bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of crystal growth and thermoelectric properties of n-type Bi-Se-Te and p-type Bi-Sb-Te nanocrystalline thin films: Effects of homogeneous irradiation with an electron beam
Authors: Takashiri Masayuki , Imai Kazuo , Uyama Masato , Hagino Harutoshi , Tanaka Saburo , Miyazaki Koji , Nishi Yoshitake
Published: June 2014

The effects of homogenous electron beam (EB) irradiation on the crystal growth and thermoelectric properties of n-type Bi-Se-Te and p-type Bi-Sb-Te thin films were investigated. Both types of thin films were prepared by flash evaporation, after which homogeneous EB irradiation was performed at an acceleration voltage of 0.17 MeV. For the n-type thin films, nanodots with a diameter of less than 10 nm were observed on the surface of rice-like nanostructures, and crystallization and crystal orientation were improved by EB irradiation. The resulting enhancement of mobility led to increased electrical conductivity and thermoelectric power factor for the n-type thin films. In contrast, the crystallization and crystal orientation of the p-type thin films were not influenced by EB irradiation. The carrier concentration increased and mobility decreased with increased EB irradiation dose, possibly because of the generation of defects. As a result, the thermoelectric power factor of p-type thin films was not improved by EB irradiation. The different crystallization behavior of the n-type and p-type thin films is attributed to atomic rearrangement during EB irradiation. Selenium in the n-type thin films is more likely to undergo atomic rearrangement than the other atoms present, so only the crystallinity of the n-type Bi-Se-Te thin films was enhanced.
Application of Fourier transform to MHD flow over an accelerated plate with partial-slippage
Authors: Ahmad Salman , Hussain Shafqat , Siddiqui Abuzar Abid , Ali Asad , Aqeel Muhammad
Published: June 2014

Magneto-Hydrodynamic (MHD) flow over an accelerated plate is investigated with partial slip conditions. Generalized Fourier Transform is used to get the exact solution not only for uniform acceleration but also for variable acceleration. The numerical solution is obtained by using linear finite element method in space and One-Step-θ-scheme in time. The resulting discretized algebraic systems are solved by applying geometric-multigrid approach. Numerical solutions are compared with the obtained Fourier transform results. Many interesting results related with slippage and MHD effects are discussed in detail through graphical sketches and tables. Application of Dirac-Delta function is one of the main features of present work.
Local excitation of strongly coupled exciton-surface plasmons polaritons by a single nanoantenna
Authors: Eizner E. , Ellenbogen T.
Published: June 2014

We demonstrate experimentally local coupling of light from free space to exciton-surface plasmon polaritons (X-SPPs). This is achieved by using a single, sub-wavelength gold nanowire on top of a thin silver film which is covered with a 30 nm thick layer of J-aggregating dyes in polyvinyl alcohol. We show that the nanowire acts as an antenna that resonantly scatters light to X-SPPs states with a Rabi splitting of 0.1 eV. The locally excited X-SPPs properties are studied by angle resolved spectroscopy of the far-field leaky photons and are compared to the large-scale response through Kretschmann reflection measurements and to theoretical calculations. The nanowire scattering properties are studied by dark-field scattering measurements and finite-difference time-domain simulations. This method to locally excite X-SPPs can potentially be useful for future applications of hybrid light matter states.
Structural and electrical properties of armchair CdS nanotubes
Authors: Das Monoj , Gupta Bikash C.
Published: June 2014

A systematic study of geometrical structures and electrical properties of CdS nanotubes is carried out within the density functional formalism. Geometrical and electrical properties such as wall thickness, curvature, stability, bandgap energies, work functions and charge redistribution analysis are done for CdS nanotubes with varied diameter for understanding their character. It is found that all the tubes remain hollow even after complete relaxation and their work function, bandgap as well as wall thickness decreases with increasing diameter. Some of these findings are in agreement with experimental observation that thermionic emission enhances with decreasing wall thickness of CdS nanotubes.
Observation of the partial reheating of the metallic vapor during the wire explosion process for nanoparticle synthesis
Authors: Bora B. , Kausik S. S. , Wong C. S. , Chin O. H. , Yap S. L. , Soto L.
Published: June 2014

In this paper, an experimental study using time resolved imaging was reported to study the expansion of the vapor as well as subsequent formation of the arc plasma during the synthesis of Cu nanoparticles by wire explosion process to understand the influences of arc plasma formation on the characteristics of the produced nanoparticles by means of partial reheating of the vapor. Arc plasma is known to form after a delay or immediately depending on the ambience and pressure when the supplied energy is sufficient to sustain the plasma. Observations of two expanding concentric cylinders one inside another by time resolved imaging in the case of delayed formation of arc plasma suggest that the vapor of the wire material is expanding in front of the expansion of the arc plasma. Due to the expansion of the vapor in front of the arc plasma, some of the wire material may not be reheated by arc plasma as opposed to the case of immediate formation of arc plasma, where the vapor is expected to be reheated completely. Thus, the arc plasma formation has strong influence on the characteristics of the produced nanoparticles in wire explosion process and most probably explains the earlier reported opposite trends observed for particle size with varying pressure for different gases.
Super-collimation by axisymmetric photonic crystals
Authors: Purlys V. , Maigyte L. , Gailevičius D. , Peckus M. , Gadonas R. , Staliunas K.
Published: June 2014

We propose and experimentally show the mechanism of beam super-collimation by axisymmetric photonic crystals, specifically by periodic (in propagation direction) structure of layers of concentric rings. The physical mechanism behind the effect is an inverse scattering cascade of diffracted wave components back into on- and near-axis angular field components, resulting in substantial enhancement of intensity of these components. We explore the super-collimation by numerical calculations and prove it experimentally. We demonstrate experimentally the axial field enhancement up to 7 times in terms of field intensity.
Diffusion length in nanoporous TiO2 films under above-band-gap illumination
Authors: Park J. D. , Son B. H. , Park J. K. , Kim Sang Yong , Park Ji-Yong , Lee Soonil , Ahn Y. H.
Published: June 2014

We determined the carrier diffusion lengths in TiO2 nanoporous layers of dye-sensitized solar cells by using scanning photocurrent microscopy using an ultraviolet laser. Here, we excited the carrier directly in the nanoporous layers where the diffusion lengths were found to 140 μm as compared to that of visible illumination measured at 90 μm. The diffusion length decreased with increasing laser modulation frequency, in which we determined the electron lifetimes and the diffusion coefficients for both visible and UV illuminations. The diffusion lengths have been studied in terms of the sintering temperatures for both cells with and without binding molecules. We found a strong correlation between the diffusion length and the overall light-to-current conversion efficiency, proving that improving the diffusion length and hence the interparticle connections, is key to improving cell efficiency.
Operational modal identification of offshore wind turbine structure based on modified stochastic subspace identification method considering harmonic interference
Authors: Dong Xiaofeng , Lian Jijian , Yang Min , Wang Haijun
Published: June 2014

The structural modal parameter information can be generally obtained from different vibration responses triggered by unknown excitations using the classic modal identification methods which are based on the assumption that the input to the structure is exactly the same or close to the stationary random white noise. For the actual projects such as the offshore wind turbine structure, however, the imposed loads cannot be considered as the pure white noise excitation because the harmonic components emerge obviously in vibration responses due to periodic rotation excitations of the rotor. When the created harmonic components have greater energy and their frequencies are close to any natural modal frequency of the structure, the classic methods can no longer separate harmonic modes from actual structural operational modes under this strong harmonic disturbance, thus false modes may be generated and the identification accuracy may be badly affected. To identify the actual structural operational modes accurately under strong harmonic excitation, a modified stochastic subspace identification (SSI) method considering harmonic interference called the harmonic modification SSI (HM-SSI) method was proposed in this paper assuming the input harmonic frequencies are known and time-invariant. Then the effectiveness and accuracy of the HM-SSI method were verified through a simple numerical model of cantilever beam excited by various harmonic inputs superimposed on random loads. Besides, the superior robustness and better accuracy of identification results affected by the level of noise and the proportion of harmonic energy were reflected. Finally, the modal parameter information under different operational conditions was obtained and the safety assessment of an operational wind turbine was made based on the measured data from one offshore wind turbine test prototype at high running speed.
Thermodynamic parameter matching ability of geothermal flash-binary power system
Authors: Luo Chao , Lu Zhenneng , Gong Yulie , Ma Weibin
Published: June 2014

Based on the numerical simulation, the effect of geothermal water temperature on net power output, thermal efficiency, and optimal temperature of flash-binary power system was discussed in this paper. The simulation results show that when the temperature is 80 °C, the net power output per geofluid is about 1.08 and 0.86 kWh/t by direct cooling and indirect cooling of flash system, respectively, when the temperature is 150 °C, the values are 6.57 and 6.35 kWh/t; the optimal temperature of the combined system is 80 °C and 85 °C, 100 °C and 115 °C, and 125 °C and 140 °C by direct cooling and indirect cooling of flash system, respectively, when the geothermal water temperature is 100 °C, 130 °C, and 150 °C. In addition, the power output of flash-binary system by direct cooling is dominated by flash power generation, while by indirect cooling is dominated by binary power generation. The flash-binary power system could provide technical support for geothermal resource utilization in China.
Vortex motion in layered superconductors Cu0.03TaS2
Authors: Lu Junchao , Zhu Xiangde , Pi Li , Sun Yuping , Zhang Yuheng
Published: June 2014

The vortex motion in Cu0.03TaS2 has been investigated by resistivity results with a special electrode arrangements. The vortex behaviors for H ∥ c are completely different from that for H ∥ ab. The analysis indicates that when H ∥ ab, the sharp ρ − T transition is the superconductive-normal transition while for H ∥ c, the broadened ρ − T transition is caused by the suppression of the superconducting weak link between the S-Ta-S layers. The existence of the vortex pancake in Cu0.03TaS2 is contradictory to the Clem's model, further demonstrating that the models for high temperature cuprates superconductors are not applicable to the layered transition metal dichalcogenides.
Cleaning graphene with a titanium sacrificial layer
Authors: Joiner C. A. , Roy T. , Hesabi Z. R. , Chakrabarti B. , Vogel E. M.
Published: June 2014

Graphene is a promising material for future electronic applications and chemical vapor deposition of graphene on copper is a promising method for synthesizing graphene on the wafer scale. The processing of such graphene films into electronic devices introduces a variety of contaminants which can be difficult to remove. An approach to cleaning residues from the graphene channel is presented in which a thin layer of titanium is deposited via thermal e-beam evaporation and immediately removed. This procedure does not damage the graphene as evidenced by Raman spectroscopy, greatly enhances the electrical performance of the fabricated graphene field effect transistors, and completely removes the chemical residues from the surface of the graphene channel as evidenced by x-ray photoelectron spectroscopy.
An automated phase correction algorithm for retrieving permittivity and permeability of electromagnetic metamaterials
Authors: Cao Z. X. , Yuan F. G. , Li L. H.
Published: June 2014

To retrieve complex-valued effective permittivity and permeability of electromagnetic metamaterials (EMMs) based on resonant effect from scattering parameters using a complex logarithmic function is not inevitable. When complex values are expressed in terms of magnitude and phase, an infinite number of permissible phase angles is permissible due to the multi-valued property of complex logarithmic functions. Special attention needs to be paid to ensure continuity of the effective permittivity and permeability of lossy metamaterials as frequency sweeps. In this paper, an automated phase correction (APC) algorithm is proposed to properly trace and compensate phase angles of the complex logarithmic function which may experience abrupt phase jumps near the resonant frequency region of the concerned EMMs, and hence the continuity of the effective optical properties of lossy metamaterials is ensured. The algorithm is then verified to extract effective optical properties from the simulated scattering parameters of the four different types of metamaterial media: a cut-wire cell array, a split ring resonator (SRR) cell array, an electric-LC (E-LC) resonator cell array, and a combined SRR and wire cell array respectively. The results demonstrate that the proposed algorithm is highly accurate and effective.
Reactions between a Ge substrate and a sputter deposited Ti film
Authors: Pelleg Joshua , Shneck Roni , Eliahu Reut
Published: June 2014

Formations of germanides in thin films of the Ti-Ge system were investigated by XRD after rapid thermal annealing (RTA) at several temperatures for various times. Phase formation depends on the conditions of the experiments and specifically on the thickness of the Ti film relative to that of the Ge. Considering the equilibrium phase diagram of the Ti-Ge system, if the composition is close the Ge rich side, TiGe2 might be expected to be the first phase to form and the phases present would be TiGe2 and Ge. However this is not the case. If the composition of the constituents is between the compounds of Ti6Ge5 and TiGe2, the first formation can be either one of these, but depends on how close it is to any of these compounds. However Ti6Ge5 is observed always to be the first phase. The presence of Ti6Ge5 and Ti5Ge3 is observed when the composition shifts to a location between these compounds on the phase diagram. Coexistence of Ti and Ti5Ge3 is a possibility when the amount of Ge is below the concentration of the phase Ti5Ge3, namely, when the Ge constituent is completely consumed and excess of Ti is left behind after the reaction. Temperature and time are major parameters that determine the outcome of the reactions between Ti and Ge during RTA and any of these can override the influence of the composition. XRD, SEM, Auger, TEM and resistivity were the experimental tools to study the Ti-Ge system and to evaluate the phases present under a set of experimental conditions.
Green emission in carbon doped ZnO films
Authors: Tseng L. T. , Yi J. B. , Zhang X. Y. , Xing G. Z. , Fan H. M. , Herng T. S. , Luo X. , Ionescu M. , Ding J. , Li S.
Published: June 2014

The emission behavior of C-doped ZnO films, which were prepared by implantation of carbon into ZnO films, is investigated. Orange/red emission is observed for the films with the thickness of 60–100 nm. However, the film with thickness of 200 nm shows strong green emission. Further investigations by annealing bulk ZnO single crystals under different environments, i.e. Ar, Zn or C vapor, indicated that the complex defects based on Zn interstitials are responsible for the strong green emission. The existence of complex defects was confirmed by electron spin resonance (ESR) and low temperature photoluminescence (PL) measurement.
Megaprojects, Neoliberalization, and State Capacities: Assessing the Medium-Term Impact of the 2004 Olympic Games on Athenian Urban Policies
Authors: Souliotis Nicos , Sayas John , Maloutas Thomas
Published: June 2014

With this paper we examine the 2004 Olympic Games as an ambivalent catalyst for the implementation of neoliberal urban policies in Athens. We draw upon two distinct analytical streams: first, regulationist scholars' conception of neoliberalization as a path-dependent and, to a large extent, state-led process, and, second, Skocpol's ‘autonomy state’ approach. We argue that the implementation of neoliberal urban policies in Athens has been shaped by a combination of centralism, low central state capacity, organizational and financial weakness of business elites, and citizen movements' opposition. We first provide an overview of Athenian urban policies since the 1960s; then we examine the preparation of the 2004 Olympic Games; and, finally, we investigate the post-Olympic use of Olympic venues, including the period of the current sovereign debt crisis. In the conclusion we emphasize that the bailout agreement between Greece and the International Monetary Fund, the European Central Bank, and the European Union aims at reboosting neoliberal public policies in a radical way.
Patterns of Elitism within Participatory Environmental Governance
Authors: Parkins John R , Sinclair A John
Published: June 2014

A close examination of venues for participatory environmental governance reveals highly constrained settings for citizen engagement. This situation is documented within the broader social milieu by Skocpol as a narrowing of public life which is characterized in this paper by professional, stakeholder, and elitist forms of participatory environmental governance. Case-study evidence is presented from three different governance settings in Canada (environmental assessment, land-use planning, and forest management) identifying two distinct types of elitism: elite representation by design and elite representation by procedure. Two options are presented as a response to this analysis. One option involves accepting elitism by strengthening the linkages between stakeholders and constituencies, and the other option involves fighting elitism by drawing on modes of community-based decision, deliberative activism, and promoting research that highlights the consequences of environmental elitism.
Mechanisms of Change in Adolescent Substance Use Treatment: How Does Treatment Work?
Authors: Black Jessica J. , Chung Tammy
Published: June 2014

Background

Adolescent substance use treatment outcome research generally shows small to moderate effects in reducing substance use, with no specific “brand” of treatment emerging as clearly superior to any other, and treatment gains that fade over time. The relatively weak and temporary effects of treatment call for improving the potency and durability of intervention effects. In response to this call, this critical narrative review summarizes research on mechanisms of change for both adults and adolescents in substance use treatment, with a particular focus on reviewing what is known regarding “how” adolescent substance use treatment works.

Methods

A comprehensive review of the adolescent (aged 11–18) substance use treatment literature was conducted to identify empirical studies that examined mediators of intervention effects. Relevant databases (e.g., PsychINFO, MEDLINE) were searched using key words (e.g., “mediator”), and relevant articles from reference sections of identified studies and review papers were considered.

Results

Studies of mechanisms of psychotherapy change are rare in the adult, and particularly adolescent, substance use treatment outcome literature. The 4 adolescent studies that examined substance use treatment mechanisms found that positive social support, motivation to abstain, and positive parenting behaviors mediated treatment effects. To date, research has not supported therapy-specific mechanisms of change, finding instead that “common” processes of change largely account for improvements in outcome across distinct “brands” of treatment.

Conclusions

The lack of empirical support for treatment-specific mechanisms of change may be due to the need for greater precision in defining and measuring treatment-specific causal chains. Future directions include neuroscience approaches to examining changes in brain functioning that are associated with treatment response and recovery and examining mechanisms in adaptive treatment designs, which can accommodate individual differences in targets for intervention and response to treatment.
Linking the Price of Agricultural Land to Use Values and Amenities
Authors: Borchers Allison , Ifft Jennifer , Kuethe Todd
Published: June 2014

The recent appreciation in agricultural land values across the United States has raised a number of important questions for farmers, farmland owners, lenders, and policy makers. While traditional economic theory suggests that farmland values are determined by the discounted stream of expected returns, previous research has shown that agricultural land values are actually driven by a complex set of factors. This study leverages the unique characteristics of a national land‐based USDA survey on farmland values and cash rents to estimate broad, national‐level determinants of the market value of cropland and pastureland. Our results support past research findings that indicate farmland values are only partially explained by agricultural returns. We find that multiple nonagricultural attributes of farmland also contribute to the market value.
TAO1 kinase maintains chromosomal stability by facilitating proper congression of chromosomes
Authors: Shrestha Roshan L. , Tamura Naoka , Fries Anna , Levin Nicolas , Clark Joanna , Draviam Viji M.
Published: June 2014

Chromosomal instability can arise from defects in chromosome–microtubule attachment. Using a variety of drug treatments, we show that TAO1 kinase is required for ensuring the normal congression of chromosomes. Depletion of TAO1 reduces the density of growing interphase and mitotic microtubules in human cells, showing TAO1's role in controlling microtubule dynamics. We demonstrate the aneugenic nature of chromosome–microtubule attachment defects in TAO1-depleted cells using an error-correction assay. Our model further strengthens the emerging paradigm that microtubule regulatory pathways are important for resolving erroneous kinetochore–microtubule attachments and maintaining the integrity of the genome, regardless of the spindle checkpoint status.
Autophagy and apoptosis: parent-of-origin genome-dependent mechanisms of cellular self-destruction
Authors: Ptak Grazyna E. , Toschi Paola , Fidanza Antonella , Czernik Marta , Zacchini Federica , Modlinski Jacek A. , Loi Pasqualino
Published: June 2014

Functional genomic imprinting is necessary for the transfer of maternal resources to mammalian embryos. Imprint-free embryos are unable to establish a viable placental vascular network necessary for the transfer of resources such as nutrients and oxygen. How the parental origin of inherited genes influences cellular response to resource limitation is currently not well understood. Because such limitations are initially realized by the placenta, we studied how maternal and paternal genomes influence the cellular self-destruction responses of this organ specifically. Here, we show that cellular autophagy is prevalent in androgenetic (i.e. having only a paternal genome) placentae, while apoptosis is prevalent in parthenogenetic (i.e. having only a maternal genome) placentae. Our findings indicate that the parental origin of inherited genes determines the placenta's cellular death pathway: autophagy for androgenotes and apoptosis for parthenogenotes. The difference in time of arrest between androgenotes and parthenogenotes can be attributed, at least in part, to their placentae's selective use of these two cell death pathways. We anticipate our findings to be a starting point for general studies on the parent-of-origin regulation of autophagy. Furthermore, our work opens the door to new studies on the involvement of autophagy in pathologies of pregnancy in which the restricted transfer of maternal resources is diagnosed.
Campylobacter fetus subsp. testudinum subsp. nov., isolated from humans and reptiles
Authors: Fitzgerald Collette , Tu Zheng chao , Patrick Mary , Stiles Tracy , Lawson Andy J. , Santovenia Monica , Gilbert Maarten J. , van Bergen Marcel , Joyce Kevin , Pruckler Janet , Stroika Steven , Duim Birgitta , Miller William G. , Loparev Vladimir , Sinnige Jan C. , Fields Patricia I. , Tauxe Robert V. , Blaser Martin J. , Wagenaar Jaap A.
Published: June 2014

A polyphasic study was undertaken to determine the taxonomic position of 13

Campylobacter fetus

-like strains from humans (n = 8) and reptiles (n = 5). The results of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS and genomic data from sap analysis, 16S rRNA gene and hsp60 sequence comparison, pulsed-field gel electrophoresis, amplified fragment length polymorphism analysis, DNA–DNA hybridization and whole genome sequencing demonstrated that these strains are closely related to

C. fetus

but clearly differentiated from recognized subspecies of

C. fetus

. Therefore, this unique cluster of 13 strains represents a novel subspecies within the species

C. fetus

, for which the name Campylobacter fetus subsp. testudinum subsp. nov. is proposed, with strain 03-427T ( = ATCC BAA-2539T = LMG 27499T) as the type strain. Although this novel taxon could not be differentiated from

C. fetus subsp. fetus

and

C. fetus subsp. venerealis

using conventional phenotypic tests, MALDI-TOF MS revealed the presence of multiple phenotypic biomarkers which distinguish Campylobacter fetus subsp. testudinum subsp. nov. from recognized subspecies of

C. fetus

.
Oceanicola
antarcticus sp. nov. and Oceanicola flagellatus sp. nov., moderately halophilic bacteria isolated from seawater
Authors: Huo Ying-Yi , Li Zheng-Yang , You Hong , Wang Chun-Sheng , Post Anton F. , Oren Aharon , Xu Xue-Wei
Published: June 2014

Two Gram-stain-negative, aerobic, moderately halophilic, rod-shaped bacteria (strains Ar-45T and DY470T) were isolated from seawater collected from the Southern Ocean and the Pacific Ocean, respectively. Growth of strain Ar-45T was observed with between 0.5 and 10.0 % (w/v) NaCl (optimally with 0.5–3.0 %) and between pH 5.5 and 9.5. Strain DY470T grew in the presence of 0.5–7.5 % (w/v) NaCl (optimally with 2.0 %) and at pH 5.5–8.5. Chemotaxonomic analysis showed Q-10 as the respiratory quinone for both strains. The major fatty acids (>5 %) of strain Ar-45T were C16 : 0, C19 : 0 cyclo ω8c and C18 : 1ω7c, while those of strain DY470T were C18 : 1ω7c, C16 : 0 and 11-methyl C18 : 1ω7c. The DNA G+C contents of the two strains were 62.0 and 61.8 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains Ar-45T and DY470T were related most closely to the genus

Oceanicola

, with sequence similarities of 97.4–94.0 and 97.7–94.7 %, respectively. The DNA–DNA hybridization value between strain Ar-45T and

Oceanicola marinus

LMG 23705T was 22.0 %. Levels of DNA–DNA relatedness between strain DY470T and

Oceanicola nitratireducens

LMG 24663T and

Oceanicola batsensis

DSM 15984T were 32.5 and 26.1 %, respectively. Based on phylogenetic, chemotaxonomic and phenotypic data, strains Ar-45T and DY470T are considered to represent two novel species of the genus

Oceanicola

, for which the names Oceanicola
antarcticus (type strain Ar-45T = CGMCC 1.12662T = LMG 27868T) and Oceanicola
flagellatus (type strain DY470T = CGMCC 1.12664T = LMG 27871T) are proposed.
Evolution of Escherichia coli for maximum HOCl resistance through constitutive expression of the OxyR regulon
Authors: Gundlach Jasmin , Winter Jeannette
Published: June 2014

Exposure of cells to stress impairs cellular functions and may cause killing or adaptation. Adaptation can be facilitated by stress-induced mutagenesis or epigenetic changes, i.e. phenotypic variation without mutations. Upon exposure to HOCl, which is produced by the innate immune system upon bacterial infection, bacteria trigger stress responses that enable increased survival against the stress. Here, we addressed the question whether bacteria can adapt to high HOCl doses and if so, how the acquired resistance is facilitated. We evolvedEscherichia colicells for maximum HOCl resistance by successively increasing the HOCl concentration in the cultivation medium. HOCl-resistant cells showed broad stress resistance but did not carry any chromosomal mutations as revealed by whole-genome sequencing. According to proteome analysis and analysis of transcript levels of stress-related genes, HOCl resistance was accompanied by altered levels of outer-membrane proteins A, C, F and W, and, most prominently, a constitutively expressed OxyR regulon. Induction of the OxyR regulon is facilitated by a partially oxidized OxyR leading to increased levels of antioxidant proteins such as Dps, AhpC/AhpF and KatG. These changes were maintained in evolved strains even when they were cultivated without stress for a prolonged time, indicating epigenetic changes contributed to stress resistance. This indicated that maximum HOCl resistance was conferred by the accumulated action of the OxyR stress response and other factors such as altered levels of outer-membrane proteins.
Newly isolated mAbs broaden the neutralizing epitope in murine norovirus
Authors: Kolawole Abimbola O. , Xia Chunsheng , Li Ming , Gamez Monica , Yu Chenchen , Rippinger Christine M. , Yucha Ryan E. , Smith Thomas J. , Wobus Christiane E.
Published: June 2014

Here, we report the isolation and functional characterization of mAbs against two murine norovirus (MNV) strains, MNV-1 and WU20, which were isolated following oral infection of mice. The mAbs were screened for reactivity against the respective homologous and heterologous MNV strain by ELISA. Selected mAbs were of IgA, IgG1, IgG2a or IgG2b isotype and showed a range of Western blot reactivities from non-binding to strong binding, suggesting recognition of conformational and linear epitopes. Some of the anti-MNV-1 antibodies neutralized both MNV-1 and WU20 infections in culture and in mice, but none of the anti-WU20 mAbs neutralized either virus. The non-neutralizing anti-MNV-1 IgG2b antibody 5C4.10 was mapped to the S domain of the MNV-1 capsid, whilst the epitopes of the neutralizing anti-MNV-1 IgA antibodies 2D3.7 and 4F9.4 were mapped to the P domain. Generation of neutralization escape viruses showed that two mutations (V339I and D348E) in the C′D′ loop of the MNV-1 P domain mediated escape from mAb 2D3.7 and 4F9.4 neutralization. These findings broaden the known neutralizing epitopes of MNV to the main surface-exposed loops of the P domain. In addition, the current panel of antibodies provides valuable reagents for studying norovirus biology and development of diagnostic tools.
A fossilOsmundafrom the Jurassic of Sweden—reconciling molecular and fossil evidence in the phylogeny of Osmundaceae
Authors: Bomfleur Benjamin , Grimm Guido W. , McLoughlin Stephen
Published: June 2014

The systematic classification of Osmundaceae has long remained controversial. Recent molecular data indicate thatOsmundais paraphyletic, and needs to be separated intoOsmundastrumandOsmunda s. str. Here we describe an exquisitely preserved JurassicOsmundarhizome (O. pulchellasp. nov.) that combines diagnostic features ofOsmundastrumandOsmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm.Osmunda pulchellaand five additional, newly identified JurassicOsmundaspecies show anatomical character suites intermediate betweenOsmundastrumandOsmunda.Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolveOsmunda s.l.as monophyletic. Our evolutionary placement analysis identifies fossil species as ancestral members of modern genera and subgenera. Altogether, the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can be elegantly reconciled under the assumption thatOsmundais indeed monophyletic; the recently proposed root-placement in Osmundaceae—based solely on molecular data—likely results from un- or misinformative out-group signals.
Origin and evolution of the self-organizing cytoskeleton in the network of eukaryotic organelles
Authors: Jékely Gáspár
Published: June 2014

The eukaryotic cytoskeleton evolved from prokaryotic cytomotive filaments. Prokaryotic filament systems show bewildering structural and dynamic complexity, and in many aspects prefigure the self-organizing properties of the eukaryotic cytoskeleton. Here I compare the dynamic properties of the prokaryotic and eukaryotic cytoskeleton, and discuss how these relate to function and the evolution of organellar networks. The evolution of new aspects of filament dynamics in eukaryotes, including severing and branching, and the advent of molecular motors converted the eukaryotic cytoskeleton into a self-organizing ‘active gel’, the dynamics of which can only be described with computational models. Advances in modeling and comparative genomics hold promise of a better understanding of the evolution of the self-organizing cytoskeleton in early eukaryotes, and its role in the evolution of novel eukaryotic functions, such as amoeboid motility, mitosis, and ciliary swimming.
Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits
Authors: Kessner Darren , Novembre John
Published: June 2014

Evolve and resequence studies combine artificial selection experiments with massively parallel sequencing technology to study the genetic basis for complex traits. In these experiments, individuals are selected for extreme values of a trait, causing alleles at quantitative trait loci (QTLs) to increase or decrease in frequency in the experimental population. We present a new analysis of the power of artificial selection experiments to detect and localize quantitative trait loci. This analysis uses a simulation framework that explicitly models whole genomes of individuals, quantitative traits, and selection based on individual trait values. We find that explicitly modeling QTL provides produces qualitatively different insights than considering independent loci with constant selection coefficients. Specifically, we observe how interference between QTLs under selection impacts the trajectories and lengthens the fixation times of selected alleles. We also show that a substantial portion of the genetic variance of the trait (50–100%) can be explained by detected QTLs in as little as 20 generations of selection, depending on the trait architecture and experimental design. Furthermore, we show that power depends crucially on the opportunity for recombination during the experiment. Finally, we show that an increase in power is obtained by leveraging founder haplotype information to obtain allele frequency estimates.
Complete plastid genome assembly of invasive plant,Centaurea diffusa
Authors: Turner Kathryn G. , Grassa Christopher J.
Published: June 2014

New genomic tools are needed to elucidate the evolution of invasive, non-model organisms. Here we present the completed plastome assembly for the problematic invasive weed,Centaurea diffusa. This new tool represents a significant contribution to future studies of the ecological genomics of invasive plants, particularly this weedy genus, and studies of the Asteraceae in general.
Simultaneous estimation of transcript abundances and transcript specific fragment distributions of RNA-Seq data with the Mix2model
Authors: Tuerk Andreas , Wiktorin Gregor
Published: June 2014

Quantification of RNA transcripts with RNA-Seq is inaccurate due to positional fragmentation bias, which is not represented appropriately by current statistical models of RNA-Seq data. Another, less investigated, source of error is the inaccuracy of transcript start and end annotations.

This article introduces the Mix2(rd. “mixquare”) model, which uses a mixture of probability distributions to model the transcript specific positional fragment bias. The parameters of the Mix2model can be efficiently trained with the EM algorithm and are tied between similar transcripts. Transcript specific shift and scale parameters allow the Mix2model to automatically correct inaccurate transcript start and end annotations. Experiments are conducted on synthetic data covering 7 genes of different complexity, 4 types of fragment bias and correct as well as incorrect transcript start and end annotations. Abundance estimates obtained by Cufflinks 2.2.0, PennSeq and the Mix2model show superior performance of the Mix2model in the vast majority of test conditions.

The Mix2software is available athttp://www.lexogen.com/fileadmin/uploads/bioinfo/mix2model.tgz, subject to the enclosed license.

Additional experimental data are available in the supplement.
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
Authors: Naccache Samia N. , Federman Scot , Veeraraghavan Narayanan , Zaharia Matei , Lee Deanna , Samayoa Erik , Bouquet Jerome , Greninger Alexander L. , Luk Ka-Cheung , Enge Barryett , Wadford Debra A. , Messenger Sharon L. , Genrich Gillian L. , Pellegrino Kristen , Grard Gilda , Leroy Eric , Schneider Bradley S. , Fair Joseph N. , Martínez Miguel A. , Isa Pavel , Crump John A. , DeRisi Joseph L. , Sittler Taylor , Hackett John , Miller Steve , Chiu Charles Y.
Published: June 2014

Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI (“sequence-based ultrarapid pathogen identification”), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7–500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times.
Phase-transformation-induced twinning of an iron(III) calix[4]pyrrolidine complex
Authors: Journot Guillaume , Neier Reinhard , Stoeckli-Evans Helen
Published: June 2014

The title compound, tetrachlorido-1κCl;2κ3Cl-(2,2,7,7,12,12,17,17-octamethyl-21,22,23,24-tetraazapentacyclo[16.2.1.13,6.18,11.113,16]tetracosane-1κ4N,N′,N′′,N′′′)-μ2-oxido-diiron(III), [Fe2Cl4O(C28H52N4)], undergoes a slow phase transformation atca173 K from monoclinic space groupP21/n, denoted form (I), to the maximal non-isomorphic subgroup, triclinic space groupP\overline{1}, denoted form (II), which is accompanied by nonmerohedral twinning [twin fractions of 0.693 (4) and 0.307 (4)]. The transformation was found to be reversible, as on raising the temperature the crystal reverted to monoclinic form (I). In the asymmetric unit of form (I),Z′ = 1, while in form (II),Z′ = 2, with a very small reduction (ca1.8%) in the unit-cell volume. The two independent molecules (AandB) in form (II) are related by a pseudo-twofold screw axis along thebaxis. The molecular overlay of moleculeAon moleculeBhas an r.m.s. deviation of 0.353 Å, with the largest distance between two equivalent atoms being 1.202 Å. The reaction of calix[4]pyrrolidine, the fully reduced form ofmeso-octamethylporphyrinogen, with FeCl3gave a red–brown solid that was recrystallized from ethanol in air, resulting in the formation of the title compound. In both forms, (I) and (II), the FeIIIatoms are coordinated to the macrocyclic ligand and have distorted octahedral FeN4OCl coordination spheres. These FeIIIatoms lie out of the mean plane of the four N atoms, displaced towards the O atom of the [OFeCl3] unit by 0.2265 (5) Å in form (I), and by 0.2210 (14) and 0.2089 (14) Å, respectively, in the two independent molecules (AandB) of form (II). The geometry of the [OFeCl3] units are similar, with each FeIIIatom having a tetrahedral coordination sphere. The NH H atoms are directed below the planes of the macrocycles and are hydrogen bonded to the coordinated Cl−ions. There are also intramolecular C—H...Cl hydrogen bonds present in both (I) and (II). In form (I), there are no significant intermolecular interactions present. In form (II), the individual molecules are arranged in alternate layers parallel to theacplane. TheBmolecules are linked by a C—H...Cl hydrogen bond, forming chains along [100].
A three-dimensional PbIIcoordination framework: poly[[μ4-(E)-2,2′-(diazene-1,2-diyl)dibenzoato]dimethanollead(II)]
Authors: Liu Lei-Lei , Yu Cai-Xia , Hua Lei , Lin Lu
Published: June 2014

In the title coordination polymer, [Pb(C14H8N2O4)(CH3OH)2]n, the asymmetric unit contains half of a PbIIcation, half of a 2,2′-(diazene-1,2-diyl)dibenzoate dianionic ligand (denotedL2−) and one methanol ligand. Each PbIIcentre is eight-coordinated by six O atoms of chelating/bridging carboxylate groups from fourL2−ligands and two O atoms from two terminal methanol ligands, forming a distorted dodecahedron. The [PbL2(MeOH)2] subunits are interlinkedviathe sharing of two carboxylate O atoms to form a one-dimensional [PbL2(MeOH)2]nchain. Adjacent chains are further connected byL2−ligands, giving rise to a two-dimensional layer, and these layers are bridged byL2−linkers to afford a three-dimensional framework with a 41263topology.
The relationship between motivation to work and workers’ pay flexibility
Authors: Stynen Dave , Forrier Anneleen , Sels Luc
Published: June 2014

Purpose

– The purpose of this paper is to explore the role of motivation to work in explaining workers’ pay flexibility – as measured by their reservation wage ratio – across the lifespan. This is important since pay inflexibility may undermine mature age workers’ retention at the workforce.

Design/methodology/approach

– Relying on self-determination theory the paper broadens the role of “motivation to work” from the overall work valence an individual attaches to work to the underlying work values (i.e. the perceived value of work for its intrinsic vs extrinsic outcomes) and work motives (i.e. the underlying autonomous vs controlled reasons regulating one's work participation). The authors conducted hierarchical linear regression analyses on a sample of 1,577 Belgian workers to explore how individuals’ work values and work motives, in addition to work valence, shape workers’ reservation wage ratios across the lifespan.

Findings

– Results indicate that work valence and holding relative intrinsic work values and relative autonomous work motives are associated with lower reservation wage ratios. Finally, age moderates all three relationships. Whereas the negative impact of work valence and relative autonomous work motives is stronger at older age, the negative impact of relative intrinsic work values is stronger at younger age.

Research limitations/implications

– Motivational predictors are differently related to reservation wage ratios across the lifespan.

Practical implications

– By fostering overall work valence and autonomous work motivation practitioners can exert influence on mature age workers’ pay flexibility.

Originality/value

– This study extends prior research on pay flexibility by focussing on the content of motivation to work (i.e. work values, work motives) and its role across the lifespan.
An integrative model of work/family interface for Chinese employees
Authors: Lu Luo , Chang Yu-Yueh
Published: June 2014

Purpose

– The purpose of this paper is to examine the mediating roles of four aspects of work and family interface (WFI: work-to-family conflict, WFC; family-to-work conflict, FWC; work-to-family enrichment, WFE; and family-to-work enrichment, FWE) in a Chinese context in Taiwan. Included in the integral model are demands and resources from the work and family domains as antecedents, and role satisfaction and burnout as consequences.

Design/methodology/approach

– Structured questionnaires were used to collect data from 499 full-time working Chinese parents in Taiwan.

Findings

– Structural equation modeling results showed that antecedents had cross-domain and within-domain effects on all aspects of the WFI; and conflict and enrichment also had cross-domain and within-domain effects on job satisfaction and family satisfaction, while influences from the work domain (WFC and WFE) had a significant impact on burnout. Overall, the partial mediation model was supported, showing that antecedent variables having both indirect (through the WFI variables) as well as direct relationships with the outcome variables.

Originality/value

– This is the first study testing a comprehensive model of the whole loop of antecedents-WFI-consequences with a non-Western sample. One unique contribution of the study is that the authors extended Western-based resources theories to Chinese employees, confirming that all four aspects of the WFI are important mediators linking up antecedents with consequences from both the work and family domains. Basing upon the findings, the authors suggests that both managers and employees should endeavor to break the destructive flow of conflict→dissatisfaction/burnout and to initiate the constructive flow of enrichment→satisfaction/free of burnout, by considering not only demands but also resources from both the work and family domains.