bluuebunny/crossref_metadata_2025 huggingface dataset:
Immunomodulatory effects of the intake of fermented milk with Lactobacillus casei DN114001 in lactating mothers and their children
Authors: Ortiz-Andrellucchi Adriana , Sánchez-Villegas Almudena , Rodríguez-Gallego Carlos , Lemes Angelina , Molero Teresa , Soria Adela , Peña-Quintana Luis , Santana Milagrosa , Ramírez Octavio , García José , Cabrera Félix , Cobo José , Serra-Majem Lluís
Published: March 2008

The healthy action of probiotics is not only due to their nutritional properties and their influence on the gastrointestinal environment, but also to their action on the immune system. The aim of the present study was to determine if 6 weeks of probiotic intake would be able to modulate the immune system in women who had recently delivered and were breast-feeding. The design consisted of a randomised, controlled and double-blind nutritional intervention study with parallel groups with a sample size of 104 women. The main variable is the T helper type 1/T helper type 2 (Th1/Th2) profile determined by measuring interferon-γ (Th1) and IL-4 (Th2) values in peripheral blood by flow cytometry. The modifications of cytokines were evaluated in maternal milk by cytometric bead array in a flow cytometer and ELISA at three stages of breast-feeding: colostrum, early milk (10 d) and mature milk (45 d). Additionally, the anthropometry and infectious and allergic episodes in the newborn were followed up throughout the first 6 months of life. After the consumption of milk fermented with Lactobacillus casei during the puerperium, we observed a non-significant increase in T and B lymphocytes and a significant increase in natural killer cells. A decrease in the pro-inflammatory cytokine TNF-α in maternal milk and fewer gastrointestinal disturbances were also observed in the breast-fed child of the mothers who consumed L. casei. The intake of milk fermented with L. casei during the lactation period modestly contributes to the modulation of the mother's immunological response after delivery and decreases the incidence of gastrointestinal episodes in the breast-fed child.
Comparison of body fat estimation using waist:height ratio using different ‘waist’ measurements in Australian adults
Authors: Kagawa Masaharu , Byrne Nuala M. , Hills Andrew P.
Published: March 2008

The objective of the present study was to determine differences in predicting total and regional adiposity using the waist:height ratio (WHtR) calculated using different ‘waist’ measurements. Body composition of ninety-five males and 121 female Australian adults (aged 20 years and above) was measured using dual-energy X-ray absorptiometry. The WHtR was calculated using: (1) the narrowest point between the lower costal border and the top of the iliac crest (WHtR-W), and (2) at the level of the umbilicus (WHtR-A). Relationships between calculated WHtR and measured body composition, such as percentage body fat (%BF) and percentage trunk fat (%TF) were determined. Values obtained from WHtR-A were significantly greater than WHtR-W in both groups (P < 0·05). While no correlation differences between WHtR-W and WHtR-A in relation to body composition variables were observed, females showed significantly lower correlation with lean mass compared with BMI. Regression analyses showed that neither WHtR had an age influence on %TF estimation. Estimated %BF and %TF were comparable for both WHtR and also with estimated values using a BMI of 25 kg/m2. Sensitivity of excess %BF and %TF increased by using WHtR-A, particularly in females. In conclusion, the umbilicus measurement may be better than using the narrowest site in the WHtR calculation, particularly in females. To improve the screening ability of the WHtR and make comparisons between studies easier there may be a need to standardise the measurement location. Further studies are recommended to confirm the findings across different ethnic groups.
Myringostapediopexy and myringolenticulopexy in mastoid surgery
Authors: Cheang P P , Kim D , Rockley T J
Published: March 2008

Objective:

To compare hearing results in patients undergoing myringostapediopexy or myringolenticulopexy in canal wall down mastoidectomy.

Study design:

Case series of one surgeon. A retrospective review of 83 consecutive mastoid cavity operations for primary cholesteatoma. Only those patients who had undergone either myringostapediopexy or myringolenticulopexy were included.

Setting:

District general hospital.

Patients:

Forty-two procedures were performed in 40 patients. The mean age was 42 years old. The average follow up was 5.9 years.

Intervention:

Seventeen patients underwent myringolenticulopexy (the incus head was excised, leaving the lenticular process attached to the stapes prior to graft placement) and 25 underwent myringostapediopexy (type III tympanoplasty).

Main outcome measures:

Audiometry three to six months after surgery, and status of mastoid cavity after a minimum follow up of one year.

Results:

Comparison of post-operative hearing results for the two groups showed a statistically significant hearing advantage for myringolenticulopexy (p = 0.029). In the myringolenticulopexy group, 92 per cent achieved a post-operative air–bone gap of less than 30 dB, compared with 62 per cent in the myringostapediopexy group. The mean post-operative air–bone gaps in the two groups were 17.5 and 24.7 dB, respectively.

Conclusion:

When surgically feasible, the technique of myringolenticulopexy is a useful method of preserving serviceable hearing in single-stage mastoid cavity surgery.
Record-linkage and capture–recapture analysis to estimate the incidence and completeness of reporting of tuberculosis in England 1999–2002
Authors: VAN HEST N. A. H. , STORY A. , GRANT A. D. , ANTOINE D. , CROFTS J. P. , WATSON J. M.
Published: March 2008

In 1999 the Enhanced Tuberculosis Surveillance (ETS) system was introduced in the United Kingdom to strengthen surveillance of tuberculosis (TB). The aim of this study was to assess the use of record-linkage and capture–recapture methodology for estimating the completeness of TB reporting in England between 1999 and 2002. Due to the size of the TB data sources sophisticated record-linkage software was required and the proportion of false-positive cases among unlinked hospital-derived TB records was estimated through a population mixture model. This study showed that record-linkage of TB data sources and cross-validation with additional TB-related datasets improved data quality as well as case ascertainment. Since the introduction of ETS observed completeness of notification in England has increased and the results were consistent with expected levels of under-notification. Completeness of notification estimated by a log-linear capture–recapture model was highly inconsistent with prior estimates and the validity of this methodology was further examined.
A statistical model investigating the prevalence of tuberculosis in New York City using counting processes with two change-points
Authors: ACHCAR J. A. , MARTINEZ E. Z. , RUFFINO-NETTO A. , PAULINO C. D. , SOARES P.
Published: March 2008

We considered a Bayesian analysis for the prevalence of tuberculosis cases in New York City from 1970 to 2000. This counting dataset presented two change-points during this period. We modelled this counting dataset considering non-homogeneous Poisson processes in the presence of the two-change points. A Bayesian analysis for the data is considered using Markov chain Monte Carlo methods. Simulated Gibbs samples for the parameters of interest were obtained using WinBugs software.
IS FINNIS WRONG?
Authors: Rodriguez-Blanco Veronica
Published: March 2008

Judges and lawyers believe that international law, customary law, and legal systems such as the Third Reich or apartheid law in South Africa are law. But how do we explain the fact that there is one concept of law when there are different conceptions of law with a variety of different features? Finnis, inspired by the Aristotelian notion of central case, adumbrates the idea that the concept of law might be unified by a primary concept which is the concept of “law as practical reason”; that is, law conceived from an ethical perspective. He advances two arguments to defend his methodology: the conceptual and the functional. Contra Finnis, the paper shows that neither the conceptual nor the functional argument can successfully support the view that “law as practical reason” is the central case of the concept of law. The study clarifies the Aristotelian notion of central case and illustrates the mistaken application of this notion to the concept of law. However, we also argue that Finnis's insight–the idea that all the different conceptions of law might be unified for the purposes of theoretical research–is fundamental and appealing. This paper aims to reconstruct Finnis's insight through the model of core resemblance. The result is that the different conceptions of law can be unified by resemblance to the concept of “law as practical reason,” though there is no identity among the different conceptions of law.
PERSONS PURSUING GOODS
Authors: Smith Steven D.
Published: March 2008

John Finnis's powerfully and deservedly influential modern classic, Natural Law and Natural Rights, expounds a theory of law and morality that is based on a picture of “persons” using practical reason to pursue certain “basic goods.” While devoting much attention to practical reason and to the goods, however, Finnis says little about the nature of personhood. This relative inattention to what “persons” are creates a risk—one that Finnis himself notices—of assuming or importing an inadequate anthropology. This essay suggests that the “new natural law” developed by Finnis suffers in places from the inadvertent adoption of (or, more likely, acquiescence in) a flawed anthropology—an anthropology under the thrall of modern individualistic commitments. To explain this suspicion, this article discusses three difficulties (or so they seem to me) in his natural law theory: difficulties in accounting for the basic good of friendship, for obligations we owe to others, and for legal authority. These difficulties may seem disconnected, but this article suggests that they may all reflect an inadequate anthropology—one that Finnis does not exactly embrace (in fact, I suspect that he would reject it) but that is pervasive today and that in places may affect his theorizing.
EUROPEAN FISCAL DISCIPLINE BEFORE AND AFTER EMU: CRASH DIET OR PERMANENT WEIGHT LOSS?
Authors: HALLETT ANDREW HUGHES , LEWIS JOHN
Published: March 2008

This paper studies the evolution of European fiscal policies in three periods: the pre-Maastricht phase (to 1991); the runup to monetary union (1992–1997), and the stability pact phase (1998 onward). Using three separate indicators, we search for structural breaks that could signify a change in the average level of discipline in these periods. We find increased fiscal discipline only up to 1997. We conclude the new fiscal discipline was a temporary phenomenon, a product of the sanction of being denied entry to the Euro. After EMU, fiscal policy gradually loosened. A single structural break test will miss these dynamic effects, and could easily generate the false conclusion that fiscal discipline had tightened since the start of phase two of EMU.
Frequentist and Bayesian approaches to prevalence estimation using examples from Johne's disease
Authors: McV. Messam Locksley L. , Branscum Adam J. , Collins Michael T. , Gardner Ian A.
Published: March 2008

Although frequentist approaches to prevalence estimation are simple to apply, there are circumstances where it is difficult to satisfy assumptions of asymptotic normality and nonsensical point estimates (greater than 1 or less than 0) may result. This is particularly true when sample sizes are small, test prevalences are low and imperfect sensitivity and specificity of diagnostic tests need to be incorporated into calculations of true prevalence. Bayesian approaches offer several advantages including direct computation of range-respecting interval estimates (e.g. intervals between 0 and 1 for prevalence) without the requirement of transformations or large-sample approximations. They also allow direct probabilistic interpretation, and the flexibility to model in a straightforward manner the probability of zero prevalence. In this review, we present frequentist and Bayesian methods for animal- and herd-level true prevalence estimation based on individual and pooled samples. We provide statistical methods for detecting differences between population prevalence and frequentist methods for sample size and power calculations. All examples are motivated usingMycobacterium aviumsubspeciesparatuberculosisinfection and we provide WinBUGS code for all examples of Bayesian estimation.
Actinobacillus pleuropneumoniaevaccines: from bacterins to new insights into vaccination strategies
Authors: Ramjeet Mahendrasingh , Deslandes Vincent , Gouré Julien , Jacques Mario
Published: March 2008

With the growing emergence of antibiotic resistance and rising consumer demands concerning food safety, vaccination to prevent bacterial infections is of increasing relevance.Actinobacillus pleuropneumoniaeis the etiological agent of porcine pleuropneumonia, a respiratory disease leading to severe economic losses in the swine industry. Despite all the research and trials that were performed withA. pleuropneumoniaevaccination in the past, a safe vaccine that offers complete protection against all serotypes has yet not reached the market. However, recent advances made in the identification of new potential vaccine candidates and in the targeting of specific immune responses, give encouraging vaccination perspectives. Here, we review past and current knowledge onA. pleuropneumoniaevaccines as well as the newly available genomic tools and vaccination strategies that could be useful in the design of an efficient vaccine againstA. pleuropneumoniaeinfection.
Microstructures in Hole 1274A peridotites, ODP Leg 209, Mid‐Atlantic Ridge: Tracking the fate of melts percolating in peridotite as the lithosphere is intercepted
Authors: Suhr Guenter , Kelemen Peter , Paulick Holger
Published: March 2008

We report the microstructures of harzburgites and dunites from ODP Leg 209, Hole 1274A, 15°39′N on the Mid‐Atlantic Ridge. A set of features in these peridotites is so unaffected by plastic flow that it must have formed very late by magmatic processes. We believe that the microstructures record the interaction between a peridotite and a percolating melt as the thermal boundary layer was progressively intercepted. The following chronology for the microstructures is derived: Group 1, resorption of orthopyroxene (opx) associated with olivine precipitation, enhanced by a migrating melt; Group 2, conversion of opx to clinopyroxene (cpx) by a percolating melt; Group 3, precipitation of cpx and spinel as intricate intergrowth (symplectite), associated with olivine dissolution, from an interstitial melt. For these reactions the ratio of melt generated to melt consumed is progressively decreasing, as expected during progressive freezing of asthenosphere. Pristine reaction microstructures analogous to Site 1274A are also found in the Lanzo Massif (Italy) and the Little Port Complex (Canada). For all three settings we infer (1) slow spreading conditions and (2) an ancient depletion event. We thus infer that preservation of the described microstructures is favored by slow spreading and a previous depletion. Slow spreading may be required since it avoids the tectonic overprint during ductile corner flow generally inferred for fast spreading ridges. Slow spreading does not tend, however, to generate highly depleted residues because a thick lithospheric lid limits the extent of melting. Residues will thus tend to be lherzolitic, not harzburgitic. However, lherzolites have a lower permeability for mafic melts than harzburgites. In order to generate the percolation‐dominated microstructures of Site 1274A, a harzburgitic host rock appears favorable. This may now explain the need for an ancient depletion event since only then can harzburgitic residues occur at the top of the mantle column during slow spreading conditions.
A semi‐empirical model of the contribution from sporadic meteoroid sources on the meteor input function in the MLT observed at Arecibo
Authors: Fentzke Jonathan T. , Janches Diego
Published: March 2008

In this paper, we present a modeling and observational study of the micrometeor input function with a focus on understanding how each of the extraterrestrial sporadic meteoroid sources contributes to the observed meteoric flux in the Mesosphere and Lower Thermosphere (MLT) atmospheric region. For this purpose, we expand the model presented by Janches et al. (2006) using a Monte Carlo technique and incorporating: 1) a widely accepted global mass flux, which is divided into different proportions among the known sporadic meteoroid sources as the initial input above Earth’s atmosphere; 2) contemporary knowledge on the source's velocity and radiant distributions; and 3) the full integration of the canonical meteor equations that describe the meteoroid entry and ablation physics. In addition, we constrain the initial input through a comparison of our modeled results with meteor observations obtained with the 430 MHz High Power and Large Aperture (HPLA) Arecibo radar in Puerto Rico that covers all seasons. The predicted meteor rates and velocity distributions are in excellent agreement with the observed ones without the need for any additional normalization factor. Our results indicate that although the Earth’s Apex centered radiant source, which is characterized by high geocentric speeds (∼55 km/s), appears to be ∼33% of the meteoroids in the Solar System at 1 AU, it accounts for ∼60% of the meteors observed by the Arecibo HPLA radar in the atmosphere. The remaining 40% of observed meteors originate mostly from the Helion and Anti‐Helion sources, with a very small, but constant during the day, contribution of the South and North Toroidal sources. These results also suggest that particles smaller than ∼10−3μg with slow velocities (<30 km/s) will not significantly ablate and never become observable meteors. The motivation of this effort is to construct a new and more precise MIF model needed for the subsequent modeling of the atmospheric phenomena related to the meteoric flux.
Attenuation in the upper mantle beneath Southern California: Physical state of the lithosphere and asthenosphere
Authors: Yang Yingjie , Forsyth Donald W.
Published: March 2008

We invert phase and amplitude data of Rayleigh waves for attenuation (Q−1) and shear wave velocities beneath southern California using teleseismic sources recorded by the TriNet/USArray network. Fundamental mode surface wave studies from 25 to 143 s period allow us to constrain the vertical variation of shear quality factor Qμ in the upper mantle. We use 2‐D sensitivity kernels for surface waves based on single‐scattering (Born) approximation to account for the effects of scattering on amplitude. A one‐dimensional shear velocity model reveals a pronounced low velocity zone (LVZ) from ∼80 km to ∼200 km underlying a high velocity lid. Qμ shows a similar pattern; large Qμ at depths shallower than 80 km and much smaller Qμ at depths greater than 100 km. Models that attribute the variations of attenuation and shear velocities with depth solely to temperature and pressure effects predict too low Qμ values if they match the shear velocities. Alternative models considering the presence of partial melt can explain the observed very low Vs velocities in the asthenosphere. Partial melt in the asthenosphere could be generated due to decompression and the reduced solidus for damp mantle when the asthenosphere rose to fill the space left by the subducted Farallon plate.
Nonspherical and spherical characterization of ice in Hurricane Erin for wideband passive microwave comparisons
Authors: Skofronick‐Jackson Gail , Heymsfield Andrew , Holthaus Eric , Albers Cerese , Kim Min‐Jeong
Published: March 2008

In order to better understand the characteristics and physical‐to‐radiative relationships of frozen hydrometeors in hurricane systems, computed brightness temperatures (TB) from 10.7 to 183 ± 10 GHz were compared with radiometric observations of Hurricane Erin (2001) from the NASA ER‐2 aircraft. The focus was on the high frequencies (≥85 GHz) that are particularly sensitive to frozen hydrometeors. In order to initialize the cloud profiles used in the radiative transfer calculations, data from airborne radars, dropsondes, and cloud models were used. Three different ice habit and size parameterizations were used with these cloud profiles to obtain the particle radiative signatures including (1) spherical particles with size distributions derived from in situ observations, (2) spherical “fluffy” snow and graupel particles with modified Marshall‐Palmer size distributions, and (3) a non‐spherical bullet rosette habit where the radiation attributes (scattering, absorption, and asymmetry properties) were computed using the Discrete Dipole Approximation. In addition, three different reflectivity to ice water content (Z‐IWC) relationships were used with the three habit and size parameterizations to provide a measure of the sensitivity of the Z‐IWC relationship. This work showed that both the scattering and asymmetry coefficients, along with the ice water content in each layer, play an important role in determining the resultant high frequency brightness temperatures. All low frequency (<40 GHz) calculations matched the observations with correlation coefficients greater than 0.9. At higher frequencies (> 90 GHz), correlation coefficients ranged from 0.7 to 0.92. Comparing between the three ice habit and size parameterizations showed less than a 0.2 difference in correlation coefficient, while the comparisons between the three Z‐IWC relationships caused changes of up to 0.15 in the correlation coefficients, but they had a significant effect on the mean differences between the observations and the calculations.
Spatial and temporal variation of sediment yield in the landscape: Example of Huanghe (Yellow River)
Authors: Hassan Marwan A. , Church Michael , Xu Jiongxin , Yan Yunxia
Published: March 2008

Regional scale relations between specific sediment yield and drainage basin area in the Huanghe basin reveal varying landscape sedimentary dynamics. Declining specific sediment yield with area is typical of disturbed agricultural areas, while increasing yields indicate the remobilization of stored sediment by bank and floodplain erosion along major tributaries. Using the developed relations, areally‐adjusted sediment yield maps are created over the entire Huanghe basin. Maps of the Loess Plateau for periods before and after 1970 reveal major changes in sediment yield, indicating that land management may have a major effect on sediment dynamics within a short period of time.
Computational enzymology: modelling the mechanisms of biological catalysts
Authors: Mulholland Adrian J.
Published: March 2008

Simulations and modelling [e.g. with combined QM/MM (quantum mechanics/molecular mechanics) methods] are increasingly important in investigations of enzyme-catalysed reaction mechanisms. Calculations offer the potential of uniquely detailed, atomic-level insight into the fundamental processes of biological catalysis. Highly accurate methods promise quantitative comparison with experiments, and reliable predictions of mechanisms, revolutionizing enzymology.
Structure determinations of human and chimaeric antibodies by solution scattering and constrained molecular modelling
Authors: Perkins Stephen J. , Bonner Alexandra
Published: March 2008

X-ray and neutron scattering and analytical ultracentrifugation provide multiparameter structural and compositional information on proteins that complements high-resolution protein crystallography and NMR studies. They are ideal methods to use when either a large protein cannot be crystallized, when scattering provides the only means to obtain a solution structure, or the protein crystal structure has been determined and it is necessary to validate this. Once these results have been obtained, we apply automated constrained modelling methods based on known subunit crystal structures to identify the best-fit structure. Using our antibody structures as examples, we describe the generation of appropriate starting models, randomizing these for trial-and-error scattering fits, identifying the final best-fit models and interpreting these in terms of function. We discuss our structure determinations for IgA and IgD, an IgA–human serum albumin complex, the dimer of IgA and secretory component associated with this and chimaeras of mouse IgG with two complement proteins. Constrained modelling confirms the experimental data analysis and produces families of best-fit molecular models. Its usage has clarified several aspects of antibody structure and function in solution.
Histidine protonation and the activation of viral fusion proteins
Authors: Mueller Daniela S. , Kampmann Thorsten , Yennamalli Ragothaman , Young Paul R. , Kobe Bostjan , Mark Alan E.
Published: March 2008

Many viral fusion proteins only become activated under mildly acidic condition (pH 4.5–6.5) close to the pKa of histidine side-chain protonation. Analysis of the sequences and structures of influenza HA (haemagglutinin) and flaviviral envelope glycoproteins has led to the identification of a number of histidine residues that are not only fully conserved themselves but have local environments that are also highly conserved [Kampmann, Mueller, Mark, Young and Kobe (2006) Structure 14, 1481–1487]. Here, we summarize studies aimed at determining the role, if any, that protonation of these potential switch histidine residues plays in the low-pH-dependent conformational changes associated with fusion activation of a flaviviral envelope protein. Specifically, we report on MD (Molecular Dynamics) simulations of the DEN2 (dengue virus type 2) envelope protein ectodomain sE (soluble E) performed under varied pH conditions designed to test the histidine switch hypothesis of Kampmann et al. (2006).
Exploiting glycogen synthase kinase 3β flexibility in molecular recognition
Authors: Mazanetz Michael P. , Withers Ian M. , Laughton Charles A. , Fischer Peter M.
Published: March 2008

GSK3β (glycogen synthase kinase 3β) is involved in the phosphorylation of various important regulatory proteins. Pharmacological inhibition of this enzyme could yield treatments for a variety of diseases including diabetes and Alzheimer's disease. The understanding of events involved in the molecular recognition of inhibitors by the active site of this enzyme is key in structure-based design strategies. The present study deals with the dynamic nature of GSK3β and highlights the importance of studying protein plasticity in structure-based drug design, exemplified by our method called ASP (active-site pressurization).
AAA proteins and the life process
Authors: Förster Andreas , Freemont Paul S. , Mayer R. John
Published: March 2008

AAAs (ATPases associated with various cellular activities) form a large group of P-loop NTPases, themselves the most abundant class of protein in all organisms. Because of their importance, since 1995, there has been a biennial meeting focusing on AAAs. The Seventh International Meeting on AAA Proteins was held on 9–13 September 2007 in Cirencester, U.K. and brought together various prominent and promising researchers in the field. The talks that are discussed herein and the corresponding papers that follow this introduction give a good overview of the current areas of research into these proteins.
Dissecting the ATP hydrolysis pathway of bacterial enhancer-binding proteins
Authors: Bose Daniel , Joly Nicolas , Pape Tillmann , Rappas Mathieu , Schumacher Jorg , Buck Martin , Zhang Xiaodong
Published: March 2008

bEBPs (bacterial enhancer-binding proteins) are AAA+ (ATPase associated with various cellular activities) transcription activators that activate gene transcription through a specific bacterial σ factor, σ54. σ54–RNAP (RNA polymerase) binds to promoter DNA sites and forms a stable closed complex, unable to proceed to transcription. The closed complex must be remodelled using energy from ATP hydrolysis provided by bEBPs to melt DNA and initiate transcription. Recently, large amounts of structural and biochemical data have produced insights into how ATP hydrolysis within the active site of bEBPs is coupled to the re-modelling of the closed complex. In the present article, we review some of the key nucleotides, mutations and techniques used and how they have contributed towards our understanding of the function of bEBPs.
The Sulfolobus solfataricus AAA protein Sso0909, a homologue of the eukaryotic ESCRT Vps4 ATPase
Authors: Hobel Cédric F.V. , Albers Sonja V. , Driessen Arnold J.M. , Lupas Andrei N.
Published: March 2008

Sso0909 is a protein of the thermo-acidophilic crenarchaeon Sulfolobus solfataricus, annotated as a p60 katanin-like ATPase. We present here results supporting the hypothesis that Sso0909 is an orthologue of the eukaryotic ESCRT (endosomal sorting complex required for transport) ATPase Vps4 (vacular protein sorting 4). The spectrum of Sso0909 homologues is limited to several orders of Crenarchaea and to three euryarchaeal Thermoplasmata species, where they were presumably acquired by lateral gene transfer. Almost invariably, Sso0909 homologues occur in the genomic vicinity of homologues of eukaryotic ESCRT-III components, which are the targets of disassembly by Vps4, as well as with a creanarchaeal-specific coiled-coil protein. S. solfataricus sso0909 is constitutively expressed under normal growth conditions and appears to be essential, as judged by the failure to obtain stable deletion mutants. We expressed Sso0909 in Escherichia coli and S. solfataricus, but have not obtained preparations with ATPase activity so far.
The AAA peroxins Pex1p and Pex6p function as dislocases for the ubiquitinated peroxisomal import receptor Pex5p
Authors: Platta Harald W. , Debelyy Mykhaylo O. , Magraoui Fouzi El , Erdmann Ralf
Published: March 2008

The discovery of the peroxisomal ATPase Pex1p triggered the beginning of the research on AAA (ATPase associated with various cellular activities) proteins and the genetic dissection of peroxisome biogenesis. Peroxisomes are virtually ubiquitous organelles, which are connected to diverse cellular functions. The highly diverse and adaptive character of peroxisomes is accomplished by modulation of their enzyme content, which is mediated by dynamically operating protein-import machineries. The import of matrix proteins into the peroxisomal lumen has been described as the ATP-consuming step, but the corresponding reaction, as well as the ATPase responsible, had been obscure for nearly 15 years. Recent work using yeast and human fibroblast cells has identified the peroxisomal AAA proteins Pex1p and Pex6p as mechano-enzymes and core components of a complex which dislocates the cycling import receptor Pex5p from the peroxisomal membrane back to the cytosol. This AAA-mediated process is regulated by the ubiquitination status of the receptor. Pex4p [Ubc10p (ubiquitin-conjugating enzyme 10)]-catalysed mono-ubiquitination of Pex5p primes the receptor for recycling, thereby enabling further rounds of matrix protein import, whereas Ubc4p-catalysed polyubiquitination targets Pex5p to proteasomal degradation.
Dynamic and functional assembly of the AAA peroxins, Pex1p and Pex6p, and their membrane receptor Pex26p involved in shuttling of the PTS1 receptor Pex5p in peroxisome biogenesis
Authors: Fujiki Yukio , Miyata Non , Matsumoto Naomi , Tamura Shigehiko
Published: March 2008

The peroxisome is a single-membrane-bound organelle found in eukaryotes. The functional importance of peroxisomes in humans is highlighted by peroxisome-deficient PBDs (peroxisome biogenesis disorders), such as Zellweger syndrome. Two AAA (ATPase associated with various cellular activities) peroxins, Pex1p and Pex6p, are encoded by PEX1 and PEX6, the causal genes for CG (complementation group) 1 and CG4 PBDs respectively. PEX26, which is responsible for CG8 PBDs, codes for Pex26p, the recruiter of Pex1p–Pex6p complexes to peroxisomes. We recently assigned the binding regions between human Pex1p and Pex6p and elucidated the pivotal roles that the AAA cassettes, D1 and D2 domains, play in Pex1p–Pex6p interaction and in peroxisome biogenesis. ATP binding to both AAA cassettes of Pex1p and Pex6p was a prerequisite for the Pex1p–Pex6p interaction and peroxisomal localization, but ATP hydrolysis by the D2 domains was not required. Pex1p exists in two distinct oligomeric forms, a homo-oligomer in the cytosol and a hetero-oligomer on peroxisome membranes, with these possibly having distinct functions in peroxisome biogenesis. AAA peroxins are involved in the export from peroxisomes of Pex5p, the PTS1 (peroxisome-targeting signal type 1) receptor.
The MCM helicase: linking checkpoints to the replication fork
Authors: Forsburg Susan L.
Published: March 2008

The MCM (minichromosome maintenance) complex is a helicase which is essential for DNA replication. Recent results suggest that the MCM helicase is important for replication fork integrity, and may function as a target of the replication checkpoint. Interactions between MCM proteins, checkpoint kinases, and repair and recovery proteins suggest that MCMs are proximal effectors of replication fork stability in the cell and are likely to play an important role in maintaining genome integrity.
Role(s) of Cdc48/p97 in mitosis
Authors: Meyer Hemmo , Popp Oliver
Published: March 2008

The ubiquitin-dependent chaperone Cdc48 (cell divison cycle 48)/p97 is involved in a variety of degradative and regulatory processes during interphase that help to maintain cellular homoeostasis. The results available so far suggest that its basic activity is to mobilize ubiquitinated substrate proteins from cellular structures or segregate them from binding partners, and then hand them over for degradation or recycling. Several studies in different organisms show that Cdc48/p97 also has critical roles in mitosis. However, many important aspects of these functions and the general perspective have remained unclear.
Molecular mechanism of force generation by dynein, a molecular motor belonging to the AAA+ family
Authors: Numata Naoki , Kon Takahide , Shima Tomohiro , Imamula Kenji , Mogami Toshifumi , Ohkura Reiko , Sutoh Keiko , Sutoh Kazuo
Published: March 2008

Dynein is an AAA+ (ATPase associated with various cellular activities)-type motor complex that utilizes ATP hydrolysis to actively drive microtubule sliding. The dynein heavy chain (molecular mass >500 kDa) contains six tandemly linked AAA+ modules and exhibits full motor activities. Detailed molecular dissection of this motor with unique architecture was hampered by the lack of an expression system for the recombinant heavy chain, as a result of its large size. However, the recent success of recombinant protein expression with full motor activities has provided a method for advances in structure–function studies in order to elucidate the molecular mechanism of force generation.
The MCM complex: (just) a replicative helicase?
Authors: Costa Alessandro , Onesti Silvia
Published: March 2008

The MCM2–MCM7 (minichromosome maintenance 2–7) complex is involved both in the initiation and the elongation step of eukaryotic DNA replication and is believed to be the replicative helicase. Whereas the mechanism of DNA unwinding at the replication fork has been extensively investigated, the role of the MCM2–MCM7 complex during initiation has not yet been characterized by biochemical studies. Here we summarize the in vivo evidence which supports a role for the MCM complex in origin melting. In addition, we present an overview of the mechanism of action of a number of AAA+ (ATPase associated with various cellular activities) initiators and hexameric helicases, which can be used in turn as models for the steps of recognition, duplex melting, loading and nucleic acid translocation of the MCM helicase.
Critical Success Factors in Destination Marketing
Authors: Baker Michael J. , Cameron Emma
Published: March 2008

As a consequence of globalisation, the marketing of places has grown in importance as countries, regions and individual destinations compete with one another to attract investment and visitors. In order to compete effectively, it is essential to identify the critical success factors (CSFs) and ensure these are incorporated into one's strategic planning. An extensive review of the literature covering place and destination marketing indicates that image and identity play an important role in differentiating between objectively similar alternatives. Accordingly, the branding of destinations has become of major importance and is analysed in depth. Thirty-three factors are identified, clustered into four categories, that may be considered CSFs to be taken into account when developing tourism strategies and plans.
Quantitative determination of vortex core dimensions in head-to-head domain walls using off-axis electron holography
Authors: Junginger F. , Kläui M. , Backes D. , Krzyk S. , Rüdiger U. , Kasama T. , Dunin-Borkowski R. E. , Feinberg J.-M. , Harrison R. J. , Heyderman L. J.
Published: March 2008

In this paper, we present a complete three-dimensional characterization of vortex core spin structures, which is important for future magnetic data storage based on vortex cores in disks and in wires. Using electron holography to examine vortices in patterned Permalloy devices we have quantitatively measured the in-plane and out-of-plane magnetization of a vortex core. Observed core widths and integrated phase shifts agree well with those derived from micromagnetic simulations.
Morphological and electrical investigations of lead zirconium titanate thin films obtained by sol-gel synthesis on indium tin oxide electrodes
Authors: Bruno E. , De Santo M. P. , Castriota M. , Marino S. , Strangi G. , Cazzanelli E. , Scaramuzza N.
Published: March 2008

In recent years, interest in PbZr0.53Ti0.47O3 (PZT) films has been rapidly increasing due to their technological applications as ferroelectric materials. In the present work, PZT films are obtained by sol-gel synthesis and deposited by spin coating on a transparent conductor substrate, with a perspective application as rectifying layers in asymmetric nematic liquid crystal cells. An extensive investigation is carried out on the effects of different annealing temperatures, with regard to the film texture and to the electric polarization properties, by using low vacuum scanning electron microscopy, atomic force microscopy, and electrostatic force microscopy. It has been observed that PZT domains self-organize into flower-like dendritic structures with a “rosetta” shape at the early stage of crystallization, occurring for annealing temperatures higher than 600 °C; the dimensions of such structures increase versus the annealing temperature. The ferroelectric properties of the PZT films have been related to the observed domains.
Oscillator strengths and line widths of dipole-allowed transitions in N214 between 89.7 and 93.5nm
Authors: Stark G. , Lewis B. R. , Heays A. N. , Yoshino K. , Smith P. L. , Ito K.
Published: March 2008

Line oscillator strengths in the 20 electric dipole-allowed bands of N214 in the 89.7–93.5nm (111480–106950cm−1) region are reported from photoabsorption measurements at an instrumental resolution of ∼6mÅ (0.7cm−1) full width at half maximum. The absorption spectrum comprises transitions to vibrational levels of the 3pσuc4′Σu+1, 3pπuc3Πu1, and 3sσgo3Πu1 Rydberg states and of the b′Σu+1 and bΠu1 valence states. The J dependences of band f values derived from the experimental line f values are reported as polynomials in J′(J′+1) and are extrapolated to J′=0 in order to facilitate comparisons with results of coupled Schrödinger-equation calculations. Most bands in this study are characterized by a strong J dependence of the band f values and display anomalous P-, Q-, and R-branch intensity patterns. Predissociation line widths, which are reported for 11 bands, also exhibit strong J dependences. The f value and line width patterns can inform current efforts to develop comprehensive spectroscopic models that incorporate rotational effects and predissociation mechanisms, and they are critical for the construction of realistic atmospheric radiative-transfer models.
Two-dimensional fluorescence resonance energy transfer as a probe for protein folding: A theoretical study
Authors: Ting Christina L. , Makarov Dmitrii E.
Published: March 2008

We describe a two-dimensional (2D), four-color fluorescence resonance energy transfer (FRET) scheme, in which the conformational dynamics of a protein is followed by simultaneously observing the FRET signal from two different donor-acceptor pairs. For a general class of models that assume Markovian conformational dynamics, we relate the properties of the emission correlation functions to the rates of elementary kinetic steps in the model. We further use a toy folding model that treats proteins as chains with breakable cross-links to examine the relationship between the cooperativity of folding and FRET data and to establish what additional information about the folding dynamics can be gleaned from 2D, as opposed to one-dimensional FRET experiments. We finally discuss the potential advantages of the four-color FRET over the three-color FRET technique.
Experimental study of hydrogen plasma reforming by intermittent spark discharges
Authors: Barni R. , Quintini A. , Piselli M. , Riccardi C.
Published: March 2008

We present an experimental analysis of an air/methane high-voltage discharge at atmospheric pressure which operates in an intermittent spark regime. The aim is to study the feasibility of hydrogen reforming through plasma processing. The structure of the spark and the electrical characteristics of the discharge were studied as a function of the air/methane mixture composition, the gas flow rate, the average current, and the external circuitry resistance. Discharge spectra in the visible and near-ultraviolet range show the production of several radicals and excited species which provide a clue to the relevant chemical kinetics in the plasma state. Detailed mass analysis of the composition of the exhaust gas flow shows a significant production of hydrogen and high conversion efficiency of methane. The dependence on the discharge operating parameters was investigated in order to clarify the optimal setup design for an efficient plasma reformer.
Radiation response of nanometric HfSiON/SiO2 gate stacks
Authors: Devine R. A. B. , Quevedo-Lopez M. A. , Alshareef H.
Published: March 2008

The x-ray irradiation sensitivity of hafnium silicon oxynitride/silicon oxide dielectric stacks deposited on Si has been measured. Clear evidence for trapped negative charge buildup is found for samples biased positively during irradiation and also for negative bias with or without radiation. A two phase buildup of trapped negative charge is observed in the case of irradiation in the presence of positive bias suggestive of different rates of electron trapping in the two layers.
CCSD calculations on C14, C18, and C22 carbon clusters
Authors: Arulmozhiraja Sundaram , Ohno Takahisa
Published: March 2008

The structure and energetics of the ring isomers of C4n+2 (n=3–5) carbon clusters were studied by using coupled-cluster singles and doubles excitation theory to overcome the vast differences existing in the literature. The results obtained in the present study clearly indicate that C14, C18, and C22 carbon rings have bond-length and bond-angle alternated acetylenic minimum energy structures. Contrarily, density functional theory calculations were unable to predict these acetylenic-type structures and they ended up with the cumulenic structures. It is found from the coupled-cluster studies that the lowest-energy ring isomer for the first two members of C4n+2 series is a bond-angle alternated cumulenic D(2n+1)h symmetry structure while the same for the remaining members is a bond-length and bond-angle alternated C(2n+1)h symmetry structure. In C4n+2 carbon rings, Peierls-type distortion, transformation from bond-angle alternated to bond-length alternated minimum energy structures, occurs at C14 carbon ring.
Tuning of magnetic properties in cobalt ferrite nanocrystals
Authors: Cedeño-Mattei Y. , Perales-Perez O. , Tomar M. S. , Roman F. , Voyles P. M. , Stratton W. G.
Published: March 2008

Cobalt ferrite (CoFe2O4) possesses excellent chemical stability, good mechanical hardness, and a large positive first order crystalline anisotropy constant, making it a promising candidate for magneto-optical recording media. In addition to precise control of the composition and structure of CoFe2O4, its practical application will require the capability to control particle size at the nanoscale. The results of a synthesis approach in which size control is achieved by modifying the oversaturation conditions during ferrite formation in water through a modified coprecipitation approach are reported. X-ray diffraction, transmission electron microscopy (TEM) diffraction, and TEM energy-dispersive x-ray spectroscopy analyses confirmed the formation of the nanoscale cobalt ferrite. M-H measurements verified the strong influence of synthesis conditions on crystal size and hence, on the magnetic properties of ferrite nanocrystals. The room-temperature coercivity values increased from 460 up to 4626Oe under optimum synthesis conditions determined from a 23 factorial design.
Mesoscopic dynamics of inhomogeneous polymers based on variable cell shape dynamic self-consistent field theory
Authors: Li Xuan , Tang Ping , Zhang Hongdong , Qiu Feng , Yang Yuliang
Published: March 2008

In this paper, we combine variable cell shape method with dynamic self-consistent field theory and extend to study structure and dynamics under shear for triblock copolymer melts. Due to shear, the calculation cell shape is variable and no longer orthogonal. Pseudospectral method is employed to solve the diffusion equation for chain propagator on the nonorthogonal coordinate and the shear periodical condition can be easily designed in terms of the variable cell shape method. By using this strategy, the shear induced morphology evolution is investigated for topologically complex polymeric systems such as linear and star triblock copolymers; the morphology of linear ABC triblock copolymers is more shear sensitive than that of star triblocks. In particular, once the chain propagator is obtained, the microscopic elastic stress and spatial stress distribution can be derived and thus the dynamic mechanical property can be calculated under shear. By imitating the dynamic storage modulus G′ corresponding to any given morphology in the oscillatory shear measurements, we explore the relationship between the morphology and the storage modulus G′ and extend to study the mechanism of phase separation dynamics as well as order-disorder transition (ODT) for linear and star triblock copolymers. The results show that the chain architecture can be easily distinguished by investigating the ODT, though the systems such as AB symmetric diblock and ABA triblock copolymers by coupling AB precursors almost exhibit similar microstructures. In addition, the storage modulus G′ and loss modulus G″ can be simultaneously determined in frequency sweeps of oscillatory shear measurements and the dependence of the moduli on phase separated patterns and the chain topology is investigated. The simulation findings are in qualitatively agreement with the experimental results.