bluuebunny/crossref_metadata_2025 huggingface dataset:
An Examination of Kernite (Na2B4O6(OH)2·3H2O) Using X-Ray and Electron Spectroscopies: Quantitative Microanalysis of a Hydrated Low-Z Mineral
Authors: Meier Douglas C. , Davis Jeffrey M. , Vicenzi Edward P.
Published: September 2011

Mineral borates, the primary industrial source of boron, are found in a large variety of compositions. One such source, kernite (Na2B4O6(OH)2·3H2O), offers an array of challenges for traditional electron-probe microanalysis (EPMA)—it is hygroscopic, an electrical insulator, composed entirely of light elements, and sensitive to both low pressures and the electron beam. However, the approximate stoichiometric composition of kernite can be analyzed with careful preparation, proper selection of reference materials, and attention to the details of quantification procedures, including correction for the time dependency of the sodium X-ray signal. Moreover, a reasonable estimation of the mineral's water content can also be made by comparing the measured oxygen to the calculated stoichiometric oxygen content. X-ray diffraction, variable-pressure electron imaging, and visual inspection elucidate the structural consequences of high vacuum treatment of kernite, while Auger electron spectroscopy and X-ray photoelectron spectroscopy confirm electron beam-driven migration of sodium and oxygen out of the near-surface region (sampling depth ≈ 2 nm). These surface effects are insufficiently large to significantly affect the EPMA results (sampling depth ≈ 400 nm at 5 keV).
The Legality Principle in Sentencing at the ECCC: Making Up Law as It Goes Along?
Authors: KIELSGARD Mark D.
Published: September 2011

Sui generis hybrid international criminal tribunals must conduct business without institutional memory and are only as effective or fair as their constitutive documents allow. The sparse guidance provided for the international crimes court in Cambodia creates uncertainty and arguably ambiguous standards that infringe upon the legality principle and undermine efforts for nulla poena sine lege.
Fighting Organized Crime in the Asia Pacific Region: New Weapons, Lost Wars
Authors: SCHLOENHARDT Andreas
Published: September 2011

This article analyses offences dealing with the incrimination of organized crime under international and domestic laws in the Asia Pacific region and develops recommendations to improve existing and proposed provisions. The article frames the arguments for and against offences such as “participation in an organized crime group”, “gangsterism”, or “racketeering”, and critically examines the rationale, elements, and application of existing and proposed organized crime offences in the Asia Pacific.
Neurodegeneration: Potential Causes, Prevention, and Future Treatment Options
Authors: Zhang Zhongtao
Published: September 2011

Here I advance a hypothesis that neurodegeneration is a natural process associated with aging due to the loss of genetic redundancy following a mathematical model R(t) = R0(1-αe(βC+γI+δEt)t), where the calorie intake (C) and immune response (I) play critical roles. The early onset of neurodegenerative diseases such as Alzheimer’s disease is due to metabolic imbalance or chronic immune reactions to various infections. Therefore, the potential treatment options for neurodegenerative diseases are to modulate metabolism and immune response.
Kinetic Simulation Algorithm Ontology
Authors: Zhukova Anna , Waltemath Dagmar , Juty Nick , Laibe Camille , Le Novère Nicolas
Published: September 2011

To enable the accurate and repeatable execution of a computational simulation task, it is important to identify both the algorithm used and the initial setup. These minimum information requirements are described by the MIASE guidelines. Since the details of some algorithms are not always publicly available, and many are implemented only in a limited number of simulation tools, it is crucial to identify alternative algorithms with similar characteristics that may be used to provide comparable results in an equivalent simulation experiment. The Kinetic Simulation Algorithm Ontology (KiSAO) was developed to address this issue by describing existing algorithms and their inter-relationships through their characteristics and parameters. The use of KiSAO in conjunction with simulation descriptions, such as SED-ML, will allow simulation software to automatically choose the best algorithm available to perform a simulation. The availability of algorithm parameters, together with their type may permit the automatic generation of user-interfaces to configure simulators. To enable making queries to KiSAO programmaticaly, from simulation experiment description editors and simulation tools, a java library libKiSAO was implemented.
Dynamic Structures in SBML
Authors: Myers Chris
Published: September 2011

This talk describes ideas on how to integrate dynamic structures in SBML.
Retinal adaptation to spatial correlations
Authors: Simmons Kristina , Prentice Jason , Homann Jan , Tkacik Gasper , Nelson Philip , Balasubramanian Vijay
Published: September 2011

The classical center-surround retinal ganglion cell receptive field is thought to remove the strong spatial correlations in natural scenes, enabling efficient use of limited bandwidth. While early studies with drifting gratings reported robust surrounds (Enroth-Cugell and Robson, 1966), recent measurements with white noise reveal weak surrounds (Chichilnisky and Kalmar, 2002). This might be evidence for dynamical weakening of the retinal surround in response to decreased spatial correlations, which would be predicted by efficient coding theory. Such adaptation is reported in LGN (Lesica et al., 2007), but whether the retina also adapts to correlations is unknown.We tested for adaptation by recording simultaneously from ~40 ganglion cells on a multi-electrode array while presenting white and exponentially correlated checkerboards and strips. Measuring from ~200 cells responding to 90 minutes each of white and correlated stimuli, we were able to extract precise spatiotemporal receptive fields (STRFs). We found that a difference-of-Gaussians was not a good fit and the surround was generally displaced from the center. Thus, to assess surround strength we found the center and surround regions and the total weight on the pixels in each region. The relative surround strength was then defined as the ratio of surround weight to center weight. Surprisingly, we found that the majority of recorded cells have a stronger surround under white noise than under correlated noise (p<.05), contrary to naive expectation from theory. The conclusion was robust to different methods of extracting STRFs and persisted with checkerboard and strip stimuli.To test, without assuming a model, whether the retina decorrelates stimuli, we also measured the pairwise correlations between spike trains of simultaneously recorded neurons under three conditions: white checkerboard, exponentially correlated noise, and scale-free noise. The typical amount of pairwise correlation increased with extent of input correlation, in line with our STRF measurements.
Systems Biology on Bio-Linux
Authors: Bicak Mesude
Published: September 2011

This presentation introduces the Bio-Linux Operating System which is a popular Computational Biology workstation with 500+ bioinformatics software. It then provides an overview of popular modelling approaches in systems biology, covering top-down, bottom-up and hybrid modelling. Finally it highlights the challenges being faced by systems biology modellers, agent-based modellers in particular, regarding standardisation efforts.
Updates to the SBML Level 3 Flux Balance Constraints (FBC) package
Authors: Olivier Brett
Published: September 2011

In this presentation I introduce the need for an SBML package and introduce recent updates to the proposal.The Flux Balance Constraints package is a proposed SBML Level 3 extension that allows the definition of constraint based (a.k.a steady state, flux balance analysis, FBA) models.
Resistant Groups in Enterprise System Implementations: A Q-Methodology Examination
Authors: Klaus Tim , Wingreen Stephen C , Blanton J Ellis
Published: September 2011

This paper is an initial investigation into types of user resistance and the management strategy expectations of users in a mandatory adoption setting. Despite its relationship to adoption, relatively little is known about user resistance. User resistance is investigated in the Enterprise System (ES) environment because the complexity and richness of ES leads users to manifest a large range of resistant behaviors and beliefs. Using Concourse Theory and Q-methodology, ES users are interviewed followed by the development of a Q-sort questionnaire, which was distributed to ES users. The results reveal eight user groups and address the management strategies preferred by each group. The results have implications for both research in the field of user resistance and adoption, and practitioners involved in system implementation.
Control of the antisymmetric mode (m = 1) for high Reynolds axisymmetric turbulent separating/reattaching flows
Authors: Weiss Pierre-Élie , Deck Sébastien
Published: September 2011

The separated flow over a three-dimensional axisymmetric step controlled by means of continuous jets is investigated numerically at a high subsonic regime using Zonal Detached Eddy Simulation (ZDES). The main objective is here to analyze the influence of two controlled devices acting in different regions of the separated flow, i.e., in the shear layer or in the recirculation area. Contrary to most flow control strategies that aim at reducing the drag, the final purpose of this study consists in controlling the antisymmetric azimuthal mode (m=1) responsible for side loads occurring on a massively separated afterbody. Thus, the design of controlled cases has been motivated both by a literature review which is detailed but especially by the previous identification of a potential area of receptiveness linked to an absolutely unstable area. The related achievement expected lies in increasing the three-dimensionality of the flow but decreasing its large scale coherence. For both controlled configurations, instantaneous, statistical, and fluctuating properties are scrutinized. In particular, the analysis exhibits that the backflow has to be considered stronger in time compared to its mean and broadly distributed in space which impacts the amount of energy needed to counteract this backflow and thus to control the flow. Then, a two-point spectral analysis is performed on the entire wall of interest of the afterbody providing a spatial representation of the fluctuating energy for a selected frequency. This last investigation permits to understand the influence of the control on the mechanisms related to the dimensionless frequency StD=0.2 and its associated antisymmetric mode. Finally, this analysis permits to predict the effect of the control on the change in the nature of the instability contained in the potentially receptive zone transitioning from fully absolute to fully convective.
Collisional relaxation of O2($X^3\Sigma _g^ -$X3Σg−, υ = 1) and O2(a1Δg, υ = 1) by atmospherically relevant species
Authors: Pejaković Dušan A. , Campbell Zachary , Kalogerakis Konstantinos S. , Copeland Richard A. , Slanger Tom G.
Published: September 2011

Laboratory measurements are reported of the rate coefficient for collisional removal of O2($X^3\Sigma _g^ -$X3Σg−, υ = 1) by O(3P), and the rate coefficients for removal of O2(a1Δg, υ = 1) by O2, CO2, and O(3P). A two-laser method is employed, in which the pulsed output of the first laser at 285 nm photolyzes ozone to produce oxygen atoms and O2(a1Δg, υ = 1), and the output of the second laser detects O2(a1Δg, υ = 1) via resonance-enhanced multiphoton ionization. The kinetics of O2($X^3\Sigma _g^ -$X3Σg−, υ = 1) + O(3P) relaxation is inferred from the temporal evolution of O2(a1Δg, υ = 1), an approach enabled by the rapid collision-induced equilibration of the O2($X^3\Sigma _g^ -$X3Σg−, υ = 1) and O2(a1Δg, υ = 1) populations in the system. The measured O2($X^3\Sigma _g^ -$X3Σg−, υ = 1) + O(3P) rate coefficient is (2.9 ± 0.6) × 10−12 cm3 s−1 at 295 K and (3.4 ± 0.6) × 10−12 cm3 s−1 at 240 K. These values are consistent with the previously reported result of (3.2 ± 1.0) × 10−12 cm3 s−1, which was obtained at 315 K using a different experimental approach [K. S. Kalogerakis, R. A. Copeland, and T. G. Slanger, J. Chem. Phys. 123, 194303 (2005)]. For removal of O2(a1Δg, υ = 1) by O(3P), the upper limits for the rate coefficient are 4 × 10−13 cm3 s−1 at 295 K and 6 × 10−13 cm3 s−1 at 240 K. The rate coefficient for removal of O2(a1Δg, υ = 1) by O2 is (5.6 ± 0.6) × 10−11 cm3 s−1 at 295 K and (5.9 ± 0.5) × 10−11 cm3 s−1 at 240 K. The O2(a1Δg, υ = 1) + CO2 rate coefficient is (1.5 ± 0.2) × 10−14 cm3 s−1 at 295 K and (1.2 ± 0.1) × 10−14 cm3 s−1 at 240 K. The implications of the measured rate coefficients for modeling of atmospheric emissions are discussed.
Pinning control of complex networks via edge snapping
Authors: DeLellis P. , di Bernardo M. , Porfiri M.
Published: September 2011

In this paper, we propose a hierarchy of novel decentralized adaptive pinning strategies for controlled synchronization of complex networks. This hierarchy addresses the fundamental need of selecting the sites to pin through a fully decentralized approach based on edge snapping. Specifically, we present three different strategies of increasing complexity which use a combination of network evolution and adaptation of the coupling and control gains. Theoretical results are complemented by extensive numerical investigations of the performance of the proposed strategies on a set of testbed examples.
Homoclinic snaking of localized states in doubly diffusive convection
Authors: Beaume Cédric , Bergeon Alain , Knobloch Edgar
Published: September 2011

Numerical continuation is used to investigate stationary spatially localized states in two-dimensional thermosolutal convection in a plane horizontal layer with no-slip boundary conditions at top and bottom. Convectons in the form of 1-pulse and 2-pulse states of both odd and even parity exhibit homoclinic snaking in a common Rayleigh number regime. In contrast to similar states in binary fluid convection, odd parity convectons do not pump concentration horizontally. Stable but time-dependent localized structures are present for Rayleigh numbers below the snaking region for stationary convectons. The computations are carried out for (inverse) Lewis number τ = 1/15 and Prandtl numbers Pr = 1 and Pr≫1.
Novel numerical method for calculating the pressure tensor in spherical coordinates for molecular systems
Authors: Nakamura Takenobu , Shinoda Wataru , Ikeshoji Tamio
Published: September 2011

We propose a novel method for computing the pressure tensor along the radial axis of a molecular system with spherical symmetry. The proposed method uses the slice averaged pressure to improve the numerical stability and precision significantly. Simplified expressions of the local pressure are derived for a conventional molecular force field including non-bond, bond stretching, angle bending, and torsion interactions; these expressions are advantageous in terms of the computational cost. We also discuss an algorithm to avoid numerical singularity. Finally, the method is successfully applied to three different molecular systems, i.e., a water droplet in oil, a spherical micelle, and a liposome.
High-temperature oxide thermoelectrics
Authors: Terasaki Ichiro
Published: September 2011

We have evaluated the power factor of transition metal oxides at high temperatures using the Heikes formula and the Ioffe–Regel conductivity. The evaluated power factor is found to be nearly independent of carrier concentration in a wide range of doping, and explains the experimental data for cobalt oxides well. This suggests that the same power factor can be obtained with a thermopower larger than 2kB/e, and also suggests a reasonably high value of the dimensionless figure of merit ZT. We propose an oxide thermoelectric power generator by using materials having a thermopower larger than 300 μV/K.
On particle spin in two-way coupled turbulent channel flow simulations
Authors: Zhao Lihao , Andersson Helge I.
Published: September 2011

The rotational motion of spherical particles suspended in a turbulent flow field may not necessarily adapt to the fluid rotation, i.e., the particle spin may be different from the fluid vorticity. The translational and rotational motions of tiny particles are described in a Lagrangian framework using the point-particle approximation. The turbulence of the fluid phase is obtained by means of direct numerical simulations in which the feed-back from the particles onto the flow field is accounted for by a two-way coupling scheme. Particles with three different response times are considered, each for which millions of particles are released randomly in a turbulent channel flow at a frictional Reynolds number 360. The lightest particles with rotational response time 0.3 times the viscous time scale exhibited preferential concentration in areas with low streamwise vorticity but rotated passively along with the local fluid. The heaviest particles with a 30 times longer response time spun strikingly different from the particle spin observed in a one-way coupled simulation. This phenomenon can be ascribed primarily to the substantial modulation of the carrier-phase turbulence caused by the feed-back from the particles in the two-way coupled approach. Due to their higher rotational inertia, these particles did not even adjust to the rotational motion of the local fluid.
Cr metal thin film memory
Authors: Hong Augustin J. , Kim Jiyoung , Kim Kyoungwhan , Wang Yong , Xiu Faxian , Jeon Jaeseok , Park Jemin , Rauda Iris , Chen Li-Min , Yang Yang , Tolbert Sarah , Zou Jin , Wang Kang L.
Published: September 2011

As state of the art flash memory technologies scale down to sub 30 nm node, conventional floating gate flash memory approaches its physical scaling limit mainly because of the high gate coupling ratio (GCR) requirement to secure proper memory window. Here, we report a novel flash memory device called Cr metal thin film memory (MTFM) that can circumvent the GCR issue and extend flash memory scalability by employing Cr thin film as a storage layer. Cr metal thin film memory devices with simple and low temperature processes produced a wide memory window of 10 V at the ±18 V voltage sweep with GCR of only 0.3. Such a large window can be adopted for multi-level cell operations, which can further increase the memory density. Also, retention measurement shows more than 10 years retention time due to higher energy barrier between Cr metal and tunnel oxide than conventional poly silicon and tunnel oxide. Cross section transmission electron microscope (TEM) images showed the structure and accurate dimensions of the Cr MTFM device with continuous Cr film and sharp interfaces. As for material characterizations, an amorphous like Cr phase was observed through TEM and x-ray diffraction (XRD). X-ray photoelectron spectroscopy (XPS) confirmed the Cr-Cr bond and Cr-O bond near the Cr surface after evaporation and rapid thermal annealing. This metal thin film memory may open a new route to achieve the terabit level flash memory.
Some properties of toroidal isodynamic magnetostatic equilibria
Authors: Aly J.-J.
Published: September 2011

We establish some general properties of a 3D isodynamic magnetostatic equilibrium admitting a family of nested toroidal flux surfaces. In particular, we use the virial theorem to prove a simple relation between the total pressure (magnetic + thermal) and the magnetic pressure on each flux surface, and we derive some useful consequences of the latter. We also show the constancy on each rational surface of two integrals along magnetic lines. As a simple application of our results, we show the nonexistence of an equilibrium with vanishing toroidal current, and of an equilibrium with closed lines.
Low-Reynolds-number gravity-driven migration and deformation of bubbles near a free surface
Authors: Pigeonneau Franck , Sellier Antoine
Published: September 2011

We investigate numerically the axisymmetric migration of bubbles toward a free surface, using a boundary-integral technique. Our careful numerical implementation allows to study the bubble(s) deformation and film drainage; it is benchmarked against several tests. The rise of one bubble toward a free surface is studied and the computed bubble shape compared with the results of Princen [J. Colloid Interface Sci. 18, 178 (1963)]. The liquid film between the bubble and the free surface is found to drain exponentially in time in full agreement with the experimental work of Debrégeas et al. [Science 279, 1704 (1998)]. Our numerical results also cast some light on the role played by the deformation of the fluid interfaces and it turns out that for weakly deformed interfaces (high surface tension or a tiny bubble) the film drainage is faster than for a large fluid deformation. By introducing one or two additional bubble(s) below the first one, we examine to which extent the previous trends are affected by bubble-bubble interactions. For instance, for a 2-bubble chain, decreasing the bubble-bubble separation increases the deformation of the last bubble in the chain. Finally, the exponential drainage of the film between the free surface and the closest bubble is preserved, yet the drainage is enhanced.
High-resolution 13C nuclear magnetic resonance evidence of phase transition of Rb,Cs-intercalated single-walled nanotubes
Authors: Bouhrara M. , Saih Y. , Wågberg T. , Goze-Bac C. , Abou-Hamad E.
Published: September 2011

We present 13 C high-resolution magic-angle-turning (MAT) and magic angle spinning nuclear magnetic resonance data of Cs and Rb intercalated single walled carbon nanotubes. We find two distinct phases at different intercalation levels. A simple charge transfer is applicable at low intercalation level. The new phase at high intercalation level is accompanied by a hybridization of alkali (s) orbitals with the carbon (sp2) orbitals of the single walled nanotubes, which indicate bundle surface sites is the most probable alkali site.
Dissipative and hysteresis loops as images of irreversible processes in nonlinear acoustic fields
Authors: Hedberg C. M. , Rudenko O. V.
Published: September 2011

Irreversible processes taking place during nonlinear acoustic wave propagation are considered using a representation by loops in a thermodynamic parameter space. For viscous and heat conducting media, the loops are constructed for quasi-harmonic and sawtooth waves and the descriptive equations are formulated. The linear and nonlinear absorptions are compared. For relaxing media, the processes are frequency-dependent. The loops broadens, narrows, and bends. The linear and nonlinear relaxation losses of wave energy are shown. Residual stresses and irreversible strains appear for hysteretic media, and here, a generalization of Rayleigh loops is pictured which takes into account the nonlinearly frequency-dependent hereditary properties. These describe the dynamic behavior, for which new equations are derived.
LC-circuit calorimetry
Authors: Bossen O. , Schilling A.
Published: September 2011

We present a new type of calorimeter in which we couple an unknown heat capacity with the aid of Peltier elements to an electrical circuit. The use of an electrical inductance and an amplifier in the circuit allows us to achieve autonomous oscillations, and the measurement of the corresponding resonance frequency makes it possible to accurately measure the heat capacity with an intrinsic statistical uncertainty that decreases as \documentclass[12pt]{minimal}\begin{document}$ \sim t_\mathrm{m}^{ -3/2}$\end{document}∼tm−3/2 with measuring time tm, as opposed to a corresponding uncertainty \documentclass[12pt]{minimal}\begin{document}$\sim t_\mathrm{m}^{-1/2}$\end{document}∼tm−1/2 in the conventional alternating current method to measure heat capacities. We have built a demonstration experiment to show the feasibility of the new technique, and we have tested it on a gadolinium sample at its transition to the ferromagnetic state.
Lithium plasma emitter for collisionless magnetized plasma experiment
Authors: Kawamori Eiichirou , Lee Jyun-Yi , Huang Yi-Jue , Syugu Wun-Jheng , Song Sung-Xuang , Hsieh Tung-Yuan , Cheng C. Z.
Published: September 2011

This paper presents a newly developed lithium plasma emitter, which can provide quiescent and low-temperature collisionless conditions for magnetized plasma experiments. This plasma emitter generates thermal emissions of lithium ions and electrons to produce a lithium plasma. Lithium type beta-eucryptite and lanthanum-hexaboride (LaB6) powders were mixed and directly heated with a tungsten heater to synthesize ion and electron emissions. As a result, a plasma with a diameter of ∼15 cm was obtained in a magnetic mirror configuration. The typical range of electron density was 1012–1013 m−3 and that of electron temperature was 0.1–0.8 eV with the emitter operation temperature of about 1500 K. The amplitude fluctuations for the plasma density were lower than 1%.
Compositional effects on the electronic structure of ZnSe1−xSx ternary quantum dots
Authors: Pandey Sumeet C. , Mountziaris T. J. , Maroudas Dimitrios
Published: September 2011

We report first-principles density functional theory calculations of the electronic structure of ZnSe1−xSx ternary quantum dots (TQDs) and the impact of composition and compositional distribution on the electron density distribution, electronic density of states, and band gap. We find that the band gaps for ZnSe/ZnS core/shell TQDs are nearly independent of the number of S atoms in the shell, whereas the presence of S in the core of alloyed TQDs modifies the electronic energy levels significantly. Our results imply that distribution of S atoms can be used to achieve quantum confinement in different regions of the TQDs.
Effect of gravity on the microstructure of Al-Si alloy for rear-passivated solar cells
Authors: Urrejola Elias , Peter Kristian , Plagwitz Heiko , Schubert Gunnar
Published: September 2011

We study the influence of the gravity field orientation on the microstructure of Al–Si forming alloy. Due to the difference between the diffusivity of aluminum and silicon, Kirkendall void formations are normally found at the back of rear-passivated solar cells instead of an eutectic layer. We show that the voids may partially be avoided by sintering the samples with the solid/liquid interface oriented opposite to the direction of the gravity field. A local back-surface-field is found underneath the voids using this approach. This phenomenon strongly applies to rear-passivated solar cells, which exhibited strong fill factor losses.
Electromagnetic properties of sapphire, ruby, and irradiated ruby at frequencies of 30–40 GHz
Authors: Krupka Jerzy , Shimada Takeshi , Ueda Itaru , Karcz Waldemar
Published: September 2011

Permittivity and electromagnetic losses of sapphire, ruby, and irradiated ruby samples were examined at frequencies of 30–40 GHz and temperatures of 4–300 K employing the whispering gallery mode technique. At room temperature, the dielectric properties of the sapphire, ruby, and irradiated ruby samples were similar. Significant differences in electromagnetic losses took place at cryogenic temperatures. Losses were related to the imaginary part of the susceptibility associated with the presence of paramagnetic Cr3+ ions as well as those introduced by structural defects caused by the irradiation of ruby samples. The presence of impurities and the structural defects result in the dielectric losses being larger than those of pure sapphire.
Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA
Authors: Kamburov Atanas , Cavill Rachel , Ebbels Timothy M. D. , Herwig Ralf , Keun Hector C.
Published: September 2011

Summary:Pathway-level analysis is a powerful approach enabling interpretation of post-genomic data at a higher level than that of individual biomolecules. Yet, it is currently hard to integrate more than one type of omics data in such an approach. Here, we present a web tool ‘IMPaLA’ for the joint pathway analysis of transcriptomics or proteomics and metabolomics data. It performs over-representation or enrichment analysis with user-specified lists of metabolites and genes using over 3000 pre-annotated pathways from 11 databases. As a result, pathways can be identified that may be disregulated on the transcriptional level, the metabolic level or both. Evidence of pathway disregulation is combined, allowing for the identification of additional pathways with changed activity that would not be highlighted when analysis is applied to any of the functional levels alone. The tool has been implemented both as an interactive website and as a web service to allow a programming interface.

Availability:The web interface of IMPaLA is available at http://impala.molgen.mpg.de. A web services programming interface is provided at http://impala.molgen.mpg.de/wsdoc.

Contact:  kamburov@molgen.mpg.de; r.cavill@imperial.ac.uk; h.keun@imperial.ac.uk

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Semi-supervised learning improves gene expression-based prediction of cancer recurrence
Authors: Shi Mingguang , Zhang Bing
Published: September 2011

Motivation: Gene expression profiling has shown great potential in outcome prediction for different types of cancers. Nevertheless, small sample size remains a bottleneck in obtaining robust and accurate classifiers. Traditional supervised learning techniques can only work with labeled data. Consequently, a large number of microarray data that do not have sufficient follow-up information are disregarded. To fully leverage all of the precious data in public databases, we turned to a semi-supervised learning technique, low density separation (LDS).

Results: Using a clinically important question of predicting recurrence risk in colorectal cancer patients, we demonstrated that (i) semi-supervised classification improved prediction accuracy as compared with the state of the art supervised method SVM, (ii) performance gain increased with the number of unlabeled samples, (iii) unlabeled data from different institutes could be employed after appropriate processing and (iv) the LDS method is robust with regard to the number of input features. To test the general applicability of this semi-supervised method, we further applied LDS on human breast cancer datasets and also observed superior performance. Our results demonstrated great potential of semi-supervised learning in gene expression-based outcome prediction for cancer patients.

Contact:  bing.zhang@vanderbilt.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Human SNM1A and XPF–ERCC1 collaborate to initiate DNA interstrand cross-link repair
Authors: Wang Anderson T. , Sengerová Blanka , Cattell Emma , Inagawa Takabumi , Hartley Janet M. , Kiakos Konstantinos , Burgess-Brown Nicola A. , Swift Lonnie P. , Enzlin Jacqueline H. , Schofield Christopher J. , Gileadi Opher , Hartley John A. , McHugh Peter J.
Published: September 2011

One of the major DNA interstrand cross-link (ICL) repair pathways in mammalian cells is coupled to replication, but the mechanistic roles of the critical factors involved remain largely elusive. Here, we show that purified human SNM1A (hSNM1A), which exhibits a 5′–3′ exonuclease activity, can load from a single DNA nick and digest past an ICL on its substrate strand. hSNM1A-depleted cells are ICL-sensitive and accumulate replication-associated DNA double-strand breaks (DSBs), akin to ERCC1-depleted cells. These DSBs are Mus81-induced, indicating that replication fork cleavage by Mus81 results from the failure of the hSNM1A- and XPF–ERCC1-dependent ICL repair pathway. Our results reveal how collaboration between hSNM1A and XPF–ERCC1 is necessary to initiate ICL repair in replicating human cells.
Ending the message: poly(A) signals then and now
Authors: Proudfoot Nick J.
Published: September 2011

Polyadenylation [poly(A)] signals (PAS) are a defining feature of eukaryotic protein-coding genes. The central sequence motif AAUAAA was identified in the mid-1970s and subsequently shown to require flanking, auxiliary elements for both 3′-end cleavage and polyadenylation of premessenger RNA (pre-mRNA) as well as to promote downstream transcriptional termination. More recent genomic analysis has established the generality of the PAS for eukaryotic mRNA. Evidence for the mechanism of mRNA 3′-end formation is outlined, as is the way this RNA processing reaction communicates with RNA polymerase II to terminate transcription. The widespread phenomenon of alternative poly(A) site usage and how this interrelates with pre-mRNA splicing is then reviewed. This shows that gene expression can be drastically affected by how the message is ended. A central theme of this review is that while genomic analysis provides generality for the importance of PAS selection, detailed mechanistic understanding still requires the direct analysis of specific genes by genetic and biochemical approaches.
Shared and unique properties of ubiquitin and SUMO interaction networks in DNA repair
Authors: van Wijk Sjoerd J.L. , Müller Stefan , Dikic Ivan
Published: September 2011

In this issue of Genes & Development, Yang and colleagues (pp. 1847–1858) identify new components of a small ubiquitin-like modifier (SUMO)-like interaction network that orchestrates and fine-tunes the Fanconi anemia (FA) pathway and replication-coupled repair. This new pathway emphasizes the intricate interplay of ubiquitin (Ub) and SUMO networks in the DNA damage response.
Family Law Proceedings, Domestic Violence and the Impact upon School: A Neglected Area of Research
Authors: Eriksson Maria , Bruno Linnéa , Näsman Elisabet
Published: September 2011

The aim of this article is to open up a discussion about an unexplored area of children’s lives at school. While there has been considerable discussion of issues about child protection and the cooperation between school and social services in that context, studies on the intersection between school and family law proceedings seem virtually non‐existent. This is also the case when it comes to family law proceedings and different forms of childhood adversity. Drawing upon previous and ongoing research on family law and domestic violence in Sweden, together with a number of other existing studies on children and domestic violence, this article outlines the potential impact of family law proceedings upon school as well as issues requiring further research exploration.
Impacts of introducing Nile tilapia on the fisheries of a tropical reservoir in North‐eastern Brazil
Authors: ATTAYDE J. L. , BRASIL J. , MENESCAL R. A.
Published: September 2011

Abstract  Nile tilapia, Oreochromis niloticus (L.), has been introduced in most tropical and subtropical regions of the world to improve inland fisheries and aquaculture. This species is generally viewed as beneficial where introduced, but the environmental impacts of its widespread introductions are uncertain and not well understood. In this study, a 30‐year time series of fisheries records from a tropical reservoir was divided into five equal periods of 6 years and compared. The introduction of Nile tilapia did not increase the total catch‐per‐unit‐of‐effort (CPUE), the number of fishers actively fishing or their per capita income. Conversely, a significant reduction in the CPUE of other commercially important species was observed after the introduction of Nile tilapia in the reservoir. Although other factors cannot be rule out as possible explanations of the observed changes in the reservoir fisheries, the results are consistent with the hypothesis that these changes may have been caused, at least partially, by the introduction of the Nile tilapia.
Hierarchical Bayesian estimation of the population viability of an epixylic moss
Authors: Ruete Alejandro , Wiklund Karin , Snäll Tord
Published: September 2011

1. Understanding the variation in population abundances requires accounting for the environmental variability and uncertainty on different scales. We developed and evaluated a Bayesian hierarchical model for the inter‐annual variation in population abundance of the epixylic bryophyte Buxbaumia viridis. The model accounts for spatio‐temporal variability on two spatial scales. We used data on population abundance and on the weather variables at regional level collected between 1996 and 2003, and data on dead wood amount collected between 1996 and 2008. We also provide a Bayesian estimate of the population viability, specifically the population stochastic growth rate (log λS), which accounts for natural variability and uncertainty.

2. Previous estimates of population viability did not account for uncertainties in a satisfactory way. First, point estimates of log λS cannot, by definition, express variation. Second, the commonly used approach to estimate log λS and its confidence interval underestimates uncertainties. The approach aims to estimate the mean of log λS, with the confidence interval representing the uncertainty in the estimate of this mean. The interval does not reflect the natural variation and uncertainty.

3. We estimated a probability distribution of log λS, where the probability distributions of the year‐specific growth rates (log λy) are accounted for. The species is likely to decline under current environmental conditions. Based on the probability distribution of log λS, we estimated this risk to be 81%.

4. We found support for the hypotheses that the population dynamics are driven by autumn frosts, by spring precipitation and temperature (regional variables), and by the preceding year’s population abundance (local variable).

5. Synthesis. Statements about the viability of populations should not be based on point estimates of log λS. Instead, the full probability distribution of log λS should be used, which explicitly accounts for the hierarchically structured natural variability and uncertainty. This distribution allows estimating the risk for a population decline, or providing an estimate of the confidence in a statement about a decline. This quantitative information can be weighed against other interests. We expect this Bayesian approach to be especially useful in the viability analysis of natural populations experiencing environmental variability.
Determination of spatial correlation functions of refractive index of living tissue
Authors: GAO WANRONG
Published: September 2011

We present what to our knowledge the first method of determination of spatial correlation functions of refractive index fluctuations of living tissues by Fourier domain optical coherence tomography (FDOCT). Based on the second‐order statistical description of the random characteristic of living tissue, a formula which clearly relates the spectral electrical power from the detector to the Fourier spectrum of the refractive index correlation function is given. The method is characterized by its capability of noninvasive measurements in vivo. It has the potential of allowing quantitative discrimination between different tissue types or the same tissue at different pathological states by determining their Fourier components of spatial correlation functions of refractive index.
Relationship between sleep‐disordered breathing and markers of systemic inflammation in women from the general population
Authors: SVENSSON MALIN , VENGE PER , JANSON CHRISTER , LINDBERG EVA
Published: September 2011

Sleep‐disordered breathing (SDB) is a risk factor for cardiovascular disease (CVD). The underlying pathogenesis is not clear. In patients with obstructive sleep apnoea syndrome (OSAS) elevated levels of inflammatory markers, such as C‐reactive protein (CRP), interleukin‐6 (IL‐6) and tumour necrosis factor α (TNFα) have been found. These markers have also been shown as independent markers of CVD in other populations. The aim of the study was to investigate the association between SDB and systemic inflammation in a population‐based cohort of women. From 6817 women who previously answered a questionnaire concerning snoring habits, 230 habitually snoring women and 170 women regardless of snoring status went through polysomnography, anthropometric measurements and blood sampling. Analyses were made for CRP, TNFα, IL‐6, myeloperoxidase (MPO) and lysozyme. The levels of CRP, IL‐6 and lysozyme were significantly higher in subjects with apnoea–hypopnoea index (AHI) ≥15 compared with women with lower AHI. All inflammatory markers except MPO correlated to AHI and oxygen desaturation measures, and to waist circumference. In multiple linear regressions adjusting for age, waist circumference and smoking, independent correlations between oxygen desaturation indices (ODI) and inflammation were found for IL‐6 (P = 0.03 for % sleep time with saturation <90%) and TNFα (P = 0.03 for ODI 3%). No significant correlations were found between AHI and inflammation. Also, for women from the general population there is an independent correlation between SDB and inflammation, even after adjusting for obesity. The results indicate that intermittent hypoxia, and not the AHI, is related to systemic inflammation seen in OSAS.
Identification and characterization of stationary phase inducible genes in Escherichia coli
Authors: Weichart Dieter , Lange Roland , Henneberg Nicola , Hengge‐Aronis Regine
Published: September 2011

During transition into stationary phase a large set of proteins is induced in Escherichia coli. Only a minority of the corresponding genes has been identified so far. Using the λplacMu system and a plate screen for carbon starvation‐induced fusion activity, a series of chromosomal lacZ fusions (csi::lacZ) was isolated. In complex medium these fusions were induced either during late exponential phase or during entry into stationary phase. csi::lacZ expression in minimal media in response to starvation for carbon, nitrogen and phosphate sources and the roles of global regulators such as the alternative sigma factor sigma;S (encoded by rpoS), cAMP/CRP and the relA gene product were investigated. The results show that almost every fusion exhibits its own characteristic pattern of expression, suggesting a complex control of stationary phase‐inducible genes that involves various combinations of regulatory mechanisms for different genes. All fusions were mapped to the E. coli chromosome. Using fine mapping by Southern hybridization, cloning, sequencing and/or phenotypic analysis, csi‐5, csi‐17, and csi‐18 could be localized in osmY (encoding a periplasmic protein), glpD (aerobic glycerol‐3‐phosphate dehydrogenase) and glgA (glycogen synthase), respectively. The other fusions seem to specify novel genes now designated csiA through to csiF. csi‐17(glpD)::lacZ was shown to produce its own glucose‐starvation induction, thus illustrating the Intricacies of gene‐fusion technology when applied to the study of gene regulation.
Xcp‐mediated protein secretion in Pseudomonas aeruginosa: identification of two additional genes and evidence for regulation of xcp gene expression
Authors: Akrim Mohammed , Bally Marc , Ball Geneviève , Tommassen Jan , Teerink Henk , Filloux Alain , Lazdunski Andrée
Published: September 2011

In Pseudomonas aeruginosa, several exoproteins synthesized with a signal sequence (elastase, lipase, phospholipases, alkaline phosphatase and exotoxin A) are secreted by a two‐step mechanism. They first cross the inner membrane in a signal sequence‐dependent way, and are further translocated across the outer membrane in a second step requiring secretion functions encoded by several xcp genes. Ten xcp genes have already been characterized (Bally et al., 1992a). In this study, two additional xcp genes, xcpP and xcpQ, are described. They are located in the 40 min region of the chromosome where they probably define an operon, divergent from the xcpR–Z operon previously characterized in this region. These two genes encode two proteins, XcpP and XcpQ, similar to PulC and PulD of the pul system of Klebsiella oxytoca. Moreover, the two divergent operons share a common regulation which is growth‐phase dependent.
Split decision: a thaumarchaeon encoding both FtsZ and Cdv cell division proteins chooses Cdv for cytokinesis
Authors: Busiek Kimberly K. , Margolin William
Published: September 2011

Cytoskeletal proteins play a pivotal role in cytokinesis in prokaryotes and eukaryotes. Most bacteria and a major branch of the archaea called the Euryarchaeota harbour a tubulin homologue, FtsZ, which assembles into a dynamic polymeric ring structure required for cytokinesis. However, Crenarchaeota, another branch of the archaea, lack FtsZ and instead use Cdv proteins, which are homologues of the ESCRT‐III‐like system involved in vesicular sorting and cytokinesis in eukaryotes, for cell division. Recently, a group of Crenarchaeota that grow in non‐extreme environments was found to be sufficiently divergent to warrant its own branch of the archaea called the Thaumarchaeota. Notably, Thaumarchaeota have both Cdv and FtsZ homologues, which begs the question of which system is used for cell division. In this issue of Molecular Microbiology,Pelve et al. (2011) Pelve and colleagues tackle this question. They found that cells of the thaumarchaeon Nitrosopumilus maritimus likely divide using the Cdv system and not FtsZ, based on localization of Cdv proteins but not FtsZ to division sites. The authors also provide evidence that the cell cycle during growth of N. maritimus differs significantly from those of other archaea.
GSK962040: a small molecule motilin receptor agonist which increases gastrointestinal motility in conscious dogs
Authors: Leming S. , Broad J. , Cozens S. J. , Otterson M. , Winchester W. , Lee K. , Dukes G. E. , Sanger G. J.
Published: September 2011

Background  GSK962040, a small molecule motilin receptor agonist, was identified to address the need for a safe, efficacious gastric prokinetic agent. However, as laboratory rodents lack a functional motilin system, studies in vivo have been limited to a single dose, which increased defecation in rabbits. Motilin agonists do not usually increase human colonic motility, so gastric prokinetic activity needs to be demonstrated.

Methods  The effect of intravenous GSK962040 on gastro‐duodenal motility was assessed in fasted dogs implanted with strain gauges. Activity was correlated with blood plasma concentrations of GSK962040 (measured by HPLC‐MS/MS) and potency of GSK962040 at the dog recombinant receptor [using a Fluorometric Imaging Plate Reader (Molecular Devices, Wokingham, UK) after expression in HEK293 cells].

Key Results  GSK962040 activated the dog motilin receptor (pEC50 5.79; intrinsic activity 0.72, compared with [Nle13]‐motilin). In vivo, GSK962040 induced phasic contractions, the duration of which was dose‐related (48 and 173 min for 3 and 6 mg kg−1), driven by mean plasma concentrations >1.14 μmol L−1. After the effects of GSK962040 faded, migrating motor complex (MMC) activity returned. Migrating motor complex restoration was unaffected by 3 mg kg−1 GSK962040 but at 6 mg kg−1, MMCs returned 253 min after dosing, compared with 101 min after saline (n = 5 each).

Conclusions & Inferences  The results are consistent with lower potency for agonists at the dog motilin receptor, compared with humans. They also define the doses of GSK962040 which stimulate gastric motility. Correlation of in vivo and in vitro data in the same species, together with plasma concentrations, guides further studies and translation to other species.