bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical study of the advanced target design for FIREX-I
Authors: Nagatomo H. , Johzaki T. , Sakagami H. , Sentoku Y. , Sunahara A. , Taguchi T. , Shiraga H. , Azechi H. , Mima K.
Published: July 2009

In the fast ignition (FI) scheme, at first high density fuel core plasma is assembled by an implosion laser and then heated by a peta watt laser to achieve the fusion burning condition. A typical target for FI is a shell fitted with a re-entrant Au cone to keep a path for the heating laser clean. Recently, for the FIREX-I scale size experiment, the CH tip of the guiding cone has advantages from the viewpoint of the generation of hot electrons and hot electron transport. As a result, from the viewpoint of implosion dynamics, cone-guided implosion with the CH tip is studied using the two-dimensional radiation hydrodynamic code. Two shockwaves caused by the leading shock of implosion and jet from the core determine the breakup time of the tip. With a sophisticated target and laser pulse shape design, CH, CD or other low-Z material tips will be realized without breaking up the cone tip before the maximum compression timing and debasement of the implosion performance.
Diffuse reflection model and noise stabilization for tangential image tomographic reconstruction (TITR) code
Authors: Banerjee Santanu , Vasu P.
Published: July 2009

A tomographic reconstruction code had been reported by us for inferring the poloidal emissivity of tokamak plasma from tangentially acquired images. Here we present modifications to the code that account for any diffuse reflections from the surfaces of walls enclosing the plasma. It is generally recognized that such reconstruction codes are highly susceptible to noise in the data. In this work we have analysed the sensitivity to noise for varying degrees of over-determinism in the set of equations; over-determinism is defined as the ratio of the number of detector signals available to the grid resolution of reconstruction. A tractable scheme for dividing the poloidal cross section into a finite number of unknown sub-tori and voids, while still keeping the over-determinism high, is incorporated. Finally it is shown that noise level >20% can be handled with over-determinism achievable from present day detector array/cameras. The singular value decomposition of the matrix, as used here, can be expected to converge even if any ill-conditioned matrix is encountered due to computational round-off errors in the estimation of chord lengths through sub-tori and voids.
Lower hybrid wave produced supra-thermal electrons and fishbone-like instability in FTU
Authors: Cesario R. , Panaccione L. , Botrugno A. , Calabrò G. , Cardinali A. , Castaldo C. , Marinucci M. , Pericoli V. , Romano A. , Smeulders P. , Tuccillo A.A. , Zonca F.
Published: July 2009

The fishbone-like internal kink instability driven by supra-thermal electrons generated by lower hybrid current drive is an important issue of burning plasma research. Indeed, the trapped particle averaged bounce characterizing the interaction of trapped alpha particles with low-frequency MHD modes in burning plasmas depends on energy, not on mass, hence the charged fusion product effects can be usefully modelled by the analogous effect induced by the fast electrons on the low-frequency MHD modes.

Fishbone-like internal kink instabilities driven by electrons were observed during experiments on Frascati Tokamak Upgrade (FTU) and interpreted in terms of an oscillating ‘fixed point’ activity followed by one of ‘limit cycle’, produced by suprathermal electrons in the presence of a q-profile with q
min ≈ 1. As an interesting behaviour of the fast electron population produced by the LH power when the q-profile meets the condition q
min ≈ 1, the fast electron bremsstrahlung data of FTU show a marked redistribution in space across layers centred at r/a ≈ 0.20–0.33. This redistribution occurs during and in phase with the fishbone oscillation observed by the MHD diagnostic, with the same time scale and at the same radial position of the peak emission seen by x-ray tomography.
Cryopump design for the ITER heating neutral beam injector
Authors: Dremel M. , Day C. , Hemsworth R. , Pearce R. , Mayaux C.
Published: July 2009

Forschungszentrum Karlsruhe (FZK) is developing cryopumps for ITER heating neutral beam injectors (NBIs). The system is characterized by high gas flows coming from different sources against which the cryopumps must maintain a pressure between 10−2 and 10−3 Pa in the beam line (BL) vessel. The design of 2001 had proposed a cylindrical vessel with a cylindrical cryopump inside with a maximized pumping area to cover the vacuum requirements. In this design the only access to all BL components was through the beam source vessel, making it necessary to dismantle the beam source for all maintenance issues on the BL. During the ongoing design investigations on the heating NBI, it was decided in 2006 to use a rectangular vessel for the BL with a top access to improve the maintenance. This necessitated a full redesign of the cryopumps. In the new geometry of the BL vessel the size of the cryopump is limited to a flat rectangular geometry of 8 m length, 2.75 m height and 0.5 m depth. To cover the vacuum requirements two cryopumps of this size must be included for each injector. Gas profile calculations using the detailed BL geometry have been used to detect the needed gas capture probability of the pumping surface to guarantee the beam pulse operation. In this paper we give an outline of the working scope done to come up with a cryopump design covering the needs of the ITER NBI. The design of the novel cryopump and the heat load calculations for the different operation scenarios will be discussed. It is shown that the cryopump for the ITER heating NBI covers all vacuum requirements and it is fully adapted to the ITER cryogenic supply.
Rac1 Modulates Stimulus-evoked Ca2+Release in Neuronal Growth Cones via Parallel Effects on Microtubule/Endoplasmic Reticulum Dynamics and Reactive Oxygen Species Production
Authors: Zhang Xiao-Feng , Forscher Paul
Published: July 2009

The small G protein Rac regulates cytoskeletal protein dynamics in neuronal growth cones and has been implicated in axon growth, guidance, and branching. Intracellular Ca2+is another well known regulator of growth cone function; however, effects of Rac activity on intracellular Ca2+metabolism have not been well characterized. Here, we investigate how Rac1 activity affects release of Ca2+from intracellular endoplasmic reticulum (ER) stores stimulated by application of serotonin (5-hydroxytriptamine). We also address how Rac1 effects on microtubule assembly dynamics affect distribution of Ca2+release sites. Multimode fluorescent microscopy was used to correlate microtubule and ER behavior, and ratiometric imaging was used to assess intracellular Ca2+dynamics. We report that Rac1 activity both promotes Ca2+release and affects its spatial distribution in neuronal growth cones. The underlying mechanism involves synergistic Rac1 effects on microtubule assembly and reactive oxygen species (ROS) production. Rac1 activity modulates Ca2+by 1) enhancing microtubule assembly which in turn promotes spread of the ER-based Ca2+release machinery into the growth cone periphery, and 2) by increasing ROS production which facilitated inositol 1,4,5-trisphosphate-dependent Ca2+release. These results cast Rac1 as a key modulator of intracellular Ca2+function in the neuronal growth cone.
Caenorhabditis elegans FOS-1 and JUN-1 Regulateplc-1Expression in the Spermatheca to Control Ovulation
Authors: Hiatt Susan M. , Duren Holli M. , Shyu Y. John , Ellis Ronald E. , Hisamoto Naoki , Matsumoto Kunihiro , Kariya Ken-ichi , Kerppola Tom K. , Hu Chang-Deng
Published: July 2009

Fos and Jun are components of activator protein-1 (AP-1) and play crucial roles in the regulation of many cellular, developmental, and physiological processes. Caenorhabditis elegans fos-1 has been shown to act in uterine and vulval development. Here, we provide evidence that C. elegans fos-1 and jun-1 control ovulation, a tightly regulated rhythmic program in animals. Knockdown of fos-1 or jun-1 blocks dilation of the distal spermathecal valve, a critical step for the entry of mature oocytes into the spermatheca for fertilization. Furthermore, fos-1 and jun-1 regulate the spermathecal-specific expression of plc-1, a gene that encodes a phospholipase C (PLC) isozyme that is rate-limiting for inositol triphosphate production and ovulation, and overexpression of PLC-1 rescues the ovulation defect in fos-1(RNAi) worms. Unlike fos-1, regulation of ovulation by jun-1 requires genetic interactions with eri-1 and lin-15B, which are involved in the RNA interference pathway and chromatin remodeling, respectively. At least two isoforms of jun-1 are coexpressed with fos-1b in the spermatheca, and different AP-1 dimers formed between these isoforms have distinct effects on the activation of a reporter gene. These findings uncover a novel role for FOS-1 and JUN-1 in the reproductive system and establish C. elegans as a model for studying AP-1 dimerization.
The Molecular Function of the Yeast Polo-like Kinase Cdc5 in Cdc14 Release during Early Anaphase
Authors: Liang Fengshan , Jin Fengzhi , Liu Hong , Wang Yanchang
Published: July 2009

In the budding yeast Saccharomyces cerevisiae , Cdc14 is sequestered within the nucleolus before anaphase entry through its association with Net1/Cfi1, a nucleolar protein. Protein phosphatase PP2ACdc55 dephosphorylates Net1 and keeps it as a hypophosphorylated form before anaphase. Activation of the Cdc fourteen early anaphase release (FEAR) pathway after anaphase entry induces a brief Cdc14 release from the nucleolus. Some of the components in the FEAR pathway, including Esp1, Slk19, and Spo12, inactivate PP2ACdc55, allowing the phosphorylation of Net1 by mitotic cyclin-dependent kinase (Cdk) (Clb2-Cdk1). However, the function of another FEAR component, the Polo-like kinase Cdc5, remains elusive. Here, we show evidence indicating that Cdc5 promotes Cdc14 release primarily by stimulating the degradation of Swe1, the inhibitory kinase for mitotic Cdk. First, we found that deletion of SWE1 partially suppresses the FEAR defects in cdc5 mutants. In contrast, high levels of Swe1 impair FEAR activation. We also demonstrated that the accumulation of Swe1 in cdc5 mutants is responsible for the decreased Net1 phosphorylation. Therefore, we conclude that the down-regulation of Swe1 protein levels by Cdc5 promotes FEAR activation by relieving the inhibition on Clb2-Cdk1, the kinase for Net1 protein.
Proteasome Inactivation Promotes p38 Mitogen-activated Protein Kinase-dependent Phosphatidylinositol 3-kinase Activation and Increases Interleukin-8 Production in Retinal Pigment Epithelial Cells
Authors: Fernandes Alexandre F. , Bian Qingning , Jiang Jian-Kang , Thomas Craig J. , Taylor Allen , Pereira Paulo , Shang Fu
Published: July 2009

Oxidative stress and inflammation are implicated in the pathogenesis of many age-related diseases. We have demonstrated previously that oxidative inactivation of the proteasome is a molecular link between oxidative stress and overexpression of interleukin (IL)-8. Here, we elucidated a novel signaling cascade that leads to up-regulation of IL-8 in response to proteasome inactivation. The sequence of events in this cascade includes proteasome inactivation, activation of mitogen-activated protein kinase kinase (MKK)3/MKK6, activation of p38 mitogen-activated protein kinase (MAPK), epidermal growth factor receptor phosphorylation, phosphatidylinositol 3-kinase (PI3K) activation and increased IL-8 expression. Blocking any of these signaling pathways abolished the up-regulation of IL-8 induced by proteasome inhibition. Although Akt is also activated in response to proteasome inactivation, we found that the PI3K-dependent up-regulation of IL-8 is independent of 3-phosphoinositide-dependent protein kinase (PDK)1 and Akt. Inhibition of PDK1 and Akt with chemical inhibitors or expression of constitutive active Akt had little effects on IL-8 expression in response to proteasome inactivation. In contrast, inhibition of interleukin 2-inducible T cell kinase, a kinase downstream of PI3K, significantly reduced the expression and secretion of IL-8 in response to proteasome inactivation. Together, these data elucidate a novel signaling network that leads to increased IL-8 production in response to proteasome inactivation.
The Peroxisomal Matrix Import of Pex8p Requires Only PTS Receptors and Pex14p
Authors: Ma Changle , Schumann Uwe , Rayapuram Naganand , Subramani Suresh
Published: July 2009

Pichia pastoris (Pp) Pex8p, the only known intraperoxisomal peroxin at steady state, is targeted to peroxisomes by either the peroxisomal targeting signal (PTS) type 1 or PTS2 pathway. Until recently, all cargoes entering the peroxisome matrix were believed to require the docking and really interesting new gene (RING) subcomplexes, proteins that bridge these two subcomplexes and the PTS receptor-recycling machinery. However, we reported recently that the import of PpPex8p into peroxisomes via the PTS2 pathway is Pex14p dependent but independent of the RING subcomplex ( Zhang et al., 2006 ). In further characterizing the peroxisome membrane-associated translocon, we show that two other components of the docking subcomplex, Pex13p and Pex17p, are dispensable for the import of Pex8p. Moreover, we demonstrate that the import of Pex8p via the PTS1 pathway also does not require the RING subcomplex or intraperoxisomal Pex8p. In receptor-recycling mutants (Δpex1, Δpex6, and Δpex4), Pex8p is largely cytosolic because Pex5p and Pex20p are unstable. However, upon overexpression of the degradation-resistant Pex20p mutant, hemagglutinin (HA)-Pex20p(K19R), in Δpex4 and Δpex6 cells, Pex8p enters peroxisome remnants. Our data support the idea that PpPex8p is a special cargo whose translocation into peroxisomes depends only on the PTS receptors and Pex14p and not on intraperoxisomal Pex8p, the RING subcomplex, or the receptor-recycling machinery.
Distinct Roles for Key Karyogamy Proteins during Yeast Nuclear Fusion
Authors: Melloy Patricia , Shen Shu , White Erin , Rose Mark D.
Published: July 2009

During yeast mating, cell fusion is followed by the congression and fusion of the two nuclei. Proteins required for nuclear fusion are found at the surface (Prm3p) and within the lumen (Kar2p, Kar5p, and Kar8p) of the nuclear envelope (NE). Electron tomography (ET) of zygotes revealed that mutations in these proteins block nuclear fusion with different morphologies, suggesting that they act in different steps of fusion. Specifically, prm3 zygotes were blocked before formation of membrane bridges, whereas kar2, kar5, and kar8 zygotes frequently contained them. Membrane bridges were significantly larger and occurred more frequently in kar2 and kar8, than in kar5 mutant zygotes. The kinetics of NE fusion in prm3, kar5, and kar8 mutants, measured by live-cell fluorescence microscopy, were well correlated with the size and frequency of bridges observed by ET. However the kar2 mutant was defective for transfer of NE lumenal GFP, but not diffusion within the lumen, suggesting that transfer was blocked at the NE fusion junction. These observations suggest that Prm3p acts before initiation of outer NE fusion, Kar5p may help dilation of the initial fusion pore, and Kar2p and Kar8p act after outer NE fusion, during inner NE fusion.
On the inference of spatial structure from population genetics data
Authors: Guillot Gilles
Published: July 2009

Motivation: In a series of recent papers, Tess, a computer program based on the concept of hidden Markov random field, has been proposed to infer the number and locations of panmictic population units from the genotypes and spatial locations of these individuals. The method seems to be of broad appeal as it is conceptually much simpler than other competing methods and it has been reported by its authors to be fast and accurate. However, this methodology is not grounded in a formal statistical inference method and seems to rely to a large extent on arbitrary choices regarding the parameters used. The present article is an investigation of the accuracy of this method and an attempt to assess whether recent results reported on the basis of this method are genuine features of the genetic process or artefacts of the method.

Method: I analyse simulated data consisting of populations at Hardy–Weinberg and linkage equilibrium and also data simulated under a scenario of isolation-by-distance at mutation–migration–drift equilibrium. Arabidopsis thaliana data previously analysed with this method are also reconsidered.

Results: Using the Tess program under the no-admixture model to analyse data consisting of several genuine HWLE populations with individuals of pure ancestries leads to highly inaccurate results; Using the Tess program under the admixture model to analyse data consisting of a continuous isolation-by-distance population leads to the inference of spurious HWLE populations whose number and features depend on the parameters used. Results previously reported about the A.thaliana using Tess seem to a large extent to be artefacts of the statistical methodology used. The findings go beyond population clustering models and can be an help to design more efficient algorithms based on graphs.

Availability: The data analysed in the present article are available from http://folk.uio.no/gillesg/Bioinformatics-HMRF

Contact:  gilles.guillot@bio.uio.no

Supplementary information:  Supplementary data are available at Bioinformatics online.
Comment on ‘On the inference of spatial structure from population genetics data’
Authors: Durand Eric , Chen Chibiao , François Olivier
Published: July 2009

Contact:  Olivier.francois@imag.fr
k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage
Authors: Bragg Lauren M. , Stone Glenn
Published: July 2009

Motivation: The clustering of expressed sequence tags (ESTs) is a crucial step in many sequence analysis studies that require a high level of redundancy. Chimeric sequences, while uncommon, can make achieving the optimal EST clustering a challenge. Single-linkage algorithms are particularly vulnerable to the effects of chimeras. To avoid chimera-facilitated erroneous merges, researchers using single-linkage algorithms are forced to use stringent sequence–similarity thresholds. Such thresholds reduce the sensitivity of the clustering algorithm.

Results: We introduce the concept of k-link clustering for EST data. We evaluate how clustering error rates vary over a range of linkage thresholds. Using k-link, we show that Type II error decreases in response to increasing the number of shared ESTs (ie. links) required. We observe a base level of Type II error likely caused by the presence of unmasked low-complexity or repetitive sequence. We find that Type I error increases gradually with increased linkage. To minimize the Type I error introduced by increased linkage requirements, we propose an extension to k-link which modifies the required number of links with respect to the size of clusters being compared.

Availability: The implementation of k-link is available under the terms of the GPL from http://www.bioinformatics.csiro.au/products.shtml. k-link is licensed under the GNU General Public License, and can be downloaded from http://www.bioinformatics.csiro.au/products.shtml. k-link is written in C++.

Contact:  lauren.bragg@csiro.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus
Authors: Nishida Hiromi , Motoyama Takayuki , Yamamoto Shogo , Aburatani Hiroyuki , Osada Hiroyuki
Published: July 2009

We identified 5 975 567 mono- and 6 995 122 di-nucleosome positions of the fungus Aspergillus fumigatus, which was detected at high resolution based on the DNA sequence data obtained from both mono- and di-nucleosomal DNA fragments. We show that the distribution of lengths of the mono-nucleosomal DNA fragments has two peaks at 135 and 150 nt, whereas the distribution of di-nucleosomal DNA fragment lengths has a single peak at 285 nt. Although the gene bodies of the active and inactive genes and the inactive gene promoters had the two peaks of the mono-nucleosomal DNA fragment lengths, the active gene promoter lost the longer peak at 150 nt. Our findings strongly suggest that the nucleosomes protecting longer DNA fragments against MNase at the promoters, thereby inhibiting high gene expression.

Contact:  hnishida@iu.a.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Gastroprotective Effect of Ginger Rhizome (Zingiber officinale) Extract: Role of Gallic Acid and Cinnamic Acid in H+, K+‐ATPase/H. pylori Inhibition and Anti‐Oxidative Mechanism
Authors: Nanjundaiah Siddaraju M. , Annaiah Harish Nayaka Mysore , Dharmesh Shylaja M.
Published: July 2009

Zinger officinale has been used as a traditional source against gastric disturbances from time immemorial. The ulcer‐preventive properties of aqueous extract of ginger rhizome (GRAE) belonging to the family Zingiberaceae is reported in the present study. GRAE at 200 mg kg−1 b.w. protected up to 86% and 77% for the swim stress‐/ethanol stress‐induced ulcers with an ulcer index (UI) of 50 ± 4.0/46 ± 4.0, respectively, similar to that of lansoprazole (80%) at 30 mg kg−1 b.w. Increased H+, K+‐ATPase activity and thiobarbituric acid reactive substances (TBARS) were observed in ulcer‐induced rats, while GRAE fed rats showed normalized levels and GRAE also normalized depleted/amplified anti‐oxidant enzymes in swim stress and ethanol stress‐induced animals. Gastric mucin damage was recovered up to 77% and 74% in swim stress and ethanol stress, respectively after GRAE treatment. GRAE also inhibited the growth of H. pylori with MIC of 300 ± 38 μg and also possessed reducing power, free radical scavenging ability with an IC50 of 6.8 ± 0.4 μg mL−1 gallic acid equivalent (GAE). DNA protection up to 90% at 0.4 μg was also observed. Toxicity studies indicated no lethal effects in rats fed up to 5 g kg−1 b.w. Compositional analysis favored by determination of the efficacy of individual phenolic acids towards their potential ulcer‐preventive ability revealed that between cinnamic (50%) and gallic (46%) phenolic acids, cinnamic acid appear to contribute to better H+, K+‐ATPase and Helicobacter pylori inhibitory activity, while gallic acid contributes significantly to anti‐oxidant activity.
Arthropod remains in the oral cavities of fossil reptiles support inference of early insectivory
Authors: Modesto Sean P. , Scott Diane M. , Reisz Robert R.
Published: July 2009

Inference of feeding preferences in fossil terrestrial vertebrates (tetrapods) has been drawn predominantly from craniodental morphology, and less so from fossil specimens preserving conclusive evidence of diet in the form of oral and/or gut contents. Recently, the pivotal role of insectivory in tetrapod evolution was emphasized by the identification of putative insectivores as the closest relatives of the oldest known herbivorous amniotes. We provide the first compelling evidence for insectivory among early tetrapods on the basis of two 280-million-year-old (late Palaeozoic) fossil specimens of a new species of acleistorhinid parareptile with preserved arthropod cuticle on their toothed palates. Their dental morphology, consisting of homodont marginal dentition with cutting edges and slightly recurved tips, is consistent with an insectivorous diet. The intimate association of arthropod cuticle with the oral region of two small reptiles, from a rich fossil locality that has otherwise not produced invertebrate remains, strongly supports the inference of insectivory in the reptiles. These fossils lend additional support to the hypothesis that the origins and earliest stages of higher vertebrate evolution are associated with relatively small terrestrial insectivores.
How universal are human mate choices? Size does not matter when Hadza foragers are choosing a mate
Authors: Sear Rebecca , Marlowe Frank W.
Published: July 2009

It has been argued that size matters on the human mate market: both stated preferences and mate choices have been found to be non-random with respect to height and weight. But how universal are these patterns? Most of the literature on human mating patterns is based on post-industrial societies. Much less is known about mating behaviour in more traditional societies. Here we investigate mate choice by analysing whether there is any evidence for non-random mating with respect to size and strength in a forager community, the Hadza of Tanzania. We test whether couples assort for height, weight, body mass index (BMI), per cent fat and grip strength. We test whether there is a male-taller norm. Finally, we test for an association between anthropometric variables and number of marriages. Our results show no evidence for assortative mating for height, weight, BMI or per cent fat; no evidence for a male-taller norm and no evidence that number of marriages is associated with our size variables. Hadza couples may assort positively for grip strength, but grip strength does not affect the number of marriages. Overall we conclude that, in contrast to post-industrial societies, mating appears to be random with respect to size in the Hadza.
Mesopredators constrain a top predator: competitive release of ravens after culling crows
Authors: Bodey Thomas W. , McDonald Robbie A. , Bearhop Stuart
Published: July 2009

Although predator control programmes rarely consider complex competitive interactions among predators, it is becoming clear that removal of larger ‘superior’ competitors often releases the ‘inferior’ ones and can precipitate trophic cascades. In contrast, our study indicates that culling hooded crows
Corvus cornix
appears to release a larger competitor, the common raven
Corvus corax
. Ravens ranged more widely, and the predation of artificial nests was significantly faster (although total predation was similar), after the removal of crows. Our study provides evidence of a novel reversal of competitive release where a larger species was freed from constraints imposed on its distribution and behaviour by a smaller species, and emphasizes the importance of considering community and ecosystem effects of predator manipulations when undertaken for conservation or game management.
Combining structure and dynamics: non-denaturing high-pressure effect on lysozyme in solution
Authors: Ortore Maria Grazia , Spinozzi Francesco , Mariani Paolo , Paciaroni Alessandro , Barbosa Leandro R. S. , Amenitsch Heinz , Steinhart Milos , Ollivier Jacques , Russo Daniela
Published: July 2009

Small-angle X-ray scattering (SAXS) and elastic and quasi-elastic neutron scattering techniques were used to investigate the high-pressure-induced changes on interactions, the low-resolution structure and the dynamics of lysozyme in solution. SAXS data, analysed using a global-fit procedure based on a new approach for hydrated protein form factor description, indicate that lysozyme completely maintains its globular structure up to 1500 bar, but significant modifications in the protein–protein interaction potential occur at approximately 600–1000 bar. Moreover, the mass density of the protein hydration water shows a clear discontinuity within this pressure range. Neutron scattering experiments indicate that the global and the local lysozyme dynamics change at a similar threshold pressure. A clear evolution of the internal protein dynamics from diffusing to more localized motions has also been probed. Protein structure and dynamics results have then been discussed in the context of protein–water interface and hydration water dynamics. According to SAXS results, the new configuration of water in the first hydration layer induced by pressure is suggested to be at the origin of the observed local mobility changes.
Maturation of high-density lipoproteins
Authors: Shih Amy Y. , Sligar Stephen G. , Schulten Klaus
Published: July 2009

Human high-density lipoproteins (HDLs) are involved in the transport of cholesterol. The mechanism by which HDL assembles and functions is not well understood owing to a lack of structural information on circulating spherical HDL. Here, we report a series of molecular dynamics simulations that describe the maturation of discoidal HDL into spherical HDL upon incorporation of cholesterol ester as well as the resulting atomic level structure of a mature circulating spherical HDL particle. Sixty cholesterol ester molecules were added in a stepwise fashion to a discoidal HDL particle containing two apolipoproteins wrapped around a 160 dipalmitoylphosphatidylcholine lipid bilayer. The resulting matured particle, captured in a coarse-grained description, was then described in a consistent all-atom representation and analysed in chemical detail. The simulations show that maturation results from the formation of a highly dynamic hydrophobic core comprised of cholesterol ester surrounded by phospholipid and protein; the two apolipoprotein strands remain in a belt-like conformation as seen in the discoidal HDL particle, but with flexible N- and C-terminal helices and a central region stabilized by salt bridges. In the otherwise flexible lipoproteins, a less mobile central region provides an ideal location to bind lecithin cholesterol acyltransferase, the key enzyme that converts cholesterol to cholesterol ester during HDL maturation.
Fluorescence two-dimensional difference gel electrophoresis for biomaterial applications
Authors: McNamara Laura E. , Dalby Matthew J. , Riehle Mathis O. , Burchmore Richard
Published: July 2009

Fluorescence two-dimensional difference gel electrophoresis (DiGE) is rapidly becoming established as a powerful technique for the characterization of differences in protein expression levels between two or more conditions. In this review, we consider the application of DiGE—both minimal and saturation labelling—to biomaterials research, considering the challenges and rewards of this approach.
Political gout: dissolute patients, deceitful physicians, and other blue devils
Authors: Rousseau George
Published: July 2009

This essay seeks to assess the renegade Thomas Beddoes through the filter of the gout diagnosis in his time. It stretches out to cover his whole life and emphasizes the need for a broad comparative historical and biographical approach. Gout is shown to have functioned then as more than a malady; it was also part of a social code embedding class, rank, affiliation, standing and political position.
His majesty's subjects: from laboratory to human experiment in pneumatic chemistry
Authors: Stewart Larry
Published: July 2009

Experiments in pneumatic chemistry paved the way for medical innovation in the last quarter of the eighteenth century. Thomas Beddoes and James Watt were instrumental in the spread of the use of new gas chemistry in pneumatic therapy, but they were far from alone. There was no shortage of experimental subjects, as the practice was quickly taken up by medics throughout Britain.
Reduced Bloch mode expansion for periodic media band structure calculations
Authors: Hussein Mahmoud I.
Published: July 2009

Reduced Bloch mode expansion (RBME) is presented for fast periodic media band structure calculations. The expansion employs a natural basis composed of a selected reduced set of Bloch eigenfunctions. The reduced basis is selected within the irreducible Brillouin zone at high symmetry points determined by the medium’s crystal structure and group theory (and possibly at additional related points). At each of the reciprocal lattice selection points, a number of Bloch eigenfunctions are selected up to the frequency/energy range of interest for the band structure calculations. As it is common to initially discretize the periodic unit cell and solution field using some choice of basis, RBME is practically a secondary expansion that uses a selected set of Bloch eigenvectors. Such expansion therefore keeps, and builds on, any favourable attributes a primary expansion approach might exhibit. Being in line with the well-known concept of modal analysis, the proposed approach maintains accuracy while reducing the computation time by up to two orders of magnitudes or more depending on the size and extent of the calculations. Results are presented for phononic, photonic and electronic band structures.
On the Maslov index of multi-pulse homoclinic orbits
Authors: Chardard Frédéric , Dias Frédéric , Bridges Thomas J.
Published: July 2009

Multi-pulse homoclinic orbits of Hamiltonian systems on

can be classified by a sequence of integers. In this paper, we find the surprising result that this string of integers encodes the value of the Maslov index of the homoclinic orbit. Our results include a computable formulation of the Maslov index for homoclinic orbits and a robust numerical method for the evaluation of the Maslov index.
Uni-axial stress–strain response and thermal conductivity degradation of ceramic matrix composite fibre tows
Authors: Tang C. , Blacklock M. , Hayhurst D. R.
Published: July 2009

A physical model, previously developed by one of the authors, has been extended to cover thermal conductivity degradation owing to the uni-axial stress–strain response of aligned groups of fibres or tows found in ceramic matrix composites. Both the stress–strain and thermal models, together with their coupling, have been shown to predict known composite behaviour qualitatively. The degradation of longitudinal thermal properties is shown to be driven by strain-controlled fibre failure; while the degradation of transverse thermal properties is because of the growth of fibre–matrix interface wake-debonded cracks, coupled with strain-driven fibre failure.
Mortality risk increases with natal dispersal distance in American martens
Authors: Johnson Cheryl A. , Fryxell John M. , Thompson Ian D. , Baker James A.
Published: July 2009

The assumption that mortality risk increases with dispersal distance has rarely been tested. We compared patterns of natal dispersal in the American marten (Martes americana) between a large regenerating forest landscape and an uncut landscape that was dominated by more mature forest to test whether mortality risk increased with dispersal distance, and whether variation in mortality risk influenced dispersal distance. Mortality risk increased with dispersal distance in both landscape treatments, but the distance-dependent increase in mortality in the regenerating landscape was twice that in the uncut landscape. Differences in body condition, supported by other data on foraging efficiency, suggested that juveniles from the regenerating landscape were less able to cope with the energetic demands of dispersal compared with juveniles from older forests. Juveniles travelled shorter distances in the regenerating versus uncut landscape. These results implied that dispersal was costly in terms of juvenile survival and that mean dispersal distance was shaped, in part, by mortality risk.
The role of pre-emptive culling in the control of foot-and-mouth disease
Authors: Tildesley Michael J. , Bessell Paul R. , Keeling Matt J. , Woolhouse Mark E. J.
Published: July 2009

The 2001 foot-and-mouth disease epidemic was controlled by culling of infectious premises and pre-emptive culling intended to limit the spread of disease. Of the control strategies adopted, routine culling of farms that were contiguous to infected premises caused the most controversy. Here we perform a retrospective analysis of the culling of contiguous premises as performed in 2001 and a simulation study of the effects of this policy on reducing the number of farms affected by disease. Our simulation results support previous studies and show that a national policy of contiguous premises (CPs) culling leads to fewer farms losing livestock. The optimal national policy for controlling the 2001 epidemic is found to be the targeting of
all
contiguous premises, whereas for localized outbreaks in high animal density regions, more extensive fixed radius ring culling is optimal. Analysis of the 2001 data suggests that the lowest-risk CPs were generally prioritized for culling, however, even in this case, the policy is predicted to be effective. A sensitivity analysis and the development of a spatially heterogeneous policy show that the optimal culling level depends upon the basic reproductive ratio of the infection and the width of the dispersal kernel. These analyses highlight an important and probably quite general result: optimal control is highly dependent upon the distance over which the pathogen can be transmitted, the transmission rate of infection and local demography where the disease is introduced.
A potent effect of observational learning on chimpanzee tool construction
Authors: Price Elizabeth E. , Lambeth Susan P. , Schapiro Steve J. , Whiten Andrew
Published: July 2009

Although tool use occurs in diverse species, its complexity may mark an important distinction between humans and other animals. Chimpanzee tool use has many similarities to that seen in humans, yet evidence of the cumulatively complex and constructive technologies common in human populations remains absent in free-ranging chimpanzees. Here we provide the first evidence that chimpanzees have a latent capacity to socially learn to construct a composite tool. Fifty chimpanzees were assigned to one of five demonstration conditions that varied in the amount and type of information available in video footage of a conspecific. Chimpanzees exposed to complete footage of a chimpanzee combining the two components to retrieve a reward learned to combine the tools significantly more than those exposed to more restricted information. In a follow-up test, chimpanzees that constructed tools after watching the complete demonstration tended to do so even when the reward was within reach of the unmodified components, whereas those that spontaneously solved the task (without seeing the modification process) combined only when necessary. Social learning, therefore, had a powerful effect in instilling a marked persistence in the use of a complex technique at the cost of efficiency, inhibiting insightful tool use.
Precocial development of locomotor performance in a ground-dwelling bird (Alectoris chukar): negotiating a three-dimensional terrestrial environment
Authors: Jackson Brandon E. , Segre Paolo , Dial Kenneth P.
Published: July 2009

Developing animals are particularly vulnerable to predation. Hence, precocial young of many taxa develop predator escape performance that rivals that of adults. Ontogenetically unique among vertebrates, birds transition from hind limb to forelimb dependence for escape behaviours, so developmental investment for immediate gains in running performance may impair flight performance later. Here, in a three-dimensional kinematic study of developing birds performing pre-flight flapping locomotor behaviours, wing-assisted incline running (WAIR) and a newly described behaviour, controlled flapping descent (CFD), we define three stages of locomotor ontogeny in a model gallinaceous bird (Alectoris chukar). In stage I (1–7 days post-hatching (dph)) birds crawl quadrupedally during ascents, and their flapping fails to reduce their acceleration during aerial descents. Stage II (8–19 dph) birds use symmetric wing beats during WAIR, and in CFD significantly reduce acceleration while controlling body pitch to land on their feet. In stage III (20 dph to adults), birds are capable of vertical WAIR and level-powered flight. In contrast to altricial species, which first fly when nearly at adult mass, we show that in a precocial bird the major requirements for flight (i.e. high power output, wing control and wing size) convene by around 8 dph (atca5% of adult mass) and yield significant gains in escape performance: immature chukars can fly by 20 dph, at only about 12 per cent of adult mass.
A new proposal concerning the botanical origin of Baltic amber
Authors: Wolfe Alexander P. , Tappert Ralf , Muehlenbachs Karlis , Boudreau Marc , McKellar Ryan C. , Basinger James F. , Garrett Amber
Published: July 2009

Baltic amber constitutes the largest known deposit of fossil plant resin and the richest repository of fossil insects of any age. Despite a remarkable legacy of archaeological, geochemical and palaeobiological investigation, the botanical origin of this exceptional resource remains controversial. Here, we use taxonomically explicit applications of solid-state Fourier-transform infrared (FTIR) microspectroscopy, coupled with multivariate clustering and palaeobotanical observations, to propose that conifers of the family Sciadopityaceae, closely allied to the sole extant representative,Sciadopitys verticillata, were involved in the genesis of Baltic amber. The fidelity of FTIR-based chemotaxonomic inferences is upheld by modern–fossil comparisons of resins from additional conifer families and genera (Cupressaceae:Metasequoia; Pinaceae:PinusandPseudolarix). Our conclusions challenge hypotheses advocating members of either of the families Araucariaceae or Pinaceae as the primary amber-producing trees and correlate favourably with the progressive demise of subtropical forest biomes from northern Europe as palaeotemperatures cooled following the Eocene climate optimum.
Mineralized soft-tissue structure and chemistry in a mummified hadrosaur from the Hell Creek Formation, North Dakota (USA)
Authors: Manning Phillip L. , Morris Peter M. , McMahon Adam , Jones Emrys , Gize Andy , Macquaker Joe H. S. , Wolff George , Thompson Anu , Marshall Jim , Taylor Kevin G. , Lyson Tyler , Gaskell Simon , Reamtong Onrapak , Sellers William I. , van Dongen Bart E. , Buckley Mike , Wogelius Roy A.
Published: July 2009

An extremely well-preserved dinosaur (
Cf. Edmontosaurus
sp.) found in the Hell Creek Formation (Upper Cretaceous, North Dakota) retains soft-tissue replacement structures and associated organic compounds. Mineral cements precipitated in the skin apparently follow original cell boundaries, partially preserving epidermis microstructure. Infrared and electron microprobe images of ossified tendon clearly show preserved mineral zonation, with silica and trapped carbon dioxide forming thin linings on Haversian canals within apatite. Furthermore, Fourier transform infrared spectroscopy (FTIR) of materials recovered from the skin and terminal ungual phalanx suggests the presence of compounds containing amide groups. Amino acid composition analyses of the mineralized skin envelope clearly differ from the surrounding matrix; however, intact proteins could not be obtained using protein mass spectrometry. The presence of endogenously derived organics from the skin was further demonstrated by pyrolysis gas chromatography mass spectrometry (Py-GCMS), indicating survival and presence of macromolecules that were in part aliphatic (see the electronic supplementary material).
A new primate from the Eocene Pondaung Formation of Myanmar and the monophyly of Burmese amphipithecids
Authors: Beard K. Christopher , Marivaux Laurent , Chaimanee Yaowalak , Jaeger Jean-Jacques , Marandat Bernard , Tafforeau Paul , Soe Aung Naing , Tun Soe Thura , Kyaw Aung Aung
Published: July 2009

The family Amphipithecidae is one of the two fossil primate taxa from Asia that appear to be early members of the anthropoid clade.
Ganlea megacanina
, gen. et sp. nov., is a new amphipithecid from the late middle Eocene Pondaung Formation of central Myanmar. The holotype of
Ganlea
is distinctive in having a relatively enormous lower canine showing heavy apical wear, indicating an important functional role of the lower canine in food preparation and ingestion. A phylogenetic analysis of amphipithecid relationships suggests that
Ganlea
is the sister taxon of
Myanmarpithecus
, a relatively small-bodied taxon that has often, but not always, been included in Amphipithecidae.
Pondaungia
is the sister taxon of the
Ganlea
+
Myanmarpithecus
clade. All three Pondaung amphipithecid genera are monophyletic with respect to
Siamopithecus
, which is the most basal amphipithecid currently known. The inclusion of
Myanmarpithecus
in Amphipithecidae diminishes the likelihood that amphipithecids are specially related to adapiform primates. Extremely heavy apical wear has been documented on the lower canines of all three genera of Burmese amphipithecids. This distinctive wear pattern suggests that Burmese amphipithecids were an endemic radiation of hard object feeders that may have been ecological analogues of living New World pitheciin monkeys.
Uropathogens from diabetic patients in Libya: virulence factors and phylogenetic groups of Escherichia coli isolates
Authors: Ghenghesh Khalifa Sifaw , Elkateb Einass , Berbash Nuri , Abdel Nada Rania , Ahmed Salwa F. , Rahouma Amal , Seif-Enasser Nadia , Elkhabroun Mohamed-Abdulwahab , Belresh Taher , Klena John D.
Published: July 2009

Urinary tract infections (UTIs) in patients with diabetes mellitus (DM) are reported mainly from developed countries. In addition to this underreporting from developing countries, there is a lack of information pertaining to the virulence factors (VFs) and phylogenetic grouping of uropathogenicEscherichia coli(UPEC) from DM and non-DM patients in developing countries. Between July 2005 and June 2006, urine specimens were collected from 135 DM and 164 non-DM patients, all with clinically diagnosed UTIs, attending Elkhadra Hospital and the Diabetic Center in Tripoli, Libya. Specimens were examined for different uropathogens using standard microbiological procedures. Isolated uropathogens were tested for their susceptibility to antimicrobial agents by a disc diffusion method. In addition, UPEC was grouped phylogenetically by PCR and subsequently tested for 19 VFs. Uropathogens were isolated from 77 (57 %) of the DM group and from 110 (67 %) of the non-DM group (P>0.05).E. coliwas isolated from 18 (13 %) and 29 (18 %),Klebsiellaspecies from 18 (13 %) and 23 (14 %), andStaphylococcus aureusfrom 12 (9 %) and 12 (7 %) of the DM and non-DM groups, respectively (P>0.05). Age, gender, education level and marital status had no significant influence on the isolation rates of different organisms from the DM group compared with the non-DM group. With very few exceptions, no differences were observed in the antimicrobial resistance profiles of uropathogens from the DM and non-DM patients. In addition, UPEC from the DM patients was significantly less virulent and was associated with phylogenetic group A, whilst UPEC from the non-DM patients was significantly more virulent and was associated with group D. The results of our surveillance of UTI infections in DM patients agree, in general, with observations reported previously from several developed countries.
Detection of Cryptococcus by conventional, serological and molecular methods
Authors: Saha Dolan Champa , Xess Immaculata , Biswas Ashutosh , Bhowmik Dipankar M. , Padma M. V.
Published: July 2009

The rising incidence of cryptococcosis in India is posing a serious threat. Due to lack of sensitive methods for diagnosis, high morbidity and mortality are associated with the disease. Early diagnosis is essential to prevent serious complications. Therefore, we attempted to find highly sensitive and specific detection methods. A comparative evaluation of the detection of cryptococcosis was done by conventional (direct microscopy and culture) and rapid diagnostic [latex agglutination test (LAT), enzyme immunoassay (EIA) and PCR] methods. The study was done on 359 samples from 52 positive patients and 30 negative controls in an Indian set-up. Evaluation was done for cerebrospinal fluid (CSF), serum and urine separately. The diagnostic value of the tests was assessed in pre-treatment samples, and follow-up tests were also done on samples obtained after initiation of treatment. PCR had the highest sensitivity, followed by EIA and LAT, both before and after treatment. The positive detection by LAT, EIA and PCR was the longest in CSF (>90 days), followed by serum (∼65 days) then urine (∼45 days) after initiation of treatment. Our results indicated that the sensitivity and specificity of PCR and EIA were comparable in urine, CSF and serum for diagnosis of cryptococcosis.