bluuebunny/crossref_metadata_2025 huggingface dataset:
Operational Momentum in Numerosity Production Judgments of Multi-Digit Number Problems
Authors: Lindemann Oliver , Tira Michael D.
Published: June 2011

The current study demonstrates a numerosity production task and investigates approximate mental calculations with two-digit numbers. Participants were required to produce random dot patterns to indicate the size of two-digit numbers and the results of addition and subtraction problems. The stimuli in the calculation task consisted of problems requiring a carry operation (e.g., 24 + 18) or no-carry problems (e.g., 24 + 53) or zero problems (e.g., 24 + 0). Our analysis revealed that the outcomes of additions were estimated to be larger than the outcomes of subtractions. Interestingly, this judgment bias was present for no-carry and zero problems but not for carry problems. Taken together, the presented data provide empirical support for the presence of an operational momentum effect (OM effect) in multi-digit number arithmetic. These findings and the dissociation of the OM effect for carry and no-carry problems are discussed in the context of recent models on multi-digit number processing.
Efficient adaptive numerical integration algorithms for the evaluation of surface radiation integrals in the high‐frequency regime
Authors: Carluccio Giorgio , Albani Matteo
Published: June 2011

The possibility of reducing the sampling point density in the numerical evaluation of radiation integrals is discussed by resorting to asymptotic high‐frequency technique concepts. It is shown that the numerical evaluation of the radiation integrals becomes computationally more efficient by introducing an adaptive sampling. Using this approach, the number of sampling points is found to be drastically smaller than that resulting from a standard Nyquist sampling rate.
Modeling of coronal mass ejections that caused particularly large geomagnetic storms using ENLIL heliosphere cone model
Authors: Taktakishvili A. , Pulkkinen A. , MacNeice P. , Kuznetsova M. , Hesse M. , Odstrcil D.
Published: June 2011

In our previous paper we reported the results of modeling of 14 selected well‐observed strong halo coronal mass ejection (CME) events using the WSA‐ENLIL cone model combination. Cone model input parameters were obtained from white light coronagraph images of the CME events using the analytical method developed by Xie et al. (2004). This work verified that coronagraph input gives reasonably good results for the CME arrival time prediction. In contrast to Taktakishvili et al. (2009), where we started the analysis by looking for clear CME signatures in the data and then proceeded to model the interplanetary consequences at 1 AU, in the present paper we start by generating a list of observed geomagnetic storm events and then work our way back to remote solar observations and carry out the corresponding CME modeling. The approach used in this study is addressing space weather forecasting and operational needs. We analyzed 36 particularly strong geomagnetic storms, then tried to associate them with particular CMEs using SOHO/LASCO catalogue, and finally modeled these CMEs using WSA‐ENLIL cone model. Recently, Pulkkinen et al. (2010) developed a novel method for automatic determination of cone model parameters. We employed both analytical and automatic methods to determine cone model input parameters. We examined the CME arrival times and magnitude of impact at 1 AU for both techniques. The results of the simulations are compared with the ACE satellite observations. This comparison demonstrated that WSA‐ENLIL model combination with coronagraph input gives reasonably good results for the CME arrival times for this set of “geoeffective” CME events as well.
Steps toward “useful” hydroclimatic scenarios for water resource management in the Murray‐Darling Basin
Authors: Kiem Anthony S. , Verdon‐Kidd Danielle C.
Published: June 2011

There is currently a distinct gap between what climate science can provide and information that is practically useful for (and needed by) natural resource managers. Improved understanding, and model representations, of interactions between the various climate drivers (both regional and global scale), combined with increased knowledge about the interactions between climate processes and hydrological processes at the regional scale, is necessary for improved attribution of climate change impacts, forecasting at a range of temporal scales and extreme event risk profiling (e.g., flood, drought, and bushfire). It is clear that the science has a long way to go in closing these research gaps; however, in the meantime water resource managers in the Murray‐Darling Basin, and elsewhere, require hydroclimatic projections (i.e., seasonal to multidecadal future scenarios) that are regionally specific and, importantly, take into account the impacts, and associated uncertainties, of both natural climate variability and anthropogenic change. The strengths and weaknesses of various approaches for supplying this information are discussed in this paper.
Subsurface characterization of groundwater contaminated by landfill leachate using microbial community profile data and a nonparametric decision‐making process
Authors: Pearce Andrea R. , Rizzo Donna M. , Mouser Paula J.
Published: June 2011

Microbial biodiversity in groundwater and soil presents a unique opportunity for improving characterization and monitoring at sites with multiple contaminants, yet few computational methods use or incorporate these data because of their high dimensionality and variability. We present a systematic, nonparametric decision‐making methodology to help characterize a water quality gradient in leachate‐contaminated groundwater using only microbiological data for input. The data‐driven methodology is based on clustering a set of molecular genetic‐based microbial community profiles. Microbes were sampled from groundwater monitoring wells located within and around an aquifer contaminated with landfill leachate. We modified a self‐organizing map (SOM) to weight the input variables by their relative importance and provide statistical guidance for classifying sample similarities. The methodology includes the following steps: (1) preprocessing the microbial data into a smaller number of independent variables using principal component analysis, (2) clustering the resulting principal component (PC) scores using a modified SOM capable of weighting the input PC scores by the percent variance explained by each score, and (3) using a nonparametric statistic to guide selection of appropriate groupings for management purposes. In this landfill leachate application, the weighted SOM assembles the microbial community data from monitoring wells into groupings believed to represent a gradient of site contamination that could aid in characterization and long‐term monitoring decisions. Groupings based solely on microbial classifications are consistent with classifications of water quality from hydrochemical information. These microbial community profile data and improved decision‐making strategy compliment traditional chemical groundwater analyses for delineating spatial zones of groundwater contamination.
Stochastic flux‐related analysis of transverse mixing in two‐dimensional heterogeneous porous media
Authors: Cirpka Olaf A. , de Barros Felipe P. J. , Chiogna Gabriele , Rolle Massimo , Nowak Wolfgang
Published: June 2011

Transverse mixing of solutes in steady state transport is of utmost importance for assessing mixing‐controlled reactions of compounds that are continuously introduced into the subsurface. Classical spatial moments analysis fails to describe mixing because the tortuous streamlines in heterogeneous formations cause plume meandering, squeezing, and stretching, which affect transverse spatial moments even if there is no mass transfer perpendicular to the direction of flow. For transverse solute mixing, however, the decisive process is the exchange of solute mass between adjacent stream tubes. We therefore reformulate the advection‐dispersion equation in streamline coordinates (i.e., in terms of the potential and the stream function values) and analyze how flux‐related second central moments of plumes increase with dropping hydraulic potential. We compare the ensemble behavior of these second central moments in random two‐dimensional heterogeneous flow fields with the moments in an equivalent homogeneous system, thus defining an equivalent effective transverse dispersion coefficient. Unlike transverse macrodispersion coefficients derived by traditional moment analysis, our mixing‐relevant, flux‐related coefficient does not increase with travel distance. We present closed‐form solutions for the mean enhancement of transverse mixing by heterogeneity in two‐dimensional isotropic media for linear laws of local‐scale transverse dispersion. The mixing enhancement factor increases with the log conductivity variance but remains fairly low. We also evaluate the variance of our cumulative measure of transverse mixing, showing that heterogeneity causes substantial uncertainty of mixing. The analytical expressions are compared to numerical Monte Carlo simulations for various values of log conductivity variance, indicating good agreement with the analytical results at low variability. In the numerical simulations, we also consider nonlinear models of local‐scale transverse dispersion.
Formation and structure of Al-Zr metallic glasses studied by Monte Carlo simulations
Authors: Li J. H. , Zhao S. Z. , Dai Y. , Cui Y. Y. , Liu B. X.
Published: June 2011

Based on the recently constructed n-body potential, both molecular dynamics and Monte Carlo simulations revealed that the Al-Zr amorphous alloy or metallic glass can be obtained within the composition range of 24–66 at. % Zr. The revealed composition range could be considered the intrinsic glass-forming range and it quantitatively indicates the glass-forming ability of the Al-Zr system. The underlying physics of the finding is that, within the composition range, the amorphous alloys are energetically favored to form. In addition, it is proposed that the energy difference between a solid solution and the amorphous phase could serve as the driving force of the crystalline to amorphous transition and the driving force should be sufficiently large for amorphization to take place. The minimum driving forces for fcc Al-based and hcp Zr-based Al-Zr solid solutions to amorphize are calculated to be about −0.05 and −0.03 eV/atom, respectively, whereas the maximum driving force is found to be −0.23 eV/atom at the alloy stoichiometry of Al60Zr40. A thermodynamics parameter γ¯, defined as the ratio of the driving force to the formation energy of the solid solution, is further proposed to indicate the glass-forming ability of an Al-Zr alloy. Thermodynamics calculations show that the glass-forming ability of the Al56Zr44 alloy is the largest, implying that the Al56Zr44 amorphous alloy is more ready to form than other alloys in the Al-Zr system. Besides, Voronoi analysis found that there exists a strong correlation between the coordinate number and structure. Amorphization could result in increase of coordinate numbers and about 1.5% volume-expansion. The volume-expansion induced by amorphization can be attributed to two factors, i.e., the total bond number of the Al-Zr amorphous phase is greater than that of the corresponding solid solution, and the averaged bond length of the Al-Zr amorphous phase is longer than that of the corresponding solid solution. For the Al-Zr alloys, especially for the Al-Zr amorphous phase, there exists a negative chemical micro-inhomogeneity in the alloys, suggesting that metallic bonds prefer to be formed between the atoms of dissimilar species. Finally, it is found that there is a weak correspondence between the bond-angle distributions of Al-Zr amorphous alloys and the solid solutions. It is further suggested that the configuration of Al-Zr amorphous alloys embodies some hybrid imprint of bcc, fcc, and hcp structures. More interestingly, the short-range order is also observed in the bond-angle distributions.
Use of Raman spectroscopy to determine the site occupancy of dopants in BaTiO3
Authors: Pokorný J. , Pasha U. M. , Ben L. , Thakur O. P. , Sinclair D. C. , Reaney I. M.
Published: June 2011

Chemical doping is one of the major methods by which the properties of BaTiO3 are modified to induce various device characteristics. Doping strategies are generally separated into iso- and alio-valent (donors and acceptors) and into A- and B-site species within the perovskite structure. The A1g octahedral breathing mode at ∼800 cm−1 in BaTiO3 is Raman inactive for compositions with single B-site species. However, this mode becomes Raman active if more than one B-site species is present, including titanium vacancies, VT′′′′. Moreover, the relative intensity of the A1g breathing mode is qualitatively related to the concentration of the species replacing Ti in the B-site. This article illustrates some clear cases where the A1g octahedral breathing mode can be utilized to verify the site occupancy of dopants in BaTiO3 when used in conjunction with more conventional indirect methods such as x-ray diffraction (Vegard’s Law) and dielectric measurements as a function of temperature.
Representations of a symplectic type subalgebra of $W^N_{\infty }$W∞N
Authors: Boyallian Carina , Meinardi Vanesa
Published: June 2011

In this paper we classify the irreducible quasifinite highest weight modules over the symplectic type Lie subalgebra of the Lie algebra of all regular differential operators on circle that kill constants. We also realize them in terms of the representations theory of the complex Lie algebra \documentclass[12pt]{minimal}\begin{document}$g\ell _\infty ^{[m]}$\end{document}gℓ∞[m] of infinite matrices with a finite number of non-zero diagonals with entries in the algebra of truncated polynomials and the corresponding subalgebras of type C.
In situ observation of the formation of hollow zinc oxide shells
Authors: Tringe J. W. , Levie H. W. , El-Dasher B. S. , Swift R. , Wall M. A.
Published: June 2011

Single crystal zinc particles, 1–2 μm in diameter, were observed in situ with transmission electron microscopy during sublimation. The rate of sublimation is strongly dependent on the presence of a surface oxide layer. Near 375 °C, minimally oxidized Zn surfaces sublime in tens of seconds, consistent with a model in which the particle behaves similarly to an isolated microscale effusion cell. By contrast, zinc particles fully enclosed by oxide sublime less than one-tenth as quickly. These results provide new insight into the synthesis mechanisms of hollow ZnO microspheres and related structures formed from metallic zinc at elevated temperatures.
Molecular association of heteronuclear vibrating square-well dumbbells in liquid-vapor phase equilibrium
Authors: Chapela Gustavo A. , de Río Fernando , Alejandre José
Published: June 2011

Molecular aggregates are formed by heteronuclear vibrating square-well dumbbells. In a recent article [G. A. Chapela and J. Alejandre, J. Chem. Phys., 132(10), 104704 (2010)], it is shown that heteronuclear vibrating square-well dumbbells with a diameter ratio between particles of 1/2 and interacting potential ratio of 4 form micelles of different sizes and shapes which manifest themselves in both the liquid and vapor phases, up to and above the critical point. This means that micellization and phase separation are present simultaneously in this simple model. These systems present a maximum in the critical temperature when plotted against the potential well depth of the second particle ε2. In the same publication, it was speculated that the formation of micelles was responsible for the appearance of the maximum. A thorough study on this phenomena is presented here and it is found that there is a threshold on the size of the second particle and its corresponding depth of interaction potential, where the micelles are formed. If the diameter and well depth of the second particle are small enough for the first and deep enough for the second, micelles are formed. For σ2/σ1 between 0.25 and 0.65 and ε2/ε1 larger than 5.7, micelles are formed up to and above the critical temperature. Outside these ranges micelles appear only at temperatures lower than the critical point. There is a strong temperature dependence on the formation and persistence of the aggregates. For the deepest wells and large enough second particles, a gel interconnected aggregate is obtained. In this work, the micelles are formed at temperatures as low as the triple point and as high as the critical point and, in some cases, persist well above it. The presence of these maxima in critical temperatures Tc when plotted against ε2 as follows. At lower values of ε2, an increase of Tc is obtained as is expected by the increase of the attractive volume as indicated by the principle of corresponding states. As ε2 increases further, the formation of molecular aggregates produce a saturation effect of the deepening of the potential well by encapsulating the particles of the second kind inside the micelles, so the resulting Tc represents a new poly disperse system of molecular aggregates and not the original heteronuclear vibrating square-well dumbbells. The surface tension is also analyzed for these systems, and it is shown that decreases with increasing attraction due to the formation of molecular aggregates.
A new grand canonical ensemble method to calculate first-order phase transitions
Authors: Tang Yiping
Published: June 2011

A theory about first-order phase transition of pure fluids is proposed. The theory is developed by combining grand canonical ensemble with density functional for homogeneous fluids. It is based on the fact that the grand partition function of one macroscopic volume is the product of the grand partition functions of its subvolumes. Density fluctuations of molecules determine the relation between the grand partition function and the free energy density. By combining pairs of subvolumes successively, the free energy density is transformed and rapidly becomes stationary. The stationary curve versus molecule density is convex and its linear segments represent phase transitions. The transform leads to the new grand canonical method to calculate phase equilibrium, which is more robust than classic ones. The transform suggests that classical van der Waals loop is physical and essential to phase transition.
Ordered structures of defect clusters in gadolinium-doped ceria
Authors: Li Zhi-Peng , Mori Toshiyuki , Ye Fei , Ou Dingrong , Zou Jin , Drennan John
Published: June 2011

The nano-domain, with short-range ordered structure, has been widely observed in rare-earth-doped ceria. Atomistic simulation has been employed to investigate the ordering structure of the nano-domain, as a result of aggregation and segregation of dopant cations and the associated oxygen vacancies in gadolinium-doped ceria. It is found that the binding energy of defect cluster increases as a function of cluster size, which provides the intrinsic driving force for the defect cluster growth. However, the ordered structures of the defect clusters are different from the chain model as previously reported. Adjacent oxygen vacancies prefer to locate along 〈110〉/2 lattice vector, which results in a unique stable structure (isosceles triangle) formation. Such isosceles triangle structure can act as the smallest unit of cluster growth to form a symmetric dumbbell structure. This unique dumbbell structure is hence considered as a building block for the development of larger defect clusters, leading to nano-domain formation in rare-earth-doped ceria.
p
-type conduction induced by N-doping in α-Fe2O3
Authors: Morikawa Takeshi , Kitazumi Kousuke , Takahashi Naoko , Arai Takeo , Kajino Tsutomu
Published: June 2011

A p-type N-doped α-Fe2O3 was developed by magnetron sputtering of a Fe2O3 target in a plasma containing N2 and Ar followed by postannealing. Photoelectrochemical measurement under visible light irradiation (>410 nm) showed that N–Fe2O3 exhibits a typical cathodic photocurrent originated from the p-type conduction. X-ray photoemission spectroscopy indicated that the atomic N incorporated substitutionally at O sites was responsible for the p-type conduction. The concentration of acceptors was very close to that for Zn-doped Fe2O3, a typical p-type α-Fe2O3. This finding would stimulate further research on p-type Fe2O3 for solar fuel generation, etc.
The 15Πg state of C2
Authors: Schmidt Timothy W. , Bacskay George B.
Published: June 2011

We report ab initio spectroscopic constants for the recently identified 15Πg state of C2 [P. Bornhauser, Y. Sych, G. Knopp, T. Gerber, and P. P. Radi, J. Chem. Phys. 134, 044302 (2011)]. The calculations are performed at the multi-reference configuration interaction level of theory with Davidson's correction using aug-cc-pV6Z basis sets and include core-valence correlation and relativistic corrections obtained with quadruple-zeta bases. Such treatment accurately reproduces the experimentally observed constants of the a3Πu and other states. Thus, we expect our calculated ωe value for the 15Πg state to be within a few  cm−1, and rotational constants to be within 0.1% of experiment. Agreement with available spectroscopic data is excellent, with the calculations strongly suggesting that the 15Πg vibrational level observed by Bornhauser et al. is v = 0.
Nonvolatile bistable all-optical switch from mechanical buckling
Authors: Intaraprasonk Varat , Fan Shanhui
Published: June 2011

We propose a nonvolatile all-optical bistable optomechanical switch comprising two parallel buckling waveguides. The bistability comes from mechanical buckling so the operation of the switch does not require maintenance power. The switching and reading of the states are all optical; they involve relatively strong and relatively weak optical pulses, respectively, similar to conventional bistable optical switches.
Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress
Authors: Charles Georgette M. , Chen Changbin , Shih Susan C. , Collins Sean R. , Beltrao Pedro , Zhang Xin , Sharma Tanu , Tan Song , Burlingame Alma L. , Krogan Nevan J. , Madhani Hiten D. , Narlikar Geeta J.
Published: June 2011

Recent work has identified several posttranslational modifications (PTMs) on chromatin-remodeling complexes. Compared with our understanding of histone PTMs, significantly less is known about the functions of PTMs on remodeling complexes, because identification of their specific roles often is hindered by the presence of redundant pathways. Remodels the Structure of Chromatin (RSC) is an essential, multifunctional ATP-dependent chromatin-remodeling enzyme of
Saccharomyces cerevisiae
that preferentially binds acetylated nucleosomes. RSC is itself acetylated by Gcn5 on lysine 25 (K25) of its Rsc4 subunit, adjacent to two tandem bromodomains. It has been shown that an intramolecular interaction between the acetylation mark and the proximal bromodomain inhibits binding of the second bromodomain to acetylated histone H3 tails. We report here that acetylation does not significantly alter the catalytic activity of RSC or its ability to recognize histone H3-acetylated nucleosomes preferentially in vitro. However, we find that Rsc4 acetylation is crucial for resistance to DNA damage in vivo. Epistatic miniarray profiling of the
rsc4-K25R
mutant reveals an interaction with mutants in the INO80 complex, a mediator of DNA damage and replication stress tolerance. In the absence of a core INO80 subunit,
rsc4-K25R
mutants display sensitivity to hydroxyurea and delayed S-phase progression under DNA damage. Thus, Rsc4 helps promote resistance to replication stress, and its single acetylation mark regulates this function. These studies offer an example of acetylation of a chromatin-remodeling enzyme controlling a biological output of the system rather than regulating its core enzymatic properties.
Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins
Authors: Gordon Blair R. G. , Li Yifei , Cote Atina , Weirauch Matthew T. , Ding Pengfei , Hughes Timothy R. , Navarre William Wiley , Xia Bin , Liu Jun
Published: June 2011

H-NS and Lsr2 are nucleoid-associated proteins from Gram-negative bacteria and
Mycobacteria
, respectively, that play an important role in the silencing of horizontally acquired foreign DNA that is more AT-rich than the resident genome. Despite the fact that Lsr2 and H-NS proteins are dissimilar in sequence and structure, they serve apparently similar functions and can functionally complement one another. The mechanism by which these xenogeneic silencers selectively target AT-rich DNA has been enigmatic. We performed high-resolution protein binding microarray analysis to simultaneously assess the binding preference of H-NS and Lsr2 for all possible 8-base sequences. Concurrently, we performed a detailed structure-function relationship analysis of their C-terminal DNA binding domains by NMR. Unexpectedly, we found that H-NS and Lsr2 use a common DNA binding mechanism where a short loop containing a “Q/RGR” motif selectively interacts with the DNA minor groove, where the highest affinity is for AT-rich sequences that lack A-tracts. Mutations of the Q/RGR motif abolished DNA binding activity. Netropsin, a DNA minor groove-binding molecule effectively outcompeted H-NS and Lsr2 for binding to AT-rich sequences. These results provide a unified molecular mechanism to explain findings related to xenogeneic silencing proteins, including their lack of apparent sequence specificity but preference for AT-rich sequences. Our findings also suggest that structural information contained within the DNA minor groove is deciphered by xenogeneic silencing proteins to distinguish genetic material that is self from nonself.
Parent-specific copy number in paired tumor–normal studies using circular binary segmentation
Authors: Olshen Adam B. , Bengtsson Henrik , Neuvial Pierre , Spellman Paul T. , Olshen Richard A. , Seshan Venkatraman E.
Published: June 2011

Motivation: High-throughput techniques facilitate the simultaneous measurement of DNA copy number at hundreds of thousands of sites on a genome. Older techniques allow measurement only of total copy number, the sum of the copy number contributions from the two parental chromosomes. Newer single nucleotide polymorphism (SNP) techniques can in addition enable quantifying parent-specific copy number (PSCN). The raw data from such experiments are two-dimensional, but are unphased. Consequently, inference based on them necessitates development of new analytic methods.

Methods: We have adapted and enhanced the circular binary segmentation (CBS) algorithm for this purpose with focus on paired test and reference samples. The essence of paired parent-specific CBS (Paired PSCBS) is to utilize the original CBS algorithm to identify regions of equal total copy number and then to further segment these regions where there have been changes in PSCN. For the final set of regions, calls are made of equal parental copy number and loss of heterozygosity (LOH). PSCN estimates are computed both before and after calling.

Results: The methodology is evaluated by simulation and on glioblastoma data. In the simulation, PSCBS compares favorably to established methods. On the glioblastoma data, PSCBS identifies interesting genomic regions, such as copy-neutral LOH.

Availability: The Paired PSCBS method is implemented in an open-source R package named PSCBS, available on CRAN (http://cran.r-project.org/).

Contact:  olshena@biostat.ucsf.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Xwalk: computing and visualizing distances in cross-linking experiments
Authors: Kahraman Abdullah , Malmström Lars , Aebersold Ruedi
Published: June 2011

Motivation: Chemical cross-linking of proteins or protein complexes and the mass spectrometry-based localization of the cross-linked amino acids in peptide sequences is a powerful method for generating distance restraints on the substrate's topology.

Results: Here, we introduce the algorithm Xwalk for predicting and validating these cross-links on existing protein structures. Xwalk calculates and displays non-linear distances between chemically cross-linked amino acids on protein surfaces, while mimicking the flexibility and non-linearity of cross-linker molecules. It returns a ‘solvent accessible surface distance’, which corresponds to the length of the shortest path between two amino acids, where the path leads through solvent occupied space without penetrating the protein surface.

Availability: Xwalk is freely available as a web server or stand-alone JAVA application at http://www.xwalk.org.

Contact:  abdullah@imsb.biol.ethz.ch; aebersold@imsb.biol.ethz.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
Pathogen detection using short-RNA deep sequencing subtraction and assembly
Authors: Isakov Ofer , Modai Shira , Shomron Noam
Published: June 2011

Motivation: Early and accurate detection of human pathogen infection is critical for treatment and therapeutics. Here we describe pathogen identification using short RNA subtraction and assembly (SRSA), a detection method that overcomes the requirement of prior knowledge and culturing of pathogens, by using degraded small RNA and deep sequencing technology. We prove our approach's efficiency through identification of a combined viral and bacterial infection in human cells.

Contact:  nshomron@post.tau.ac.il
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates
Authors: Yang Yuedong , Faraggi Eshel , Zhao Huiying , Zhou Yaoqi
Published: June 2011

Motivation: In recent years, development of a single-method fold-recognition server lags behind consensus and multiple template techniques. However, a good consensus prediction relies on the accuracy of individual methods. This article reports our efforts to further improve a single-method fold recognition technique called SPARKS by changing the alignment scoring function and incorporating the SPINE-X techniques that make improved prediction of secondary structure, backbone torsion angle and solvent accessible surface area.

Results: The new method called SPARKS-X was tested with the SALIGN benchmark for alignment accuracy, Lindahl and SCOP benchmarks for fold recognition, and CASP 9 blind test for structure prediction. The method is compared to several state-of-the-art techniques such as HHPRED and BoostThreader. Results show that SPARKS-X is one of the best single-method fold recognition techniques. We further note that incorporating multiple templates and refinement in model building will likely further improve SPARKS-X.

Availability: The method is available as a SPARKS-X server at http://sparks.informatics.iupui.edu/

Contact:  yqzhou@iupui.edu
MGV: a generic graph viewer for comparative omics data
Authors: Symons Stephan , Nieselt Kay
Published: June 2011

Motivation: High-throughput transcriptomics, proteomics and metabolomics methods have revolutionized our knowledge of biological systems. To gain knowledge from comparative omics studies, strong data integration and visualization features are required. Knowledge gained from these studies is often available in the form of graphs, and their visualization is especially useful in a wide range of systems biology topics, including pathway analysis, interaction networks or gene models. Especially, it is necessary to compare biological models with measured data. This allows the identification of new models and new insights into existing ones.

Results: We present MGV, a versatile generic graph viewer for multiomics data. MGV is integrated into Mayday (Battke et al., 2010). It extends Mayday's visual analytics capabilities by integrating a wide range of biological models, high-throughput data and meta information to display enriched graphs that combine data and models. A wide range of tools is available for visualization of nodes, data-aware graph layout as well as automatic and manual aggregation and refinement of the data. We show the usefulness of MGV applied to several problems, including differential expression of alternative transcripts, transcription factor interaction, cross-study clustering comparison and integration of transcriptomics and metabolomics data for pathway analysis.

Availability: MGV is a open-source software implemented in Java and freely available as a part of Mayday at www.microarray-analysis.org/mayday.

Contact:  symons@informatik.uni-tuebingen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Age, growth, and maturity of the whitebrow skate, Bathyraja minispinosa, from the eastern Bering Sea
Authors: Ainsley Shaara M. , Ebert David A. , Cailliet Gregor M.
Published: June 2011

Ainsley, S. M., Ebert, D. A., and Cailliet, G. M. 2011. Age, growth, and maturity of the whitebrow skate, Bathyraja minispinosa, from the eastern Bering Sea. – ICES Journal of Marine Science, 68: 1426–1434. Skates are a common bycatch in groundfish fisheries in the Bering Sea; however, their life-history characteristics are not well known. The study is the first to investigate the age, growth, and age at maturity of Bathyraja minispinosa. Ages were estimated using sectioned vertebrae and several growth models were compared. The Gompertz model was the best fit and no significant differences were detected between sexes for any model. The maximum age estimated was 37 years, and parameter estimates generated from the three-parameter von Bertalanffy model were k = 0.02 year−1 and L∞ = 146.9 cm total length (TL). Males reached their size at 50% maturity larger than females (70.1 and 67.4 cm, respectively), but no significant differences in the estimated size or age at maturity were found. Whereas B. minispinosa is smaller than many skate species in the eastern Bering Sea, it has a considerably longer estimated lifespan, indicating that size may not be a reliable method of estimating the vulnerability of a rajid species to population declines in the eastern North Pacific.
Misspent youth: does catching immature fish affect fisheries sustainability?
Authors: Vasilakopoulos Paraskevas , O'Neill Finbarr G. , Marshall C. Tara
Published: June 2011

Vasilakopoulos, P., O'Neill, F. G., and Marshall, C. T. 2011. Misspent youth: does catching immature fish affect fisheries sustainability? – ICES Journal of Marine Science, 68: 1525–1534. The “spawn-at-least-once” principle suggests that sustainability is secured if fish become vulnerable to commercial gears only after they have spawned. However, some studies suggest that protecting immature fish is not essential to sustainability because extrinsic factors determine both recruitment and stock status. A meta-analysis was conducted to quantify the independent effects of exploitation pattern and exploitation rate on current stock status. The analysis used empirical data for 38 fish stocks of 13 species in the NE Atlantic. Two metrics of exploitation pattern were used and their sensitivity was compared. As expected, exploitation rate had a significant negative effect on current stock status. Exploitation patterns associated with high proportional fishing mortality of immature fish also had a significant negative effect on current stock status, providing empirical support for the “spawn-at-least-once” principle. When the fishing mortality of immature fish exceeds half that of mature fish, stock status falls below precautionary limits. Our results suggest that a sensitive metric of exploitation pattern could provide useful information about an aspect of exploitation that is currently overlooked by fisheries management regimes that focus primarily on exploitation rate.
Modelling the economic and ecological impacts of the transition to individual transferable quotas in the multispecies US west coast groundfish trawl fleet
Authors: Toft Jodie E. , Punt André E. , Little L. Richard
Published: June 2011

Toft, J. E., Punt, A. E., and Little, L. R. 2011. Modelling the economic and ecological impacts of the transition to individual transferable quotas in the multispecies US west coast groundfish trawl fleet. – ICES Journal of Marine Science, 68: 1566–1579. There is a need to understand the potential impacts on ecosystems and economies from shifting fisheries management towards individual transferable quota (ITQ) programmes. Multispecies fisheries present the challenge of understanding spatial patterns in fisher behaviour as they strive to balance profitable target catches while avoiding species with low catch limits. A spatially explicit model of biological and fleet dynamics was constructed to evaluate how the limited-entry groundfish trawl fleet off the US west coast and selected groundfish species (targeted Dover sole, and overfished darkblotched rockfish) were affected by two approaches to management: trip limits and ITQs. The model includes regional populations for both species, provides biological and socio-economic outputs, and determines quota price endogenously when applied for ITQs. Under ITQ management, effort and the total landings of the overfished species, darkblotched rockfish, were lower, coastwide profits higher, and the centre of fishing activity shifted south to areas with lower landing rates of darkblotched rockfish. The framework presented holds promise for obtaining insight about how new, untested management alternatives affect coastal and marine resources and those who rely on them.
Clifford Hiley Mortimer. 27 February 1911 — 11 May 2010
Authors: Brooks A. S. , Lund J. W. G. , Talling J. F.
Published: June 2011

The passing of Clifford Hiley Mortimer, shortly before the centenary of his birth, ended a scientific career that was as varied and versatile as it was long. Few investigators of a natural environment—here that of lakes—penetrated so deeply and widely over the range of physics, chemistry and biology. In this setting he won worldwide respect; he was ‘at home’ with personal relations, language and professional enterprise in Britain, central Europe and North America. In science he had an ability to combine ‘hands on’ practicality with deep theoretical penetration. He could combine his science with historical essay, elegant draughtsmanship, the inspiration of students and the administration of a research institute. All these appeared in the first half of his life. He worked methodically and with tenacity of purpose, even in the vicissitudes of extreme age. In his nineties he published a major book centred on the physics of Lake Michigan, beside which lake he then lived. The near-final draft of another work, intended to inform students on water density within inland waters, was in existence on his death in his hundredth year.
Strong influence of regional species pools on continent-wide structuring of local communities
Authors: Lessard Jean-Philippe , Borregaard Michael K. , Fordyce James A. , Rahbek Carsten , Weiser Michael D. , Dunn Robert R. , Sanders Nathan J.
Published: June 2011

There is a long tradition in ecology of evaluating the relative contribution of the regional species pool and local interactions on the structure of local communities. Similarly, a growing number of studies assess the phylogenetic structure of communities, relative to that in the regional species pool, to examine the interplay between broad-scale evolutionary and fine-scale ecological processes. Finally, a renewed interest in the influence of species source pools on communities has shown that the definition of the source pool influences interpretations of patterns of community structure. We use a continent-wide dataset of local ant communities and implement ecologically explicit source pool definitions to examine the relative importance of regional species pools and local interactions for shaping community structure. Then we assess which factors underlie systematic variation in the structure of communities along climatic gradients. We find that the average phylogenetic relatedness of species in ant communities decreases from tropical to temperate regions, but the strength of this relationship depends on the level of ecological realism in the definition of source pools. We conclude that the evolution of climatic niches influences the phylogenetic structure of regional source pools and that the influence of regional source pools on local community structure is strong.
Drastic historic shifts in bumble-bee community composition in Sweden
Authors: Bommarco Riccardo , Lundin Ola , Smith Henrik G. , Rundlöf Maj
Published: June 2011

The species richness of flower-visiting insects has declined in past decades, raising concerns that the ecosystem service they provide by pollinating crops and wild plants is threatened. The relative commonness of different species with shared ecological traits can play a pervasive role in determining ecosystem functioning, but information on changes in abundances of pollinators over time is lacking. We gathered data on relative abundances of bumble-bee species in Swedish red clover fields during three periods in the last 70 years (1940s, 1960s and present), and on clover seed yields since 1921. We found drastic decreases in bumble-bee community evenness, with potential consequences for level and stability of red clover seed yield. The relative abundances of two short-tongued bumble-bees have increased from 40 per cent in the 1940s to entirely dominate present communities with 89 per cent. Average seed yield declined in recent years and variation in yield doubled, suggesting that the current dependence on few species for pollination has been especially detrimental to stability in seed yield. Our results suggest a need to develop management schemes that promote not only species-rich but also more evenly composed communities of service-providing organisms.
Increase in Tomato Locule Number Is Controlled by Two Single-Nucleotide Polymorphisms Located NearWUSCHEL
Authors: Muños Stéphane , Ranc Nicolas , Botton Emmanuel , Bérard Aurélie , Rolland Sophie , Duffé Philippe , Carretero Yolande , Le Paslier Marie-Christine , Delalande Corinne , Bouzayen Mondher , Brunel Dominique , Causse Mathilde
Published: June 2011

In tomato (Solanum lycopersicum) fruit, the number of locules (cavities containing seeds that are derived from carpels) varies from two to up to 10 or more. Locule number affects fruit shape and size and is controlled by several quantitative trait loci (QTLs). The large majority of the phenotypic variation is explained by two of these QTLs, fasciated (fas) and locule number (lc), that interact epistatically with one another. FAS has been cloned, and mutations in the gene are described as key factors leading to the increase in fruit size in modern varieties. Here, we report the map-based cloning of lc. The lc QTL includes a 1,600-bp region that is located 1,080 bp from the 3′ end of WUSCHEL, which encodes a homeodomain protein that regulates stem cell fate in plants. The molecular evolution of lc showed a reduction of diversity in cultivated accessions with the exception of two single-nucleotide polymorphisms. These two single-nucleotide polymorphisms were shown to be responsible for the increase in locule number. An evolutionary model of locule number is proposed herein, suggesting that the fas mutation appeared after the mutation in the lc locus to confer the extreme high-locule-number phenotype.
Prospective multicentre cohort study of heparin‐induced thrombocytopenia in acute ischaemic stroke patients
Authors: Kawano Hiroyuki , Yamamoto Haruko , Miyata Shigeki , Izumi Manabu , Hirano Teruyuki , Toratani Naomi , Kakutani Isami , Sheppard Jo‐Ann I. , Warkentin Theodore E. , Kada Akiko , Sato Shoichiro , Okamoto Sadahisa , Nagatsuka Kazuyuki , Naritomi Hiroaki , Toyoda Kazunori , Uchino Makoto , Minematsu Kazuo
Published: June 2011

Acute ischaemic stroke patients sometimes receive heparin for treatment and/or prophylaxis of thromboembolic complications. This study was designed to elucidate the incidence and clinical features of heparin‐induced thrombocytopenia (HIT) in acute stroke patients treated with heparin. We conducted a prospective multicentre cohort study of 267 patients who were admitted to three stroke centres within 7 d after stroke onset. We examined clinical data until discharge and collected blood samples on days 1 and 14 of hospitalization to test anti‐platelet factor 4/heparin antibodies (anti‐PF4/H Abs) using an enzyme‐linked immunosorbent assay (ELISA); platelet‐activating antibodies were identified by serotonin‐release assay (SRA). Patients with a 4Ts score ≥4 points, positive‐ELISA, and positive‐SRA were diagnosed as definite HIT. Heparin was administered to 172 patients (64·4%: heparin group). Anti‐PF4/H Abs were detected by ELISA in 22 cases (12·8%) in the heparin group. Seven patients had 4Ts ≥ 4 points. Among them, three patients (1·7% overall) were also positive by both ELISA and SRA. National Institutes of Health Stroke Scale score on admission was high (range, 16–23) and in‐hospital mortality was very high (66·7%) in definite HIT patients. In this study, the incidence of definite HIT in acute ischaemic stroke patients treated with heparin was 1·7% (95% confidence interval: 0·4–5·0). The clinical severity and outcome of definite HIT were unfavourable.
Antigen-specific T cell responses to BK polyomavirus antigens identify functional anti-viral immunity and may help to guide immunosuppression following renal transplantation
Authors: Chakera A , Bennett S , Lawrence S , Morteau O , Mason P D , O'Callaghan C A , Cornall R J
Published: June 2011

Infection with the polyoma virus BK (BKV) is a major cause of morbidity following renal transplantation. Limited understanding of the anti-viral immune response has prevented the design of a strategy that balances treatment with the preservation of graft function. The proven utility of interferon-gamma enzyme-linked immunospot (ELISPOT) assays to measure T cell responses in immunocompetent hosts was the basis for trying to develop a rational approach to the management of BKV following renal transplantation. In a sample of transplant recipients and healthy controls, comparisons were made between T cell responses to the complete panel of BKV antigens, the Epstein–Barr virus (EBV) antigens, BZLF1 and EBNA1, and the mitogen phytohaemagglutinin (PHA). Correlations between responses to individual antigens and immunosuppressive regimens were also analysed. Antigen-specific T cell responses were a specific indicator of recent or ongoing recovery from BKV infection (P < 0·05), with responses to different BKV antigens being highly heterogeneous. Significant BKV immunity was undetectable in transplant patients with persistent viral replication or no history of BKV reactivation. Responses to EBV antigens and mitogen were reduced in patients with BKV reactivation, but these differences were not statistically significant. The T cell response to BKV antigens is a useful and specific guide to recovery from BKV reactivation in renal transplant recipients, provided that the full range of antigenic responses is measured.
Resolution-associated molecular patterns (RAMP): RAMParts defending immunological homeostasis?
Authors: Shields A M , Panayi G S , Corrigall V M
Published: June 2011

The resolution of inflammation is central to the maintenance of good health and immune homeostasis. Recently, several intracellular stress proteins have been described as having extracellular properties that are anti-inflammatory or favour the resolution of inflammation. We propose that these molecules should be defined as resolution-associated molecular patterns (RAMPs). RAMPs are released at times of cellular stress and help to counterbalance the inflammatory effects of pathogen-associated (PAMPs) and damage-associated (DAMPs) molecular patterns. We propose that heat shock protein 10 (HSP10), αB-crystallin (αBC), HSP27 and binding immunoglobulin protein (BiP) should be considered founding members of the RAMP family. A greater understanding of RAMP biology may herald the development of novel immunotherapies.