bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal variability in area burned for the province of Ontario, Canada, during the past 200 years inferred from tree rings
Authors: Girardin Martin P. , Tardif Jacques , Flannigan Mike D.
Published: September 2006

Area burned variability in the province of Ontario, Canada, was inferred from 25 tree ring width chronologies covering A.D. 1781–1982 and distributed largely across the Boreal Shield. The area burned estimates account for 39.5% of the variance in the actual area burned recorded from 1917 to 1981 and were verified using a split sample calibration‐verification scheme. The reconstruction showed that a positive trend in area burned from circa 1970–1981 was preceded by three decades during which area burned was amongst the lowest during the past 200 years. The area burned exhibited a trend toward increasing variance during the past century, recently reaching magnitudes similar to those seen prior to 1850. Signal analyses further identified the presence of two prominent periodic components in area burned that related to decade‐to‐decade variations. This will help to place the recent increase in area burned in a context relative to the long‐term history of the province.
Evidence for locally derived, ultramafic intracrater materials in Amazonis Planitia, Mars
Authors: Schneider Romy D. , Hamilton Victoria E.
Published: September 2006

We studied a dark, intracrater feature in Amazonis Planitia using visible, thermal, and spectral data from the Mars Global Surveyor (MGS) Thermal Emission Spectrometer (TES), MGS Mars Orbiter Camera (MOC), and 2001 Mars Odyssey Thermal Emission Imaging System (ODY THEMIS) instruments. Visible and thermal data indicate that there are heterogeneities within the dark feature at meter to kilometer scales and suggest that it represents eroded terrain containing inactive ripple‐like bed forms (possibly armored or indurated) as well as loose, possibly actively saltating, sediment. In addition, part of the dark intracrater material may be covered with dust, either as an optically thin (few microns thick) layer or as thicker discontinuous patches. The thermal properties of the dark material are consistent with a mixture of sand, rock, and bedrock, whereas the rest of the crater floor has thermal characteristics of fine (∼35 μm) particulates. Spectral data indicate that the crater floor is covered by a layer of dust that is spectrally and compositionally similar to the globally homogenized surface dust in other high‐albedo regions on Mars. The mineralogy of the dark materials is mafic (dominated modally by pyroxene and olivine); however, unlike other lithologies common in low‐albedo regions (i.e., surface types I and II), its derived bulk chemistry indicates that it is an ultramafic lithology with the lowest silica content detected on Mars to date. Sheet silicates and glasses are not identified above detection limits, and as such, the materials do not display evidence for significant chemical weathering. The geomorphology and visible distribution of the dark, intracrater materials combined with the lack of an obvious source in the region outside the crater suggest they are the product of erosion of a local source.
A comparative study of detrital mineral and bedrock age‐elevation methods for estimating erosion rates
Authors: Huntington Katharine W. , Hodges Kip V.
Published: September 2006

The age‐elevation pattern of thermochronologic data has been used for many years to estimate apparent erosion rates in orogenic settings. Recently, it has been suggested that thermochronologic data for detrital minerals from active river system sediments can be used as an effective proxy for bedrock age‐elevation distributions, serving as an alternative method for erosion rate studies. This “detrital mineral thermochronology” (DMT) method is easier, faster, and more cost‐effective than the traditional bedrock approach, and provides additional information about transients in topography and sediment delivery that may vary on diurnal to millennial timescales for a particular sampling site. However, two variants of the DMT method have been described in the literature, and they can yield very different erosion rate estimates. We tested both of these approaches against the traditional age‐elevation method using detrital and bedrock 40Ar/39Ar muscovite data sets from a single river catchment in the Annapurna Range, Nepal Himalaya. A nominal erosion rate estimate of ∼0.6 km/Myr for the 5.0–2.5 Ma period was calculated from the bedrock data, presented here for the first time. This result agrees with the ∼0.7 km/Myr (maximum) estimate from the detrital data set, which was derived from the DMT variant that emphasizes the range of single‐grain ages for a detrital sample, in this case, 11–2.5 Ma. However, the other DMT variant, which emphasizes the mean of the sample age distribution, yields an erosion rate estimate of ∼2.3 km/Myr. The simplest explanation for this discrepancy is that erosion rate increased significantly after ∼2.5 Ma, a scenario that is supported by apatite fission track data from the catchment.
Understanding shallow magma emplacement at volcanoes: Orthogonal feeder dikes during the 2002–2003 Stromboli (Italy) eruption
Authors: Acocella V. , Neri M. , Scarlato P.
Published: September 2006

Understanding how shallow magma is emplaced within volcanoes is crucial for hazard assessment. The 2002–2003 Stromboli eruption provides the opportunity to investigate shallow magma emplacement resulting from orthogonal feeder dikes and its possible effects. Stromboli erupted in 2002–2003, when effusive activity replaced Strombolian activity. On December 28, a NE‐SW fissure propagated from the lava‐filled northernmost summit crater. On December 29, a NW‐SE fissure propagated north of the craters, feeding NW‐SE aligned vents. On December 30, this area collapsed, reaching the sea and generating a tsunami. In mid February 2003, the NW‐SE fissure became inactive, while the NE‐SW effusive fissure continued until July. A model for shallow magma emplacement is proposed. The lateral propagation of a NE‐SW dike from the northernmost crater was triggered. Below, a NW‐SE dike, propagating from the magma‐filled NE tip of the NE‐SW elongated conduit, fed the NW‐SE aligned vents. In February, the conduit periphery became solidified, freezing the NW‐SE dike, and the transport of magma was limited to the central part, focusing its rise below the craters. This fed the NE‐SW fissure until the supply decreased further (July), returning to the ordinary level sustaining Strombolian activity. Orthogonal dike emplacement followed the trajectories of the maximum (gravitational) stress σ1, partly controlled by the irregular topography of the uppermost edifice. The emplacement of orthogonal dikes in a limited area is feasible at non‐perfectly conical active volcanoes, where the maximum gravitational stress may show variations from a purely radial path.
Transient D″ discontinuity revealed by seismic migration
Authors: Chambers K. , Woodhouse J. H.
Published: September 2006

The D″ region beneath North Central Asia is investigated using a weighted migration based on the Generalised Radon Transform. We image complex structure including a D″ discontinuity with variable topography and velocity contrast. We also present observations of an area where the D″ reflector stops. Using synthetic data sets generated for distributions of point scatterers we show that this is not due to deficiencies in the data coverage, but requires that the D″ discontinuity is not a continuous surface. The termination of the discontinuity appears to restrict it to a region high seismic velocity. This could be interpreted as confirmatory evidence for the existence and behaviour of the post‐perovskite phase transformation. However, compositional variations may also play a role.
A dynamical attractor governs beach response to storms
Authors: Plant Nathaniel G. , Todd Holland K. , Holman Rob A.
Published: September 2006

Sandbars are ubiquitous, yet not well understood beach features that change their position and shape in response to changing wave conditions. We propose and test a simple empirical model consisting of two coupled linear differential equations that represents bar dynamics in terms of wave forcing and two other state variables: (1) the mean cross‐shore bar position and (2) the alongshore variability about that mean. Model coefficients are constrained by fitting to a 2‐month data set, and the modeled behavior is examined with a stability analysis. The system is found to be stable and, hence, predictable. Rates of change of the bar position and its alongshore variability are found to be significantly coupled, such that prediction of one variable requires information about the other. The system response time is slow compared to the storm wave cycle such that the bar response continually orbits time‐varying equilibrium points in the state variable phase plane.
Wave front active control by a digital-signal-processor-driven deformable membrane mirror
Authors: Bonora S. , Capraro I. , Poletto L. , Romanin M. , Trestino C. , Villoresi P.
Published: September 2006

The correction of the beam wave front degradations, introduced by optical aberrations or by medium inhomogeneities, has a widespread relevance in several areas of optics. We describe here an adaptive optics system aimed to the optical optimization of the beam wave front in few seconds using an electrostatic deformable mirror and a controller based on a fixed-point digital signal processor. The correction system acts the wave front modification by a deformable mirror in closed loop with a genetic algorithm. We also studied the dynamics of the mirror for its use in beam wander correction due to atmospheric turbulence in free space classical and quantum optical communications.
Optics for five-dimensional measurement for correction of vertical displacement error due to attitude of floating body in superconducting magnetic levitation system
Authors: Shiota Fuyuhiko , Morokuma Tadashi
Published: September 2006

An improved optical system for five-dimensional measurement has been developed for the correction of vertical displacement error due to the attitude change of a superconducting floating body that shows five degrees of freedom besides a vertical displacement of 10mm. The available solid angle for the optical measurement is extremely limited because of the cryogenic laser interferometer sharing the optical window of a vacuum chamber in addition to the basic structure of the cryogenic vessel for liquid helium. The aim of the design was to develop a more practical as well as better optical system compared with the prototype system. Various artifices were built into this optical system and the result shows a satisfactory performance and easy operation overcoming the extremely severe spatial difficulty in the levitation system. Although the system described here is specifically designed for our magnetic levitation system, the concept and each artifice will be applicable to the optical measurement system for an object in a high-vacuum chamber and/or cryogenic vessel where the available solid angle for an optical path is extremely limited.
Quantum Monte Carlo calculations of the dissociation energy of the water dimer
Authors: Benedek N. A. , Snook I. K. , Towler M. D. , Needs R. J.
Published: September 2006

We report diffusion quantum Monte Carlo (DMC) calculations of the equilibrium dissociation energy De of the water dimer. The dissociation energy measured experimentally, D0, can be estimated from De by adding a correction for vibrational effects. Using the measured dissociation energy and the modern value of the vibrational energy Mas et al., [J. Chem. Phys. 113, 6687 (2000)] leads to De=5.00±0.7kcalmol−1, although the result Curtiss et al., [J. Chem. Phys. 71, 2703 (1979)] De=5.44±0.7kcalmol−1, which uses an earlier estimate of the vibrational energy, has been widely quoted. High-level coupled cluster calculations Klopper et al., [Phys. Chem. Chem. Phys. 2, 2227 (2000)] have yielded De=5.02±0.05kcalmol−1. In an attempt to shed new light on this old problem, we have performed all-electron DMC calculations on the water monomer and dimer using Slater-Jastrow wave functions with both Hartree-Fock approximation (HF) and B3LYP density functional theory single-particle orbitals. We obtain equilibrium dissociation energies for the dimer of 5.02±0.18kcalmol−1 (HF orbitals) and 5.21±0.18kcalmol−1 (B3LYP orbitals), in good agreement with the coupled cluster results.
Multipass laser mass spectrometer with extreme jet-cooled pulsed gas
Authors: Kirihara Naotoshi , Takahashi Kenji , Kitada Norifumi , Tanaka Mizuho , Suzuki Yasuo
Published: September 2006

We have developed a photon accumulated laser mass spectrometer that enables us to identify isomers of polychlorinated dibenzo-p-dioxin and polychlorinated dibenzofuran. This system is comprised of a high temperature (230°C) pulsed gas injector (PGI), multimirror multipath system (MMS), and the conventional time-of-flight mass spectrometer. The PGI induces the formation of a choked supersonic jet gas pulse that cools down to a temperature to restrain fragmentation and reduces vibrational and rotational thermal noises. The results suggest that the excited lifetime numbers and fragment dynamics of these species change completely with jet cooling of molecules. The MMS enhances the soft ionization efficiency (by a factor of 1000 over a single path system) through photon accumulation by extending the irradiation duration (to about 40ns) and volume, and it further minimizes fragmentation by carefully controlling the laser intensity distribution within the ionization volume. For the typical isomer 2,3,4,7,8-pentachlorodibenzofuran, the system achieved a detection threshold (S/N ratio=3) of 410ppq (equivalent to 4.4ng∕Nm3).
Self-consistent Ornstein-Zernike approximation for molecules with soft cores
Authors: Høye J. S. , Reiner A.
Published: September 2006

The self-consistent Ornstein-Zernike approximation (SCOZA) is an accurate liquid state theory. So far it has been tied to interactions composed of hard core repulsion and long-range attraction, whereas real molecules have soft core repulsion at short distances. In the present work, this is taken into account through the introduction of an effective hard core with a diameter that depends upon temperature only. It is found that the contribution to the configurational internal energy due to the repulsive reference fluid is of prime importance and must be included in the thermodynamic self-consistency requirement on which SCOZA is based. An approximate but accurate evaluation of this contribution relies on the virial theorem to gauge the amplitude of the pair distribution function close to the molecular surface. Finally, the SCOZA equation is transformed by which the problem is reformulated in terms of the usual SCOZA with fixed hard core reference system and temperature-dependent interaction.
Prediction of the Phase Behaviour of Hydrogen-Bonded Polymer Blends
Authors: Coleman Michael M. , Painter Paul C.
Published: September 2006

In the early 1990s your authors believed that they had essentially solved the problem of predicting the phase behaviour of hydrogen-bonded polymer blends. A text devoted to this subject, Specific Interactions and the Miscibility of Polymer Blends, was published and we thought that it was now time to look around for something else to do. This was before a colleague, Boris Veytsman, pointed out that there was a flaw in our derivation of the free energy of mixing equation. It has taken us some 15 years to correct the theory and match the predictions of the phase behaviour of hydrogen-bonded blends that we presented in our 1991 book. So we have come full circle. The subject has become far more complicated, but at the same time far more interesting. Along the way we have discovered that the phase behaviour of hydrogen-bonded polymer blends can be successfully predicted using equilibrium constants determined from appropriate low molecular weight analogues, if chain connectivity effects such as intermolecular screening and functional group accessibility are included.
Disulfide isomerization switches tissue factor from coagulation to cell signaling
Authors: Ahamed Jasimuddin , Versteeg Henri H. , Kerver Marjolein , Chen Vivien M. , Mueller Barbara M. , Hogg Philip J. , Ruf Wolfram
Published: September 2006

Cell-surface tissue factor (TF) binds the serine protease factor VIIa to activate coagulation or, alternatively, to trigger signaling through the G protein-coupled, protease-activated receptor 2 (PAR2) relevant to inflammation and angiogenesis. Here we demonstrate that TF·VIIa-mediated coagulation and cell signaling involve distinct cellular pools of TF. The surface-accessible, extracellular Cys
186
–Cys
209
disulfide bond of TF is critical for coagulation, and protein disulfide isomerase (PDI) disables coagulation by targeting this disulfide. A TF mutant (TF C209A) with an unpaired Cys
186
retains TF·VIIa signaling activity, and it has reduced affinity for VIIa, a characteristic of signaling TF on cells with constitutive TF expression. We further show that PDI suppresses TF coagulant activity in a nitric oxide-dependent pathway, linking the regulation of TF thrombogenicity to oxidative stress in the vasculature. Furthermore, a unique monoclonal antibody recognizes only the noncoagulant, cryptic conformation of TF. This antibody inhibits formation of the TF·PAR2 complex and TF·VIIa signaling, but it does not prevent coagulation activation. These experiments delineate an upstream regulatory mechanism that controls TF function, and they provide initial evidence that TF·VIIa signaling can be specifically inhibited with minimal effects on coagulation.
Safety in stereotypes? The impact of gender and ‘race’ on young people's perceptions of their post‐compulsory education and labour market opportunities
Authors: Beck Vanessa , Fuller Alison , Unwin Lorna
Published: September 2006

This article examines the impact of gender and ‘race’ on young people's perceptions of the educational and labour market opportunities available to them after they complete their compulsory schooling in England. Its findings are based on a study of the views of girls and boys about the government‐supported ‘Apprenticeships’ programme, which, because it reflects labour market conditions, is highly gendered and also segregated by ethnicity. The research shows that young people receive very little practical information and guidance about the consequences of pursuing particular occupational pathways, and are not engaged in any formal opportunities to debate gender and ethnic stereotyping as related to the labour market. This is particularly worrying for females, who populate apprenticeships in sectors with lower completion rates and levels of pay, and which create less opportunity for progression. In addition, the research reveals that young people from non‐White backgrounds are more reliant on ‘official’ sources of guidance (as opposed to friends and families) for their labour market knowledge. The article argues that, because good‐quality apprenticeships can provide a strong platform for lifelong learning and career progression, young people need much more detailed information about how to compare a work‐based pathway with full‐time education. At the same time, they also need to understand that apprenticeships (and jobs more generally) in some sectors may result in very limited opportunities for career advancement.
The new skills agenda: increased lifelong learning or new sites of inequality?
Authors: Appleby Yvon , Bathmaker Ann Marie
Published: September 2006

The last five years have seen a radical transformation in adult education in England with a concentrated emphasis on national basic skills provision. This was prompted initially by a government response to low levels of literacy in the British adult population, identified by an influential international survey, showing unfavourable comparisons with other European countries. The response to the disclosure that seven million adults in England were not functionally literate saw the creation in 2001 of a national basic skills strategy in England entitled Skills for Life. It is a far‐reaching strategy creating a new infrastructure to support adult basic skills learning opportunities over a seven‐year period. It also created the entitlement to free basic skills learning opportunities, as a cornerstone to creating national economic competitiveness and social cohesion. Such an entitlement could be interpreted as a commitment to providing wider access to foundation skills for adults who had previously missed out, as part of a lifelong learning agenda. However, a critical reading of the policy texts, and recent funding priorities, show the strategy rooted more in a response to what is perceived as the skills demands of a knowledge economy for global competitiveness than to issues of social inclusion and increased opportunities for lifelong learning. The result of this may well be the creation of new sites of inequality that affect older women and adult ESOL (English for Speakers of Other Languages) learners disproportionately, the very people that are identified as being needed to fill skill gaps in the economy.
The double-stranded RNA-induced apoptosis pathway is involved in the cytopathogenicity of cytopathogenic Bovine viral diarrhea virus
Authors: Yamane Daisuke , Kato Kentaro , Tohya Yukinobu , Akashi Hiroomi
Published: September 2006

Bovine viral diarrhea virus (BVDV), which is classified in the genus Pestivirus, family Flaviviridae, can be divided into two biotypes according to its ability to induce a cytopathic effect in tissue culture cells. The mechanisms through which cytopathogenic (cp) BVDV induces cell death and non-cytopathogenic (ncp) BVDV causes persistent infection without producing cell death remain unclear. Here, it was found that the overexpression of four apoptosis-related cellular mRNAs in cells infected with cpBVDV could also be caused by synthetic dsRNA. In fact, it was found that the amount of dsRNA produced by cpBVDV considerably exceeded the amount yielded by ncpBVDV. To evaluate the possible involvement of dsRNA in the induction of apoptosis, this study examined whether RNAi-mediated depletion of two dsRNA-reactive cellular factors, dsRNA-dependent protein kinase and 2′,5′-oligoadenylate synthetase 1, resulted in the prevention of cpBVDV-induced apoptosis. Although the induction of apoptosis was reduced after the suppression of either factor alone, the simultaneous silencing of both factors resulted in an almost complete inhibition of apoptosis without affecting viral titre. These results showed that dsRNA is the main trigger of apoptosis in cpBVDV-infected cells and that the cytopathogenicity of BVDV depends on the yield potential of dsRNA. In contrast, ncpBVDV yielded minimal levels of dsRNA, thereby establishing a persistent infection without inducing apoptosis. This report supports the significance of viral dsRNA as a trigger of innate immune responses.
Analysis of Epstein–Barr virus latent gene expression in endemic Burkitt's lymphoma and nasopharyngeal carcinoma tumour cells by using quantitative real-time PCR assays
Authors: Bell Andrew I. , Groves Katherine , Kelly Gemma L. , Croom-Carter Debbie , Hui Edwin , Chan Anthony T. C. , Rickinson Alan B.
Published: September 2006

Studies of Epstein–Barr virus (EBV)-positive cell lines have identified several forms of virus latency, but the patterns of virus gene expression in EBV-positive tumour cells appear more variable. However, it is unclear to what extent these differences merely reflect the increased sensitivities of different detection methods. Here, the design and validation of novel real-time RT-PCR assays to quantify relative levels of EBV transcripts are described. When the new assays were used to screen a collection of endemic Burkitt's lymphoma tumours, abundant Qp-driven EBNA1 expression was found, whereas the other latent transcripts (with the exception of LMP2A) were either absent or detectable only at trace levels. Analysis of 12 nasopharyngeal carcinoma biopsies revealed significant levels of EBNA1 and LMP2A transcripts in almost every case but, in contrast to previous reports, LMP1 expression was undetectable. These new quantitative assays may help to provide a clearer picture of EBV gene expression in tumour material.
Application of an immunocapillary electrophoresis assay to the detection of abnormal prion protein in brain, spleen and blood specimens from patients with variant Creutzfeldt–Jakob disease
Authors: Lourenco Paula C. , Schmerr Mary Jo , MacGregor Ian , Will Robert G. , Ironside James W. , Head Mark W.
Published: September 2006

Sensitive and specific detection of abnormal prion protein in blood could provide a diagnostic test or screening assay for animal and human prion diseases. Here, the application of an immunocapillary electrophoresis (ICE) method developed for sheep scrapie to brain, spleen and blood from patients with Creutzfeldt–Jakob disease (CJD) is described. The assay involves organic-solvent extraction, a competitive immunoassay using fluorescently labelled synthetic prion protein peptides and polyclonal antibodies specific for those sequences, and analysis by capillary electrophoresis using laser-induced fluorescence detection. The test was evaluated by using clinical blood specimens from patients with variant (n=5) or sporadic (n=4) CJD and patients initially suspected of having CJD who were given an alternative diagnosis (n=6). In this context, the ICE assay was specific, but incompletely sensitive (55 %). The method was unable to detect abnormal prion protein in variant CJD brain or spleen reference materials due to its loss during the extraction process.
Herpes simplex virus type 1 ICP0 localizes in the stromal layer of infected rabbit corneas and resides predominantly in the cytoplasm and/or perinuclear region of rabbit keratocytes
Authors: Morishige Naoyuki , Jester James V. , Naito Julie , Osorio Nelson , Wahlert Andrew , Jones Clinton , Everett Roger D. , Wechsler Steven L. , Perng Guey Chuen
Published: September 2006

Herpes stromal keratitis (HSK) results from the reactivation of herpes simplex virus type-1 (HSV-1) in the cornea. The subsequent corneal inflammation and neovascularization may lead to scarring and visual loss. The cellular and molecular mechanisms underlying HSK remain unknown. The presence of stromal HSV-1 viral proteins or antigens in the HSK cornea remains a subject of debate. It was recently reported that HSV-1 ICP0 rapidly diffuses out of infected rabbit corneas. To investigate further the presence of HSV-1 ICP0 in the infected cornea, particularly in the corneal stroma, ex vivo confocal microscopy was used to scan rabbit corneas infected with the virus ICP0–EYFP, an HSV-1 derivative (strain 17+) that expresses ICP0 fused to the enhanced yellow fluorescent protein (EYFP). These results demonstrate that ICP0 is expressed in the corneal epithelium and stromal cells (keratocytes) of infected rabbit corneas throughout acute infection. Furthermore, expression of ICP0–EYFP appears localized to punctate, granular deposits within stromal keratocytes, showing both a cytoplasmic and perinuclear localization. These findings provide new data demonstrating that anterior corneal keratocytes become infected and express ICP0 during acute HSV-1 infection.
Peptide display on Potato virus X: molecular features of the coat protein-fused peptide affecting cell-to-cell and phloem movement of chimeric virus particles
Authors: Lico Chiara , Capuano Floriana , Renzone Giovanni , Donini Marcello , Marusic Carla , Scaloni Andrea , Benvenuto Eugenio , Baschieri Selene
Published: September 2006

The potexvirusPotato virus X(PVX) can be modified genetically to generate chimeric virus particles (CVPs) carrying heterologous peptides fused to coat protein (CP) subunits. A spontaneous PVX mutant expressing a truncated, but functional, form of the CP has been isolated. With the aim of exploiting this virus to display peptides useful for vaccine formulations, two novel viral expression vectors based on pPVX201 (bearing the wild-type PVX genome) were constructed encoding the truncated CP. Both vectors were able to produce infectious virus particlesin plantaand were used to insert a panel of sequences encoding peptides of biopharmaceutical interest as N-terminal fusions to the truncatedcpgene. The analysis of infection progression induced by the different constructs enabled identification of two important structural features of the fused peptide, namely tryptophan content and isoelectric point, critically affecting the formation of PVX CVPs and virus movement through the plant. These results are discussed in view of the rising interest in engineered plant viruses for development of peptide-based epitope vaccines.
Cell target genes of Epstein–Barr virus transcription factor EBNA-2: induction of the p55α regulatory subunit of PI3-kinase and its role in survival of EREB2.5 cells
Authors: Spender Lindsay C. , Lucchesi Walter , Bodelon Gustavo , Bilancio Antonio , Karstegl Claudio Elgueta , Asano Tomoichiro , Dittrich-Breiholz Oliver , Kracht Michael , Vanhaesebroeck Bart , Farrell Paul J.
Published: September 2006

Microarray analysis covering most of the annotated RNAs in the human genome identified a panel of genes induced by the Epstein–Barr virus (EBV) EBNA-2 transcription factor in the EREB2.5 human B-lymphoblastoid cell line without the need for any intermediate protein synthesis. Previous data indicating that PIK3R1 RNA (theαregulatory subunit of PI3-kinase) was induced were confirmed, but it is now shown that it is the p55αregulatory subunit that is induced. Several EBV-immortalized lymphoblastoid cell lines were shown to express p55α. Expression of PI3-kinase p85 regulatory and p110 catalytic subunits was not regulated by EBNA-2. Proliferation of EREB2.5 lymphoblastoid cells was inhibited by RNAi knock-down of p55αprotein expression, loss of p55αbeing accompanied by an increase in apoptosis. p55αis thus a functional target of EBNA2 in EREB2.5 cells and the specific regulation of p55αby EBV will provide an opportunity to investigate the physiological function of p55αin this human cell line.
Isolation and Purification of Tetrahymena Nuclei
Authors: Sweet Melody T. , Allis C. David
Published: September 2006

INTRODUCTION

The procedures described below allow the isolation of nuclei from all stages of the Tetrahymena life cycle in high yield with a high degree of purity. This method gives highly purified populations of both micronuclei and macronuclei.
Antibody Addition to Drosophila Specimens and Detection Using Enzyme-Linked Reagents
Authors: Harlow Ed , Lane David
Published: September 2006

INTRODUCTION

Enzyme-linked reagents give excellent sensitivity and use a simple light microscope for detection. A range of enzymes is available, but for staining in situ, horseradish peroxidase will suit most needs. Diaminobenzidine (DAB) is one of the most sensitive substrates for horseradish peroxidase. It yields an intense brown product that is insoluble in both water and alcohol. It can be made more sensitive by adding metal salts such as cobalt or nickel to the substrate solution. The reaction products are slate gray to black, and they are stable in both water and alcohol. DAB/metal staining is compatible with a wide range of common histological stains.
Lysing Tissue-Culture Cells for Immunoprecipitation
Authors: Harlow Ed , Lane David
Published: September 2006

INTRODUCTION

For cells grown in tissue culture, the most useful method of lysis is treating with detergents, as described in this protocol. Non-ionic detergents, such as NP-40, solubilize the plasma and intracellular membranes, break many weak intermolecular bonds, and solubilize most of the commonly studied protein antigens. RIPA lysis buffer, which contains non-ionic detergents mixed with ionic detergents, may be used as a more rigorous extraction buffer to release all but the insoluble proteins of the cell and to break most weak noncovalent interactions. The resulting lysate is ready for preclearing.
Genome-Wide Analysis of Protein-Protein Interactions Using a Two-Hybrid Array: Amplification of ORFs
Authors: Hazbun Tony R. , Miller John P.
Published: September 2006

INTRODUCTION

The two-hybrid array method described in this protocol was applied to ~6000 open reading frames (ORFs) of the Saccharomyces cerevisiae genome, but it could be applied to any collection of ORFs, including the genome complements of other organisms or smaller sets of functionally related ORFs. The method relies on a spatially ordered set of yeast strains, each expressing a different protein fused to the Gal4 activation domain (AD). A mating strategy is used in which a strain expressing a protein fused to the Gal4 DNA-binding domain (BD) (the bait) is mated to each array strain (the prey). Construction of the array is achieved using polymerase chain reaction (PCR) and recombinational cloning in conjunction with high-throughput transformation of the appropriate yeast strain. To capitalize on the advantageous use of the mating procedure, the array strains must be haploid yeast. This allows the introduction of the Gal4 BD and AD fusions into the same diploid cell by mating of the haploid array strains with a haploid strain of the opposite mating type containing the BD. Diploid yeast strains expressing both of these protein fusions are selected using auxotrophic media, and subsequently, two-hybrid positives are selected for the activation of a reporter gene that allows their growth on the appropriate media. This protocol describes the first step in constructing an array: amplification of the predicted ORFs that are to be included in the array. Gene-specific primers containing vector-specific flanking sequences that facilitate recombinational cloning are used to amplify each ORF. A secondary amplification can be used to extend the length of the homologous vector sequence flanking the ORF.
Efficacy and safety of melphalan, arsenic trioxide and ascorbic acid combination therapy in patients with relapsed or refractory multiple myeloma: a prospective, multicentre, phase II, single‐arm study
Authors: Berenson James R. , Boccia Ralph , Siegel David , Bozdech Marek , Bessudo Alberto , Stadtmauer Edward , Talisman Pomeroy J. , Steis Ronald , Flam Marshall , Lutzky Jose , Jilani Syed , Volk Joseph , Wong Siu‐Fun , Moss Robert , Patel Ravi , Ferretti Delina , Russell Kit , Louie Robert , Yeh Howard S. , Swift Regina A.
Published: September 2006

We assessed the safety and efficacy of melphalan, arsenic trioxide (ATO) and ascorbic acid (AA) (MAC) combination therapy for patients with multiple myeloma (MM) who failed more than two different prior regimens. Patients received melphalan (0·1 mg/kg p.o.), ATO (0·25 mg/kg i.v.) and AA (1 g i.v) on days 1–4 of week 1, ATO and AA twice weekly during weeks 2–5 and no treatment during week 6 of cycle 1; during cycles 2–6, the schedule remained the same except ATO and AA were given twice weekly in week 1. Objective responses occurred in 31 of 65 (48%) patients, including two complete, 15 partial and 14 minor responses. Median progression‐free survival and overall survival were 7 and 19 months respectively. Twenty‐two patients had elevated serum creatinine levels (SCr) at baseline, and 18 of 22 (82%) showed decreased SCr levels during treatment. Specific grade 3/4 haematological (3%) or cardiac adverse events occurred infrequently. Frequent grade 3/4 non‐haematological adverse events included fever/chills (15%), pain (8%) and fatigue (6%). This steroid‐free regimen was effective and well tolerated in this heavily pretreated group. These results indicate that the MAC regimen is a new therapeutic option for patients with relapsed or refractory MM.
Congenital hypothyroidism caused by new mutations in the thyroid oxidase 2 (THOX2) gene
Authors: Pfarr Nicole , Korsch Eckhard , Kaspers Stefan , Herbst Antje , Stach Armin , Zimmer Claudia , Pohlenz Joachim
Published: September 2006

Objective  Congenital primary hypothyroidism (CH) occurs in one of 4000 births and in 20% of the cases CH is due to a defect in thyroid hormonogenesis. Candidate genes were examined to determine the precise aetiology of suspected dyshormonogenesis in CH.

Design  The genes that code for thyroid peroxidase (TPO), pendrin (PDS), sodium iodide symporter (NIS) and thyroid oxidase 2 (THOX2) were sequenced directly from genomic DNA.

Patients  Two girls found to have CH in the neonatal screening programme and suspected of having thyroid dyshormonogenesis were investigated to identify their molecular defect.

Results  Patient A had a novel heterozygous 1 bp insertion in the THOX2 gene (ins602g). This insertion results in a frameshift that predicts a premature stop at codon 300. Analysis of cDNA, transcribed from lymphocyte RNA, showed that this mutation causes skipping of exon 5, resulting in a frameshift and a premature stop at codon 254. The euthyroid mother was also a heterozygous carrier of the mutation whereas the father was homozygous for the wild‐type THOX2 gene. In patient B, compound heterozygous mutations (ins602g→fsX300 and D506N) were identified. D506N was present in one allele of the clinically unaffected mother and in a brother, whereas the euthyroid father was heterozygous for ins602g. Sixty normal individuals did not harbour the mutations. Sequencing of the TPO, PDS and NIS genes revealed no mutations.

Conclusions  The identified THOX2 mutations, which have not been described previously, are the probable causes of CH in the patients. Mutations in the THOX2 gene should be considered as the molecular cause of CH in young patients with thyroid dyshormonogenesis.
Thermoregulatory trade‐offs result from vegetation removal by a harvester ant
Authors: BUCY AVE MARIE , BREED MICHAEL D.
Published: September 2006

Abstract 1. Analyses of ecological trade‐offs help to explain how organisms balance competing demands. Harvester ants (Pogonomyrmex occidentalis), are conspicuous residents of shortgrass prairie in western North America; worker P. occidentalis actively clear all vegetation from the immediate vicinity of their large gravel mounds. This study is based on the prediction that vegetation clearing yields a thermal trade‐off by increasing soil temperatures; during cool periods the resulting increase in soil temperature opens new time windows for activity, while during hot periods the soil temperature is more likely to exceed the maximum thermal tolerance for this species. To test the hypothesis that daily and seasonal trade‐offs in ant activity result from vegetation removal, the effects of experimentally applied shade on activity patterns were measured.

2. Harvester ant activity correlated highly with ground temperature; experimental shading of ant mounds shifted daily activity patterns by lowering ground temperature. Shading in the morning significantly delayed the onset of ant activity by preventing solar warming of the mound. In contrast, mid‐day experimental shading prevented elevation of ground temperatures to above 50 °C and allowed ants to remain active when lethally high temperatures would normally force them inside the mound.

3. A model derived from field data predicted surface ground temperature (and therefore ant activity) based on air temperature and solar radiation, under conditions of sun and shade. For each of six seasons modelled, shade removal yielded a net gain of activity time. These results indicate that vegetation removal by harvester ants produces an advantageous thermoregulatory effect by helping to maximise activity time.
An evaluation of renal inpatient meals against Renal Nutrition Group standards
Authors: Rai E. M. , Hartley G. H.
Published: September 2006

Background The Renal Nutrition Group (RNG) of the British Dietetic Association has developed standards for the nutritional composition of meals provided to renal patients in hospital. However, no data are available as to whether these are achievable. The purpose of this study was to determine whether renal inpatient meals can meet the standards set by the RNG.

Method A prospective 10‐day weighed food analysis of hospital meals provided to renal patients was undertaken. Two sample meals were analysed at each mealtime to include (1) the most energy dense choice and (2) the most frequent patient choice (FPC).

Results Energy dense choice meals achieved the standard for protein provision on 90% of days, but provided too little energy on 100% of days (for men) and on 30% of days (for women). Although daily standards for potassium were met on 70% of days, those for sodium and phosphate were exceeded. FPC meals met the daily standards for potassium, sodium and phosphate on at least 80% of days, but provided too little protein on 40% of days and too little energy on 100% of days (for men and women).

Conclusion The majority of hospital meals fail to meet the RNG standards. Problems exist in providing sufficient energy and protein whilst restricting sodium, potassium and phosphate.
Home delivery of dietary products in inherited metabolic disorders reduces prescription and dispensing errors
Authors: MacDonald A. , Manji N. , Evans S. , Davies P. , Daly A. , Hendriksz C. , Chakrapani A.
Published: September 2006

In the UK, for patients with inherited metabolic disorders (IMD) the traditional system for acquiring essential dietary products [patient prompted prescriptions generated by a medical general practitioner (GP) and dispensed by a chemist] is problematic.

Objective  To investigate the efficacy of a home delivery service (HDS) for essential dietary products (EDP) (i.e. protein substitutes, milk replacements, energy and vitamin and mineral supplements) for subjects with IMD, particularly examining any prescription and dispensing errors, metabolic control and consumer satisfaction.

Methods  A prospective, controlled, home delivery trial for EDP was conducted in patients with IMD for 12 months. Sixty‐two patients with IMD [50 with phenylketonuria (PKU); 12 with other IMD: aged 6 months–30 years] were recruited. Thirty subjects used a monthly HDS (Homeward: Nutricia) to receive EDP, 32 remained on the traditional system. Each month, the HDS checked home stock levels of EDP, obtained their prescriptions directly from GP's, and then delivered them to the subjects’ homes. An independent researcher completed monthly telephone interviews with patients/parents about any EDP prescription errors or delay in receipt.

Results  Incorrect protein substitute was dispensed once by the HDS compared with nine subjects who had 12 errors in the control group (P = 0.01); incorrect flavours of protein substitute were dispensed to the home delivery group once compared with eight subjects getting 11 errors via the chemist (P = 0.03). The HDS delayed delivery of protein substitute for one subject on three occasions compared with 39 occasions in 16 subjects via the chemist (P = 0.001). In patients with PKU, plasma phenylalanine control deteriorated in the control group (P < 0.05) but not in the HDS group.

Conclusions  The long‐term use of a HDS for EDP in IMD is safer, effective and more reliable than conventional systems.
Who should receive a statin these days? Lessons from recent clinical trials
Authors: SHEPHERD J.
Published: September 2006

The 3‐hydroxy‐3‐methylglutaryl coenzyme A reductase inhibitors or statins are the most successful cardiovascular drugs of all time. By interrupting cholesterol synthesis in the liver, they activate hepatocyte low‐density lipoprotein (LDL) receptors and produce consistent and predictable reductions in circulating LDL cholesterol with resulting reproducible improvements in cardiovascular risk by retarding or even regressing the march of atherosclerosis in all major arterial trees (coronary, cerebral and peripheral). Clinical trials have demonstrated their capacity not only to extend life, but also to improve its quality by retarding the progression of diabetes mellitus and chronic renal disease and by enhancing central and peripheral blood flow.

They are amongst the most extensively investigated pharmaceutical agents in current clinical use. In cardiovascular end‐point trials they have proven ability to help prevent that first and all important myocardial infarction and to reduce the likelihood of a recurrence in those who do succumb. They are equally effective in men and women of all ages and at all levels of cardiovascular risk, whether caused by hypercholesterolaemia, hypertension, cigarette smoking, diabetes mellitus or the metabolic syndrome. In addition, they improve the outlook of patients with familial hypercholesterolaemia whose LDL receptor function is deficient or defective; and all of this comes at minimal risk to the recipient. Their most important potential side effect is myopathy, which on very rare occasions may lead to rhabdomyolysis. Clinical experience shows that myopathic symptoms with creatine kinase levels raised to more than 10 times the upper limit of normal is seen in <0.01% of recipients and progression to fatal rhabdomyolysis because of renal failure has been recorded in only 0.15 cases per million prescriptions. Liver function abnormalities are also, rarely, seen. Again, the frequency of raised aspartate or alanine aminotransferase to more than three times the normal limit is encountered in no more than 1–2% of all treated patients and is completely reversible upon withdrawal of treatment. Progression to hepatitis or liver failure does not occur.

This constellation of benefits with little side effect penalty has resulted in the comparison of statins with antibiotics in the global battle against cardiovascular disease.
Long‐Term Voluntary Exercise and the Mouse Hypothalamic‐Pituitary‐Adrenocortical Axis: Impact of Concurrent Treatment with the Antidepressant Drug Tianeptine
Authors: Droste S. K. , Schweizer M. C. , Ulbricht S. , Reul J. M. H. M.
Published: September 2006

We investigated whether voluntary exercise and concurrent antidepressant treatment (tianeptine; 20 mg/kg/day; 4 weeks) exert synergistic effects on the mouse hypothalamic‐pituitary‐adrenocortical (HPA) axis. Animals had access to a running wheel, were treated with the antidepressant, or received both conditions combined. Control mice received no running wheel and no drug treatment. Exercise resulted in asymmetric changes in the adrenal glands. Whereas sedentary mice had larger left adrenals than right ones, this situation was abolished in exercising animals, mainly due to enlargement of the right adrenal cortex. However, antidepressant treatment alone was ineffective whereas the combination of antidepressant treatment and exercise resulted in an enlargement of both adrenal cortices. In these respective conditions, the levels of tyrosine hydroxylase (TH) mRNA expression in the left and right adrenal medullas varied greatly in parallel to the changes observed in the adrenal cortex sizes. TH mRNA expression in the locus coeruleus of exercising mice was significantly increased irrespective of concomitant tianeptine treatment. Corticotrophin‐releasing factor mRNA levels in the hypothalamic paraventricular nucleus were decreased after voluntary exercise but were unaffected by tianeptine. Exercise, particularly in combination with tianeptine treatment, resulted in decreased early morning baseline plasma levels of corticosterone. If animals were exposed to novelty (i.e. a mild psychological stressor), a decreased response in plasma corticosterone levels was observed in the exercising mice. By contrast, after restraint, a mixed physical and psychological stressor, exercising mice showed an enhanced response in plasma corticosterone compared to the controls; a response which was even further boosted in exercising mice concomitantly treated with tianeptine. Under either condition, plasma adrenocorticotrophic hormone levels were not different between groups. Thus, voluntary exercise impacts substantially on HPA axis regulation. Concurrent tianeptine treatment results in synergistic actions, mainly at the adrenal level, affecting both its structure and function.