bluuebunny/crossref_metadata_2025 huggingface dataset:
Dietary cholesterol-oxidation products accumulate in serum and liver in apolipoprotein E-deficient mice, but do not accelerate atherosclerosis
Authors: Ando Miyuki , Tomoyori Hiroko , Imaizumi Katsumi
Published: October 2009

There are conflicting reports regarding the effect of dietary cholesterol-oxidation products (oxysterols) on the development of atherosclerosis in experimental animals. To address this issue, apolipoprotein (Apo) E-deficient mice were fed a purified diet (AIN-93) or the same purified diet containing 0·2 g cholesterol or 0·2 g oxysterols/kg. The dietary oxysterols had no significant effect on the serum lipid levels. Although all of the diet-derived oxysterols (cholest-5-en-3β,7α-diol, cholest-5-en-3β,7β-diol, cholestan-5α,6α-epoxy-3β-ol, cholestan-5β,6β-epoxy-3β-ol, cholestan-3β, 5α, 6β-triol, cholest-5-en-3β-ol-7-one and cholest-5-en-3β, 25-diol) accumulated in the serum and liver, only cholest-5-en-3β-ol-7-one and cholestan-3β, 5α, 6β-triol accumulated significantly (P<0·05) in the aorta. The oxysterol diet did not result in elevation of the aortic cholesterol level or the lesion volume in the aortic valve. These present results indicate that exogenous oxysterols do not promote the development of atherosclerosis in ApoE-deficient mice.
An RCT Comparing Effect of Two Types of Support on Severity of Symptoms for People Completing Internet-Based Cognitive Behaviour Therapy for Social Phobia
Authors: Titov Nickolai , Andrews Gavin , Schwencke Genevieve , Solley Karen , Johnston Luke , Robinson Emma
Published: October 2009

Objective: The present study (Shyness 6) compares the benefits and acceptability of two types of guidance on severity of symptoms during Internet treatment for social phobia.

Methods: Non-inferiority randomized controlled trial of Internet treatment, supplemented with weekly telephone calls from a technician (computerized cognitive-behavioural treatment (CCBT + Tel), or regular access to a clinician-moderated online discussion forum (CCBT + Forum), was carried out. An intention-to-treat model was used for data analyses. The participants consisted of 82 volunteers with social phobia. The intervention consisted of six lessons of CCBT for social phobia (the Shyness programme) with complex automated reminders. The main outcome measures were the Social Interaction Anxiety Scale and Social Phobia Scale.

Results: A total of 79% of CCBT + Tel and 79% of CCBT + Forum group participants completed all six lessons. Large mean within-groups effect sizes (Cohen's d) for the two social phobia measures were found for the CCBT + Tel and CCBT + Forum groups (1.31 and 1.54, respectively). Each participant in the CCBT + Tel group received a mean total of 38 min of technician time over the 8 week programme, while participants in the CCBT + Forum group received a mean total of 37 min of clinician time. Quantitative and qualitative data indicate that both the CCBT + Tel and CCBT + Forum procedures were equally and highly acceptable to participants.

Conclusions: The Shyness programme with either telephone support or access to a clinician-moderated online forum resulted in good clinical outcomes with equivalent patient acceptability. These results confirm that people with social phobia may significantly benefit from a highly structured education programme administered by clinical or non-clinical staff.
Effects of positive and negative delusional ideation on memory
Authors: Sugimori Eriko , Tanno Yoshihiko
Published: October 2009

We investigated the relationship between levels of delusional ideation (whether positive or negative delusions) and the activation and distortion of memory by using pairs of positive and negative adjectives describing personality traits where those adjectives had similar meanings. We presented one of each pair of adjectives in the learning phase. Immediately after the learning phase in Experiment 1, we asked whether each adjective had been presented. Participants with high (positive or negative) delusional ideation were more likely to indicate that they had learned adjectives that they had not actually learned. This finding suggested that non‐learned positive (or negative) adjectives that were associated with learned negative (or positive) adjectives were more likely to be activated in participants prone to positive (or negative) delusional ideation. However, in Experiment 2, two forced‐choice tests were conducted immediately after the learning phase. In this context, participants, regardless of their proneness to delusional ideation, could almost always correctly distinguish what had and had not been presented, suggesting that the activation of learned items was still stronger than that for non‐learned items in the immediate test. As time passed, the proportion of false alarms for positive or negative adjectives was higher in the two forced‐choice tests among those with high proneness to (positive or negative) delusional ideation, suggesting that participants with delusional ideation were increasingly likely to depend on internal conditions for retrieval over time.
Amygdaloid Neurosurgery for Aggressive Behaviour, Sydney, 1967–1977: Chronological Narrative
Authors: White Richard , Williams Sid
Published: October 2009

Objective: The aim of this paper is to record an historical narrative of amygdaloid neurosurgery at Callan Park Mental Hospital, Sydney in the period 1967–1977. In this paper, this is denoted the Amygdaloid Neurosurgery Project (ANP). The goal of the project was to ameliorate aggressive or self-harming behaviour by selective ablative surgery on the amygdaloid nucleus.

Conclusions: In 1964, Professor Leslie Gordon Kiloh became acting director of the newly built neurosurgical research facility at Callan Park Mental Hospital. In 1966, he advised bilateral amygdaloidotomy for the treatment of a 16-year-old aggressive and self-harming male patient. Following major improvement in that patient's condition, a further 19 patients were treated by amygdaloid surgery. In 1974, Kiloh's team reported that 39% of the first 18 patients treated had persisting improvement but one patient sustained persisting hemiplegia. The program was suspended in 1977 by the New South Wales (NSW) Government, following allegations by a senior nurse that patients at the neurosurgical unit had been mistreated. A Ministerial Committee of Inquiry proposed that stringent legislative controls should be applied to psychosurgery. The Committee expressed reservations about amygdaloid psychosurgery in particular. Psychosurgery referrals declined after that date. Since 2007, under the revised NSW Mental Health Act, all forms of neurosurgery for psychiatric disorder are prohibited.
Community Mental Health Care in Mongolia: Adapting Best Practice to Local Culture
Authors: Altanzul Narmandakh , Erdenebayar Luvsandorj , Ng Chee , Byambasuren Sandag , Sharma Nalin , Tsetsegdary Gombodorj
Published: October 2009

Objectives: The aim of this paper is to describe the development of community mental health care in Mongolia, as exemplified by a best practice model of care in the community.

Conclusion: Through the Asia-Pacific Community Mental Health Development Project, Mongolia has identified local best practice such as the ‘Ger’ project that provides community psychosocial rehabilitation, which has been adapted according to local conditions and culture. Cultural considerations are important in producing effective clinical outcomes and a better quality of life for people with mental illness. The project has also shown that it is possible for persons with mental illness to receive rehabilitation effectively in local community settings. Inter-sectoral collaboration with multiple stakeholders is essential to achieve optimal community mental health service development.
BUOYANT BUBBLES IN INTRACLUSTER GAS: EFFECTS OF MAGNETIC FIELDS AND ANISOTROPIC VISCOSITY
Authors: Dong Ruobing , Stone James M.
Published: October 2009

Recent observations by Chandra and XMM-Newton indicate that there are complex structures at the cores of galaxy clusters, such as cavities and filaments. One plausible model for the formation of such structures is the interaction of radio jets with the intracluster medium (ICM). To investigate this idea, we use three-dimensional magnetohydrodynamic simulations including anisotropic (Braginskii) viscosity to study the effect of magnetic fields on the evolution and morphology of buoyant bubbles in the ICM. We investigate a range of different initial magnetic field geometries and strengths, and study the resulting X-ray surface brightness distribution for comparison to observed clusters. Magnetic tension forces and viscous transport along field lines tend to suppress instabilities parallel, but not perpendicular, to field lines. Thus, the evolution of the bubble depends strongly on the initial field geometry. We find that toroidal field loops initially confined to the interior of the bubble are best able to reproduce the observed cavity structures.
An area-preserving mapping in natural canonical coordinates for magnetic field line trajectories in the DIII-D tokamak
Authors: Punjabi Alkesh
Published: October 2009

The new approach of integrating magnetic field line trajectories in natural canonical coordinates (Punjabi and Ali 2008 Phys. Plasmas
15 122502) in divertor tokamaks is used for the DIII-D tokamak (Luxon and Davis1985 Fusion Technol.
8 441). The equilibrium EFIT data (Evans et al 2004 Phys. Rev. Lett.
92 235003, Lao et al 2005 Fusion Sci. Technol.
48 968) for the DIII-D tokamak shot 115467 at 3000 ms is used to construct the equilibrium generating function (EGF) for the DIII-D in natural canonical coordinates. The EGF gives quite an accurate representation of the closed and open equilibrium magnetic surfaces near the separatrix, the separatrix, the position of the X-point and the poloidal magnetic flux inside the ideal separatrix in the DIII-D. The equilibrium safety factor q from the EGF is somewhat smaller than the DIII-D EFIT q profile. The equilibrium safety factor is calculated from EGF as described in the previous paper (Punjabi and Ali 2008 Phys. Plasmas
15 122502). Here the safety factor for the open surfaces in the DIII-D is calculated. A canonical transformation is used to construct a symplectic mapping for magnetic field line trajectories in the DIII-D in natural canonical coordinates. The map is explored in more detail in this work, and is used to calculate field line trajectories in the DIII-D tokamak. The continuous analogue of the map does not distort the DIII-D magnetic surfaces in different toroidal planes between successive iterations of the map. The map parameter k can represent effects of magnetic asymmetries in the DIII-D. These effects in the DIII-D are illustrated. The DIII-D map is then used to calculate stochastic broadening of the ideal separatrix from the topological noise and field errors, the low mn, the high mn and peeling–ballooning magnetic perturbations in the DIII-D. The width of the stochastic layer scales as 1/2 power of amplitude with a maximum deviation of 6% from the Boozer–Rechester scaling (Boozer and Rechester 1978 Phys. Fluids
21 682). The loss of poloidal flux scales linearly with the amplitude of perturbation with a maximum deviation of 10% from linearity. Perturbations with higher mode numbers result in higher stochasticity. The higher the complexity and coupling in the equilibrium magnetic geometry, the closer is the scaling to the Boozer–Rechester scaling of width. The comparison of the EGF for the simple map (Punjabi et al 1992 Phys. Rev. Lett.
69 3322) with that of the DIII-D shows that the more complex the magnetic geometry and the more coupling of modes in equilibrium, the more robust or resilient is the system against the chaos-inducing, symmetry-breaking perturbations.
Charge carrier dynamics in semiconducting mercury cluster anions
Authors: Young Ryan M , Griffin Graham B , Ehrler Oli T , Kammrath Aster , Bragg Arthur E , Verlet Jan R R , Cheshnovsky Ori , Neumark Daniel M
Published: October 2009

We have examined size-dependent electronic relaxation dynamics in isolated semiconducting mercury cluster anions using time-resolved photoelectron imaging. Relaxation following excitation from within the conduction (p-) band occurs on an ∼3–40 ps timescale and is attributed to non-adiabatic relaxation through the p-band. Exciting an electron from the valence (s-) band into the conduction band creates an electron–hole pair that relaxes prior to Auger emission. The dynamics associated with this feature occur on an ∼500 fs timescale and are attributed to either a hole-induced contraction of the cluster or electron–electron scattering.
Hyperspherical and related views of the dynamics of nanoclusters
Authors: Lombardi A , Palazzetti F , Grossi G , Aquilanti V , Castro Palacio J C , Rubayo Soneira J
Published: October 2009

In this paper, we give an account of recent progress in understanding properties of nanoaggregates, following their dynamical behavior by classical mechanics simulations and utilizing tools based on extensions of hyperspherical and related techniques, originally developed for the quantum mechanical treatment of few-body atomic and molecular systems. After an outline of the underlying theory, recent applications exemplifying statistical and thermodynamic aspects of nanoclusters are discussed.
Stability of metallic hollow cluster systems
Authors: Verkhovtsev A V , Polozkov R G , Ivanov V K , Solov'yov A V
Published: October 2009

The results of calculations of electron structure for cluster systems with a spherical hole are presented. The calculations are performed within the jellium model using the Hartree–Fock and local density approximations for the electronic subsystem. It has been found that the total energy of the cluster has two minima as a function of the radius of the hole.
Photofragment angular momentum distribution beyond the axial-recoil approximation
Authors: Kuznetsov V V , Shternin P S , Vasyutinskii O S
Published: October 2009

The paper reviews recent advantages in the theory of the rapidly growing field of the angular momentum orientation and alignment in photolysis of small molecules. Particular emphasis is put on the photofragment orbital orientation and alignment in molecular photolysis beyond the axial-recoil approximation. One of the most important recent achievements is derivation of a universal expression for the recoil-angle dependence of the polarization cross section in terms of the anisotropy parameters (anisotropy transforming coefficients), which is valid for one photon photolysis reaction of any diatomic or polyatomic molecule irrespective of the reaction mechanism. The anisotropy parameters contain all information about the reaction dynamics in the frame of the quantum scattering theory, they can be either determined from experiment or calculated from ab initio theory. Expressions for the anisotropy parameters for the photolysis of rotating diatomic/linear molecules are analyzed, which contain information on radial and Coriolis nonadiabatic interactions as well as on the full range of interference effects. In the case of direct photodissociation, the molecular rotation is taken into consideration in the quasi-classical approximation by introducing the set of rotation factors, which depend on the molecular axis rotation angle γ and on the quantum numbers of the photon polarization matrix. In the case of slow predissociation, the molecular rotation is taken into consideration by introducing the set of reduction factors. As shown, in most cases molecular rotation decreases the angular momentum polarization of the photofragments.
Interactions and collisions of cold metal atoms in magnetic traps
Authors: Buchachenko A A , Suleimanov Yu V , Szczęśniak M M , Chałasiński G
Published: October 2009

Current research in magnetic trapping of the metal atoms is commented upon from the viewpoint of the theory of interatomic interactions and collision dynamics at sub-kelvin temperatures. Atom–atom interactions that lead to collision-induced transitions between different Zeeman states of complex atoms are discussed using the concept of interaction anisotropy. Theoretical results for Zeeman relaxation dynamics for lanthanides, transition and heavy main group metals are reviewed and compared with recent experimental findings. Possible directions of future research are outlined.
Depolarization of rotational angular momentum in open-shell collisions: OH+rare gases
Authors: Paterson Grant , Marinakis Sarandis , Costen Matthew L , McKendrick Kenneth G
Published: October 2009

This paper addresses recent progress in studies of collisional depolarization of rotational angular momentum in open-shell molecules. The application of the polarization spectroscopy (PS) technique to the OH radical in collisions with the rare gases He and Ar is described. The capacity of quantum mechanical scattering calculations on ab initio potential energy surfaces to reproduce the experimental results is considered. We explain how the very recent progress in theoretical methodology has enhanced the value of this comparison, reflect more generally on the relationship to other experimental methods and molecular systems, and speculate on some promising future directions for this research field.
Nonadiabatic effects in inelastic collisional processes
Authors: Belyaev Andrey K
Published: October 2009

The standard adiabatic Born–Oppenheimer approach to inelastic collisional processes is revised. It is shown that the widely used standard interpretation of this approach has fundamental limitations leading to physical artefacts or to uncertainties in numerical calculations due to neglecting the electron translation problem. It is demonstrated that the Born–Oppenheimer approach itself does not have such limitations. The particular full quantum solution of the electron translation problem within the Born–Oppenheimer approach by means of the reprojection procedure is discussed in the paper together with the practical applications.
Analytical semiclassical theory for general non-adiabatic transition and tunneling
Authors: Zhu Chaoyuan
Published: October 2009

A semiclassical solution of general two-state non-adiabatic transition and tunneling is found analytically within the Wentzel–Kramers–Brillouin (WKB) semiclassical framework associated with the Stokes phenomenon in mathematics. The non-adiabatic scattering matrix is determined by a complex quantity called the Stokes constant, which can be directly connected to the complex transition points of the WKB solution. An accurate and compact analytical solution is found for this Stokes constant which is a function of three parameters, one of which corresponds to the diabatic-to-adiabatic transformation angle that is interpreted as a type of non-adiabatic transition. Numerical examples demonstrate that the present unified analytical semiclassical theory works very well for both non-adiabatic transition and non-adiabatic tunneling. The present analytical semiclassical method can be a very powerful tool for application to multidimensional non-adiabatic dynamic processes.
State-to-state reactive scattering using reactant–product decoupling
Authors: Cvitaš Marko T , Althorpe Stuart C
Published: October 2009

In this paper, we review a quantum wave packet method for computing state-to-state quantum dynamics of three-atom and four-atom bimolecular reactions using the reactant–product decoupling (RPD) approach. The long propagation times needed in order to extract state-to-state observables cover geometries at which the fragments are far apart on the reactant and product side of the reaction valley. To alleviate the coordinate problem, we partition the coordinate space into three regions, describing reactants, products and the interaction region each using a basis set optimized for the particular region. The wave packet is propagated simultaneously over all three regions, and it is transferred between the regions using a system of artificial reflecting and absorbing potentials. We review the accuracy and efficiency of the method and comment on its prospects for yielding accurate differential cross sections of four-atom reactions in the near future.
A comparative study of hydrogen-atom release dynamics in radical–radical reactions
Authors: Choi Jong-Ho
Published: October 2009

This paper presents a comparative study of the atomic hydrogen release dynamics in the oxidation reactions of saturated and unsaturated hydrocarbon radicals. The prototypal radical–radical reactive scattering processes were examined by applying a combination of crossed beams and high-resolution vacuum-ultraviolet laser-induced fluorescence spectroscopy. With the aid of ab initio and statistical calculations, remarkable dynamic features were uncovered in the Doppler profile analysis of the atomic hydrogen products. The difference in the reactivity of saturated and unsaturated hydrocarbon radicals could be rationalized in terms of the characteristic geometry of the transition state and activation barriers along the exit channel on the doublet potential energy surface.
Gerade–ungerade symmetry breaking in bound states localized in the II′ 1Πg outer potential well of HD
Authors: Grozdanov Tasko P , McCarroll Ronald
Published: October 2009

Gerade–ungerade symmetry breaking in HD for the bound states associated with the 1Πg outer well potential is investigated theoretically. The asymptotic behaviour of all the relevant non-adiabatic couplings between the states correlated to the n=2 dissociation limit has been determined. The calculation of the energies of states with f-parity reduces to finding the eigenvalues of a set of two coupled differential equations. For states of e-parity, a three-state model is required to represent the system correctly. The calculated energies are in excellent agreement with recent high resolution spectroscopic measurements.
Generalized diatomics-in-molecule method for polyatomics
Authors: Belyaev A K , Tiukanov A S , Domcke W
Published: October 2009

A new derivation of the generalized diatomics-in-molecule (GDIM) method for the description of electronically stationary and quasi-stationary states of a polyatomic molecule is given in the partial-wave representation of the electron continuum. The method is based on the combination of the projection-operator approach of scattering theory with the diatomics-in-molecule fragmentation of the fixed-nuclei Hamiltonian, resulting in the construction of diabatic discrete states, electron-molecule scattering continua and discrete–continuum couplings from the corresponding data of the fragments. The GDIM method is applied to the H3
− anion. The ground-state local-complex-potential surface (both the real and the imaginary parts) is obtained. Classical trajectories of H−+H2 collisions with inclusion of the electron detachment channel are calculated.
States of a hydrogen atom in an impenetrable cubic cavity
Authors: Kretov M K , Scherbinin A V , Pupyshev V I
Published: October 2009

Changes in the relative positions of energy levels of a hydrogen atom placed into an impenetrable cubic cavity under both variations of the cavity size and nuclear displacements off the center alongside the fourfold symmetry axes are studied. Numerical estimates for the energies of the states corresponding to 1s, 2s, 2p, 3d states in the free atom, are performed using the collocation method for cavities with edge lengths within 1 to 6 au. Qualitative methods that may be used to analyze the changes in the atomic states in a cubic cavity under variations of its form or nuclear displacements are discussed.
Pancreatic Ductal Morphogenesis and the Pdx1 Homeodomain Transcription Factor
Authors: Wescott Melanie P. , Rovira Meritxell , Reichert Maximilian , von Burstin Johannes , Means Anna , Leach Steven D. , Rustgi Anil K.
Published: October 2009

Embryonic development of the pancreas is marked by an early phase of dramatic morphogenesis, in which pluripotent progenitor cells of the developing pancreatic epithelium give rise to the full array of mature exocrine and endocrine cell types. The genetic determinants of acinar and islet cell lineages are somewhat well defined; however, the molecular mechanisms directing ductal formation and differentiation remain to be elucidated. The complex ductal architecture of the pancreas is established by a reiterative program of progenitor cell expansion and migration known as branching morphogenesis, or tubulogenesis, which proceeds in mouse development concomitantly with peak Pdx1 transcription factor expression. We therefore evaluated Pdx1 expression with respect to lineage-specific markers in embryonic sections of the pancreas spanning this critical period of duct formation and discovered an unexpected population of nonislet Pdx1-positive cells displaying physical traits of branching. We then established a 3D cell culture model of branching morphogenesis using primary pancreatic duct cells and identified a transient surge of Pdx1 expression exclusive to branching cells. From these observations we propose that Pdx1 might be involved temporally in a program of gene expression sufficient to facilitate the biochemical and morphological changes necessary for branching morphogenesis.
Computing the shortest elementary flux modes in genome-scale metabolic networks
Authors: de Figueiredo Luis F. , Podhorski Adam , Rubio Angel , Kaleta Christoph , Beasley John E. , Schuster Stefan , Planes Francisco J.
Published: October 2009

Motivation: Elementary flux modes (EFMs) represent a key concept to analyze metabolic networks from a pathway-oriented perspective. In spite of considerable work in this field, the computation of the full set of elementary flux modes in large-scale metabolic networks still constitutes a challenging issue due to its underlying combinatorial complexity.

Results: In this article, we illustrate that the full set of EFMs can be enumerated in increasing order of number of reactions via integer linear programming. In this light, we present a novel procedure to efficiently determine the K-shortest EFMs in large-scale metabolic networks. Our method was applied to find the K-shortest EFMs that produce lysine in the genome-scale metabolic networks of Escherichia coli and Corynebacterium glutamicum. A detailed analysis of the biological significance of the K-shortest EFMs was conducted, finding that glucose catabolism, ammonium assimilation, lysine anabolism and cofactor balancing were correctly predicted. The work presented here represents an important step forward in the analysis and computation of EFMs for large-scale metabolic networks, where traditional methods fail for networks of even moderate size.

Contact:  fplanes@tecnun.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
W-ChIPMotifs: a web application tool forde novomotif discovery from ChIP-based high-throughput data
Authors: Jin Victor X. , Apostolos Jeff , Nagisetty Naga Satya Venkateswara Ra , Farnham Peggy J.
Published: October 2009

Summary: W-ChIPMotifs is a web application tool that provides a user friendly interface for de novo motif discovery. The web tool is based on our previous ChIPMotifs program which is a de novo motif finding tool developed for ChIP-based high-throughput data and incorporated various ab initio motif discovery tools such as MEME, MaMF, Weeder and optimized the significance of the detected motifs by using a bootstrap resampling statistic method and a Fisher test. Use of a randomized statistical model like bootstrap resampling can significantly increase the accuracy of the detected motifs. In our web tool, we have modified the program in two aspects: (i) we have refined the P-value with a Bonferroni correction; (ii) we have incorporated the STAMP tool to infer phylogenetic information and to determine the detected motifs if they are novel and known using the TRANSFAC and JASPAR databases. A comprehensive result file is mailed to users.

Availability:  http://motif.bmi.ohio-state.edu/ChIPMotifs. Data used in the article may be downloaded from http://motif.bmi.ohio-state.edu/ChIPMotifs/examples.shtml.

Contact:  victor.jin@osumc.edu
United States Bank Rescue Politics, 2008–2009: A Business Historian's View
Authors: Rose Mark H.
Published: October 2009

First I describe my background in American historical scholarship. Thereafter, I assess the efforts of Presidents George W. Bush and Barack H. Obama and their senior advisors to stabilize American financial institutions during the period 2008–2009. My fundamental contention is that state actors such as Bush and Obama structured financial industries and markets. Despite the ubiquitous presence of these state actors, however, American business and political leaders maintained the fiction that state and business were, and properly ought to remain, separate entities. In Part III, I return to my scholarly background and to a proposed scaffolding for historical scholarship focused on the political economy of U.S. financial institutions since 1970.
Small within-day increases in temperature affects boldness and alters personality in coral reef fish
Authors: Biro Peter A. , Beckmann Christa , Stamps Judy A.
Published: October 2009

Consistent individual differences in behaviour, termed personality, are common in animal populations and can constrain their responses to ecological and environmental variation, such as temperature. Here, we show for the first time that normal within-daytime fluctuations in temperature of less than 3°C have large effects on personality for two species of juvenile coral reef fish in both observational and manipulative experiments. On average, individual scores on three personality traits (PTs), activity, boldness and aggressiveness, increased from 2.5- to sixfold as a function of temperature. However, whereas most individuals became more active, aggressive and bold across temperature contexts (were plastic), others did not; this changed the individual rank order across temperatures and thus altered personality. In addition, correlations between PTs were consistent across temperature contexts, e.g. fish that were active at a given temperature also tended to be both bold and aggressive. These results (i) highlight the importance of very carefully controlling for temperature when studying behavioural variation among and within individuals and (ii) suggest that individual differences in energy metabolism may contribute to animal personality, given that temperature has large direct effects on metabolic rates in ectotherms.
Tuberculosis in Dr Granville's mummy: a molecular re-examination of the earliest known Egyptian mummy to be scientifically examined and given a medical diagnosis
Authors: Donoghue Helen D. , Lee Oona Y.-C. , Minnikin David E. , Besra Gurdyal S. , Taylor John H. , Spigelman Mark
Published: October 2009

‘Dr Granville's mummy’ was described to the Royal Society of London in 1825 and was the first ancient Egyptian mummy to be subjected to a scientific autopsy. The remains are those of a woman, Irtyersenu, aged about 50, from the necropolis of Thebes and dated to about 600 BC. Augustus Bozzi Granville (1783–1872), an eminent physician and obstetrician, described many organs still
in situ
and attributed the cause of death to a tumour of the ovary. However, subsequent histological investigations indicate that the tumour is a benign cystadenoma. Histology of the lungs demonstrated a potentially fatal pulmonary exudate and earlier studies attempted to associate this with particular disease conditions. Palaeopathology and ancient DNA analyses show that tuberculosis was widespread in ancient Egypt, so a systematic search for tuberculosis was made, using specific DNA and lipid biomarker analyses. Clear evidence for
Mycobacterium tuberculosis
complex DNA was obtained in lung tissue and gall bladder samples, based on nested PCR of the IS
6110
locus. Lung and femurs were positive for specific
M. tuberculosis
complex cell-wall mycolic acids, demonstrated by high-performance liquid chromatography of pyrenebutyric acid–pentafluorobenzyl mycolates. Therefore, tuberculosis is likely to have been the major cause of death of Irtyersenu.
Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time
Authors: Harder Nathalie , Mora-Bermúdez Felipe , Godinez William J. , Wünsche Annelie , Eils Roland , Ellenberg Jan , Rohr Karl
Published: October 2009

Live-cell imaging allows detailed dynamic cellular phenotyping for cell biology and, in combination with small molecule or drug libraries, for high-content screening. Fully automated analysis of live cell movies has been hampered by the lack of computational approaches that allow tracking and recognition of individual cell fates over time in a precise manner. Here, we present a fully automated approach to analyze time-lapse movies of dividing cells. Our method dynamically categorizes cells into seven phases of the cell cycle and five aberrant morphological phenotypes over time. It reliably tracks cells and their progeny and can thus measure the length of mitotic phases and detect cause and effect if mitosis goes awry. We applied our computational scheme to annotate mitotic phenotypes induced by RNAi gene knockdown of CKAP5 (also known as ch-TOG) or by treatment with the drug nocodazole. Our approach can be readily applied to comparable assays aiming at uncovering the dynamic cause of cell division phenotypes.
Rapid identification of homologous recombinants and determination of gene copy number with reference/query pyrosequencing (RQPS)
Authors: Liu Zhenyi , Obenauf Anna C. , Speicher Michael R. , Kopan Raphael
Published: October 2009

Manipulating the mouse genome is a widespread technology with important applications in many biological fields ranging from cancer research to developmental biology. Likewise, correlations between copy number variations (CNVs) and human diseases are emerging. We have developed the reference-query pyrosequencing (RQPS) method, which is based on quantitative pyrosequencing and uniquely designed probes containing single nucleotide variations (SNVs), to offer a simple and affordable genotyping solution capable of identifying homologous recombinants independent of the homology arm size, determining the micro-amplification status of endogenous human loci, and quantifying virus/transgene copy number in experimental or commercial species. In addition, we also present a simple pyrosequencing-based protocol that could be used for the enrichment of homologous recombinant embryonic stem (ES) cells.
Sleep deprivation and Pavlovian fear conditioning
Authors: Cai Denise J. , Shuman Tristan , Harrison Elizabeth M. , Sage Jennifer R. , Anagnostaras Stephan G.
Published: October 2009

Sleep has been suggested to play a role in memory consolidation. Prior rodent studies have used sleep deprivation to examine this relationship. First, we reexamined the effects of sleep deprivation on Pavlovian fear conditioning. We found that the deprivation method itself (i.e., gentle handling) induced deficits independent of sleep. Second, we examined an alternative method of sleep deprivation using amphetamine and found that this method failed to induce amnesia. These data indicate that sleep deprivation is a problematic way to examine the role of sleep in memory consolidation, and an alternative paradigm is proposed.
The amygdala is not necessary for unconditioned stimulus inflation after Pavlovian fear conditioning in rats
Authors: Rabinak Christine A. , Orsini Caitlin A. , Zimmerman Joshua M. , Maren Stephen
Published: October 2009

The basolateral complex (BLA) and central nucleus (CEA) of the amygdala play critical roles in associative learning, including Pavlovian conditioning. However, the precise role for these structures in Pavlovian conditioning is not clear. Recent work in appetitive conditioning paradigms suggests that the amygdala, particularly the BLA, has an important role in representing the value of the unconditioned stimulus (US). It is not known whether the amygdala performs such a function in aversive paradigms, such as Pavlovian fear conditioning in rats. To address this issue, Experiments 1 and 2 used temporary pharmacological inactivation of the amygdala prior to a US inflation procedure to assess its role in revaluing shock USs after either overtraining (Experiment 1) or limited training (Experiment 2), respectively. Inactivation of the BLA or CEA during the inflation session did not affect subsequent increases in conditioned freezing observed to either the tone conditioned stimulus (CS) or the conditioning context in either experiment. In Experiment 3, NBQX infusions into the BLA impaired the acquisition of auditory fear conditioning with an inflation-magnitude US, indicating that the amygdala is required for associative learning with intense USs. Together, these results suggest that the amygdala is not required for revaluing an aversive US despite being required for the acquisition of fear to that US.
Histone acetylation is recruited in consolidation as a molecular feature of stronger memories
Authors: Federman Noel , Fustiñana Maria Sol , Romano Arturo
Published: October 2009

Gene expression is a key process for memory consolidation. Recently, the participation of epigenetic mechanisms like histone acetylation was evidenced in long-term memories. However, until now the training strength required and the persistence of the chromatin acetylation recruited are not well characterized. Here we studied whether histone acetylation is involved in consolidation in invertebrates, whether it depends on the training strength, and whether it is a permanent or transient mechanism. We used a well-characterized memory model in invertebrates, the context-signal memory in crabs. Our results show no changes in histone 3 (H3) acetylation during consolidation of a standard training protocol. However, strong training induced a significant increase in H3 acetylation 1-h post-training, returning to basal levels afterward. Accordingly, the administration of histone deacetylase inhibitors sodium butyrate (NaB) and trichostatin A allowed a weak training to induce long-term memory. NaB enhanced memory in two phases during consolidation. These findings support that H3 acetylation (1) is involved in consolidation, (2) occurs only after strong training, (3) is a transient process, and (4) memory is enhanced in two phases. The coincidence of these phases with other mechanisms of gene expression is discussed.
The Parasitoid Wasp Nasonia: An Emerging Model System with Haploid Male Genetics
Authors: Werren John H. , Loehlin David W.
Published: October 2009

INTRODUCTION

Nasonia is a complex of four closely related species of wasps that is rapidly emerging as a model for evolutionary and developmental genetics. It has several features that make it an excellent genetic system, including a short generation time, ease of rearing, interfertile species, visible and molecular markers, and a sequenced genome. The form of sex determination, called “haplodiploidy,” makes Nasonia particularly suitable as a genetic tool. Females are diploid and develop from fertilized eggs, whereas males are haploid and develop from unfertilized eggs. This allows geneticists to exploit many of the advantages of haploid genetics in an otherwise complex eukaryotic organism. Nasonia readily inbreeds, permitting production of isogenic lines, and the four species in the genus are interfertile (after removal of the endosymbiont Wolbachia), facilitating movement of genes between the species for efficient positional cloning of quantitative trait loci (QTL). Genome sequencing of the genetic model Nasonia vitripennis and two interfertile species, Nasonia giraulti and Nasonia longicornis, is now completed. This genome project provides a wealth of interspecies polymorphisms (e.g., single nucleotide polymorphisms [SNPs], insertion-deletions [indels], microsatellites) to facilitate positional cloning of genes involved in species differences in behavior, morphology, and development. Advances in the genetics of this system also open a path for improvement of parasitoid insects as agents of pest control.
Haploview: Visualization and Analysis of SNP Genotype Data
Authors: Barrett Jeffrey C.
Published: October 2009

INTRODUCTION

Association studies involve accessing, parsing, generating, and analyzing large volumes of data, often carried out in many steps over many months. Large-scale surveys of genetic variation, such as the International HapMap Project, and rapidly increasing volumes of single-nucleotide polymorphism (SNP) genotyping data have created exciting opportunities for association studies. However, they have further exacerbated the difficulty of curating and analyzing such data. Haploview is a program developed in Mark Daly’s lab at the Broad Institute of MIT and Harvard, which is designed to bundle many everyday analysis tasks into one easy-to-use package. Haploview has several features that are useful throughout different phases of association studies. Several of these features are illustrated in this article by following a hypothetical association study from design to execution. Haploview is used to (1) analyze HapMap data and choose tag-SNPs, (2) evaluate the quality of disease genotype data, (3) test for association, and (4) evaluate a region for follow-up of a positive association.
High-Resolution Dual-Trap Optical Tweezers with Differential Detection: Data Collection and Instrument Calibration: Figure 1.
Authors: Bustamante Carlos , Chemla Yann R. , Moffitt Jeffrey R.
Published: October 2009

INTRODUCTION

Optical traps or “optical tweezers” have become an indispensable tool in understanding fundamental biological processes. Dual-trap optical tweezers with differential detection have the advantage that the instrument is decoupled from sources of environmental noise, thereby minimizing interference of signal and maximizing stability and spatial resolution. In this article, we describe methods of data detection and calibration for our dual-trap design.
High-Resolution Dual-Trap Optical Tweezers with Differential Detection: Minimizing the Influence of Measurement Noise
Authors: Bustamante Carlos , Chemla Yann R. , Moffitt Jeffrey R.
Published: October 2009

INTRODUCTION

Optical traps or “optical tweezers” have become an indispensable tool in understanding fundamental biological processes. The environment, the instrument components, and the overall design all have important roles in determining the spatial resolution of an optical trap. However, even with careful attention to these details, the spatial resolution of the optical tweezers is still fundamentally limited by the forces that induce Brownian fluctuations of the trapped microspheres. In this article, we focus on the ways in which the design and implementation of an experiment--the choice of bead size, tether length, and even the method in which the motions of the beads are monitored--can have a large impact on the fundamental resolution of the measurement. By investigating how the Brownian fluctuations depend on experimental parameters and the detection method, we develop a set of guidelines for designing a high-resolution experiment, with a prescription for minimizing the effect of Brownian fluctuations, thus maximizing the resolution of the experiment.
High-Resolution Dual-Trap Optical Tweezers with Differential Detection: Alignment of Instrument Components: Figure 1.
Authors: Bustamante Carlos , Chemla Yann R. , Moffitt Jeffrey R.
Published: October 2009

INTRODUCTION

Optical traps or “optical tweezers” have become an indispensable tool in understanding fundamental biological processes. Using our design, a dual-trap optical tweezers with differential detection, we can detect length changes to a DNA molecule tethering the trapped beads of 1 bp. By forming two traps from the same laser and maximizing the common optical paths of the two trapping beams, we decouple the instrument from many sources of environmental and instrumental noise that typically limit spatial resolution. The performance of a high-resolution instrument--the formation of strong traps, the minimization of background signals from trap movements, or the mitigation of the axial coupling, for example--can be greatly improved through careful alignment. This procedure, which is described in this article, starts from the laser and advances through the instrument, component by component. Alignment is complicated by the fact that the trapping light is in the near infrared (NIR) spectrum. Standard infrared viewing cards are commonly used to locate the beam, but unfortunately, bleach quickly. As an alternative, we use an IR-viewing charge-coupled device (CCD) camera equipped with a C-mount telephoto lens and display its image on a monitor. By visualizing the scattered light on a pair of irises of identical height separated by >12 in., the beam direction can be set very accurately along a fixed axis.
Extraction of RNA from the Plant Kalanchoë daigremontiana
Authors: Garcês Helena , Sinha Neelima
Published: October 2009

INTRODUCTION

This protocol describes how to isolate total RNA from several tissues of Kalanchoë daigremontiana. Total RNA can be isolated by using the TRI-reagent method, scaled up for processing 2 g of tissue, or by using the protocol described here, which gives higher concentrations of high quality RNA. The resulting RNA can be used for various applications including generation of cDNA for reverse transcriptase-PCR (RT-PCR), Northern blots, or other purposes.
Refined candidate region specified by haplotype sharing for Escherichia coli F4ab/F4ac susceptibility alleles in pigs
Authors: Jacobsen M. , Kracht S. S. , Esteso G. , Cirera S. , Edfors I. , Archibald A. L. , Bendixen C. , Andersson L. , Fredholm M. , Jørgensen C. B.
Published: October 2009

Infection of the small intestine by enterotoxigenic Escherichia coli F4ab/ac is a major welfare problem and financial burden for the pig industry. Natural resistance to this infection is inherited as a Mendelian recessive trait, and a polymorphism in the MUC4 gene segregating for susceptibility/resistance is presently used in a selection programme by the Danish pig breeding industry. To elucidate the genetic background involved in E. coli F4ab/ac susceptibility in pigs, a detailed haplotype map of the porcine candidate region was established. This region covers approximately 3.7 Mb. The material used for the study is a three generation family, where the founders are two Wild boars and eight Large White sows. All pigs have been phenotyped for susceptibility to F4ab/ac using an adhesion assay. Their haplotypes are known from segregation analysis using flanking markers. By a targeted approach, the candidate region was subjected to screening for polymorphisms, mainly focusing on intronic sequences. A total of 18 genes were partially sequenced, and polymorphisms were identified in GP5, CENTB2, APOD, PCYT1A, OSTalpha, ZDHHC19, TFRC, ACK1, MUC4, MUC20, KIAA0226, LRCH3 and MUC13. Overall, 227 polymorphisms were discovered in the founder generation. The analysis revealed a large haplotype block, spanning at least 1.5 Mb around MUC4, to be associated with F4ab/ac susceptibility.
The phenotypic and functional characteristics of umbilical cord blood and peripheral blood natural killer cells
Authors: Verneris Michael R. , Miller Jeffrey S.
Published: October 2009

Allogeneic hematopoietic cell transplantation can be curative for patients with high‐risk acute leukaemia. Umbilical cord blood (UCB) is an increasingly used source of allogeneic stem cells for patients who are in need of a transplant, but do not have a sibling donor. This review highlights the similarities and differences between the natural killer (NK) cells obtained from adult peripheral blood (PB) and UCB. These two cell sources show similar percentages of NK cells, including the major CD56dim and CD56bright subpopulations. UCB also contains an additional CD56−CD16+ subset, not typically found in PB. In addition, there are a number of progenitor cell populations in UCB that can give rise to NK cells. Some studies showed that UCB NK cells express a relatively higher percentage of inhibitory receptors (CD94/NKG2A and killer‐cell immunoglobulin‐like receptors) and less adhesion molecules. Resting UCB NK cells also show significantly less cytotoxicity compared to PB NK cells. However, following cytokine stimulation, the cytotoxicity of UCB NK cells can be rapidly increased to levels that are comparable to PB NK cells. Activation and expansion protocols for UCB NK cells are briefly reviewed. Lastly, we outline the early use of UCB NK cells in clinical trials.