bluuebunny/crossref_metadata_2025 huggingface dataset:
Resolving confusion of tongues in statistics and machine learning: A primer for biologists and bioinformaticians
Authors: van Iterson Maarten , van Haagen Herman H. H. B. M. , Goeman Jelle J.
Published: January 2012

Bioinformatics is the field where computational methods from various domains have come together for analysis of biological data. Each domain has introduced its own specific jargon. However, in closely related domains, e.g. machine learning and statistics, concordant and discordant terminology occurs, the later can lead to confusion. This article aims to help solve the confusion of tongues arising from these two closely related domains, which are frequently used in bioinformatics. We provide a short summary of the most commonly applied machine learning and statistical approaches to data analysis in bioinformatics, i.e. classification and statistical hypothesis testing. We explain differences and similarities in common terminology used in various domains, such as precision, recall, sensitivity and true positive rate. This primer can serve as a guide to the terminology used in these fields.
The methylproteome and the intracellular methylation network
Authors: Erce Melissa A. , Pang Chi N. I. , Hart‐Smith Gene , Wilkins Marc R.
Published: January 2012

Since its discovery more than 50 years ago, post‐translational modification (PTM) of proteins via methylation has grown in prominence, its involvement having been recognised in a number of central processes in the cell. Of these, the best characterised is its role in the epigenetic code. However, there is increasing evidence that its role extends far beyond this and we propose that it is a key regulator in interactome dynamics. In this review, we focus on the role of methylation in regulating protein‐protein interactions and illustrate, by providing a broad‐scale summary of our current knowledge of methylation and its impact on systems biology, how this can ultimately affect interactome dynamics. We describe the variety of analytical techniques available for the study of the methylproteome, comment on their advantages and limitations, and consider how these tools can help elucidate how methylation regulates the dynamics of the interactome. The insights gained from methyltransferase‐substrate networks will be summarised and the ability of protein methylation to facilitate or block protein‐protein interactions as well as their interplay with other post‐translational modifications, in particular phosphorylation, is highlighted. Finally, the importance of methylation in pathology‐associated protein interaction networks will be discussed using examples involving human diseases and the p53 protein.
Using SILAC and quantitative proteomics to investigate the interactions between viral and host proteomes
Authors: Munday Diane C. , Surtees Rebecca , Emmott Edward , Dove Brian K. , Digard Paul , Barr John N. , Whitehouse Adrian , Matthews David , Hiscox Julian A.
Published: January 2012

Viruses continue to pose some of the greatest threats to human and animal health, and food security worldwide. Therefore, new approaches are required to increase our understanding of virus‐host cell interactions and subsequently design more effective therapeutic countermeasures. Quantitative proteomics based on stable isotope labeling by amino acids in cell culture (SILAC), coupled to LC‐MS/MS and bioinformatic analysis, is providing an excellent resource for studying host cell proteomes and can readily be applied for the study of virus infection. Here, we review this approach and discuss how virus‐host cell interactions can best be studied, what is realistically feasible, and the potential limitations. For example, sub‐cellular fractionation can reduce sample complexity for LC‐MS/MS, increase data return and provide information regarding protein trafficking between different cellular compartments. The key to successful quantitative proteomics combines good experimental design and appropriate sample preparation with statistical analysis and validation of the MS data through the use of independent techniques and functional analysis. The annotation of the human genome and the increasing availability of biological reagents such as antibodies, provide the optimum parameters for studying viruses that infect humans, in human cell lines. SILAC‐based quantitative proteomics can also be used to study the interactome of viral proteins with the host cell. Coupling proteomic studies with global transcriptomic and RNA depletion experiments will provide great insights into the complexity of the infection process, and potentially reveal new antiviral targets.
β‐Tubulins in Gibberella zeae: their characterization and contribution to carbendazim resistance
Authors: Qiu JianBo , Huang TingTing , Xu JianQiang , Bi ChaoWei , Chen ChangJun , Zhou MingGuo
Published: January 2012

BACKGROUND: Fusarium head blight caused by Gibberella zeae is an important disease of wheat and barley because it reduces grain yield and quality and results in the contamination of grain with mycotoxins. Recent studies have shown that carbendazim resistance in field strains of G. zeae is not caused by mutation of the β‐tubulin gene (β1tub), which is the case with other filamentous fungi, but that fungicide resistance is greatly increased by deletion of β1tub. The aim of the present study was to clarify the function of β1tub and its role in carbendazim resistance in G. zeae by artificial gene operation.

RESULTS: Deletion of β1tub reduced vegetative growth and pathogenicity but increased asexual reproduction in G. zeae. All the mutants were more resistant to carbendazim than parent strains. A three‐dimensional model of β1tub was constructed, and the possible carbendazim binding site was analysed.

CONCLUSION: β1tub is not an essential gene in G. zeae, but it affects the sensitivity of the fungus to carbendazim. Copyright © 2012 Society of Chemical Industry
AZO/Au/AZO multilayer as a transparent conductive electrode
Authors: Lee Seungjun , Bang Seokhwan , Park Joohyun , Park Soyeon , Ko Youngbin , Jeon Hyeongtag
Published: January 2012

A multilayer of Al doped ZnO/gold/Al doped ZnO (AZO/Au/AZO) was deposited by atomic layer deposition (ALD), and its structural, electrical, and optical properties were investigated. The thin Au interlayer was deposited by e‐beam evaporator and showed a series of islands. As the Au interlayer thickness increased, the Au islands coalesced resulting in a continuous Au film at 12 nm or thicker. As the Au interlayer thickness increased to 12 nm, the carrier concentration increased from 1.3 × 1020 to 4.2 × 1021 cm−3, the Hall mobility increased from 13.4 to 22.4 cm2/Vs, and the resistivity decreased from 2.6 × 10−3 to 1.2 × 10−4 Ωcm. However, the transmittance decreased from 80 to 48%. Additionally, the AZO/Au/AZO multilayer was less crystalline than a single AZO layer.
Mixed effect Poisson log‐linear models for clinical and epidemiological sleep hypnogram data
Authors: Swihart Bruce J. , Caffo Brian S. , Crainiceanu Ciprian M. , Punjabi Naresh M.
Published: January 2012

Bayesian Poisson log‐linear multilevel models scalable to epidemiological studies are proposed to investigate population variability in sleep state transition rates. Hierarchical random effects are used to account for pairings of subjects and repeated measures within those subjects, as comparing diseased with non‐diseased subjects while minimizing bias is of importance. Essentially, non‐parametric piecewise constant hazards are estimated and smoothed, allowing for time‐varying covariates and segment of the night comparisons. The Bayesian Poisson regression is justified through a re‐derivation of a classical algebraic likelihood equivalence of Poisson regression with a log(time) offset and survival regression assuming exponentially distributed survival times. Such re‐derivation allows synthesis of two methods currently used to analyze sleep transition phenomena: stratified multi‐state proportional hazards models and log‐linear generalized estimating equations (GEE) models for transition counts. An example data set from the Sleep Heart Health Study is analyzed. Supplementary material includes the analyzed data set as well as the code for a reproducible analysis. Copyright © 2012 John Wiley & Sons, Ltd.
The analysis of binary longitudinal data with time‐dependent covariates
Authors: Guerra Matthew W. , Shults Justine , Amsterdam Jay , Ten‐Have Thomas
Published: January 2012

We consider longitudinal studies with binary outcomes that are measured repeatedly on subjects over time. The goal of our analysis was to fit a logistic model that relates the expected value of the outcomes with explanatory variables that are measured on each subject. However, additional care must be taken to adjust for the association between the repeated measurements on each subject. We propose a new maximum likelihood method for covariates that may be fixed or time varying. We also implement and make comparisons with two other approaches: generalized estimating equations, which may be more robust to misspecification of the true correlation structure, and alternating logistic regression, which models association via odds ratios that are subject to less restrictive constraints than are correlations. The proposed estimation procedure will yield consistent and asymptotically normal estimates of the regression and correlation parameters if the correlation on consecutive measurements on a subject is correctly specified. Simulations demonstrate that our approach can yield improved efficiency in estimation of the regression parameter; for equally spaced and complete data, the gains in efficiency were greatest for the parameter associated with a time‐by‐group interaction term and for stronger values of the correlation. For unequally spaced data and with dropout according to a missing‐at‐random mechanism, MARK1ML with correctly specified consecutive correlations yielded substantial improvements in terms of both bias and efficiency. We present an analysis to demonstrate application of the methods we consider. We also offer an R function for easy implementation of our approach. Copyright © 2012 John Wiley & Sons, Ltd.
Does female representation in top management improve firm performance? A panel data investigation
Authors: Dezsö Cristian L. , Ross David Gaddis
Published: January 2012

We argue that female representation in top management brings informational and social diversity benefits to the top management team, enriches the behaviors exhibited by managers throughout the firm, and motivates women in middle management. The result should be improved managerial task performance and thus better firm performance. We test our theory using 15 years of panel data on the top management teams of the S&P 1,500 firms. We find that female representation in top management improves firm performance but only to the extent that a firm's strategy is focused on innovation, in which context the informational and social benefits of gender diversity and the behaviors associated with women in management are likely to be especially important for managerial task performance. Copyright © 2012 John Wiley & Sons, Ltd.
Enrichment of Fe‐Containing Phases and Recovery of Iron and Its Oxides by Magnetic Separation from BOF Slags
Authors: Wang Deyong , Jiang Maofa , Liu Chengjun , Min Yi , Cui Yuyuan , Liu Jian , Zhang Yongcang
Published: January 2012

Steel slag normally contains a large amount of iron and its oxides. Therefore, it is a potential renewable resource in case of inadequate iron ore supply. To recover the metals from steel slag, two types of BOF slags were remelted at 1873 K. The liquid slags were cooled using four types of cooling conditions, namely, water granulation, splashing, air cooling, and furnace cooling, to investigate the influence of cooling rate on mineral components, especially the enrichment behavior of Fe‐containing minerals. Subsequently, wet magnetic separation was conducted to examine the relations between iron recovery ratio and cooling conditions. The results show that the slags under the four cooling conditions mainly contained dicalcium silicate, RO phase, FetO, 2CaO(Fe,Al)2O3, and calcium ferrite. However, tricalcium silicate, 12CaO·7Al2O3, M‐A spinel, and free CaO and MgO were occasionally observed. The amount of glass matrix decreased, the Fe‐containing minerals increased, and the minerals more fully crystallized when the cooling rate of the liquid slag was decreased. From granulation to furnace cooling of the slags, the iron content in the recovered concentrate and the iron recovery ratio both increased. This result is in agreement with the findings on phase transformation through SEM analysis.
Effect of TiO2 on the Viscosity and Slag Structure in Blast Furnace Type Slags
Authors: Park Hyunsik , Park Jun‐Young , Kim Gi Hyun , Sohn Il
Published: January 2012

TiO2 additions up to 10 mass% behaved as a basic oxide and lowered the viscosity in the CaO–SiO2–17 mass% Al2O3–10 mass% MgO‐based slags by depolymerizing the silicate network structure. Raman spectroscopy revealed the sum of NBO/Si 1 and 3 decreased while the sum of NBO/Si 2 and 4 increased with TiO2 content. Unlike the silicate structures, the aluminate structures seems to be relatively unaffected by TiO2 additions according to the FTIR results. 5 mass% TiO2 significantly decreased the viscosity compared to the TiO2 free slags, but beyond 5 mass% TiO2 meaningful changes in the viscosity was not observed. From the comparison of the viscosity at constant TiO2 of 5 and 10 mass% and varying CaO/SiO2 ratio, increasing the CaO/SiO2 ratio was more effective in decreasing the viscosity than TiO2 additions.
The Encounter between Jews and America in the Gilded Age and Progressive Era
Authors: Diner Hasia
Published: January 2012

The period after 1870 through the middle of the 1920s, the Gilded Age and Progressive Era, coincided with the mass migration of Jews to the United States. Nearly three million Jews, primarily from eastern Europe, overwhelmed the numerically small Jewish community already resident in America. Of the Jews who left Europe in those years, approximately 85 percent opted for the United States, a society that took some of its basic characteristics from the particular developments of this transitional historical period. This essay focuses on five aspects of Gilded Age and Progressive Era America and their impact on the Jews. These features of American society both stimulated the mass migration and made possible a relatively harmonious, although complicated, integration. Those forces included the broader contours of immigration, the nation's obsession with race, its vast industrial and economic expansion, its valorization of religion, and its two-party system in which neither the Democrats or the Republicans had any stake in demonizing the growing number of Jewish voters.
A free plate surface and weak oceanic crust produce single‐sided subduction on Earth
Authors: Crameri F. , Tackley P. J. , Meilick I. , Gerya T. V. , Kaus B. J. P.
Published: January 2012

Earth's lithosphere is characterized by the relative movement of almost rigid plates as part of global mantle convection. Subduction zones on present‐day Earth are strongly asymmetric features composed of an overriding plate above a subducting plate that sinks into the mantle. While global self‐consistent numerical models of mantle convection have reproduced some aspects of plate tectonics, the assumptions behind these models do not allow for realistic single‐sided subduction. Here we demonstrate that the asymmetry of subduction results from two major features of terrestrial plates: (1) the presence of a free deformable upper surface and (2) the presence of weak hydrated crust atop subducting slabs. We show that assuming a free surface, rather than the conventional free‐slip surface, allows the dynamical behavior at convergent plate boundaries to change from double‐sided to single‐sided. A weak crustal layer further improves the behavior towards steady single‐sided subduction by acting as lubricating layer between the sinking and the overriding plate. This is a first order finding of the causes of single‐sided subduction, which by its own produces important features like the arcuate curvature of subduction trenches.
Hot oxygen atoms in the Venus nightside exosphere
Authors: Gröller H. , Lammer H. , Lichtenegger H. I. M. , Pfleger M. , Dutuit O. , Shematovich V. I. , Kulikov Y. N. , Biernat H. K.
Published: January 2012

The nightside oxygen exosphere of Venus is investigated for high and moderate solar activity by means of a Monte‐Carlo model. Hot O atoms are assumed to be produced by dissociative recombination of O2+ and NO+ molecular ions and by charge transfer processes between ionospheric O+ ions and neutral O and H atoms. The model considers rotational and vibrational excitation of the initial energy distribution of hot O atoms, includes elastic, inelastic, and quenching collisions between the suprathermal atoms and the ambient neutral atmosphere species, and uses differential cross sections for the determination of the scattering angle in the collisions. The results indicate that dissociative recombination of O2+ is, like at Venus' dayside, the most efficient source of hot O atoms at the planet's nightside. For high solar activity, the nightside exospheric density of hot O atoms is about one order of magnitude lower compared to the dayside, although between 2–10 times higher than in previous studies.
A phenomenological model for the flow resistance over submerged vegetation
Authors: Konings Alexandra G. , Katul Gabriel G. , Thompson Sally E.
Published: January 2012

The bulk velocity Ub in streams is conventionally estimated from Manning's equation, but difficulties remain in parameterizing the roughness coefficient n when the streambed is covered with vegetation. A two‐layer velocity model is proposed to determine n and Ub for the submerged vegetation case. The modeled n is derived as a function of flow and vegetation properties that can be inferred from remote sensing platforms, such as canopy height, leaf area density, and flow depth. The main novelty in the proposed formulation is that the shear stress is related to the mean velocity profile by considering both ejective and sweeping motions by dominant eddies. The proposed model is tested against a large data set from the literature and is shown to perform well, particularly for rigid vegetation. Poorer model performance for flexible vegetation can be partially attributed to the shape of the assumed mean velocity profile. The roughness coefficient n is found to be robust to variations in the average spacing between canopy elements, allowing the model to be applied to heterogeneous canopies.
Sediment dynamics in a sand bed stream with riparian vegetation
Authors: Gorrick Sam , Rodríguez José F.
Published: January 2012

The characteristic bed morphology of streams results from the action of various sediment fluxes. Sediment fluxes are difficult to quantify, and as a result, few studies have been able to characterize the relative importance of different transport mechanisms in shaping a river's bed at the reach scale. Even fewer studies have been able to address the impacts of introduced riparian vegetation on those fluxes. This study provides the first comprehensive set of flow and sediment measurements required to compute the fluxes in a sand bed stream with riparian vegetation. Data were collected in a reduced‐scale laboratory model of a reach of a sand bed stream in southeastern Australia that is undergoing rehabilitation using in‐stream riparian vegetation. The reach has a large‐radius meander and a variable width. Laboratory measurements included streamwise and transverse velocities, bed shear stresses, bed load transport, suspended sediment concentrations, and bed topography with and without riparian vegetation placed along the outer bank of the bend. The results unveiled the importance of secondary circulation as well as converging and diverging flow patterns in shaping the bed topography. Modifications due to the vegetation included a shift of the main flow away from the vegetated outer bank and an overall straightening of the flow in the reach, resulting in an increased deposition near the vegetated bank and a reduced deposition near the inner bank. This highlights the need for overall reach assessment of flow and sediment dynamics before revegetation, as its effects go beyond local bank protection.
The anglerfish deception
Authors: Wickson Fern , Wynne Brian
Published: January 2012

A recent proposal to reform the EU's policy on the use of genetically modified crops looks good at first sight, but there are dangers for science lurking in the background.
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
Authors: Soergel David A W , Dey Neelendu , Knight Rob , Brenner Steven E
Published: January 2012

Microbial community profiling using 16S rRNA gene sequences requires accurate taxonomy assignments. ‘Universal’ primers target conserved sequences and amplify sequences from many taxa, but they provide variable coverage of different environments, and regions of the rRNA gene differ in taxonomic informativeness—especially when high-throughput short-read sequencing technologies (for example, 454 and Illumina) are used. We introduce a new evaluation procedure that provides an improved measure of expected taxonomic precision when classifying environmental sequence reads from a given primer. Applying this measure to thousands of combinations of primers and read lengths, simulating single-ended and paired-end sequencing, reveals that these choices greatly affect taxonomic informativeness. The most informative sequence region may differ by environment, partly due to variable coverage of different environments in reference databases. Using our Rtax method of classifying paired-end reads, we found that paired-end sequencing provides substantial benefit in some environments including human gut, but not in others. Optimal primer choice for short reads totaling 96 nt provides 82–100% of the confident genus classifications available from longer reads.
Infrared spectra and ultraviolet-tunable laser induced photochemistry of matrix-isolated phenol and phenol-d5
Authors: Giuliano Barbara Michela , Reva Igor , Lapinski Leszek , Fausto Rui
Published: January 2012

Monomers of phenol and its ring-perdeuterated isotopologue phenol-d5 were isolated in argon matrices at 15 K. The infrared (IR) spectra of these species were recorded and analyzed. In situ photochemical transformations of phenol and phenol-d5 were induced by tunable UV laser light. The photoproducts have been characterized by IR spectroscopy supported by theoretical calculations of the infrared spectra. The primary product photogenerated from phenol was shown to be the phenoxyl radical. The analysis of the progress of the observed phototransformations led to identification of 2,5-cyclohexadienone as one of the secondary photoproducts. Spectral indications of other secondary products, such as the Dewar isomer and the open-ring ketene, were also detected. Identification of the photoproducts provided a guide for the interpretation of the mechanisms of the observed photoreactions.
(PbS)32: A baby crystal
Authors: Kiran B. , Kandalam Anil K. , Rallabandi Rameshu , Koirala Pratik , Li Xiang , Tang Xin , Wang Yi , Fairbrother Howard , Gantefoer Gerd , Bowen Kit
Published: January 2012

Theoretical calculations based on density functional theory have found (PbS)32 to be the smallest cubic cluster for which its inner (PbS)4 core enjoys bulk-like coordination. Cubic (PbS)32 is thus a “baby crystal,” i.e., the smallest cluster, exhibiting sixfold coordination, that can be replicated to obtain the bulk crystal. The calculated dimensions of the (PbS)32 cluster further provide a rubric for understanding the pattern of aggregation when (PbS)32 clusters are deposited on a suitable surface, i.e., the formation of square and rectangular, crystalline nano-blocks with predictable dimensions. Experiments in which mass-selected (PbS)32 clusters were soft-landed onto a highly ordered pyrolytic graphite surface and the resulting aggregates imaged by scanning tunneling microscopy provide evidence in direct support of the computational results.
Relation of astrophysical turbulence and magnetic reconnection
Authors: Lazarian A. , Eyink Gregory L. , Vishniac E. T.
Published: January 2012

Astrophysical fluids are generically turbulent and this must be taken into account for most transport processes. We discuss how the preexisting turbulence modifies magnetic reconnection and how magnetic reconnection affects the MHD turbulent cascade. We show the intrinsic interdependence and interrelation of magnetic turbulence and magnetic reconnection, in particular, that strong magnetic turbulence in 3D requires reconnection and 3D magnetic turbulence entails fast reconnection. We follow the approach in Eyink et al. [Astrophys. J. 743, 51 (2011)] to show that the expressions of fast magnetic reconnection in A. Lazarian and E. T. Vishniac [Astrophys. J. 517, 700 (1999)] can be recovered if Richardson diffusion of turbulent flows is used instead of ordinary Ohmic diffusion. This does not revive, however, the concept of magnetic turbulent diffusion which assumes that magnetic fields can be mixed up in a passive way down to a very small dissipation scales. On the contrary, we are dealing the reconnection of dynamically important magnetic field bundles which strongly resist bending and have well defined mean direction weakly perturbed by turbulence. We argue that in the presence of turbulence the very concept of flux-freezing requires modification. The diffusion that arises from magnetic turbulence can be called reconnection diffusion as it based on reconnection of magnetic field lines. The reconnection diffusion has important implications for the continuous transport processes in magnetized plasmas and for star formation. In addition, fast magnetic reconnection in turbulent media induces the First order Fermi acceleration of energetic particles, can explain solar flares and gamma ray bursts. However, the most dramatic consequence of these developments is the fact that the standard flux freezing concept must be radically modified in the presence of turbulence.
Electronic structure of the [MgO3]+ cation
Authors: Ben Houria A. , Yazidi O. , Jaidane N. , Senent M. L. , Hochlaf M.
Published: January 2012

Accurate ab initio calculations are performed to investigate the stable isomers of [MgO3]+ and its lowest electronic states at both molecular and asymptotic regions. The calculations are done using large basis sets and configuration interaction methods including the complete active space self-consistent field, the internally contracted multi-reference configuration interaction, the standard coupled cluster (RCCSD(T)) approaches and the newly implemented explicitly correlated coupled cluster method (RCCSD(T)-F12). The presence of three stable forms is predicted: a cyclic global minimum c-MgO3+, which is followed by a quasi-linear isomer, l2-MgO3+. A third isomer of Cs symmetry (l1-MgO3+) is also found. Moreover, we computed the one-dimensional cuts of the six-dimensional potential energy surfaces of the lowest doublet and quartet electronic states of [MgO3]+ along the RMgO and ROO stretching coordinates covering both the molecular and the asymptotic regions. These curves are used later for discussing the metastability of this cation and to propose plausible mechanisms for the Mg+ + O3 atmospherically important ion–molecule reaction and related reactive channels.
Studies of pure and nitrogen-incorporated hydrogenated amorphous carbon thin films and their possible application for amorphous silicon solar cells
Authors: Dwivedi Neeraj , Kumar Sushil , Malik Hitendra K.
Published: January 2012

Hydrogenated amorphous carbon (a-C:H) and nitrogen-incorporated a-C:H (a-C:N:H) thin films were deposited using radio frequency–plasma-enhanced chemical vapor deposition technique and studied for their electrical, optical, and nano-mechanical properties. Introduction of nitrogen and increase of self bias enhanced the conductivity of a-C:H and a-C:N:H films, whereas current-voltage measurement reveals heterojunction formation due to their rectifying behavior. The bandgap of these films was changed over wide range from 1.9 eV to 3.45 eV by varying self bias and the nitrogen incorporation. Further, activation energy was correlated with the electronic structure of a-C:H and a-C:N:H films, and conductivity was discussed as a function of bandgap. Moreover, a-C:N:H films exhibited high hardness and elastic modulus, with maximum values as 42 GPa and 430 GPa, respectively, at −100 V. Observed fascinating electrical, optical, and nano-mechanical properties made it a material of great utility in the development of optoelectronic devices, such as solar cells. In addition, we also performed simulation study for an a-Si:H solar cell, considering a-C:H and C:N:H as window layers, and compared their performance with the a-Si:H solar cell having a-SiC:H as window layer. We also proposed several structures for the development of a near full-spectrum solar cell. Moreover, due to high hardness, a-C:N:H films can be used as a protective and encapsulate layer on solar cells, especially in n-i-p configuration on metal substrate. Nevertheless, a-C:H and a-C:N:H as a window layer can avoid the use of additional hard and protective coating and, hence, minimize the cost of the product.
Oxygen-induced metal-insulator-transition on single crystalline metal oxide wires
Authors: Berengue O. M. , Amorim C. A. , Kamimura H. , Chiquito A. J. , Leite E. R.
Published: January 2012

In this work we report on the transition from metal to insulator conduction of individual single crystalline In2O3 wires induced by different oxygen concentration during their growth. The transport measurements revealed that the metallic conduction was mainly governed by the acoustic phonon scattering and the insulating character was addressed by the variable range hopping mechanism, which in turn can be considered as a first evidence of the occurrence of an Anderson-like metal-insulator-transition (MIT). The experimental data provided the critical carrier density to be 8×1018 cm-3 corresponding to a critical impurities spacing of 2.5 nm, which was found to be in agreement with previous reported data on polycrystalline indium oxide samples and with our recent finding on In2O3 semiconducting samples. The approach presented here can be used to grow other metal oxide systems in which oxygen vacancies play a fundamental role for the electron transport features.
Origin of large dielectric constant in La modified BiFeO3-PbTiO3 multiferroic
Authors: Singh Anupinder , Chatterjee Ratnamala , Mishra S. K. , Krishna P. S. R. , Chaplot S. L.
Published: January 2012

The presence of superlattice reflections and detailed analysis of the powder neutron and x-ray diffraction data reveals that La rich BLF-PT (BFO0.50–LF0.50)0.50–(PT)0.50 has a ferroelectric rhombohedral crystal structure with space group R3c at ambient condition. Impedance spectroscopy, dielectric spectroscopy is subset of impedance spectroscopy and ac conductivity measurements were performed in the temperature range 483 K ≤ T ≤ 573 K to probe the origin of large remnant polarization and frequency dependent broad transitions with large dielectric constant near TcFE. Results of impedance spectroscopy measurements clearly show contributions of both grain and grain boundaries throughout the frequency range (1 kHz ≤ f ≤ 10 MHz). It could be concluded that the grain boundaries are more resistive and capacitive as compared to the grains, resulting in inhomogeneity in the sample and cause broad frequency dependent dielectric transitions. The Maxwell-Wagner model fits very well up to ∼105 Hz. Enhancement in dielectric constant and remnant polarization values are possibly due to space charge polarization caused by piling of charges at the interface of grain and grain boundaries.
Microfluidic carbon-blackened polydimethylsiloxane device with reduced ultra violet background fluorescence for simultaneous two-color ultra violet/visible-laser induced fluorescence detection in single cell analysis
Authors: Galla Lukas , Greif Dominik , Regtmeier Jan , Anselmetti Dario
Published: January 2012

In single cell analysis (SCA), individual cell-specific properties and inhomogeneous cellular responses are being investigated that is not subjected to ensemble-averaging or heterogeneous cell population effects. For proteomic single cell analysis, ultra-sensitive and reproducible separation and detection techniques are essential. Microfluidic devices combined with UV laser induced fluorescence (UV-LIF) detection have been proposed to fulfill these requirements. Here, we report on a novel microfluidic chip fabrication procedure that combines straightforward production of polydimethylsiloxane (PDMS) chips with a reduced UV fluorescence background (83%-reduction) by using PDMS droplets with carbon black pigments (CBP) as additives. The CBP-droplet is placed at the point of detection, whereas the rest of the chip remains transparent, ensuring full optical control of the chip. We systematically studied the relation of the UV background fluorescence at CBP to PDMS ratios (varying from 1:10 to 1:1000) for different UV laser powers. Using a CBP/PDMS ratio of 1:20, detection of a 100 nM tryptophan solution (S/N = 3.5) was possible, providing a theoretical limit of detection of 86 nM (with S/N = 3). Via simultaneous two color UV/VIS-LIF detection, we were able to demonstrate the electrophoretic separation of an analyte mixture of 500 nM tryptophan (UV) and 5 nM fluorescein (VIS) within 30 s. As an application, two color LIF detection was also used for the electrophoretic separation of the protein content from a GFP-labeled single Spodoptera frugiperda (Sf9) insect cell. Thereby just one single peak could be measured in the visible spectral range that could be correlated with one single peak among others in the ultraviolet spectra. This indicates an identification of the labeled protein γ-PKC and envisions a further feasible identification of more than one single protein in the future.
Graphene covered SiC powder as advanced photocatalytic material
Authors: Zhu Kaixing , Guo Liwei , Lin Jingjing , Hao Weichang , Shang Jun , Jia Yuping , Chen Lianlian , Jin Shifeng , Wang Wenjun , Chen Xiaolong
Published: January 2012

Graphene covered SiC powder (GCSP) has been fabricated by well established method of high temperature thermal decomposition of SiC. The structural and photocatalystic characteristics of the prepared GCSP were investigated and compared with that of the pristine SiC powder. Under UV illumination, more than 100% enhancement in photocatalystic activity is achieved in degradation of Rhodamine B (Rh B) by GCSP catalyst than by pristine SiC powder. The possible mechanisms underlining the observed results are discussed. The results suggested that GCSP as a composite of graphene based material has great potential for use as a high performance photocatalyst.
Magnetic transport apparatus for the production of ultracold atomic gases in the vicinity of a dielectric surface
Authors: Händel S. , Marchant A. L. , Wiles T. P. , Hopkins S. A. , Cornish S. L.
Published: January 2012

We present an apparatus designed for studies of atom-surface interactions using quantum degenerate gases of 85Rb and 87Rb in the vicinity of a room temperature dielectric surface. The surface to be investigated is a super-polished face of a glass Dove prism mounted in a glass cell under ultra-high vacuum. To maintain excellent optical access to the region surrounding the surface, magnetic transport is used to deliver ultracold atoms from a separate vacuum chamber housing the magneto-optical trap (MOT). We present a detailed description of the vacuum apparatus highlighting the novel design features; a low profile MOT chamber and the inclusion of an obstacle in the transport path. We report the characterization and optimization of the magnetic transport around the obstacle, achieving transport efficiencies of 70% with negligible heating. Finally, we demonstrate the loading of a hybrid optical-magnetic trap with 87Rb and the creation of Bose-Einstein condensates via forced evaporative cooling close to the dielectric surface.
Effect of explosive emission on runaway electron generation
Authors: Levko D. , Yatom S. , Vekselman V. , Gleizer J. Z. , Gurovich V. Tz. , Krasik Ya. E.
Published: January 2012

The results of numerical simulations of the generation of runaway electrons in a nitrogen-filled coaxial diode with electron emission governed by field emission that transfers to explosive emission with a variable time delay are presented. It is shown that the time when the explosive emission turns on influences significantly the generation of runaway electrons. Namely, an explosive emission turn-on prior to the formation of the virtual cathode leads to an increase in the current amplitude of the runaway electrons and a decrease in its duration. Conversely, an explosive emission turn-on after the formation of the virtual cathode and during the high-voltage pulse rise time does not influence the generation of runaway electrons significantly. When the explosive emission turns on during the fall of the high-voltage pulse and after the virtual cathode formation, one obtains additional runaway electron generation. Finally, a comparison between electron energy distributions obtained with and without explosive emission turn-on showed that the former increases the number of electrons in the high-energy tail and the electrons’ largest energy. The comparison of both the simulated electron energy distributions with the experimentally obtained electron spectrum has shown that the best fit is obtained when the explosive emission is considered in the simulation.
Plasmon-enhanced upconversion fluorescence in NaYF4:Yb/Er/Gd nanorods coated with Au nanoparticles or nanoshells
Authors: Li Z. Q. , Chen S. , Li J. J. , Liu Q. Q. , Sun Z. , Wang Z. B. , Huang S. M.
Published: January 2012

We investigate plasmon-enhanced upconversion (UC) fluorescence in Yb3+-Er3+-Gd+3 codoped sodium yttrium fluoride (NaYF4:Yb/Er/Gd) nanorods using gold nanoparticles or nanoshells. A simple method was proposed for the preparation of core/shell NaYF4/Au structures, with dispersed Au nanoparticles or uniform Au coating on the surface of the UC nanorod. Pure hexagonal-phase NaYF4:Yb/Er/Gd nanorods were synthesized via a liquid-solid reaction in oleic acid and ethanol solvent. A one-step approach was introduced to modify the hydrophobic surfaces of the as-deposited NaYF4:Yb/Er/Gd nanorods. After this surface modification, Au nanoparticles or nanoshells were successfully attached on the surfaces of NaYF4:Yb/Er/Gd nanorods. The as-deposited UC nanorods showed a strong UC emission in green and red bands under 980 nm laser excitation. The attachment of Au nanoparticles onto NaYF4:Yb/Er/Gd nanorods resulted in a more than three-fold increase in UC emissions, whereas the formation of continuous and compact Au shells around the nanorods suppressed the emissions. The related interaction mechanisms of the UC emission of NaYF4:Yb/Er/Gd nanorods with plasmon modes in Au nanostructures are analyzed and discussed.
Large area ceramic thin films on plastics: A versatile route via solution processing
Authors: Kozuka H. , Yamano A. , Fukui T. , Uchiyama H. , Takahashi M. , Yoki M. , Akase T.
Published: January 2012

A new general route for large area, submicron thick ceramic thin films (crystalline metal oxide thin films) on plastic substrates is presented, where the crystallization of films is guaranteed by a firing process. Gel films are deposited on silicon substrates with a release layer and fired to be ceramic films, followed by transferring onto plastic substrates using adhesives. The ceramic films thus fabricated on plastics exhibit a certain degree of flexibility, implying the possibility of the technique to be applied to high-throughput roll-to-roll processes. Using this technique, we successfully realized transparent anatase thin films that provide high optical reflectance and transparent indium tin oxide thin films that exhibit electrical conductivity on polycarbonate and acrylic resin substrates, respectively. Crystallographically oriented zinc oxide films and patterned zinc oxide films are also demonstrated to be realized on acrylic resin substrates.
Amplification factors in shock-turbulence interactions: Effect of shock thickness
Authors: Donzis Diego A.
Published: January 2012

Amplification factors of streamwise velocity are investigated in canonical shock-turbulence interactions. The ratio of laminar shock thickness to the Kolmogorov length scale is suggested as the appropriate parameter to understand data from simulations and experiments. The different regimes of the interaction suggested in the literature can also be understood in terms of this parameter.
The effects of translating the Multidimensional Sexuality Questionnaire from English to Mandarin: a test of reliability and validity
Authors: Tao Peng , Coates Rosemary , Zhao Yun , Maycock Bruce
Published: January 2012

Background
In China, sexuality studies using validated psychosexual instruments are limited, with no valid Mandarin language version of a sexuality inventory with psychometric properties available for use. Thus, the Mandarin version of the Multidimensional Sexuality Questionnaire (M-MSQ), comprising four subscales, originating from the Multidimensional Sexuality Questionnaire, was tested for its psychometric properties.
Methods: A convenience sampling technique was employed to recruit 200 oil workers (100 males and 100 females) in northern China. Originally, 158 participants (84 males and 74 females) completed the questionnaire; these accounted for 79% of the total study sample. From this group, a subsample of 50 participants (25 males and 25 females) was randomly selected to investigate the test–retest reliability. Of these, the responses of 33 participants (18 males and 15 females) were valid. The analysis on reliability was based on Cronbach’s α, Pearson’s correlation coefficient (r) and the intraclass correlation coefficient, also including evaluation on criterion validity and discriminatory validity.
Results: The M-MSQ was found to be homogeneous in factor structure, comparing well with the original questionnaire. Both the discriminatory validity and the criterion-related validity were satisfactory in the total sample and gender groups, in addition, the overall reliability of the M-MSQ was sound in internal consistency with Cronbach’s α = 0.900–0.931. The results of the test–retest showed that the stability of the M-MSQ achieved a positive statistically significant standard assessed by Pearson’s coefficient and the intraclass correlation coefficient.
Conclusion: The M-MSQ is reliable in these four subscales, and may be used as a measure of sexual esteem, sexual conscious, sexual motivation and sexual satisfaction in Mandarin speakers.
Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin
Authors: Westfall Patrick J. , Pitera Douglas J. , Lenihan Jacob R. , Eng Diana , Woolard Frank X. , Regentin Rika , Horning Tizita , Tsuruta Hiroko , Melis David J. , Owens Andrew , Fickes Scott , Diola Don , Benjamin Kirsten R. , Keasling Jay D. , Leavell Michael D. , McPhee Derek J. , Renninger Neil S. , Newman Jack D. , Paddon Chris J.
Published: January 2012

Malaria, caused by
Plasmodium sp
, results in almost one million deaths and over 200 million new infections annually. The World Health Organization has recommended that artemisinin-based combination therapies be used for treatment of malaria. Artemisinin is a sesquiterpene lactone isolated from the plant
Artemisia annua
. However, the supply and price of artemisinin fluctuate greatly, and an alternative production method would be valuable to increase availability. We describe progress toward the goal of developing a supply of semisynthetic artemisinin based on production of the artemisinin precursor amorpha-4,11-diene by fermentation from engineered
Saccharomyces cerevisiae
, and its chemical conversion to dihydroartemisinic acid, which can be subsequently converted to artemisinin. Previous efforts to produce artemisinin precursors used
S. cerevisiae
S288C overexpressing selected genes of the mevalonate pathway [Ro et al. (2006)
Nature
440:940–943]. We have now overexpressed every enzyme of the mevalonate pathway to
ERG20
in
S. cerevisiae
CEN.PK2, and compared production to CEN.PK2 engineered identically to the previously engineered S288C strain. Overexpressing every enzyme of the mevalonate pathway doubled artemisinic acid production, however, amorpha-4,11-diene production was 10-fold higher than artemisinic acid. We therefore focused on amorpha-4,11-diene production. Development of fermentation processes for the reengineered CEN.PK2 amorpha-4,11-diene strain led to production of > 40 g/L product. A chemical process was developed to convert amorpha-4,11-diene to dihydroartemisinic acid, which could subsequently be converted to artemisinin. The strains and procedures described represent a complete process for production of semisynthetic artemisinin.
METALLICITY DISTRIBUTION FUNCTIONS OF THE OLD POPULATIONS OF THE MAGELLANIC CLOUDS FROM RR Lyrae STARS
Authors: Haschke Raoul , Grebel Eva K. , Duffau Sonia , Jin Shoko
Published: January 2012

We present the first metallicity distribution functions of the old field populations in the Magellanic Clouds (MCs). Our metallicities are based on the Fourier decomposition of Type ab RR Lyrae light curves from the Optical Gravitational Lensing Experiment. On the metallicity scale of Zinn & West, we find a mean metallicity of [Fe/H] = −1.50 ± 0.24 dex based on 16,776 RR Lyrae stars in the Large Magellanic Cloud (LMC). For the Small Magellanic Cloud (SMC) we obtain −1.70 ± 0.27 dex based on 1831 RR Lyrae stars. These uncertainties represent the intrinsic spread in the population rather than the standard deviation of the mean. Our results are in good agreement with the few existing spectroscopic metallicity determinations for LMC RR Lyrae stars from the literature. For both the LMC and the SMC the metallicity spread exceeds 1 dex in [Fe/H]. The distribution of metallicities in both Clouds is very uniform, and no significant metallicity gradient is detectable. We also do not find any pronounced populations of extremely metal-poor RR Lyrae candidates with metallicities well below −2 dex, although we need to caution that the photometric method used may overestimate the metallicities of metal-deficient stars. Moreover, because of stellar evolutionary effects one does not expect to observe many RR Lyrae stars among very metal-poor horizontal branch stars. We suggest that the MCs experienced fairly rapid and efficient early enrichment involving pre-enriched gas as well as possibly gas infall, while metal loss through outflows does not seem to have played a significant role. Moreover, we suggest that the differences in the metallicities of the old population of LMC and SMC make an origin from a single, common progenitor unlikely, unless the separation happened very early on.
Effect of the annealing treatments on the electroluminescence efficiency of SiO2 layers doped with Si and Er
Authors: Jambois O , Ramírez J M , Berencén Y , Navarro-Urrios D , Anopchenko A , Marconi A , Prtljaga N , Tengattini A , Pellegrino P , Daldosso N , Pavesi L , Colonna J-P , Fedeli J-M , Garrido B
Published: January 2012

We studied the effect of rapid thermal processing and furnace annealing on the transport properties and electroluminescence (EL) of SiO2 layers doped with Si and Er ions. The results show that for the same annealing temperature, furnace annealing decreases the electrical conductivity and increases the probability of impact excitation, which leads to an improved external quantum efficiency. Correlations between predictions from phenomenological transport models, annealing regimes and erbium EL are observed and discussed.