bluuebunny/crossref_metadata_2025 huggingface dataset:
A pattern approach to software inspection process improvement
Authors: Harjumaa Lasse
Published: December 2005

Concrete guidelines are often helpful when planning software process improvement. Small companies, in particular, need detailed and unambiguous instructions detailing what process areas to improve, and how to achieve the improvement. This article introduces a set of patterns to direct the improvement of the software inspection process. The pattern approach has been applied, since it has been used very successfully for knowledge‐sharing purposes and other areas of software engineering. The approach involves an evaluation of the inspection process capability, setting an overall goal for the improvement and updating the process according to pre‐defined actions. Experiments with initial patterns show that the method provides a feasible and quick way of making inspections more effective. Using patterns may also be beneficial when launching more wide‐ranging SPI activities, as companies can run preliminary trials of the improvement process on a smaller scale first. Copyright © 2005 John Wiley & Sons, Ltd.
Intention‐driven modeling for flexible workflow applications
Authors: Nurcan Selmin , Edme Marc‐Henri
Published: December 2005

During the early 1990s, workflow technologies were the only ones to offer a transversal integration capacity to the enterprise applications, thus allowing the representation and the enactment of business processes. However, the formalisms developed for workflow specifications were almost systematically activity oriented. Consequently, the resulting process definitions have the advantage to be easily transformable in executable code, but the disadvantage of being prescriptive and rigid. Recent works underline the needs in term of flexible and adaptive workflows, whose execution can evolve according to situations that cannot always be prescribed. In fact, a flexible representation of business processes is an asset to maintain the fit between business processes and their supporting systems in an evolving environment. This article proposes a conceptual framework for an intention‐driven modeling of flexible workflow applications. The purpose of the underlying modeling formalism is to define an integration/orchestration for islands of business process chunks and their support systems in order to create and to maintain the fit between them. The modeling framework offers the ability to represent in the same business process definition the well‐structured process chunks as well as the ill‐structured orad hocones. Copyright © 2005 John Wiley & Sons, Ltd.
Efficacy of mu‐opioid agonists in the treatment of evoked neuropathic pain: Systematic review of randomized controlled trials
Authors: Eisenberg Elon , McNicol Ewan D. , Carr Daniel B.
Published: December 2005

Several reviews of randomized controlled trials (RCTs) have shown the efficacy of mu‐opioids in reducing spontaneous neuropathic pain (NP). However, relatively little is known about their specific efficacy for evoked pain, which is a significant problem for many patients with NP. The present systematic review assesses the efficacy of opioid agonists for the treatment of evoked NP based upon published RCTs. We searched articles in any language using the MEDLINE database (1966 to December 2004), the Cochrane Central Register of Controlled Trials (4th quarter, 2004) and the reference lists of retrieved papers, employing search terms for RCTs, opioids and NP. Only RCTs in which opioid agonists were given to treat NP of any etiology, and evoked pain was assessed were included. Data were extracted by two independent investigators. Nine articles met inclusion criteria and were classified as short‐term (less than 24 h; n = 7) or intermediate‐term trials (4 weeks; n = 2). Although the scarcity of retrieved data precluded formal meta‐analysis of short‐term trials, we found that the intensity of dynamic mechanical allodynia was significantly attenuated by opioids relative to placebo in all studies. In contrast, no consistent effects on the magnitude of static allodynia, the threshold for mechanical allodynia or the threshold or magnitude of heat allodynia were found. The threshold and magnitude of cold‐induced allodynia generally responded positively to opioid treatments in patients with peripheral pain syndromes, but not central pain syndromes. Evoked pain was studied in only two intermediate‐term trials, in both of which oxycodone was significantly superior to placebo. The results of the two trials were combinable for a meta‐analysis that showed an overall 24 points difference in endpoint pain intensities between patients given opioids and those treated with placebo (95% CI −33 to −15; p < 0.00001). In conclusion: short‐term studies show that opioids can reduce the intensity of dynamic mechanical allodynia and perhaps of cold allodynia in peripheral NP. Insufficient evidence precludes drawing conclusions regarding the effect of opioids on other forms of evoked NP. A meta‐analysis of intermediate‐term studies demonstrates the efficacy of opioids over placebo for evoked NP. These findings are clinically relevant because dynamic mechanical allodynia and cold allodynia are the most prevalent types of evoked pain in NP.
Laser-driven generation of high-current ion beams using skin-layer
ponderomotive acceleration
Authors: BADZIAK J. , GŁOWACZ S. , JABŁOŃSKI S. , PARYS P. , WOŁOWSKI J. , HORA H.
Published: December 2005

Basic properties of generation of high-current ion beams using the
skin-layer ponderomotive acceleration (S-LPA) mechanism, induced by a
short laser pulse interacting with a solid target are studied. Simplified
scaling laws for the ion energies, the ion current densities, the ion beam
intensities, and the efficiency of ions' production are derived for
the cases of subrelativistic and relativistic laser-plasma interactions.
The results of the time-of-flight measurements performed for both
backward-accelerated ion beams from a massive target and
forward-accelerated beams from a thin foil target irradiated by 1-ps laser
pulse of intensity up to ∼ 1017 W/cm2 are
presented. The ion current densities and the ion beam intensities at the
source obtained from these measurements are compared to the ones achieved
in recent short-pulse experiments using the target normal sheath
acceleration (TNSA) mechanism at relativistic (>1019
W/cm2) laser intensities. The possibility of application of
high-current ion beams produced by S-LPA at relativistic intensities for
fast ignition of fusion target is considered. Using the derived scaling
laws for the ion beam parameters, the achievement conditions for ignition
of compressed DT fuel with ion beams driven by ps laser pulses of total
energy ≤ 100 kJ is shown.
Laser-produced blast wave and numerical simulation using the FLASH
code
Authors: FARLEY D.R. , SHIGEMORI K. , AZECHI H.
Published: December 2005

Two-dimensional (2D) FLASH simulations were run with Spitzer-Härm
conductivity on and off in an attempt to simulate a laser-produced blast
wave. Dissociation, ionization, recombination, and radiative cooling were
not included. An initial Gaussian temperature profile with
T0 = 120 eV and spot radius r0 =
25 μm was used assuming 1 μm thickness of the CH disk is ablated
into the background nitrogen gas. Evolution of the blast wave differs
slightly between the cases of Spitzer-Härm on and off, and neither
case matches well with experiment. Due to the high temperatures involved,
a thermal wave should be expected such that the Spitzer-Härm
conductivity on case is more likely. A simulation run with an initial
temperature of ∼ 4 keV might match better with experiment.
Idealized slab plasma approach for the study of warm dense
matter
Authors: NG A. , AO T. , PERROT F. , DHARMA-WARDANA M.W.C. , FOORD M.E.
Published: December 2005

Recently, warm dense matter has emerged as an interdisciplinary field
that draws increasing interest in plasma physics, condensed matter
physics, high pressure science, astrophysics, inertial confinement fusion,
as well as material science under extreme conditions. To allow the study
of well-defined warm dense matter states, we introduced the concept of
idealized slab plasma (ISP) that can be realized in the laboratory via (1)
the isochoric heating of a solid and (2) the propagation of a shock wave
in a solid. The application of this concept provides new means for probing
AC conductivity, equation of state, ionization, and opacity. These
approaches are presented here using results derived from numerical
simulations.
Supershort electron beam from air filled diode at atmospheric
pressure
Authors: TARASENKO V.F. , SHUNAILOV S.A. , SHPAK V.G. , KOSTYRYA I.D.
Published: December 2005

The properties of an electron beam (e-beam) formed in air under
atmospheric pressure are reported. The nanosecond generators RADAN-303
(two devices) and RADAN-220, producing nanosecond voltage pulses with
amplitude of up to 400 kV and subnanosecond rise time were used in the
experiments. It was shown for the first time that the duration of e-beam
current of gas diode behind the foil does not exceed 0.1 ns. The maximum
amplitude of current of a supershort avalanche electron beam (SAEB) behind
the foil was ∼400 A. The data on the influence of various parameters
on e-beam current amplitude measured behind the foil were obtained. An
electron beam with energy less than 60 keV and powerful X-ray radiation
were formed in discharge gap simultaneously with SAEB.
The internationalization of fire protection: in pursuit of municipal networks in Edwardian Birmingham
Authors: EWEN SHANE
Published: December 2005

Through a case study of Birmingham fire brigade, this article examines the plethora of international networking activities undertaken during the late Victorian and early Edwardian period. Birmingham fire brigade, under the control of Alfred Tozer, led British municipal participation in early international fire networks, attending international congresses and exhibitions in Berlin and London, and also visiting continental cities to inspect fire brigades and their appliances. Locating the study firmly within historical debates concerning the embryonic international municipal movement, this article demonstrates that municipal institutions participated in networking activities as part of a policy learning and knowledge-transfer process.
Research in urban history: a review of recent theses
Authors: MILLER CAROLINE L.
Published: December 2005

Researching and producing this review of theses poses many challenges, the least of which is how to produce a meaningful summary of an abstract that already summarizes some 200–400 pages of detailed research, while avoiding sounding clichéd. However, undertaking this review for four years does give one the opportunity to consider the patterns and changes that have emerged. Thus this article will commence with a short review of the sources of theses, their numbers and the themes they had pursued.
Definitional, personal, and mechanical constraints on part of speech annotation performance
Authors: BABARCZY ANNA , CARROLL JOHN , SAMPSON GEOFFREY
Published: December 2005

For one aspect of grammatical annotation, part-of-speech tagging, we investigate experimentally whether the ceiling on accuracy stems from limits to the precision of tag definition or limits to analysts' ability to apply precise definitions, and we examine how analysts' performance is affected by alternative types of semi-automatic support. We find that, even for analysts very well-versed in a part-of-speech tagging scheme, human ability to conform to the scheme is a more serious constraint than precision of scheme definition. We also find that although semi-automatic techniques can greatly increase speed relative to manual tagging, they have little effect on accuracy, either positively (by suggesting valid candidate tags) or negatively (by lending an appearance of authority to incorrect tag assignments). On the other hand, it emerges that there are large differences between individual analysts with respect to usability of particular types of semi-automatic support.
Earthquake fracture energy inferred from kinematic rupture models on extended faults
Authors: Tinti E. , Spudich P. , Cocco M.
Published: December 2005

We estimate fracture energy on extended faults for several recent earthquakes by retrieving dynamic traction evolution at each point on the fault plane from slip history imaged by inverting ground motion waveforms. We define the breakdown work (Wb) as the excess of work over some minimum traction level achieved during slip.Wbis equivalent to "seismological" fracture energy (G) in previous investigations. Our numerical approach uses slip velocity as a boundary condition on the fault. We employ a three‐dimensional finite difference algorithm to compute the dynamic traction evolution in the time domain during the earthquake rupture. We estimateWbby calculating the scalar product between dynamic traction and slip velocity vectors. This approach does not require specifying a constitutive law and assuming dynamic traction to be collinear with slip velocity. If these vectors are not collinear, the inferred breakdown work depends on the initial traction level. We show that breakdown work depends on the square of slip. The spatial distribution of breakdown work in a single earthquake is strongly correlated with the slip distribution. Breakdown work density and its integral over the fault, breakdown energy, scale with seismic moment according to a power law (with exponent 0.59 and 1.18, respectively). Our estimates of breakdown work range between 4 × 105and 2 × 107J/m2for earthquakes having moment magnitudes between 5.6 and 7.2. We also compare our inferred values with geologic surface energies. This comparison might suggest that breakdown work for large earthquakes goes primarily into heat production.
Clues to Martian brines based on halogens in salts from nakhlites and MER samples
Authors: Rao M. N. , Sutton S. R. , McKay D. S. , Dreibus G.
Published: December 2005

Chlorine and Br abundances in fracture‐filling secondary salts in Nakhla veins determined in this study by Synchrotron X‐ray Microprobe (Br) and Electron Microprobe (Cl) techniques compare well to the halogens determined recently by APXS instruments in soils and rock rinds at the Gusev and Meridiani sites. The salts in these Mars rocks arise from Martian brines that have undergone evaporative or freezing concentration. The halogen abundances in these salts are corrected for “dilution effect” (because of mixing with halogen‐poor phases) to obtain their “true” abundances, which seem to be close to the halogen abundances in terrestrial sea brines. Consistent with the petrographic evidence for evaporative salt deposition sequence of carbonate‐sulfate‐halite in nakhlite meteorites, Nakhla veins yield high Br (∼250 ppm) and low Cl/Br ratios (∼10–50), suggesting possible salt deposition from concentrated brines, whereas Lafayette iddingsite, with low Br (11 ppm) and high Cl/Br ratios (∼250–300), indicates salt deposition from dilute brines on Mars. The low Cl/Br ratios (∼20 to 80) in salts from Gusev and Meridiani rock rinds indicate that they presumably originate from concentrated subsurface Martian brines. The high Cl/Br ratio (∼270) in salts deposited by dilute solutions in Lafayette and Adirondack is similar to the chondritic Cl/Br ratio, which seems to characterize the dilute brines on Mars (prior to halite precipitation) including “Early Mars Waters” (Noachian or earlier). Our results seem to be consistent with the Burt‐Knauth model involving density stratification during evaporation/freezing of brine solutions in Martian regolith.
Mineralogy of Martian atmospheric dust inferred from thermal infrared spectra of aerosols
Authors: Hamilton Victoria E. , McSween Harry Y. , Hapke Bruce
Published: December 2005

We have utilized optical constants derived from thermal infrared spectra acquired by the Mariner 9 Infrared Interferometer Spectrometer (M9 IRIS) and Mars Global Surveyor Thermal Emission Spectrometer (MGS TES), during periods of relatively high dust/low water ice opacity, to generate synthetic transmission and emission spectra of the atmospheric dust. Using libraries of transmission and emission spectra of common rock‐forming minerals and their alteration products, we applied a linear deconvolution algorithm to the spectra to model the dust mineralogy. Models of the M9 IRIS transmission data generally are of poor quality, and the mineralogical results of these fits are unlikely to be valid. Fits to the TES transmission spectrum and TES and IRIS emission spectra are of better quality and suggest that the dust mineralogy is dominated by framework silicates (feldspar and/or zeolite) with carbonate, sulfate, pyroxene, and olivine, identified near, but below, generalized detection limits. Evidence for phyllosilicates is not robust. Our results, combined with those from in situ measurements and other visible to infrared spectral studies, suggest that framework silicates (probably feldspar) dominate the dust mineralogy, with lesser amounts of olivine, pyroxene, amorphous material, hematite, and magnetite, and that the dust largely is the product of mechanical weathering of basaltic rocks with minor chemical alteration.
Impact of vegetation on flow routing and sedimentation patterns: Three‐dimensional modeling for a tidal marsh
Authors: Temmerman S. , Bouma T. J. , Govers G. , Wang Z. B. , De Vries M. B. , Herman P. M. J.
Published: December 2005

A three‐dimensional hydrodynamic and sediment transport model was used to study the relative impact of (1) vegetation, (2) micro‐topography, and (3) water level fluctuations on the spatial flow and sedimentation patterns in a tidal marsh landscape during single inundation events. The model incorporates three‐dimensional (3‐D) effects of vegetation on the flow (drag and turbulence). After extensive calibration and validation against field data, the model showed that the 3‐D vegetation structure is determinant for the flow and sedimentation patterns. As long as the water level is below the top of the vegetation, differences in flow resistance between vegetated and unvegetated areas result in faster flow routing over unvegetated areas, so that vegetated areas are flooded from unvegetated areas, with flow directions more or less perpendicular to the vegetation edge. At the vegetation edge, flow velocities are reduced and sediments are rapidly trapped. In contrast, in between vegetated areas, flow velocities are enhanced, resulting in reduced sedimentation or erosion. As the water level overtops the vegetation, the flow paths described above change to more large‐scale sheet flow crossing both vegetated and unvegetated areas. As a result, sedimentation patterns are then spatially more homogeneous. Our results suggest that the presence of a vegetation cover is the key factor controlling the long‐term geomorphic development of tidal marsh landforms, leading to the formation of (1) unvegetated tidal channels and (2) vegetated platforms with a levee‐basin topography in between these channels.
Reduction of ferric haemoproteins by tetrahydropterins: a kinetic study
Authors: Capeillere-Blandin Chantal , Mathieu Delphine , Mansuy Daniel
Published: December 2005

We previously showed that one-electron transfer from tetrahydropterins to iron porphyrins is a very general reaction, with formation of an intermediate cation radical similar to the one detected in NO synthase. As a model reaction, the rates of reduction of eight haemoproteins by diMePH4 (6,7-dimethyltetrahydropterin) have been studied and correlated with their one-electron reduction potentials, Em (FeIII/FeII). On the basis of kinetic data analyses, a bimolecular collisional mechanism is proposed for the electron transfer from diMePH4 to ferrihaemoproteins. Haemoproteins with reduction potentials below −160 mV were shown not to be reduced by diMePH4 to the corresponding ferrohaemoproteins. For haemoproteins with reduction potentials more positive than −160 mV, such as chloroperoxidase, cytochrome b5, methaemoglobin and cytochrome c, there was a good correlation between the second-order reduction rate constant and the redox potential, Em (FeIII/FeII):The rate of reduction of cytochrome c by BH4 [(6R)-5,6,7,8-tetrahydrobiopterin] was determined to be similar to that of the reduction of cytochrome c by diMePH4. These results confirm the role of tetrahydropterins as one-electron donors to FeIII porphyrins.
Intracellular colocalization and interaction of IGF-binding protein-2 with the cyclin-dependent kinase inhibitor p21CIP1/WAF1 during growth inhibition
Authors: Terrien Xavier , Bonvin Elise , Corroyer Sophie , Tabary Olivier , Clement Annick , Henrion Caude Alexandra
Published: December 2005

It is presently unknown whether any member of the IGFBP (insulin-like growth factor binding protein) family directly participates in the control of cell proliferation. We have previously documented that induction of IGFBP-2 was associated with inhibition of DNA synthesis in lung alveolar epithelial cells. In the present study, we investigated the relationship between IGFBP-2 and the cell cycle inhibitor p21CIP1/WAF1 further. We used serum deprivation to inhibit the proliferation of MLE (mouse lung epithelial)-12 cells, and characterized the spatial localization of IGFBP-2. We found that growth inhibition, which was supported by the strong induction of p21CIP1/WAF1, was correlated with increased secretion of IGFBP-2 and, unexpectedly, with its increased localization in the nucleus and particularly in the cytoplasm. By coimmunoprecipitation, we discovered that IGFBP-2 is capable of binding to p21CIP1/WAF1. Interaction between these two proteins was further supported by colocalization of the proteins within growth-arrested cells, as visualized by confocal microscopy. Furthermore, this interaction increased with the duration of the stress, but was suppressed when proliferation was restimulated by the addition of serum. The recombinant expression of GFP (green fluorescent protein)-tagged IGFBP-2 in transfected MLE-12 cells demonstrated its ability to bind specifically to p21CIP1/WAF1. Taken together, these results provide a link between IGFBP-2 and p21CIP1/WAF1 in the regulation of alveolar lung cell proliferation.
Distinct domains of the sodium channel β3-subunit modulate channel-gating kinetics and subcellular location
Authors: Yu Esther J. , Ko Seong-Hoon , Lenkowski Paul W. , Pance Alena , Patel Manoj K. , Jackson Antony P.
Published: December 2005

Electrical excitability in neurons depends on the expression and activity of voltage-gated sodium channels in the neuronal plasma membrane. The ion-conducting α-subunit of the channel is associated with auxiliary β-subunits of which there are four known types. In the present study, we describe the first detailed structure/function analysis of the β3-subunit. We correlate the effect of point mutations and deletions in β3 with the functional properties of the sodium channel and its membrane-targeting behaviour. We show that the extracellular domain influences sodium channel gating properties, but is not required for the delivery of β3 to the plasma membrane when expressed with the α-subunit. In contrast, the intracellular domain is essential for correct subunit targeting. Our results reveal the crucial importance of the Cys21–Cys96 disulphide bond in maintaining the functionally correct β3 structure and establish a role for a second putative disulphide bond (Cys2–Cys24) in modulating channel inactivation kinetics. Surprisingly, our results imply that the wild-type β3 molecule can traverse the secretory pathway independently of the α-subunit.
Regulation of ERK1 gene expression by coactivator proteins
Authors: Chu Beanca Y. , Tran Kim , Ku Tony K. S. , Crowe David L.
Published: December 2005

RARs (retinoic acid receptors) mediate the effect of their ligand RA (retinoic acid) on gene expression. We previously showed that RA inhibited cellular proliferation in part by decreasing expression of the mitogen activated protein kinase ERK1 (extracellular signal regulated kinase 1). However, the mechanism by which RA regulates ERK1 expression is largely uncharacterized. The present study characterizes coactivator-mediated regulation of RA target gene expression by analysing ERK1 promoter activation. CBP (CREB-binding protein) and PCAF (p300/CBP associated factor) are transcriptional coactivators that interact with nuclear hormone receptors such as RARs. CBP and PCAF differentially regulated ERK1 expression in stable clones. CBP clones expressed higher ERK1 protein levels, proliferated faster in culture and were resistant to RA-mediated growth inhibition. PCAF clones expressed lower levels of ERK1 protein and cells grew more slowly than controls. CBP and PCAF regulation of the ERK1 promoter was dependent on two Sp1 (specificity protein 1) sites located between −86 and −115 bp. Immunoprecipitation and yeast two-hybrid analysis revealed that PCAF interacted with Sp1 via CBP. A putative p53 binding site at −360 bp functioned as a major repressor of ERK1 promoter activity even in the absence of exogenous p53 expression. CBP and PCAF occupancy of the proximal ERK1 promoter was dramatically decreased by RA treatment. PCAF mediated inhibition of ERK1 expression was due to decreased stability of the kinase mRNA. We conclude that CBP and PCAF coactivators mediate ERK1 gene expression at both the transcriptional and post-transcriptional level.
Specific role for p85/p110β in GTP-binding-protein-mediated activation of Akt
Authors: Kubo Hiroshi , Hazeki Kaoru , Takasuga Shunsuke , Hazeki Osamu
Published: December 2005

We prepared CHO (Chinese hamster ovary) cells expressing both IR (insulin receptor) and A1R (A1 adenosine receptor). Treatment of the cells with insulin or PIA [N6-(2-phenylisopropyl)adenosine], a specific A1R agonist increased Akt activity in the cells in a PI3K- (phosphoinositide 3-kinase) dependent manner. Transfection of p110β into the cells augmented the action of PIA with little effect on insulin. Introduction of a pH1 vector producing shRNA (short hairpin RNA) that targets p110β abolished PIA-induced Akt activation. By contrast, an shRNA probe targeting p110α did not impair the effects of PIA. The effect of PIA in p110α-deficient cells was attenuated effectively by both Δp85 and βARK-CT (β-adrenergic receptor kinase-C-terminal peptide). A Δp85-derived protein possessing point mutations in its two SH2 domains did not impair PIA action. These results suggest that tyrosine-phosphorylated proteins and Gβγ (βγ subunits of GTP-binding protein) are necessary for the specific function of p110β in intact cells. The p110β-middle (middle part of p110β) may play an important role in signal reception from GPCRs (GTP-binding-protein-coupled receptor), because transfection of the middle part impaired PIA sensitivity.
The in situ observation of the temperature and pressure stability of recombinant Aspergillus aculeatus pectin methylesterase with Fourier transform IR spectroscopy reveals an unusual pressure stability of β-helices
Authors: Dirix Carolien , Duvetter Thomas , Loey Ann Van , Hendrickx Marc , Heremans Karel
Published: December 2005

The stability of recombinant Aspergillus aculeatus PME (pectin methylesterase), an enzyme with high β-helix content, was studied as a function of pressure and temperature. The conformational stability was monitored using FTIR (Fourier transform IR) spectroscopy whereas the functional enzyme stability was monitored by inactivation studies. Protein unfolding followed by amorphous aggregation, which makes the process irreversible, was observed at temperatures above 50 °C. This could be correlated to the irreversible enzyme inactivation observed at that temperature. Hydrostatic pressure greater than 1 GPa was necessary to induce changes in the enzyme's secondary structure. No enzyme inactivation was observed at up to 700 MPa. Pressure increased PME stability towards thermal denaturation. At 200 MPa, temperatures above 60 °C were necessary to cause significant PME unfolding and loss of activity. These results may be relevant for an understanding of the extreme stability of amyloid fibrils for which β-helices have been proposed as a structural element.
An AU-rich stem–loop structure is a critical feature of the perinuclear localization signal of c-mycmRNA
Authors: Chabanon Hervé , Mickleburgh Ian , Burtle Brian , Pedder Christopher , Hesketh John
Published: December 2005

In eukaryotic cells, several mRNAs including those of c-myc and c-fos are localized to the perinuclear cytoplasm and associated with the cytoskeleton. The localization element of c-myc mRNA is present within its 3′UTR (3′-untranslated region) but the precise nature of this signal has remained unidentified. Chemical/enzymatic cleavage with RNases (ribonucleases) and lead have identified single-stranded and double-stranded regions in RNA transcripts of nucleotides 194–280 of the c-myc 3′UTR. Combined with computer predicted structure these results indicate that this region folds so that part of it forms a stem-loop structure. A mutation, that has been previously shown to prevent localization, leads to a different secondary RNA structure in this region as indicated by altered cleavage patterns. Competitive gel-retardation assays, using labelled transcripts corresponding to nucleotides 205–280 of c-myc 3′UTR, and fibroblast extracts revealed that the stem-loop region was sufficient for RNA–protein complex formation. In situ hybridization studies in cells transfected with reporter constructs, in which all or parts of the region corresponding to this stem-loop were linked to β-globin, indicated that this region was sufficient for localization and that deletion of the nucleotides corresponding to the proposed upper-stem or terminal loop prevented localization. Our hypothesis is that an AU-rich stem-loop structure within nt 222–267 in the c-myc 3′UTR forms the perinuclear localization signal. Bioinformatic analysis suggests that this signal shares features with 3′UTRs of other localized mRNAs and that these features may represent a conserved form of signal in mRNA localization mechanisms.
Induction of apoptosis by lipophilic activators of CTP:phosphocholine cytidylyltransferase α (CCTα)
Authors: Lagace Thomas A. , Ridgway Neale D.
Published: December 2005

Farnesol (FOH) inhibits the CDP-choline pathway for PtdCho (phosphatidylcholine) synthesis, an activity that is involved in subsequent induction of apoptosis. Interestingly, the rate-limiting enzyme in this pathway, CCTα (CTP:phosphocholine cytidylyltransferase α), is rapidly activated, cleaved by caspases and exported from the nucleus during FOH-induced apoptosis. The purpose of the present study was to determine how CCTα activity and PtdCho synthesis contributed to induction of apoptosis by FOH and oleyl alcohol. Contrary to previous reports, we show that the initial effect of FOH and oleyl alcohol was a rapid (10–30 min) and transient activation of PtdCho synthesis. During this period, the mass of DAG (diacylglycerol) decreased by 40%, indicating that subsequent CDP-choline accumulation and inhibition of PtdCho synthesis could be due to substrate depletion. At later time points (>1 h), FOH and oleyl alcohol promoted caspase cleavage and nuclear export of CCTα, which was prevented by treatment with oleate or DiC8 (dioctanoylglycerol). Protection from FOH-induced apoptosis required CCTα activity and PtdCho synthesis since (i) DiC8 and oleate restored PtdCho synthesis, but not endogenous DAG levels, and (ii) partial resistance was conferred by stable overexpression of CCTα and increased PtdCho synthesis in CCTα-deficient MT58 cells. These results show that DAG depletion by FOH or oleyl alcohol could be involved in inhibition of PtdCho synthesis. However, decreased DAG was not sufficient to induce apoptosis provided nuclear CCTα and PtdCho syntheses were sustained.
Tetravalent single-chain avidin: from subunits to protein domains via circularly permuted avidins
Authors: Nordlund Henri R. , Hytönen Vesa P. , Hörhä Jarno , Määttä Juha A. E. , White Daniel J. , Halling Katrin , Porkka Eevaleena J. , Slotte J. Peter , Laitinen Olli H. , Kulomaa Markku S.
Published: December 2005

scAvd (single-chain avidin, where two dcAvd are joined in a single polypeptide chain), having four biotin-binding domains, was constructed by fusion of topologically modified avidin units. scAvd showed similar biotin binding and thermal stability properties as chicken avidin. The DNA construct encoding scAvd contains four circularly permuted avidin domains, plus short linkers connecting the four domains into a single polypeptide chain. In contrast with wild-type avidin, which contains four identical avidin monomers, scAvd enables each one of the four avidin domains to be independently modified by protein engineering. Therefore the scAvd scaffold can be used to construct spatially and stoichiometrically defined pseudotetrameric avidin molecules showing different domain characteristics. In addition, unmodified scAvd could be used as a fusion partner, since it provides a unique non-oligomeric structure, which is fully functional with four high-affinity biotin-binding sites. Furthermore, the subunit-to-domain strategy described in the present study could be applied to other proteins and protein complexes, facilitating the development of sophisticated protein tools for applications in nanotechnology and life sciences.
Analysis of hepatic gene transcription in mice expressing insulin-insensitive GSK3
Authors: Lipina Christopher , Huang Xu , Finlay David , J McManus Edward , R. Alessi Dario , Sutherland Calum
Published: December 2005

GSK3 (glycogen synthase kinase-3) regulation is proposed to play a key role in the hormonal control of many cellular processes. Inhibition of GSK3 in animal models of diabetes leads to normalization of blood glucose levels, while high GSK3 activity has been reported in Type II diabetes. Insulin inhibits GSK3 by promoting phosphorylation of a serine residue (Ser-21 in GSK3α, Ser-9 in GSK3β), thereby relieving GSK3 inhibition of glycogen synthesis in muscle. GSK3 inhibition in liver reduces expression of the gluconeogenic genes PEPCK (phosphoenolpyruvate carboxykinase), G6Pase (glucose-6-phosphatase), as well as IGFBP1 (insulin-like growth factor binding protein-1). Overexpression of GSK3 in cells antagonizes insulin regulation of these genes. In the present study we demonstrate that regulation of these three genes by feeding is normal in mice that express insulin-insensitive GSK3. Therefore inactivation of GSK3 is not a prerequisite for insulin repression of these genes, despite the previous finding that GSK3 activity is absolutely required for maintaining their expression. Interestingly, insulin injection of wild-type mice, which activates PKB (protein kinase B) and inhibits GSK3 to a greater degree than feeding (50% versus 25%), does not repress these genes. We suggest for the first time that although pharmacological inhibition of GSK3 reduces hepatic glucose production even in insulin-resistant states, feeding can repress the gluconeogenic genes without inhibiting GSK3.
Molecular cloning and expression of a human hST8Sia VI (α2,8-sialyltransferase) responsible for the synthesis of the diSia motif on O-glycosylproteins
Authors: Teintenier-Lelièvre Mélanie , Julien Sylvain , Juliant Sylvie , Guerardel Yann , Duonor-Cérutti Martine , Delannoy Philippe , Harduin-Lepers Anne
Published: December 2005

Based on BLAST analysis of the human and mouse genome databases using the human CMP sialic acid; α2,8-sialyltransferase cDNA (hST8Sia I; EC 2.4.99.8), a putative sialyltransferase gene, was identified on human chromosome 10. The genomic organization was found to be similar to that of hST8Sia I and hST8Sia V. Transcriptional expression analysis showed that the newly identified gene was constitutively expressed at low levels in various human tissues and cell lines. We have isolated a full-length cDNA clone from the breast cancer cell line MCF-7 that encoded a type II membrane protein of 398 amino acid residues with the conserved motifs of sialyltransferases. We have established a mammary cell line (MDA-MB-231) stably transfected with the full-length hST8Sia VI and the analysis of sialylated carbohydrate structures expressed at the cell surface clearly indicated the disappearance of Neu5Acα2-3-sialylated structures. The transient expression of a truncated soluble form of the enzyme in either COS-7 cells or insect Sf-9 cells led to the production of an active enzyme in which substrate specificity was determined. Detailed substrate specificity analysis of the hST8Sia VI recombinant enzyme in vitro, revealed that this enzyme required the trisaccharide Neu5Acα2-3Galβ1-3GalNAc (where Neu5Ac is N-acetylneuraminic acid and GalNAc is N-acetylgalactosamine) to generate diSia (disialic acid) motifs specifically on O-glycans.
EGFR kinase possesses a broad specificity for ErbB phosphorylation sites, and ligand increases catalytic-centre activity without affecting substrate binding affinity
Authors: Fan Ying-Xin , Wong Lily , Johnson Gibbes R.
Published: December 2005

We previously found that EGF (epidermal growth factor) increases the EGFR (EGF receptor) kinase-binding affinity towards the major tyrosine phosphorylation sites in downstream adaptor proteins such as Gab1 (Grb2-associated binding protein 1) and Shc [Src homology 2 (SH2) domain and collagen containing protein], but not that towards EGFR autophosphorylation sites [Fan, Wong, Deb and Johnson (2004) J. Biol. Chem. 279, 38143–38150]. EGFR activation can also result in transphosphorylation of tyrosine resides in the C-terminal region of the related receptors ErbB2, ErbB3 and ErbB4 in heterodimers which are formed upon ligand stimulation. In the present study, we investigated the specificity of EGFR kinase by comparing the steady state kinetic parameters for peptides derived from all four ErbBs in the absence or presence of EGF. Our results demonstrated that (i) EGFR kinase can efficiently phosphorylate a broad range of diverse peptide sequences representing ErbB sites; (ii) certain ErbB2, ErbB3 and ErbB4 sites had higher specificity constants than any EGFR sequence and (iii) EGF stimulation consistently increases the kcat approx. 5-fold, but does not significantly alter the Km for any ErbB peptides. Furthermore, peptides containing lysine at position −2 or −3 N-terminal to the target tyrosine were found to be poor EGFR kinase substrates, and substitution of these lysines with glutamine decreased the Km and increased the kcat for these substrates. We conclude that EGFR kinase-mediated ErbB transphosphorylations are mostly controlled at the level of oligomerization, and not by a preference of the EGFR kinase for phosphorylation sites in any particular ErbB. The results also demonstrated that, unlike phosphorylation sites in select downstream targets, EGF does not regulate the recognition of phosphorylation sites in the C-terminal region of any of the ErbBs.
Far-red fluorescent proteins evolved from a blue chromoprotein from Actinia equina
Authors: Shkrob Maria A. , Yanushevich Yurii G. , Chudakov Dmitriy M. , Gurskaya Nadya G. , Labas Yulii A. , Poponov Sergey Y. , Mudrik Nikolay N. , Lukyanov Sergey , Lukyanov Konstantin A.
Published: December 2005

Proteins of the GFP (green fluorescent protein) family demonstrate a great spectral and phylogenetic diversity. However, there is still an intense demand for red-shifted GFP-like proteins in both basic and applied science. To obtain GFP-like chromoproteins with red-shifted absorption, we performed a broad search in blue-coloured Anthozoa species. We revealed specimens of Actinia equina (beadlet anemone) exhibiting a bright blue circle band at the edge of the basal disc. A novel blue chromoprotein, aeCP597, with an absorption maximum at 597 nm determining the coloration of the anemone basal disk was cloned. AeCP597 carries a chromophore chemically identical with that of the well-studied DsRed (red fluorescent protein from Discosoma sp.). Thus a strong 42-nm bathochromic shift of aeCP597 absorption compared with DsRed is determined by peculiarities of chromophore environment. Site-directed and random mutagenesis of aeCP597 resulted in far-red fluorescent mutants with emission maxima at up to 663 nm. The most bright and stable mutant AQ143 possessed excitation and emission maxima at 595 and 655 nm respectively. Thus aeCP597 and its fluorescent mutants set a new record of red-shifted absorption and emission maxima among GFP-like proteins.
Role for a P-type H+-ATPase in the acidification of the endocytic pathway of Trypanosoma cruzi
Authors: Vieira Mauricio , Rohloff Peter , Luo Shuhong , Cunha-E-Silva Narcisa L. , De Souza Wanderley , Docampo Roberto
Published: December 2005

Previous studies in Trypanosoma cruzi, the etiologic agent of Chagas disease, have resulted in the cloning and sequencing of a pair of tandemly linked genes (TcHA1 and TcHA2) that encode P (phospho-intermediate form)-type H+-ATPases with homology to fungal and plant proton-pumping ATPases. In the present study, we demonstrate that these pumps are present in the plasma membrane and intracellular compartments of three different stages of T. cruzi. The main intracellular compartment containing these ATPases in epimastigotes was identified as the reservosome. This identification was achieved by immunofluorescence assays and immunoelectron microscopy showing their co-localization with cruzipain, and by subcellular fractionation and detection of their activity. ATP-dependent proton transport by isolated reservosomes was sensitive to vanadate and insensitive to bafilomycin A1, which is in agreement with the localization of P-type H+-ATPases in these organelles. Analysis by confocal immunofluorescence microscopy revealed that epitope–tagged TcHA1-Ty1 and TcHA2-Ty1 gene products are localized in the reservosomes, whereas the TcHA1-Ty1 gene product is additionally present in the plasma membrane. Immunogold electron microscopy showed the presence of the H+-ATPases in other compartments of the endocytic pathway such as the cytostome and endosomal vesicles, suggesting that in contrast with most cells investigated until now, the endocytic pathway of T. cruzi is acidified by a P-type H+-ATPase.
Visualizing Large-Scale Data in Educational, Behavioral, Psychometrical and Social Sciences: Utilities and Design Patterns of the SEER Computational and Graphical Statistics
Authors: Chiu Christopher WT , Pashley Peter , Seastrom Marilyn , Carr Peggy
Published: December 2005

This paper introduces a graphical method SEE Repeated-measure data (SEER) to visually analyze data commonly collected in large-scale surveys, market research, biostatistics, and educational and psychological measurement. Many researchers in these disciplines encounter large amounts of data. Examples include the Law School Admission Test (LSAT) repeater scores, career paths of students graduated from college, essays scores in the writing assessments of the National Assessment of Educational Progress (NAEP), and scores derived from different test equating methods in the discipline of psychometrics. Efficiency, ease-of-interpretations, applicability, user interactions are challenges due to the graphical complexity in visualizing large-scale data sets. To overcome these challenges, the author expands a systematic data-visualization technique, called SEER. The SEER technique was originally designed to depict career paths and occupational stability for professionals in the science and engineering discipline. In this paper, the author summarizes this example and highlights its applications in legal education, psychometrics, and other related areas. The author also, (a) expands this technique to examine repeat test takers' scores, (b) illustrates how to monitor inter-rater consistency for essay scoring and for depicting multi-faceted data that involve human judgments, and (c) demonstrates how to investigate differences of test equating and scaling methodology using the SEER method. The broader impacts and design patterns of the SEER method are discussed.
Water-carbon dioxide mixtures at high temperatures and pressures: Local order in the water rich phase investigated by vibrational spectroscopy
Authors: Oparin R. , Tassaing T. , Danten Y. , Besnard M.
Published: December 2005

Raman scattering combined with near- and midinfrared absorption spectroscopies was used to investigate the evolution of the local order in the water rich phase of water-CO2 mixtures under isobaric heating (T=40–360°C,P=250bars). The quantitative analysis of the spectra shows that tetramers and larger oligomers are the main constituents of water at moderate temperatures below 80 °C. As the temperature increases, the dimer and trimer concentrations considerably increase at the expense of larger oligomers. Finally, water dimers are predominant at the highest temperature investigated close to the temperature of total miscibility of the mixture (T=366°C,P=250bars). This result is consistent with our previous investigation [R. Oparin T. Tassaing, Y. Danten, and M. Besnard, J. Chem. Phys. 120, 10691 (2004)] on water dissolved in the CO2 rich phase where we found that close to the temperature of total miscibility water also exists mainly under dimeric form. The current study combined with that mentioned above provides a model investigation of the evolution of the state of aggregation of water molecules in binary mixture involving a hydrophobic solvent in a wide range of temperature.
Investigation of aging process of Si–SiOx structures with silicon quantum dots
Authors: Baran M. , Khomenkova L. , Korsunska N. , Stara T. , Sheinkman M. , Goldstein Y. , Jedrzejewski J. , Savir E.
Published: December 2005

In this work the aging processes of magnetron-sputtered Si–SiOx structures with silicon quantum dots are investigated by photoluminescence, electronic paramagnetic resonance, infrared absorption, and Raman-scattering methods. It is observed that oxidation of the silicon dots, change in the defect concentration in the oxide matrix, and oxidation of the silicon amorphous phase occur during storage in air at room temperature. A comparison of the variation of parameters of sputtered structures and porous silicon layers caused by the aging process is made. It is shown that the rate of oxidation of silicon dots and the decrease of their sizes in sputtered structures are essentially less than that in porous silicon. It is also shown that in Si–SiOx, layers in contrast to porous silicon, the intensity and spectral position of the emission band caused by exciton recombination in Si crystallites do not change practically during aging.
Remote-charge-scattering limited mobility in field-effect transistors with SiO2 and Al2O3∕SiO2 gate stacks
Authors: Saito Shin-ichi , Torii Kazuyoshi , Shimamoto Yasuhiro , Tonomura Osamu , Hisamoto Digh , Onai Takahiro , Hiratani Masahiko , Kimura Shin’ichiro , Manabe Yukiko , Caymax Matty , Maes Jan Willem
Published: December 2005

We examined, both experimentally and theoretically, the mobility reduction in metal-insulator-semiconductor field-effect transistors (MISFETs) limited by remote charge scattering. The accuracy of the mobility calculations was confirmed by agreement with experiments on MISFETs with pure SiO2 gate dielectrics, in which mobility is reduced due to scattering from the depletion charges in the polycrystalline silicon gate. In MISFETs with Al2O3∕SiO2 gate stacks, we could not identify the contributions from the remote phonon scattering by using low-temperature measurements of the mobility. The experimental mobility reduction is explained by a model in which both negative and positive charges are located at the Al2O3∕SiO2 interface. According to this model, the mobility increases with the interfacial SiO2 thickness. We confirmed this by fabricating MISFETs with various interfacial SiO2 thicknesses.
Electrical current effect in phase-separated La5∕8−yPryCa3∕8MnO3: Charge order melting versus Joule heating
Authors: Sacanell Joaquin , Leyva A. G. , Levy P.
Published: December 2005

We have studied the effect of electric field on transport properties of the prototypical phase-separated manganite La5∕8−yPryCa3∕8MnO3 with y=0.34. Our results show that the suggested image, in which the charge ordered state is melted by the appliance of an electric current and∕or voltage, has to be revised. We explain the observed resistivity drop in terms of an artifact related to Joule heating and the particular hysteresis that the system under study displays, common to many other phase-separated manganites.