcass side of each animal were swabbed immediately following slaughter.Campylobacterspp. were isolated from 322 (54%) of the 600 rectal faecal samples.Campylobacter jejuniandC. coliaccounted for 69 and 29.7% of the isolate recovered, respectively. A total of 159 environmental samples were examined, of theseCampylobacterspp. was isolated from 46 samples (29%).Campylobacter jejuniandC. coliaccounted for 35 and 59% of these isolates, respectively.Campylobacterspp. was not isolated from any of the dressed carcasses. Logistic regression indicated prevalence ofCampylobacterspp. faecal shedding within pens was positively correlated to the pen, the month of sampling and theCampylobacterspp. contamination status of the pen dividing bars and the water trough surface.Campylobacterspp. should be considered as a pathogen shed in the faeces of a substantial proportion of feedlot cattle. However, with good hygienic practice during harvest, a very low level of this pathogen can be achieved on dressed carcasses.
Schoolchildren's abilities to frame, understand and successfully manipulate food label information: enabling consumer choice through education
Authors: Stuart Stephen A. , Schröder Monika J.A. , Bower John A.
Published: October 2010

At a time when the major dialogue in food labelling is directed towards the volume and type of information presented, it is important to understand whether adolescents leaving education have the abilities to comprehend and use the current label as they represent the next generation of consumers.

Legislation has been created to protect consumers and to enable them to make informed food choices. Food labels carry a significant volume of mandatory and voluntary information, designed to fulfil a variety of commercial and consumer functions. For these laws to be effective at an individual level, it is important that information is framed correctly, and that people can manipulate the data in an accurate and meaningful manner.

In order to optimise food label information consumers require some competence across three different conceptual dimensions: maths, English comprehension, and health and nutrition. Most individuals acquire such skills at school.

The pilot research that this paper describes investigates changes in   the   abilities   to   frame,   comprehend   and   manipulate label information, of 19 schoolchildren at one secondary school in Scotland. The main research, to be conducted in 2003, will include over a thousand children from another seven Scottish schools.

Statistical analysis indicates that there is a significant improvement in the dimensions of both maths and English comprehension between levels S1 and S5, whilst the health and nutrition dimension does not show such significance.

Each dimension has been measured against attitudes towards the use of labels in shopping and cooking to determine if the differences between those who use labels and those who do not are significant

The research also proposes a new method of presenting nutrition information to make it more meaningful to individuals across a wide spectrum of competence by reducing the number of conceptual components required to comprehend it.
Determination of isoprene and α‐/β‐pinene oxidation products in boreal forest aerosols from Hyytiälä, Finland: diel variations and possible link with particle formation events
Authors: Kourtchev I. , Ruuskanen T. M. , Keronen P. , Sogacheva L. , Dal Maso M. , Reissell A. , Chi X. , Vermeylen R. , Kulmala M. , Maenhaut W. , Claeys M.
Published: October 2010

Biogenic volatile organic compounds (VOCs), such as isoprene and α‐/β‐pinene, are photo‐oxidized in the atmosphere to non‐volatile species resulting in secondary organic aerosol (SOA). The goal of this study was to examine time trends and diel variations of oxidation products of isoprene and α‐/β‐pinene in order to investigate whether they are linked with meteorological parameters or trace gases. Separate day‐night aerosol samples (PM1) were collected in a Scots pine dominated forest in southern Finland during 28 July–11 August 2005 and analyzed with gas chromatography/mass spectrometry (GC/MS). In addition, inorganic trace gases (SO2, CO, NOx, and O3), meteorological parameters, and the particle number concentration were monitored. The median total concentration of terpenoic acids (i.e., pinic acid, norpinic acid, and two novel compounds, 3‐hydroxyglutaric acid and 2‐hydroxy‐4‐isopropyladipic acid) was 65 ng m−3, while that of isoprene oxidation products (i.e., 2‐methyltetrols and C5 alkene triols) was 17.2 ng m−3. The 2‐methyltetrols exhibited day/night variations with maxima during day‐time, while α‐/β‐pinene oxidation products did not show any diel variation. The sampling period was marked by a relatively high condensation sink, caused by pre‐existing aerosol particles, and no nucleation events. In general, the concentration trends of the SOA compounds reflected those of the inorganic trace gases, meteorological parameters, and condensation sink. Both the isoprene and α‐/β‐pinene SOA products were strongly influenced by SO2, which is consistent with earlier reports that acidity plays a role in SOA formation. The results support previous proposals that oxygenated VOCs contribute to particle growth processes above boreal forest.
Why plant volatile analysis needs bioinformatics – detecting signal from noise in increasingly complex profiles
Authors: Van Dam N. M. , Poppy G. M.
Published: October 2010

Plant volatile analysis may be the oldest form of what now is called plant “metabolomic” analysis. A wide array of volatile organic compounds (VOCs), such as alkanes, alcohols, isoprenoids, and esters, can be collected simultaneously from the plant headspace, either within the laboratory or in the field. Increasingly faster and more sensitive analysis techniques allow detection of an ever‐growing number of compounds in decreasing concentrations. However, the myriads of data becoming available from such experiments do not automatically increase our ecological and evolutionary understanding of the roles these VOCs play in plant‐insect interactions. Herbivores and parasitoids responding to changes in VOC emissions are able to perceive minute changes within a complex VOC background. Plants modified in genes involved in VOC synthesis may be valuable for the evaluation of changes in plant‐animal interactions compared to tests with synthetic compounds, as they allow changes to be made within the context of a more complex profile. We argue that bioinformatics is an essential tool to integrate statistical analysis of plant VOC profiles with insect behavioural data. The implementation of statistical techniques such as multivariate analysis (MVA) and meta‐analysis is of the utmost importance to interpreting changes in plant VOC mixtures. MVA focuses on differences in volatile patterns rather than in single compounds. Therefore, it more closely resembles the information processing in insects that base their behavioural decisions on differences in VOC profiles between plants. Meta‐analysis of different datasets will reveal general patterns pertaining to the ecological role of VOC in plant‐insect interactions. Successful implementation of bioinformatics in VOC research also includes the development of MVA that integrate time‐resolved chemical and behavioural analyses, as well as databases that link plant VOCs to their effects on insects.
Modeling volatile isoprenoid emissions – a story with split ends
Authors: Grote R. , Niinemets Ü.
Published: October 2010

Accurate prediction of plant‐generated volatile isoprenoid fluxes is necessary for reliable estimation of atmospheric ozone and aerosol formation potentials. In recent years, significant progress has been made in understanding the environmental and physiological controls on isoprenoid emission and in scaling these emissions to canopy and landscape levels. We summarize recent developments and compare different approaches for simulating volatile isoprenoid emission and scaling up to whole forest canopies with complex architecture. We show that the current developments in modeling volatile isoprenoid emissions are “split‐ended” with simultaneous but separated efforts in fine‐tuning the empirical emission algorithms and in constructing process‐based models. In modeling volatile isoprenoid emissions, simplified leaf‐level emission algorithms (Guenther algorithms) are highly successful, particularly after scaling these models up to whole regions, where the influences of different ecosystem types, ontogenetic stages, and variations in environmental conditions on emission rates and dynamics partly cancel out. However, recent experimental evidence indicates important environmental effects yet unconsidered and emphasize, the importance of a highly dynamic plant acclimation in space and time. This suggests that current parameterizations are unlikely to hold in a globally changing and dynamic environment. Therefore, long‐term predictions using empirical algorithms are not necessarily reliable. We show that process‐based models have large potential to capture the influence of changing environmental conditions, in particular if the leaf models are linked with physiologically based whole‐plant models. This combination is also promising in considering the possible feedback impacts of emissions on plant physiological status such as mitigation of thermal and oxidative stresses by volatile isoprenoids. It might be further worth while to incorporate main features of these approaches in regional empirically‐based emission estimations thereby merging the “split ends”.
Foliar limonene uptake scales positively with leaf lipid content: “non‐emitting” species absorb and release monoterpenes
Authors: Noe S. M. , Copolovici L. , Niinemets Ü. , Vaino E.
Published: October 2010

Monoterpenes synthesized and released by emitting vegetation can be taken up by neighboring non‐emitting plants, but the uptake capacity of non‐emitting species has not been studied extensively. We investigated the foliar uptake potential of the hydrophobic monoterpene limonene in 13 species of contrasting leaf structure and lipid content to determine the structural and chemical controls of monoterpene uptake. Leaf dry mass per unit area (MA,D) varied 6.5‐fold, dry to fresh mass ratio (DF) 2.7‐fold, lipid content per dry mass (LM) 2.5‐fold and per unit area (LA) 4.6‐fold across the studied species. Average foliar limonene uptake rate (UA) from air at saturating limonene partial pressures varied from 0.9 to 6 nmol m−2 s−1, and limonene leaf to air partition coefficient (KFA, ratio of limonene content per dry mass to limonene partial pressure) from 0.7 to 6.8 μmol kg−1 Pa−1. UA and KFA scaled positively with leaf lipid content, and were independent of DF, indicating that variation in leaf lipid content was the primary determinant of species differences in monoterpene uptake rate and KFA. Mass‐based limonene uptake rates further suggested that thinner leaves with greater surface area per unit dry mass have higher uptake rates. In addition, limonene lipid to air partition coefficient (KLA = KFA/LM) varied 19‐fold, indicating large differences in limonene uptake capacity at common leaf lipid content. We suggest that the significant uptake of hydrophobic monoterpenes when monoterpene ambient air concentration is high and release when the concentration is low should be included in large‐scale monoterpene emission models.
Extended fast-ion D-alpha diagnostic on DIII-D
Authors: Muscatello C. M. , Heidbrink W. W. , Taussig D. , Burrell K. H.
Published: October 2010

A fast-ion deuterium-alpha (FIDA) diagnostic, first commissioned on DIII-D in 2005, relies on Doppler-shifted light from charge-exchange between beam neutrals and energetic ions. The second generation (2G) system was installed on DIII-D in 2009. Its most obvious improvement is the spatial coverage with 11 active in-beam and three passive off-beam views; the latter allows for simultaneous monitoring of the background signal. Providing extended coverage in fast-ion velocity space, the new views possess a more tangential component with respect to the toroidal field compared to their first generation counterparts. Each viewing chord consists of a bundle of three 1.5 mm core fibers to maximize light gathering. For greater throughput, fast f/1.8 optical components are used throughout. The signal is transmitted via fiber optics to a patch panel, so the user is able to choose the detector. FIDA was originally installed with a spectrometer and charge-coupled device (CCD) camera to monitor the full Dα spectrum for two spatial views. 2G adds another spectrometer and CCD that monitor the blue-shifted wing for six spatial views at 1 kHz. In addition, a photomultiplier tube and fast digitizer provide wavelength-integrated signals at 1 MHz for eight spatial views.
FePtAg–C nanogranular films fabricated on a heat resistant glass substrate for perpendicular magnetic recording
Authors: Perumal A. , Zhang L. , Takahashi Y. K. , Hono K.
Published: October 2010

We report (001)-oriented FePtAg–C nanogranular films consisting of fine particle size of about 5 nm with a narrow size distribution of 3.3 nm in variance that were grown on a Fe–Ta–C nanocrystalline soft magnetic underlayer (SUL) through MgO/SiO2 intermediate layers. The degree of L10 order, c-axis orientation and resulting magnetic properties of FePtAg–C nanogranular films grown at low temperatures are improved by the post annealing effect without changing the nanogranular microstructure dramatically. Square-shaped perpendicular hysteresis loops with large negative nucleation field of 3.8 kOe, 100% squareness, coercivity of ∼8 kOe, and high energy barrier of 2.13 eV were obtained for the double-layered medium. Temperature dependent Kerr loops measurement reveals that the coercivity and nucleation field decrease at a rate of 26 Oe/°C and 20 Oe/°C, respectively. These results suggest that the (001) textured FePtAg–C nanogranular films with perpendicular anisotropy on SUL may be suitable as a recording medium to realize ultrahigh-density perpendicular recording in the conventional recording system.
Iterative Monte Carlo formulation of real-time correlation functions
Authors: Baltaretu Cristian O. , Makri Nancy
Published: October 2010

We present an iterative Monte Carlo path integral methodology for evaluating thermally averaged real-time correlation functions. Standard path integral Monte Carlo methods are used to sample paths along the imaginary time contour. Propagation of the density matrix is performed iteratively on a grid composed of the end points of the sampled paths. Minimally oscillatory propagators are constructed using energy filtering techniques. A single propagation yields the values of the correlation function at all intermediate time points. Model calculations suggest that the method yields accurate results over several oscillation periods and the statistical error grows slowly with increasing propagation time.
Diameter dependence of oxidative stability in multiwalled carbon nanotubes: Role of defects and effect of vacuum annealing
Authors: Singh Dilip K. , Iyer Parameswar K. , Giri P. K.
Published: October 2010

While the oxidative stability of single walled carbon nanotubes has been studied extensively, very little is known about the diameter dependence of oxidative stability in multiwalled carbon nanotubes (MWNTs) and the effect of vacuum annealing on such stability. We have investigated six sets of samples with different diameters in the range of 5–100 nm systematically by thermogravimetric analysis (TGA) before and after vacuum annealing. High resolution transmission electron microscopy studies provide evidence for structural defects in the nanotube walls. Further, it reveals that with increasing diameter, interlayer d-spacing between concentric tubes decreases. Experimental TGA profile is found to constitute multiple components of oxidation as revealed from reverse Sigmoidal fitting. Analysis of the TGA profile shows that the oxidation temperature follows an exponential recovery function with increasing diameter, while width of the differentiated TGA spectra decreases. It is shown that oxidative stability of lower diameter MWNTs are primarily controlled by lattice strain, while that of large diameter MWNTs is decided by the defects in the nanotube wall. High vacuum annealing studies in the temperature range 300–1000 °C show major improvement in the structure and oxidative stability for MWNTs annealed at 500 °C. Results are compared with those of the single walled nanotubes. The observed diameter dependence is explained on the basis of strain in the nanotube lattice and defects in the nanotube walls.