bluuebunny/crossref_metadata_2025 huggingface dataset:
Research Spotlight: Reservoirs affect irrigation and river discharge to oceans
Authors: Tretkoff Ernie
Published: June 2011

Humans have long altered the water cycle by damming rivers to create reservoirs to store water. To examine the effects of large reservoirs on the global water cycle and the availability of water for irrigation, Biemans et al. analyzed reservoir operations with a global‐scale hydrology and vegetation model. They found that at continental and global scales, irrigation and reservoir operation affect the timing and amount of water reaching the oceans. For instance, in Europe, reservoir operation increased February river discharge to oceans by 8% but decreased May discharge by 10%. Over a year, irrigation decreases global discharge to oceans by about 2.1%. Furthermore, the researchers found that global surface water extractions for irrigation have increased substantially along with the construction of large reservoirs during the past century. They estimate that around 460 cubic kilometers of water for irrigation is withdrawn from reservoirs annually. The authors note that by storing water and redistributing it, reservoirs significantly increase the amount available for irrigation, but in some regions the current reservoir system might not be enough to meet growing demand for water. (Water Resources Research, doi:10.1029/2009WR008929, 2011)
Research Spotlight: New analysis can better anticipate the likelihood of flood occurrence
Authors: Kumar Mohi
Published: June 2011

To manage freshwater resources, communities need information on how likely the volume of flow for a river or stream will equal or exceed a certain value of interest. Such information, for example, helps engineers know how much water to release into dams' spillways, guides urban planners in anticipating flash floods, and provides scientists with information on how changing precipitation patterns may influence flood frequency. Central to gaining these insights are flow duration curves (FDCs), which help to quantify the likelihood that streamflow will be greater than a specific level. Traditional period‐of‐record FDCs are a representation of the entire record of observation of a particular stream, whereas annual FDCs yield a picture on an annual basis. Serinaldi shows that both FDCs and annual FDCs can be complemented with confidence intervals based on a unique theoretical framework, which confirms the dual nature of the two approaches.
Inhibiting myosin-ATPase reveals a dynamic range of mitochondrial respiratory control in skeletal muscle
Authors: Perry Christopher G. R. , Kane Daniel A. , Lin Chien-Te , Kozy Rachel , Cathey Brook L. , Lark Daniel S. , Kane Constance L. , Brophy Patricia M. , Gavin Timothy P. , Anderson Ethan J. , Neufer P. Darrell
Published: June 2011

Assessment of mitochondrial ADP-stimulated respiratory kinetics in PmFBs (permeabilized fibre bundles) is increasingly used in clinical diagnostic and basic research settings. However, estimates of the Km for ADP vary considerably (~20–300 μM) and tend to overestimate respiration at rest. Noting that PmFBs spontaneously contract during respiration experiments, we systematically determined the impact of contraction, temperature and oxygenation on ADP-stimulated respiratory kinetics. BLEB (blebbistatin), a myosin II ATPase inhibitor, blocked contraction under all conditions and yielded high Km values for ADP of >~250 and ~80 μM in red and white rat PmFBs respectively. In the absence of BLEB, PmFBs contracted and the Km for ADP decreased ~2–10-fold in a temperature-dependent manner. PmFBs were sensitive to hyperoxia (increased Km) in the absence of BLEB (contracted) at 30 °C but not 37 °C. In PmFBs from humans, contraction elicited high sensitivity to ADP (Km<100 μM), whereas blocking contraction (+BLEB) and including a phosphocreatine/creatine ratio of 2:1 to mimic the resting energetic state yielded a Km for ADP of ~1560 μM, consistent with estimates of in vivo resting respiratory rates of <1% maximum. These results demonstrate that the sensitivity of muscle to ADP varies over a wide range in relation to contractile state and cellular energy charge, providing evidence that enzymatic coupling of energy transfer within skeletal muscle becomes more efficient in the working state.
Comment on “Long time evolution of phase oscillator systems” [Chaos 19, 023117 (2009)]
Authors: Ott Edward , Hunt Brian R. , Antonsen Thomas M.
Published: June 2011

In a recent paper by Ott and Antonsen [Chaos 19, 023117 (2009)], it was shown for the case of Lorentzian distributions of oscillator frequencies that the dynamics of a very general class of large systems of coupled phase oscillators time-asymptotes to a particular simplified form given by Ott and Antonsen [Chaos 18, 037113 (2008)]. This comment extends this previous result to a broad class of oscillator distribution functions.
Local synchronization in complex networks of coupled oscillators
Authors: Stout John , Whiteway Matthew , Ott Edward , Girvan Michelle , Antonsen Thomas M.
Published: June 2011

We investigate the effects that network topology, natural frequency distribution, and system size have on the path to global synchronization as the overall coupling strength between oscillators is increased in a Kuramoto network. In particular, we study the scenario recently found by Gómez-Gardeñes et al. [Phys. Rev. E 73, 056124 (2006)] in which macroscopic global synchronization emerges through a process whereby many small synchronized clusters form, grow, and merge, eventually leading to a macroscopic giant synchronized component. Our main result is that this scenario is robust to an increase in the number of oscillators or a change in the distribution function of the oscillators’ natural frequencies, but becomes less prominent as the number of links per oscillator increases.
Breakdown of order preservation in symmetric oscillator networks with pulse-coupling
Authors: Kielblock Hinrich , Kirst Christoph , Timme Marc
Published: June 2011

Symmetric networks of coupled dynamical units exhibit invariant subspaces with two or more units synchronized. In time-continuously coupled systems, these invariant sets constitute barriers for the dynamics. For networks of units with local dynamics defined on the real line, this implies that the units’ ordering is preserved and that their winding number is identical. Here, we show that in permutation-symmetric networks with pulse-coupling, the order is often no longer preserved. We analytically study a class of pulse-coupled oscillators (characterizing for instance the dynamics of spiking neural networks) and derive quantitative conditions for the breakdown of order preservation. We find that in general pulse-coupling yields additional dimensions to the state space such that units may change their order by avoiding the invariant sets. We identify a system of two symmetrically pulse-coupled identical oscillators where, contrary to intuition, the oscillators’ average frequencies and thus their winding numbers are different.
The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode
Authors: Costanzo Francesca , Sulpizi Marialore , Valle Raffaele Guido Della , Sprik Michiel
Published: June 2011

The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H+) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H3O+). Using the computed solvation free energy of H+ as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pKa and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]10.1063/1.3250438. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pKa, NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent.
Study of the piezoresistivity of doped nanocrystalline silicon thin films
Authors: Alpuim P. , Gaspar J. , Gieschke P. , Ehling C. , Kistner J. , Gonçalves N. J. , Vasilevskiy M. I. , Paul O.
Published: June 2011

The piezoresistive response of n- and p-type hydrogenated nanocrystalline silicon thin films, deposited by hot-wire (HW) and plasma-enhanced chemical vapor deposition (PECVD) on thermally oxidized silicon wafers, has been studied using four-point bending tests. The piezoresistive gauge factor (GF) was measured on patterned thin-film micro-resistors rotated by an angle θ with respect to the principal strain axis. Both longitudinal (GFL) and transverse (GFT) GFs, corresponding to θ = 0° and 90°, respectively, are negative for n-type and positive for p-type films. For other values of θ (30°, 45°, 120°, and 135°) GFs have the same signal as GFL and GFT and their value is proportional to the normal strain associated with planes rotated by θ relative to the principal strain axis. It is concluded that the films are isotropic in the growth plane since the GF values follow a Mohr’s circle with the principal axes coinciding with those of the strain tensor. The strongest p-type pirezoresistive response (GFL = 41.0, GFT = 2.84) was found in a film deposited by PECVD at a substrate temperature of 250 °C and working pressure of 0.250 Torr, with dark conductivity 1.6 Ω−1cm−1. The strongest n-type response (GFL =− 28.1, GFT =− 5.60) was found in a film deposited by PECVD at 150 °C and working pressure of 3 Torr, with dark conductivity 9.7 Ω−1cm−1. A model for the piezoresistivity of nc-Si is proposed, based on a mean-field approximation for the conductivity of an ensemble of randomly oriented crystallites and neglecting grain boundary effects. The model is able to reproduce the measured GFL values for both n- and p-type films. It fails, however, to explain the transversal GFT data. Both experimental and theoretical data show that nanocrystalline silicon can have an isotropic piezoresistive effect of the order of 40% of the maximum response of crystalline silicon.
Real-time monitoring of nucleation-growth cycle of carbon nanoparticles in acetylene plasmas
Authors: Hundt Morten , Sadler Patrick , Levchenko Igor , Wolter Matthias , Kersten Holger , Ostrikov Kostya (Ken)
Published: June 2011

Quantum cascade laser absorption spectroscopy was used to measure the absolute concentration of acetylene in situ during the nanoparticle growth in Ar + C2H2 RF plasmas. It is demonstrated that the nanoparticle growth exhibits a periodical behavior, with the growth cycle period strongly dependent on the initial acetylene concentration in the chamber. Being 300 s at 7.5% of acetylene in the gas mixture, the growth cycle period decreases with the acetylene concentration increasing; the growth eventually disappears when the acetylene concentration exceeds 32%. During the nanoparticle growth, the acetylene concentration is small and does not exceed 4.2% at radio frequency (RF) power of 4 W, and 0.5% at RF power of 20 W. An injection of a single acetylene pulse into the discharge also results in the nanoparticle nucleation and growth. The absorption spectroscopy technique was found to be very effective for the time-resolved measurement of the hydrocarbon content in nanoparticle-generating plasmas.
Compact, rugged in-chamber transmission spectrometers (7–28 keV) for the Sandia Z facility
Authors: Sinars D. B. , Wenger D. F. , Pikuz S. A. , Jones B. , Geissel M. , Hansen S. B. , Coverdale C. A. , Ampleford D. J. , Cuneo M. E. , McPherson L. A. , Rochau G. A.
Published: June 2011

We describe a pair of time-integrated transmission spectrometers that are designed to survey 7–28 keV (1.9 to 0.43 Å) x-ray photons produced by experiments on the Sandia Z pulsed power facility. Each spectrometer uses a quartz 10–11 crystal in a Cauchois geometry with a slit to provide spatial resolution along one dimension. The spectrometers are located in the harsh environment of the Z vacuum chamber, which necessitates that their design be compact and rugged. Example data from calibration tests and Z experiments are shown that illustrate the utility of the instruments.
Analytical evaluation of first-order electrical properties based on the spin-free Dirac-Coulomb Hamiltonian
Authors: Cheng Lan , Gauss Jürgen
Published: June 2011

We report an analytical scheme for the calculation of first-order electrical properties using the spin-free Dirac-Coulomb (SFDC) Hamiltonian, thereby exploiting the well-developed density-matrix formulations in nonrelativistic coupled-cluster (CC) derivative theory. Orbital relaxation effects are fully accounted for by including the relaxation of the correlated orbitals with respect to orbitals of all types, viz., frozen-core, occupied, virtual, and negative energy state orbitals. To demonstrate the applicability of the presented scheme, we report benchmark calculations for first-order electrical properties of the hydrogen halides, HX with X = F, Cl, Br, I, At, and a first application to the iodo(fluoro)methanes, CHnF3 − nI, n = 0–3. The results obtained from the SFDC calculations are compared to those from nonrelativistic calculations, those obtained via leading-order direct perturbation theory as well as those from full Dirac-Coulomb calculations. It is shown that the full inclusion of spin-free (SF) relativistic effects is necessary to obtain accurate first-order electrical properties in the presence of fifth-row elements. The SFDC scheme is also recommended for applications to systems containing lighter elements because it introduces no extra cost in the rate-determining steps of a CC calculation in comparison to the nonrelativistic case. On the other hand, spin-orbit contributions are generally small for first-order electrical properties of closed-shell molecules and may be handled efficiently by means of perturbation theory.
Spectroscopy of annular drums and quantum rings: Perturbative and nonperturbative results
Authors: Alvarado Carlos , Amore Paolo
Published: June 2011

We obtain systematic approximations to the states (energies and wave functions) of quantum rings (annular drums) of arbitrary shape by conformally mapping the annular domain to a simply connected domain. Extending the general results of Amore [J. Math. Phys. 51, 052105 (2010)]10.1063/1.3364792, we obtain an analytical formula for the spectrum of quantum ring of arbitrary shape: for the cases of a circular annulus and of an asymmetric annulus considered here this formula is remarkably simple and precise. We also obtain precise variational bounds for the ground state of different quantum rings. Finally, we extend the conformal collocation method of Amore [J. Math. Phys. 51, 052105 (2010)10.1063/1.3364792; J. Phys. A 41, 265206 (2008)]10.1088/1751-8113/41/26/265206 to the class of problems considered here and calculate precise numerical solutions for a large number of states (≈2000).
Electron-rich sheath dynamics. I. Transient currents and sheath-plasma instabilities
Authors: Stenzel R. L. , Gruenwald J. , Ionita C. , Schrittwieser R.
Published: June 2011

The evolution of an electron-rich sheath on a plane electrode has been investigated experimentally. A rapidly rising voltage is applied to a plane gridded electrode in a weakly ionized, low temperature, and field-free discharge plasma. Transient currents during the transition from ion-rich to electron-rich sheath are explained including the current closure. Time-resolved current-voltage characteristics of the electrode are presented. The time scale for the formation of an electron-rich sheath is determined by the ion dynamics and takes about an ion plasma period. When the ions have been expelled from the sheath a high-frequency sheath-plasma instability grows. The electric field contracts into the electron-rich sheath which implies that the potential outside the sheath drops. It occurs abruptly and creates a large current pulse on the electrode which is not a conduction but a displacement current. The expulsion of ions from the vicinity of the electrode lowers the electron density, electrode current, and the frequency of the sheath-plasma oscillations. Electron energization in the sheath creates ionization which reduces the space charge density, hence sheath electric field. The sheath-plasma instability is weakened or vanishes. The ionization rate decreases, and the sheath electric field recovers. A relaxation instability with repeated current transients can arise which is presented in a companion paper. Only for voltages below the ionization potential a quiescent electron rich-sheath is observed.
Electron-rich sheath dynamics. II. Sheath ionization and relaxation instabilities
Authors: Stenzel R. L. , Gruenwald J. , Ionita C. , Schrittwieser R.
Published: June 2011

Instabilities in an electron-rich sheath on a plane electrode in a discharge plasma have been investigated experimentally. The high-frequency sheath-plasma instability near the electron plasma frequency is observed. With increasing dc voltage, the instability exhibits bursty amplitude and frequency jumps. The electrode current shows spikes and jumps, and the plasma potential near the electrode shows large fluctuations below the ion plasma frequency. Sheath-ionization has been identified as the cause for these low frequency instabilities. Electrons energized in the sheath produce ions which reduce the space charge in the sheath and the electric field and the ionization rate. Ions are ejected from the sheath which increases the charge density, electric field, and ionization rate. The positive feedback between these processes leads to a relaxation instability whose time scale is determined by ion inertia and ionization rates. The associated density and potential fluctuations affect the amplitude and frequency of the sheath-plasma instability. When the sheath ionization rate exceeds the ion losses, the sheath expands into an anode plasma or “fireball.” The potential drop across the sheath decreases and the sheath-plasma instability vanishes. The electrode current-voltage characteristics develop a region of negative conductance. For short grid voltage pulses, the ionization effects can be avoided.
Vibration transfers to measure the performance of vibration isolated platforms on site using background noise excitation
Authors: Segerink F. B. , Korterik J. P. , Offerhaus H. L.
Published: June 2011

This article demonstrates a quick and easy way of quantifying the performance of a vibration-isolated platform. We measure the vibration transfer from floor to table using background noise excitation from the floor. As no excitation device is needed, our setup only requires two identical sensors (in our case, low noise accelerometers), a data acquisition system, and processing software. Background noise excitation from the floor has the additional advantage that any non-linearity in the suspension system relevant to the actual vibration amplitudes will be taken into account. Measurement time is typically a few minutes, depending on the amount of background noise. The (coherent) transfer of the vibrations in the floor to the platform, as well as the (non-coherent) acoustical noise pick-up by the platform are measured. Since we use calibrated sensors, the absolute value of the vibration levels is established and can be expressed in vibration criterion curves. Transfer measurements are shown and discussed for two pneumatic isolated optical tables, a spring suspension system, and a simple foam suspension system.
Effect of central slotted screen with a high solidity ratio on the secondary resonance phenomenon for liquid sloshing in a rectangular tank
Authors: Faltinsen O. M. , Firoozkoohi R. , Timokha A. N.
Published: June 2011

Mounting a screen with a high solidity ratio (0.5 ≲ Sn < 1) at the center of a rectangular tank qualitatively changes the secondary resonance phenomenon for liquid sloshing. In contrast to the clean tank, the steady-state sloshing due to lateral excitation is then characterized by multi-peak response curves in a neighborhood of the primary resonance frequency. The present paper revises the adaptive nonlinear multimodal method to study the secondary resonance phenomenon for the screen-affected resonant sloshing with a finite liquid depth and, thereby, clarify earlier experimental results of the authors.
Well-aligned graphene arrays for field emission displays
Authors: Huang Cheng-Kuang , Ou Yongxi , Bie Yaqing , Zhao Qing , Yu Dapeng
Published: June 2011

Well-aligned graphene field emission arrays were fabricated on copper foils via simple photolithography and wet etching techniques. The method offered high-ordered micro sized graphene pattern in the array elements. Field emission measurement revealed a turn-on field of 7.2 V/μm at 100 nA/cm2 and a good emission current stability. Exposed graphene edges were produced on each array element edge and found to be the significant contributors to the emission current. Owing to the obvious advantages of low cost and easy for scale-up production, this method demonstrates the feasibility of utilizing such graphene field emission array configurations in display applications.
Strong coupling between excitons in J-aggregates and waveguide modes in thin polymer films
Authors: Ellenbogen Tal , Steinvurzel Paul , Crozier Kenneth B.
Published: June 2011

We observe a large room temperature Rabi splitting for the transverse electric (190 meV) and transverse magnetic (125 meV) waveguide modes of a thin polymer film doped with J-aggregating dye, indicating strong coupling between propagating light modes and localized molecular excitons. We show that the difference in the measured splitting results from the different field distribution of the cross polarized modes. Numerical simulations indicate that the exciton-waveguide modes are as strongly coupled as exciton-surface plasmon polaritons supported by the same system.
Enhanced conversion efficiency of InGaN multiple quantum well solar cells grown on a patterned sapphire substrate
Authors: Lee Ya-Ju , Lee Min-Hung , Cheng Chun-Mao , Yang Chia-Hao
Published: June 2011

This study demonstrated the enhanced conversion efficiency of an indium gallium nitride (InGaN) multiple quantum well (MQW) solar cell fabricated on a patterned sapphire substrate (PSS). Compared to conventional solar cells grown on a planar sapphire substrate, threading dislocation defects were found to be reduced from 1.28 × 109 to 3.62 × 108 cm−2, leading to an increase in short-circuit current density (JSC = 1.09 mA·cm−2) of approximately 60%. In addition, the open-circuit voltage and fill factor (VOC = 2.05 V; FF = 51%) of the solar cells grown on PSS were nearly identical to those of conventional devices. The enhanced performance is primarily due to improvements in the crystalline quality of the epitaxial layers, reducing the trapping of photogenerated electrons and holes by nonradiative recombination centers in MQW, with a corresponding increase in the transport efficiency of the carriers outside the device.
MicroRNA regulation of homeostatic synaptic plasticity
Authors: Cohen Jonathan E. , Lee Philip R. , Chen Shan , Li Wei , Fields R. Douglas
Published: June 2011

Homeostatic mechanisms are required to control formation and maintenance of synaptic connections to maintain the general level of neural impulse activity within normal limits. How genes controlling these processes are co-coordinately regulated during homeostatic synaptic plasticity is unknown. MicroRNAs (miRNAs) exert regulatory control over mRNA stability and translation and may contribute to local and activity-dependent posttranscriptional control of synapse-associated mRNAs. However, identifying miRNAs that function through posttranscriptional gene silencing at synapses has remained elusive. Using a bioinformatics screen to identify sequence motifs enriched in the 3′UTR of rapidly destabilized mRNAs, we identified a developmentally and activity-regulated miRNA (miR-485) that controls dendritic spine number and synapse formation in an activity-dependent homeostatic manner. We find that many plasticity-associated genes contain predicted miR-485 binding sites and further identify the presynaptic protein SV2A as a target of miR-485. miR-485 negatively regulated dendritic spine density, postsynaptic density 95 (PSD-95) clustering, and surface expression of GluR2. Furthermore, miR-485 overexpression reduced spontaneous synaptic responses and transmitter release, as measured by miniature excitatory postsynaptic current (EPSC) analysis and FM 1–43 staining. SV2A knockdown mimicked the effects of miR-485, and these effects were reversed by SV2A overexpression. Moreover, 5 d of increased synaptic activity induced homeostatic changes in synaptic specializations that were blocked by a miR-485 inhibitor. Our findings reveal a role for this previously uncharacterized miRNA and the presynaptic protein SV2A in homeostatic plasticity and nervous system development, with possible implications in neurological disorders (e.g., Huntington and Alzheimer's disease), where miR-485 has been found to be dysregulated.
Li experiments on T-11M and T-10 in support of a steady-state tokamak concept with Li closed loop circulation
Authors: Mirnov S.V. , Azizov E.A. , Alekseev A.G. , Lazarev V.B. , Khayrutdinov R.R. , Lyublinski I.E. , Vertkov A.V. , Vershkov V.A.
Published: June 2011

This paper presents a review of the last T-11M and T-10 tokamak activity in the field of Li plasma facing component (PFC) investigation. Attention is mainly paid to the realization of the concept of closed loop lithium circulation as a solution of the PFC problem of a steady-state DT volumetric neutron source on a tokamak basis. Realization of the Li PFC concept demands the decision of three main tasks: lithium injection into the plasma, Li collection before its deposition on the vacuum vessel and the return of Li to the injection zone from the collector. This emitter–collector concept assumes that the main heat flux from a hot plasma to the PFC (limiters and divertor plates) can be dissipated on the entire vessel wall surface by non-coronal Li radiation, which will smoothen the local heat load PFC. A rail limiter on the basis of a capillary porous system manufactured from tungsten felt and provided with W wings was successfully tested in the last T-11M experiments as a prototype of steady-state Li emitter–collector. A witness-sample analysis showed that the lateral sides of the rail and ring limiters crossing the plasma scrape-off layer can collect a significant (∼80%) part of Li, injected into the plasma during discharges. This can be used in the future for closing Li loop circulation. As was shown by Li pellet injection in T-10, the probability of Li penetration into the hot plasma core from its boundary is lower than that of deuterium by a factor of 5–10. This result can explain the effect of plasma cleaning (Z
eff (0) ∼ 1) during T-10 Li experiments. Some different schemes of future lithium circulation loops are discussed.
ontoCAT: an R package for ontology traversal and search
Authors: Kurbatova Natalja , Adamusiak Tomasz , Kurnosov Pavel , Swertz Morris A. , Kapushesky Misha
Published: June 2011

Motivation: There exist few simple and easily accessible methods to integrate ontologies programmatically in the R environment. We present ontoCAT—an R package to access ontologies in widely used standard formats, stored locally in the filesystem or available online. The ontoCAT package supports a number of traversal and search functions on a single ontology, as well as searching for ontology terms across multiple ontologies and in major ontology repositories.

Availability: The package and sources are freely available in Bioconductor starting from version 2.8: http://bioconductor.org/help/bioc-views/release/bioc/html/ontoCAT.html or via the OntoCAT website http://www.ontocat.org/wiki/r.

Contact:  natalja@ebi.ac.uk; natalja@ebi.ac.uk
Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS
Authors: Aggio Raphael , Villas−Bôas Silas Granato , Ruggiero Katya
Published: June 2011

Motivation: The Automated Mass Spectral Deconvolution and Identification System (AMDIS) is freeware extensively applied in metabolomics. However, datasets processed by AMDIS require extensive data correction, filtering and reshaping to create reliable datasets for further downstream analysis. Performed manually, these processes are laborious and extremely time consuming. Furthermore, manual corrections increase the chance of human error and can introduce additional technical variability to the data. Thus, an automated pipeline for curating GC-MS data is urgently needed.

Results: We present the Metab R package designed to automate the pipeline for analysis of metabolomics GC-MS datasets processed by AMDIS.

Availability: The Metab package, the AMDIS library and the reference ion library are available at www.metabolomics.auckland.ac.nz/index.php/downloads.

Contact:  k.ruggiero@auckland.ac.nz
CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages
Authors: Bot Jan J. , Reinders Marcel J. T.
Published: June 2011

Summary: CytoscapeRPC is a plugin for Cytoscape which allows users to create, query and modify Cytoscape networks from any programming language which supports XML-RPC. This enables them to access Cytoscape functionality and visualize their data interactively without leaving the programming environment with which they are familiar.

Availability: Install through the Cytoscape plugin manager or visit the web page: http://wiki.nbic.nl/index.php/CytoscapeRPC for the user tutorial and download.

Contact:  j.j.bot@tudelft.nl; j.j.bot@tudelft.nl
BRISK—research-oriented storage kit for biology-related data
Authors: Tan Alan , Tripp Ben , Daley Denise
Published: June 2011

Motivation: In genetic science, large-scale international research collaborations represent a growing trend. These collaborations have demanding and challenging database, storage, retrieval and communication needs. These studies typically involve demographic and clinical data, in addition to the results from numerous genomic studies (omics studies) such as gene expression, eQTL, genome-wide association and methylation studies, which present numerous challenges, thus the need for data integration platforms that can handle these complex data structures. Inefficient methods of data transfer and access control still plague research collaboration. As science becomes more and more collaborative in nature, the need for a system that adequately manages data sharing becomes paramount.

Results: Biology-Related Information Storage Kit (BRISK) is a package of several web-based data management tools that provide a cohesive data integration and management platform. It was specifically designed to provide the architecture necessary to promote collaboration and expedite data sharing between scientists.

Availability and Implementation: The software, documentation, Java source code and demo are available at http://genapha.icapture.ubc.ca/brisk/index.jsp. BRISK was developed in Java, and tested on an Apache Tomcat 6 server with a MySQL database.

Contact:  denise.daley@hli.ubc.ca
Integration and visualization of host–pathogen data related to infectious diseases
Authors: Driscoll Timothy , Gabbard Joseph L. , Mao Chunhong , Dalay Oral , Shukla Maulik , Freifeld Clark C. , Hoen Anne Gatewood , Brownstein John S. , Sobral Bruno W.
Published: June 2011

Motivation: Infectious disease research is generating an increasing amount of disparate data on pathogenic systems. There is a growing need for resources that effectively integrate, analyze, deliver and visualize these data, both to improve our understanding of infectious diseases and to facilitate the development of strategies for disease control and prevention.

Results: We have developed Disease View, an online host–pathogen resource that enables infectious disease-centric access, analysis and visualization of host–pathogen interactions. In this resource, we associate infectious diseases with corresponding pathogens, provide information on pathogens, pathogen virulence genes and the genetic and chemical evidences for the human genes that are associated with the diseases. We also deliver the relationships between pathogens, genes and diseases in an interactive graph and provide the geolocation reports of associated diseases around the globe in real time. Unlike many other resources, we have applied an iterative, user-centered design process to the entire resource development, including data acquisition, analysis and visualization.

Availability and Implementation: Freely available at http://www.patricbrc.org; all major web browsers supported.

Contact:  cmao@vbi.vt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Developmental Stage-dependent Persistent Impact of Propofol Anesthesia on Dendritic Spines in the Rat Medial Prefrontal Cortex
Authors: Briner Adrian , Nikonenko Irina , De Roo Mathias , Dayer Alexandre , Muller Dominique , Vutskits Laszlo
Published: June 2011

Background

Recent observations demonstrate that anesthetics rapidly impair synaptogenesis during neuronal circuitry development. Whether these effects are lasting and depend on the developmental stage at which these drugs are administered remains, however, to be explored.

Methods

Wistar rats received propofol anesthesia at defined developmental stages during early postnatal life. The acute and long-term effects of these treatments on neuronal cytoarchitecture were evaluated by Neurolucida and confocal microscopy analysis after iontophoretic injections of Lucifer Yellow into layer 5 pyramidal neurons in the medial prefrontal cortex. Quantitative electron microscopy was applied to investigate synapse density.

Results

Layer 5 pyramidal neurons of the medial prefrontal cortex displayed intense dendritic growth and spinogenesis during the first postnatal month. Exposure of rat pups to propofol at postnatal days 5 and 10 significantly decreased dendritic spine density, whereas this drug induced a significant increase in spine density when administered at postnatal days 15, 20, or 30. Quantitative electron microscopy revealed that the propofol-induced increase in spine density was accompanied by a significant increase in the number of synapses. Importantly, the propofol-induced modifications in dendritic spine densities persisted up to postnatal day 90.

Conclusion

These new results demonstrate that propofol anesthesia can rapidly induce significant changes in dendritic spine density and that these effects are developmental stage-dependent, persist into adulthood, and are accompanied by alterations in synapse number. These data suggest that anesthesia in the early postnatal period might permanently impair circuit assembly in the developing brain.
Maternal Psychopathology and Psychomotor Development of Children With GERD
Authors: Karacetin Gul , Demir Turkay , Erkan Tulay , Cokugras Fugen Cullu , Sonmez Burcin Alsancak
Published: June 2011

Objectives:

The relation between gastroesophageal reflux disease (GERD) and maternal psychopathology as well as the role of impairments in mother–child interactions in the perpetuation of feeding problems in children with GERD was previously implicated but not confirmed. The present study aimed to study the relation between maternal psychopathology and feeding problems in children with GERD and the effects of GERD on the psychomotor development of children.

Subjects and Methods:

The case group included 39 children with GERD and their mothers and the comparison group included 39 healthy children and their mothers. The groups were matched for age, gestational age, socioeconomic status, and sex. Scales used for the psychiatric assessment of mothers were the Beck Anxiety Inventory, Hamilton Rating Scale for Depression, Eating Attitudes Test, and Experiences in Close Relationships‐Revised. The children's developmental levels were assessed by the Brunet‐Lezine Revised test.

Results:

Maternal Beck Anxiety Inventory, Hamilton Rating Scale for Depression, Eating Attitudes Test, and Experiences in Close Relationships‐Revised scores were significantly higher in the case group. Forced feeding and maternal thoughts of the child's feeding as insufficient were associated with a high level of maternal attachment‐related anxiety and avoidance. Children with GERD had significantly lower Brunet‐Lezine‐Revised scores.

Conclusions:

Maternal psychopathology, especially insecure attachment, may play a role in the feeding problems in children with GERD. Children with GERD should be examined for maternal psychopathology and feeding problems so that maladaptive feeding behaviors can receive appropriate intervention before the development of negative reinforcement to feeding. The psychomotor development of children should be kept in mind.
Modelling the effects of past and future climate on the risk of bluetongue emergence in Europe
Authors: Guis Helene , Caminade Cyril , Calvete Carlos , Morse Andrew P. , Tran Annelise , Baylis Matthew
Published: June 2011

Vector-borne diseases are among those most sensitive to climate because the ecology of vectors and the development rate of pathogens within them are highly dependent on environmental conditions. Bluetongue (BT), a recently emerged arboviral disease of ruminants in Europe, is often cited as an illustration of climate's impact on disease emergence, although no study has yet tested this association. Here, we develop a framework to quantitatively evaluate the effects of climate on BT's emergence in Europe by integrating high-resolution climate observations and model simulations within a mechanistic model of BT transmission risk. We demonstrate that a climate-driven model explains, in both space and time, many aspects of BT's recent emergence and spread, including the 2006 BT outbreak in northwest Europe which occurred in the year of highest projected risk since at least 1960. Furthermore, the model provides mechanistic insight into BT's emergence, suggesting that the drivers of emergence across Europe differ between the South and the North. Driven by simulated future climate from an ensemble of 11 regional climate models, the model projects increase in the future risk of BT emergence across most of Europe with uncertainty in rate but not in trend. The framework described here is adaptable and applicable to other diseases, where the link between climate and disease transmission risk can be quantified, permitting the evaluation of scale and uncertainty in climate change's impact on the future of such diseases.
Spectral tuning and evolution of primate short-wavelength-sensitive visual pigments
Authors: Carvalho Livia S. , Davies Wayne L. , Robinson Phyllis R. , Hunt David M.
Published: June 2011

The peak sensitivities (λmax) of the short-wavelength-sensitive-1 (SWS1) pigments in mammals range from the ultraviolet (UV) (360–400 nm) to the violet (400–450 nm) regions of the spectrum. In most cases, a UV or violet peak is determined by the residue present at site 86, with Phe conferring UV sensitivity (UVS) and either Ser, Tyr or Val causing a shift to violet wavelengths. In primates, however, the tuning mechanism of violet-sensitive (VS) pigments would appear to differ. In this study, we examine the tuning mechanisms of prosimian SWS1 pigments. One species, the aye-aye, possesses a pigment with Phe86 butin vitrospectral analysis reveals a VS rather than a UVS pigment. Other residues (Cys, Ser and Val) at site 86 in prosimians also gave VS pigments. Substitution at site 86 is not, therefore, the primary mechanism for the tuning of VS pigments in primates, and phylogenetic analysis indicates that substitutions at site 86 have occurred at least five times in primate evolution. The sole potential tuning site that is conserved in all primate VS pigments is Pro93, which when substituted by Thr (as found in mammalian UVS pigments) in the aye-aye pigment shifted the peak absorbance into the UV region with aλmaxvalue at 371 nm. We, therefore, conclude that the tuning of VS pigments in primates depends on Pro93, not Tyr86 as in other mammals. However, it remains uncertain whether the initial event that gave rise to the VS pigment in the ancestral primate was achieved by a Thr93Pro or a Phe86Tyr substitution.
Decomposing variation in population growth into contributions from environment and phenotypes in an age-structured population
Authors: Pelletier Fanie , Moyes Kelly , Clutton-Brock Tim H. , Coulson Tim
Published: June 2011

Evaluating the relative importance of ecological drivers responsible for natural population fluctuations in size is challenging. Longitudinal studies where most individuals are monitored from birth to death and where environmental conditions are known provide a valuable resource to characterize complex ecological interactions. We used a recently developed approach to decompose the observed fluctuation in population growth of the red deer population on the Isle of Rum into contributions from climate, density and their interaction and to quantify their relative importance. We also quantified the contribution of individual covariates, including phenotypic and life-history traits, to population growth. Fluctuations in composition in age and sex classes ((st)age structure) of the population contributed substantially to the population dynamics. Density, climate, birth weight and reproductive status contributed less and approximately equally to the population growth. Our results support the contention that fluctuations in the population's (st)age structure have important consequences for population dynamics and underline the importance of including information on population composition to understand the effect of human-driven changes on population performance of long-lived species.
Restrictions that control herpes simplex virus type 1 infection in mouse brain ex vivo
Authors: Cohen Meytal , Braun Efrat , Tsalenchuck Yael , Panet Amos , Steiner Israel
Published: June 2011

Elucidating the cellular and molecular factors governing herpes simplex virus type 1 (HSV-1) neurotropism is a prerequisite for understanding HSV-1 encephalitis and for targeting HSV-1-derived vectors for gene transfer to the brain. Earlier we had described anex vivosystem of mouse brain slices and demonstrated a selective and unique infection pattern, mostly around the ventricles. Here, we examined tissue factors controlling HSV-1 infection of brain slices. We demonstrated that heparan sulphate, while an important factor, does not determine the infection pattern. Hyaluronic acid, but not collagen, appears to enhance HSV-1 brain infection. To investigate whether tissue distribution of viral receptors determines the infection pattern, we examined transcription of herpes virus entry mediator and nectin-1 receptor genes in infected and uninfected brain regions. Both the infected and the uninfected regions express the receptors. We also explored the influence of intra-cellular factors. HSV-1 does not preferentially infect proliferating cells in the brain slices, despite its predilection to the ventricular zones. To delineate the step at which the HSV-1 infection cascade is restricted, mRNA was isolated following tissue infection, and transcription of the immediate-early and late viral genes was evaluated. The results indicated that HSV-1 genes are not expressed in regions that do not express a viral reporter gene. Therefore, we conclude that tissue resistance to infection is associated with a block at or prior to the immediate-early mRNA synthesis. Taken together, using theex vivosystem of organotypic culture we describe here extra-cellular and intra-cellular restriction levels of HSV-1 brain infection.
Identification of an antibody-binding epitope on the rotavirus A non-structural protein NSP2 using phage display analysis
Authors: Donker Nicole C. , Foley Michael , Tamvakis Debra C. , Bishop Ruth , Kirkwood Carl D.
Published: June 2011

The non-structural protein 2 (NSP2) of rotavirus has important roles in rotavirus replication associated with RNA binding, hydrolysis of NTPs and RNA, and helix destabilizing properties. A cell-culture assay using an NSP2-specific mAb and polyclonal antiserum to block virus replication showed a 73 and 96 % reduction in the amount of virus produced during replication, respectively. Phage display technology was used to identify the antibody-binding region on the NSP2 protein with the motif 244T-(Y/F)-Ø-Ø-Ø-X-K-Ø-G252, where Ø is a hydrophilic residue and X is any amino acid. This region was mapped to the three-dimensional NSP2 crystal structure to visualize the epitope. Analysis revealed identity to a region on NSP2 that mapped to a site exposed on the surface of the protein, which could possibly interfere with a functionally important region of the protein. Antibody binding to this region could disrupt the essential roles of NSP2, such as the formation of viroplasms with NSP5 or the interaction with viral RNA, thereby indicating a possible mechanism for the observed inhibition of virus replication. Genetic analysis of the putative binding region of NSP2 revealed a high level of conservation, suggesting that the region is under strict control.
Serine/arginine-rich protein 30c activates human papillomavirus type 16 L1 mRNA expression via a bimodal mechanism
Authors: Somberg Monika , Li Xiaoze , Johansson Cecilia , Orru Beatrice , Chang Roger , Rush Margaret , Fay Joanna , Ryan Fergus , Schwartz Stefan
Published: June 2011

Two splice sites on the human papillomavirus type 16 (HPV-16) genome are used exclusively by the late capsid protein L1 mRNAs: SD3632 and SA5639. These splice sites are suppressed in mitotic cells. This study showed that serine/arginine-rich protein 30c (SRp30c), also named SFRS9, activated both SD3632 and SA5639 and induced production of L1 mRNA. Activation of HPV-16 L1 mRNA splicing by SRp30c required an intact arginine/serine-repeat (RS) domain of SRp30c. In addition to this effect, SRp30c could enhance L1 mRNA production indirectly by inhibiting the early 3′-splice site SA3358, which competed with the late 3′-splice site SA5639. SRp30c bound directly to sequences downstream of SA3358, suggesting that SRp30c inhibited the enhancer at SA3358 and caused a redirection of splicing to the late 3′-splice site SA5639. This inhibitory effect of SRp30c was independent of its RS domain. These results suggest that SRp30c can activate HPV-16 L1 mRNA expression via a bimodal mechanism: directly by stimulating splicing to late splice sites and indirectly by inhibiting competing early splice sites.