bluuebunny/crossref_metadata_2025 huggingface dataset:
Soft-sphere soft glasses
Authors: Heyes D. M. , Clarke S. M. , Brańka A. C.
Published: December 2009

Molecular dynamics simulations have been used to compute physical properties of model fluids in which the particles interacted via the soft-sphere pair potential (SSP) ϕ(r)=ϵ(σ/r)n, where ϵ and σ are the characteristic energy and distance, respectively. The emphasis is on small values of n, tending to the lower theromodynamically allowed bound of 3+. An accurate equation of state for the SSP fluid is obtained, consisting of two terms, and as n→3+, the compressibility factor, Z tends to Z=B2ζn/3 for ζ>0, where B2 is the second virial coefficient, and ζ=πNσ3/6V is a nominal packing fraction for N particles in volume V. A simple formula for the position of the first peak in the radial distribution function in the soft particle limit is proposed and shown to agree with the simulation data. The fluid phase velocity autocorrelation function at fluid-solid coexistence becomes more oscillatory as n decreases. Values for the self-diffusion coefficient D and shear viscosity η were calculated as a function of n and density, and these were used to estimate the n-dependence of an ideal glass transition. The glass transition shifts relatively further into the solid part of the phase diagram as softness (∼1/n) increases. D decreases by ca. 75% and η increases by about a factor of 3 along the fluid-solid coexistence line from n=∞ to 3.25. Non-Gaussian behavior was calculated from the particle displacements as a function of particle softness. A screened soft-sphere potential, SSSP, was introduced to explore the effects for small n of the long range part of the potential in relation to the scale of the local structure. The SSSP with suitable analytic form and parameters can give statistically indistinguishable results from the full SSP for the static properties, D and η.
Intense ultrafast light kick by rotational Raman wake in atmosphere
Authors: Wu Jian , Cai Hua , Lu Peifen , Bai Xueshi , Ding Liang’en , Zeng Heping
Published: December 2009

We report that intense ultrafast light can be particlelike kicked through the rotational Raman wake of the impulsively pre-excited diatomic molecules in atmosphere, manifested by controllable repulsion and attraction of intense pulses delayed by molecular alignment revival periods, and by mutual fusion of orthogonally polarized intense pulses nearby zero time delay. The rotational Raman wake facilitates longer ranges of interaction on the intense ultrafast light kicks than the plasma wake and Kerr effect.
Resolution of identity approximation for the Coulomb term in molecular and periodic systems
Authors: Burow Asbjörn M. , Sierka Marek , Mohamed Fawzi
Published: December 2009

A new formulation of resolution of identity approximation for the Coulomb term is presented, which uses atom-centered basis and auxiliary basis functions and treats molecular and periodic systems of any dimensionality on an equal footing. It relies on the decomposition of an auxiliary charge density into charged and chargeless components. Applying the Coulomb metric under periodic boundary conditions constrains the explicit form of the charged part. The chargeless component is determined variationally and converged Coulomb lattice sums needed for its determination are obtained using chargeless linear combinations of auxiliary basis functions. The lattice sums are partitioned in near- and far-field portions which are treated through an analytical integration scheme employing two- and three-center electron repulsion integrals and multipole expansions, respectively, operating exclusively in real space. Our preliminary implementation within the TURBOMOLE program package demonstrates consistent accuracy of the method across molecular and periodic systems. Using common auxiliary basis sets the errors of the approximation are small, in average about 20 μhartree per atom, for both molecular and periodic systems.
A computational study of ion conductance in the KcsA K+ channel using a Nernst–Planck model with explicit resident ions
Authors: Jung Yong-Woon , Lu Benzhuo , Mascagni Michael
Published: December 2009

The biophysical mechanisms underlying the relationship between the structure and function of the KcsA K+ channel are described. Because of the conciseness of electrodiffusion theory and the computational advantages of a continuum approach, the Nernst–Planck (NP) type models, such as the Goldman–Hodgkin–Katz and Poisson-NP (PNP) models, have been used to describe currents in ion channels. However, the standard PNP (SPNP) model is known to be inapplicable to narrow ion channels because it cannot handle discrete ion properties. To overcome this weakness, the explicit resident ions NP (ERINP) model was formulated, which applies a local explicit model where the continuum model fails. Then, the effects of the ERI Coulomb potential, the ERI induced potential, and the ERI dielectric constant for ion conductance were tested in the ERINP model. The current-voltage (I-V) and current-concentration (I-C) relationships determined in the ERINP model provided biologically significant information that the traditional continuum model could not, explicitly taking into account the effects of resident ions inside the KcsA K+ channel. In addition, a mathematical analysis of the K+ ion dynamics established a tight structure-function system with a shallow well, a deep well, and two K+ ions resident in the selectivity filter. Furthermore, the ERINP model not only reproduced the experimental results with a realistic set of parameters, but it also reduced CPU costs.
Effects of Ru diffusion in exchange-biased MgO magnetic tunnel junctions prepared by in situ annealing
Authors: Shin Il-Jae , Min Byoung-Chul , Hong Jin Pyo , Shin Kyung-Ho
Published: December 2009

We study the effect of Ru diffusion in exchange-biased MgO magnetic tunnel junctions prepared by high-temperature in situ annealing above 400 °C, circumventing Mn diffusion conventionally caused by postannealing process. The high temperature in situ annealing leads to Ru diffusion at the CoFeB/Ru interfaces, and thereby results in a reduction in tunnel magnetoresistance (TMR). The minimization of Ru diffusion during the in situ annealing provides a large TMR of 294% at room temperature with an exchange-bias field of 280 Oe. In addition, the temperature and voltage dependence of TMR reveals that there is neither significant spin-exchange scattering nor severe impurity-assisted scattering in the MgO barrier.
Three crystallographers share this year’s chemistry Nobel
Authors: Day Charles
Published: December 2009

The ribosome is a massive molecule that decodes genes to make proteins. In 2000, three independent groups determined its structure with atomic resolution.
Sensitive cantilevers detect the persistent currents in normal-metal rings
Authors: Wilson Mark
Published: December 2009

A torque magnetometer can measure the currents with a precision two orders of magnitude greater than is possible with the usual tool of choice, a superconducting quantum interference device.
JET gets new wall to prep for ITER
Authors: Feder Toni
Published: December 2009

An elaborate, remote-controlled revamping of JET has begun.
Augustine panel urges more autonomy for NASA
Authors: Kramer David
Published: December 2009

Congressionally imposed restrictions limit NASA managers’ capacity to streamline operations.
DOE names winners of long-shot energy research grants
Authors: Kramer David
Published: December 2009

Billions of dollars will flow into “smart grid” projects.
Lighting and astronomy
Authors: Luginbuhl Christian B. , Walker Constance E. , Wainscoat Richard J.
Published: December 2009

The rapid growth of light pollution threatens the future of astronomical observation. Detailed modeling of how light from the ground propagates through the atmosphere suggests ways to limit the damage.
Charles Sanders Peirce and the first absolute measurement standard
Authors: Crease Robert P.
Published: December 2009

In his brilliant but troubled life, Peirce was a pioneer in both metrology and philosophy.
What causes road noise?
Authors: Rasmussen Robert Otto , Donavan Paul R.
Published: December 2009

Scientists understand the individual characteristics of roads and tires that contribute to tire-pavement noise. Nonetheless, engineering a quiet ride remains a challenge.
Essential roles of CKIδ and CKIε in the mammalian circadian clock
Authors: Lee Hyeongmin , Chen Rongmin , Lee Yongjin , Yoo Seunghee , Lee Choogon
Published: December 2009

Circadian rhythms in mammals are generated by a negative transcriptional feedback loop in which PERIOD (PER) is rate-limiting for feedback inhibition. Casein kinases Iδ and Iε (CKIδ/ε) can regulate temporal abundance/activity of PER by phosphorylation-mediated degradation and cellular localization. Despite their potentially crucial effects on PER, it has not been demonstrated in a mammalian system that these kinases play essential roles in circadian rhythm generation as does their homolog in
Drosophila
. To disrupt both CKIδ/ε while avoiding the embryonic lethality of CKIδ disruption in mice, we used CKIδ-deficient

Per2
Luc

mouse embryonic fibroblasts (MEFs) and overexpressed a dominant-negative mutant CKIε (DN-CKIε) in the mutant MEFs. CKIδ-deficient MEFs exhibited a robust circadian rhythm, albeit with a longer period, suggesting that the cells possess a way to compensate for CKIδ loss. When CKIε activity was disrupted by the DN-CKIε in the mutant MEFs, circadian bioluminescence rhythms were eliminated and rhythms in endogenous PER abundance and phosphorylation were severely compromised, demonstrating that CKIδ/ε are indeed essential kinases for the clockwork. This is further supported by abolition of circadian rhythms when physical interaction between PER and CKIδ/ε was disrupted by overexpressing the CKIδ/ε binding domain of PER2 (CKBD-P2). Interestingly, CKBD-P2 overexpression led to dramatically low levels of endogenous PER, while PER-binding, kinase-inactive DN-CKIε did not, suggesting that CKIδ/ε may have a non-catalytic role in stabilizing PER. Our results show that an essential role of CKIδ/ε is conserved between
Drosophila
and mammals, but CKIδ/ε and DBT may have divergent non-catalytic functions in the clockwork as well.
EIN3/EIL1 cooperate with PIF1 to prevent photo-oxidation and to promote greening of
Arabidopsis
seedlings
Authors: Zhong Shangwei , Zhao Mantong , Shi Tianying , Shi Hui , An Fengying , Zhao Qiong , Guo Hongwei
Published: December 2009

The ability to switch from skotomorphogenesis to photomorphogenesis is essential for seedling development and plant survival. Recent studies revealed that COP1 and phytochrome-interacting factors (PIFs) are key regulators of this transition by repressing the photomorphogenic responses and/or maintaining the skotomorphogenic state of etiolated seedlings. Here we report that the plant hormone ethylene plays a crucial role in the transition from skotomorphogenesis to photomorphogenesis by facilitating greening of etiolated seedlings upon light irradiation. Activation of EIN3/EIL1 is both necessary and sufficient for ethylene-induced enhancement of seedling greening, as well as repression of the accumulation of protochlorophyllide, a phototoxic intermediate of chlorophyll synthesis. EIN3/EIL1 were found to induce gene expression of two key enzymes in the chlorophyll synthesis pathway, protochlorophyllide oxidoreductase A and B (PORA/B). ChIP and EMSA assays demonstrated that EIN3 directly binds to the specific elements present in the
PORA
and
PORB
promoters. Genetic studies revealed that EIN3/EIL1 function in cooperation with PIF1 in preventing photo-oxidative damage and promoting cotyledon greening. Moreover, activation of EIN3 reverses the blockage of greening triggered by
cop1
mutation or far-red light irradiation. Consistently, EIN3 acts downstream of COP1 and its protein accumulation is enhanced by COP1 but decreased by light. Taken together, EIN3/EIL1 represent a new class of transcriptional regulators along with PIF1 to optimize de-etiolation of
Arabidopsis
seedlings. Our study highlights the essential role of ethylene in enhancing seedling development and survival through protecting etiolated seedlings against photo-oxidative damage.
Anger Management Training in Incarcerated Male Offenders: Differential Impact on Proactive and Reactive Criminal Thinking
Authors: Walters GlennD.
Published: December 2009

Forty-seven male federal prison inmates who completed a six-week/eight-hour anger management class were administered the 35-item short form of the Psychological Inventory of Criminal Thinking Styles (PICTS) during the first class session and again during the final class session. It was hypothesized that anger management training would have an ameliorative effect on the hostile or reactive component of criminal thinking, as measured by the PICTS Reactive (R) criminal thinking scale, but have little or no effect on the instrumental or proactive component of criminal thinking, as measured by the PICTS Proactive (P) criminal thinking scale. Consistent with this hypothesis, the R scale displayed a significant pre-test/post-test decline, whereas the P scale showed no significant change between the two testings. The theoretical and clinical implications of these findings are discussed.
The effect of pseudoephedrine on self‐paced endurance cycling performance
Authors: Betteridge Scott , Mündel Toby , Stannard Stephen
Published: December 2009

The purpose of this study was to investigate the effects of pseudoephedrine ingestion on endurance cycling performance. Using a double‐blind, randomized cross‐over design, eight well‐trained cyclists (VO2max=69±2 ml · kg−1 · min−1) performed two self‐paced performance time‐trials in the laboratory at least 6 days apart. Ninety minutes before the trial, the participants consumed either placebo or pseudoephedrine (2.5 mg · kg−1bw). The time‐trial required completion of a set amount of work, equivalent to riding at 150 min at a power output calculated to elicit 70% VO2max. Venous blood samples were collected just before starting the trial, then at every 20% increment completed work until the required work was completed. Although time to complete the trial was quicker for five of the eight participants, there was no significant effect of pseudoephedrine on performance (P=0.235), or blood glucose or lactate, between trials. However, heart rate was significantly higher with pseudoephedrine consumption compared with placebo (P< 0.05). The results of this study indicate that pseudoephedrine has no effect on self‐paced endurance exercise performance, but may affect the cardiac response to exercise.
Semantic Ambiguity within and across Languages: An Integrative Review
Authors: Degani Tamar , Tokowicz Natasha
Published: December 2009

Semantic ambiguity often occurs within a language (e.g., the word “organ” in English means both a body part and a musical instrument), but it can also cross a language boundary, such that a given word form is shared in two languages, but its meanings are different (e.g., the word “angel” means “sting” in Dutch). Bilingual individuals are therefore faced not only with ambiguity in each of their languages, but also with ambiguity across languages. The current review focuses on studies that explored such cross-language ambiguity and examines how the results from these studies can be integrated with what we have learned about within-language ambiguity resolution. In particular, this review examines how interactions of frequency and context manifest themselves in ambiguity that crosses a language boundary and call for the inclusion of language context as a contributing factor. An extension of the monolingual reordered access model (Duffy, Morris, & Rayner, 1988) is outlined to discuss the interactions between these factors. Furthermore, the effects of the similarity between the two meanings, task differences, and individual differences are explored. This review highlights the need for studies that test within- and cross-language ambiguity in the same individuals before strong conclusions can be made about the nature of interactions between frequency, semantic context, and language context.
Imipenem Resistance in Pseudomonas aeruginosa Emergence, Epidemiology, and Impact on Clinical and Economic Outcomes
Authors: Lautenbach Ebbing , Synnestvedt Marie , Weiner Mark G. , Bilker Warren B. , Vo Lien , Schein Jeff , Kim Myoung
Published: December 2009

Background.

Pseudomonas aeruginosa is one of the most common gram-negative hospital-acquired pathogens. Resistance of this organism to imipenem complicates treatment.

Objective.

To elucidate the risk factors for imipenem-resistant P. aeruginosa (IRPA) infection or colonization and to identify the effect of resistance on clinical and economic outcomes.

Methods.

Longitudinal trends in prevalence of IRPA from 2 centers were characterized during the period from 1989 through 2006. For P. aeruginosa isolates obtained during the period from 2001 through 2006, a case-control study was conducted to investigate the association between prior carbapenem use and IRPA infection or colonization, and a cohort study was performed to identify the effect of IRPA infection or colonization on mortality, length of stay after culture, and hospital cost after culture.

Results.

From 1989 through 2006, the proportion of P. aeruginosa isolates demonstrating resistance to imipenem increased from 13% to 20% (P< .001, trend). During the period from 2001 through 2006, there were 2,542 unique patients with P. aeruginosa isolates, and 253 (10.0%) had IRPA isolates. Prior carbapenem use was independently associated with IRPA infection or colonization (adjusted odds ratio [OR], 7.92 [95% confidence interval {CI}, 4.78-13.11]). Patients with an IRPA isolate recovered had higher in-hospital mortality than did patients with an imipenem-susceptible P. aeruginosa isolate (17.4% vs 13.4%; P = .01). IRPA infection or colonization was an independent risk factor for mortality among patients with isolates recovered from blood (adjusted OR, 5.43 [95% CI, 1.72-17.10]; P = .004) but not among patients with isolates recovered from other anatomic sites (adjusted OR, 0.78 [95% CI, 0.51-1.21]; P = .27). Isolation of IRPA was associated with longer hospital stay after culture (P<.001) and greater hospital cost after culture (P<.001) than was isolation of an imipenem-susceptible strain. In multivariable analysis, IRPA infection or colonization remained an independent risk factor for both longer hospital stay after culture (coefficient, 0.20 [95% CI, 0.04-0.36]; P = .02) and greater hospital cost after culture (coefficient, 0.30 [95% CI, 0.06-0.54]; P = .02).

Conclusions.

The prevalence of IRPA infection or colonization has increased significantly, with important implications for both clinical and economic outcomes. Interventions to curb this continued increase and strategies to optimize therapy are urgently needed.
Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila
Authors: Lu Jian , Clark Andrew G.
Published: December 2009

Transposable elements (TEs) are mobile DNA sequences that make up a large fraction of eukaryotic genomes. Recently it was discovered that PIWI-interacting RNAs (piRNAs), a class of small RNA molecules that are mainly generated from transposable elements, are crucial repressors of active TEs in the germline of fruit flies. By quantifying expression levels of 32 TE families in piRNA pathway mutants relative to wild-type fruit flies, we provide evidence that piRNAs can severely silence the activities of retrotransposons. We incorporate piRNAs into a population genetic framework for retrotransposons and perform forward simulations to model the population dynamics of piRNA loci and their targets. Using parameters optimized for Drosophila melanogaster, our simulation results indicate that (1) piRNAs can significantly reduce the fitness cost of retrotransposons; (2) retrotransposons that generate piRNAs (piRTs) are selectively more advantageous, and such retrotransposon insertions more easily attain high frequency or fixation; (3) retrotransposons that are repressed by piRNAs (targetRTs), however, also have an elevated probability of reaching high frequency or fixation in the population because their deleterious effects are attenuated. By surveying the polymorphisms of piRT and targetRT insertions across nine strains of D. melanogaster, we verified these theoretical predictions with population genomic data. Our theoretical and empirical analysis suggests that piRNAs can significantly increase the fitness of individuals that bear them; however, piRNAs may provide a shelter or Trojan horse for retrotransposons, allowing them to increase in frequency in a population by shielding the host from the deleterious consequences of retrotransposition.
Dignam and Roeder Nuclear Extract Preparation
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T.
Published: December 2009

INTRODUCTION

In this protocol for Dignam and Roeder nuclear extract preparation, HeLa cells are harvested by centrifugation, washed, and resuspended in a hypotonic buffer, which causes the cells to swell. Subsequently, the cells are lysed with a handheld Dounce homogenizer. The nuclei are pelleted by centrifugation, the cytoplasmic supernatant is decanted, and the nuclear pellet is resuspended by Dounce homogenization in a moderate salt buffer. After stirring the suspension for 30 min to allow extraction of transcription factors, the nuclei are centrifuged again, and the resulting supernatant or extract is dialyzed for use in transcription experiments. Generally, 1 L of culture (i.e., 1-2 g of cells, depending on cell density at harvest) yields 1-2 mL of extract at 6-10 mg/mL. This should provide enough extract for ~50-100 in vitro transcription reactions, depending on the scale.
Surgery on Tammar Wallaby (Macropus eugenii) Pouch Young
Authors: Hickford Danielle , Frankenberg Stephen , Renfree Marilyn B.
Published: December 2009

INTRODUCTION

Two features of marsupial young make them ideal for developmental studies: (1) Their immune system, like that of the thyroid and thermoregulation, develops relatively late after birth, and (2) they tolerate xenografts. This late development allows transplants to grow and survive in the recipient for at least 150 d without the use of immunosuppressants. The immaturity of the organ systems and the tiny size of the neonate pose difficulties for anesthesia. However, because the pouch young are completely heterothermic until at least 3 mo of age, cooling can be used as an anesthetic agent. In practice, however, we use hypothermia for neonates and young up to the age of 25-30 d, and injectable anethetics thereafter. Healing is remarkably rapid. This tolerance of xenografts and the ability and ease with which hypothermia can be applied to marsupial young provides a unique approach to understanding developmental processes that normally take place in utero in eutherians. This protocol describes surgical procedures and post-surgical care performed on tammar wallaby (Macropus eugenii) pouch young (PY).
Immunohistochemical Staining of Sectioned Tammar Wallaby (Macropus eugenii) Tissue
Authors: Hickford Danielle , Frankenberg Stephen , Renfree Marilyn B.
Published: December 2009

INTRODUCTION

Although standard immunohistochemical protocols are used for staining tammar wallaby (Macropus eugenii) tissues, sometimes the tammar protein sequence differs slightly from that of the species against which the antibody was raised. If possible, obtain sequence for the marsupial protein to see which regions of the protein are the most highly conserved between marsupials and eutherians. When purchasing an antibody, if possible, choose one that has shown reactivity across a broad range of species, and preferably choose a polyclonal rather than a monoclonal. Because a tammar epitope may differ slightly from the one against which an antibody was raised, it may be affected differently by fixation, especially if fixatives (such as paraformaldehyde [PFA] or formalin) that cross-link proteins are used. When testing a new antibody on tammar tissues, we therefore routinely test numerous pretreatments to see which one gives optimal staining. In some cases, the optimal pretreatment differs from that suggested by the manufacturer of the antibody. This protocol describes how to use the avidin-biotin complex detection method on paraffin-embedded specimens.
Analyzing Microorganisms in Environmental Samples Using Stable Isotope Probing with H218O
Authors: Schwartz Egbert
Published: December 2009

INTRODUCTION

When analyzing environmental samples of microorganisms by stable isotope probing (SIP), labeling the DNA with H218O, instead of organic or nitrogenous compounds, offers important advantages because water cannot be used as an energy, carbon, or nitrogen source. As a result, addition of the label is unlikely to influence microbial growth rates in soil directly, and microbial communities can be exposed to the label for long periods of time because they are not exposed to abnormally high substrate concentrations. Because all organisms incorporate water into their DNA, performing SIP with H218O is a method for identifying microorganisms that have grown during incubation with H218O, as well as microorganisms that have not grown (i.e., did not incorporate the label) but survived the incubation. This protocol describes the use of SIP with H218O to study soil microorganisms.
Electroporation of Transgenic DNAs in the Sea Squirt Ciona
Authors: Christiaen Lionel , Wagner Eileen , Shi Weiyang , Levine Michael
Published: December 2009

INTRODUCTION

The electroporation method described here is probably the mainstay of sea squirt (Ciona) research, because the utility of transgene expression in staged embryo populations enables a wide array of biological questions to be addressed. It allows rapid identification and characterization of cis-regulatory DNA, such as tissue-specific enhancers. Electroporation of plasmids expressing fluorescent reporter genes permits live imaging and lineage tracing. Finally, structure-function relationships can be examined by expressing dominant-negative or constitutively active forms of specific proteins using appropriate cell-specific enhancers.
X-gal Staining of Electroporated Sea Squirt (Ciona) Embryos
Authors: Christiaen Lionel , Wagner Eileen , Shi Weiyang , Levine Michael
Published: December 2009

INTRODUCTION

This protocol describes the fixation, staining, and mounting of sea squirt (Ciona intestinalis) embryos and larvae that have been electroporated with a plasmid DNA containing a cis-regulatory DNA (e.g., tissue-specific enhancer) fused to the lacZ reporter gene. Green fluorescent protein (GFP) reporter genes can be directly visualized in living embryos and larvae, although fixed preparations can use aspects of this protocol.
Whole-Mount In Situ Hybridization on Sea Squirt (Ciona intestinalis) Embryos
Authors: Christiaen Lionel , Wagner Eileen , Shi Weiyang , Levine Michael
Published: December 2009

INTRODUCTION

This protocol describes whole-mount in situ hybridization on sea squirt (Ciona intestinalis) embryos. This method is a mainstay of the sea squirt (Ciona) research community. It permits the detailed visualization of gene expression at single-cell resolution. It has been used to detect localized maternal mRNAs in the fertilized egg and to identify restricted patterns of gene expression within individual cells of the developing central nervous system at advanced stages of development, including swimming tadpoles.
Fluorescent Protein Tracking and Detection: Applications Using Fluorescent Proteins in Living Cells
Authors: Rizzo Mark A. , Davidson Michael W. , Piston David W.
Published: December 2009

INTRODUCTION

Fluorescent proteins (FPs) are quite versatile imaging probes and have been successfully employed in almost every biological discipline from microbiology to systems physiology. They are extremely useful as reporters for gene-expression studies in cultured cells, excised tissues, and whole animals. In this article, the discussion of FP applications will be focused on live cell microscopy techniques. In live cells, FPs are most commonly used to track the localization and dynamics of proteins, organelles, and other cellular compartments. FPs can also be used to assess protein-protein interactions in living cells through the use of fluorescence resonance energy transfer (FRET). This article provides some general tips for the practical aspects of using and imaging enhanced green fluorescent protein (EGFP) and newer members of the color palette, as well as quantitative imaging of FPs and imaging of several FPs at the same time. Finally, an overview is provided for the different types of biosensors that have been derived from FPs.
Computational Modeling and Molecular Physiology Experiments Reveal New Insights into Shoot Branching in Pea
Authors: Dun Elizabeth A. , Hanan Jim , Beveridge Christine A.
Published: December 2009

Bud outgrowth is regulated by the interplay of multiple hormones, including auxin, cytokinin, strigolactones, and an unidentified long-distance feedback signal that moves from shoot to root. The model of bud outgrowth regulation in pea (Pisum sativum) includes these signals and a network of five RAMOSUS (RMS) genes that operate in a shoot-root-shoot loop to regulate the synthesis of, and response to, strigolactones. The number of components in this network renders the integration of new and existing hypotheses both complex and cumbersome. A hypothesis-driven computational model was therefore developed to help understand regulation of shoot branching. The model evolved in parallel with stepwise laboratory research, helping to define and test key hypotheses. The computational model was used to verify new mechanisms involved in the regulation of shoot branching by confirming that the new hypotheses captured all relevant biological data sets. Based on cytokinin and RMS1 expression analyses, this model is extended to include subtle but important differences in the function of RMS3 and RMS4 genes in the shoot and rootstock. Additionally, this research indicates that a branch-derived signal upregulates RMS1 expression independent of the other feedback signal. Furthermore, we propose xylem-sap cytokinin promotes sustained bud outgrowth, rather than acting at the earlier stage of bud release.
Phylogeny of the genusPalmanura(Collembola: Neanuridae)
Authors: Vargas José G. Palacios , García‐Barros Enrique , Simón Benito José C.
Published: December 2009

In order to assess the phylogenetic structure of the springtail genusPalmanura, as well as to test the monophyly of the tribe Sensillanurini (Neanuridae: Neanurinae), a data matrix of morphological (chaetotactic and other) characters of members of this group was assembled and analysed in the light of Wagner parsimony. The data matrix included all the known members of the Neotropical genusPalmanura, plus representatives ofSensillanuraandAmericanura. Although not all the clades obtained were highly supported by bootstrap resampling, some structures were relatively constant under different approaches. Alternative analyses (unordered and ordered character states, rescaled weighting procedure) were applied. While alternative solutions were obtained, a number of structures were shared by the results irrespective of the method used. On this basis, the results suggest that some further reassessment is required to confirm formally the monophyly of the tribe Sensillanurini. The generaPalmanuraandAmericanuraare mutually poly/paraphyletic; we thus suggest thatPalmanurashould be considered as a synonym ofAmericanura, although some character reassessment and more varied outgroup species may be necessary before a formal generic redefinition can be proposed. Finally, a comparison of the performance of the characters under Wagner parsimony analysis indicated that differences in the characters’ retention indexes are due not to the topological (tagmal) position of the traits involved, but to character coding: the characters describing quantitative features (generally numbers of setae) generally performed worse than other types of characters under parsimony. An updated list of the known members of the Sensillanurini (Collembola: Neanuridae: Neanurinae) is presented. © The Willi Hennig Society 2009.
Inter‐hospital transfers of acutely ill adults in Scotland*
Authors: Fried M. J. , Bruce J. , Colquhoun R. , Smith G.
Published: December 2009

The transfer of acutely ill adults who were transported between hospitals by the Scottish Ambulance Service was audited in order to determine the number of transfers and to quantify the incidence of adverse events. Patients over 16 years of age requiring intervention/vital signs monitoring during transfer or a nursing/medical escort from the outset were defined as acutely ill adults. Three thousand and forty‐eight audit forms were received, of which 2396 were suitable for inclusion in the audit. Transfers primarily occurred for specialist management (1580; 66%) or specialist investigation (550; 23%). Clinicians escorted 825 (34%) patients and were away from their hospital a median (IQR [range]) of 2 h (01:24–3:30 [00:05–17:33]) h:min Clinical intervention was required in 84 transfers (4%). The median (IQR [range]) time for 248 transfers (10.3%) requiring assisted ventilation was 28 min (00:17–00:50 [00:04–02:55]). The incidence of unsecured medical equipment (in escorted transfers only) was significantly lower in dedicated transport teams (2/205, 1%) vs non‐dedicated (113/620, 18%; p = 0.004). Medical equipment failures were less common in the transfer of patients requiring assisted ventilation (1/156, 0.6% vs 9/97, 9%; p = 0.001).
Comparative study of early interactions in mother–child dyads and care centre staff–child within the context of Chilean crèches
Authors: Pía Santelices M. , Olhaberry M. , Paz Pérez‐Salas C. , Carvacho C.
Published: December 2009

Background  Bowlby developed the concept of ‘caregiver’ to refer to significant adults with whom young children interact daily. Not only parents are considered significant caregivers but also the care centre staff where the child attends regularly. Within caregiver–infant interactions, sensitive response on the part of the adult is a key concept in the assessment of the quality of the relationship, as it integrates the experiences and emotions that will influence the attainment of a secure attachment and a favourable emotional, social and cognitive development in the child.

Methods  This study is a comparative analysis between the dyadic interactions between a child and its principal caregivers in the home and in the crèche; it is based on a group of 185 children between 8 and 24 months old, who attend a crèche regularly. The Care‐Index instrument was used to assess interaction between children and adults, analysing sensitive response in the adults and cooperativeness in the children.

Results  The sensitive response of adults to children was complementary; mothers and primary caregivers showed greater sensitivity in the affective aspects of the interaction, while the care centre staff showed greater sensitivity in the cognitive aspects. The fact that caregivers show significant differences in response sensitivity is consistent with existing studies, as are corresponding significant differences in the children's cooperativeness, which demonstrates that a child could benefit from interacting with adults whose different skills could strengthen diverse aspects of health child development.

Conclusions  The presence of children in the crèche can be a positive experience in that it favours quality exchanges with the child, developing cognitive aspects of the interaction which are cultivated to a lesser degree by mothers or primary caregivers who principally develop affective aspects.
Benefit finding in survivors of childhood cancer and their parents: further empirical support for the Benefit Finding Scale for Children
Authors: Michel G. , Taylor N. , Absolom K. , Eiser C.
Published: December 2009

Background  Diagnosis of a life‐threatening condition has been linked to post‐traumatic stress. However, only recently has it been acknowledged that positive outcomes including post‐traumatic growth or benefit finding may also occur. The aim of our study was to extend previous work describing benefit finding among survivors of childhood cancer, by determining the contribution of demographic and medical variables and associations between child benefit finding and parent post‐traumatic growth.

Methods  Survivors of any child cancer (leukaemia, central nervous system or solid tumour; age 12–15 years; completed treatment >2 years) were recruited from routine follow‐up clinics and asked to complete questionnaires [Benefit Finding Scale for Children (BFSC), quality of life (QOL), post‐traumatic stress (PTS), illness perception and optimism]. Parents completed parallel measures to describe their own post‐traumatic growth (PTG), QOL, PTS and illness perception.

Results  Forty‐eight survivors and parents completed questionnaires (response rate: 81%). The BFSC showed good internal reliability (alpha = 0.91). Diagnosis of leukaemia, greater optimism and reports that the illness still affects their life today were associated with higher scores on the BFSC among survivors themselves. For parents, perceptions of how much the illness still affects them emotionally was associated with PTG. There was no association between children's benefit finding and parents' PTG.

Conclusions  The BFSC is a useful and reliable instrument to assess positive outcomes after cancer in children. The extent to which survivors are optimistic and perceive on‐going effects of the illness on their daily lives is significantly associated with the ability to find benefit after end of treatment.
Adolescent obesity in Syria: prevalence and associated factors
Authors: Nasreddine L. , Mehio‐Sibai A. , Mrayati M. , Adra N. , Hwalla N.
Published: December 2009

Background Data on the prevalence of overweight and obesity in Eastern Mediterranean countries remain scarce, particularly for children and adolescents. The objective of this study is to estimate the prevalence of obesity and examine associated factors and covariates amongst school adolescents in Syria.

Methods A cross‐sectional survey of a representative sample of 776 adolescents (386 males and 390 females), aged 15–18 years, was conducted in six randomly chosen secondary schools in Damascus, the capital city of Syria. Anthropometric measurements and dietary assessment data were collected using standard methods and techniques. Overweight and obesity were defined according to World Health Organization 2007 child growth standards.

Results The prevalence rates of overweight and obesity were estimated at 18.9 and 8.6%, respectively. Carbohydrate and saturated fatty acid intakes were significantly higher amongst overweight and obese (250.66 and 32.82 g/day, respectively) as compared with normal weight adolescents (218.12 and 26.10 g/day, respectively). Regression analysis showed that the likelihood of obesity was significantly greater amongst adolescent boys than girls (OR = 2.30,P< 0.05) and amongst subjects reporting family history of obesity (OR = 2.98,P< 0.05). The odds of obesity increased consistently with increasing educational attainment of both parents and was higher (OR = 1.63) amongst adolescents reporting lower crowding index than their counterparts.

Conclusion Our findings of a positive association between obesity and socio‐economic status measured by parental education and crowding index call for intervention strategies for the promotion of healthy dietary practices not only amongst school adolescents but also parents, targeting families as the unit of intervention. Further studies are needed to examine nutritional habits and food choices amongst families of different socio‐economic strata.
Controlled source electromagnetic three‐dimensional grid‐modelling based on a complex resistivity structure of the seafloor: effects of acquisition parameters and geometry of multi‐layered resistors
Authors: Bhuyian Anwar H. , Thrane Bård P. , Landrø Martin , Johansen Ståle E.
Published: December 2009

A comprehensive controlled source electromagnetic (CSEM) modelling study, based on complex resistivity structures in a deep marine geological setting, is conducted. The study demonstrates the effects of acquisition parameters and multi‐layered resistors on CSEM responses. Three‐dimensional (3D) finite difference time domain (FDTD) grid‐modelling is used for CSEM sensitivity analysis. Interpolation of normalized CSEM responses provides attributes representing relative sensitivity of the modelled structures. Modelling results show that fine grid, 1 × 1 km receiver spacing, provides good correlations between CSEM responses and the modelled structures, irrespective of source orientation. The resolution of CSEM attributes decreases for receiver spacing >2 × 2 km, when using only in‐line data. Broadside data in the grid geometry increase data density by 100 – approximately 200% by filling in in‐line responses and improve the resolution of CSEM attributes. Optimized source orientation (i.e., oblique to the strike of an elongated resistor) improves the structural definition of the CSEM anomalies for coarse‐grid geometries (receiver spacing ≥3 × 3 km). The study also shows that a multi‐resistor anomaly is not simply the summation but a cumulative response with mutual interference between constituent resistors. The combined response of constituent resistors is approximately 50% higher than the cumulative response of the multi‐resistor for 0.5 Hz at 4000 m offset. A gradual inverse variation of offset and frequency allows differentiation of CSEM anomalies for multi‐layered resistors. Similar frequency‐offset variations for laterally persistent high‐resistivity facies show visual continuity with varying geometric expressions. 3D grid‐modelling is an effective and adequate tool for CSEM survey design and sensitivity analysis.
On shear‐wave triplications in a multilayered transeversely isotropic medium with vertical symmetry axis
Authors: Roganov Yuriy , Stovas Alexey
Published: December 2009

The presence of triplications (caustics) can be a serious problem in seismic data processing and analysis. The traveltime curve becomes multi‐valued and the geometrical spreading correction factor tends to zero due to energy focusing.

We analyse the conditions for the qSV‐wave triplications in a homogeneous transversely isotropic medium with vertical symmetry axis. The proposed technique can easily be extended to the case of horizontally layered vertical symmetry axis medium. We show that the triplications of the qSV‐wave in a multilayered medium imply certain algebra. We illustrate this algebra on a two‐layer vertical symmetry axis model.
Drosophila G9a is implicated in germ cell development
Authors: Lee K.‐S. , Yoon J. , Park J. S. , Kang Y.‐K.
Published: December 2009

In Drosophila ovaries, germline stem cells (GSCs) divide asymmetrically in the germaria to produce daughter GSCs and cystoblasts. Single cystoblasts differentiate to form germline cysts with 16 germline cells, all of which are connected by the fusome, a vesiculated structure critical for oocyte specification. We here show that histone H3K9 methyltransferase dg9a is associated with spectrosome/fusome formation in the germarium; dG9a13414 mutant ovaries have disorganized spectrosome/fusome in about half the germaria, with reduced levels of hu‐li tai shao and α‐SPECTRIN proteins. We found that the amount of germline cells within cysts was reduced and that oocyte determination often failed in egg chambers of the dG9a13414 mutant ovaries. These results suggest that a mutation in dG9a gene gives rise to anomalous spectrosome/fusome structures, which in turn lead to faulty germ‐cell development in Drosophila ovaries.
Influence of factors related to implant stability detected by wireless resonance frequency analysis device
Authors: OHTA K. , TAKECHI M. , MINAMI M. , SHIGEISHI H. , HIRAOKA M. , NISHIMURA M. , KAMATA N.
Published: December 2009

Summary  Resonance frequency analysis (RFA) was introduced as a method for measuring implant stability more than a decade ago. Implant stability quotient (ISQ) values obtained using a recently introduced wireless RFA device have made it possible to evaluate stability in a non‐invasive technique; however, there are few studies of the factors that affect ISQ values determined using this device. The aim of the present study was to evaluate the association between ISQ values determined by wireless RFA and various factors related to dental implant stability using a pig cortical bone model. Dental implants (Replace® Select Tapered implants) with a length of 10 mm were placed into pig cortical bone samples, then, ISQ values were determined using wireless RFA under various conditions (probe orientation, diameter of implant, insertion torque and peri‐implant bone loss). The results of this study showed that ISQ values were not affected by the direction of the probe from parallel to perpendicular to the long axis of the pig bone or to the smart peg. In addition, the diameter of the implant did not have a significant effect on the measured ISQ values. Statistically significant correlations were found between insertion torque and ISQ values (Spearman’s test, P < 0·05), and lower ISQ values were observed for deeper peri‐implant vertical defects (Mann–Whitney U‐test, P < 0·05). A wireless RFA device appears to be useful for measuring implant stability within the limits of the present in vitro study.
Soy extract phytoestrogens with high dose of isoflavones for menopausal symptoms
Authors: Ferrari Augusto
Published: December 2009

Aim:  The aim of the present study was to assess the efficacy and safety of a standardized compound based on an extract of soy phytoestrogens, with high doses of isoflavones in the management of menopausal hot flushes.

Methods:  A total of 180 women aged 40–65 years with a minimum of five moderate‐to‐severe hot flushes in the last 7 days at baseline and absence of menstruation for at least 6 months participated in a 12‐week prospective, randomized, double‐blind, placebo‐controlled multicenter trial. After a 2‐week run‐in period, women received one tablet a day of 80 mg isoflavones (corresponding to 60 mg of genistein) or a matching placebo.

Results:  The mean daily number of moderate‐to‐severe hot flushes decreased in both study groups, but the reduction was greater in the isoflavones arm at 6 (36.2%) and 12 weeks (41.2%) than in the placebo arm (24.0% at 6 weeks, 29.3% at 12 weeks), with a difference of 1.1 (95% CI [−2.0 to −0.06]) (P = 0.038) at 6 weeks and 1.1 (95% CI [−2.05 to −0.15]) (P = 0.023) at 12 weeks. Similar findings were obtained for hot flushes of any intensity. The Kupperman index decreased in both study groups. Relief of hot flushes was greater when time to menopause was ≥12 months and in cases of BMI ≥27 kg/m2.

Conclusion:  In daily practice conditions, high doses of isoflavones, particularly genistein, can be used for the management of hot flushes in postmenopausal women not treated with hormone replacement therapy due to their superior efficacy to placebo and very good safety profile.