bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrical conductivity of Sr2−xVMoO6−y (x = 0.0, 0.1, 0.2) double perovskites
Authors: Childs Nicholas B. , Weisenstein Adam , Smith Richard , Sofie Stephen , Key Camas
Published: June 2013

Electrical conductivity of Sr2-xVMoO6-y (x = 0.0, 0.1, 0.2) double perovskites has been investigated in a reducing atmosphere at temperatures up to 800 °C. This material has a key application in solid oxide fuel cell anodes as a mixed ion and electron conductor. A solid state synthesis technique was used to fabricate materials and crystal structure was verified through x-ray diffraction. Subsequent to conventional sintering in a reducing environment, elemental valence states were indentified through x-ray photoemission spectroscopy on the double perovskite material before and after annealing in a hydrogen environment. Samples exhibited metallic like conduction with electrical conductivities of 1250 S/cm (Sr2VMoO6-y′), 2530 S/cm (Sr1.8VMoO6-y″), and 3610 S/cm (Sr1.9VMoO6-y‴) at 800 °C in 5% H2/95% N2, with a substantial increase in conductivity upon cooling to room temperature. Room temperature electrical conductivity values for Sr1.9VMoO6-y‴ make it a candidate as the highest electrically conductive oxide known. Highly insulating secondary surface phases, Sr3V2O8, and SrMoO4, begin to reduce at 400 °C in a hydrogen environment, as confirmed by X-ray photoemission and thermal gravimetric analysis. This reduction, from V5+ and Mo6+ to lower valence states, leads to a large increase in sample electrical conductivity.
Investigation of ripple-limited low-field mobility in large-scale graphene nanoribbons
Authors: Luisier M. , Boykin T. B. , Ye Z. , Martini A. , Klimeck G. , Kharche N. , Jiang X. , Nayak S.
Published: June 2013

Combining molecular dynamics and quantum transport simulations, we study the degradation of mobility in graphene nanoribbons caused by substrate-induced ripples. First, the atom coordinates of large-scale structures are relaxed such that surface properties are consistent with those of graphene on a substrate. Then, the electron current and low-field mobility of the resulting non-flat nanoribbons are calculated within the Non-equilibrium Green's Function formalism in the coherent transport limit. An accurate tight-binding basis coupling the σ- and π-bands of graphene is used for this purpose. It is found that the presence of ripples decreases the mobility of graphene nanoribbons on SiO2 below 3000 cm2/Vs, which is comparable to experimentally reported values.
Buoyancy storms in a zonal stream on the polar beta-plane: Experiments with altimetry
Authors: Sui Y. , Afanasyev Y. D.
Published: June 2013

Results from a new series of experiments on flows generated by localized heating in the presence of a background zonal current on the polar β-plane are presented. The flow induced by a heater without the background zonal flow is in the form of a β-plume. Zonal jets of alternating directions are formed within the plume. The westward transport velocity in the plume is proportional to the upwelling velocity above the heater in agreement with linear theory. When the background flow in the form of the eastward zonal current is present, the β-plume can be overwhelmed by the eastward current. The main control parameters of the experiment are the strength of the heater and strength of the sink which is used to create the background flow. The regime diagram shows the area where a β-plume can exist in the parameter space. The critical value of the velocity of the zonal flow below which the β-plume can exist is obtained by considering barotropic Rossby waves emitted by the baroclinic eddies in the heated area.
Laser direct patterning of a reduced-graphene oxide transparent circuit on a graphene oxide thin film
Authors: Yung K. C. , Liem H. , Choy H. S. , Chen Z. C. , Cheng K. H. , Cai Z. X.
Published: June 2013

In this study, reduced-graphene oxide (GO) circuits were directly patterned on glass using an industrially available excimer laser system. A threshold of laser energy density was observed, which provided a clear differentiation on whether the GO was reduced. A sharp drop of resistance by a factor of 104 was measured as the laser energy density increased from 65 to 75 mJ/cm2. The highest conductivity measured was ∼1.33 × 104 S/m, which is among the best reported in the literature for any laser reduction method. Raman analysis of the excimer laser-reduced GO film revealed the formation of a prominent 2D peak at 2700 cm−1. The relative signal strength between the Raman D and G peaks suggests that the amount of structural disorder in the reduced GO is insignificant. The reduced GO displays a transmittance greater than 80% across the entire range from 450 to 800 nm. The outstanding electrical, optical, and morphological properties have enabled graphene to display promising applications, and this nano-processing method makes graphene even more attractive when used as a transparent electrode for touch screens and in many more applications.
In situ atomic layer deposition study of HfO2 growth on NH4OH and atomic hydrogen treated Al0.25Ga0.75N
Authors: Qin Xiaoye , Brennan Barry , Dong Hong , Kim Jiyoung , Hinkle Christopher L. , Wallace Robert M.
Published: June 2013

The atomic layer deposition (ALD) of HfO2 on the native oxide, NH4OH, and atomic hydrogen treated Al0.25Ga0.75N surface was studied using in situ X-ray photoelectron spectroscopy (XPS), after each individual “half cycle” of the ALD process. During the deposition process, minimal change in the chemical states of Ga and Al is detected, with no evidence of interfacial oxide generation. The initial HfO2 growth rate on the native oxide Al0.25Ga0.75N surface is very low, however, exposure of the Al0.25Ga0.75N surface to atomic hydrogen decreases the concentration of carbon and oxygen and enhances the HfO2 growth rate.
Dielectric properties and phase transitions of [001], [110], and [111] oriented Pb(Zn1/3Nb2/3)O3-6%PbTiO3 single crystals
Authors: Amin Hentati Mouhamed , Dammak Hichem , Khemakhem Hamadi , Pham Thi Mai
Published: June 2013

Phase transformations of [001], [110], and [111] oriented Pb(Zn1/3Nb2/3)O3-6%PbTiO3 (PZN-6%PT) single crystals have been investigated by means of dielectric permittivity and loss, x-ray diffraction and depolarization current as function of temperature (from 250 to 500 K). The unpoled samples undergo R-T-C phase transition sequence during zero field heating (ZFH), where R, T, and C are rhombohedral, tetragonal, and cubic phases, respectively. Under electric field (0.5 kV/cm), an intermediate orthorhombic (O) phase is induced between the T and R phases in the field cooling (FC) process. This phase reappears during subsequent zero field heating of the poled sample (zero field heating after field cooling: ZFHaFC). The existence range of this O phase depends on both the crystal orientation and the measurement conditions (FC or ZFHaFC). Finally, for the [001] direction, it was found that the piezoelectric activity of the intermediate phase is the highest.
Molecular dynamics investigation of the thermomechanical behavior of monolayer GaN
Authors: Sarma J. V. N. , Chowdhury Rajib , Jayaganthan R.
Published: June 2013

Molecular dynamics simulations are performed on monolayer gallium nitride to study their mechanical behavior at various temperatures in the range of 10 to 1700 K. The transition from brittle to ductile nature has been illustrated from the evolution of fracture at two different temperatures of 700 and 1300 K. Brittle to ductile transition temperatures TBDT are obtained from the plots of logarithm of yield stress and inverse temperature at different strain rates and compared qualitatively with the same system in the presence of single and diatomic vacancies. Logarithm of strain rate against inverse of TBDT thus obtained represents an Arrhenius plot, the slope of which corresponds to the activation energy of dislocation glide that is found to be approximately 2.0 ± 0.05 eV for the present case. This suggests that the brittle to ductile transition is controlled by the dislocation mobility as in the case of other semiconductors like silicon and germanium. This behavior is found to be consistent with the presented underlying models. In addition, thermal conductivities are obtained over a temperature range of 300 to 2000 K from the equilibrium Green-Kubo formulations and compared with the (25,0) nanotube that is generated from the same system of monolayer GaN. The values are found to be decreased in both the cases as compared to the bulk gallium nitride, and the reduction in the values of thermal conductivity can be attributed to the finite size effects, increased surface inelastic scattering, and change of phonon spectrum at low dimensions, respectively.
Field-accelerated structural relaxation in the amorphous state of phase change memory
Authors: Fantini P. , Ferro M. , Calderoni A.
Published: June 2013

This work shows the experimental evidence of the acceleration of the resistance drift phenomenon over time by means of a constant bias applied to a phase change memory cell programmed in the amorphous state. The experimental findings, highlighting the role of electric field in the drift phenomenon, are supported by a bias-controlled kinetic model describing the amorphous network in terms of many two-level systems evolving over time to lower its own total system energy.
Phase transition and electric field induced strain properties in Sm modified lead zirconate stannate titanate based antiferroelectric ceramics
Authors: Zhang Qingfeng , Yang Tongqing , Zhang Yangyang , Yao Xi
Published: June 2013

The effect of Sm addition on the crystal structures and electrical properties of Pb1−3x/2Smx(Zr0.63Sn0.26Ti0.11)O3 ceramics were investigated in this work. X-ray diffraction analysis showed that with increasing Sm content from 0.005 to 0.03, the phase structure of the specimens underwent transition from ferroelectric (FE) to antiferroelectric (AFE) state due to the substitution of Sm3+ with smaller ion radius for Pb2+ decreasing the tolerance factor of the ceramics. In addition, it was observed that with the improvement of Sm3+ content, the strain of the specimens first increased and then decreased, and the largest value of 0.735% was obtained in the sample with x = 0.015 near AFE/FE phase boundary at the measuring frequency 1 Hz. This is because the reversal of the domains, which produces the strain, is more consummate in this composition. Further, the strain at different frequencies was nearly the same at high electric field, which was attributed to that the electric field applied to the sample was so large that the reorientation of the domains could finish in all measuring frequencies. Both a high strain level and a relatively good frequency stability in the specimen with x = 0.015 make a potential candidate for actuators applications over a wide-frequency working range.
Villain's fractal growth of poly[1-[4-(3-carboxy-4-hydroxyphenylazo) benzenesulfonamido]-1,2-ethanediyl, sodium salt] J-aggregates onto layer-by-layer films and its effect on film absorbance spectrum
Authors: Ferreira Quirina , António Ribeiro Paulo , Raposo Maria
Published: June 2013

Morphology of poly(allylamine hydrochloride) and poly[1-[4-(3-carboxy-4-hydroxyphenylazo) benzenesulfonamido]-1,2-ethanediyl, sodium salt] (PAZO) layer-by-layer (LBL) films is shown to influence the orientation of PAZO chromophores with respect to solid support surface, which in turn is related with observed red-shifts changes of the chromophore absorbance peak position relative to that of solution spectrum, as the bilayers are being deposited. For the first bilayers, an increase of red shift values is observed, while roughness and grain radius are kept practically constant; after the 5th bilayer, the red-shift values decrease, while grain sizes increase and the number of grains decreases. This behavior is consistent with adsorption of coiled PAZO molecules, treated as pseudo-particles, with the chromophores head-to-head oriented-J aggregates. These aggregates adsorb perpendicularly to the substrate surface for the first layers and, as roughness and grain radius increase, the adsorption of the J aggregates takes place parallel to the solid support surface, which gives rise to a decrease in the red shift value. Moreover, the adsorption of these pseudo-particles follows a fractal growth characterized by a scaling exponent of α = 0.80 ± 0.02 and a temporal growth exponent of β = 0.17 ± 0.02. These values suggest a layer growth according with Villain model, which accounts for the interactions between deposited particles and the surface. This is in accordance with the electrostatic forces driving LbL film formation and accounts for the observed morphology behavior for the different number of layers.
Tuning the effective refractive index of a thin air gap region sandwiched by metallic metamaterials by lateral displacements
Authors: Akiyama Koichi , Shibuya Kyoji , Takano Keisuke , Abe Yuji , Tokuda Yasunori , Hangyo Masanori
Published: June 2013

We theoretically and experimentally investigate the terahertz transmission of two metallic slabs with periodic cut-through slit arrays. It is revealed that the air gap region between the metallic slabs can be modeled as a medium with an effective refractive index depending on the slab arrangement, that is, depending on the vertical distance and the lateral displacement between the slabs. This property is interpreted in terms of the optical length of the electromagnetic waves propagating in the narrow slit between the two slabs. The result provides a new guide for designing the structure of metallic slab systems.
The transition mechanism from a symmetric single period discharge to a period-doubling discharge in atmospheric helium dielectric-barrier discharge
Authors: Zhang Dingzong , Wang Yanhui , Wang Dezhen
Published: June 2013

Period-doubling and chaos phenomenon have been frequently observed in atmospheric-pressure dielectric-barrier discharges. However, how a normal single period discharge bifurcates into period-doubling state is still unclear. In this paper, by changing the driving frequency, we study numerically the transition mechanisms from a normal single period discharge to a period-doubling state using a one-dimensional self-consistent fluid model. The results show that before a discharge bifurcates into a period-doubling state, it first deviates from its normal operation and transforms into an asymmetric single period discharge mode. Then the weaker discharge in this asymmetric discharge will be enhanced gradually with increasing of the frequency until it makes the subsequent discharge weaken and results in the discharge entering a period-doubling state. In the whole transition process, the spatial distribution of the charged particle density and the electric field plays a definitive role. The conclusions are further confirmed by changing the gap width and the amplitude of the applied voltage.
Lattice Boltzmann numerical simulation and experimental research of dynamic flow in an expansion-contraction microchannel
Authors: Jiang Di , Sun Dongke , Xiang Nan , Chen Ke , Yi Hong , Ni Zhonghua
Published: June 2013

This paper applies the lattice Boltzmann method (LBM) to a 3D simulation of micro flows in an expansion-contraction microchannel. We investigate the flow field under various inlet flow rates and cavity structures, and then systematically study the flow features of the vortex and Dean flow in this channel. Vortex formation analysis demonstrates that there is no observable vortex generated when the inlet flow rate is low enough. As the inlet flow rate increases, a small vortex first appears near the inlet, and then this vortex region will keep expanding until it fully occupies the cavity. A smaller cavity width may result in a larger vortex but the vortex is less influenced by cavity length. The Dean flow features at the outlet become more apparent with increasing inlet flow rate and more recirculation regions can be observed in the cross-section under over high inlet flow rate. In order to support the simulation results, some experimental processes are conducted successfully. It validates that the applied model can accurately characterize the flow in the microchannel. Results of simulations and experiments in this paper provide insights into the design and operation of microfluidic systems for particle/cell manipulation.
Optical and magnetic properties of porous anodic alumina/Ni nanocomposite films
Authors: Zhang Jing-Jing , Li Zi-Yue , Zhang Zhi-Jun , Wu Tian-Shan , Sun Hui-Yuan
Published: June 2013

A simple method to tune the optical properties of porous anodic alumina (PAA) films embedded with Ni is reported. The films display highly saturated colors after being synthesized by an ac electrodeposition method. The optical properties of the samples can be effectively tuned by varying the oxidation time of aluminum. The ultrashort Ni nanowires (100 nm long and 50 nm in diameter) present only fcc phase and show no apparent averaged effective magnetic anisotropy. The coercivity mechanism of the Ni nanowires in our case is consistent with fanning mechanism based on a chain-of-spheres model. PAA/Ni films with structural color and magnetic properties have friability-resistant feature and can be used in many areas, including decoration, display, and multifunctional anti-counterfeiting technology.
Spin torque on the surface of graphene in the presence of spin orbit splitting
Authors: Chen Ji , Jalil Mansoor Bin Abdul , Tan Seng Ghee
Published: June 2013

We study theoretically the spin transfer torque of a ferromagnetic layer coupled to (deposited onto) a graphene surface in the presence of the Rashba spin orbit coupling (RSOC). We show that the RSOC induces an effective magnetic field, which will result in the spin precession of conduction electrons. We derive correspondingly the generalized Landau-Lifshitz-Gilbert (LLG) equation, which describes the precessional motion of local magnetization under the influence of the spin orbit effect. Our theoretical estimate indicates that the spin orbit spin torque may have significant effect on the magnetization dynamics of the ferromagnetic layer coupled to the graphene surface.
Regulation of anionic lipids in binary membrane upon the adsorption of polyelectrolyte: A Monte Carlo simulation
Authors: Duan Xiaozheng , Li Yunqi , Zhang Ran , Shi Tongfei , An Lijia , Huang Qingrong
Published: June 2013

We employ Monte Carlo simulations to investigate the interaction between an adsorbing linear flexible cationic polyelectrolyte and a binary fluid membrane. The membrane contains neutral phosphatidyl–choline, PC) and multivalent anionic (phosphatidylinositol, PIP2) lipids. We systematically study the influences of the solution ionic strength, the chain length and the bead charge density of the polyelectrolyte on the lateral rearrangement and the restricted mobility of the multivalent anionic lipids in the membrane. Our findings show that, the cooperativity effect and the electrostatic interaction of the polyelectrolyte beads can significantly affect the segregation extent and the concentration gradients of the PIP2 molecules, and further cooperate to induce the complicated hierarchical mobility behaviors of PIP2 molecules. In addition, when the polyelectrolyte brings a large amount of charges, it can form a robust electrostatic well to trap all PIP2 and results in local overcharge of the membrane. This work presents a mechanism to explain the membrane heterogeneity formation induced by the adsorption of charged macromolecule.
Coarse wavelength division (de)multiplexer using an interleaved angled multimode interferometer structure
Authors: Hu Y. , Gardes F. Y. , Thomson D. J. , Mashanovich G. Z. , Reed G. T.
Published: June 2013

We have demonstrated a coarse wavelength (de)multiplexing structure on the silicon-on-insulator platform. It comprises two 4-channel angled multimode interferometers interleaved with an imbalanced Mach-Zehnder interferometer (MZI) leading to an 8-channel multiplexing device. The device requires only single lithography and etching steps for fabrication and has a good tolerance to fabrication errors in terms of waveguide width. The insertion loss and crosstalk achieved are 3-4 dB and –(15–20) dB, respectively. Potential is shown for achieving improved performance using larger waveguide bending radii in the MZI arms and/or (a) local heater(s) for refractive index tuning.
Characterization of GaN microstructures grown by plasma-assisted molecular beam epitaxy
Authors: Lo Ikai , Pang Wen-Yuan , Chen Wen-Yen , Hsu Yu-Chi , Hsieh Chia-Ho , Shih Cheng-Hung , Chou Mitch M. C. , Hsu Tzu-Min , Hsu Gary Z. L.
Published: June 2013

The characterization of GaN microstructures grown by plasma-assisted molecular beam epitaxy on LiAlO2 substrate was studied by cathodoluminescence and photoluminescence measurements. We demonstrated that the cathodoluminescence from oblique semi-polar surfaces of mushroom-shaped GaN was much brighter than that from top polar surface due to the reduction of polarization field on the oblique semi-polar surfaces. It implies that the oblique semi-polar surface is superior for the light-emitting surface of wurtzite nano-devices.
Resonant magnetoelectric response of cantilevers with magnetostrictive and piezoelectric layers on opposite sides of the substrate
Authors: Krantz Matthias C. , Gugat Jascha L. , Gerken Martina
Published: June 2013

A theory is derived for the bending-mode magnetoelectric coefficients at resonance for magnetostrictive and piezoelectric layers on opposite sides of a substrate. Results are given for the transverse ME coefficient in the Metglas-Si-AlN system with magnetic field excitation parallel and electric polarization perpendicular to the cantilever. The center-substrate layer sequence is found to produce about 50 % enhancement of the magnetoelectric effect compared to magnetoelectric bilayers on one side of a substrate. Up to about 10 % additional enhancement of the ME effect is predicted if the magnetostrictive and piezoelectric layers are separated from the substrate by spacer layers with lower Youngs modulus. Lowest order bending mode resonance frequencies are given.
Structure of NKp65 bound to its keratinocyte ligand reveals basis for genetically linked recognition in natural killer gene complex
Authors: Li Yili , Wang Qian , Chen Sharon , Brown Patrick H. , Mariuzza Roy A.
Published: June 2013

The natural killer (NK) gene complex (NKC) encodes numerous C-type lectin-like receptors that govern the activity of NK cells. Although some of these receptors (Ly49s, NKG2D, CD94/NKG2A) recognize MHC or MHC-like molecules, others (Nkrp1, NKRP1A, NKp80, NKp65) instead bind C-type lectin-like ligands to which they are genetically linked in the NKC. To understand the basis for this recognition, we determined the structure of human NKp65, an activating receptor implicated in the immunosurveillance of skin, bound to its NKC-encoded ligand keratinocyte-associated C-type lectin (KACL). Whereas KACL forms a homodimer resembling other C-type lectin-like dimers, NKp65 is monomeric. The binding mode in the NKp65–KACL complex, in which a monomeric receptor engages a dimeric ligand, is completely distinct from those used by Ly49s, NKG2D, or CD94/NKG2A. The structure explains the exceptionally high affinity of the NKp65–KACL interaction compared with other cell–cell interaction pairs (
K
D
= 6.7 × 10
−10
M), which may compensate for the monomeric nature of NKp65 to achieve cell activation. This previously unreported structure of an NKC-encoded receptor–ligand complex, coupled with mutational analysis of the interface, establishes a docking template that is directly applicable to other genetically linked pairs in the NKC, including Nkrp1–Clr, NKRP1A–LLT1, and NKp80–AICL.
Empowerment as Contested Terrain
Authors: Pruijt Hans , Yerkes Mara A.
Published: June 2013

Sociological analysis has mainly portrayed empowerment as a manipulative, masking discourse. However, various actors in society view it as the opposite of domination and espouse it as a goal. Empowerment can constitute a discursive field shaped by its internal contractions between autonomy and control, between ambition and risk of programmed failure, exacerbated by the emphasis on responsibility, and between focus and stigmatization. The paper presents a case study of controversies and interventions concerning employability in The Netherlands. Employability can be seen as empowerment in matters of career. The study is based on 41 interviews with policy makers, managers, union and employers' leaders and politicians. It shows that actors drawing on the principle of empowerment as a goal in itself can reset or reclaim a drifting empowerment project in its inceptive phase and add their own twist during execution, evaluation and efforts to engineer improvements.
Ventilator-Associated Tracheobronchitis Increases the Length of Intensive Care Unit Stay
Authors: Karvouniaris Marios , Makris Demosthenes , Manoulakas Efstratios , Zygoulis Paris , Mantzarlis Konstantinos , Triantaris Apostolos , Chatzi Maria , Zakynthinos Epaminondas
Published: June 2013

Objective.

To investigate prospectively the clinical course and risk factors for ventilator-associated tracheobronchitis (VAT) and the impact of VAT on intensive care unit (ICU) morbidity and mortality.

Design.

Prospective cohort study.

Setting.

University Hospital Larissa, Larissa, Greece

Patients.

Critical care patients who received mechanical ventilation for more than 48 hours were prospectively studied between 2009 and 2011.

Methods.

The modified Clinical Pulmonary Infection Score, white blood cell count, and C-reactive protein level were systematically assessed every 2 days for the first 2 weeks of ICU stay. Bronchial secretions were assessed daily. Quantitative cultures of endotracheal secretions were performed on the first ICU day for every patient and every 2 days thereafter for the first 2 weeks or more at the discretion of the attending physicians. Definition of VAT was based on previously published criteria.

Results.

A total of 236 patients were observed; 42 patients (18%) presented with VAT. Gram-negative pathogens, which were usually multidrug resistant, were responsible for 92.9% of cases. Patients with a neurosurgical admission presented with VAT significantly more often than did other ICU patients (28.5% vs 14.1%; P = .02). The occurrence of VAT was a significant risk factor for increased duration of ICU stay (OR [95% CI], 3.04 [1.35-6.85]; P = .01). Age (OR [95% CI], 1.04 [1.015-1.06]; P = .02), Acute Physiology and Chronic Health Evaluation II score (OR [95% CI], 1.08 [1.015-1.16]; P = .02), and C-reactive protein level at admission (OR [95% CI], 1.05 [1.011.1]; P = .02) were independent factors for ICU mortality.

Conclusions.

VAT is a nosocomial infection that might be associated with prolonged stay in the ICU, especially in neurocritical patients. VAT was not associated with increased mortality in our study.
Mucosal Barrier Injury Laboratory-Confirmed Bloodstream Infection: Results from a Field Test of a New National Healthcare Safety Network Definition
Authors: See Isaac , Iwamoto Martha , Allen-Bridson Kathy , Horan Teresa , Magill Shelley S. , Thompson Nicola D.
Published: June 2013

Objective.

To assess challenges to implementation of a new National Healthcare Safety Network (NHSN) surveillance definition, mucosal barrier injury laboratory-confirmed bloodstream infection (MBI-LCBI).

Design.

Multicenter field test.

Setting.

Selected locations of acute care hospitals participating in NHSN central line-associated bloodstream infection (CLABSI) surveillance.

Methods.

Hospital staff augmented their CLABSI surveillance for 2 months to incorporate MBI-LCBI: a primary bloodstream infection due to a selected group of organisms in patients with either neutropenia or an allogeneic hematopoietic stem cell transplant with gastrointestinal graft-versus-host disease or diarrhea. Centers for Disease Control and Prevention (CDC) staff reviewed submitted data to verify whether CLABSIs met MBI-LCBI criteria and summarized the descriptive epidemiology of cases reported.

Results.

Eight cancer, 2 pediatric, and 28 general acute care hospitals including 193 inpatient units (49% oncology/bone marrow transplant [BMT], 21% adult ward, 20% adult critical care, 6% pediatric, 4% step-down) conducted field testing. Among 906 positive blood cultures reviewed, 282 CLABSIs were identified. Of the 103 CLABSIs that also met MBI-LCBI criteria, 100 (97%) were reported from oncology/BMT locations. Agreement between hospital staff and CDC classification of reported CLABSIs as meeting the MBI-LCBI definition was high (90%; k= 0.82). Most MBI-LCBIs (91%) occurred in patients meeting neutropenia criteria. Some hospitals indicated that their laboratories' methods of reporting cell counts prevented application of neutropenia criteria; revised neutropenia criteria were created using data from field testing.

Conclusions.

Hospital staff applied the MBI-LCBI definition accurately. Field testing informed modifications for the January 2013 implementation of MBI-LCBI in the NHSN.
From bench to bar: careers in patent law for molecular biologists
Authors: Machin Nathan A.
Published: June 2013

Leaving science to pursue a career in patent law requires a considerable investment of time and energy, and possibly money, with no guarantee of finding a job or of returning to science should the decision prove infelicitous. Yet the large number of former scientists now practicing patent law shows that it can be done. I provide suggestions for investigating the potential opportunities, costs, risks, and rewards of this career path.
FuncISH: learning a functional representation of neural ISH images
Authors: Liscovitch Noa , Shalit Uri , Chechik Gal
Published: June 2013

Motivation: High-spatial resolution imaging datasets of mammalian brains have recently become available in unprecedented amounts. Images now reveal highly complex patterns of gene expression varying on multiple scales. The challenge in analyzing these images is both in extracting the patterns that are most relevant functionally and in providing a meaningful representation that allows neuroscientists to interpret the extracted patterns.

Results: Here, we present FuncISH—a method to learn functional representations of neural in situ hybridization (ISH) images. We represent images using a histogram of local descriptors in several scales, and we use this representation to learn detectors of functional (GO) categories for every image. As a result, each image is represented as a point in a low-dimensional space whose axes correspond to meaningful functional annotations. The resulting representations define similarities between ISH images that can be easily explained by functional categories. We applied our method to the genomic set of mouse neural ISH images available at the Allen Brain Atlas, finding that most neural biological processes can be inferred from spatial expression patterns with high accuracy. Using functional representations, we predict several gene interaction properties, such as protein–protein interactions and cell-type specificity, more accurately than competing methods based on global correlations. We used FuncISH to identify similar expression patterns of GABAergic neuronal markers that were not previously identified and to infer new gene function based on image–image similarities.

Contact:  noalis@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding
Authors: Cannistraci Carlo Vittorio , Alanis-Lobato Gregorio , Ravasi Timothy
Published: June 2013

Motivation: Most functions within the cell emerge thanks to protein–protein interactions (PPIs), yet experimental determination of PPIs is both expensive and time-consuming. PPI networks present significant levels of noise and incompleteness. Predicting interactions using only PPI-network topology (topological prediction) is difficult but essential when prior biological knowledge is absent or unreliable.

Methods: Network embedding emphasizes the relations between network proteins embedded in a low-dimensional space, in which protein pairs that are closer to each other represent good candidate interactions. To achieve network denoising, which boosts prediction performance, we first applied minimum curvilinear embedding (MCE), and then adopted shortest path (SP) in the reduced space to assign likelihood scores to candidate interactions. Furthermore, we introduce (i) a new valid variation of MCE, named non-centred MCE (ncMCE); (ii) two automatic strategies for selecting the appropriate embedding dimension; and (iii) two new randomized procedures for evaluating predictions.

Results: We compared our method against several unsupervised and supervisedly tuned embedding approaches and node neighbourhood techniques. Despite its computational simplicity, ncMCE-SP was the overall leader, outperforming the current methods in topological link prediction.

Conclusion: Minimum curvilinearity is a valuable non-linear framework that we successfully applied to the embedding of protein networks for the unsupervised prediction of novel PPIs. The rationale for our approach is that biological and evolutionary information is imprinted in the non-linear patterns hidden behind the protein network topology, and can be exploited for predicting new protein links. The predicted PPIs represent good candidates for testing in high-throughput experiments or for exploitation in systems biology tools such as those used for network-based inference and prediction of disease-related functional modules.

Availability:  https://sites.google.com/site/carlovittoriocannistraci/home

Contact:  kalokagathos.agon@gmail.com or timothy.ravasi@kaust.edu.sa

Supplementary information:  Supplementary data are available at Bioinformatics online.
Poly(A) motif prediction using spectral latent features from human DNA sequences
Authors: Xie Bo , Jankovic Boris R. , Bajic Vladimir B. , Song Le , Gao Xin
Published: June 2013

Motivation: Polyadenylation is the addition of a poly(A) tail to an RNA molecule. Identifying DNA sequence motifs that signal the addition of poly(A) tails is essential to improved genome annotation and better understanding of the regulatory mechanisms and stability of mRNA.

Existing poly(A) motif predictors demonstrate that information extracted from the surrounding nucleotide sequences of candidate poly(A) motifs can differentiate true motifs from the false ones to a great extent. A variety of sophisticated features has been explored, including sequential, structural, statistical, thermodynamic and evolutionary properties. However, most of these methods involve extensive manual feature engineering, which can be time-consuming and can require in-depth domain knowledge.

Results: We propose a novel machine-learning method for poly(A) motif prediction by marrying generative learning (hidden Markov models) and discriminative learning (support vector machines). Generative learning provides a rich palette on which the uncertainty and diversity of sequence information can be handled, while discriminative learning allows the performance of the classification task to be directly optimized. Here, we used hidden Markov models for fitting the DNA sequence dynamics, and developed an efficient spectral algorithm for extracting latent variable information from these models. These spectral latent features were then fed into support vector machines to fine-tune the classification performance.

We evaluated our proposed method on a comprehensive human poly(A) dataset that consists of 14 740 samples from 12 of the most abundant variants of human poly(A) motifs. Compared with one of the previous state-of-the-art methods in the literature (the random forest model with expert-crafted features), our method reduces the average error rate, false-negative rate and false-positive rate by 26, 15 and 35%, respectively. Meanwhile, our method makes ∼30% fewer error predictions relative to the other string kernels. Furthermore, our method can be used to visualize the importance of oligomers and positions in predicting poly(A) motifs, from which we can observe a number of characteristics in the surrounding regions of true and false motifs that have not been reported before.

Availability:  http://sfb.kaust.edu.sa/Pages/Software.aspx

Contact:  lsong@cc.gatech.edu or xin.gao@kaust.edu.sa

Supplementary information:  Supplementary data are available at Bioinformatics online.
IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
Authors: Peng Yu , Leung Henry C. M. , Yiu Siu-Ming , Lv Ming-Ju , Zhu Xin-Guang , Chin Francis Y. L.
Published: June 2013

Motivation: RNA sequencing based on next-generation sequencing technology is effective for analyzing transcriptomes. Like de novo genome assembly, de novo transcriptome assembly does not rely on any reference genome or additional annotation information, but is more difficult. In particular, isoforms can have very uneven expression levels (e.g. 1:100), which make it very difficult to identify low-expressed isoforms. One challenge is to remove erroneous vertices/edges with high multiplicity (produced by high-expressed isoforms) in the de Bruijn graph without removing correct ones with not-so-high multiplicity from low-expressed isoforms. Failing to do so will result in the loss of low-expressed isoforms or having complicated subgraphs with transcripts of different genes mixed together due to erroneous vertices/edges.

Contributions: Unlike existing tools, which remove erroneous vertices/edges with multiplicities lower than a global threshold, we use a probabilistic progressive approach to iteratively remove them with local thresholds. This enables us to decompose the graph into disconnected components, each containing a few genes, if not a single gene, while retaining many correct vertices/edges of low-expressed isoforms. Combined with existing techniques, IDBA-Tran is able to assemble both high-expressed and low-expressed transcripts and outperform existing assemblers in terms of sensitivity and specificity for both simulated and real data.

Availability:  http://www.cs.hku.hk/∼alse/idba_tran.

Contact:  chin@cs.hku.hk

Supplementary information:  Supplementary data are available at Bioinformatics online.
A graph kernel approach for alignment-free domain–peptide interaction prediction with an application to human SH3 domains
Authors: Kundu Kousik , Costa Fabrizio , Backofen Rolf
Published: June 2013

Motivation: State-of-the-art experimental data for determining binding specificities of peptide recognition modules (PRMs) is obtained by high-throughput approaches like peptide arrays. Most prediction tools applicable to this kind of data are based on an initial multiple alignment of the peptide ligands. Building an initial alignment can be error-prone, especially in the case of the proline-rich peptides bound by the SH3 domains.

Results: Here, we present a machine-learning approach based on an efficient graph-kernel technique to predict the specificity of a large set of 70 human SH3 domains, which are an important class of PRMs. The graph-kernel strategy allows us to (i) integrate several types of physico-chemical information for each amino acid, (ii) consider high-order correlations between these features and (iii) eliminate the need for an initial peptide alignment. We build specialized models for each human SH3 domain and achieve competitive predictive performance of 0.73 area under precision-recall curve, compared with 0.27 area under precision-recall curve for state-of-the-art methods based on position weight matrices.

We show that better models can be obtained when we use information on the noninteracting peptides (negative examples), which is currently not used by the state-of-the art approaches based on position weight matrices. To this end, we analyze two strategies to identify subsets of high confidence negative data.

The techniques introduced here are more general and hence can also be used for any other protein domains, which interact with short peptides (i.e. other PRMs).

Availability: The program with the predictive models can be found at http://www.bioinf.uni-freiburg.de/Software/SH3PepInt/SH3PepInt.tar.gz. We also provide a genome-wide prediction for all 70 human SH3 domains, which can be found under http://www.bioinf.uni-freiburg.de/Software/SH3PepInt/Genome-Wide-Predictions.tar.gz.

Contact:  backofen@informatik.uni-freiburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers
Authors: Orenstein Yaron , Shamir Ron
Published: June 2013

Motivation: Novel technologies can generate large sets of short double-stranded DNA sequences that can be used to measure their regulatory effects. Microarrays can measure in vitro the binding intensity of a protein to thousands of probes. Synthetic enhancer sequences inserted into an organism’s genome allow us to measure in vivo the effect of such sequences on the phenotype. In both applications, by using sequence probes that cover all k-mers, a comprehensive picture of the effect of all possible short sequences on gene regulation is obtained. The value of k that can be used in practice is, however, severely limited by cost and space considerations. A key challenge is, therefore, to cover all k-mers with a minimal number of probes. The standard way to do this uses the de Bruijn sequence of length . However, as probes are double stranded, when a k-mer is included in a probe, its reverse complement k-mer is accounted for as well.

Results: Here, we show how to efficiently create a shortest possible sequence with the property that it contains each k-mer or its reverse complement, but not necessarily both. The length of the resulting sequence approaches half that of the de Bruijn sequence as k increases resulting in a more efficient array, which allows covering more longer sequences; alternatively, additional sequences with redundant k-mers of interest can be added.

Availability: The software is freely available from our website http://acgt.cs.tau.ac.il/shortcake/.

Contact: rshamir@tau.ac.il
Predicting drug-target interactions using restricted Boltzmann machines
Authors: Wang Yuhao , Zeng Jianyang
Published: June 2013

Motivation:  In silico prediction of drug-target interactions plays an important role toward identifying and developing new uses of existing or abandoned drugs. Network-based approaches have recently become a popular tool for discovering new drug-target interactions (DTIs). Unfortunately, most of these network-based approaches can only predict binary interactions between drugs and targets, and information about different types of interactions has not been well exploited for DTI prediction in previous studies. On the other hand, incorporating additional information about drug-target relationships or drug modes of action can improve prediction of DTIs. Furthermore, the predicted types of DTIs can broaden our understanding about the molecular basis of drug action.

Results: We propose a first machine learning approach to integrate multiple types of DTIs and predict unknown drug-target relationships or drug modes of action. We cast the new DTI prediction problem into a two-layer graphical model, called restricted Boltzmann machine, and apply a practical learning algorithm to train our model and make predictions. Tests on two public databases show that our restricted Boltzmann machine model can effectively capture the latent features of a DTI network and achieve excellent performance on predicting different types of DTIs, with the area under precision-recall curve up to 89.6. In addition, we demonstrate that integrating multiple types of DTIs can significantly outperform other predictions either by simply mixing multiple types of interactions without distinction or using only a single interaction type. Further tests show that our approach can infer a high fraction of novel DTIs that has been validated by known experiments in the literature or other databases. These results indicate that our approach can have highly practical relevance to DTI prediction and drug repositioning, and hence advance the drug discovery process.

Availability: Software and datasets are available on request.

Contact:  zengjy321@tsinghua.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Simple topological properties predict functional misannotations in a metabolic network
Authors: Liberal Rodrigo , Pinney John W.
Published: June 2013

Motivation: Misannotation in sequence databases is an important obstacle for automated tools for gene function annotation, which rely extensively on comparison with sequences with known function. To improve current annotations and prevent future propagation of errors, sequence-independent tools are, therefore, needed to assist in the identification of misannotated gene products. In the case of enzymatic functions, each functional assignment implies the existence of a reaction within the organism’s metabolic network; a first approximation to a genome-scale metabolic model can be obtained directly from an automated genome annotation. Any obvious problems in the network, such as dead end or disconnected reactions, can, therefore, be strong indications of misannotation.

Results: We demonstrate that a machine-learning approach using only network topological features can successfully predict the validity of enzyme annotations. The predictions are tested at three different levels. A random forest using topological features of the metabolic network and trained on curated sets of correct and incorrect enzyme assignments was found to have an accuracy of up to 86% in 5-fold cross-validation experiments. Further cross-validation against unseen enzyme superfamilies indicates that this classifier can successfully extrapolate beyond the classes of enzyme present in the training data. The random forest model was applied to several automated genome annotations, achieving an accuracy of in most cases when validated against recent genome-scale metabolic models. We also observe that when applied to draft metabolic networks for multiple species, a clear negative correlation is observed between predicted annotation quality and phylogenetic distance to the major model organism for biochemistry (Escherichia coli for prokaryotes and Homo sapiens for eukaryotes).

Contact:  j.pinney@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.