bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of GSK‐3 in synaptic plasticity
Authors: Peineau S , Bradley C , Taghibiglou C , Doherty A , Bortolotto Z A , Wang Y T , Collingridge G L
Published: March 2008

Glycogen synthase kinase‐3 (GSK‐3), an important component of the glycogen metabolism pathway, is highly expressed in the CNS. It has been implicated in major neurological disorders including Alzheimer's disease, schizophrenia and bipolar disorders. Despite its central role in these conditions it was not known until recently whether GSK‐3 has neuronal‐specific functions under normal conditions. However recent work has shown that GSK‐3 is involved in the regulation of, and cross‐talk between, two major forms of synaptic plasticity, N‐methyl‐D‐aspartate receptor (NMDAR)‐dependent long‐term potentiation (LTP) and NMDAR‐dependent long‐term depression (LTD). The present article summarizes this recent work and discusses its potential relevance to the treatment of neurological disorders.

British Journal of Pharmacology (2008) 153, S428–S437; doi:10.1038/bjp.2008.2
Influence of the metabolic profile on the in vivo antioxidant activity of quercetin under a low dosage oral regimen in rats
Authors: Santos M R , Rodríguez‐Gómez M J , Justino G C , Charro N , Florencio M H , Mira L
Published: March 2008

Background and purpose

Flavonoids are known to possess a broad set of pharmacological effects, some of which have been attributed to their antioxidant properties and, more recently, to cell signalling modulation. Nevertheless, flavonoids are extensively metabolized and their metabolites are the potential bioactive forms in vivo. Therefore, a first and crucial step to understand the mechanisms underlying potential health benefits of flavonoids is knowledge of their metabolites and their biological activities.

Experimental approach

To approximate a human dietary pattern of intake of flavonoids, regular rat chow was supplemented with 0.02% quercetin and fed to Sprague–Dawley rats over 3 weeks. Plasma samples were analysed by HPLC and electrospray tandem mass spectrometry, and plasma antioxidant capacity was measured by the 2,2′‐azino‐bis(3‐ethylbenzothiazoline sulphonate) assay.

Key results

Major metabolites were 3′‐methylquercetin (isorhamnetin) glucuronide sulphate conjugates, the most plausible conjugation positions being at the 3‐, 5‐ and 7‐hydroxyl positions. Isorhamnetin conjugates are methylated at the 3′‐OH position, which decreases the high antioxidant activity of quercetin and its metabolites and their contribution to plasma antioxidant potential.

Conclusions and implications

This metabolic pattern differs from that observed after a single high‐dose administration, where the major metabolites were quercetin conjugates at 5‐ and 7‐hydroxyl positions and a significantly increased plasma antioxidant activity was observed. These data show altogether that the different metabolic patterns obtained under a prolonged low‐dosage regimen or after a single high dose, crucially affected the antioxidant potential of plasma in treated animals. Our data also allow for the establishment of structure–antioxidant activity relationships for quercetin metabolites.

British Journal of Pharmacology (2008) 153, 1750–1761; doi:10.1038/bjp.2008.46; published online 3 March 2008
Asthma from a pharmacogenomic point of view
Authors: Szalai C , Ungvári I , Pelyhe L , Tölgyesi G , Falus A
Published: March 2008

Pharmacogenomics, a fascinating, emerging area of biomedical research is strongly influenced by growing availability of genomic databases, high‐throughput genomic technologies, bioinformatic tools and artificial computational modelling approaches. One main area of pharmacogenomics is the discovery of new drugs and drug targets with molecular genetic, genomic or even bioinformatic methods; the other is the study of how genomic differences influence the variability in patients' responses to drugs. From a genetic point of view, asthma is multifactorial, which means that the susceptibility to the disease is determined by interactions between multiple genes, and involves important non‐genetic factors such as the environment for their expression. In this review, we summarize collective evidence from linkage and association studies that have consistently reported suggestive linkage or association of asthma or its associated phenotypes to polymorphic markers and single nucleotide polymorphisms in selected chromosomes. Genes that have been found implicated in the disease are potential new drug targets and several pharmacological investigations are underway to utilize these new discoveries. Next, we will focus on the inter‐individual variability in anti‐asthmatic drug responses and review the recent results in this topic.

British Journal of Pharmacology (2008) 153, 1602–1614; doi:10.1038/bjp.2008.55; published online 3 March 2008
Clinical pharmacological issues in the development of acute stroke therapies
Authors: Ford G A
Published: March 2008

The demonstration of the ischaemic penumbra in animal models and the effectiveness of reperfusion therapy in humans led to considerable optimism for neuroprotection in acute stroke. Initial experience with failure of phase II and III trials led to the STAIR recommendations for pre‐clinical and clinical studies. Review of pre‐clinical studies suggests that selection of agents for clinical development may not have been optimal. The neuroprotective agent NXY‐059 fulfilled pre‐clinical and many clinical STAIR criteria but a second large phase III study failed to demonstrate any benefit. Many of the STAIR criteria have not been fulfilled in the development of recent neuroprotective agents. Other issues not addressed include the use of animal models more reflective of older stroke patients with physiological derangement, demonstration of drug distribution to the proposed site of action in humans, selection of patients with salvageable tissue, achieving very early treatment, refinement of measurement of neurological impairment and disability, and physiological optimization in proof of concept human studies. Increasing the number and quality of clinical centres undertaking acute stroke research, use of surrogate imaging markers and adaptive dose designs in phase II trials could improve the likelihood of identifying an effective neuroprotective. Neuroprotection in acute stroke remains a significant challenge but has not been clearly shown to be ineffective. Given the profound burden of stroke and limited applicability of reperfusion to currently at best 10% patients, further proof of concept studies of neuroprotection remain indicated with careful review of pre‐clinical data and more rigorous phase II trial design.

British Journal of Pharmacology (2008) 153, S112–S119; doi:10.1038/sj.bjp.0707654
Vanishing of ferromagnetic order in (Ga,Mn)As films at high hole concentrations: beyond the mean field Zener model
Authors: Cho Y. J. , Liu X. , Furdyna J. K.
Published: March 2008

The effect of relative Mn and hole concentrations on ferromagnetic order in thin (Ga,Mn)As films is investigated in using modulation doped (Al,Ga,Be)As∕(Ga,Mn)As heterostructures grown by molecular beam epitaxy. Our Hall effect measurements indicate that the hole concentration p in the (Ga,Mn)As layers increases with the amount of Be in the (Al,Ga,Be)As barrier. At low Be amount in the barrier, the Curie temperature TC of the (Ga,Mn)As layer is enhanced compared to that observed without Be doping. However, as the Be content in the (Al,Ga,Be)As barrier is increased further, this trend is reversed: TC is observed to decrease, and eventually the ferromagnetic order in (Ga,Mn)As disappears altogether, as seen in magnetization measurements. This behavior is in disagreement with the mean field Zener model of magnetic semiconductors, since that model predicts TC to be simply proportional to p1∕3. Our results suggest that this model fails at very high values of p, especially when p exceeds the Mn concentration in (Ga,Mn)As.
Angular dependence of spin-wave resonance and relaxation in half-metallic Sr2FeMoO6 films
Authors: Nosach Tetiana , Mullady Gabriella , Leifer Nicole , Adyam Venimadhav , Li Qi , Greenbaum Steven , Ren Yuhang
Published: March 2008

We investigated the magnetic anisotropic parameters and spin-wave relaxation of thin films of the ferromagnetic half-metallic Sr2FeMoO6 by ferromagnetic resonance technique. The resonance field and linewidth were recorded as a function of relative angle between applied magnetic field and crystallographic axes of the sample. The resonance field varies sinusoidally and considerable linewidth broadening occurs when the applied field is rotated parallel to the sample plane. The results are described using higher order components of anisotropy fields. We obtain the values of the cubic anisotropic field, 2K4∥∕M=0.09611T, the effective demagnetization field, 4πM−2K2⊥∕M=0.1216T, and the planar anisotropic field, 2K4⊥∕M=−0.108T. Moreover, we estimated the spin relaxation time (damping factor) from the analysis of the angular dependence of peak-to-peak linewidth, leading to an intrinsic value of α∼0.00025 (Gilbert damping).
Effect of magnetic field on the mechanical properties of magnetostrictive iron-gallium nanowires
Authors: Downey Patrick R. , Flatau Alison B. , McGary Patrick D. , Stadler Bethanie J. H.
Published: March 2008

This study experimentally investigates the elastic properties of individual iron-gallium nanowires with and without an applied magnetic bias field. The experiments were conducted with a custom manipulator stage designed for use within a scanning electron microscope, where nanowires were mechanically tested both statically and dynamically. Experiments were also performed in the presence of a 20Oe dc magnetic field in order to identify any variation in wire properties. The results suggest that iron-gallium nanowires possess an elastic modulus very similar to the macroscale value, tensile strengths of more than double the bulk material, and minor magnetic field induced stiffening at low stresses.
Pinholes in thin low resistance MgO-based magnetic tunnel junctions probed by temperature dependent transport measurements
Authors: Ventura J. , Teixeira J. M. , Araujo J. P. , Sousa J. B. , Wisniowski P. , Freitas P. P.
Published: March 2008

Magnetic tunnel junctions (MTJs) with thin crystalline MgO(001) barriers displaying large tunnel magnetoresistance (TMR) and low resistance-area product (R×A) will likely be used as the next generation sensors in read heads of ultrahigh density hard drives. However, the thin insulting barrier may result in the unwanted presence of metallic pinholes joining the two electrodes. Here we study the transport properties of thin MgO-based low resistance MTJs (barrier thickness, t=0.6nm), deposited by physical vapor deposition, with R×A values as low as 8Ωμm2 and TMR as high as 70% at room temperature. We performed temperature dependent (300–20K) resistance and magnetoresistance measurements on different samples of the same series and observed different behaviors for different samples and magnetic states. All samples showed positive dR∕dT for the parallel state due to the presence of pinholes in the barrier. However, in the antiparallel state the R(T) curves always exhibit a mixed character, with dR∕dT changing from negative to positive with decreasing temperature. Our results then show an interesting competition between tunnel and metallic transport in the studied samples.
Electron acoustic soliton in a quantum magnetoplasma
Authors: Masood W. , Mushtaq A.
Published: March 2008

A theoretical investigation is carried out for the first time to understand the linear and nonlinear properties of obliquely propagating electron-acoustic solitary waves (EASWs) in a two-electron population quantum magnetoplasma. A dispersion relation in the linear regime and the Zakharov–Kuznetsov (ZK) equation in the nonlinear regime are derived by using a quantum hydrodynamic set of equations. It is observed that the magnetic field contributes in the wave dispersion through the weakly transverse direction in the ZK equation. It is also found that propagation characteristics of the EASW are significantly affected by the presence of quantum corrections and the ratio of hot to cold electron concentration. The results presented in this study may be helpful to understand the salient features of the finite-amplitude localized electron acoustic solitary pulses in a two-population electron Fermi gas observed in laser-produced plasmas.
Toroidal field stabilization of the rotational instability in field-reversed configurations
Authors: Milroy R. D. , Steinhauer L. C.
Published: March 2008

The rotational instability almost always appears in dynamically formed field-reversed configurations (FRC). It generally appears as an m=2 mode (azimuthal mode number). Driven by the gravitylike centrifugal effect in rotating plasmas, it is akin to a gravitational mode. On the other hand, translated FRCs often do not exhibit this instability. A recent analysis [H. Y. Guo et al., Phys. Rev. Lett. 95, 17001 (2005)] suggested that magnetic shear effects associated with a modest toroidal field can stabilize it. Here the stabilizing effect of a modest toroidal field is investigated numerically using the NIMROD code [C. R. Sovinec et al., J. Comput. Phys. 195, 355 (2004)] and analytically using the modified energy principle. The analysis predicts the growth rate as a function of toroidal field strength, as well as a stability condition. The three-dimensional numerical calculations are in basic agreement with the analysis, although complete stability is not predicted due to the appearance of a distinct mode structure that persists in the open field-line region.
Ion-acoustic solitary waves in fully relativistic electron-ion plasmas
Authors: Lee Nam C.
Published: March 2008

The possibility of ion-acoustic solitary waves in a fully relativistic plasma comprised of electrons and ions is investigated by the pseudopotential method. Applying the gas-dynamic approach developed by McKenzie [Phys. Plasmas 9, 800 (2002)] to the energy conservation laws, it is shown that, as in nonrelativistic plasmas, only compressive ion-acoustic solitary waves are possible in two-component relativistic plasmas in the case where the ions are supersonic and electrons are subsonic. It is also shown that, by introducing the relativistic ion-acoustic velocity, various existence conditions for the solitary waves in relativistic two-fluid plasmas can be cast into forms that are identical to the nonrelativistic counterparts found by the gas-dynamic approach. It can be suggested that the method presented in this study can be extended for the investigation of other kinds of electrostatic solitary waves in relativistic multicomponent plasmas.
Calculation of scalar structure functions from a vortex model of turbulent passive scalar transport
Authors: Higgins Keith , Ooi Andrew , Chong M. S.
Published: March 2008

A Saffman and Pullin [Phys. Fluids 8, 3072 (1996)] type vortex model for passive scalar structure functions is formulated. The intermittent turbulent fine-scale dynamics in the model is represented by numerical solutions of the advection-diffusion and Navier–Stokes equations in the form of axially strained vortex-scalar structures. The use of these structures is motivated by Pullin and Lundgren’s [Phys. Fluids 13, 2553 (2001)] asymptotic strained spiral vortex model of turbulent passive scalar transport. Ensemble-averaged scalar structure functions, of even orders 2–10, are calculated from a range of vortex-scalar structures using Monte Carlo integration. For axisymmetric strained scalar fields, acceptable agreement of the second-order structure function with experimental data reported by Antonia and Van Atta [J. Fluid Mech. 84, 561 (1978)] is obtained. Structure functions are also calculated for a range of passive scalar spiral structures. These are generated by the winding of single and double scalar patches in single strained vortex patches and in merging strained vortices. Power-law scaling of the second- and higher-order structure functions is obtained from cases involving the winding of single scalar patches in an axisymmetric strained vortex patch. The second-order scaling exponents from these cases are in reasonable agreement with Kolmogorov–Oboukhov–Corrsin scaling and the experimental results of Antonia et al. [Phys. Rev. A 30, 2704 (1984)] and Gylfason and Warhaft [Phys. Fluids 16, 4012 (2004)]. However, the higher-order scaling exponents from these cases fall below theoretical predictions and experimental results. Higher-order moments are sensitive to the composition of the vortex-scalar structures, and various improvements are suggested that could enhance the performance of the model. The present approach is promising, and it is the first demonstration that a vortex model using simplified Navier–Stokes dynamics can produce some scalar structure functions that compare favorably with experimental observations.
Cascades and fluxes in two-dimensional turbulence
Authors: Davidson P. A.
Published: March 2008

We develop simple models of forced and unforced turbulence at large but finite Reynolds number. These models yield a number of predictions, such as (i) the form of the second- and third-order structure functions in the inertial range; (ii) the rate of generation of palinstrophy in forced and unforced turbulence; (iii) the rate of destruction of enstrophy in decaying turbulence; (iv) the rate of change of Loitsyansky’s integral in decaying turbulence; and, again for decaying turbulence; and (v) the existence of an inverse energy cascade, embedded within the direct enstrophy cascade. We show that these predictions are not mere artifacts of our simple models, but rather genuine features of two-dimensional turbulence. The most surprising findings relate to (iii), (iv), and (v) above, where we show that, once the turbulence is fully developed, the enstrophy dissipation rate scales as β∼⟨ω2⟩3∕2∕ln(Re), Loitsyansky’s integral grows at a rate proportional to βℓ6∕ln(Re), and the filamentation of vorticity fuels an inverse energy cascade with a flux of order βℓ2∕ln(Re). (Here, ω is the vorticity, ℓ is the integral scale, β the enstrophy dissipation rate, and Re the Reynolds number.) This suggests that, in the limit of Re→∞, the enstrophy dissipation rate tends to zero and the inverse energy cascade progressively shuts down. Loitsyansky’s integral is also an invariant in this limit, provided that ℓ remains finite as Re→∞.
On the dimension of subspaces with bounded Schmidt rank
Authors: Cubitt Toby , Montanaro Ashley , Winter Andreas
Published: March 2008

We consider the question of how large a subspace of a given bipartite quantum system can be when the subspace contains only highly entangled states. This is motivated in part by results of Hayden et al. [e-print arXiv:quant-ph∕0407049; Commun. Math. Phys., 265, 95 (2006)], which show that in large d×d-dimensional systems there exist random subspaces of dimension almost d2, all of whose states have entropy of entanglement at least logd−O(1). It is also a generalization of results on the dimension of completely entangled subspaces, which have connections with the construction of unextendible product bases. Here we take as entanglement measure the Schmidt rank, and determine, for every pair of local dimensions dA and dB, and every r, the largest dimension of a subspace consisting only of entangled states of Schmidt rank r or larger. This exact answer is a significant improvement on the best bounds that can be obtained using the random subspace techniques in Hayden et al. We also determine the converse: the largest dimension of a subspace with an upper bound on the Schmidt rank. Finally, we discuss the question of subspaces containing only states with Schmidt equal to r.
Control landscapes for observable preparation with open quantum systems
Authors: Wu Rebing , Pechen Alexander , Rabitz Herschel , Hsieh Michael , Tsou Benjamin
Published: March 2008

A quantum control landscape is defined as the observable as a function(al) of the system control variables. Such landscapes were introduced to provide a basis to understand the increasing number of successful experiments controlling quantum dynamics phenomena. This paper extends the concept to encompass the broader context of the environment having an influence. For the case that the open system dynamics are fully controllable, it is shown that the control landscape for open systems can be lifted to the analysis of an equivalent auxiliary landscape of a closed composite system that contains the environmental interactions. This inherent connection can be analyzed to provide relevant information about the topology of the original open system landscape. Application to the optimization of an observable expectation value reveals the same landscape simplicity observed in former studies on closed systems. In particular, no false suboptimal traps exist in the system control landscape when seeking to optimize an observable, even in the presence of complex environments. Moreover, a quantitative study of the control landscape of a system interacting with a thermal environment shows that the enhanced controllability attainable with open dynamics significantly broadens the range of the achievable observable values over the control landscape.
Indentation depth dependence of the mechanical strength of Ni films
Authors: Ma Zengsheng , Long Shiguo , Pan Yong , Zhou Yichun
Published: March 2008

The indentation depth effect has been systematically examined on the mechanical properties of electrodeposited nickel films under 0% and 10% tensile strains. It is found that the indentation depth is proportional to the square root of the loads applied and the depth profiles of hardness and elastic modulus follow the similar trend of change with maximal values at the surface skins. The hardness and modulus then attenuate to a value of about half of the maximum, which follows the model proposed by Graca et al., Surf. Coat. Technol. (in press) with the mechanism of geometrically necessary dislocations and surface free energy. We suggest that the effect of surface oxidation and surface bond contraction [C. Q. Sun, Prog. Solid State Chem. 35, 1 (2007)] contributes intrinsically to the anomalous skin strengthening because of the local strain and energy trapping caused by surface bonds breaking.
Application of quantum cascade lasers in studies of low-pressure plasmas: Characterization of rapid passage effects on density and temperature measurements
Authors: van Helden J. H. , Horrocks S. J. , Ritchie G. A. D.
Published: March 2008

The application of quantum cascade lasers in the intrapulse operation mode for low-pressure plasma spectroscopy is hampered by the observation of rapid passage effects, leading to lower quantitative accuracy. We demonstrate that accurate densities and rotational temperatures of CH4 within a CH4 plasma can be obtained by characterizing the rapid passage effects in gas phase conditions prior to carrying out the plasma measurements. Furthermore, we show that the ratios of the integrated absorption of two transitions are not affected by the rapid passage effect and, thus, rotational temperatures of species can be obtained.
Noise reduction by multiple referencing in surface plasmon resonance imaging
Authors: Boecker Daniel , Zybin Alexander , Niemax Kay , Grunwald Christian , Mirsky Vladimir M.
Published: March 2008

The analytical performance of surface plasmon resonance imaging with charge coupled device detection can be improved significantly by splitting a macroscopic sensing surface into multiple microscopic neighboring sensing and referencing subareas. It is shown that such a multiple referencing reduces intensity fluctuations across the total sensing area and, therefore, improves the signal/noise (S/N) ratio proportional to the splitting factor. The approach is demonstrated by detection of biotin binding to a monolayer of streptavidin. An effective variation of the reflected intensity of about 10−4, which corresponds to the refraction index variation of 3×10−6, was detected with a S/N ratio about 10 without any temperature stabilization of the sensing area.
Sea Perch is a fun, hands-on approach to teaching science
Authors: Kramer David
Published: March 2008

Children at K–12 levels learn physics and engineering by assembling their own working underwater vehicles.
Magnetoreception in animals
Authors: Johnsen Sönke , Lohmann Kenneth J.
Published: March 2008

Determining how animals orient themselves using Earth’s magnetic field can be even more difficult than finding a needle in a haystack. It is like finding a needle in a stack of needles.
Little cup of helium, big science
Authors: van Delft Dirk
Published: March 2008

One hundred years ago, Heike Kamerlingh Onnes first liquefied helium in a cryogenic laboratory whose excellence and scale were unparalleled. Creating, staffing, and running the Leiden laboratory required more than just scientific skill.
Cell-Penetrating Peptide-Mediated Delivery of Peptide Nucleic Acid (PNA) Oligomers
Authors: Lundberg Pontus , Kilk Kalle , Langel Ülo
Published: March 2008

INTRODUCTION

Techniques for knockdown of specific genes and nonviral DNA delivery are important for studying protein functions, and are a means for future therapeutics. The problems with many techniques are low bioavailability and toxicity, especially in vivo. Some cationic peptides are able to translocate across the plasma membrane, and more importantly, to carry a cargo many times their own size, which may improve the bioavailability of hydrophilic macromolecules. These cationic peptides, often referred to as cell-penetrating peptides, have been used to transport a wide variety of cargos, including gene-regulating oligonucleotides and analogs, both in vitro and in vivo. One oligonucleotide analog that shows great potential in protein knockdown is peptide nucleic acid (PNA). PNA is a DNA-mimicking molecule that binds more strongly to DNA and RNA than DNA itself does and is more stable than its DNA counterpart. Furthermore, it is also easily synthesized and modified using standard peptide synthesis protocols. This protocol presents a synthesis strategy for covalently linking a cell-penetrating peptide (CPP) to PNA using a disulfide bridge. This can improve existing protocols for protein knockdown as well as DNA delivery, due to its relatively high efficacy and low toxicity.
Vital Stain for Plant Cytoplasm
Authors: Schwab Birgit , Hülskamp Martin
Published: March 2008

INTRODUCTION

This protocol describes a vital stain for plant cytoplasm. Fluorescein diacetate is used to identify viable cells, which will emit a greenish fluorescence. Dead cells will fluoresce red in the presence of propidium iodide, which does not enter live cells.
Phenotypic Analysis of Arabidopsis Mutants: Quantitative Analysis of Root Growth
Authors: Doerner Peter
Published: March 2008

INTRODUCTION

The growth of plant roots is very easy to measure and is particularly straightforward in Arabidopsis thaliana, because the increase in organ size is essentially restricted to one dimension. The precise measurement of root apical growth can be used to accurately determine growth activity (the rate of growth at a given time) during development in mutants, transgenic backgrounds, or in response to experimental treatments. Root growth is measured in a number of ways, the simplest of which is to grow the seedlings in a Petri dish and record the position of the advancing root tip at appropriate time points. The increase in root length is measured with a ruler and the data are entered into Microsoft Excel for analysis. When dealing with large numbers of seedlings, however, this procedure can be tedious, as well as inaccurate. An alternative approach, described in this protocol, uses “snapshots” of the growing plants, which are taken using gel-documentation equipment (i.e., a video camera with a frame-grabber unit, now commonly used to capture images from ethidium-bromide-stained electrophoresis gels). The images are analyzed using publicly available software (NIH-Image), which allows the user simply to cut and paste data into Microsoft Excel.
DNA Immunoprecipitation (DIP) for the Determination of DNA-Binding Specificity
Authors: Gossett Andrea J. , Lieb Jason D.
Published: March 2008

INTRODUCTION

Knowledge of the DNA-binding specificity of a transcription factor aids in understanding the function of that factor in the regulation of gene transcription. One popular method of identifying the genomic DNA sites bound by a given protein in vivo is the Chromatin ImmunoPrecipitation with microarray analysis (ChIP-chip) technique. However, this method reveals a binding pattern influenced by in vivo phenomena that may mask the actual DNA-binding specificity of the factor, such as chromatin effects and competitive or cooperative protein-protein interactions. ChIP-chip also requires adequate expression of the protein in the cell type chosen to create the extract used for immunoprecipitation. DNA Immunoprecipitation (DIP) is an alternative technique that allows one to take advantage of the favorable properties of both in vivo and traditional in vitro techniques (e.g., electromobility shift assay [EMSA] and binding site selection [SELEX]). DIP utilizes naked genomic DNA as a binding substrate for one or more purified recombinant proteins. Because genomic DNA is used as a template in DIP reactions, the results are directly comparable to ChIP-chip or ChIP-seq data. DIP can be carried out in the presence of cofactors such as heterodimer partners, competitors, or small molecule binding inhibitors. After DNA is isolated by DIP, it is most efficiently detected using a highly parallel genomic technique such as a DNA microarray (DIP-chip) or high-throughput sequencing (DIP-seq). In this protocol, we describe a DIP of a yeast (Saccharomyces cerevisiae) protein with yeast genomic DNA.
Purification of His-Tagged Proteins Using Fractogel-Cobalt
Authors: Tom Roseanne , Bisson Louis , Durocher Yves
Published: March 2008

INTRODUCTION

Fast and efficient production of recombinant proteins (r-proteins) remains a major challenge for the academic and biopharmaceutical communities. Such proteins often need to be as pure as possible before any characterization study can begin. Although many types of protein tag are available, histidine is the most popular. Although small-scale immobilized metal-affinity column (IMAC) purification of such proteins (e.g., <500 mL of culture medium) can easily be achieved using gravity chromatography columns, larger volumes can be processed with the aid of automated chromatography systems. This protocol describes an IMAC purification technique for secreted proteins using a cobalt-loaded resin. Preliminary small-scale trials using this technique can be used to determine the production scale that will be needed to provide enough pure material for a given study.
Human blood dendritic cells from allergic subjects have impaired capacity to produce interferon‐α via toll‐like receptor 9
Authors: Tversky J. R. , Le T. V. , Bieneman A. P. , Chichester K. L. , Hamilton R. G. , Schroeder J. T.
Published: March 2008

Background
High‐affinity IgE receptor (FcɛRI) expression on blood dendritic cells reportedly correlates with serum IgE levels. Our studies demonstrate that plasmacytoid dendritic cells (pDCs) secrete pro‐inflammatory cytokines (IL‐6, TNF‐α) following FcɛRI stimulation – a mode of activation that simultaneously reduces expression of Toll‐like receptor 9 (TLR9). Whether or not TLR9 and/or FcɛRI levels and their function on dendritic cells relate to allergic status is unknown.

Objective
The aim of this study is to compare the innate (TLR9‐mediated) immune response of human pDCs to TLR9 and FcɛRIα receptor expression in allergic and non‐allergic subjects.

Methods
Basophil‐depleted mononuclear cell fractions containing pDCs were prepared from peripheral blood of allergic and non‐allergic subjects. Intracellular TLR9 and surface FcɛRIα expression in blood dendritic cell antigen‐2‐positive cells were determined by flow cytometry. Activating anti‐IgE antibody, anti‐FcɛRIα antibody, and TLR9 agonist were used to stimulate cell suspensions, with cytokine levels determined by ELISA.

Results
No difference in the frequency of pDCs was detected among allergic (n=9) vs. non‐allergic (n=11) subjects (P=0.261). While there was also no difference in the baseline expression of TLR9, pDCs from allergic subjects produced sixfold less IFN‐α when stimulated with CpG (P=0.002). Conversely, there was higher FcɛRIα expression (P=0.01) on the pDCs of allergic subjects.

Conclusions
Impaired TLR9‐dependent immune responses in human pDCs are associated with allergic status and inversely correlated with FcɛRIα expression. This impaired innate immune response among dendritic cells of allergic subjects may lead to more targeted therapeutic approaches and could provide a better understanding of the mechanisms underlying conventional and CpG‐based immunotherapy.
Genetic differentiation in diapause response along a latitudinal cline in European yellow dung fly populations
Authors: DEMONT MARCO , BLANCKENHORN WOLF U.
Published: March 2008

Abstract1. Seasonality is a prime selective factor expected to result in local adaptation of life cycles and dormancy. Genetic differentiation in diapause response was investigated along a European latitudinal cline in the dung flyScathophaga stercoraria(Diptera: Scathophagidae). Such differentiation may be mediated by additive or dominance genetic and/or maternal effects, which need to be distinguished.

2. Replicate sibships from five European populations (Lugano, Switzerland: 46.00°N; Zurich, Switzerland: 47.37°N; Oxford, U.K.: 51.75°N; Lund, Sweden: 55.70°N; Reykjavik, Iceland: 64.15°N) were raised in a common laboratory environment known to induce pupal winter diapause (12 °C and 12 h light), revealing a genetic latitudinal cline in both the proportion of individuals entering diapause and diapause duration in response to winter length estimated from weather data.

3. Populations from the extremes of the cline (Lugano and Reykjavik) were further reciprocally crossed to investigate the underlying genetics. This experiment revealed evidence for diapause induction at 12 °C being dominant (i.e. not merely additive) and clearly rejected maternal effects as the primary source of this between‐population variation.
Changing transcriptional initiation sites and alternative 5′‐ and 3′‐splice site selection of the first intron deploys Arabidopsis PROTEIN ISOASPARTYL METHYLTRANSFERASE2 variants to different subcellular compartments
Authors: Dinkins Randy D. , Majee Susmita Maitra , Nayak Nihar R. , Martin David , Xu Qilong , Belcastro Marisa P. , Houtz Robert L. , Beach Carol M. , Downie A. Bruce
Published: March 2008

Arabidopsis thaliana (L.) Heynh. possesses two PROTEIN‐L‐ISOASPARTATE METHYLTRANSFERASE (PIMT) genes encoding enzymes (EC 2.1.1.77) capable of converting uncoded l‐isoaspartyl residues, arising spontaneously at l‐asparaginyl and l‐aspartyl sites in proteins, to l‐aspartate. PIMT2 produces at least eight transcripts by using four transcriptional initiation sites (TIS; resulting in three different initiating methionines) and both 5′‐ and 3′‐alternative splice site selection of the first intron. The transcripts produce mature proteins capable of converting l‐isoaspartate to l‐aspartate in small peptide substrates. PIMT:GFP fusion proteins generated a detectable signal in the nucleus. However, whether the protein was also detectable in the cytoplasm, endo‐membrane system, chloroplasts, and/or mitochondria, depended on the transcript from which it was produced. On‐blot‐methylation of proteins, prior to the completion of germination, indicated that cruciferin subunits contain isoaspartate. The implications of using transcriptional mechanisms to expand a single gene’s repertoire to protein variants capable of entry into the cell’s various compartments are discussed in light of PIMT’s presumed role in repairing the proteome.
Puzzling practice: A strategy for working with clinical practice issues
Authors: Walsh Kenneth , Moss Cheryle , Lawless Jane , McKelvie Rhonda , Duncan Lindsay
Published: March 2008

In this paper we aim to share the evolution of innovative ways to explore, ‘unpack’ and reframe clinical issues that exist in everyday practice. The elements of these processes, which we call ‘puzzling practice’, and the techniques associated with them, were delineated over a two year period by the four authors using action theory based processes. The authors have evolved several different frameworks for ‘puzzling practice’ which we draw on and use in our practice development work and in our research practice. This paper pays attention to a particular form of puzzling practice that we have found to be useful in assisting individual clinicians and teams to explore and find workable solutions to practice issues.

The paper uses a semi‐fictitious example of ‘Puzzling Practice’ gleaned from our experience as practice development facilitators. In this example ‘puzzling practice’ uses seven different elements; naming the issue; puzzling the issue; testing the puzzle exploring the heart of out practice; formulating the puzzle question; visualizing the future; and generating new strategies for action. Each of the elements is illustrated by the story and the key foundations and ideas behind each element is explored.
Demands of immigration among nurses from Canada and the Philippines
Authors: Victorino Beechinor Linda A , Fitzpatrick Joyce J
Published: March 2008

The purpose of this study was to describe and compare the demands of immigration on nurses from Canada and those from the Philippines, who immigrate to the USA and work in Hawaii. The findings can assist policy‐makers in formulating plans to alleviate the shortage of nurses through effective immigration recruitment practices. Nurse educators can gain support for the recruitment of students from a diverse array of cultures. Managers and nursing leaders can use this information in designing recruitment, orientation, support and retention programmes for nurses that are specific to their cultural needs. The two groups of nurses were sampled from acute care staff nurse populations in Hawaii. Aroian's instrument, the Demands of Immigration scale, was used to measure and compare the distress levels of the nurses. The findings include a higher level of distress experienced by nurses from Canada compared with nurses from the Philippines. This might be attributed to a preponderance of social and collegial support available to the Philippine nurses in Hawaii where one‐fourth of the population is derived from their country of origin.
Risk factors for anastomotic leakage after rectal cancer surgery: a case‐control study
Authors: Jestin P. , Påhlman L. , Gunnarsson U.
Published: March 2008

Background  With introduction of the total mesorectal excision technique and preoperative radiotherapy in rectal cancer surgery, the local recurrence rate has decreased and the overall survival has improved. One drawback, however, is the high anastomotic leakage rate of approximately 10–18%. Male gender and low anastomoses are known risk factors for such leakage. The aim of this study was to identify potentially modifiable risk factors.

Method  In a case‐control study, data from the Swedish Rectal Cancer Registry (1995–2000) were analysed. Cases were all patients with anastomotic leakage after an anterior resection (n = 134). Two controls were randomly selected for each case. The medical records (n = 402) were checked against a study protocol. Due to incorrect recording two cases and 28 controls were excluded from further analyses.

Results  In the multivariate analysis significant risk factors were American Society of Anesthesiologists score > 2 [OR = 1.40 (95% CI 1.05–1.83)], preoperative radiotherapy [OR = 1.34 (95% CI 1.06–1.69)], intraoperative adverse events [OR = 1.85 (95% CI 1.32–2.58)], level of anastomosis ≤ 6 cm [OR = 1.39 (95% CI 1.01–1.90)] and severe bleeding [OR = 1.45 (95% CI 1.14–1.84)]. Diverting stoma protected from leakage [OR = 0.68 (95% CI 0.52–0.88)]. Male gender was a risk factor in the univariate but not in the multivariate analysis [OR = 1.30 (95% CI 1.04–1.63) and OR = 1.26 (95% CI 1.00–1.58), respectively]. Except for a protective stoma, none of the variables considered as possible targets for improvement, such as postoperative epidural anaesthesia, observation at intensive care unit for more than 24 h, and intraabdominal drainage, proved to be protective factors either in the univariate or in the multivariate analyses.

Conclusion  The most important risk factors for leakage were adverse intraoperative events, low anastomoses and preoperative radiotherapy. A diverting stoma is protective and can reduce the consequences when leakage occurs. Further analyses with focus on the surgical technique and individual surgeon may be valuable in identifying targets for improvement.
Children's Planning of Classroom Plays with Adult or Child Direction
Authors: Baker‐Sennett Jacquelyn , Matusov Eugene , Rogoff Barbara
Published: March 2008

This study examined the planning that occurred when children participated in classroom playcrafting with either adult or child leadership. In a first‐/second‐grade classroom in an innovative public school, we videotaped 11 sessions in which children volunteered to develop a play with small groups of classmates and seven sessions in which adult volunteers (parents and a grandparent) developed plays with small groups of children. The plays were crafted in one session of about an hour, and then usually performed for the class.

More planning took place during child‐ than adult‐directed sessions (averaging 92 vs. 35 percent of the session's duration). The groups led by children were more frequently involved in planning of themes, planning of details of the themes, and especially in improvisationally mindstorming ideas than were the groups led by adults. In adult‐directed sessions, the adults often planned the play before the children joined the activity, and the children spent most of the session in non‐playplanning activities such as gluing and coloring puppets or rehearsal of lines designed by the adult in advance. We argue that opportunities to observe and participate in planning—which occurred more frequently in child‐directed than adult‐directed sessions—are important to the development of planning skills and of co‐ordination of plans with others.
Positional Accuracy of Spatial Data: Non‐Normal Distributions and a Critique of the National Standard for Spatial Data Accuracy
Authors: Zandbergen Paul A
Published: March 2008

Spatial data quality is a paramount concern in all GIS applications. Existing spatial data accuracy standards, including the National Standard for Spatial Data Accuracy (NSSDA) used in the United States, commonly assume the positional error of spatial data is normally distributed. This research has characterized the distribution of the positional error in four types of spatial data: GPS locations, street geocoding, TIGER roads, and LIDAR elevation data. The positional error in GPS locations can be approximated with a Rayleigh distribution, the positional error in street geocoding and TIGER roads can be approximated with a log‐normal distribution, and the positional error in LIDAR elevation data can be approximated with a normal distribution of the original vertical error values after removal of a small number of outliers. For all four data types considered, however, these solutions are only approximations, and some evidence of non‐stationary behavior resulting in lack of normality was observed in all four datasets. Monte‐Carlo simulation of the robustness of accuracy statistics revealed that the conventional 100% Root Mean Square Error (RMSE) statistic is not reliable for non‐normal distributions. Some degree of data trimming is recommended through the use of 90% and 95% RMSE statistics. Percentiles, however, are not very robust as single positional accuracy statistics. The non‐normal distribution of positional errors in spatial data has implications for spatial data accuracy standards and error propagation modeling. Specific recommendations are formulated for revisions of the NSSDA.
Comparing Student Performance in Online and Blended Sections of a GIS Programming Class
Authors: Detwiler James E
Published: March 2008

Educators and non‐educators alike commonly assume that online courses cannot match the effectiveness of their traditional, face‐to‐face counterparts. This article describes a comparative study of the performance and study habits of two groups of students in a course in Geographic Information Systems (GIS) software programming and customization: one delivered online to adult professionals working asynchronously; the other delivered in a blended, online/face‐to‐face environment to upper‐level undergraduates in residence. Course grades show that the undergraduate cohort underperformed in comparison to the online cohort, in spite of the fact that their version of the course included face‐to‐face lecture and lab time in addition to the online course materials. To explore differences in the study habits of the two groups, all students were asked to keep a diary of the time they devoted to coursework. Information from these diaries suggest that a student's ability to meet learning objectives is less dependent on the course content delivery mechanism than it is on the student's motivation, maturity and time management skills.
Resection of Pulmonary Metastases in Canine Osteosarcoma: 36 Cases (1983–1992)
Authors: O'BRIEN M. G. , STRAW R. C. , WITHROW S. J. , POWERS B. E. , JAMESON V. J. , LAFFERTY M. , OGILVIE G. K. , LaRUE S. M.
Published: March 2008

Thirty‐six dogs underwent pulmonary metastatectomy for osteosarcoma. All patients had been treated for histologically confirmed osteosarcoma of the appendicular skeleton. Treatment for the primary tumor consisted of amputation or a limb sparing procedure in conjunction with adjuvant chemotherapy, local radiation therapy, or both.

Significant factors in determining prognosis included the disease‐free interval (DFI) between treatment of the primary tumor and development of pulmonary metastases and the number of metastatic nodules present at surgery. Dogs that developed pulmonary metastases 300 days or more after diagnosis of the primary tumor had a median DFI of 128 days after metastatectomy. Dogs that developed pulmonary metastases fewer than 300 days after diagnosis had a median DFI of 58 days. Dogs with one or two metastatic nodules removed had a median DFI of 95 days, whereas dogs with three or more nodules removed had a median DFI of 53 days. The results of this study indicate that prognostic variables exist for dogs with metastatic pulmonary osteosarcoma and can help predict survival after metastatectomy. These variables are similar to the prognostic variables that have been determined for human patients undergoing pulmonary metastatectomy because of osteosarcoma. Though a controversial procedure, pulmonary metastatectomy seems to be a valid treatment option for selected dogs with metastatic pulmonary osteosarcoma.