bluuebunny/crossref_metadata_2025 huggingface dataset:
External noise-induced phenomena in CO oxidation on single crystal surfaces
Authors: Pineda M. , Toral R.
Published: March 2009

The influence of external noise on minimalistic models for the catalytic CO oxidation on Ir(111) and Pt(111) is studied by means of the adiabatic elimination technique. Two models, which reproduce the bistable behavior usually observed in CO oxidation on Pt group metal surfaces, are analyzed. The noise is superposed on the fraction of CO in the constant gas flow directed at the surfaces and the resulting stochastic systems are reduced after the adiabatic elimination of oxygen coverage. This reduction allows us to analyze theoretically the interplay between external noise and the kinetic bistability of CO oxidation. We report the phenomena of noise-induced shifts of steady states and noise-induced jumps between stable steady states. We also present evidence for noise-induced transitions from mono- to bistability. The theoretical results are compared with simulations of the original two-variable stochastic reaction systems.
In-depth agglomeration of d-metals at Si-on-Mo interfaces
Authors: Tsarfati Tim , Zoethout Erwin , van de Kruijs Robbert , Bijkerk Fred
Published: March 2009

Reflective Si/Mo multilayer mirrors with protective d-metal surfaces onto a range of upper Mo and Si layer thicknesses have been grown with physical vapor deposition and investigated on diffusion and in-depth compound formation. Laterally inhomogeneous upward Si and downward d-metal diffusion occurs through Mo layers up to 2 nm thickness. Especially Ru and Rh agglomerate and form silicides such as Ru2Si3 and Rh2Si not in the midst of the Si layer but at the Si/Mo interface. This appears to be mediated by MoSi2 presence at the Si/Mo interface that acts as precursor via better lattice compatibility and lowering of formation energy.
Citizenship's Place: The State's Creation of Public Space and Street Vendors' Culture of Informality in Bogotá, Colombia
Authors: Hunt Stacey
Published: March 2009

In this paper I seek to move beyond understandings of Colombia as a failed state or qualified democracy by exploring how the state continues to govern despite widespread shortcomings. I argue that two technologies of governance are central to contemporary rule in Colombia: state fragmentation and citizen education. These technologies are exemplified by the recovery of public space from street vendors in order to preserve it as a privileged site for citizenship. This process is made possible by the proliferation of state agencies, policies, and plans which define the problem of public space as one of its invasion by ambulant vendors, and the solution to this invasion as the relocation of vendors to spatially marginalized and state-regulated markets where they are taught to overcome their ‘culture of informality’ by participating in political and economic transactions in state-prescribed ways. I argue that the recovery of public space and relocation of street vendors is a spatial technology of governance that codes structural inequalities as a question of culture while producing new forms of segregation in which citizens and street vendors have differentiated places and rights to mobility. This study analyzes the relationship between state and citizen construction while considering the pedagogical work implicated in the resilience of both democracy and neoliberal economic policies.
The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5′ splice site-like sequences
Authors: Loughlin Fionna E. , Mansfield Robyn E. , Vaz Paula M. , McGrath Aaron P. , Setiyaputra Surya , Gamsjaeger Roland , Chen Eva S. , Morris Brian J. , Guss J. Mitchell , Mackay Joel P.
Published: March 2009

The alternative splicing of mRNA is a critical process in higher eukaryotes that generates substantial proteomic diversity. Many of the proteins that are essential to this process contain arginine/serine-rich (RS) domains. ZRANB2 is a widely-expressed and highly-conserved RS-domain protein that can regulate alternative splicing but lacks canonical RNA-binding domains. Instead, it contains 2 RanBP2-type zinc finger (ZnF) domains. We demonstrate that these ZnFs recognize ssRNA with high affinity and specificity. Each ZnF binds to a single AGGUAA motif and the 2 domains combine to recognize AGGUAA(N
x
)AGGUAA double sites, suggesting that ZRANB2 regulates alternative splicing via a direct interaction with pre-mRNA at sites that resemble the consensus 5′ splice site. We show using X-ray crystallography that recognition of an AGGUAA motif by a single ZnF is dominated by side-chain hydrogen bonds to the bases and formation of a guanine-tryptophan-guanine “ladder.” A number of other human proteins that function in RNA processing also contain RanBP2 ZnFs in which the RNA-binding residues of ZRANB2 are conserved. The ZnFs of ZRANB2 therefore define another class of RNA-binding domain, advancing our understanding of RNA recognition and emphasizing the versatility of ZnF domains in molecular recognition.
The mosaic genome structure of the
Wolbachia w
Ri strain infecting
Drosophila simulans
Authors: Klasson Lisa , Westberg Joakim , Sapountzis Panagiotis , Näslund Kristina , Lutnaes Ylva , Darby Alistair C. , Veneti Zoe , Chen Lanming , Braig Henk R. , Garrett Roger , Bourtzis Kostas , Andersson Siv G. E.
Published: March 2009

The obligate intracellular bacterium
Wolbachia pipientis
infects around 20% of all insect species. It is maternally inherited and induces reproductive alterations of insect populations by male killing, feminization, parthenogenesis, or cytoplasmic incompatibility. Here, we present the 1,445,873-bp genome of
W. pipientis
strain
w
Ri that induces very strong cytoplasmic incompatibility in its natural host
Drosophila simulans
. A comparison with the previously sequenced genome of
W. pipientis
strain
w
Mel from
Drosophila melanogaster
identified 35 breakpoints associated with mobile elements and repeated sequences that are stable in
Drosophila
lines transinfected with
w
Ri. Additionally, 450 genes with orthologs in
w
Ri and
w
Mel were sequenced from the
W. pipientis
strain
w
Uni, responsible for the induction of parthenogenesis in the parasitoid wasp
Muscidifurax uniraptor
. The comparison of these A-group
Wolbachia
strains uncovered the most highly recombining intracellular bacterial genomes known to date. This was manifested in a 500-fold variation in sequence divergences at synonymous sites, with different genes and gene segments supporting different strain relationships. The substitution-frequency profile resembled that of
Neisseria meningitidis
, which is characterized by rampant intraspecies recombination, rather than that of
Rickettsia
, where genes mostly diverge by nucleotide substitutions. The data further revealed diversification of ankyrin repeat genes by short tandem duplications and provided examples of horizontal gene transfer across A- and B-group strains that infect
D. simulans
. These results suggest that the transmission dynamics of
Wolbachia
and the opportunity for coinfections have created a freely recombining intracellular bacterial community with mosaic genomes.
Curvature-driven lipid sorting needs proximity to a demixing point and is aided by proteins
Authors: Sorre Benoit , Callan-Jones Andrew , Manneville Jean-Baptiste , Nassoy Pierre , Joanny Jean-François , Prost Jacques , Goud Bruno , Bassereau Patricia
Published: March 2009

Sorting of lipids and proteins is a key process allowing eukaryotic cells to execute efficient and accurate intracellular transport and to maintain membrane homeostasis. It occurs during the formation of highly curved transport intermediates that shuttle between cell compartments. Protein sorting is reasonably well described, but lipid sorting is much less understood. Lipid sorting has been proposed to be mediated by a physical mechanism based on the coupling between membrane composition and high curvature of the transport intermediates. To test this hypothesis, we have performed a combination of fluorescence and force measurements on membrane tubes of controlled diameters pulled from giant unilamellar vesicles. A model based on membrane elasticity and nonideal solution theory has also been developed to explain our results. We quantitatively show, using 2 independent approaches, that a difference in lipid composition can build up between a curved and a noncurved membrane. Importantly, and consistent with our theory, lipid sorting occurs only if the system is close to a demixing point. Remarkably, this process is amplified when even a low fraction of lipids is clustered upon cholera toxin binding. This can be explained by the reduction of the entropic penalty of lipid sorting when some lipids are bound together by the toxin. Our results show that curvature-induced lipid sorting results from the collective behavior of lipids and is even amplified in the presence of lipid-clustering proteins. In addition, they suggest a generic mechanism by which proteins can facilitate lipid segregation in vivo.
A nontransferring dry adhesive with hierarchical polymer nanohairs
Authors: Jeong Hoon Eui , Lee Jin-Kwan , Kim Hong Nam , Moon Sang Heup , Suh Kahp Y.
Published: March 2009

We present a simple yet robust method for fabricating angled, hierarchically patterned high-aspect-ratio polymer nanohairs to generate directionally sensitive dry adhesives. The slanted polymeric nanostructures were molded from an etched polySi substrate containing slanted nanoholes. An angled etching technique was developed to fabricate slanted nanoholes with flat tips by inserting an etch-stop layer of silicon dioxide. This unique etching method was equipped with a Faraday cage system to control the ion-incident angles in the conventional plasma etching system. The polymeric nanohairs were fabricated with tailored leaning angles, sizes, tip shapes, and hierarchical structures. As a result of controlled leaning angle and bulged flat top of the nanohairs, the replicated, slanted nanohairs showed excellent directional adhesion, exhibiting strong shear attachment (≈26 N/cm2in maximum) in the angled direction and easy detachment (≈2.2 N/cm2) in the opposite direction, with a hysteresis value of ≈10. In addition to single scale nanohairs, monolithic, micro-nanoscale combined hierarchical hairs were also fabricated by using a 2-step UV-assisted molding technique. These hierarchical nanoscale patterns maintained their adhesive force even on a rough surface (roughness <20 μm) because of an increase in the contact area by the enhanced height of hierarchy, whereas simple nanohairs lost their adhesion strength. To demonstrate the potential applications of the adhesive patch, the dry adhesive was used to transport a large-area glass (47.5 × 37.5 cm2, second-generation TFT-LCD glass), which could replace the current electrostatic transport/holding system with further optimization.
Synaptic transmission block by presynaptic injection of oligomeric amyloid beta
Authors: Moreno Herman , Yu Eunah , Pigino Gustavo , Hernandez Alejandro I. , Kim Natalia , Moreira Jorge E. , Sugimori Mutsuyuki , Llinás Rodolfo R.
Published: March 2009

Early Alzheimer's disease (AD) pathophysiology is characterized by synaptic changes induced by degradation products of amyloid precursor protein (APP). The exact mechanisms of such modulation are unknown. Here, we report that nanomolar concentrations of intraaxonal oligomeric (o)Aβ42, but not oAβ40 or extracellular oAβ42, acutely inhibited synaptic transmission at the squid giant synapse. Further characterization of this phenotype demonstrated that presynaptic calcium currents were unaffected. However, electron microscopy experiments revealed diminished docked synaptic vesicles in oAβ42-microinjected terminals, without affecting clathrin-coated vesicles. The molecular events of this modulation involved casein kinase 2 and the synaptic vesicle rapid endocytosis pathway. These findings open the possibility of a new therapeutic target aimed at ameliorating synaptic dysfunction in AD.
HLA-G homodimer-induced cytokine secretion through HLA-G receptors on human decidual macrophages and natural killer cells
Authors: Li Changlin , Houser Brandy L. , Nicotra Matthew L. , Strominger Jack L.
Published: March 2009

Human decidual CD14+macrophages and CD56+NK cells were isolated from material obtained after first-trimester pregnancy terminations. Each cell type expressed a specific surface receptor for histocompatibility leukocyte antigen (HLA)-G (an MHC class Ib protein that is expressed on extravillous trophoblasts), LILRB1 on CD14+macrophages and KIR2DL4 on CD56+NK cells. Cross-linking with anti-LILRB1 or anti-KIR2DL4 resulted in up-regulation of a small subset of mRNAs including those for IL-6, IL-8, and TNFα detected using a microarray representing 114 cytokines. Incubation with transfectants expressing the HLA-G homodimer (but not with transfectants expressing the HLA-G monomer) resulted in secretion of the same cytokine proteins from both leukocyte sets. Moreover, cytokine secretion from both leukocyte sets was blocked by both the appropriate anti-receptor mAb and by anti-HLA-G. The amount of these cytokines secreted by decidual macrophages was substantially greater than that secreted by decidual NK cells. VEGF was constitutively secreted by both cell types. LILRB1, which contains an immunoreceptor tyrosine-based switch motif, functions here as an activating receptor, although it has been known as an inhibitory receptor. KIR2DL4 also functions as an activating receptor, although it also has the potential to function as an inhibitory receptor. Secretion of proinflammatory and proangiogenic proteins supports a role for these leukocytes in important processes that are essential for successful pregnancy, but they may represent only a portion of the proteins that are secreted.
Rational development of high-affinity T-cell receptor-like antibodies
Authors: Stewart-Jones Guillaume , Wadle Andreas , Hombach Anja , Shenderov Eugene , Held Gerhard , Fischer Eliane , Kleber Sascha , Nuber Natko , Stenner-Liewen Frank , Bauer Stefan , McMichael Andrew , Knuth Alexander , Abken Hinrich , Hombach Andreas A. , Cerundolo Vincenzo , Jones E. Yvonne , Renner Christoph
Published: March 2009

T-cell interaction with a target cell is a key event in the adaptive immune response and primarily driven by T-cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes. TCR avidity for a given pMHC is determined by number of MHC molecules, availability of coreceptors, and TCR affinity for MHC or peptide, respectively, with peptide recognition being the most important factor to confer target specificity. Here we present high-resolution crystal structures of 2 Fab antibodies in complex with the immunodominant NY-ESO-1
157–165
peptide analogue (SLLMWITQV) presented by HLA-A*0201 and compare them with a TCR recognizing the same pMHC. Binding to the central methionine-tryptophan peptide motif and orientation of binding were almost identical for Fabs and TCR. As the MW “peg” dominates the contacts between Fab and peptide, we estimated the contributions of individual amino acids between the Fab and peptide to provide the rational basis for a peptide-focused second-generation, high-affinity antibody library. The final Fab candidate achieved better peptide binding by 2 light-chain mutations, giving a 20-fold affinity improvement to 2–4 nM, exceeding the affinity of the TCR by 1,000-fold. The high-affinity Fab when grafted as recombinant TCR on T cells conferred specific killing of HLA-A*0201/NY-ESO-1
157–165
target cells. In summary, we prove that affinity maturation of antibodies mimicking a TCR is possible and provide a strategy for engineering high-affinity antibodies that can be used in targeting specific pMHC complexes for diagnostic and therapeutic purposes.
Identification of intracellular carriers for the endocannabinoid anandamide
Authors: Kaczocha Martin , Glaser Sherrye T. , Deutsch Dale G.
Published: March 2009

The endocannabinoid anandamide (arachidonoyl ethanolamide, AEA) is an uncharged neuromodulatory lipid that, similar to many neurotransmitters, is inactivated through its cellular uptake and subsequent catabolism. AEA is hydrolyzed by fatty acid amide hydrolase (FAAH), an enzyme localized on the endoplasmic reticulum. In contrast to most neuromodulators, the hydrophilic cytosol poses a diffusional barrier for the efficient delivery of AEA to its site of catabolism. Therefore, AEA likely traverses the cytosol with the assistance of an intracellular carrier that increases its solubility and rate of diffusion. To study this process, AEA uptake and hydrolysis were examined in COS-7 cells expressing FAAH restricted to the endoplasmic reticulum, mitochondria, or the Golgi apparatus. AEA hydrolysis was detectable at the earliest measurable time point (3 seconds), suggesting that COS-7 cells, normally devoid of an endocannabinoid system, possess an efficient cytosolic trafficking mechanism for AEA. Three fatty acid binding proteins (FABPs) known to be expressed in brain were examined as possible intracellular AEA carriers. AEA uptake and hydrolysis were significantly potentiated in N18TG2 neuroblastoma cells after overexpression of FABP5 or FABP7, but not FABP3. Similar results were observed in COS-7 cells stably expressing FAAH. Consistent with the roles of FABP as AEA carriers, administration of the competitive FABP ligand oleic acid or the selective non-lipid FABP inhibitor BMS309403 attenuated AEA uptake and hydrolysis by ≈50% in N18TG2 and COS-7 cells. Taken together, FABPs represent the first proteins known to transport AEA from the plasma membrane to FAAH for inactivation and may therefore be novel pharmacological targets.
Psychosocial risk factors for depression during pregnancy
Authors: BUNEVICIUS ROBERTAS , KUSMINSKAS LAIMA , BUNEVICIUS ADOMAS , NADISAUSKIENE RUTA J. , JURENIENE KRISTINA , POP VICTOR J.M.
Published: March 2009

Objective. To assess the prevalence of antenatal depressive disorder in different trimesters and to evaluate the relation of psychosocial risk factors to antenatal depressive disorder. Design. Cohort follow‐up. Setting. University Hospital, Kaunas, Lithuania. Sample. Two hundred and thirty pregnant women consecutively admitted. Methods. At 12–16 weeks, 22–26 weeks, and 32–36 weeks of pregnancy, participants were screened for depression using the World Health Organization's Composite International Diagnostic Interview Short Form (CIDI‐SF). Women who gave at least one positive answer to the CIDI‐SF depression‐screening question were evaluated for depressive disorder using the non‐patient version of the Structured Clinical Interview for DSM‐III‐R (SCID‐NP). Psychosocial stressors and two Big Five Personality dimensions, neuroticism and extraversion, were also evaluated. Main outcome measures. Prevalence of depressive disorder. Results. The prevalence of the antenatal depressive disorder at 12–16 weeks’ gestation was 6.1%, at 22–26 weeks 3.5%, and at 32–36 weeks 4.4%. In the first trimester, a greater prevalence of current depressive disorder was independently associated with unplanned and unwanted pregnancy, high neuroticism, low education, and a previous history of depression; in the second trimester with unplanned and unwanted pregnancy and high neuroticism; in the third trimester with unplanned and unwanted pregnancy, high neuroticism, and the occurrence of psychosocial stressors during the last year. Conclusions. The highest prevalence of depressive disorders was found in the first trimester, the lowest in mid‐pregnancy. Several determinants (unwanted and unplanned pregnancy, high neuroticism) were independent predictors of antenatal depressive disorders throughout whole pregnancy, while other determinants (low education, previous history of depression, the occurrence of psychosocial stressors at the end of pregnancy) were trimester specific.
International framework of traceability for radiation dosimetry quantities
Authors: Allisy Penelope J , Burns David T , Andreo Pedro
Published: March 2009

An overview of the international framework that supports the dissemination of the dosimetry quantities for ionizing radiation is presented. The aim of international traceability is for confidence in such measurements around the world, which is particularly important for the equivalence of patient treatment regimes as required in international clinical trials for radiotherapy but also for fields as diverse as industrial processing, diagnostic medicine and radiation protection. This paper gives some explanation of the comparison system for national primary standards in the field of dosimetry and shows how these can support the claims for the calibration and measurement capabilities of national metrology institutes represented in the BIPM key comparison database.
2D characterization of core thermal topology changes in controlled RFX-mod QSH states
Authors: Bonomo Federica , Alfier Alberto , Gobbin Marco , Auriemma Fulvio , Franz Paolo , Marrelli Lionello , Pasqualotto Roberto , Spizzo Gianluca , Terranova David
Published: March 2009

In the reversed field pinch RFX-mod device, the achievement of high plasma currents (I
p ⩾ 1.3 MA) has allowed the appearance of a new kind of large thermal structures emerging in the plasma core during the so-called quasi-single helicity (QSH) regimes. These structures correspond to a helical equilibrium established in the plasma, which has been dubbed as the single helical axis (SHAx) state. The topological features of this new type of thermal structures covering most of the plasma core have been experimentally investigated here. Analyses have been performed by means of three diagnostics, simultaneously and routinely running on RFX-mod: the soft x-ray (SXR) camera, the Thomson scattering diagnostic for the electron temperature (T
e) profile estimation and the SXR tomography. In particular, a 2D map reconstruction of T
e has been performed: the core electron temperature asymmetries mostly account for the ones in the reconstructed SXR emissivity. The magnetic topology of these QSH thermal structures has also been analysed and numerically investigated by the Hamiltonian guiding centre code ORBIT: magnetic and thermal structures have been identified, in position and topological features. Also the T
e profile temporal evolution, provided by the tomographic diagnostic and the SXR camera, has been investigated, showing that the transition to SHAx does not develop in a unique way.
High density physics in reversed field pinches: comparison with tokamaks and stellarators
Authors: Puiatti M.E. , Scarin P. , Spizzo G. , Valisa M. , Agostini M. , Alfier A. , Canton A. , Carraro L. , Gazza E. , Lorenzini R. , Paccagnella R. , Predebon I. , Terranova D. , Bonfiglio D. , Cappello S. , Cavazzana R. , Dal Bello S. , Innocente P. , Marrelli L. , Piovan R. , Piovesan P. , Sattin F. , Zanca P.
Published: March 2009

Reversed field pinches (RFPs) share with tokamaks and stellarators the experimental evidence of an upper limit for the maximum value of the electron density at which they can operate. Above a certain density level, well described by the Greenwald law for tokamaks and RFPs, a radiative collapse with strong plasma cooling is observed, predominantly due to processes occurring at the plasma boundary. In the RFX-mod RFP close to the density limit a radiating belt, poloidally symmetric and toroidally localized, develops in the region where the plasma is shrunk as an effect of the m = 0 tearing modes. The phenomenology recalls that of MARFES or plasma detachment, though, unlike tokamaks, the appearance of the radiating belt is associated with a soft landing of the plasma discharge.

The paper reports the experimental pattern of the RFX-mod plasmas close to the density limit, including density and radiation profiles, plasma flow and turbulence. Particles are toroidally conveyed towards the region of maximum shrinking of the plasma column where they accumulate. The interpretation is related to the topology of MHD m = 0 and m = 1 modes: the reconstruction of the magnetic topology shows that the highly radiating region corresponds to the presence of peripheral m = 0 magnetic islands well detached from the wall. The emerging indication is that in RFPs a reduction of the m = 0 activity could be a way to overcome the density limit.
The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance
Authors: Gifford Robert J. , Liu Tommy F. , Rhee Soo-Yon , Kiuchi Mark , Hue Stephane , Pillay Deenan , Shafer Robert W.
Published: March 2009

Summary: The calibrated population resistance (CPR) tool is a web-accessible program for performing standardized genotypic estimation of transmitted HIV-1 drug resistance. The program is linked to the Stanford HIV drug resistance database and can additionally perform viral genotyping and algorithmic estimation of resistance to specific antiretroviral drugs.

Availability:  http://cpr.stanford.edu/cpr/index.html

Contact:  robjgiff@gmail.com
Local RNA structure alignment with incomplete sequence
Authors: Kolbe Diana L. , Eddy Sean R.
Published: March 2009

Motivation: Accuracy of automated structural RNA alignment is improved by using models that consider not only primary sequence but also secondary structure information. However, current RNA structural alignment approaches tend to perform poorly on incomplete sequence fragments, such as single reads from metagenomic environmental surveys, because nucleotides that are expected to be base paired are missing.

Results: We present a local RNA structural alignment algorithm, trCYK, for aligning and scoring incomplete sequences under a model using primary sequence conservation and secondary structure information when possible. The trCYK algorithm improves alignment accuracy and coverage of sequence fragments of structural RNAs in simulated metagenomic shotgun datasets.

Availability: The source code for Infernal 1.0, which includes trCYK, is available at http://infernal.janelia.org

Contact:  kolbed@janelia.hhmi.org; eddys@janelia.hhmi.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Automated diagnosis of LC-MS/MS performance
Authors: Xu Hua , Freitas Michael A.
Published: March 2009

Summary: We report a software scheme for automated diagnosis of liquid chromatography tandem mass spectrometry (LC-MS/MS) system performance. The proposed software scheme provides a robust framework for establishing automated diagnosis of LC-MS/MS system performance for a variety of instruments and experiments. This schematic consists of four main software components: (i) data conversion, (ii) peptide identification, (iii) LC retention time analysis and (iv) system performance evaluation. The implementation of a standard approach for assessing LC-MS/MS system performance enables researchers to apply reliable metrics to assess their workflows performance over different batch experiments. Furthermore, the results from system diagnosis can provide feedback to the workflow to stop batch analysis if system performance falls below prescribed thresholds. A basic implementation of the approach based on the MassMatrix database search and LC retention time analysis programs is presented.

Availability: An open source implementation of the LC-MS/MS system diagnosis software based on the MassMatrix database search program is freely available to non-commercial users and can be downloaded at www.massmatrix.net.

Contact:  huaxu@uic.edu; freitas.5@osu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models
Authors: Bois Frédéric Y.
Published: March 2009

Summary: Statistical inference about the parameter values of complex models, such as the ones routinely developed in systems biology, is efficiently performed through Bayesian numerical techniques. In that framework, prior information and multiple levels of uncertainty can be seamlessly integrated. GNU MCSim was precisely developed to achieve those aims, in a general non-linear differential context. Starting with version 5.3.0, GNU MCSim reads in and simulates Systems Biology Markup Language models. Markov chain Monte Carlo simulations can be used to generate samples from the joint posterior distribution of the model parameters, given a dataset and prior distributions. Hierarchical statistical models can be used. Optimal design of experiments can also be investigated.

Availability and Implementation: The GNU GPL source is available at http://savannah.gnu.org/projects/mcsim. A distribution package is at http://www.gnu.org/software/mcsim. GNU MCSim is written in standard C and runs on any platform supporting a C compiler. Supplementary Material is available online at http://www.gnu.org/software/mcsim.

Contact:  frederic.bois@ineris.fr
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Authors: Cock Peter J. A. , Antao Tiago , Chang Jeffrey T. , Chapman Brad A. , Cox Cymon J. , Dalke Andrew , Friedberg Iddo , Hamelryck Thomas , Kauff Frank , Wilczynski Bartek , de Hoon Michiel J. L.
Published: March 2009

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.

Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license.

Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk.
BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server
Authors: Geeleher Paul , Morris Dermot , Hinde John P. , Golden Aaron
Published: March 2009

Summary: BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian package provided to upgrade an existing Ubuntu installation. In its current version, several microarray analysis pipelines are supported including oligonucleotide, dual-or single-dye experiments, including post-processing with Gene Set Enrichment Analysis. BioconductorBuntu is designed to be extensible, by server-side integration of further relevant Bioconductor modules as required, facilitated by its straightforward underlying Python-based infrastructure. BioconductorBuntu offers an ideal environment for the development of processing procedures to facilitate the analysis of next-generation sequencing datasets.

Availability: BioconductorBuntu is available for download under a creative commons license along with additional documentation and a tutorial from http://bioinf.nuigalway.ie

Contact:  paul.geeleher@nuigalway.ie
Investigating and mitigating uncertainties in the assessment of Scottish Nephrops norvegicus populations using simulated underwater television data
Authors: Campbell N. , Dobby H. , Bailey N.
Published: March 2009

Campbell, N., Dobby, H., and Bailey, N. 2009. Investigating and mitigating uncertainties in the assessment of Scottish Nephrops norvegicus populations using simulated underwater television data. – ICES Journal of Marine Science, 66: 646–655. Nephrops norvegicus is a commercially significant decapod crustacean that excavates and inhabits burrows in muddy sediments throughout the Northeast Atlantic and Mediterranean Sea. Because of its variable emergence behaviour, traditional surveys are considered a poor indicator of the status of its populations, and underwater television (TV) survey methods have been developed. The approach involves towing a TV camera over patches of muddy sediment and counting the number of Nephrops burrow complexes within a known area. Assuming a 1:1 rate of occupancy, the average population density can be estimated. This is raised to the known area of suitable sediment to give a measure of population size. Recently, underwater TV surveys have been used to provide absolute measures of abundance for a number of Nephrops stocks in the North Sea and Northeast Atlantic. It is therefore imperative to identify, quantify, and control for uncertainties in this process. Previous workers have suggested that visual recognition of Nephrops burrows and “edge effects”, where single openings of burrow complexes at the sides of the viewed transect are counted, are important sources of uncertainty. This study shows edge effects to be responsible for an overestimation of population size of between 4 and 55%, depending on the width of the field of view and the mean size of the burrow complex. This overestimation is countered to some extent by variability in burrow entrance structure, which leads to Nephrops burrows going unrecognized. The scales of these errors are discussed in relation to observed sediment softness, sediment distribution, and burrow dimensions from sites around Scotland.
Cylinder loading in transient motion representing flow under a wave group
Authors: Stallard T. , Taylor P.H. , Williamson C.H.K. , Borthwick A.G.L.
Published: March 2009

There are a great many studies that investigate the force on bodies in periodic oscillatory motions, but almost no studies that focus on the kinds of fluid loading that are of great relevance to offshore structure designers; namely, the problem of a cylinder subjected to the forces from ocean wave groups, especially those of large amplitude. In this study, we move a vertical circular cylinder in non-periodic horizontal orbital motion through stationary fluid, in a towing tank at
Re
≲1.15×10
4
. The motion is chosen to represent the relative fluid motion incident upon a horizontal cylinder with its axis aligned parallel to the crest of a large ocean wave group, as defined by the ‘NewWave’ formulation. The vector form of the well-known Morison equation provides a good representation of the measured forces. By measuring the force components in the radial and azimuthal directions, we clearly demonstrate that the presence of vigorous force fluctuations at a higher frequency than the orbital motion are associated with vortex shedding that is otherwise masked by the choice of coordinates. We find vortex frequencies comparable with those for flow past fixed bodies and a ‘transverse’ force magnitude similar to the fixed flow case at the same average speed. Finally, we show that by retaining only an azimuthal (constant) drag coefficient term to represent the fluid loading throughout the wave group orbits, the resolved
X
- and
Y
-force fluctuations agree well with measured forces. This demonstrates that we can obtain a reasonable estimate of time-varying forces using a single term. It is expected that such a simple force representation will become less effective in shallower fluids and for smaller wave amplitudes relative to body size.
Asymmetric quantum codes: constructions, bounds and performance
Authors: Sarvepalli Pradeep Kiran , Klappenecker Andreas , Rötteler Martin
Published: March 2009

Recently, quantum error-correcting codes have been proposed that capitalize on the fact that many physical error models lead to a significant asymmetry between the probabilities for bit- and phase-flip errors. An example for a channel that exhibits such asymmetry is the combined amplitude damping and dephasing channel, where the probabilities of bit and phase flips can be related to relaxation and dephasing time, respectively. We study asymmetric quantum codes that are obtained from the Calderbank–Shor–Steane (CSS) construction. For such codes, we derive upper bounds on the code parameters using linear programming. A central result of this paper is the explicit construction of some new families of asymmetric quantum stabilizer codes from pairs of nested classical codes. For instance, we derive asymmetric codes using a combination of Bose–Chaudhuri–Hocquenghem (BCH) and finite geometry low-density parity-check (LDPC) codes. We show that the asymmetric quantum codes offer two advantages, namely to allow a higher rate without sacrificing performance when compared with symmetric codes and vice versa to allow a higher performance when compared with symmetric codes of comparable rates. Our approach is based on a CSS construction that combines BCH and finite geometry LDPC codes.
Strain-induced polarization in non-ideal chiral nematic elastomers
Authors: Biggins J.S.
Published: March 2009

Symmetry arguments are advanced that, although ideal chiral nematic elastomers cannot show strain-induced electrical polarization, non-ideal ones can. Phenomenological arguments are then presented, which predict a simple and universal form for the direction and strain dependence of the polarization. A microscopic minimal model is also developed, which predicts the same form. Finally, an example of a polarization–strain curve is calculated for a typical experimental geometry. In this geometry, the polarization is exactly zero at both small and large strains, but pronounced for a large set of intermediate strains corresponding to the strains that cause incremental rotation of the nematic director.
Pursuit and an evolutionary game
Authors: Wei Ermin , Justh Eric W. , Krishnaprasad P.S.
Published: March 2009

Pursuit is a familiar mechanical activity that humans and animals engage in—athletes chasing balls, predators seeking prey and insects manoeuvring in aerial territorial battles. In this paper, we discuss and compare strategies for pursuit, the occurrence in nature of a strategy known asmotion camouflage, and some evolutionary arguments to support claims of prevalence ofthisstrategy, as opposed to alternatives. We discuss feedback laws for a pursuer to realize motion camouflage, as well as two alternative strategies. We then set up a discrete-time evolutionary game to model competition among these strategies. This leads to a dynamics in the probability simplex in three dimensions, which captures the mean-field aspects of the evolutionary game. The analysis of this dynamics as an ascent equation solving a linear programming problem is consistent with observed behaviour in Monte Carlo experiments, and lends support to an evolutionary basis for prevalence of motion camouflage.
A pyritized lepidocoleid machaeridian (Annelida) from the Lower Devonian Hunsrück Slate, Germany
Authors: Högström Anette E.S. , Briggs Derek E.G. , Bartels Christoph
Published: March 2009

A machaeridian,
Lepidocoleus hohensteini
sp. nov., is described from the Hunsrück Slate (Lower Emsian) of Germany. The available material includes a unique example preserving evidence of the soft tissues, only the second machaeridian specimen to do so and the first lepidocoleid. This specimen shows that the plates are attached to alternate segments in the trunk. The morphology is consistent with an annelid affinity of the Lepidocoleidae and confirms the unity of the Machaeridia. This discovery adds an important group to the known diversity of this famous late Palaeozoic marine Konservat-Lagerstätte.
The basolateral amygdala is necessary for the encoding and the expression of odor memory
Authors: Sevelinges Yannick , Desgranges Bertrand , Ferreira Guillaume
Published: March 2009

Conditioned odor avoidance (COA) results from the association between a novel odor and a delayed visceral illness. The present experiments investigated the role of the basolateral amygdala (BLA) in acquisition and retrieval of COA memory. To address this, we used the GABAA agonist muscimol to temporarily inactivate the BLA during COA acquisition or expression. BLA inactivation before odor–malaise pairing greatly impaired COA tested 3 d later. In contrast, muscimol microinfusion between odor and malaise spared retention. Moreover, inactivation of the BLA before pre-exposure to the odor prevented latent inhibition of COA. This suggests that neural activity in the BLA is essential for the formation of odor representation. BLA inactivation before the retrieval test also blocked COA memory expression when performed either 3 d (recent memory) or 28 d (remote memory) after acquisition. This effect was transitory as muscimol-treated animals were not different from controls during the subsequent extinction tests. Moreover, muscimol infusion in the BLA neither affected olfactory perception nor avoidance behavior, and it did not induce a state-dependent learning. Altogether, these findings suggest that neural activity in the BLA is required for the encoding and the retrieval of odor memory. Moreover, the BLA seems to play a permanent role in the expression of COA.
Storage or retrieval deficit: The yin and yang of amnesia
Authors: Hardt Oliver , Wang Szu-Han , Nader Karim
Published: March 2009

To this day, it remains unresolved whether experimental amnesia reflects failed memory storage or the inability to retrieve otherwise intact memory. Methodological as well as conceptual reasons prevented deciding between these two alternatives: The absence of recovery from amnesia is typically taken as supporting storage impairment interpretations; however, this absence of recovery does not positively demonstrate nonexistence of memory, allowing for alternative interpretations of amnesia as impairment of memory retrieval. To address this shortcoming, we present a novel approach to study the nature of amnesia that makes positive, i.e., falsifiable, predictions for the absence of memory. Applying this paradigm, we demonstrate here that infusing anisomycin into the dorsal hippocampus induces amnesia by impairing memory storage, not retrieval.
The hippocampus supports encoding of between-domain associations within working memory
Authors: Piekema Carinne , Kessels Roy P.C. , Rijpkema Mark , Fernández Guillén
Published: March 2009

It has been established that the medial temporal lobe, including the hippocampus, is crucial for associative memory. The aim of the current functional magnetic resonance imaging (fMRI) study was to investigate whether the hippocampus is differentially activated for associations between items processed in the same neocortical region (within-domain) as compared with associations between items processed in different neocortical regions (between-domain). Here, we show that the hippocampus is significantly more active for between-domain associations compared with within-domain associations. Thus, the hippocampus is important for associative encoding, and furthermore, shows greater activation when the stimuli to be associated come from different stimulus categories.
Phospholipase D Activation Is an Early Component of the Salicylic Acid Signaling Pathway in Arabidopsis Cell Suspensions
Authors: Krinke Ondřej , Flemr Matyáš , Vergnolle Chantal , Collin Sylvie , Renou Jean-Pierre , Taconnat Ludivine , Yu Agnès , Burketová Lenka , Valentová Olga , Zachowski Alain , Ruelland Eric
Published: March 2009

Salicylic acid (SA) plays a central role in defense against pathogen attack, as well as in germination, flowering, senescence, and the acquisition of thermotolerance. In this report we investigate the involvement of phospholipase D (PLD) in the SA signaling pathway. In presence of exogenous primary alcohols, the production of phosphatidic acid by PLD is diverted toward the formation of phosphatidylalcohols through a reaction called transphosphatidylation. By in vivo metabolic phospholipid labeling with 33Pi, PLD activity was found to be induced 45 min after addition of SA. We show that incubation of Arabidopsis (Arabidopsis thaliana) cell suspensions with primary alcohols inhibited the induction of two SA-responsive genes, PATHOGENESIS-RELATED1 and WRKY38, in a dose-dependent manner. This inhibitory effect was more pronounced when the primary alcohols were more hydrophobic. Secondary or tertiary alcohols had no inhibitory effect. These results provide compelling arguments for PLD activity being upstream of the induction of these genes by SA. A subsequent study of n-butanol effects on the SA-responsive transcriptome identified 1,327 genes differentially expressed upon SA treatment. Strikingly, the SA response of 380 of these genes was inhibited by n-butanol but not by tert-butanol. A detailed analysis of the regulation of these genes showed that PLD could act both positively and negatively, either on gene induction or gene repression. The overlap with the previously described phosphatidylinositol-4-kinase pathway is discussed.
The Synthetic Elicitor 3,5-Dichloroanthranilic Acid InducesNPR1-Dependent andNPR1-Independent Mechanisms of Disease Resistance in Arabidopsis
Authors: Knoth Colleen , Salus Melinda S. , Girke Thomas , Eulgem Thomas
Published: March 2009

Immune responses of Arabidopsis (Arabidopsis thaliana) are at least partially mediated by coordinated transcriptional up-regulation of plant defense genes, such as the Late/sustained Up-regulation in Response to Hyaloperonospora parasitica (LURP) cluster. We found a defined region in the promoter of the LURP member CaBP22 to be important for this response. Using a CaBP22 promoter-reporter fusion, we have established a robust and specific high-throughput screening system for synthetic defense elicitors that can be used to trigger defined subsets of plant immune responses. Screening a collection of 42,000 diversity-oriented molecules, we identified 114 candidate LURP inducers. One representative, 3,5-dichloroanthranilic acid (DCA), efficiently induced defense reactions to the phytopathogens H. parasitica and Pseudomonas syringae. In contrast to known salicylic acid analogs, such as 2,6-dichloroisonicotinic acid (INA), which exhibit a long-lasting defense-inducing activity and are fully dependent on the transcriptional cofactor NPR1 (for Nonexpresser of Pathogenesis-Related genes1), DCA acts transiently and is only partially dependent on NPR1. Microarray analyses revealed a cluster of 142 DCA- and INA-responsive genes that show a pattern of differential expression coinciding with the kinetics of DCA-mediated disease resistance. These ACID genes (for Associated with Chemically Induced Defense) constitute a core gene set associated with chemically induced disease resistance, many of which appear to encode components of the natural immune system of Arabidopsis.
The Analysis of Arabidopsis Nicotianamine Synthase Mutants Reveals Functions for Nicotianamine in Seed Iron Loading and Iron Deficiency Responses
Authors: Klatte Marco , Schuler Mara , Wirtz Markus , Fink-Straube Claudia , Hell Rüdiger , Bauer Petra
Published: March 2009

Nicotianamine chelates and transports micronutrient metal ions in plants. It has been speculated that nicotianamine is involved in seed loading with micronutrients. A tomato (Solanum lycopersicum) mutant (chloronerva) and a tobacco (Nicotiana tabacum) transgenic line have been utilized to analyze the effects of nicotianamine loss. These mutants showed early leaf chlorosis and had sterile flowers. Arabidopsis (Arabidopsis thaliana) has four NICOTIANAMINE SYNTHASE (NAS) genes. We constructed two quadruple nas mutants: one had full loss of NAS function, was sterile, and showed a chloronerva-like phenotype (nas4x-2); another mutant, with intermediate phenotype (nas4x-1), developed chlorotic leaves, which became severe upon transition from the vegetative to the reproductive phase and upon iron (Fe) deficiency. Residual nicotianamine levels were sufficient to sustain the life cycle. Therefore, the nas4x-1 mutant enabled us to study late nicotianamine functions. This mutant had no detectable nicotianamine in rosette leaves of the reproductive stage but low nicotianamine levels in vegetative rosette leaves and seeds. Fe accumulated in the rosette leaves, while less Fe was present in flowers and seeds. Leaves, roots, and flowers showed symptoms of Fe deficiency, whereas leaves also showed signs of sufficient Fe supply, as revealed by molecular-physiological analysis. The mutant was not able to fully mobilize Fe to sustain Fe supply of flowers and seeds in the normal way. Thus, nicotianamine is needed for correct supply of seeds with Fe. These results are fundamental for plant manipulation approaches to modify Fe homeostasis regulation through alterations of NAS genes.