bluuebunny/crossref_metadata_2025 huggingface dataset:
Localised quantum states of atomic and molecular particles physisorbed on carbon-based nanoparticles
Authors: Kaprálová-Žďánská Petra Ruth , Trachta Michal , Bludský Ota , Špirko Vladimír
Published: September 2014

The vibrational states of atomic and molecular particles adsorbed on long linear nanographenes are described using reliable theoretical potentials and appropriate vibrational (lateral) Hamiltonians. Although they rigorously obey the Bloch theorem only for infinite nanographenes, the energy patterns of the probed states closely resemble the usual Bloch bands and gaps. In addition, for any finite nanographene, these patterns are enriched by the presence of “solitary” energy levels and the “resonance” structure of the bands. While typical band states are profoundly delocalised due to a fast tunneling of the adsorbed particle, the “solitary” and “resonance” states exhibit strong localisation, similar to the behaviour of the states of the Wannier-Stark ladders in optical and semiconductor superlattices.
Mixed quantum/classical theory for inelastic scattering of asymmetric-top-rotor + atom in the body-fixed reference frame and application to the H2O + He system
Authors: Semenov Alexander , Dubernet Marie-Lise , Babikov Dmitri
Published: September 2014

The mixed quantum/classical theory (MQCT) for inelastic molecule-atom scattering developed recently [A. Semenov and D. Babikov, J. Chem. Phys. 139, 174108 (2013)] is extended to treat a general case of an asymmetric-top-rotor molecule in the body-fixed reference frame. This complements a similar theory formulated in the space-fixed reference-frame [M. Ivanov, M.-L. Dubernet, and D. Babikov, J. Chem. Phys. 140, 134301 (2014)]. Here, the goal was to develop an approximate computationally affordable treatment of the rotationally inelastic scattering and apply it to H2O + He. We found that MQCT is somewhat less accurate at lower scattering energies. For example, below E = 1000 cm−1 the typical errors in the values of inelastic scattering cross sections are on the order of 10%. However, at higher scattering energies MQCT method appears to be rather accurate. Thus, at scattering energies above 2000 cm−1 the errors are consistently in the range of 1%–2%, which is basically our convergence criterion with respect to the number of trajectories. At these conditions our MQCT method remains computationally affordable. We found that computational cost of the fully-coupled MQCT calculations scales as n2, where n is the number of channels. This is more favorable than the full-quantum inelastic scattering calculations that scale as n3. Our conclusion is that for complex systems (heavy collision partners with many internal states) and at higher scattering energies MQCT may offer significant computational advantages.
Novel electrochemical method of fast and reproducible fabrication of metallic nanoelectrodes
Authors: Silva E. L. , Silva R. F. , Zheludkevich M. , Oliveira F. J.
Published: September 2014

A novel electrochemical wire etching method of fabrication of ultrasharp nanoelectrodes is reported. Tungsten wires can be sharpened to less than 10 nm tip radius in a reproducible manner in less than 1 min by using controllable hydrodynamic electrolyte flow combined with optimized electrochemical etching parameters. The method relies on the variations of the electric field at the surface of a metal wire, while the electrolyte solution is in motion, rather than on the ionic gradient generated in a static solution.
The Hölder continuity of spectral measures of an extended CMV matrix
Authors: Munger Paul E. , Ong Darren C.
Published: September 2014

We prove results about the Hölder continuity of the spectral measures of the extended CMV matrix, given power law bounds of the solution of the eigenvalue equation. We thus arrive at a unitary analogue of the results of Damanik, Killip, and Lenz [“Uniform spectral properties of one-dimensional quasicrystals, III. α-continuity,” Commun. Math. Phys. 212, 191–204 (2000)] about the spectral measure of the discrete Schrödinger operator.
Highly durable superhydrophobic coatings with gradient density by movable spray method
Authors: Tenjimbayashi Mizuki , Shiratori Seimei
Published: September 2014

Superhydrophobic surface is expected to be applied in anti-fouling, anti-icing, and anti-bacterial. However, practical use is interrupted by low mechanical strength, time-consuming process, and limited coating substrate. Here highly durable superhydrophobic coatings were prepared by simple and novel spraying method, which sprays with changing the “spray distance between substrate and spray” (SD), named “movable spray method.” We prepared the solution that changes wettability and durability with spraying distance by mixing SiO2 nanoparticles and ethyl alpha cyanoacrylate polymer (EAC). Then, we evaluated the chemical components and surface morphologies of each spraying distance coatings (0 ∼ 50 cm) by XPS, SEM, and laser scanning microscope. It revealed that surface roughness and SiO2/EAC ratio increased as the SD increases. Thus, durable superhydrophobic coatings were designed by spraying with increasing SD gradually. Glow discharge-optical emission spectrometry analysis revealed that designed coatings showed the gradual increase of SiO2/EAC ratio. As a result, coatings prepared on glass, wood, or aluminum substrates maintained their superhydrophobicity up to the abrasion at 40 kPa. This movable spray method is simple coating by the wet process and prepares robust hydrophobic coating on complex shape and large area substrates. The gradient functional surface was found to have mechanical durability and superhydrophobicity, and wide area applications will be expected.
Equilibration of complexes of DNA and H-NS proteins on charged surfaces: A coarse-grained model point of view
Authors: Joyeux Marc
Published: September 2014

The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes, the precise structure of complexes of DNA and H-NS proteins is still not well understood. In particular, it is not clear whether the structure of DNA/H-NS complexes in the living cell is similar to that of complexes deposited on mica surfaces, which may be observed by AFM microscopy. A coarse-grained model, which helps getting more insight into this question, is described and analyzed in the present paper. This model is able of describing both the bridging of bacterial DNA by H-NS in the bulk and the deposition and equilibration of the complex on a charged surface. Simulations performed with the model reveal that a slight attraction between DNA and the charged surface is sufficient to let DNA/H-NS complexes reorganize from 3D coils to planar plasmids bridged by H-NS proteins similar to those observed by AFM microscopy. They furthermore highlight the antagonistic effects of the interactions between DNA and the surface. Indeed, increasing these interactions slows down the equilibration of naked plasmids on the surface but, on the other hand, enables a faster equilibration of DNA/H-NS complexes. Based on the distribution of the lifetimes of H-NS bridges and the time evolution of the number of trans-binding protein dimers during equilibration of the complexes on the surface, it is argued that the decrease of the equilibration time of the complex upon increase of the interaction strength between DNA and the surface is ascribable to the associated decrease of the probability to form new bridges between DNA and the proteins.
Uniaxial magnetic anisotropy induced low field anomalous anisotropic magnetoresistance in manganite thin films
Authors: Liao Zhaoliang , Huijben Mark , Koster Gertjan , Rijnders Guus
Published: September 2014

La2/3Sr1/3MnO3 films with uniaxial magnetic anisotropy were coherently grown on NdGaO3 (110) substrates. The uniaxial anisotropy has strong effect on magnetoresistance (MR). A positive MR was observed when the current is along magnetic easy axis under the current-field perpendicular geometry. In contrast, no positive MR is observed when current is along the magnetic hard axis regardless of the field direction. Our analysis indicates that the anomalous anisotropic MR effect arises from the uniaxial magnetic anisotropy caused stripe domains which contribute to strong anisotropic domain wall resistivity.
In situ preparation, electrical and surface analytical characterization of pentacene thin film transistors
Authors: Lassnig R. , Striedinger B. , Hollerer M. , Fian A. , Stadlober B. , Winkler A.
Published: September 2014

The fabrication of organic thin film transistors with highly reproducible characteristics presents a very challenging task. We have prepared and analyzed model pentacene thin film transistors under ultra-high vacuum conditions, employing surface analytical tools and methods. Intentionally contaminating the gold contacts and SiO2 channel area with carbon through repeated adsorption, dissociation, and desorption of pentacene proved to be very advantageous in the creation of devices with stable and reproducible parameters. We mainly focused on the device properties, such as mobility and threshold voltage, as a function of film morphology and preparation temperature. At 300 K, pentacene displays Stranski-Krastanov growth, whereas at 200 K fine-grained, layer-like film growth takes place, which predominantly influences the threshold voltage. Temperature dependent mobility measurements demonstrate good agreement with the established multiple trapping and release model, which in turn indicates a predominant concentration of shallow traps in the crystal grains and at the oxide-semiconductor interface. Mobility and threshold voltage measurements as a function of coverage reveal that up to four full monolayers contribute to the overall charge transport. A significant influence on the effective mobility also stems from the access resistance at the gold contact-semiconductor interface, which is again strongly influenced by the temperature dependent, characteristic film growth mode.
Manipulating surface diffusion and elastic interactions to obtain quantum dot multilayer arrangements over different length scales
Authors: Placidi E. , Arciprete F. , Latini V. , Latini S. , Magri R. , Scuderi M. , Nicotra G. , Patella F.
Published: September 2014

An innovative multilayer growth of InAs quantum dots on GaAs(100) is demonstrated to lead to self-aggregation of correlated quantum dot chains over mesoscopic distances. The fundamental idea is that at critical growth conditions is possible to drive the dot nucleation only at precise locations corresponding to the local minima of the Indium chemical potential. Differently from the known dot multilayers, where nucleation of new dots on top of the buried ones is driven by the surface strain originating from the dots below, here the spatial correlations and nucleation of additional dots are mostly dictated by a self-engineering of the surface occurring during the growth, close to the critical conditions for dot formation under the fixed oblique direction of the incoming As flux, that drives the In surface diffusion.
Decreased coherence and functional connectivity of electroencephalograph in Alzheimer's disease
Authors: Wang Ruofan , Wang Jiang , Yu Haitao , Wei Xile , Yang Chen , Deng Bin
Published: September 2014

In this paper, we investigate the abnormalities of electroencephalograph (EEG) signals in the Alzheimer's disease (AD) by analyzing 16-scalp electrodes EEG signals and make a comparison with the normal controls. Coherence is introduced to measure the pair-wise normalized linear synchrony and functional correlations between two EEG signals in different frequency domains, and graph analysis is further used to investigate the influence of AD on the functional connectivity of human brain. Data analysis results show that, compared with the control group, the pair-wise coherence of AD group is significantly decreased, especially for the theta and alpha frequency bands in the frontal and parieto-occipital regions. Furthermore, functional connectivity among different brain regions is reconstructed based on EEG, which exhibit obvious small-world properties. Graph analysis demonstrates that the local functional connections between regions for AD decrease. In addition, it is found that small-world properties of AD networks are largely weakened, by calculating its average path lengths, clustering coefficients, global efficiency, local efficiency, and small-worldness. The obtained results show that both pair-wise coherence and functional network can be taken as effective measures to distinguish AD patients from the normal, which may benefit our understanding of the disease.
Alternative p-doped hole transport material for low operating voltage and high efficiency organic light-emitting diodes
Authors: Murawski Caroline , Fuchs Cornelius , Hofmann Simone , Leo Karl , Gather Malte C.
Published: September 2014

We investigate the properties of N,N′-[(Diphenyl-N,N′-bis)9,9,-dimethyl-fluoren-2-yl]-benzidine (BF-DPB) as hole transport material (HTL) in organic light-emitting diodes (OLEDs) and compare BF-DPB to the commonly used HTLs N,N,N′,N′-tetrakis(4-methoxyphenyl)-benzidine (MeO-TPD), 2,2′,7,7′-tetrakis(N,N′-di-p-methylphenylamino)-9,9′-spirobifluorene (Spiro-TTB), and N,N′-di(naphtalene-1-yl)-N,N′-diphenylbenzidine (NPB). The influence of 2,2′-(perfluoronaphthalene-2,6-diylidene)dimalononitrile (F6-TCNNQ p-dopant) concentration in BF-DPB on the operation voltage and efficiency of red and green phosphorescent OLEDs is studied; best results are achieved at 4 wt. % doping. Without any light extraction structure, BF-DPB based red (green) OLEDs achieve a luminous efficacy of 35 .1 lm/W (74 .0 lm/W) at 1000 cd/m2 and reach a very high brightness of 10 000 cd/m2 at a very low voltage of 3.2 V (3.1 V). We attribute this exceptionally low driving voltage to the high ionization potential of BF-DPB which enables more efficient hole injection from BF-DPB to the adjacent electron blocking layer. The high efficiency and low driving voltage lead to a significantly lower luminous efficacy roll-off compared to the other compounds and render BF-DPB an excellent HTL material for highly efficient OLEDs.
Communication: A rotationally resolved (2OH) overtone band in the water dimer (H2O)2
Authors: Földes T. , Vanfleteren T. , Herman M.
Published: September 2014

Cw-CRDS spectra of water-rare gas supersonic expansions were recorded between 7229 and 7262 cm−1. The effective absorption pathlength was about 1 km in jet-cooled gas and the resolution about 1 × 10−4 cm−1. Many well-resolved structures are observed that could be assigned from experimental evidence to H2O-Ar/Kr bands. Eight broader unresolved features are more specifically reported and assigned to small H2O multimers, in good agreement and refining previous observations by Nizkorodov et al. [J. Chem. Phys. 122, 194316 (2005)]. Among these, the band at 7256.5 cm−1 is shown to be a Q branch of the water dimer with accompanying R and very weak P lines. The band is assigned to a Ka = 0 ← 1 transition and rotationally analyzed, leading to a restricted set of upper state rotational constants. The upper state lifetime (60 ± 3 ps) is extracted from the linewidths.
Electric-field-controlled interface strain coupling and non-volatile resistance switching of La1-xBaxMnO3 thin films epitaxially grown on relaxor-based ferroelectric single crystals
Authors: Zheng Ming , Zhu Qiu-Xiang , Li Xue-Yan , Yang Ming-Min , Wang Yu , Li Xiao-Min , Shi Xun , Luo Hao-Su , Zheng Ren-Kui
Published: September 2014

We have fabricated magnetoelectric heterostructures by growing ferromagnetic La1-xBaxMnO3 (x = 0.2, 0.4) thin films on (001)-, (110)-, and (111)-oriented 0.31Pb(In1/2Nb1/2)O3-0.35Pb(Mg1/3Nb1/2)O3-0.34PbTiO3 (PINT) ferroelectric single-crystal substrates. Upon poling along the [001], [110], or [111] crystal direction, the electric-field-induced non-180° domain switching gives rise to a decrease in the resistance and an enhancement of the metal-to-insulator transition temperature TC of the films. By taking advantage of the 180° ferroelectric domain switching, we identify that such changes in the resistance and TC are caused by domain switching-induced strain but not domain switching-induced accumulation or depletion of charge carriers at the interface. Further, we found that the domain switching-induced strain effects can be efficiently controlled by a magnetic field, mediated by the electronic phase separation. Moreover, we determined the evolution of the strength of the electronic phase separation against temperature and magnetic field by recording the strain-tunability of the resistance [(ΔR/R)strain] under magnetic fields. Additionally, opposing effects of domain switching-induced strain on ferromagnetism above and below 197 K for the La0.8Ba0.2MnO3 film and 150 K for the La0.6Ba0.4MnO3 film, respectively, were observed and explained by the magnetoelastic effect through adjusting the magnetic anisotropy. Finally, using the reversible ferroelastic domain switching of the PINT, we realized non-volatile resistance switching of the films at room temperature, implying potential applications of the magnetoelectric heterostructure in non-volatile memory devices.
Communication: Hartree-Fock description of excited states of H2
Authors: Barca Giuseppe M. J. , Gilbert Andrew T. B. , Gill Peter M. W.
Published: September 2014

Hartree-Fock (HF) theory is most often applied to study the electronic ground states of molecular systems. However, with the advent of numerical techniques for locating higher solutions of the self-consistent field equations, it is now possible to examine the extent to which such mean-field solutions are useful approximations to electronic excited states. In this Communication, we use the maximum overlap method to locate 11 low-energy solutions of the HF equation for the H2 molecule and we find that, with only one exception, these yield surprisingly accurate models for the low-lying excited states of this molecule. This finding suggests that the HF solutions could be useful first-order approximations for correlated excited state wavefunctions.
Effect of tensile strain on the electronic structure of Ge: A first-principles calculation
Authors: Liu Li , Zhang Miao , Hu Lijuan , Di Zengfeng , Zhao Shi-Jin
Published: September 2014

Taking the change of L-point conduction band valley degeneracy under strain into consideration, we investigate the effect of biaxially tensile strain (parallel to the (001), (110), and (111) planes) and uniaxially tensile strain (along the [001], [110], and [111] directions) on the electronic structure of Ge using density functional theory calculations. Our calculation shows that biaxial tension parallel to (001) is the most efficient way to transform Ge into a direct bandgap material among all tensile strains considered. [111]-tension is the best choice among all uniaxial approaches for an indirect- to direct-bandgap transition of Ge. The calculation results, which are further elaborated by bond-orbital approximation, provide a useful guidance on the optical applications of Ge through strain engineering.
Enhanced higher temperature (20–30 K) transport properties and irreversibility field in nano-Dy2O3 doped advanced internal Mg infiltration processed MgB2 composites
Authors: Li G. Z. , Sumption M. D. , Rindfleisch M. A. , Thong C. J. , Tomsic M. J. , Collings E. W.
Published: September 2014

A series of MgB2 superconducting composite strands co-doped with Dy2O3 and C was prepared via an advanced internal Mg infiltration (AIMI) route. The transport properties and MgB2 layer growth were studied in terms of the Dy2O3 doping level, reaction temperature, and reaction time. Transport studies showed that both critical current densities, Jcs, and irreversibility fields, Birrs, were increased with Dy2O3 doping. The highest layer Jc was 1.35 × 105 A/cm2 at 4.2 K, 10 T, 30% higher than that of the best AIMI wires without Dy2O3 doping. The highest “non-barrier” Jc reached 3.6 × 104 A/cm2 at 4.2 K, 10 T, which was among the best results reported so far. The improvements were even more pronounced at higher temperatures where the field at which the layer Jc reached 104 A/cm2 was pushed out by 0.9 T at 20 K, 1.2 T at 25 K, and 1.4 T at 30 K. While little or no enhancement in Birr was seen at 10 K and 15 K, the increases in Jc at higher temperatures were consistent with observed increases in Birr of 17% at 20 K, 44% at 25 K, and 400% at 30 K. Also, there were some indications that the reaction and layer growth of MgB2 were enhanced by Dy2O3 doping.
Direct real space observation of magneto-electronic inhomogeneity in ultra-thin film La0.5Sr0.5CoO3−δ on SrTiO3(001)
Authors: Kelly S. , Galli F. , Aarts J. , Bose Shameek , Sharma M. , Leighton C.
Published: September 2014

Recent magnetotransport and neutron scattering measurements implicate interfacial magneto-electronic phase separation as the origin of the degradation in transport and magnetism in ultra-thin film La1−xSrxCoO3 on SrTiO3(001). Here, using low temperature scanning tunneling microscopy and spectroscopy the first direct, real space observation of this nanoscopic electronic inhomogeneity is provided. Films of thickness 12.4 nm (32 unit cells) are found to exhibit spatially uniform conductance, in stark contrast to 4.7 nm (12 unit cell) films that display rich variations in conductance, and thus local density of states. The electronic heterogeneity occurs across a hierarchy of length scales (5–50 nm), with complex correlations with both topography and applied magnetic fields. These results thus provide a direct observation of magneto-electronic inhomogeneity in SrTiO3(001)/La0.5Sr0.5CoO3 at thicknesses below 6–7 nm, in good agreement with less direct techniques.
Highly conducting SrMoO3 thin films for microwave applications
Authors: Radetinac Aldin , Mani Arzhang , Melnyk Sergiy , Nikfalazar Mohammad , Ziegler Jürgen , Zheng Yuliang , Jakoby Rolf , Alff Lambert , Komissinskiy Philipp
Published: September 2014

We have measured the microwave resistance of highly conducting perovskite oxide SrMoO3 thin film coplanar waveguides. The epitaxial SrMoO3 thin films were grown by pulsed laser deposition and showed low mosaicity and smooth surfaces with a root mean square roughness below 0.3 nm. Layer-by-layer growth could be achieved for film thicknesses up to 400 nm as monitored by reflection high-energy electron diffraction and confirmed by X-ray diffraction. We obtained a constant microwave resistivity of 29 μΩ·cm between 0.1 and 20 GHz by refining the frequency dependence of the transmission coefficients. Our result shows that SrMoO3 is a viable candidate as a highly conducting electrode material for all-oxide microwave electronic devices.
Ablation enhancement of silicon by ultrashort double-pulse laser ablation
Authors: Zhao Xin , Shin Yung C.
Published: September 2014

In this study, the ultrashort double-pulse ablation of silicon is investigated. An atomistic simulation model is developed to analyze the underlying physics. It is revealed that the double-pulse ablation could significantly increase the ablation rate of silicon, compared with the single pulse ablation with the same total pulse energy, which is totally different from the case of metals. In the long pulse delay range (over 1 ps), the enhancement is caused by the metallic transition of melted silicon with the corresponding absorption efficiency. At ultrashort pulse delay (below 1 ps), the enhancement is due to the electron excitation by the first pulse. The enhancement only occurs at low and moderate laser fluence. The ablation is suppressed at high fluence due to the strong plasma shielding effect.
The use of reported speech and the perceived neutrality of court interpreters
Authors: Cheung Andrew K. F
Published: September 2014

A mock trial, with two-way consecutive interpreting between Cantonese and English, was used to test perceptions of a court interpreter’s neutrality when interpreting into Cantonese in reported rather than direct speech. Monolingual Cantonese speakers played the part of witnesses using the interpreter. Three groups were created: a control group (16 participants), receiving interpretation of all English utterances into Cantonese in direct speech; and two experimental groups (17 participants each). The experimental groups received interpretation with occasional switches to reported speech. These were introduced by third person pronouns (e.g., “he said”) for one group (the ‘pronoun group’), and by professional titles (e.g., “the judge said”) for the other group (the ‘title group’). Participants afterwards completed a questionnaire, assessing neutrality and alignment on a 5-point Likert scale. The title group not only perceived the interpreter to be aligned with the English speakers, but also gave a significantly different assessment of neutrality from the control group. The pronoun group perceived the interpreter to be aligned with them, but did not differ significantly from the control group in their perception of neutrality. Use of pronouns or professional titles in the reporting clauses thus affected the interpreter’s perceived neutrality differently.
What is special about orthographic processing?
Authors: Grainger Jonathan , Hannagan Thomas
Published: September 2014

Starting from a generic architecture for reading words in alphabetic scripts, we examine the special status of letters as the building block of single word reading. After briefly describing the overall architecture that defines the interaction between orthographic and phonological processes during silent reading for meaning, we then focus on orthographic processing. We describe the nature of orthographic representations as hypothesized in our approach and we discuss how such representations might be learned during reading acquisition. We present the hypothesis that such learning involves the adaptation of basic object identification mechanisms to the specific constraints of reading, and we provide examples of this adaptation. In the light of this, we then compare the function of letters as constituents of written words relative to the role of object parts in other kinds of familiar visual stimuli (e.g. faces, numbers). We explain why we think letters must have a special status and we provide some preliminary empirical evidence in favor of this special status for letters as parts of words. Keywords: reading; orthography; visual word recognition; orthographic learning; letter strings; object identification
Morphological spellings in English
Authors: Berg Kristian , Buchmann Franziska , Dybiec Katharina , Fuhrhop Nanna
Published: September 2014

Morphologically motivated spellings in English are usually thought to be restricted to cases like 〈electric – electrician – electricity〉, where the stem final letter 〈c〉 is kept constant in spelling although the corresponding phoneme varies in spoken language. However, there are many more – and fundamentally different – spellings that refer to morphological information. We will show this by systematically going through the three major parts of morphology: inflection, derivation, and compounding. In each area, we will identify spellings that can best be explained with reference to morphology. As a result, we will present an overview of formal and functional means of morphological spellings which goes far beyond the ubiquitous example cited above. Keywords: English; spelling; writing system; morphology; stem constancy
RAMONA: a Web application for gene set analysis on multilevel omics data
Authors: Sass Steffen , Buettner Florian , Mueller Nikola S. , Theis Fabian J.
Published: September 2014

Summary: Decreasing costs of modern high-throughput experiments allow for the simultaneous analysis of altered gene activity on various molecular levels. However, these multi-omics approaches lead to a large amount of data, which is hard to interpret for a non-bioinformatician. Here, we present the r emotely a ccessible m ultilevel on tology a nalysis (RAMONA). It offers an easy-to-use interface for the simultaneous gene set analysis of combined omics datasets and is an extension of the previously introduced MONA approach. RAMONA is based on a Bayesian enrichment method for the inference of overrepresented biological processes among given gene sets. Overrepresentation is quantified by interpretable term probabilities. It is able to handle data from various molecular levels, while in parallel coping with redundancies arising from gene set overlaps and related multiple testing problems. The comprehensive output of RAMONA is easy to interpret and thus allows for functional insight into the affected biological processes. With RAMONA, we provide an efficient implementation of the Bayesian inference problem such that ontologies consisting of thousands of terms can be processed in the order of seconds.

Availability and implementation: RAMONA is implemented as ASP.NET Web application and publicly available at http://icb.helmholtz-muenchen.de/ramona .

Contact:  fabian.theis@helmholtz-muenchen.de
Angiography for Management of Perioperative Myocardial Ischemia: Does it Have Any Role?
Authors: Narayan Pradeep , Bandyopadhyay Manujesh , Khan Mohammed Wasim , Sarkar Kunal
Published: September 2014

Objective

Perioperative myocardial ischemia (PMI) is a relatively rare but potentially fatal complication after coronary artery bypass grafting and is due to graft-related problems in a significant proportion of cases. The usual indicators of MI in the postoperative setting are unreliable and therefore have uncertain diagnostic value. Angiography, the criterion standard for preoperative angina, remains underused for evaluation of PMI. The aim of this study was to evaluate the role of angiography in the management of PMI.

Methods

Between January 2011 and September 2012, a total of 2312 isolated primary consecutive coronary artery bypass graft surgeries were performed, of which 2057 (89%) were carried out on the beating heart. Twenty-six (1.12%) of these patients needed perioperative angiography. The patients needing angiography were selected on the basis of a number of clinical, biochemical, and other diagnostic parameters

Results

Twenty-six patients with PMI required angiography, of which 18 (69 %) were found to have graft-related issues. The mean (SD) time between operation and angiography was 24.58 (6.71) hours. Of the 18 patients, 17 (94.44%) required surgical intervention and 1 patient was treated with angioplasty. There were 2 deaths (11.1%) in the group undergoing intervention. Angiographic findings included occluded vein graft (n = 7), narrowing of the left internal mammary artery (n = 3), and kinking or stretching of grafts (n = 8).

Conclusions

Angiography is useful in diagnosing graft-related problems in the perioperative period. In presence of signs of graft compromise, we suggest that having a low threshold for angiographic graft evaluation may be beneficial in a carefully selected subset of patients after coronary artery bypass.
Off-Pump Tricuspid Valved Stent Implantation: Real-Time Three-Dimensional Transesophageal Echocardiography for Guidance and Assessment
Authors: Pokorny Saskia , Huenges Katharina , Gundlach Jan-Paul , Frank Derk , Groß Justus , Cremer Jochen , Lutter Georg
Published: September 2014

In this case report, the value of real-time three-dimensional transesophageal echocardiography (TEE) for guidance and assessment of orthotopic tricuspid valved stent implantation in the beating heart is assessed in four pigs. A full two-dimensional TEE evaluation of standardized parameters was conducted. Three-dimensional TEE provided dependable imaging of anatomical structures of the right side of the heart, the delivery system, and the valved stent, allowing easier orientation and more accurate views for the surgical team. Although visualization of the tricuspid valve in the porcine model is challenging, it contributed highly to the successful implantation of the tricuspid valved stent.
Midterm Outcomes after Transcatheter Aortic Valve Implantation
Authors: Lotfi Shahram , Dohmen Guido , Götzenich Andreas , Haushofer Marcus , Spillner Jan Wilhelm , Autschbach Rüdiger , Hoffmann Rainer
Published: September 2014

Objective

Transcatheter aortic valve implantation (TAVI) has become a therapeutic option for high-risk or nonoperable patients with severe symptomatic aortic valve stenosis. The best known and most frequently implanted prostheses are the CoreValve and SAPIEN prostheses. We report our experiences and analyze the results of our TAVI program.

Methods

A total of 357 patients underwent transfemoral (TF) and transapical (TA) TAVI in our center between January 2008 and October 2012. The procedure was performed in 190 patients with CoreValve, in 155 patients with SAPIEN, and in 12 patients with ACURATE TA prostheses. Transfemoral access was used in 190 patients. In 167 patients, TA access was used. The mean age was 80.2 ± 6.4 years. All patients were nonoperable or had a high risk for a conventional aortic valve replacement. The mean logistic EuroSCORE I was 25.92 ± 14.51%. The TF/CoreValve (190 patients) and TA/SAPIEN (155 patients) groups showed significant difference in the patients’ mean age (81.7 ± 6.3 years vs. 79.5 ± 6.6 years, P = 0.002) and in mean logistic EuroSCORE I (22.16 ± 13.05% vs. 31.04 ± 16.40, P < 0.001).

Results

The overall 30-day mortality (357 patients) was 9.80% (TF, 8.42%; TA, 11.37%); overall 1-year mortality (275 patients), 21.45% (TF, 23.74%; TA, 19.12%); overall 2-year mortality (199 patients), 29.15% (TF, 35.96%; TA, 23.64%); overall 3-year mortality (133 patients), 37.59% (TF, 43.86%; TA, 32.89%); and overall 4-year mortality (38 patients), 39.47% (TF, 45%; TA, 33.33%). The rate of pacemaker implantation after TAVI was significantly higher in the CoreValve group than in the SAPIEN group: 44.74% (85/190 patients) versus 6.45% (10/155 patients), P < 0.001. Stroke rate was higher in the TF-CoreValve group than in the TA-SAPIEN group: 4.21% versus 0.64%, P = 0.045.

Conclusions

Outcomes after TAVI were, in our population of nonoperable and high-risk patients, encouraging. The differences in midterm outcomes between the TF-CoreValve TAVI and the TA-SAPIEN TAVI were not significant.
Brucella papionis sp. nov., isolated from baboons (Papio spp.)
Authors: Whatmore Adrian M. , Davison Nicholas , Cloeckaert Axel , Al Dahouk Sascha , Zygmunt Michel S. , Brew Simon D. , Perrett Lorraine L. , Koylass Mark S. , Vergnaud Gilles , Quance Christine , Scholz Holger C. , Dick Edward J. , Hubbard Gene , Schlabritz-Loutsevitch Natalia E.
Published: September 2014

Two Gram-negative, non-motile, non-spore-forming coccoid bacteria (strains F8/08-60T and F8/08-61) isolated from clinical specimens obtained from baboons (Papio spp.) that had delivered stillborn offspring were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA gene sequence similarities, both strains, which possessed identical sequences, were assigned to the genus

Brucella

. This placement was confirmed by extended multilocus sequence analysis (MLSA), where both strains possessed identical sequences, and whole-genome sequencing of a representative isolate. All of the above analyses suggested that the two strains represent a novel lineage within the genus

Brucella

. The strains also possessed a unique profile when subjected to the phenotyping approach classically used to separate species of the genus

Brucella,
reacting only with Brucella A monospecific antiserum, being sensitive to the dyes thionin and fuchsin, being lysed by bacteriophage Wb, Bk2 and Fi phage at routine test dilution (RTD) but only partially sensitive to bacteriophage Tb, and with no requirement for CO2 and no production of H2S but strong urease activity. Biochemical profiling revealed a pattern of enzyme activity and metabolic capabilities distinct from existing species of the genus

Brucella

. Molecular analysis of the omp2 locus genes showed that both strains had a novel combination of two highly similar omp2b gene copies. The two strains shared a unique fingerprint profile of the multiple-copy Brucella-specific element IS711. Like MLSA, a multilocus variable number of tandem repeat analysis (MLVA) showed that the isolates clustered together very closely, but represent a distinct group within the genus

Brucella

. Isolates F8/08-60T and F8/08-61 could be distinguished clearly from all known species of the genus

Brucella

and their biovars by both phenotypic and molecular properties. Therefore, by applying the species concept for the genus

Brucella

suggested by the ICSP Subcommittee on the Taxonomy of Brucella, they represent a novel species within the genus

Brucella

, for which the name Brucella papionis sp. nov. is proposed, with the type strain F8/08-60T ( = NCTC 13660T = CIRMBP 0958T).
Origins and impacts of new mammalian exons
Authors: Merkin Jason , Chen Ping , Alexis Maria , Hautaniemi Sampsa , Burge Christopher B.
Published: September 2014

Mammalian genes are composed of exons, but the evolutionary origins and functions of new internal exons are poorly understood. Here, we analyzed patterns of exon gain using deep cDNA sequencing data from five mammals and one bird, identifying thousands of species- and lineage-specific exons. Most new exons derived from unique rather than repetitive intronic sequence. Unlike exons conserved across mammals, species-specific internal exons were mostly located in 5′ untranslated regions and alternatively spliced. They were associated with upstream intronic deletions, increased nucleosome occupancy, and RNA polymerase II pausing. Genes containing new internal exons had increased gene expression, but only in tissues where the exon was included. Increased expression correlated with level of exon inclusion, promoter proximity, and signatures of cotranscriptional splicing. Together these findings suggest that splicing at the 5′ ends of genes enhances expression and that changes in 5′ end splicing alter gene expression between tissues and between species.
Pinwheel-dipole configuration in cat early visual cortex
Authors: Ribot Jérôme , Romagnoni Alberto , Milleret Chantal , Bennequin Daniel , Touboul Jonathan
Published: September 2014

In the early visual cortex, information is processed within functional maps whose layouts are thought to underlie visual perception. However, the precise organization of these functional maps as well as their interrelationships remains largely unknown. Here, we show that spatial frequency representation in cat early visual cortex exhibits singularities around which the map organizes like an electric dipole potential. These singularities are precisely co-located with singularities of the orientation map: the pinwheel centers. To show this, we used high resolution intrinsic optical imaging in cat areas 17 and 18. First, we show that a majority of pinwheel centers exhibit in their neighborhood both semi-global maximum and minimum in the spatial frequency map, contradicting pioneering studies suggesting that pinwheel centers are placed at the locus of a single spatial frequency extremum. Based on an analogy with electromagnetism, we proposed a mathematical model for a dipolar structure, accurately fitting optical imaging data. We conclude that a majority of orientation pinwheel centers form spatial frequency dipoles in cat early visual cortex. Given the functional specificities of neurons at singularities in the visual cortex, it is argued that the dipolar organization of spatial frequency around pinwheel centers could be fundamental for visual processing.

ABBREVIATIONS

OR

Orientation

SF

Spatial frequency

PC

Pinwheel center

A17

Area 17

A18

Area 18
Self-fertilization and 1 inbreeding limit the scope for sexual antagonism
Authors: Tazzyman Samuel J. , Abbott Jessica K.
Published: September 2014

Sexual antagonism occurs when there is a positive intersexual genetic correlation in trait expression but opposite fitness effects of the trait(s) in males and females. As such, it constrains the evolution of sexual dimorphism and may therefore have implications for adaptive evolution. There is currently considerable evidence for the existence of sexually antagonistic genetic variation in laboratory and natural populations, but how sexual antagonism interacts with other evolutionary phenomena is still poorly understood in many cases. Here we explore how self-fertilization and inbreeding affect the maintenance of polymorphism for sexually antagonistic loci. We expecteda priorithat selfing should reduce the region of polymorphism, since inbreeding reduces the frequency of heterozygotes and speeds fixation. Although this expectation was supported, our results show that there is an interactive effect between the degree of selfing and dominance such that those segregating sexually antagonistic loci that do exist are more likely to be partially dominant. In addition, inbreeding effects may influence population persistence and genomic location of sexually antagonistic loci in separate-sexed organisms.
DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly
Authors: Scheinin Ilari , Sie Daoud , Bengtsson Henrik , van de Wiel Mark A. , Olshen Adam B. , van Thuijl Hinke F. , van Essen Hendrik F. , Eijk Paul P. , Rustenburg François , Meijer Gerrit A. , Reijneveld Jaap C. , Wesseling Pieter , Pinkel Daniel , Albertson Donna G. , Ylstra Bauke
Published: September 2014

Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with ∼0.1× genome coverage. We improve on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions was previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1000 samples, most of which were obtained from the fixed tissue archives of more than 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost.
Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles
Authors: Nandi Tannistha , Holden Matthew T.G. , Didelot Xavier , Mehershahi Kurosh , Boddey Justin A. , Beacham Ifor , Peak Ian , Harting John , Baybayan Primo , Guo Yan , Wang Susana , How Lee Chee , Sim Bernice , Essex-Lopresti Angela , Sarkar-Tyson Mitali , Nelson Michelle , Smither Sophie , Ong Catherine , Aw Lay Tin , Hoon Chua Hui , Michell Stephen , Studholme David J. , Titball Richard , Chen Swaine L. , Parkhill Julian , Tan Patrick
Published: September 2014

Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental strains from a restricted Asian locale. Whole-genome phylogenies resolved multiple genomic clades of Bp, largely congruent with multilocus sequence typing (MLST). We discovered widespread recombination in the Bp core genome, involving hundreds of regions associated with multiple haplotypes. Highly recombinant regions exhibited functional enrichments that may contribute to virulence. We observed clade-specific patterns of recombination and accessory gene exchange, and provide evidence that this is likely due to ongoing recombination between clade members. Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms restricting gene flow between clades. Interrogation of accessory elements revealed that each clade harbored a distinct complement of restriction-modification (RM) systems, predicted to cause clade-specific patterns of DNA methylation. Using methylome sequencing, we confirmed that representative strains from separate clades indeed exhibit distinct methylation profiles. Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit uptake of non-self DNA. Our data suggest that RM systems borne on mobile elements, besides preventing foreign DNA invasion, may also contribute to limiting exchanges of genetic material between individuals of the same species. Genomic clades may thus represent functional units of genetic isolation in Bp, modulating intraspecies genetic diversity.
Crystal structure of 4-chloro-2-[(5-ethoxy-1,3,4-thiadiazol-2-yl)methyl]-5-(piperidin-1-yl)pyridazin-3(2H)-one
Authors: Li Hongsen , Ren Xinfeng , Li Ya , Zhao Linjing
Published: September 2014

In the title molecule, C14H18ClN5O2S, the six atoms of the 1,6-dihydropyridazine ring are essentially coplanar (r.m.s. deviation = 0.008 Å), and the dihedral angle between this and the 1,3,4-thiadiazole ring is 62.06 (10)°. In the crystal, centrosymmetrically related molecules are linked by intermolecular C—H—O hydrogen bonding to form a supramolecular dimer. The terminal ethyl group is statistically disordered over two positions.
Crystal structure of tris(ethylenediammonium) hexasulfatopraseodymium(III) hexahydrate
Authors: Held Peter
Published: September 2014

In the title salt, (C2H10N2)3[Pr2(SO4)6]·6H2O, the PrIIIcation is surrounded ninefold by five sulfate groups (two monodentate and three chelating) and by one water molecule [range of Pr—O bond lengths 2.383 (3) to 2.582 (3) Å]. The [Pr(SO4)5(H2O)] groups are arranged in sheets parallel to (010). Two crystal water molecules and two ethylenediammonium cations (one with point group symmetry -1) connect the sheetsviaO—H...O and N—H...O hydrogen bonds from weak up to medium strength into a three-dimensional framework structure.