bluuebunny/crossref_metadata_2025 huggingface dataset:
Control of electrolysis-generated microbubbles for sensor surface passivation
Authors: Lucas T. M. , Harnett C. K.
Published: January 2011

This letter outlines our work in generating and controlling microbubbles as protective “lids” for samples collected from the environment. The fabrication method uses “strain architecture” to construct three-dimensional cages with high surface area. These structures confine the bubbles and perform as electrodes for electrochemical sample collection and electrolysis-based gas bubble generation. The focus of this article is on the interaction between the microcages and generated bubbles, including the bubble generation mechanism, bubble growth rate, response to hydrostatic pressure, effect of interfacial-tension modifying coatings, and long-term stability.
Birth and death of genes linked to chromosomal inversion
Authors: Furuta Yoshikazu , Kawai Mikihiko , Yahara Koji , Takahashi Noriko , Handa Naofumi , Tsuru Takeshi , Oshima Kenshiro , Yoshida Masaru , Azuma Takeshi , Hattori Masahira , Uchiyama Ikuo , Kobayashi Ichizo
Published: January 2011

The birth and death of genes is central to adaptive evolution, yet the underlying genome dynamics remain elusive. The availability of closely related complete genome sequences helps to follow changes in gene contents and clarify their relationship to overall genome organization.
Helicobacter pylori
, bacteria in our stomach, are known for their extreme genome plasticity through mutation and recombination and will make a good target for such an analysis. In comparing their complete genome sequences, we found that gain and loss of genes (loci) for outer membrane proteins, which mediate host interaction, occurred at breakpoints of chromosomal inversions. Sequence comparison there revealed a unique mechanism of DNA duplication: DNA duplication associated with inversion. In this process, a DNA segment at one chromosomal locus is copied and inserted, in an inverted orientation, into a distant locus on the same chromosome, while the entire region between these two loci is also inverted. Recognition of this and three more inversion modes, which occur through reciprocal recombination between long or short sequence similarity or adjacent to a mobile element, allowed reconstruction of synteny evolution through inversion events in this species. These results will guide the interpretation of extensive DNA sequencing results for understanding long- and short-term genome evolution in various organisms and in cancer cells.
Tailoring the magnetism of GaMnAs films by ion irradiation
Authors: Li Lin , Yao S D , Zhou Shengqiang , Bürger D , Roshchupkina O , Akhmadaliev S , Rushforth A W , Campion R P , Fassbender J , Helm M , Gallagher B L , Timm C , Schmidt H
Published: January 2011

Ion irradiation of semiconductors is a well-understood method to tune the carrier concentration in a controlled manner. We show that the ferromagnetism in GaMnAs films, known to be hole-mediated, can be modified by He ion irradiation. The coercivity can be increased by more than three times. The magnetization, Curie temperature and the saturation field along the out-of-plane hard axis all decrease as the fluence increases. The electrical and structural characterization of the irradiated GaMnAs layers indicates that the controlled tailoring of magnetism results from a compensation of holes by the generated electrical defects.
Gas phase optical emission spectroscopy during remote plasma chemical vapour deposition of GaN and relation to the growth dynamics
Authors: Corr Cormac , Boswell Rod , Carman Robert
Published: January 2011

A remote plasma chemical vapour deposition (RPCVD) system for the growth of gallium nitride (GaN) thin films is investigated using optical emission spectroscopy (OES). The intensities of the various excited species in pure nitrogen as well as nitrogen/hydrogen plasmas are correlated with GaN film growth characteristics. We show a correlation between the plasma source spectrum, the downstream spectrum where trimethylgallium is introduced and the GaN film quality. In particular, we investigate the addition of hydrogen, which greatly affects the gas phase species and the GaN film characteristics. OES is demonstrated to be a valuable monitoring tool in a RPCVD system for optimization of GaN growth.
Three-dimensional numerical modelling of gas discharges at atmospheric pressure incorporating photoionization phenomena
Authors: Papageorgiou L , Metaxas A C , Georghiou G E
Published: January 2011

A three-dimensional (3D) numerical model for the characterization of gas discharges in air at atmospheric pressure incorporating photoionization through the solution of the Helmholtz equation is presented. Initially, comparisons with a two-dimensional (2D) axi-symmetric model are performed in order to assess the validity of the model. Subsequently several discharge instabilities (plasma spots and low pressure inhomogeneities) are considered in order to study their effect on streamer branching and off-axis propagation. Depending on the magnitude and position of the plasma spot, deformations and off-axis propagation of the main discharge channel were obtained. No tendency for branching in small (of the order of 0.1 cm) overvolted discharge gaps was observed.
On subspace-hypercyclic operators
Authors: Le Can
Published: January 2011

In this paper we study an operator

T
T

on a Banach space

E
E

which is

M
M

-hypercyclic for some subspace

M
M

of

E
E

. We give a sufficient condition for such an operator to be

M
M

-hypercyclic and use it to answer negatively two questions asked by Madore and Martínez-Avendaño. We also give a sufficient condition for

T
T

to be

M
M

-hypercyclic for all finite co-dimensional subspaces

M
M

in

E
E

.
On the asymptotic formula for the solution of degenerate elliptic partial differential equations
Authors: Wei Dong-Huang
Published: January 2011

This paper gives an asymptotic expansion for the solution of the boundary problem with respect to the Laplace-Beltrami operator. We also consider some examples in the domain whose boundary is real ellipsoid, where the boundary problem does not have a

C
n

C^n

solution up to the boundary.
The Potential Supply of Carbon Dioxide Offsets from the Anaerobic Digestion of Dairy Waste in the United States
Authors: Gloy Brent A.
Published: January 2011

Anaerobic digestion allows farmers to create renewable energy and significantly reduce manure methane emissions. Estimates of the aggregate supply curve for carbon dioxide (CO2) equivalent offsets from the adoption of anaerobic digestion (AD) were developed based upon dairy farm data collected by the National Agricultural Statistics Service/Economic Research Service Agricultural Resource and Management Survey. The estimated supply curve demonstrates how the supply of CO2 offsets from AD would be influenced by offset prices. A sensitivity analysis examines how changes in capital and operating costs, as well as energy prices, would influence the supply of offsets. Under a base set of assumptions, offset prices in excess of $15 per ton of CO2 equivalent would be required to reduce methane emissions from manure storages by 50% from 2005 levels.
Should all fish in mark–recapture experiments be double-tagged? Lessons learned from tagging coastal cod (Gadus morhua)
Authors: Björnsson Björn , Karlsson Hjalti , Thorsteinsson Vilhjálmur , Solmundsson Jón
Published: January 2011

Björnsson, B., Karlsson, H., Thorsteinsson, V., and Solmundsson, J. 2011. Should all fish in mark–recapture experiments be double-tagged? Lessons learned from tagging coastal cod (Gadus morhua). – ICES Journal of Marine Science, 68: . Cod (Gadus morhua) were tagged outside and inside “herds” formed by anthropogenic feeding in an Icelandic fjord. Recapture rates were twice as high for fish double-tagged with one surgically implanted electronic tag and one anchor tag (46.6 and 62.2%) than with fish tagged with only a single anchor tag (20.0 and 29.2%) outside and inside the herds, respectively. The two main reasons for the differences observed in recapture rates were higher detection and reporting rates for the double-tagged fish. In cage experiments, 8% of the fish receiving implanted tags died during the first 2 d after tagging. For double-tagged fish, tag loss was ∼10% for both tag types. About 80% of the tags were returned by fishers and 20% by fish processors. The tag detection rate by fishers was estimated at ∼45 and ∼80% for single- and double-tagged fish, and the reporting rate at ∼74 and ∼100% for single- and double-tagged fish, respectively. It is proposed for future tagging studies to double-tag all fish routinely, placing one tag dorsally and one ventrally, to enhance the detection rate and to account for tag loss.
Some operational uses of satellite remote sensing and marine GIS for sustainable fisheries and aquaculture
Authors: Saitoh Sei-Ichi , Mugo Robinson , Radiarta I Nyoman , Asaga Shinsuke , Takahashi Fumihiro , Hirawake Toru , Ishikawa Yoichi , Awaji Toshiyuki , In Teiji , Shima Shigeki
Published: January 2011

Saitoh, S-I., Mugo, R., Radiarta, I N., Asaga, S., Takahashi, F., Hirawake, T., Ishikawa, Y., Awaji, T., In, T., and Shima, S. 2011. Some operational uses of satellite remote sensing and marine GIS for sustainable fisheries and aquaculture. – ICES Journal of Marine Science, 68: 687–695. An overview of satellite remote-sensing (SRS) operational applications in fisheries is presented, and includes two case studies illustrating the societal benefits of SRS. The first describes the use of satellite-based vessel monitoring systems (VMS) and SRS data in a skipjack tuna (Katsuwonus pelamis) fishery, including a simple algorithm for determining fishing activity from vessel speed. The second case study illustrates the application of remotely sensed information in determining the impact of climate change on site suitability for scallop (Mizuhopecten yessoensis) aquaculture. Global warming simulated according to Intergovernmental Panel on Climate Change scenarios had a significant impact on sites with the greatest suitability for scallop aquaculture. Some challenges in the field of fisheries information systems are also discussed.
First Report of Cucurbit aphid-borne yellows virus in Squash in the Czech Republic
Authors: Svoboda J. , Leisova-Svobodova L. , Lecoq H.
Published: January 2011

A yellowing of buttercup squash (Cucurbita pepo L. var. oleifera Pietsch) leaves was observed on plants in southern Moravia, the main squash-growing area of the Czech Republic. Forty leaf samples were collected in September 2009 and examined for the presence of possible cucurbit viruses by double-antibody sandwich-ELISA. Thirty-three samples were infected with Zucchini yellow mosaic virus and five with Cucurbit aphid-borne yellows virus (CABYV). The positive samples of CABYV originated near the villages of Josefov and Prušánky (one per sample) and Rakvice (three samples), and the virus isolates were named Jos-5, Pr-15, Rak-1, Rak-4, and Rak-5, respectively. CABYV was immediately transmitted from leaves collected in the field to summer squash (Cucurbita pepo L. convar. giromontiina Grebenšcikov) plants by aphids in a persistent manner. Green peach aphids, Myzus persicae (Sulzer), were used to inoculate squash plants with acquisition and inoculation feeding times of 2 and 5 days, respectively. Twenty-one plants were inoculated with 20 aphids per plant. Transmission was successful in 25% of the plants as assessed by ELISA. Infected plants showed very mild yellowing 2 weeks after transmission and were shorter compared with noninoculated controls. Leaf samples of newly infected plants were examined by electron microscopy and isometric particles of approximately 25 nm in diameter, corresponding in size and shape to described particles of CABYV (3), were observed. The presence of CABYV was verified by reverse transcription (RT)-PCR using a primer pair specific to the CABYV coat protein gene (2). The amplicons were sequenced (GenBank Accession Nos. HM771269–HM771273) and 100% sequence identity was found between isolates Jos-5 and Pr-15 and among the isolates Rak-1, Rak-2, and Rak-3. Sequence identity between these two groups was 99.3%. Blast analysis (4) showed that the Czech CABYV isolates are closely related to the Slovak isolates SK-1 (Accession No. FJ428797) and IR-3 (Accession No. FJ428800) with nucleotide sequence identities of 99.6 and 99.1%, respectively. These results indicate a similar origin between the Czech and Slovak isolates. To our knowledge, this is the first report of the natural occurrence of CABYV in the Czech Republic. CABYV is a widespread virus that reduces the yield of cucurbit vegetables (1). Protection against epidemics should be based on the control of aphid vectors, protecting plants with very fine mesh netting, keeping the cultivation area free of weeds, or planting cultivars resistant to CABYV.

References: (1) Anonymous. Research Report 1995-1996, 117. Vegetable Breeding Station, INRA, Montfavet, France, 1998. (2) M. Juarez at al., Plant Dis. 88:907, 2004. (3) H. Lecoq et al. Plant Pathol. 41:749, 1992. (4) Z. Zhang Z. et al. J. Comput. Biol. 7:203, 2000.
First Report of the Ash Dieback Pathogen Hymenoscyphus pseudoalbidus (Anamorph Chalara fraxinea) on Fraxinus excelsior in Belgium
Authors: Chandelier A. , Delhaye N. , Helson M.
Published: January 2011

Since the early 1990s, European ash (Fraxinus excelsior L.) has been affected by a lethal disease caused by the ascomycete fungus, Hymenoscyphus pseudoalbidus, originally known under the name of its anamorph, Chalara fraxinea (2,4). Pathogenicity of H. pseudoalbidus was demonstrated by inoculations on young trees (3). This emerging pathogen induces necrosis of leaf rachises, leaf wilting and shedding, bark necrosis, and wood discoloration as well as shoot, twig, and branch dieback. First observed in Poland, ash dieback now occurs in many parts of Europe. Since 2009, a survey of ash dieback caused by H. pseudoalbidus has been conducted in Wallonia (southern Belgium). Sampling units were selected to take the occurrence of ash stands and the potential points of entry of the pathogen into the country (nurseries, sawmills, rivers, and roads) into account. While the disease was not detected in 2009, young, naturally regenerated trees displaying typical symptoms of ash dieback were found in June 2010 in Silly, a village in the province of Hainaut. Symptomatic trees were located along a road in front of a large ash stand. Examination of shoots with bark necrosis from three symptomatic trees yielded positive results on the basis of a real time PCR test developed in our laboratory for the detection of H. pseudoalbidus (1). To confirm the molecular identification, fungal isolation from discolored wood onto malt extract agar supplemented with 100 mg liter–1 of streptomycin sulfate was attempted. After 18 days at 20 to 22°C in the dark, slow-growing, dull white colonies with gray patches, resembling those of C. fraxinea, had formed. The nuclear ribosomal internal transcribed spacer region (ITS) was amplified with primers ITS1 and ITS4 (4) and partly sequenced (GenBank Accession No. FR667687). A BLASTn search in GenBank revealed that the sequence of the Belgian isolate (452 bp) displayed 100% identity with sequences of a H. pseudoalbidus isolate from Switzerland (GenBank Accession No GU586932). In contrast, the sequence showed some mismatches with that of the closely related and probably strictly saprotrophic fungus, Hymenoscyphus albidus (GenBank Accession No GU586891.1). The strain was deposited as reference material in the Fungal Biology collection (CBS 128012). To our knowledge, this is the first report of ash dieback caused by H. pseudoalbidus in Belgium. The discovery of this aggressive tree pathogen in Wallonia documents its further westward spread in Europe. In the future, we expect that H. pseudoalbidus will continue its range expansion into areas that have so far not been affected by ash dieback.

References: (1) A. Chandelier et al. For. Pathol. 40:87, 2010. (2) T. Kowalski. For. Pathol. 36:264, 2006. (3) T. Kowalski and O. Holdenrieder. For. Pathol. 39:1, 2009. (4) V. Queloz et al. For. Pathol. Online publication. doi:10.1111/j.1439-0329.2010.00645.x, 2010.
Evolutionary transitions between mechanisms of sex determination in vertebrates
Authors: Quinn Alexander E. , Sarre Stephen D. , Ezaz Tariq , Marshall Graves Jennifer A. , Georges Arthur
Published: January 2011

Sex in many organisms is a dichotomous phenotype—individuals are either male or female. The molecular pathways underlying sex determination are governed by the genetic contribution of parents to the zygote, the environment in which the zygote develops or interaction of the two, depending on the species. Systems in which multiple interacting influences or a continuously varying influence (such as temperature) determines a dichotomous outcome have at least one threshold. We show that when sex is viewed as a threshold trait, evolution in that threshold can permit novel transitions between genotypic and temperature-dependent sex determination (TSD) and remarkably, between male (XX/XY) and female (ZZ/ZW) heterogamety. Transitions are possible without substantive genotypic innovation of novel sex-determining mutations or transpositions, so that the master sex gene and sex chromosome pair can be retained in ZW–XY transitions. We also show that evolution in the threshold can explain all observed patterns in vertebrate TSD, when coupled with evolution in embryonic survivorship limits.
Elastohydrodynamics of wet bristles, carpets and brushes
Authors: Gopinath A. , Mahadevan L.
Published: January 2011

Surfaces covered by bristles, hairs, polymers and other filamentous structures arise in a variety of natural settings in science such as the active lining of many biological organs, e.g. lungs, reproductive tracts, etc., and have increasingly begun to be used in technological applications. We derive an effective field theory for the elastohydrodynamics of ordered brushes and disordered carpets that are made of a large number of elastic filaments grafted on to a substrate and interspersed in a fluid. Our formulation for the elastohydrodynamic response of these materials leads naturally to a set of constitutive equations coupling bed deformation to fluid flow, accounts for the anisotropic properties of the medium, and generalizes the theory of poroelasticity to these systems. We use the effective medium equations to study three canonical problems—the normal settling of a rigid sphere onto a carpet, the squeeze flow in a carpet and the tangential shearing motion of a rigid sphere over the carpet, all problems of relevance in mechanosensation in biology with implications for biomimetic devices.
Pseudomonas aeruginosa fosfomycin resistance mechanisms affect non-inherited fluoroquinolone tolerance
Authors: De Groote Valerie N. , Fauvart Maarten , Kint Cyrielle I. , Verstraeten Natalie , Jans Ann , Cornelis Pierre , Michiels Jan
Published: January 2011

Pseudomonas aeruginosa is an opportunistic pathogen that poses a threat in clinical settings due to its intrinsic and acquired resistance to a wide spectrum of antibiotics. Additionally, the presence of a subpopulation of cells surviving high concentrations of antibiotics, called persisters, makes it virtually impossible to eradicate a chronic infection. The mechanism underlying persistence is still unclear, partly due to the fact that it is a non-inherited phenotype. Based on our findings from a previously performed screening effort for P. aeruginosa persistence genes, we hypothesize that crosstalk can occur between two clinically relevant mechanisms: the persistence phenomenon and antibiotic resistance. This was tested by determining the persistence phenotype of P. aeruginosa strains that are resistant to the antibiotic fosfomycin due to either of two unrelated fosfomycin resistance mechanisms. Overexpression of fosA (PA1129) confers fosfomycin resistance by enzymic modification of the antibiotic, and in addition causes a decrease in the number of persister cells surviving ofloxacin treatment. Both phenotypes require the enzymic function of FosA, as mutation of the Arg119 residue abolishes fosfomycin resistance as well as low persistence. The role for fosfomycin resistance mechanisms in persistence is corroborated by demonstrating a similar phenotype in a strain with a mutation in glpT (PA5235), which encodes a glycerol-3-phosphate transporter essential for fosfomycin uptake. These results indicate that fosfomycin resistance, conferred by glpT mutation or by overexpression of fosA, results in a decrease in the number of persister cells after treatment with ofloxacin and additionally stress that further research into the interplay between fosfomycin resistance and persistence is warranted.
Evaluation of three phenotypic identification systems for clinical isolates of Raoultella ornithinolytica
Authors: Park Jeong Su , Hong Ki Ho , Lee Hyun Jung , Choi Soon Hee , Song Sang Hoon , Song Kyoung-Ho , Kim Hong Bin , Park Kyoung Un , Song Junghan , Kim Eui-Chong
Published: January 2011

Raoultella spp. have recently been separated from the genus Klebsiella based on their molecular characteristics. It was discovered that Raoultella ornithinolytica can be misidentified as Klebsiella oxytoca by commonly used phenotypic identification systems. Therefore, this study evaluated the ability of three phenotypic systems to identify R. ornithinolytica compared with the genotypic methods sequence-specific primer PCR (SSP-PCR), 16S rRNA gene sequence analysis using the MicroSeq 500 system16S rDNA bacterial identification system or comparison with GenBank sequences using blast. The phenotypic systems examined in this study were the VITEK 2 GN ID card, the MicroScan Neg Combo 32 panel and API 20E. The SSP-PCR panel was able to distinguish the R. ornithinolytica reference strain from other Raoultella spp. and K. oxytoca. Of the 27 isolates identified as R. ornithinolytica by SSP-PCR, VITEK 2 identified all of them as R. ornithinolytica. MicroScan and API identified 25 isolates (92.6 %) and 24 isolates (88.9 %) as K. oxytoca, respectively. These isolates were ornithine decarboxylase (ODC) negative in all three phenotypic systems. MicroSeq 500 identified 24 isolates (88.9 %) as R. ornithinolytica, whereas GenBank identification was heterogeneous. Of the 68 isolates identified as K. oxytoca by SSP-PCR, 66 isolates (97.1 %) were identified as K. oxytoca by VITEK 2, MicroScan and API. MicroScan and API require additional biochemical tests to differentiate between ODC-negative R. ornithinolytica and K. oxytoca.
Ler of pathogenic Escherichia coli forms toroidal protein–DNA complexes
Authors: Mellies Jay L. , Benison Gregory , McNitt William , Mavor David , Boniface Chris , Larabee Frederick J.
Published: January 2011

Enteropathogenic and enterohaemorrhagic Escherichia coli are related pathotypes of bacteria that cause acute watery diarrhoea and haemorrhagic colitis, respectively, and enterohaemorrhagic E. coli can lead to a serious complication known as haemolytic uraemic syndrome. In both bacteria the global regulatory protein Ler controls virulence. The ler gene is found within the locus of enterocyte effacement, or LEE, encoding a type III secretion system necessary for injecting effector proteins into intestinal epithelial cells and causing net secretory diarrhoea. The nucleoid-associated protein H-NS silences, whereas Ler serves as an anti-silencer of, multiple LEE operons. Although Ler has a higher affinity for DNA than does H-NS, the precise molecular mechanism by which Ler increases LEE transcription remains to be determined. In this report we investigate the oligomerization activity of Ler. In solution, Ler forms dimers and soluble aggregates of up to 5000 kDa molecular mass, and appears to oligomerize more readily than the related protein H-NS. An insertional mutation into the Ler linker region diminished oligomerization activity. Despite being proteins of similar mass and having homologous DNA-binding domains, Ler and H-NS complexed to DNA migrated to distinct locations, as determined by an electrophoretic mobility shift assay, implying that the related proteins form different 3D shapes in the presence of DNA. Lastly, we present electron microscopy images of toroidal Ler–DNA structures that are predicted to be involved in stimulating gene expression.
Natural Variation of Root Hydraulics in Arabidopsis Grown in Normal and Salt-Stressed Conditions
Authors: Sutka Moira , Li Guowei , Boudet Julie , Boursiac Yann , Doumas Patrick , Maurel Christophe
Published: January 2011

To gain insights into the natural variation of root hydraulics and its molecular components, genotypic differences related to root water transport and plasma membrane intrinsic protein (PIP) aquaporin expression were investigated in 13 natural accessions of Arabidopsis (Arabidopsis thaliana). The hydraulic conductivity of excised root systems (Lpr) showed a 2-fold variation among accessions. The contribution of aquaporins to water uptake was characterized using as inhibitors mercury, propionic acid, and azide. The aquaporin-dependent and -independent paths of water transport made variable contributions to the total hydraulic conductivity in the different accessions. The distinct suberization patterns observed among accessions were not correlated with their root hydraulic properties. Real-time reverse transcription-polymerase chain reaction revealed, by contrast, a positive overall correlation between Lpr and certain highly expressed PIP transcripts. Root hydraulic responses to salt stress were characterized in a subset of five accessions (Bulhary-1, Catania-1, Columbia-0, Dijon-M, and Monte-Tosso-0 [Mr-0]). Lpr was down-regulated in all accessions except Mr-0. In Mr-0 and Catania-1, cortical cell hydraulic conductivity was unresponsive to salt, whereas it was down-regulated in the three other accessions. By contrast, the five accessions showed qualitatively similar aquaporin transcriptional profiles in response to salt. The overall work provides clues on how hydraulic regulation allows plant adaptation to salt stress. It also shows that a wide range of root hydraulic profiles, as previously reported in various species, can be observed in a single model species. This work paves the way for a quantitative genetics analysis of root hydraulics.
Comparative Effectiveness of Mixed Reality-Based Virtual Environments in Collaborative Design
Authors: Wang Xiangyu , Dunston Phillip S.
Published: January 2011

This paper presents two mixed-reality (MR) environments that provide alternative mediums that allow groups of people to share the same work and communication space in face-to-face and remote manners. Two experiments were executed to test the capabilities of the two MR systems in realistic environment and collaborative tasks against prevalent methods. Results indicated that the two MR systems significantly reduced the performance time for the collaborative design error detection task. Results also indicated less mental effort for the MR systems, suggesting that some of the mental interpretation for the error detection task is offloaded to the MR systems.
Does diurnal temperature variability affect growth in juvenile Atlantic salmon Salmo salar?
Authors: Imholt C. , Malcolm I. A. , Bacon P. J. , Gibbins C. N. , Soulsby C. , Miles M. , Fryer R. J.
Published: January 2011

This study investigated the effects of diurnal temperature variability (>7° C) on the growth of 1+ year Atlantic salmon Salmo salar. Experimental manipulation of water temperature was used to simulate: (1) constant and (2) naturally varying thermal regimes with similar daily mean values. Data from two replicates of four treatments (two thermal and two feeding regimes) were collected over 6 months corresponding to the main spring to summer growth period. Fish growth was assessed at fortnightly intervals. Small but significant differences in mean fork length (LF) and mass were observed between temperature treatments, with smaller, lighter fish under the variable temperature regime. The effects of temperature regime on growth were independent of food ration. At termination of the experiment, the median LF and mass of fish exposed to the variable temperature regime were estimated, respectively, to be 2· 6 and 8· 0% less than those under the constant regime. Given the relatively small differences in growth attributable to variable temperature regime in these experiments, it is suggested that mean daily temperatures are adequate to inform juvenile growth models for field‐based studies.
Early infection of discus Symphysodon aequifasciatus altricial larvae by Sciadicleithrum variabilum (Monogenea)
Authors: ÖNal U. , ÇElik İ. , Tokşen E. , Sepil A. , ÇAydan E.
Published: January 2011

The occurrence of Sciadicleithrum variabilum on the gills of discus Symphysodon aequifasciatus larvae 7 days after hatching is reported for the first time. This suggests that altricial larvae are susceptible to Monogenea following gill differentiation and before complete yolk resorption.
Using data from an encounter sampler to model fish dispersal
Authors: Obaza A. , DeAngelis D. L. , Trexler J. C.
Published: January 2011

A method to estimate speed of free‐ranging fishes using a passive sampling device is described and illustrated with data from the Everglades, U.S.A. Catch per unit effort (CPUE) from minnow traps embedded in drift fences was treated as an encounter rate and used to estimate speed, when combined with an independent estimate of density obtained by use of throw traps that enclose 1 m2 of marsh habitat. Underwater video was used to evaluate capture efficiency and species‐specific bias of minnow traps and two sampling studies were used to estimate trap saturation and diel‐movement patterns; these results were used to optimize sampling and derive correction factors to adjust species‐specific encounter rates for bias and capture efficiency. Sailfin mollies Poecilia latipinna displayed a high frequency of escape from traps, whereas eastern mosquitofish Gambusia holbrooki were most likely to avoid a trap once they encountered it; dollar sunfish Lepomis marginatus were least likely to avoid the trap once they encountered it or to escape once they were captured. Length of sampling and time of day affected CPUE; fishes generally had a very low retention rate over a 24 h sample time and only the Everglades pygmy sunfish Elassoma evergladei were commonly captured at night. Dispersal speed of fishes in the Florida Everglades, U.S.A., was shown to vary seasonally and among species, ranging from 0· 05 to 0· 15 m s−1 for small poeciliids and fundulids to 0· 1 to 1· 8 m s−1 for L. marginatus. Speed was generally highest late in the wet season and lowest in the dry season, possibly tied to dispersal behaviours linked to finding and remaining in dry‐season refuges. These speed estimates can be used to estimate the diffusive movement rate, which is commonly employed in spatial ecological models.
An alternative approach for the measurement of trimethylamine oxide in body fluid samples of elasmobranchs
Authors: Anderson W. G. , Allen P. J.
Published: January 2011

The present study examined an alternative approach to the measurement of trimethylamine oxide (TMAO) in body fluids of an elasmobranch, the little skate Leucoraja erinacea. Using ion exchange chromatography, the values measured compared favourably with values from the same samples measured using a recognized and frequently published spectrophotometric technique.
The frequency and management of asparaginase‐related thrombosis in paediatric and adult patients with acute lymphoblastic leukaemia treated on Dana‐Farber Cancer Institute consortium protocols
Authors: Grace Rachael F. , Dahlberg Suzanne E. , Neuberg Donna , Sallan Stephen E. , Connors Jean M. , Neufeld Ellis J. , DeAngelo Daniel J. , Silverman Lewis B.
Published: January 2011

The optimal management of asparaginase‐associated thrombotic complications is not well‐defined. We report the features, management and outcome of paediatric (ages 0–18 years) and adult (18–50 years) patients with acute lymphoblastic leukaemia (ALL) with asparaginase‐related venous thromboembolic events (VTE) treated at Dana‐Farber Cancer Institute on clinical trials for newly diagnosed ALL between 1991–2008. Of 548 patients, 43 (8%) had VTE, including 27/501 (5%) paediatric and 16/47 (34%) adult patients. Sinus venous thrombosis occurred in 1·6% of patients. Age was the only significant predictor of VTE, with those aged >30 years at very high risk (VTE rate 42%). 74% of patients received low molecular weight heparin after VTE. Complications of anticoagulation included epistaxis (9%), bruising (2%) and, in two adult patients, major bleeding. Thirty patients (70%) ultimately received at least 85% of the intended doses of asparaginase. 33% of patients experienced recurrent VTE (paediatric 17% vs. adults 47%, P = 0·07). The 48‐month event‐free survival for patients with VTE was 85 ± 6% compared with 88 ± 2% for those without VTE (P = 0·36). This study confirms that, after VTE, asparaginase can be restarted with closely monitored anticoagulation after imaging demonstrates clot stabilization or improvement. With this management strategy, a history of VTE does not appear to adversely impact prognosis.
How I manage haematology patients with septic shock
Authors: Cohen Jon , Drage Stephen
Published: January 2011

Patients with a variety of haematological conditions are at risk of infection and its most serious complication: septic shock. Mortality for septic shock remains high and especially so in patients with haematological malignancy and following bone marrow transplantation. However, advances in the treatment of severe sepsis have improved mortality rates even though evidence for the management of severe sepsis in haematology patients is limited. Wherever possible this review will concentrate on evidence directly applicable to haematology patients but inevitably will have to extrapolate evidence from other patient groups. The Surviving Sepsis Guidelines 2008 provide information on best practice in the management of patients with severe sepsis and septic shock and are broadly applicable though not specific to haematology patients. This review summarizes a practical approach to the management of severe sepsis in haematology patients and highlights areas of research which may bring new treatments in the future. The review is limited to the management and initial resuscitation of septic shock in adult haematology patients and will not address the detailed intensive care management of these patients or the management of severe sepsis in children.
Elimination of blood group antigens: hope and reality
Authors: Bagnis Claude , Chiaroni Jacques , Bailly Pascal
Published: January 2011

In transfusion medicine, three major issues, i.e. heterogeneity of human blood groups, dependence of blood supply on donation, and shortage of some phenotypes, oblige clinicians to juggle with available biological material to avoid or limit post‐transfusion reactions. This ‘fact of life’ has given impetus to a 30‐year‐old quest to achieve interchangeability of blood products between donors and recipients by eliminating blood group antigens.
Compositional trends of fisheries in the River Ganges, India
Authors: MONTAÑA C. G. , CHOUDHARY S. K. , DEY S. , WINEMILLER K. O.
Published: January 2011

Abstract  Monthly surveys of local fisheries from five principal landing sites on the River Ganges at Bhagalpur, India, were conducted from 2001 to 2007. Fishes of a range of sizes with mostly periodic‐type life‐history strategies, including many catfishes and carps, dominated the catch. Average annual yield (total mean monthly catch in units of biomass) was highly variable but trended downward during the study. Statistical ordination revealed associations between assemblage composition and hydrological seasons. Overall yields in this reach of the River Ganges tended to be greatest when the annual flood pulse was sustained longer. Patterns of average stock yields and inter‐annual variability of yields were associated with species life‐history strategies, with the most abundant and least variable species having periodic‐type strategies of seasonal spawning, high fecundity, small eggs and no parental care. Although not appearing to have declined precipitously during the study, many stocks in this stretch of the River Ganges, including those of the largest and most valuable species, nonetheless seemed to remain below historical yield levels because of multiple impacts, including chronic intense fishing and other anthropogenic impacts.
Monitoring species abundance and distribution at the landscape scale
Authors: Jones Julia P. G.
Published: January 2011

1. The abundance and distribution of a species are affected by processes which operate at multiple scales. Large‐scale dynamics are increasingly recognized in conservation responses such as metapopulation management, transfrontier protected areas and softening the agricultural matrix. Landscape‐scale monitoring is needed both to inform and judge their efficacy. In this Special Profile we address some of the challenges presented by monitoring at the landscape scale, how models of species distribution can be used to inform policy, and we discuss how monitoring at the global‐scale could be approached.

2. Collecting data over a large area is inherently costly, so methods which can provide robust information at low‐cost are particularly valuable. We present two papers which test low‐cost approaches against more data‐hungry methods (indices of abundance vs. direct density estimates, and species distribution models built from presence‐only vs. presence/absence data).

3. Occupancy modelling is a useful approach for landscape‐scale monitoring due to the relatively low‐cost of collecting detection/non‐detection data. We discuss challenges, such as non‐random sampling locations and periodical unavailability for detection, in using detection/non‐detection data for monitoring species distribution. Such data can also provide estimates of abundance and we show how existing models have been modified to allow the abundance of multiple species to be estimated simultaneously.

4. Models of species distribution can be used to project likely future scenarios and thus inform conservation planning where distributions are likely to change because of climate change or changing disturbance patterns. We also discuss how an optimization framework can be used to make efficient management decisions for invasive species management in the light of imperfect information.

5. Synthesis and applications. Monitoring is needed for many purposes including auditing past management decisions and informing future choices. Much monitoring data are collected at the site scale, although management authorities increasingly recognize landscape‐scale dynamics. Recent global targets for conservation require monitoring which can report trends at the global‐scale. Integrating data collected at a variety of scales to draw robust inference at the scale required is a challenge which deserves more attention from applied ecologists.
Habitat‐specific demography across dune fixation stages in a semi‐arid sandland: understanding the expansion, stabilization and decline of a dominant shrub
Authors: Li Shou‐Li , Yu Fei‐Hai , Werger Marinus J. A. , Dong Ming , Zuidema Pieter A.
Published: January 2011

1. Maintaining viable populations in different habitats requires physiological, morphological and demographic adaptations of plants. In sandland environments, plants experience substantial variation in growing conditions during the dune fixation process, with high sand mobility in early stages and denser vegetation cover in later stages.

2. We studied the changes in demography of a dominant shrub, Artemisia ordosica, at three stages of dune fixation: semi‐fixed dunes, fixed dunes and fixed dunes covered with microbiotic crust. Demographic data from three annual censuses were used to parameterize integral projection models (IPMs) to conduct comparative demographic analyses.

3. Plant growth and reproduction decreased strongly as dunes became more fixed. Shrinkage in plant height occurred very frequently, particularly in the fixed dunes with microbiotic crust. Population growth rate (λ) declined substantially with dune fixation: from rapid expansion in semi‐fixed dunes (λ = 1.35–1.09) to moderate decline in fixed dunes with microbiotic crust (λ = 0.94–0.89).

4. Elasticity analysis revealed that survival was a key vital rate for population growth in all habitats. Growth and fecundity were of higher importance in the semi‐fixed habitat than in the other two habitats where shrinkage became an important factor determining λ. Seedlings and small plants were critical for population growth in semi‐fixed dunes, whereas moderate to large‐sized plants were most important in the other habitats.

5. Results of life table response experiments showed that the observed strong decrease in λ during dune fixation was mainly caused by reduction in fecundity, but with additional and considerable contributions from reduced plant growth and increased occurrence of shrinkage. Thus, populations in semi‐fixed dunes are able to expand rapidly due to a much higher fecundity compared to those in other habitats.

6. Synthesis. Artemisia ordosica adopts different life history strategies along the dune fixation process. Fast expansion in semi‐fixed dunes is enabled by high seed production and effective recruitment, while populations at later dune fixation stages are maintained through frequent plant shrinkage. Integral projection models are highly appropriate tools for analysing such life history changes as they are based on statistical comparisons of vital rates across habitats.
Invasion of Norway spruce diversifies the fire regime in boreal European forests
Authors: Ohlson Mikael , Brown Kendrick J. , Birks H. John B. , Grytnes John‐Arvid , Hörnberg Greger , Niklasson Mats , Seppä Heikki , Bradshaw Richard H. W.
Published: January 2011

1. Global wildfire activity and biomass burning have varied substantially during the Holocene in both time and space. At the regional to continental scale, macroclimate is considered to be the predominant control regulating wildfire activity. By contrast, the role of forest tree composition is often considered as a subsidiary factor in studies addressing temporal variation in regional wildfire activity.

2. Here, we assemble a spatially comprehensive data set of 75 macroscopic charcoal records that reflect local burning and forest landscapes that are spread over a substantial part of the European boreal forest, spanning both oceanic and continental climates.

3. We show that the late‐Holocene invasion of Norway spruce Picea abies, a new forest dominant in northern Europe, significantly reduced wildfire activity, thus altering forest disturbance dynamics at a subcontinental scale.

4. Synthesis. Our findings show that a biotic change in the local forest ecosystem altered the fire regime largely independent of regional climate change, illustrating that forest composition is an important parameter that must be considered when modelling future fire risk and carbon dynamics in boreal forests.
Childhood obesity and co‐morbid problems: effects of Epstein's family‐based behavioural treatment in an Icelandic sample
Authors: Gunnarsdottir Thrudur , Njardvik Urdur , Olafsdottir Anna S. , Craighead Linda , Bjarnason Ragnar
Published: January 2011

Objective  This study assessed the effects of Epstein's family‐based behavioural treatment in a clinical sample of obese children in Iceland. Also, it explored whether co‐morbid concerns affect treatment outcome.

Methods  Eighty‐four obese children [mean body‐mass‐index standard‐deviation‐scores (BMI‐SDS) = 3.11, aged 7.5–13.6 years] and a participating parent initiated treatment in response to a school‐based screening. Sixty‐one families completed treatment and were followed for 1 year post treatment. Measurements included height, weight, reports of psychological well‐being (Strengths and Difficulties Questionnaire, Multidimensional Anxiety Scale for Children, Children's Depression Inventory, Piers–Harris Self Concept Scale, Social Skills Rating System) and academic competencies.

Results  Among treatment completers a large effect size was obtained for change in BMI‐SDS during treatment (mean difference = −0.40, SD = 0.29). Psychological well‐being improved and treatment effects were maintained at 1‐year follow‐up. At baseline, 69% of the children presented with one or more co‐morbid concerns. Children who scored above cut‐off for concern on parent‐reported hyperactivity (Strengths and Difficulties Questionnaire subscale T‐score ≥ 65) reduced their BMI‐SDS less during treatment than children with lower hyperactivity scores whereas children who scored in the clinical range for social anxiety (Multidimensional Anxiety Scale for Children subscale T‐score ≥ 65) reduced their BMI‐SDS significantly more than children with lower social anxiety scores. The social anxiety effect was still present at 1‐year follow‐up, but not the hyperactivity effect (P > 0.05). No differential response was shown for children with higher depression scores, lower self‐concept or low academic competencies.

Conclusions  Epstein's family‐based behavioural treatment produced promising effects in both the short and the longer term in a clinical sample of Icelandic children with substantial rates of co‐morbid concerns. Co‐morbid problems affect outcome and tailoring treatment to address co‐morbid concerns might improve outcomes for certain subgroups.
Evaluating the degree of knowledge on oral cancer among general practitioners and dentists in Qazvin
Authors: Borhan‐Mojabi Katayoun , Moradi Aboozar , Yazdabadi Anosha
Published: January 2011

Rationale, aims and objectives  Despite easy accessibility of the oral cavity to examination most oral cancers are only identified at advanced stages. The aim of this study was to assess the knowledge of general doctors and dentists on oral cancer in Qazvin to form the basis of development of undergraduate and postgraduate education programmes for early detection and prevention of oral cancer.

Methods  A cross‐sectional questionnaire‐based study was performed on general medical practitioners and general dental practitioners in 2009. Analysis was performed using spss software.

Results  The mean knowledge score of all participants was at moderate level and there was no significant difference between the two groups. There was a significant correlation between knowledge score and age, time from graduation and the interval since the last refresher course on oral cancer (P < 0.05). Smoking (78%) and alcohol consumption (34.9%) were noted as the two major risk factors by the entire population study. Approximately 80.9% of participants identified the tongue as among the most common sites for oral cancers while only 25.7% identified the floor of the mouth and 28.3% the lips as other areas of occurrence.

Conclusion  This study demonstrated an inadequate level of knowledge on oral cancers in both groups. Additional training in universities as well as continuing educational programmes on prevention and early detection of oral cancers is recommended.