bluuebunny/crossref_metadata_2025 huggingface dataset:
Coherent Josephson phase qubit with a single crystal silicon capacitor
Authors: Patel U. , Gao Y. , Hover D. , Ribeill G. J. , Sendelbach S. , McDermott R.
Published: January 2013

We have incorporated a single crystal silicon shunt capacitor into a Josephson phase qubit. The capacitor is derived from a commercial silicon-on-insulator wafer. Bosch reactive ion etching is used to create a suspended silicon membrane; subsequent metallization on both sides is used to form the capacitor. The superior dielectric loss of the crystalline silicon leads to a significant increase in qubit energy relaxation times. T1 times up to 1.6 μs were measured, more than a factor of two greater than those seen in amorphous phase qubits. The design is readily scalable to larger integrated circuits incorporating multiple qubits and resonators.
H2O photodissociation in the first absorption band: Entangled trajectory molecular dynamics method
Authors: Xu Feng , Wang Lifei , Martens Craig C. , Zheng Yujun
Published: January 2013

We investigate \documentclass[12pt]{minimal}\begin{document}$\rm {H_2O}$\end{document}H2O photodissociation in its first absorption band using entangled trajectory molecular dynamics method. We compare our results of entangled trajectories with exact quantum mechanical calculations, the overall agreement with the exact results is reasonable. To help understanding we show the photodissociation process with our entangled trajectories and the effect of the entangled trajectories in the system.
Emission spectroscopy of the interior of optically dense post-detonation fireballs
Authors: Lewis W. K. , Rumchik C. G. , Smith M. J.
Published: January 2013

In recent years, emission spectroscopy has been applied to the study of post-detonation combustion in explosives, often yielding valuable information on temperatures and chemical dynamics. The post-detonation fireballs that form as under-oxidized detonation products burn in the surrounding air are optically dense and the corresponding emission spectra sample only the material at or near the surface of the fireball. In the present study, we exploit the large optical density in order to probe the dynamics occurring in the interior of the fireball. Emission spectra are collected following detonation of 20 g aluminized Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) charges using fiber optics located behind the flame front and then compared with the corresponding spectra of the surface layer collected from outside the fireball. We find that in the early evolution of the fireball (t ≤ 60 μs and r ≤ 10 cm in the current study), combustion and light emission are predominantly confined to the surface, while the interior is dark. Later, after the fireball expands and mixes with the surrounding air (t ≥ 120 μs or r ≥ 30 cm), combustion and emission occur throughout, and we find no significant differences between the spectra collected from the interior of the fireball versus those from its surface.
An atomic layer deposition reactor with dose quantification for precursor adsorption and reactivity studies
Authors: Larrabee T. J. , Mallouk T. E. , Allara D. L.
Published: January 2013

An atomic layer deposition reactor has been constructed with quantitative, precision dose control for studying precursor adsorption characteristics and to relate dose quantity and exposure dynamics to fluid flow in both the viscous and molecular flow regimes. A fixed volume of gas, held at a controlled temperature and measured pressure, is dosed into the reaction chamber by computer-controlled pneumatic valves. Dual in situ quartz crystal microbalances provide parallel mass measurement onto two differently coated substrates, which allows adsorption coverage and relative sticking coefficients to be determined. Gas composition in the reaction chamber was analyzed in situ by a quadrupole mass spectrometer. Absolute reactant exposure is unambiguously calculated from the impingement flux, and is related to dose, surface area, and growth rates. A range of control over the dose amount is demonstrated and consequences for film growth control are demonstrated and proposed.
Observation of spin-glass behavior in nickel adsorbed few layer graphene
Authors: Mitra Sreemanta , Mondal Oindrila , Banerjee Sourish , Chakravorty Dipankar
Published: January 2013

Nickel-adsorbed graphene was prepared by first synthesizing graphite oxide (GO) by modified Hummers' method and then reducing a solution containing both GO and Ni2+. Energy dispersive X-ray spectroscopy analysis showed 31 at. % nickel was present. Magnetization measurements under both dc and ac magnetic fields were carried out in the temperature range 2 K to 300 K. The zero field cooled and field cooled magnetization data showed a pronounced irreversibility at a temperature around 20 K. The analysis of the ac susceptibility data was carried out by both Vogel-Fulcher as well as power law. From dynamic scaling analysis, the microscopic flipping time τ0∼10−13s and critical exponent zν=5.9±0.1 were found, indicating the presence of conventional spin glass in the system. The spin glass transition temperature was estimated as 19.5 K. Decay of thermoremanent magnetization was explained by stretched exponential function with a value of the exponent as 0.6. From the results, it is concluded that nickel adsorbed graphene behaves like a spin-glass.
A pillar-based microfilter for isolation of white blood cells on elastomeric substrate
Authors: Alvankarian Jafar , Bahadorimehr Alireza , Yeop Majlis Burhanuddin
Published: January 2013

Our goal is to design, fabricate, and characterize a pillar-based microfluidic device for size-based separation of human blood cells on an elastomeric substrate with application in the low-cost rapid prototyping of lab-chip devices. The single inlet single outlet device is using parallel U-shape arrays of pillars with cutoff size of 5.5 μm for trapping white blood cells (WBCs) in a pillar chamber with internal dead-volume of less than 1.0 μl. The microstructures are designed to limit the elastomeric deformation against fluid pressures. Numerical analysis showed that at maximum pressure loss of 15 kPa which is lower than the device conformal bonding strength, the pillar elastomeric deformation is less than 5% for flow rates of up to 1.0 ml min−1. Molding technique was employed for device prototyping using polyurethane methacrylate (PUMA) resin and polydimethylsiloxane (PDMS) mold. Characterization of the dual-layer device with beads and blood samples is performed. Tests with blood injection showed that ∼18%–25% of WBCs are trapped and ∼84%–89% of red blood cells (RBCs) are passed at flow rates of 15–50 μl min−1 with a slight decrease of WBCs trap and improve of the RBCs pass at higher flow rates. Similar results were obtained by separation of mixed microspheres of different size injected at flow rates of up to 400 μl min−1. Tests with blood samples stained by fluorescent gel demonstrated that the WBCs are accumulated in the arrays of pillars that later end up to blockage of the device. Filtration results of using elastomeric substrate present a good consistency with the trend of separation efficiencies of the similar silicon-based filters.
Impact of hydrogen and oxygen defects on the lattice parameter of chemical vapor deposited zinc sulfide
Authors: McCloy J. S. , Wolf W. , Wimmer E. , Zelinski B. J.
Published: January 2013

The lattice parameter of cubic chemical vapor deposited (CVD) ZnS with measured oxygen concentrations <0.6 at. % and hydrogen impurities of <0.015 at. % has been measured and found to vary between −0.10% and +0.09% relative to the reference lattice parameter (5.4093 Å) of oxygen-free cubic ZnS as reported in the literature. Defects other than substitutional O must be invoked to explain these observed volume changes. The structure and thermodynamic stability of a wide range of native and impurity induced defects in ZnS have been determined by ab initio calculations. Lattice contraction is caused by S-vacancies, substitutional O on S sites, Zn vacancies, H in S vacancies, peroxy defects, and dissociated water in S-vacancies. The lattice is expanded by interstitial H, H in Zn vacancies, dihydroxy defects, interstitial oxygen, Zn and [ZnHn] complexes (n = 1,…,4), interstitial Zn, and S2 dumbbells. Oxygen, though present, likely forms substitutional defects for sulfur resulting in lattice contraction rather than as interstitial oxygen resulting in lattice expansion. It is concluded based on measurement and calculations that excess zinc atoms either at anti-sites (i.e., Zn atoms on S-sites) or possibly as interstitial Zn are responsible for the relative increase of the lattice parameter of commercially produced CVD ZnS.
Band offsets and heterostructures of two-dimensional semiconductors
Authors: Kang Jun , Tongay Sefaattin , Zhou Jian , Li Jingbo , Wu Junqiao
Published: January 2013

The band offsets and heterostructures of monolayer and few-layer transition-metal dichalcogenides MX2 (M = Mo, W; X = S, Se, Te) are investigated from first principles calculations. The band alignments between different MX2 monolayers are calculated using the vacuum level as reference, and a simple model is proposed to explain the observed chemical trends. Some of the monolayers and their heterostructures show band alignments suitable for potential applications in spontaneous water splitting, photovoltaics, and optoelectronics. The strong dependence of the band offset on the number of layers also implicates a possible way of patterning quantum structures with thickness engineering.
Manganese nanoclusters and MnSi∼1.7 nanowires formed on Si(110): A comparative x-ray photoelectron spectroscopy study
Authors: Zou Zhi-Qiang , Shi Gao-Ming , Sun Li-Min , Liu Xiao-Yong
Published: January 2013

The growth of Mn on a Si(110) surface at room temperature (RT) and 550 °C has been investigated by scanning tunneling spectroscopy (STM) and X-ray photoelectron spectroscopy (XPS). STM observation shows that the growth at 550 °C results in the formation of nanowires (NWs), while that at RT produces only nanoclusters. The Mn 2p XPS spectra unambiguously reveal that the NWs are composed of MnSi∼1.7 and the nanoclusters are composed of Mn. Curve-fitting analysis of the spectra shows that 64.9% of the NWs were oxidized due to atmospheric exposure during sample transfer, while the Mn nanoclusters were completely oxidized under the same conditions. This fact indicates that the MnSi∼1.7 NWs have better oxidation resistance than the Mn clusters, which can be attributed to the protection effect of the SiO2 layer formed on the NWs and the smaller surface to volume ratio of the NWs comparing with the clusters. The binding energy of Mn 2p for the NWs exhibits a negative shift of ∼0.5 eV with respect to the Mn metallic state, which is similar to the silicide state of earlier transition metals Ti and Cr, but different from that of later transition metals Fe and Ni. This negative shift can be attributed to the contribution of Madelung potential.
Origin of colossal permittivity in BaTiO3 via broadband dielectric spectroscopy
Authors: Han Hyuksu , Voisin Christophe , Guillemet-Fritsch Sophie , Dufour Pascal , Tenailleau Christophe , Turner Christopher , Nino Juan C.
Published: January 2013

Barium titanate (BT) ceramics with Ba/Ti ratios of 0.95 and 1.00 were synthesized using spark plasma sintering (SPS) technique. Dielectric spectroscopy (frequency range from 40 Hz to 1 MHz and temperature range from 300 K to 30 K) was performed on those ceramics (SPS BT). SPS BT showed extremely high permittivity up to ∼105, which can be referred to as colossal permittivity, with relatively low dielectric loss of ∼0.05. Data analyses following Debye relaxation and universal dielectric response models indicate that the origin of colossal permittivity in BT ceramics is the result of a hopping polaron within semiconducting grains in combination with interfacial polarization at the insulating grain boundary. Furthermore, the contributions of each polarization mechanism to the colossal permittivity in SPS BT, such as a hopping polarization, internal barrier layer capacitance effect, and electrode effect, were estimated.
Laplace deep level transient spectroscopy of electron traps in epitaxial metalorganic chemical vapor deposition grown n-GaSb
Authors: Venter A. , Botha J. R. , Wagener V. , Murape D. M.
Published: January 2013

Three prominent electron traps, 0.167 eV, 0.243 eV, and 0.295 eV below the conduction band minimum were detected in Te doped MOCVD grown n-GaSb using an Au Schottky barrier diode. The free carrier concentration of the ∼3 μm epilayer grown on n+ (>1018 cm−3) substrate, confirmed by Hall and capacitance-voltage measurements, was 5–7 × 1016 cm−3. The low doping concentration of the epitaxial layers was achieved using diethyl tellurium as the dopant source. Defect concentration profiles suggest that Ec-0.167 eV and Ec-0.243 are predominantly confined to the surface of the epilayer and that the concentration, thereof, approximates the free carrier concentration of the material close to the metal-semiconductor interface.
Searching for room temperature ferromagnetism in transition metal implanted ZnO and GaN
Authors: Pereira L. M. C. , Araújo J. P. , Wahl U. , Decoster S. , Van Bael M. J. , Temst K. , Vantomme A.
Published: January 2013

Significant progress in the field of wide-gap dilute magnetic semiconductors (DMS) depends on the discovery of a material system which not only shows high-temperature ferromagnetism but is also simple to prepare and thus easy to reproduce. In this context, ion implantation is an attractive doping method, being both relatively simple and highly reproducible. Here, we report on the search for high-temperature ferromagnetism in ZnO and GaN implanted with Mn, Fe, and Co, prepared under a wide range of implantation and post-processing conditions. We focused on the low concentration regime (∼0.3−4%) in order to avoid phase segregation and applied strict experimental procedures to avoid ferromagnetic contamination. Despite the wide range of materials, implantation and post-processing conditions, none of the DMS systems showed room-temperature ferromagnetism. These results support the view that dilute transition-metal moments do not order ferromagnetically in ZnO and GaN.
Nanomechanical characterization of rod-like superlattice assembled from tobacco mosaic viruses
Authors: Wang Haoran , Wang Xinnan , Li Tao , Lee Byeongdu
Published: January 2013

Tobacco mosaic virus (TMV) and TMV-derived materials have demonstrated their great potential in biomedical applications, where the mechanical properties are determining factors for their proper functionalities and structural integrity. Recently, it has been found that a superlattice structure can be formed by two-dimensional hexagonal packing TMV self-assembly in Barium ions solution. In parallel to the exploration of possible applications of TMV superlattice, the mechanical properties were characterized by the atomic force microscopy based nanoindentation. The elastic modulus of 2.14 GPa was obtained by application of the extended Johnson-Kendall-Roberts (JKR) model with the force vs sample deformation data. The adhesion force was taken into consideration, and an easy-to-implement approach of using the extended JKR model was proposed by processing both the theoretical model and the experimental data. Finite element analysis was conducted to evaluate the reinforcing effect of the like-charge forces between the TMVs and the mechanical properties of the TMV superlattice. Using the Halpin-Tsai model, the transverse elastic modulus of the superlattice sample varied within 2.00–4.38 GPa, depending on the indentation locations. Attraction-repulsion equilibrium was found to maintain the packing of TMVs. This provides useful information to address the sources of the attraction and repulsion forces to control the TMV assembly.
Fermi level tuning of topological insulator Bi2(SexTe1−x)3 nanoplates
Authors: Hao Guolin , Qi Xiang , Xue Lin , Cai Canying , Li Jun , Wei Xiaolin , Zhong Jianxin
Published: January 2013

The crystal structures and morphologies of ternary Bi2(SexTe1−x)3 nanoplates have been systematically characterized by employing atomic force microscopy, scanning electron microscopy, high-resolution transmission electron microscopy equipped with the energy dispersive X-ray spectrometer, and the X-ray diffraction. We find that the Bi2(SexTe1−x)3 nanoplates exhibit uniform charge and surface potential distributions. And their Fermi levels can be effectively tuned up to 0.23 eV by varying the selenium/tellurium composition ratios.
Electron molecular beam epitaxy: Layer-by-layer growth of complex oxides via pulsed electron-beam deposition
Authors: Comes Ryan , Gu Man , Khokhlov Mikhail , Liu Hongxue , Lu Jiwei , Wolf Stuart A.
Published: January 2013

Complex oxide epitaxial film growth is a rich and exciting field, owing to the wide variety of physical properties present in oxides. These properties include ferroelectricity, ferromagnetism, spin-polarization, and a variety of other correlated phenomena. Traditionally, high quality epitaxial oxide films have been grown via oxide molecular beam epitaxy or pulsed laser deposition. Here, we present the growth of high quality epitaxial films using an alternative approach, the pulsed electron-beam deposition technique. We demonstrate all three epitaxial growth modes in different oxide systems: Frank-van der Merwe (layer-by-layer); Stranski-Krastanov (layer-then-island); and Volmer-Weber (island). Analysis of film quality and morphology is presented and techniques to optimize the morphology of films are discussed.
Synthesis and photoluminescence of fluorinated graphene quantum dots
Authors: Feng Qian , Cao Qingqi , Li Ming , Liu Fuchi , Tang Nujiang , Du Youwei
Published: January 2013

Fluorinated graphene quantum dots (F-GQDs) were synthesized by cutting fluorinated graphene through a hydrothermal approach. The F-GQDs with oxygen-rich functional groups have a F/C atomic ratio of ca. 23.68% and diameter of 1-7 nm. The photoluminescence (PL) properties of the F-GQDs were investigated. The results showed that besides exhibiting bright blue PL, the F-GQDs display a clear upconversion PL.
Optically tunable long wavelength infrared quantum cascade laser operated at room temperature
Authors: Suchalkin S. , Jung S. , Tober R. , Belkin M. A. , Belenky G.
Published: January 2013

We demonstrate rapid tuning of the emission frequency of a room-temperature mid-infrared quantum cascade laser by external optical pumping. Emission frequency tuning over 0.3 cm−1 (10 GHz) has been achieved for a λ = 9 μm device by optical generation of electron-hole pairs along the entire length of the laser stripe. Measurements indicate that this approach allows for rapid broadband frequency-modulation of mid-infrared quantum cascade lasers at above 300 MHz modulation frequencies.
Electron spin dynamics study of bulk p-GaAs: The screening effect
Authors: Zhao Chunbo , Yan Tengfei , Ni Haiqiao , Niu Zhichuan , Zhang Xinhui
Published: January 2013

In this work, the electron spin dynamics of bulk p-GaAs doped with Be grown by molecular beam epitaxy is investigated by using the time-resolved magneto-optical Kerr rotation technique. The spin relaxation/dephasing times T1 and T2* are systematically investigated as a function of hole doping density and photo-excitation density as well as temperature. The complex hole doping density dependence of spin relaxation times T1 and T2* is observed experimentally, which agrees well with predictions of the kinetic spin Bloch equation theory published previously [J. Jiang and M. Wu, Phys. Rev. B 79, 125206 (2009)]. D'yakonov-Perel's mechanism [M. Dyakonov and V. Perel, Sov. Phys. Solid State 13, 3023 (1972)] is discussed to dominate the electron spin relaxation process in p-GaAs, with the effect of hole screening proven to play an important role.
Drought survival of Australian rainforest seedlings is influenced by species evolutionary history and soil type
Authors: Curran Timothy J. , Clarke Peter J. , Warwick Nigel W. M.
Published: January 2013

Water availability influences regional tree distributions in rainforests, often by affecting survival of seedlings. The occurrence of ‘dry rainforest’ species in subhumid climates has been attributed to the evolution of drought-resistant species from their mesic rainforest congeners. Many genera are found in both dry and mesic rainforest of Australia but the extent to which this is due to differential drought resistance has not been confirmed experimentally. We compared drought survival within three congeneric pairs of dry and mesic rainforest taxa in a glasshouse dry-down experiment. Soil type could also play a role, with dry rainforests mostly occurring on fine-textured soils such as loams, which have a high available water-holding capacity, compensating for lower rainfall. Hence, we grew plants in loam or sand soil. In all pairs, the dry rainforest taxon was better able to survive drought, providing support for the climate-induced evolution of a dry rainforest flora and further confirming that drought resistance of seedlings can shape tree species distributions at regional scales. Two of three pairs had higher seedling survival on basalt-derived loam soil, suggesting that such soils may aid seedling persistence during drought. Over evolutionary time, this may have resulted in the high fidelity of dry rainforest for these soils.
Development and Evaluation of a Raman Flow Cell for Monitoring Continuous Flow Reactions
Authors: Chaplain Grant , Haswell Stephen J. , Fletcher Paul D. I. , Kelly Stephen M. , Mansfield Andrew
Published: January 2013

We show how in-line Raman spectroscopy can be used to monitor both reactant and product concentrations for a heterogeneously catalysed Suzuki cross reaction operating in continuous flow. The flow system consisted of an HPLC pump to drive a homogeneous mixture of the reactants (4-bromobenzonitrile, phenylboronic acid, and potassium carbonate) through an oven heated (80°C) palladium catalyst immobilised on a silica monolith. A custom built PTFE in-line flow cell with a quartz window enabled the coupling of an Ocean Optics Raman spectrometer probe to monitor both the reactants and product (4-cyanobiphenyl). Calibration was based on obtaining multivariate spectral data in the range 1530 cm–1 and 1640 cm–1 and using partial least-squares regression (PLSR) to obtain a calibration model which was validated using gas chromatography–mass spectrometry (GCMS) analysis. In-line Raman monitoring of the reactant and product concentrations enable (i) determination of reaction kinetic information such as the empirical rate law and associated rate constant and (ii) optimisation of either the product conversion (61 % at 0.02 mL min–1 generating 17 g h–1) or product yield (14 % at 0.24 mL min–1 generating 53 g h–1).
LRP-6 is a coreceptor for multiple fibrogenic signaling pathways in pericytes and myofibroblasts that are inhibited by DKK-1
Authors: Ren Shuyu , Johnson Bryce G. , Kida Yujiro , Ip Colin , Davidson Kathryn C. , Lin Shuei-Liong , Kobayashi Akio , Lang Richard A. , Hadjantonakis Anna-Katerina , Moon Randall T. , Duffield Jeremy S.
Published: January 2013

Fibrosis of vital organs is a major public health problem with limited therapeutic options. Mesenchymal cells including microvascular mural cells (pericytes) are major progenitors of scar-forming myofibroblasts in kidney and other organs. Here we show pericytes in healthy kidneys have active WNT/β-catenin signaling responses that are markedly up-regulated following kidney injury. Dickkopf-related protein 1 (DKK-1), a ligand for the WNT coreceptors low-density lipoprotein receptor-related proteins 5 and 6 (LRP-5 and LRP-6) and an inhibitor of WNT/β-catenin signaling, effectively inhibits pericyte activation, detachment, and transition to myofibroblasts in vivo in response to kidney injury, resulting in attenuated fibrogenesis, capillary rarefaction, and inflammation. DKK-1 blocks activation and proliferation of established myofibroblasts in vitro and blocks pericyte proliferation to PDGF, pericyte migration, gene activation, and cytoskeletal reorganization to TGF-β or connective tissue growth factor. These effects are largely independent of inhibition of downstream β-catenin signaling. DKK-1 acts predominantly by inhibiting PDGF-, TGF-β–, and connective tissue growth factor-activated MAPK and JNK signaling cascades, acting via LRP-6 with associated WNT ligand. Biochemically, LRP-6 interacts closely with PDGF receptor β and TGF-β receptor 1 at the cell membrane, suggesting that it may have roles in pathways other than WNT/β-catenin. In summary, DKK-1 blocks many of the changes in pericytes required for myofibroblast transition and attenuates established myofibroblast proliferation/activation by mechanisms dependent on LRP-6 and WNT ligands but not the downstream β-catenin pathway.
Rare-earth vs. heavy metal pigments and their colors from first principles
Authors: Tomczak Jan M. , Pourovskii Leonid V. , Vaugier Loig , Georges Antoine , Biermann Silke
Published: January 2013

Many inorganic pigments contain heavy metals hazardous to health and environment. Much attention has been devoted to the quest for nontoxic alternatives based on rare-earth elements. However, the computation of colors from first principles is a challenge to electronic structure methods, especially for materials with localized
f
-orbitals. Here, starting from atomic positions only, we compute the colors of the red pigment cerium fluorosulfide as well as mercury sulfide (classic vermilion). Our methodology uses many-body theories to compute the optical absorption combined with an intermediate length-scale modelization to assess how coloration depends on film thickness, pigment concentration, and granularity. We introduce a quantitative criterion for the performance of a pigment. While for mercury sulfide, this criterion is satisfied because of large transition matrix elements between wide bands, cerium fluorosulfide presents an alternative paradigm: the bright red color is shown to stem from the combined effect of the quasi-2D and the localized nature of

states. Our work shows the power of modern computational methods, with implications for the theoretical design of materials with specific optical properties.
Women in Praise of Women: Female Poets and Female Patrons in Qajar Iran
Authors: Brookshaw Dominic Parviz
Published: January 2013

This study examines the poetry of two women of nineteenth-century Iran—one royal, one non-royal—and the women patrons for whom they composed praise poetry. Through the reconstruction of female-centered patronage networks and associated female-only performance venues, and via an examination of the active roles played by female patrons both in affairs of state and in the management of the immense royal harem, this study highlights the various ways in which members of several generations of women in Qajar Iran were involved in the production, dissemination and appreciation of poetry. It is argued here that these patronage and poetry production networks should be read as evidence of a female-centered literary tradition, one that was in dialogue with (and often intersected) the dominant male tradition; one that empowered the women actors within it to create a sisterhood of poets through which their art could be passed on from mother to daughter, and from daughter to granddaughter (and occasionally from mother to son).
Aversion to Injection Limits Acceptability of Extended-Release Naltrexone among Homeless, Alcohol-Dependent Patients
Authors: Friedmann Peter D. , Mello Dawn , Lonergan Sean , Bourgault Claire , O'Toole Thomas P.
Published: January 2013

Background: Ending homelessness is a major priority of the Department of Veteran Affairs (VA), and alcohol use can be a barrier to stable housing. Clinical trials suggest that depot extended-release naltrexone (XR-NTX) is efficacious in reducing alcohol consumption among alcohol-dependent subjects. Methods: An open-label, randomized pilot study sought to examine the feasibility and effectiveness of XR-NTX versus oral naltrexone to improve alcohol consumption and housing stability among homeless, alcohol-dependent veterans at the Providence Veteran Affairs Medical Center. Results: Of 215 potential candidates approached over a 16-month recruitment period, only 15 agreed to consider study entry and 7 were randomized. The primary reasons given for refusal were not wanting an injection; fear of needles; and not wanting to change drinking habits. Only 1 participant in the XR-NTX group returned after the first injection. Three participants in the oral naltrexone group attended all 7 visits and had good outcomes. Conclusions: Although XR-NTX has demonstrated efficacy in reducing heavy drinking, limited acceptance of the injection might reduce its effectiveness among homeless, alcohol-dependent patients.
The influence of age, sex, and theism on ethical judgments
Authors: Smith Raymond D. , DeBode Jason D. , Walker Alan G.
Published: January 2013

The authors develop a model of ethical orientation based on responses to a series of ethically questionable vignettes using factor analysis and a categorical regression procedure. The factors used to explain variance in responses are theism orientation, age, sex, and intrinsic and extrinsic religious motivation orientation. The results confirm earlier research in that age and sex are not significant in and of themselves. An important finding is that theistic orientation is significant and also displays a strong relation to extrinsic orientation. Interaction effects between sex and theism are also discovered and explained. The results are illuminating in highlighting the importance to ethical orientation not of religious orientation per se but of the extrinsic orientation and its interaction with sex. The paper, thus, illuminates more deeply the sex–ethics connection. Last, while not particularly significant, there is also an identified age effect on ethical orientation which confirms moral development theory.
The effects of personality and spirituality on workplace incivility perceptions
Authors: Naimon Erik C. , Mullins Morell E. , Osatuke Katerine
Published: January 2013

The relationships between negative affectivity (NA), locus of control, agreeableness, and workplace spirituality were tested with workplace incivility perceptions. Hundred and two part-time and full-time college students, 90 of whom were aged 25 and older, completed measures of the
previous variables; measures of remaining Five Factor Model traits, civility, and social desirability were administered for supplemental purposes. Significant relationships were found between NA and incivility, agreeableness and incivility, and workplace spirituality and incivility. Workplace
spirituality provided a unique contribution in the prediction of incivility perceptions. The spirituality measure was factor analyzed to test factors’ relationships with incivility when controlling for the related construct of civility. Spirituality components of meaning and spiritual
blocks were found to predict incivility perceptions independently of civility scores. Results suggest that spirituality levels affect incivility perceptions above and beyond that of traditional personality variables.
Women in cell biology: a seat at the table and a place at the podium
Authors: Masur Sandra Kazahn
Published: January 2013

The Women in Cell Biology (WICB) committee of the American Society for Cell Biology (ASCB) was started in the 1970s in response to the documented underrepresentation of women in academia in general and cell biology in particular. By coincidence or causal relationship, I am happy to say that since WICB became a standing ASCB committee, women have been well represented in ASCB's leadership and as symposium speakers at the annual meeting. However, the need to provide opportunities and information useful to women in developing their careers in cell biology is still vital, given the continuing bias women face in the larger scientific arena. With its emphasis on mentoring, many of WICB's activities benefit the development of both men and women cell biologists. The WICB “Career Column” in the monthly ASCB Newsletter is a source of accessible wisdom. At the annual ASCB meeting, WICB organizes the career discussion and mentoring roundtables, childcare awards, Mentoring Theater, career-related panel and workshop, and career recognition awards. Finally, the WICB Speaker Referral Service provides a list of outstanding women whom organizers of scientific meetings, scientific review panels, and university symposia/lecture series can reach out to when facing the proverbial dilemma, “I just don't know any women who are experts.”
Sequential steps in DNA replication are inhibited to ensure reduction of ploidy in meiosis
Authors: Hua Hui , Namdar Mandana , Ganier Olivier , Gregan Juraj , Méchali Marcel , Kearsey Stephen E.
Published: January 2013

Meiosis involves two successive rounds of chromosome segregation without an intervening S phase. Exit from meiosis I is distinct from mitotic exit, in that replication origins are not licensed by Mcm2-7 chromatin binding, but spindle disassembly occurs during a transient interphase-like state before meiosis II. The absence of licensing is assumed to explain the block to DNA replication, but this has not been formally tested. Here we attempt to subvert this block by expressing the licensing control factors Cdc18 and Cdt1 during the interval between meiotic nuclear divisions. Surprisingly, this leads only to a partial round of DNA replication, even when these factors are overexpressed and effect clear Mcm2-7 chromatin binding. Combining Cdc18 and Cdt1 expression with modulation of cyclin-dependent kinase activity, activation of Dbf4-dependent kinase, or deletion of the Spd1 inhibitor of ribonucleotide reductase has little additional effect on the extent of DNA replication. Single-molecule analysis indicates this partial round of replication results from inefficient progression of replication forks, and thus both initiation and elongation replication steps may be inhibited in late meiosis. In addition, DNA replication or damage during the meiosis I–II interval fails to arrest meiotic progress, suggesting absence of checkpoint regulation of meiosis II entry.
Predictors and prognostic implications of incident heart failure following the first diagnosis of atrial fibrillation in patients with structurally normal hearts: the Belgrade Atrial Fibrillation Study
Authors: Potpara Tatjana S. , Polovina Marija M. , Licina Marina M. , Marinkovic Jelena M. , Lip Gregory Y. H.
Published: January 2013

Aim

Atrial fibrillation (AF) commonly co‐exists with heart failure (HF). The risk factors for and prognostic implications of incident HF development in patients with first‐diagnosed AF and structurally normal hearts are poorly defined. In a cohort of patients with first‐diagnosed AF and structurally normal hearts on baseline echocardiography, we investigated baseline risk factors for the development of incident HF and tested the hypothesis that incident HF was an independent predictor of adverse outcomes during a mean 10‐year follow‐up period.

Methods and results

This was a registry‐based, observational cohort study of 842 patients initially diagnosed between 1992 and 2007 (mean age 51.6 ± 12.4 years), whereby 83 (9.9%) developed HF. The linearized rate of incident HF was 0.97% [95% confidence interval (CI) 0.78–1.19%] per 100 patient‐years. Baseline history of hypertension, diabetes mellitus, dilated left atrium, and low‐normal LVEF (50–54%) were multivariable predictors of subsequent HF (all P < 0.05). HF development was significantly associated with increased number of hospitalizations, AF progression, any stroke/peripheral thrombo‐embolism, ischaemic stroke, cardiovascular death, and all‐cause mortality (all P < 0.001). Kaplan–Meier 10‐year estimates of survival free of the composite endpoint of AF progression, thrombo‐embolism, and mortality were significantly worse for AF patients with incident HF compared with those without HF (68.8%; 95% CI 64.7–72.9 vs. 25.9% 95% CI 15.7–36.1, P < 0.001).

Conclusion

Underlying co‐morbidities or subtle alterations such as mild left atrial dilatation or low‐normal LVEF in the absence of overt underlying heart disease are baseline independent risk factors for incident HF during a long‐term follow‐up. Incident HF was an independent predictor of adverse outcomes in patients initially diagnosed with first‐diagnosed AF and structurally normal hearts. These findings could facilitate the identification of AF patients at increased risk for adverse outcomes within the cohort perceived as being at ‘low risk’ given a structurally normal heart on echocardiography.
Shifts between gelatinous and crustacean plankton in a coastal upwelling region
Authors: Bode Antonio , Álvarez-Ossorio Maria Teresa , Miranda Ana , Ruiz-Villarreal Manuel
Published: January 2013

Bode, A., Álvarez-Ossorio M. T., Miranda, A., and Ruiz-Villarreal, M. 2013. Shifts between gelatinous and crustacean plankton in a coastal upwelling region. – ICES Journal of Marine Science, 70: 934–942. Variability in the dominance of copepods vs. gelatinous plankton was analysed using monthly time-series covering the last 55 years and related to changes in climatic, oceanographic, and fishery conditions in the upwelling region of Galicia (NW Spain). Seasonality was generally the main component of variability in all groups, both along the coast and in the nearby ocean, but no common long-term trend was found. Coastal copepods increased since the early 1990s, and gelatinous plankton increased in the ocean during the 1980s. Different trends were found for gelatinous plankton in two coastal sites, characterized by increases in either medusae or tunicates. In all series, multiyear periods of relative dominance of gelatinous vs. copepod plankton were evident. In general, copepod periods were observed in positive phases of the main modes of regional climatic variability. Conversely, gelatinous periods occurred during negative climatic phases. However, the low correlations between gelatinous plankton and climatic, oceanographic, or fishery variables suggest that local factors play a major role in their proliferations.
Fishing, Commitment, and Communication: A Proposal for Comprehensive Nonbinding Research Registration
Authors: Humphreys Macartan , Sanchez de la Sierra Raul , van der Windt Peter
Published: January 2013

Social scientists generally enjoy substantial latitude in selecting measures and models for hypothesis testing. Coupled with publication and related biases, this latitude raises the concern that researchers may intentionally or unintentionally select models that yield positive findings, leading to an unreliable body of published research. To combat this “fishing” problem in medical studies, leading journals now require preregistration of designs that emphasize the prior identification of dependent and independent variables. However, we demonstrate here that even with this level of advanced specification, the scope for fishing is considerable when there is latitude over selection of covariates, subgroups, and other elements of an analysis plan. These concerns could be addressed through the use of a form of comprehensive registration. We experiment with such an approach in the context of an ongoing field experiment for which we drafted a complete “mock report” of findings using fake data on treatment assignment. We describe the advantages and disadvantages of this form of registration and propose that a comprehensive but nonbinding approach be adopted as a first step to combat fishing by social scientists. Likely effects of comprehensive but nonbinding registration are discussed, the principal advantage being communication rather than commitment, in particular that it generates a clear distinction between exploratory analyses and genuine tests.
Sequence Variation in Two Protein-Coding Genes Correlates with Mycelial Compatibility Groupings in Sclerotium rolfsii
Authors: Remesal Efrén , Landa Blanca B. , Jiménez-Gasco María del Mar , Navas-Cortés Juan A.
Published: January 2013

Populations of Sclerotium rolfsii, the causal organism of Sclerotium root-rot on a wide range of hosts, can be placed into mycelial compatibility groups (MCGs). In this study, we evaluated three different molecular approaches to unequivocally identify each of 12 previously identified MCGs. These included restriction fragment length polymorphism (RFLP) patterns of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (rDNA) and sequence analysis of two protein-coding genes: translation elongation factor 1α (EF1α) and RNA polymerase II subunit two (RPB2). A collection of 238 single-sclerotial isolates representing 12 MCGs of S. rolfsii were obtained from diseased sugar beet plants from Chile, Italy, Portugal, and Spain. ITS-RFLP analysis using four restriction enzymes (AluI, HpaII, RsaI, and MboI) displayed a low degree of variability among MCGs. Only three different restriction profiles were identified among S. rolfsii isolates, with no correlation to MCG or to geographic origin. Based on nucleotide polymorphisms, the RPB2 gene was more variable among MCGs compared with the EF1α gene. Thus, 10 of 12 MCGs could be characterized utilizing the RPB2 region only, while the EF1α region resolved 7 MCGs. However, the analysis of combined partial sequences of EF1α and RPB2 genes allowed discrimination among each of the 12 MCGs. All isolates belonging to the same MCG showed identical nucleotide sequences that differed by at least in one nucleotide from a different MCG. The consistency of our results to identify the MCG of a given S. rolfsii isolate using the combined sequences of EF1α and RPB2 genes was confirmed using blind trials. Our study demonstrates that sequence variation in the protein-coding genes EF1α and RPB2 may be exploited as a diagnostic tool for MCG typing in S. rolfsii as well as to identify previously undescribed MCGs.
L-form bacteria, cell walls and the origins of life
Authors: Errington Jeff
Published: January 2013

The peptidoglycan wall is a defining feature of bacterial cells and was probably already present in their last common ancestor. L-forms are bacterial variants that lack a cell wall and divide by a variety of processes involving membrane blebbing, tubulation, vesiculation and fission. Their unusual mode of proliferation provides a model for primitive cells and is reminiscent of recently developed
in vitro
vesicle reproduction processes. Invention of the cell wall may have underpinned the explosion of bacterial life on the Earth. Later innovations in cell envelope structure, particularly the emergence of the outer membrane of Gram-negative bacteria, possibly in an early endospore former, seem to have spurned further major evolutionary radiations. Comparative studies of bacterial cell envelope structure may help to resolve the early key steps in evolutionary development of the bacterial domain of life.
Human cytomegalovirus chemokine receptor US28 induces migration of cells on a CX3CL1-presenting surface
Authors: Hjortø Gertrud M. , Kiilerich-Pedersen Katrine , Selmeczi David , Kledal Thomas N. , Larsen Niels B.
Published: January 2013

Human cytomegalovirus (HCMV)-encoded G protein-coupled-receptor US28 is believed to participate in virus dissemination through modulation of cell migration and immune evasion. US28 binds different CC chemokines and the CX3C chemokine CX3CL1. Membrane-anchored CX3CL1 is expressed by immune-activated endothelial cells, causing redirection of CX3CR1-expressing leukocytes in the blood to sites of infection. Here, we used stable transfected cell lines to examine how US28 expression affects cell migration on immobilized full-length CX3CL1, to model how HCMV-infected leukocytes interact with inflamed endothelium. We observed that US28-expressing cells migrated more than CX3CR1-expressing cells when adhering to immobilized CX3CL1. US28-induced migration was G protein-signalling dependent and was blocked by the phospholipase Cβ inhibitor U73122 and the intracellular calcium chelator BAPTA-AM. In addition, migration was inhibited in a dose-dependent manner by competition from CCL2 and CCL5, whereas CCL3 had little effect. Instead of migrating, CX3CR1-expressing cells performed ‘dancing-on-the-spot’ movements, demonstrating that anchored CX3CL1 acts as a strong tether for these cells. At low receptor expression levels, however, no significant difference in migration potential was observed when comparing the migration of CX3CR1- and US28-expressing cells. Thus, these data showed that, in contrast to CX3CR1, which promotes efficient cell capture upon binding to anchored CX3CL1, US28 acts to increase the migration of cells upon binding to the same ligand. Overall, this indicates that infected cells probably move more than uninfected cells in inflamed tissues with high CX3CL1 expression, with soluble chemokines affecting the final migration.
Epstein–Barr virus LMP2A increases IL-10 production in mitogen-stimulated primary B-cells and B-cell lymphomas
Authors: Incrocci Ryan , McCormack Molly , Swanson-Mungerson Michelle
Published: January 2013

Epstein–Barr virus (EBV) latently infected B-cells are the precursors of EBV-associated malignancies. EBV-infection induces the production of pro-survival and anti-inflammatory cytokines that may be important in the transition between latency and malignancy. One EBV protein, LMP2A, can be detected in both latently infected resting B-cells and in EBV-associated malignancies. Therefore, we tested the ability of LMP2A to influence cytokine production using both LMP2A-Tg primary B-cells and LMP2A-expressing B-cell lines. Our data demonstrate that LMP2A does not globally alter B-cell-produced cytokine levels, but specifically targets IL-10. Additional studies using ELISA and real-time-RT-PCR confirm that LMP2A utilizes PI3-kinase to increase IL-10 levels. Finally, the data demonstrate that LMP2A-expressing B-cell lines are more dependent on IL-10 for survival in comparison to LMP2A-negative B-cell lines. These data identify a novel function of LMP2A in the alteration of a cytokine that is important for both tumour survival and anti-tumour responses.
Mouse TU tagging: a chemical/genetic intersectional method for purifying cell type-specific nascent RNA
Authors: Gay Leslie , Miller Michael R. , Ventura P. Britten , Devasthali Vidusha , Vue Zer , Thompson Heather L. , Temple Sally , Zong Hui , Cleary Michael D. , Stankunas Kryn , Doe Chris Q.
Published: January 2013

Transcriptional profiling is a powerful approach for understanding development and disease. Current cell type-specific RNA purification methods have limitations, including cell dissociation trauma or inability to identify all RNA species. Here, we describe “mouse thiouracil (TU) tagging,” a genetic and chemical intersectional method for covalent labeling and purification of cell type-specific RNA in vivo. Cre-induced expression of uracil phosphoribosyltransferase (UPRT) provides spatial specificity; injection of 4-thiouracil (4TU) provides temporal specificity. Only UPRT+ cells exposed to 4TU produce thio-RNA, which is then purified for RNA sequencing (RNA-seq). This method can purify transcripts from spatially complex and rare (<5%) cells, such as Tie2:Cre+ brain endothelia/microglia (76% validated by expression pattern), or temporally dynamic transcripts, such as those acutely induced by lipopolysaccharide (LPS) injection. Moreover, generating chimeric mice via UPRT+ bone marrow transplants identifies immune versus niche spleen RNA. TU tagging provides a novel method for identifying actively transcribed genes in specific cells at specific times within intact mice.