bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation of ion dynamics and structure of superionic tellurite glasses
Authors: Dutta D. , Ghosh A.
Published: February 2008

Ion dynamics and structure of a series of superionic AgI-doped silver tellurite glasses have been investigated in this paper. The composition dependence of the dc conductivity and the activation energy of these glasses has been compared with those of AgI-doped silver phosphate and borate glasses. We have observed that the conductivity increases and the activation energy decreases with increase of AgI content and that the tellurite glasses have higher conductivity than those for phosphate or borate glasses. We have analyzed the ac electrical data in the framework of the power law and the electric modulus formalisms. We have established a correlation between the crossover rate of the mobile silver ions and the rearrangement of the structural units in tellurite glasses. The scaling of the conductivity spectra has been used to interpret the temperature and composition dependence of the relaxation dynamics. Analysis of the dielectric relaxation in the framework of modulus formalism indicates an increase in the ion-ion cooperation in the glass compositions with increasing AgI content.
Water polyamorphism: Reversibility and (dis)continuity
Authors: Winkel Katrin , Elsaesser Michael S. , Mayer Erwin , Loerting Thomas
Published: February 2008

An understanding of water’s anomalies is closely linked to an understanding of the phase diagram of water’s metastable noncrystalline states. Despite the considerable effort, such an understanding has remained elusive and many puzzles regarding phase transitions in supercooled liquid water and their possible amorphous proxies at low temperatures remain. Here, decompression of very high density amorphous ice (VHDA) from 1.1to0.02GPa at 140K is studied by means of dilatometry and powder x-ray diffraction of quench-recovered states. It is shown that the three amorphous states of ice are reversibly connected to each other, i.e., LDA↔e-HDA↔VHDA. However, while the downstroke VHDA→e-HDA transition takes place in the pressure range of 0.06GPa<p<0.40GPa, the e-HDA→LDA transition takes place quasi-discontinuously at p∼0.06GPa. That is, two amorphous-amorphous transitions of a distinct nature are observed for the first time in a one-component system–a first-order-like transition (e-HDA→LDA) and a transition which is not first-order like but possibly of higher order (VHDA→e-HDA). VHDA and e-HDA are established as the most stable and limiting states in the course of the transition. We interpret this as evidence disfavoring the hypothesis of multiple first-order liquid-liquid transitions (and the option of a third critical point), but favoring a single first-order liquid-liquid transition (and the option of a second critical point).
Propagators and related descriptors for non-Markovian asymmetric random walks with and without boundaries
Authors: Berezhkovskii Alexander M. , Weiss George H.
Published: February 2008

There are many current applications of the continuous-time random walk (CTRW), particularly in describing kinetic and transport processes in different chemical and biophysical phenomena. We derive exact solutions for the Laplace transforms of the propagators for non-Markovian asymmetric one-dimensional CTRW’s in an infinite space and in the presence of an absorbing boundary. The former is used to produce exact results for the Laplace transforms of the first two moments of the displacement of the random walker, the asymptotic behavior of the moments as t→∞, and the effective diffusion constant. We show that in the infinite space, the propagator satisfies a relation that can be interpreted as a generalized fluctuation theorem since it reduces to the conventional fluctuation theorem at large times. Based on the Laplace transform of the propagator in the presence of an absorbing boundary, we derive the Laplace transform of the survival probability of the random walker, which is then used to find the mean lifetime for terminated trajectories of the random walk.
Excitation energies in density functional theory: An evaluation and a diagnostic test
Authors: Peach Michael J. G. , Benfield Peter , Helgaker Trygve , Tozer David J.
Published: February 2008

Electronic excitation energies are determined using the CAM-B3LYP Coulomb-attenuated functional [T. Yanai et al. Chem. Phys. Lett. 393, 51 (2004)], together with a standard generalized gradient approximation (GGA) and hybrid functional. The degree of spatial overlap between the occupied and virtual orbitals involved in an excitation is measured using a quantity Λ, and the extent to which excitation energy errors correlate with Λ is quantified. For a set of 59 excitations of local, Rydberg, and intramolecular charge-transfer character in 18 theoretically challenging main-group molecules, CAM-B3LYP provides by far the best overall performance; no correlation is observed between excitation energy errors and Λ, reflecting the good quality, balanced description of all three categories of excitation. By contrast, a clear correlation is observed for the GGA and, to a lesser extent, the hybrid functional, allowing a simple diagnostic test to be proposed for judging the reliability of a general excitation from these functionals—when Λ falls below a prescribed threshold, excitations are likely to be in very significant error. The study highlights the ambiguous nature of the term “charge transfer,” providing insight into the observation that while many charge-transfer excitations are poorly described by GGA and hybrid functionals, others are accurately reproduced.
First-principles calculation of capacitance including interfacial effects
Authors: Lee Bora , Lee Choong-Ki , Han Seungwu , Lee Jaichan , Hwang Cheol Seong
Published: February 2008

An efficient computational method is proposed within a first-principles framework to calculate capacitances of metal-insulator-metal structures including interfacial effects. In this approach, we employ metal-insulator models under external electric fields to calculate dielectric responses near the interface region. Macroscopically averaged potentials allow for evaluating the capacitance and local dielectric constants of the corresponding metal-insulator-metal capacitor. We apply this method to calculate the capacitance of Au/MgO(100)/Au and Ni/ZrO2(110)/Ni with dielectric thicknesses of nanometers. While the Au/MgO interface is relatively free of interfacial effects, the computational results for Ni/ZrO2 indicate the presence of interfacial regions with dielectric constants noticeably lower than that of the bulk. Microscopic origins are discussed.
Fifty years of Physics of Fluids
Authors: Scott John T.
Published: February 2008

Physics of Fluids celebrates its 50th anniversary with this issue. This brief history summarizes the launching of the journal in 1958 under its first editor François Frenkiel, who held the position for more than 20 years; reviews the next 16years under the guidance of Andreas Acrivos, a fertile period during which the journal grew and spun off its sibling, Physics of Plasmas; and then reaches the current era under the present two editors.
Photoacoustic infrared spectroscopy at the Canadian Light Source: Commissioning experiments
Authors: Michaelian K. H. , May T. E. , Hyett C.
Published: February 2008

The commissioning of synchrotron radiation (SR) photoacoustic (PA) infrared spectroscopy at the Canadian Light Source is described in this article. Aperture tests demonstrated an exponential relationship between the wavenumber where SR and thermal-source PA intensities are equal and beam diameter. Total PA intensity increased linearly with aperture size up to 1.5mm (SR) or 3mm (thermal source). At larger apertures, this intensity approached a limiting value. The SR beam diameter in the spectrometer was estimated to be about 0.8mm in these tests. The low-frequency noise and dc offset that characterize SR PA spectra are suppressed through the calculation of average interferograms prior to Fourier transformation.
Invariant classification of the rotationally symmetric R-separable webs for the Laplace equation in Euclidean space
Authors: Chanachowicz Mark , Chanu Claudia M. , McLenaghan Raymond G.
Published: February 2008

An invariant characterization of the rotationally symmetric R-separable webs for the Laplace equation in Euclidean space is given in terms of invariants and covariants of a real binary quartic canonically associated with the characteristic conformal Killing tensor which defines the webs.
Nonresonant power transfer in plasma-surface interactions via two-surface wave decay
Authors: Akimov Yu. A. , Ostrikov K.
Published: February 2008

The excitation of pairs of electron surface waves via nonresonant decay of plasma waves incident onto a solid surface is studied in the context of controlling the interaction of pulsed electromagnetic radiation with plasma-exposed solid surfaces. The role of the plasma-exposed surfaces in nonlinear heating of the plasma edge and related power transfer is discussed. It is shown that the maximum efficiency of the power transfer at solid surfaces with dielectric permittivity εd<3 corresponds to the resonant two-surface wave decay. On the other hand, for solids with εd>3 the maximum power transfer efficiency is achieved through nonresonant excitation of the quasistatic surface waves. In this case the plasma waves generated by external radiation dissipate their energy into the plasma periphery most effectively.
Magnetic properties and magnetic domains of Nd–Fe–B thin films
Authors: Chen S. L. , Liu W. , Zhang Z. D. , Gunaratne G. H.
Published: February 2008

Anisotropic Nd–Fe–B thin films are fabricated by direct current magnetron sputtering on Si substrates heated to temperatures over a wide range. Surface morphology and magnetic domains of the Nd–Fe–B thin films prepared at different sputtering temperatures (25–600 °C) are observed by a scanning probe microscopy. The magnetic domains exhibit a rich variety of textures, changing from striped via maze to cloudlike as the sputtering temperature is increased. Variations in magnetic domains with substrate temperature are discussed using phase components and magnetic anisotropies of the thin films. In addition, patterns of magnetic domains are analyzed using the “disorder functions,” a set of characterizations of complex patterns with labyrinthine structures. The disorder function δ(1) and the structure factor δk do not change appreciably until a substrate temperature of 350 °C, but increases significantly beyond 400 °C. The disorder in magnetic domains increases with increasing sputtering temperature. A simultaneous enhancement of the anisotropic c texture and the hard-magnetic properties of the thin films are observed. The significant change of the disorder function at Ts=400 °C appears to be a precursor to the hardening of the Nd–Fe–B film. The most disordered magnetic domains of the film with the substrate temperature of 600 °C correspond to the optimum magnetic properties, with the maximum energy product (BH)max of 22.4 MG Oe.
Thermal stability of Cu nanowires on a sapphire substrate
Authors: Li Hongwei , Biser Jeffrey M. , Perkins Jason T. , Dutta Sreya , Vinci Richard P. , Chan Helen M.
Published: February 2008

Cu nanowires with widths ranging from 110 to 300 nm were fabricated on a c-plane sapphire substrate using E-beam lithography and lift-off processes. Thermal annealing of these polycrystalline metal nanowires at 700 °C in an inert (nitrogen) atmosphere showed that for lines of width 160 nm or less, there was complete breakdown into widely spaced, individual beads in a short time (1 h). It was shown that the morphological changes were driven by reduction in the surface energy, with surface diffusion as the predominant transport mechanism. The spacing between the beads was approximately 1.8 times greater than the values predicted by Rayleigh instability theory for a free standing rod with equivalent radius. Based on thermodynamic and kinetic considerations, discrepancies between the experimental observations and the predictions of Rayleigh instability theory were attributed to the stabilization effect of the substrate.
Resonant Raman spectroscopy of (Mn,Co)-codoped ZnO films
Authors: Du C. L. , Gu Z. B. , You Y. M. , Kasim J. , Yu T. , Shen Z. X. , Ni Z. H. , Ma Y. , Cheng G. X. , Chen Y. F.
Published: February 2008

Resonant Raman spectroscopy studies of (Mn, Co)-codoped ZnO films were carried out using the 325 nm laser as the excitation source. The mixed mode character of the longitudinal optical (LO) phonon reveals that the resonant Raman spectra of the films can be used to test the c-axis orientation degree of their crystallite grains. The ratio of integrated Raman intensities between the 2LO to LO changes as a function of annealing temperatures, which reaches maximum at about 800 °C and demonstrates the variation of electron-LO phonon coupling in the films. These can provide helpful information for the fabrication of ZnO based functional films and for the development of their future applications.
Changing Modes of Service Delivery: How Past Choices Structure Future Choices
Authors: Brown Trevor L , Potoski Matthew , Van Slyke David M
Published: February 2008

Public managers and their political overseers can choose from several approaches as they decide how to structure the delivery of goods and services to citizens. The three most common service-delivery modes are: internal service delivery, in which the government produces the entire service; contracts with other governments, private firms, or nonprofit organizations; and joint service-delivery arrangements. Traditionally, governments' decision to ‘make or buy’ has been framed statically: public managers and their political overseers select one delivery mode over alternatives and then remain committed to that delivery approach. Of course, in practice, service-delivery choices can be more fluid: internal service delivery can later change to contracts, and contracts can later be internalized. Changing service-delivery modes is a potentially costly undertaking. Governments that elect to switch typically make changes to existing production systems and management systems. Varying costs associated with the alteration of existing production and management systems make switching from some modes of service delivery easier than others, depending in part on how the service was initially delivered. In general, the costs of changing from direct service delivery to contract service delivery are likely to be high: managers have to dedicate significant time and effort to dismantling existing production and management systems and building new ones. On the other hand, the service-delivery decisions of contracting governments are likely to be more dynamic because they have typically already incurred the costs of changing at a previous date. Sometimes governments internalize services when they have been using joint or contracted service delivery, whereas at other times they remain in the market by switching vendor type. In this paper we examine how governments' previous service-delivery choices structure their future choices. We analyze panel data from the 1992 and 1997 International City/County Manager Association's Alternative Service Delivery surveys along with data from the US Census and other sources. Our results suggest that service-delivery choices exhibit strong inertia, although when change occurs the previous service-delivery mode influences the likelihood of changing to other service-delivery modes in important ways. In general, governments which have already internalized the upfront costs of changing modes of service delivery are more likely to approach service-delivery choices more dynamically in future decision making.
From Identity to the Economy: Analysing the Evolution of the Decentralisation Discourse
Authors: Rodriguez-Pose Andrés , Sandall Richard
Published: February 2008

Few global phenomena have been as pervasive over the lifetime of Government and Policy as the drive towards decentralisation. The number of countries transferring authority and resources to subnational tiers of government has multiplied over the last twenty-five years. Yet the motives behind this trend remain relatively unknown. We explore these motives by analysing changes in the decentralisation discourse across a number of countries. We find that, while arguments about democracy and good governance have been at the heart of the reasoning for decentralisation, identity has progressively been relegated in favour of the economy and the promise of an economic dividend as the other main motivating factor. However, this shift from identity to the economy is highly contingent on who is driving the process. Despite noticeable shifts towards economic arguments in the discourse of nationalist and secessionist movements, identity remains strong in bottom-up discourses. In contrast, it has almost disappeared—if it ever existed—when the process of decentralisation is undertaken by the state or is encouraged by international organisations.
Contingent Valuation Design and Data Treatment: If You Can't Shoot the Messenger, Change the Message
Authors: Spash Clive L
Published: February 2008

The contingent valuation method has become an established and major part of the toolbox used to produce monetary values for evaluating environmental changes. It has been used to inform everything from the value of ecosystem services to cultural heritage to loss of life. The method has been highly controversial at various stages but despite this, or perhaps due to the publicity, it has grown in scope and scale. Numerous occurrences of ‘bias’ and ‘anomalies’ in results have been addressed by improved design, so providing guidance on perfected approaches to making sure respondents reveal preferences in accord with theoretical expectations. That respondents may not wish to and often fail to conform is seen as a challenge for the design team to be more ingenious with their incentive mechanisms which get respondents to act ‘rationally’. Failing this, data can be classified and treated to derive ‘conservative’ results. I document in this paper how whole areas of evidence from contingent valuation have been removed from consideration by design, with respondents expected to conform to an idealised rational agent model or to suffer branding and exclusion as having the ‘wrong motives’. While the method is then susceptible to manipulation (eg to meet sponsors' requirements), if used more scientifically it also holds the potential to reveal fundamental flaws in economic theory and ways to advance that same theory.
Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction
Authors: Zhang Xing , Settembre Ethan , Xu Chen , Dormitzer Philip R. , Bellamy Richard , Harrison Stephen C. , Grigorieff Nikolaus
Published: February 2008

Electron cryomicroscopy (cryo-EM) yields images of macromolecular assemblies and their components, from which 3D structures can be determined, by using an image processing method commonly known as “single-particle reconstruction.” During the past two decades, this technique has become an important tool for 3D structure determination, but it generally has not been possible to determine atomic models. In principle, individual molecular images contain high-resolution information contaminated by a much higher level of noise. In practice, it has been unclear whether current averaging methods are adequate to extract this information from the background. We present here a reconstruction, obtained by using recently developed image processing methods, of the rotavirus inner capsid particle (“double-layer particle” or DLP) at a resolution suitable for interpretation by an atomic model. The result establishes single-particle reconstruction as a high-resolution technique. We show by direct comparison that the cryo-EM reconstruction of viral protein 6 (VP6) of the rotavirus DLP is similar in clarity to a 3.8-Å resolution map obtained from x-ray crystallography. At this resolution, most of the amino acid side chains produce recognizable density. The icosahedral symmetry of the particle was an important factor in achieving this resolution in the cryo-EM analysis, but as the size of recordable datasets increases, single-particle reconstruction also is likely to yield structures at comparable resolution from samples of much lower symmetry. This potential has broad implications for structural cell biology.
The nature of O
2
activation by the ethylene-forming enzyme 1-aminocyclopropane-1-carboxylic acid oxidase
Authors: Mirica Liviu M. , Klinman Judith P.
Published: February 2008

Ethylene is a plant hormone important in many aspects of plant growth and development such as germination, fruit ripening, and senescence. 1-Aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACCO), an O
2
-activating ascorbate-dependent nonheme iron enzyme, catalyzes the last step in ethylene biosynthesis. The O
2
activation process by ACCO was investigated using steady-state kinetics, solvent isotope effects (SIEs), and competitive oxygen kinetic isotope effects (
18
O KIEs) to provide insights into the nature of the activated oxygen species formed at the active-site iron center and its dependence on ascorbic acid. The observed large
18
O KIE of 1.0215 ± 0.0005 strongly supports a rate-determining step formation of an Fe
IV

O species, which acts as the reactive intermediate in substrate oxidation. The large SIE on
k
cat
/
K
m
(O
2
) of 5.0 ± 0.9 suggests that formation of this Fe
IV

O species is linked to a rate-limiting proton or hydrogen atom transfer step. Based on the observed decrease in SIE and
18
O KIE values for ACCO at limiting ascorbate concentrations, ascorbate is proposed to bind in a random manner, depending on its concentration. We conclude that ascorbate is not essential for initial O
2
binding and activation but is required for rapid Fe
IV

O formation under catalytic turnover. Similar studies can be performed for other nonheme iron enzymes, with the
18
O KIEs providing a kinetic probe into the chemical nature of Fe/O
2
intermediates formed in the first irreversible step of the O
2
activation.
Coexisting generalist herbivores occupy unique nutritional feeding niches
Authors: Behmer Spencer T. , Joern Anthony
Published: February 2008

A mainstay of ecological theory and practice is that coexisting species use different resources, leading to the local development of biodiversity. However, a problem arises for understanding coexistence of multiple species if they share critical resources too generally. Here, we employ an experimental framework grounded in nutritional physiology to show that closely related, cooccurring and generalist-feeding herbivores (seven grasshopper species in the genusMelanoplus; Orthoptera: Acrididae) eat protein and carbohydrate in different absolute amounts and ratios even if they eat the same plant taxa. The existence of species-specific nutritional niches provides a cryptic mechanism that helps explain how generalist herbivores with broadly overlapping diets might coexist. We also show that performance by grasshoppers allowed to mix their diets and thus regulate their protein–carbohydrate intake matched optimal performance peaks generated from no-choice treatments. These results indicate the active nature of diet selection to achieve balanced diets and provide buffering capacity in the face of variable food quality. Our empirical findings and experimental approach can be extended to generate and test predictions concerning the intensity of biotic interactions between species, the relative abundance of species, yearly fluctuations in population size, and the nature of interactions with natural enemies in tritrophic niche space.
Girls Most of the Time, Boys Some of the Time: Gender Differences in Toddlers' Use of Maternal Proximity and Comfort Seeking
Authors: Buss Kristin A. , Brooker Rebecca J. , Leuty Melanie
Published: February 2008

How children experience, express, and regulate distress has important implications for adjustment. Factors influencing individual differences in these aspects of affective behavior include temperament, context of situation, and parents, to name a few. Gender differences in the expression of affective behaviors have also been implicated in past research. However, differences are not always found, especially before preschool ages. This study examined the presence of gender differences and moderating influences of gender on the expression of distress and mother‐oriented behaviors (e.g., comfort seeking and proximity to mother) in 24‐month‐old toddlers during a series of situations designed to elicit either fear or frustration. Girls were more likely to seek contact from mother and stay in closer proximity to her compared to boys even after controlling for distress. However, the association between distress and contact seeking or proximity was significant for boys but not for girls. The discussion focuses on implications for biological and socialization effects of sex‐typed behavior and consequences for adjustment.
Infants' Attention and Responsiveness to Television Increases With Prior Exposure and Parental Interaction
Authors: Barr Rachel , Zack Elizabeth , Garcia Amaya , Muentener Paul
Published: February 2008

This study examined the relation between early television exposure and parental interaction style during infant‐directed television programs on 2 outcomes: infant looking time and infant responsiveness. By quasi‐experimental design half of the 12‐ to 18‐month‐old infants had prior exposure to the program content and the other half did not. Cluster analysis based on parental verbalizations revealed 3 types of parental coviewing style: high, medium, and low scaffold. Looking time was significantly higher for infants previously exposed to these videos than for those who were not. Infant looking time was also significantly higher, and infants responded more, when parents provided high levels of scaffolding in the form of questions and labels or descriptions. The results suggest that both prior exposure and parental style are associated with infant attention and responsiveness to television and have important implications for both parents and television producers.
Overcoming the Effects of Variation in Infant Speech Segmentation: Influences of Word Familiarity
Authors: Singh Leher , Nestor Sarah S. , Bortfeld Heather
Published: February 2008

Previous studies have shown that 7.5‐month‐olds can track and encode words in fluent speech, but they fail to equate instances of a word that contrast in talker gender, vocal affect, and fundamental frequency. By 10.5 months, they succeed at generalizing across such variability, marking a clear transition period during which infants' word recognition skills become qualitatively more mature. Here we explore the role of word familiarity in this critical transition and, in particular, whether words that occur frequently in a child's listening environment (i.e., “Mommy” and “Daddy”) are more easily recognized when they differ in surface characteristics than those that infants have not previously encountered (termed nonwords). Results demonstrate that words are segmented from continuous speech in a more linguistically mature fashion than nonwords at 7.5 months, but at 10.5 months, both words and nonwords are segmented in a relatively mature fashion. These findings suggest that early word recognition is facilitated in cases where infants have had significant exposure to items, but at later stages, infants are able to segment items regardless of their presumed familiarity.
Behavior of Mothers and Infants With and Without Down Syndrome During the Still‐Face Procedure
Authors: Moore Derek G. , Oates John M. , Goodwin Julia , Hobson R. Peter
Published: February 2008

There has been limited study of how the constitutional characteristics of infants with Down syndrome (DS) influence the patterning of their relations with caregivers. To assess natural and perturbed interactions between infants with DS and their mothers, we tested ten 6‐month‐old infants with DS and 20 typically developing (TD) 4‐month‐old of similar mental age. Participants were videotaped with their mothers in a natural face‐to‐face interaction, a brief period when the mothers adopted a still‐face, and a subsequent reengagement phase. There was little to distinguish the infants in the initial phase of natural interaction, but the mothers of infants with DS were more likely to show assertive warmth, and unlike in the case of mothers of TD infants, high maternal directiveness tended to be associated with lower levels of infant looking and lack of fussing. During the still‐face episode, infants of both groups showed reduced looking and smiling, although infants with DS tended to show lower levels of fussing and fewer in this group showed fussing in the reengagement phase. Therefore DS infants were somewhat similar to TD infants of comparable mental age in being responsive to the still‐face procedure, but showed indications of group differences in intense emotional reactivity.
Downward Trends in Surgical Site and Urinary Tract Infections After Cesarean Delivery in a French Surveillance Network, 1997–2003
Authors: Vincent Agnès , Ayzac Louis , Girard Raphaële , Caillat-Vallet Emmanuelle , Chapuis Catherine , Depaix Florence , Dumas Anne-Marie , Gignoux Chantal , Haond Catherine , Lafarge-Leboucher Joëlle , Launay Carine , Tissot-Guerraz Françoise , Fabry Jacques ,   Mater Sud-Est Study Group
Published: February 2008

Objective.

To evaluate whether the adjusted rates of surgical site infection (SSI) and urinary tract infection (UTI) after cesarean delivery decrease in maternity units that perform active healthcare-associated infection surveillance.

Design.

Trend analysis by means of multiple logistic regression.

Setting.

A total of 80 maternity units participating in the Mater Sud-Est surveillance network.

Patients.

A total of 37,074 cesarean deliveries were included in the surveillance from January 1, 1997, through December 31, 2003.

Methods.

We used a logistic regression model to estimate risk-adjusted post–cesarean delivery infection odds ratios. The variables included were the maternity units' annual rate of operative procedures, the level of dispensed neonatal care, the year of delivery, maternal risk factors, and the characteristics of cesarean delivery. The trend of risk-adjusted odds ratios for SSI and UTI during the study period was studied by linear regression.

Results.

The crude rates of SSI and UTI after cesarean delivery were 1.5% (571 of 37,074 patients) and 1.8% (685 of 37,074 patients), respectively. During the study period, the decrease in SSI and UTI adjusted odds ratios was statistically significant (R = −0.823 [P = .023] and R = −0.906 [P = .005], respectively).

Conclusion.

Reductions of 48% in the SSI rate and 52% in the UTI rate were observed in the maternity units. These unbiased trends could be related to progress in preventive practices as a result of the increased dissemination of national standards and a collaborative surveillance with benchmarking of rates.
Vancomycin-Resistant Enterococci in Canada: Results from the Canadian Nosocomial Infection Surveillance Program, 1999–2005
Authors: Ofner-Agostini Marianna , Johnston B. Lynn , Simor Andrew E. , Embil John , Matlow Anne , Mulvey Michael , Ormiston Debbie , Conly John ,   Canadian Nosocomial Infection Surveillance Program
Published: February 2008

Surveillance for vancomycin-resistant enterococci (VRE) in sentinel Canadian hospitals has been conducted since 1999. From 1999 to 2005, the rate of VRE detection increased from 0.37 to 1.32 cases per 1,000 patients admitted, and the rate of VRE infection increased from 0.02 to 0.05 cases per 1,000 patients admitted. Thirty-three percent of all patients with VRE detected that were reported during 1999-2005 were identified in 2005, with increases seen in all regions of Canada. Although the incidence rate of VRE carriage in Canada is increasing, it remains very low.
Biological pathway kinetic rate constants are scale-invariant
Authors: Grandison Scott , Morris Richard J.
Published: February 2008

Motivation: Scale-free networks have had a profound impact in Biology. Network theory is now used routinely to visualize, navigate through, and help understand gene networks, protein–protein interactions, regulatory networks and metabolic pathways. Here we analyse the numerical rather than topological properties of biological networks and focus on the study of kinetic rate constants within pathways.

Results: We have analysed all current entries in the BioModels database and show that the kinetic rate parameters follow Benford's; law closely. The cumulative histogram plot reveals an underlying power-law. This implies that these data are scale-invariant, thus placing biological network topology and their chemistry on an equivalent ‘scale-free’ power-law foundation.

Contact:  Richard.Morris@bbsrc.ac.uk
(In)visibility: Dislocation in French and the Voice of the Translator
Authors: McLaughlin Mairi
Published: February 2008

This article presents the results of the investigation of a corpus consisting of translated and original French taken from contemporary prize-winning fiction. The focus of the inquiry is the difference between original and translated French and the consequences for the voice of the translator. The differences between the two language types are examined through a case study of the syntactic structure known as dislocation. Through careful analysis of the form, function and usage of this construction in the two language types, I arrive at several conclusions. First, the very existence of formal, functional and usage variation highlights the differences between translated and original language, and this may in future play a greater role in governing the composition of corpora in linguistic research. Second, the way in which this variation manifests itself has consequences for the status that translation holds in a specific culture and the effects that translation can have on the target language. Finally, variation between the two language types is shown to be relevant to the debate regarding the voice of the translator: Lawrence Venuti's invisibility theory is reworked to include three types of invisibility.
Cavemen Among Us: Genealogies of Atavism from Zola's
La Bête humaine
to Chabrol's
Le Boucher
Authors: Bell Dorian
Published: February 2008

Although critics have rightly linked Claude Chabrol's film
Le Boucher
(1969) to Zola's novel
La Bête humaine
(1890), the two have yet to be considered in the context of the century-long tradition of thought about atavism that informs them both. This article reconstructs that tradition, examining how
Le Boucher
's modern-day caveman suggests twentieth-century cultural continuities with nineteenth-century notions of man's relation to his evolutionary forebears. Noting
Le Boucher
's debt to a Freudian conception of atavism — a conception heavily influenced by the very same scientific paradigm that shaped Zola's fascination with man's prehistoric self — I argue that Chabrol's film revives a nineteenth-century European anxiety of proximity whereby technological and scientific advances prompted unease about ever closer contact with the distant reaches of humanity. Chabrol achieves this by building on Zola's proto-cinematic vision, refracting it through a Freudian lens in which atavism and the cinema occupy common psychological space, and updating the thematics of atavism for a twentieth century chastised by the colonial experiment.
Influence of the Columbia River plume (USA) on the vertical and horizontal distribution of mesozooplankton over the Washington and Oregon shelf
Authors: Peterson Jay O. , Peterson William T.
Published: February 2008

Peterson, J. O., and Peterson, W. T. 2008. Influence of the Columbia River plume (USA) on the vertical and horizontal distribution of mesozooplankton over the Washington and Oregon shelf. – ICES Journal of Marine Science, 65: 477–483. River plumes extending out over continental shelf waters have distinct frontal boundaries along their leading edges that concentrate highly buoyant particles, including zooplankton. The margin between the base of the plume and the underlying oceanic waters is often many times larger in spatial extent than the visible surface front, but the influence of this region of a river plume on the vertical and horizontal distribution of zooplankton is less well understood. Using a laser optical plankton counter (LOPC) and a conductivity–temperature–depth sensor (CTD) mounted to a rapidly undulating tow body, we examined the horizontal and vertical distribution of zooplankton proximate to the Columbia River plume, to study how plume waters affect zooplankton over the continental shelf. Overall, vertically integrated zooplankton abundance and biovolume was elevated close to “aged” plume waters. Zooplankton tended to aggregate near the surface close to river plume waters. When plume waters are present at the surface, zooplankton aggregations tended to be in the upper 10 m of the water column, compared with 25 m when the plume was not present. The presence of river plumes may be ecologically and energetically important to surface feeding planktivores such as larval and juvenile fish.
Stochastic extinction and the selection of the transmission mode in microparasites
Authors: Bahi-Jaber Narges , Fouchet David , Pontier Dominique
Published: February 2008

Stochastic fluctuations in the transmission process of microparasites generate a risk of parasite extinction that cannot be assessed by deterministic models, especially in host populations of small size. While this risk of extinction represents a strong selection pressure for microparasites, it is usually not clearly separated from the deterministic ones. We suggest here that this stochastic selection pressure can affect the selection of the transmission mode of microparasites. To avoid extinction, parasites should maximize their inter-population transmission to ensure frequent reintroductions. Since the types of contacts may differ if congeners belong to the same or distinct populations, strains that are mainly transmitted through inter-population contacts might be selected. To examine this assumption, we analyse the issue of the competition between two strains differing in their transmission mode using a stochastic metapopulation model in which hosts may display different behaviours inside and outside their populations. We show that stochastic selection pressures may drive parasite evolution towards a transmission mode that maximizes the persistence of the parasite. We study the conditions under which stochastic selection pressures may surpass the deterministic ones. Our results are illustrated by the cases of feline immunodeficiency virus in cats and of sexually transmitted diseases in mammals.
Probability, ergodicity, irreversibility and dynamical systems
Authors: Lucia Umberto
Published: February 2008

The problem of irreversibility is difficult and part of this difficulty is due to dealing with the statistical mechanics of a large number of particles. The ergodic theory, founded on the link between thermodynamics and its statistical probability, introduced the ergodic theorem that consists of the equality of microcanonical phase average and the time average of the observables. Moreover, a global approach has been introduced, starting from non-equilibrium thermodynamics and obtaining a general principle of investigation, the principle of maximum entropy generation for the open systems. Here, a general approach to the investigation of irreversible systems and the application of entropy generation to the study of the dynamical systems will be developed.
Cdc28–Clb5 (CDK-S) and Cdc7–Dbf4 (DDK) collaborate to initiate meiotic recombination in yeast
Authors: Wan Lihong , Niu Hengyao , Futcher Bruce , Zhang Chao , Shokat Kevan M. , Boulton Simon J. , Hollingsworth Nancy M.
Published: February 2008

S-phase cyclin-dependent kinase Cdc28–Clb5 (CDK-S) and Dbf4-dependent kinase Cdc7–Dbf4 (DDK) are highly conserved kinases well known for their roles in the initiation of DNA replication. CDK-S is also essential for initiation of meiotic recombination because it phosphorylates Ser30 of Mer2, a meiosis-specific double-strand break (DSB) protein. This work shows that the phosphorylation of Mer2 Ser30 by CDK-S primes Mer2 for subsequent phosphorylation by DDK on Ser29, creating a negatively charged “patch” necessary for DSB formation. CDK-S and DDK phosphorylation of Mer2 S30 and S29 can be bypassed by phosphomimetic amino acids, but break formation under these conditions is still dependent on DDK and CDK-S activity. Coordination between premeiotic S and DSB formation may be achieved by using CDK-S and DDK to initiate both processes. Many other proteins important for replication, recombination, repair, and chromosome segregation contain combination DDK/CDK sites, raising the possibility that this is a common regulatory mechanism.
ATR signaling can drive cells into senescence in the absence of DNA breaks
Authors: Toledo Luis I. , Murga Matilde , Gutierrez-Martinez Paula , Soria Rebeca , Fernandez-Capetillo Oscar
Published: February 2008

The ATR kinase is a key transducer of “replicative stress,” the type of genomic damage that has been postulated to be induced by oncogenes. Here we describe a cellular system in which we can unleash ATR activity at will, in the absence of any actual damage or additional signaling pathways triggered by DNA breaks. We demonstrate that activating ATR is sufficient to promote cell cycle arrest and, if persistent, triggers p53-dependent but Ink4a/ARF-independent senescence. Moreover, we show that an ectopic activation of ATR leads to a G1/S arrest in ATM−/− cells, providing the first evidence of functional complementation of ATM deficiency by ATR. Our system provides a novel platform for the study of the specific functions of ATR signaling and adds evidence for the tumor-suppressive potential of the DNA damage response.
Preparation of Double-Stranded RNA for Drosophila RNA Interference (RNAi)
Authors: Misquitta Leonie , Wei Qin , Paterson Bruce M.
Published: February 2008

INTRODUCTION

RNA interference (RNAi) is a powerful method for determining the role of specific genes during Drosophila embryogenesis. It has been used in our laboratory to phenocopy a series of known mutations in Drosophila, including twist, engrailed, daughterless, Dmef2, and, to a lesser extent, white in the adult eye. This protocol describes the preparation of dsRNA by in vitro transcription of complementary strands of a cloned DNA fragment that codes for all or a portion of the gene of interest, followed by annealing of the transcribed RNA.
Injection of dsRNA into Drosophila Embryos for RNA Interference (RNAi): Figure 1.
Authors: Misquitta Leonie , Wei Qin , Paterson Bruce M.
Published: February 2008

INTRODUCTION

RNA interference (RNAi) is a powerful method for determining the role of specific genes during Drosophila embryogenesis. This protocol describes a technique by which Drosophila embryos can be injected with dsRNA in order to disrupt targeted gene function. The approach is straightforward, utilizing improved methods for injecting the dsRNA directly through the chorion of the embryo. This strategy minimizes problems normally associated with desiccation of the dechorionated embryo and facilitates post-injection analysis of gene expression.
Mounting Live Cells Attached to Coverslips for Microscopy
Authors: Fischer Andrew H. , Jacobson Kenneth A. , Rose Jack , Zeller Rolf
Published: February 2008

INTRODUCTION

This article describes the mounting of coverslips containing live cells onto microscope slides.
Labeling the Components of the Plasma Membrane with Fluorescent Dyes for Imaging
Authors: Chazotte Brad
Published: February 2008

INTRODUCTION

The eukaryotic cell has evolved to compartmentalize its functions and transport various metabolites among cellular compartments. Therefore, in cell biology, the study of organization and structure/function relationships are of great importance. The plasma membrane provides the essential dynamic boundary and a vital selective interface between the cell compartment and its environment. This article describes four methods for labeling the plasma membrane with fluorescent probes. Each method labels a distinct class of membrane molecules.
Labeling the Golgi Apparatus with BODIPY-FL-Ceramide (C5-DMB-ceramide) for Imaging
Authors: Chazotte Brad
Published: February 2008

INTRODUCTION

The eukaryotic cell has evolved to compartmentalize its functions and transport various metabolites among cellular compartments. Therefore, in cell biology, the study of organization and structure/function relationships are of great importance. The Golgi apparatus is composed of a series of flattened, disk-shaped cisternae typically located near the cell nucleus. It is thought that the Golgi may be a principal organizer of macromolecular traffic in the cell because many molecules, such as secreted proteins, glycoproteins, glycolipids, and plasma membrane glycoproteins, pass through the Golgi during their maturation. In this protocol, fluorescent probes of the Golgi make use of this function to allow labeling of the Golgi.
Calculation of Spot Reliability Evaluation Scores (SRED) for DNA Microarray Data
Authors: Shimokawa Kazuro , Kodzius Rimantas , Matsumura Yonehiro , Hayashizaki Yoshihide
Published: February 2008

INTRODUCTION

In terms of cost per measurement, the use of DNA microarrays for comprehensive and quantitative expression measurements is vastly superior to other methods such as Northern blotting or quantitative reverse transcriptase polymerase chain reaction (QRT-PCR). However, the output values of DNA microarrays are not always highly reliable or accurate compared with other techniques, and the output data sometimes consist of measurements of relative expression (treated sample vs. untreated) rather than absolute expression values as desired. In effect, some measurements from some laboratories do not represent absolute expression values (such as the number of transcripts) and as such are experimentally deficient. This protocol addresses one problem in some microarray data: the absence of accurate measurements. Spot reliability evaluation score for DNA microarrays (SRED) offers a reliability value for each spot in the microarray. SRED does not require an entire microarray to assess the reliability, but rather analyzes the reliability of individual spots of the microarray. The calculation of a reliability index can be used for different microarray systems, which facilitates the analysis of multiple microarray data sets from different experimental platforms.
Calculation of Absolute Expression Values for DNA Microarray Data
Authors: Shimokawa Kazuro , Kodzius Rimantas , Matsumura Yonehiro , Hayashizaki Yoshihide
Published: February 2008

INTRODUCTION

In terms of cost per measurement, the use of DNA microarrays for comprehensive and quantitative expression measurements is vastly superior to other methods such as Northern blotting or quantitative reverse transcriptase polymerase chain reaction (QRT-PCR). However, the output values of DNA microarrays are not always highly reliable or accurate compared with other techniques, and the output data sometimes consist of measurements of relative expression (treated sample vs. untreated) rather than absolute expression values as desired. In effect, some measurements from some laboratories do not represent absolute expression values (such as the number of transcripts) and as such are experimentally deficient. To address the problem that some microarray data sets fail to reflect the number of mRNA molecules sufficiently in a given sample (i.e., fail to provide absolute expression levels), additional methods are required. The procedure described here provides a new method for converting microarray data to absolute expression values with the use of external data such as expressed sequence tags (ESTs) and cap analysis of gene expression (CAGE) tags.