bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial correlation of hydrometeor occurrence, reflectivity, and rain rate from CloudSat
Authors: Marchand Roger
Published: February 2012

This paper examines the along‐track vertical and horizontal structure of hydrometeor occurrence, reflectivity, and column rain rate derived from CloudSat. The analysis assumes hydrometeors statistics in a given region are horizontally invariant, with the probability of hydrometeor co‐occurrence obtained simply by determining the relative frequency at which hydrometeors can be found at two points (which may be at different altitudes and offset by a horizontal distance, Δx). A correlation function is introduced (gamma correlation) that normalizes hydrometeor co‐occurrence values to the range of 1 to −1, with a value of 0 meaning uncorrelated in the usual sense. This correlation function is a generalization of the alpha overlap parameter that has been used in recent studies to describe the overlap between cloud (or hydrometeor) layers. Examples of joint histograms of reflectivity at two points are also examined. The analysis shows that the traditional linear (or Pearson) correlation coefficient provides a useful one‐to‐one measure of the strength of the relationship between hydrometeor reflectivity at two points in the horizontal (that is, two points at the same altitude). While also potentially useful in the vertical direction, the relationship between reflectivity values at different altitudes is not as well described by the linear correlation coefficient. The decrease in correlation of hydrometeor occurrence and reflectivity with horizontal distance, as well as precipitation occurrence and column rain rate, can be reasonably well fit with a simple two‐parameter exponential model. In this paper, the North Pacific and tropical western Pacific are examined in detail, as is the zonal dependence.
Apatite thermochronometry within a knickzone near the Higher Himalaya front, central Nepal: No resolvable fault motion in the past one million years
Authors: Nadin Elisabeth S. , Martin Aaron J.
Published: February 2012

We combine apatite fission track ages and track‐length measurements with apatite (U‐Th)/He ages to test the hypothesis that active near‐surface faulting is absent at the transition between the Higher and Lower Himalayan physiographic provinces in central Nepal. Fifteen samples define a 2.5‐km‐long, nearly constant‐elevation transect that crosses the largest knickzone on the Modi River in central Nepal. This knickzone could have resulted from modern faulting near the ancient Main Central thrust or from river incision following landslide dam breaching. Apatite fission track ages from the transect are generally ca. 1 Ma, and apatite He ages, selected by considering He concentrations, are 0.5–0.8 Ma. There is no discernable age difference between any of the samples outside 2σ uncertainty. Cooling rates are >100°C/Myr and are uniform across the sample transect. We calculate an average exhumation rate of ∼3 mm/yr across the region, with rates deduced from the fission track data equal to those extracted from the He ages. According to our new data, no fault in our study area has undergone a time‐averaged slip rate faster than 4 mm/yr during the past 1 Myr.
The second generation Singapore high resolution proton beam writing facility
Authors: van Kan J. A. , Malar P. , Baysic de Vera Armin
Published: February 2012

A new proton beam focusing facility, designed for proton beam writing (PBW) applications has been tested. PBW allows for proximity free structuring of high aspect ratio, high-density 3D nanostructures. The new facility is designed around OM52 compact quadrupole lenses capable of operating in a variety of high demagnification configurations. Performance tests show that proton beams can be focused down to 19.0 × 29.9 nm2 and single line scans show a beam width of 12.6 nm. The ultimate goal of sub 10 nm structuring with MeV protons will be discussed.
Comparison between off-resonance and electron Bernstein waves heating regime in a microwave discharge ion source
Authors: Castro G. , Mascali D. , Romano F. P. , Celona L. , Gammino S. , Lanaia D. , Di Giugno R. , Miracoli R. , Serafino T. , Di Bartolo F. , Gambino N. , Ciavola G.
Published: February 2012

A microwave discharge ion source (MDIS) operating at the Laboratori Nazionali del Sud of INFN, Catania has been used to compare the traditional electron cyclotron resonance (ECR) heating with an innovative mechanisms of plasma ignition based on the electrostatic Bernstein waves (EBW). EBW are obtained via the inner plasma electromagnetic-to-electrostatic wave conversion and they are absorbed by the plasma at cyclotron resonance harmonics. The heating of plasma by means of EBW at particular frequencies enabled us to reach densities much larger than the cutoff ones. Evidences of EBW generation and absorption together with X-ray emissions due to high energy electrons will be shown. A characterization of the discharge heating process in MDISs as a generalization of the ECR heating mechanism by means of ray tracing will be shown in order to highlight the fundamental physical differences between ECR and EBW heating.
Molecular and negative ion production by a standard electron cyclotron resonance ion source
Authors: Rácz R. , Biri S. , Juhász Z. , Sulik B. , Pálinkás J.
Published: February 2012

Molecular and negative ion beams, usually produced in special ion sources, play an increasingly important role in fundamental and applied atomic physics. The ATOMKI-ECRIS is a standard ECR ion source, designed to provide highly charged ion (HCI) plasmas and beams. In the present work, H−, O−, OH−, O2−, C−, C60− negative ions and H2+, H3+, OH+, H2O+, H3O+, O2+ positive molecular ions were generated in this HCI-ECRIS. Without any major modification in the source and without any commonly applied tricks (such as usage of cesium or magnetic filter), negative ion beams of several μA and positive molecular ion beams in the mA range were successfully obtained.
Angular distribution of plasma in the vacuum arc ion source
Authors: Nikolaev A. G. , Yushkov G. Yu. , Savkin K. P. , Oks E. M.
Published: February 2012

This paper presents measurements of the angular distribution of the plasma components and different charge states of metal ions generated by a MEVVA-type ion source and measured by a time-of-flight mass-spectrometer. The experiments were performed for different cathode materials (Al, Cu, and Ti) and for different parameters of the vacuum arc discharge. The results are compared with prior results reported by other authors. The influence of different discharge parameters on the angular distribution in a vacuum arc source is discussed.
Elastomeric silicone substrates for terahertz fishnet metamaterials
Authors: Khodasevych I. E. , Shah C. M. , Sriram S. , Bhaskaran M. , Withayachumnankul W. , Ung B. S. Y. , Lin H. , Rowe W. S. T. , Abbott D. , Mitchell A.
Published: February 2012

In this work, we characterize the electromagnetic properties of polydimethylsiloxane (PDMS) and use this as a free-standing substrate for the realization of flexible fishnet metamaterials at terahertz frequencies. Across the 0.2–2.5 THz band, the refractive index and absorption coefficient of PDMS are estimated as 1.55 and 0–22 cm−1, respectively. Electromagnetic modeling, multi-layer flexible electronics microfabrication, and terahertz time-domain spectroscopy are used in the design, fabrication, and characterization of the metamaterials, respectively. The properties of PDMS add a degree of freedom to terahertz metamaterials, with the potential for tuning by elastic deformation or integrated microfluidics.
Magnetic properties and microstructures of iron oxide@mesoporous silica core-shell composite for applications in magnetic dye separation
Authors: Hao Weichang , Xi Yang , Hu Jingwei , Wang Tianmin , Du Y. , Wang X. L.
Published: February 2012

In this report, hollow mesoporous silica (HMS) and iron oxide-hollow mesoporous silica (FexOy@HMS) core-shell composite were prepared by a one-step facile fabrication method. Transmission electron microscopy, X-ray diffraction, N2 adsorption–desorption isotherms, and vibrating sample magnetometer were used to characterize the morphology, microstructure, and magnetic properties of the HMS and core-shell composite. The magnetic separability of FexOy@HMS core-shell composite was tested in Rhodamine B (Rh.B) dye solution. The results indicate that the core-shell composite can absorb Rh.B dyes molecules effectively up to 90.1%.
Nanometer size effects on magnetic order in La1−xCaxMnO3 (x = 0.5 and 0.6) manganites, probed by ferromagnetic resonance
Authors: Shames A. I. , Rozenberg E. , Sominski E. , Gedanken A.
Published: February 2012

The data on X-band ferromagnetic resonance (FMR) in the half and electron-doped La0.5Ca0.5MnO3 (Ca0.5) and La0.4Ca0.6MnO3 (Ca0.6) nano-crystals and bulk ceramics are reported. The FMR data for considered nano-samples appeared to be strongly different, reflecting a difference in their magnetic/electronic order. An enhancement of the FMR signal intensities is observed in both nano Ca0.5 and Ca0.6 as compared to those in bulk. The peak intensity of such signal in nano Ca0.5 exceeds about two orders of magnitude the corresponding value in nano Ca0.6. This finding evidences on the respective ferromagnetic like and charge ordered antiferromagnetic ground states in Ca0.5 and Ca0.6.
The compressive stress effect on the magnetostriction and magnetization for Sm-Dy-Fe composites
Authors: Wang Bowen , Wang Zhihua , Hao Yanming , Weng Ling , Huang Wenmei , Yan Weili
Published: February 2012

Sm0.88Dy0.12Fe2 rod composites were fabricated under a compaction pressure of 800 MPa along the rod direction and in a magnetic field of 200 kA/m along the direction, perpendicular to the rod axis. It is found that the magnetostriction λ|| parallel to the rod direction is almost unchanged with increasing the compressive stress up to 20 MPa and shows a large unsaturated magnetostriction value of −620 × 10−6 at 600 kA/m. The magnetostriction λ⊥ perpendicular to rod axis increases with increasing the compressive stress when the magnetic field is larger than 300 kA/m. The variation of the magnetostriction and magnetization with compressive stress has been discussed. This result is very important to application of Sm-Dy-Fe composites.
Application of length vernier in phase coincidence detection and precision frequency measurement
Authors: Miao Miao , Wei Zhou , Bin Wang
Published: February 2012

For comparison of arbitrary frequency signals, the paper proposed two levels of length vernier based on the time-space relationship are used in three levels of phase coincidence detecting circuits to extract the phase coincidence information by proper logic calculation. The length/phase of each vernier is respectively corresponding to the accuracy and the resolution of detecting circuit. The time-space relationship is based on high-stability, high-accuracy, and high-speed of signal transmission. The method is effective to reduce the fuzzy region in the phase coincidence information and reach a higher measuring precision.
A capillary absorption spectrometer for stable carbon isotope ratio (13C/12C) analysis in very small samples
Authors: Kelly J. F. , Sams R. L. , Blake T. A. , Newburn M. , Moran J. , Alexander M. L. , Kreuzer H.
Published: February 2012

A capillary absorption spectrometer (CAS) suitable for IR laser isotope analysis of small CO2 samples is presented. The system employs a continuous-wave (cw) quantum cascade laser to study nearly adjacent rovibrational transitions of different isotopologues of CO2 near 2307 cm−1 (4.34 μm). This initial CAS system can achieve relative isotopic precision of about 10 ppm 13C, or ∼1‰ (per mil in delta notation relative to Vienna Pee Dee Belemnite) with 20–100 picomoles of entrained sample within the hollow waveguide for CO2 concentrations ∼400–750 ppm. Isotopic analyses of such gas fills in a 1-mm ID hollow waveguide of 0.8 m overall physical path length can be carried out down to ∼2 Torr. Overall 13C/12C ratios can be calibrated to ∼2‰ accuracy with diluted CO2 standards. A novel, low-cost method to reduce cw-fringing noise resulting from multipath distortions in the hollow waveguide is presented, which allows weak absorbance features to be studied at the few ppm level (peak-to-rms) after 1000 scans are co-added in ∼10 s. The CAS is meant to work directly with converted CO2 samples from a laser ablation-catalytic combustion micro-sampler to provide 13C/12C ratios of small biological isolates currently operating with spatial resolutions ∼50 μm.
Conformational properties of macromolecular pyramoids and their potential use as nano-containers
Authors: Kosmas M. , Efthymiopoulos P.
Published: February 2012

We study the macroscopic behavior of a pyramid-like nano-construct made of linear macromolecular chains. The average mean square end-to-end distances of the six edges of the pyramoid are evaluated by means of the Gaussian chain model and are found smaller than those of free chains because of architecture confinement. We also evaluate the average areas of the four faces which give a first estimate of the open windows towards the interior space of the macromolecular construct and its loading capacity. The average volume of the polymeric nano-container, which provides a measure of its interior emptiness and carrying ability, is estimated as well. The density of monomers at each point of the construct shows the three-dimensional character of the nano-cage and the location of its entrances and voids.
Normalization schemes for ultrafast x-ray diffraction using a table-top laser-driven plasma source
Authors: Schick D. , Bojahr A. , Herzog M. , Schmising C. von Korff , Shayduk R. , Leitenberger W. , Gaal P. , Bargheer M.
Published: February 2012

We present an experimental setup of a laser-driven x-ray plasma source for femtosecond x-ray diffraction. Different normalization schemes accounting for x-ray source intensity fluctuations are discussed in detail. We apply these schemes to measure the temporal evolution of Bragg peak intensities of perovskite superlattices after ultrafast laser excitation.
Electrically driven nanopyramid green light emitting diode
Authors: Chang S.-P. , Chen Y.-C. , Huang J.-K. , Cheng Y.-J. , Chang J.-R. , Sou K.-P. , Kang Y.-T. , Yang H.-C. , Hsu T.-C. , Kuo H.-C. , Chang C.-Y.
Published: February 2012

An electrically driven nanopyramid green light emitting diode (LED) was demonstrated. The nanopyramid arrays were fabricated from a GaN substrate by patterned nanopillar etch, pillar side wall passivation, and epitaxial regrowth. Multiple quantum wells were selectively grown on the facets of the nanopyramids. The fabricated LED emits green wavelength under electrical injection. The emission exhibits a less carrier density dependent wavelength shift and higher internal quantum efficiency as compared with a reference c-plane sample at the same wavelength. It shows a promising potential for using nanopyramid in high In content LED applications.
Effects of particles on stability of flow-induced precursors
Authors: Zhu Peng-Wei , Phillips Andrew W. , Edward Graham
Published: February 2012

The effect of two colorant particles with different surface geometries on the stability of shear-induced precursors in isotactic polypropylene was studied after the cessation of shear flow at 140 °C. In the absence of particles, the shear-induced precursors survived for at least 100 s after the shear flow ended. The presence of particles was found to stabilize lower molecular weight chains assisting in the formation of additional shear-induced precursors. The precursors thus formed in the samples containing particles contained two oriented clusters with different molecular weights. Incorporation of lower molecular weight chains in the precursors led to increased dissolution rates of the shear-induced precursors. Particle surface geometry was found to influence precursor dissolution, with planar particles stabilizing the shear-induced precursors to a much greater extent than curved particles. The particles investigated thus act like structural probes to follow quantitatively the dissolution process of precursors after shear and importantly to infer the formation of precursors during shear.
An explosively driven high-power microwave pulsed power system
Authors: Elsayed M. A. , Neuber A. A. , Dickens J. C. , Walter J. W. , Kristiansen M. , Altgilbers L. L.
Published: February 2012

The increased popularity of high power microwave systems and the various sources to drive them is the motivation behind the work to be presented. A stand-alone, self-contained explosively driven high power microwave pulsed power system has been designed, built, and tested at Texas Tech University's Center for Pulsed Power and Power Electronics. The system integrates four different sub-units that are composed of a battery driven prime power source utilizing capacitive energy storage, a dual stage helical flux compression generator as the main energy amplification device, an integrated power conditioning system with inductive energy storage including a fast opening electro-explosive switch, and a triode reflex geometry virtual cathode oscillator as the microwave radiating source. This system has displayed a measured electrical source power level of over 5 GW and peak radiated microwaves of about 200 MW. It is contained within a 15 cm diameter housing and measures 2 m in length, giving a housing volume of slightly less than 39 l. The system and its sub-components have been extensively studied, both as integrated and individual units, to further expand on components behavior and operation physics. This report will serve as a detailed design overview of each of the four subcomponents and provide detailed analysis of the overall system performance and benchmarks.
Dielectric properties of Yb3+ and Nb5+ doped RbTiOPO4 single crystals
Authors: Gavaldà Jna. , Carvajal J. J. , Mateos X. , Aguiló M. , Díaz F.
Published: February 2012

The influence of niobium and ytterbium doping in the electrical properties of the RbTiOPO4 (RTP) crystals has been analyzed along the three crystallographic axes. While Yb3+ does not change the ionic conductivity of RTP, Nb5+ increases it considerably. These effects are also observed for the activation energies of these samples doped with Yb3+ and Nb5+, and different relaxation mechanisms have been observed for the different dopants. RTP and Nb:RTP sample show a non-Debye relaxation mechanism, while Yb:RTP and Nb,Yb:RTP samples show a Debye relaxation mechanism.
Planar waveguide with “twisted” boundary conditions: Small width
Authors: Borisov Denis , Cardone Giuseppe
Published: February 2012

We consider a planar waveguide with “twisted” boundary conditions. By twisting we mean a special combination of Dirichlet and Neumann boundary conditions. Assuming that the width of the waveguide goes to zero, we identify the effective (limiting) operator as the width of the waveguide tends to zero, establishes the uniform resolvent convergence in various possible operator norms, and gives the estimates for the rates of convergence. We show that studying the resolvent convergence can be treated as a certain threshold effect and we present an elegant technique which justifies such point of view.
Stochastic mapping of the Michaelis-Menten mechanism
Authors: Dóka Éva , Lente Gábor
Published: February 2012

The Michaelis-Menten mechanism is an extremely important tool for understanding enzyme-catalyzed transformation of substrates into final products. In this work, a computationally viable, full stochastic description of the Michaelis-Menten kinetic scheme is introduced based on a stochastic equivalent of the steady-state assumption. The full solution derived is free of restrictions on amounts of substance or parameter values and is used to create stochastic maps of the Michaelis-Menten mechanism, which show the regions in the parameter space of the scheme where the use of the stochastic kinetic approach is inevitable. The stochastic aspects of recently published examples of single-enzyme kinetic studies are analyzed using these maps.
Sub-250 nm room-temperature optical gain from AlGaN/AlN multiple quantum wells with strong band-structure potential fluctuations
Authors: Francesco Pecora Emanuele , Zhang Wei , Yu. Nikiforov A. , Zhou Lin , Smith David J. , Yin Jian , Paiella Roberto , Dal Negro Luca , Moustakas T. D.
Published: February 2012

Deep-UV optical gain has been demonstrated in Al0.7Ga0.3N/AlN multiple quantum wells under femtosecond optical pumping. Samples were grown by molecular beam epitaxy under a growth mode that introduces band structure potential fluctuations and high-density nanocluster-like features within the AlGaN wells. A maximum net modal gain value of 118 ± 9 cm−1 has been measured and the transparency threshold of 5 ± 1 µJ/cm2 was experimentally determined, corresponding to 1.4 × 1017 cm−3 excited carriers. These findings pave the way for the demonstration of solid-state lasers with sub-250 nm emission at room temperature.
Interplay of point defects, biaxial strain, and thermal conductivity in homoepitaxial SrTiO3 thin films
Authors: Wiedigen S. , Kramer T. , Feuchter M. , Knorr I. , Nee N. , Hoffmann J. , Kamlah M. , Volkert C. A. , Jooss Ch.
Published: February 2012

Separating out effects of point defects and lattice strain on thermal conductivity is essential for improvement of thermoelectric properties of SrTiO3. We study relations between defects generated during deposition, induced lattice strain, and their impact on thermal conductivity κ in homoepitaxial SrTiO3 films prepared by ion-beam sputtering. Lowering the deposition temperature gives rise to lattice expansion by enhancement of point defect density which increases the hardness of the films. Due to a fully coherent substrate-film interface, the lattice misfit induces a large biaxial strain. However, we can show that the temperature dependence of κ is mainly sensitive on the defect concentration.
Two-dimensional electrostatic lattices for indirect excitons
Authors: Remeika M. , Fogler M. M. , Butov L. V. , Hanson M. , Gossard A. C.
Published: February 2012

We report on a method for the realization of two-dimensional electrostatic lattices for excitons using patterned interdigitated electrodes. Lattice structure is set by the electrode pattern and depth of the lattice potential is controlled by applied voltages. We demonstrate square, hexagonal, and honeycomb lattices created by this method.
Ultraviolet electroluminescence from colloidal ZnO quantum dots in an all-inorganic multilayer light-emitting device
Authors: Omata T. , Tani Y. , Kobayashi S. , Takahashi K. , Miyanaga A. , Maeda Y. , Otsuka-Yao-Matsuo S.
Published: February 2012

We report ultraviolet (UV) electroluminescence (EL) at 3.30 eV of colloidal ZnO quantum dots (QDs) in an inorganic multilayer thin-film EL device. The EL spectrum was identical to the photoluminescence spectrum of the source solution of ZnO QDs, and the emission is attributable to quantum confined electron hole pair recombination. The UV emission was successful when the ZnO QD layer was sandwiched by thin MgO layers, while only a defect-related visible emission appeared without MgO layers. The type-I quantum well structure of MgO/ZnO/MgO and surface passivation of ZnO QDs by MgO must be important for the UV EL emission.
Analysis of Gouy phase shift for optimizing terahertz air-biased-coherent-detection
Authors: He Huanyu , Zhang X.-C.
Published: February 2012

Terahertz (THz) air-biased-coherent-detection (ABCD) uses a local oscillator to enhance THz-wave detection sensitivity by mixing an optical field, a THz field, and a biased electric field (local oscillator) in air. The width of the electrodes providing the local oscillator, the longitudinal distribution of the optical and THz waves, both play important roles in the overall detection sensitivity. By analyzing the effect of the Gouy phase shift on the electric field distribution at the mixing location, we determine the optimal electrode width and observe an enhancement of the detection efficiency by a factor of two relative to the traditional THz-ABCD system using thin-wire electrodes.
Tunable piezoresistance and noise in gate-all-around nanowire field-effect-transistor
Authors: Singh Pushpapraj , Park Woo-Tae , Miao Jianmin , Shao Lichun , Krishna Kotlanka Rama , Kwong Dim-Lee
Published: February 2012

The piezoresistance and noise of n-type gate-all-around nanowire field-effect-transistor (NWFET) is investigated as a function of gate bias. With narrow gate bias span of 0.6 V near threshold region, the piezoresistive coefficient of NWFET enhances up to seven times from 29 × 10−11 Pa−1 to 207 × 10−11 Pa−1 under compressive and tensile strain conditions. Results reveal that the low frequency noise is reduced when operated in subthreshold region. The higher piezoresistive coefficient and reduced noise improve the sensor resolution (minimum detectable strain) by sixteen times. NWFET operates at low bias with higher piezoresistance and signal-to-noise ratio and offers promising applications in strain sensors.
Waveguide-integrated near-infrared detector with self-assembled metal silicide nanoparticles embedded in a silicon p-n junction
Authors: Zhu Shiyang , Chu H. S. , Lo G. Q. , Bai P. , Kwong D. L.
Published: February 2012

An all-silicon photodetector integrated in a silicon-on-insulator waveguide for the telecom regime is proposed. The device is based on internal photoemission from electrically floating metal silicide nanoparticles (NPs) embedded in the space charge region of a Si p-n junction. Numerical simulation indicates that the light absorption could be enhanced if localized surface plasmon resonances are excited on the metal silicide nanoparticles, thus enabling to shrink the detector’s footprint to a submicron scale. A proof-of-concept detector fabricated using standard silicon complementary metal-oxide-semiconductor technology exhibits a peak responsivity of ∼30 mA/W at 5-V reverse bias and a 3-dB bandwidth of ∼6 GHz. It is expected that the overall performance would be significantly improved by optimization of both the detector’s configuration and the fabrication parameters.
Dependence of negative differential resistance on electronic phase separation in unpatterned manganite films
Authors: Ding J. F. , Jin K. X. , Zhang Z. , Wu T.
Published: February 2012

Here, we report that small but well-defined negative differential resistance (NDR) steps can be observed at critical voltages in unpatterned millimeter-scale manganite films of Pr0.65(Ca0.75Sr0.25)0.35MnO3. We systematically investigate the magneto-transport properties of strained thin films grown on LaAlO3 and SrTiO3 substrates and map out their phase diagrams which show temperature- and magnetic-field-dependent electronic phase separation (EPS). Our data suggest that the onset of NDR only occurs “deep” within the regions of EPS, underscoring the subtle nature of filamentary transport in manganite thin films with competing phases.
Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates
Authors: Huang Ruiqi , Hippauf Frank , Rohrbeck Diana , Haustein Maria , Wenke Katrin , Feike Janie , Sorrelle Noah , Piechulla Birgit , Barkman Todd J.
Published: February 2012

In this study, we investigated the role for ancestral functional variation that may be selected upon to generate protein functional shifts using ancestral protein resurrection, statistical tests for positive selection, forward and reverse evolutionary genetics, and enzyme functional assays. Data are presented for three instances of protein functional change in the salicylic acid/benzoic acid/theobromine (SABATH) lineage of plant secondary metabolite-producing enzymes. In each case, we demonstrate that ancestral nonpreferred activities were improved upon in a daughter enzyme after gene duplication, and that these functional shifts were likely coincident with positive selection. Both forward and reverse mutagenesis studies validate the impact of one or a few sites toward increasing activity with ancestrally nonpreferred substrates. In one case, we document the occurrence of an evolutionary reversal of an active site residue that reversed enzyme properties. Furthermore, these studies show that functionally important amino acid replacements result in substrate discrimination as reflected in evolutionary changes in the specificity constant (
k
cat
/
K
M
) for competing substrates, even though adaptive substitutions may affect
K
M
and
k
cat
separately. In total, these results indicate that nonpreferred, or even latent, ancestral protein activities may be coopted at later times to become the primary or preferred protein activities.
Charged linker sequence modulates eukaryotic heat shock protein 90 (Hsp90) chaperone activity
Authors: Tsutsumi Shinji , Mollapour Mehdi , Prodromou Chrisostomos , Lee Chung-Tien , Panaretou Barry , Yoshida Soichiro , Mayer Matthias P. , Neckers Leonard M.
Published: February 2012

Hsp90 is an essential and highly conserved modular molecular chaperone whose N and middle domains are separated by a disordered region termed the charged linker. Although its importance has been previously disregarded, because a minimal linker length is sufficient for Hsp90 activity, the evolutionary persistence of extensive charged linkers of divergent sequence in Hsp90 proteins of most eukaryotes remains unexplained. To examine this question further, we introduced human and plasmodium native and length-matched artificial linkers into yeast Hsp90. After evaluating ATPase activity and biophysical characteristics in vitro, and chaperone function in vivo, we conclude that linker sequence affects Hsp90 function, cochaperone interaction, and conformation. We propose that the charged linker, in addition to providing the flexibility necessary for Hsp90 domain rearrangements—likely its original purpose—has evolved in eukaryotes to serve as a rheostat for the Hsp90 chaperone machine.
Genomic epidemiology of the
Escherichia coli
O104:H4 outbreaks in Europe, 2011
Authors: Grad Yonatan H. , Lipsitch Marc , Feldgarden Michael , Arachchi Harindra M. , Cerqueira Gustavo C. , FitzGerald Michael , Godfrey Paul , Haas Brian J. , Murphy Cheryl I. , Russ Carsten , Sykes Sean , Walker Bruce J. , Wortman Jennifer R. , Young Sarah , Zeng Qiandong , Abouelleil Amr , Bochicchio James , Chauvin Sara , DeSmet Timothy , Gujja Sharvari , McCowan Caryn , Montmayeur Anna , Steelman Scott , Frimodt-Møller Jakob , Petersen Andreas M. , Struve Carsten , Krogfelt Karen A. , Bingen Edouard , Weill François-Xavier , Lander Eric S. , Nusbaum Chad , Birren Bruce W. , Hung Deborah T. , Hanage William P.
Published: February 2012

The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of
Escherichia coli
O104:H4 from the outbreak centered in Germany in May–July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two
E. coli
outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak.
Arabidopsis
circadian clock protein, TOC1, is a DNA-binding transcription factor
Authors: Gendron Joshua M. , Pruneda-Paz José L. , Doherty Colleen J. , Gross Andrew M. , Kang S. Earl , Kay Steve A.
Published: February 2012

The first described feedback loop of the
Arabidopsis
circadian clock is based on reciprocal regulation between TIMING OF CAB EXPRESSION 1 (TOC1) and CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1)/LATE ELONGATED HYPOCOTYL (LHY). CCA1 and LHY are Myb transcription factors that bind directly to the
TOC1
promoter to negatively regulate its expression. Conversely, the activity of TOC1 has remained less well characterized. Genetic data support that TOC1 is necessary for the reactivation of
CCA1
/
LHY
, but there is little description of its biochemical function. Here we show that TOC1 occupies specific genomic regions in the
CCA1
and
LHY
promoters. Purified TOC1 binds directly to DNA through its CCT domain, which is similar to known DNA-binding domains. Chemical induction and transient overexpression of
TOC1
in
Arabidopsis
seedlings cause repression of
CCA1
/
LHY
expression, demonstrating that TOC1 can repress direct targets, and mutation or deletion of the CCT domain prevents this repression showing that DNA-binding is necessary for TOC1 action. Furthermore, we use the Gal4/UAS system in
Arabidopsis
to show that TOC1 acts as a general transcriptional repressor, and that repression activity is in the pseudoreceiver domain of the protein. To identify the genes regulated by TOC1 on a genomic scale, we couple
TOC1
chemical induction with microarray analysis and identify previously unexplored potential TOC1 targets and output pathways. Taken together, these results define a biochemical action for the core clock protein TOC1 and refine our perspective on how plant clocks function.
Caveat Emptor: The Role of Suboptimal Bronchoscope Repair Practices by a Third-Party Vendor in a Pseudo-Outbreak ofPseudomonasin Bronchoalveolar Lavage Specimens
Authors: Cosgrove Sara E. , Ristaino Polly , Caston-Gaa Anne , Fellerman Donna P. , Nowakowski Elaine F. , Carroll Karen C. , Orens Jonathan B. , Perl Trish M. , Maragakis Lisa L.
Published: February 2012

Objective.

To describe a pseudo-outbreak associated with loose bronchoscope biopsy ports caused by inadequate bronchoscope repair practices by third-party vendors and to alert healthcare personnel to assess bronchoscope repair practices.

Design.

Outbreak investigation.

Setting.

A 925-bed tertiary care hospital in Baltimore, Maryland.

Patients.

Patients who underwent bronchoscopy with certain bronchoscopes after they had been repaired by a third-party vendor.

Methods.

An epidemiologic investigation was conducted to determine the cause ofPseudomonas putidagrowth in 4 bronchoalveolar lavage (BAL) specimens within a 3-day period in May 2008. All bronchoscopes were inspected, and cultures were obtained from bronchoscopes and the environment. Bronchoscope cleaning and maintenance practices were reviewed. Microbiologic results from BAL specimens and medical records were reviewed to find additional cases.

Results.

All 4 case patients had undergone bronchoscopy with one of 2 bronchoscopes, both of which had loose biopsy ports. Bronchoscope cultures grewP. putida, Pseudomonas aeruginosa,andStenotrophomonas.TheP. putidastrains from the bronchoscopes matched those from the patients. Specimens from 12 additional patients who underwent bronchoscopy with these bronchoscopes grewP. putida, P. aeruginosa,orStenotrophomonas.No patients developed clinical signs or symptoms of infection, but 7 were treated with antibiotics. Investigation revealed that the implicated bronchoscopes had been sent to an external vendor for repair; examination by the manufacturer revealed irregularities in repairs and nonstandard part replacements.

Conclusions.

Third-party vendors without access to proprietary information may contribute to mechanical malfunction of medical devices, which can lead to contamination and incomplete disinfection.

Infect Control Hosp Epidemiol2012;33(3):224-229
Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs
Authors: Vesely Cornelia , Tauber Stefanie , Sedlazeck Fritz J. , von Haeseler Arndt , Jantsch Michael F.
Published: February 2012

Adenosine deaminases that act on RNA bind double-stranded and structured RNAs and convert adenosines to inosines by hydrolytic deamination. Inosines are recognized as guanosines, and, hence, RNA editing alters the sequence information but also structure of RNAs. Editing by ADARs is widespread and essential for normal life and development. Precursors of miRNAs are abundantly edited by ADARs, but neither the abundance nor the consequences of miRNA editing has been firmly established. Using transgenic mouse embryos that are deficient in the two enzymatically active editing enzymes ADAR and ADARB1, we compare relative frequencies but also sequence composition of miRNAs in these genetically modified backgrounds to wild-type mice by “next-generation sequencing.” Deficiency of ADARB1 leads to a reproducible change in abundance of specific miRNAs and their predicted targets. Changes in miRNA abundance seem unrelated to editing events. Additional deletion of ADAR has surprisingly little impact on the mature miRNA repertoire, indicating that miRNA expression is primarily dependent on ADARB1. A-to-G transitions reflecting A-to-I editing events can be detected at few sites and at low frequency during the early embryonic stage investigated. Again, most editing events are ADARB1-dependent with only few editing sites being specifically edited by ADAR. Besides known editing events in miRNAs, a few novel, previously unknown editing events were identified. Some editing events are located to the seed region of miRNAs, opening the possibility that editing leads to their retargeting.
Siliques Are Red1 from Arabidopsis Acts as a Bidirectional Amino Acid Transporter That Is Crucial for the Amino Acid Homeostasis of Siliques
Authors: Ladwig Friederike , Stahl Mark , Ludewig Uwe , Hirner Axel A. , Hammes Ulrich Z. , Stadler Ruth , Harter Klaus , Koch Wolfgang
Published: February 2012

Many membrane proteins are involved in the transport of nutrients in plants. While the import of amino acids into plant cells is, in principle, well understood, their export has been insufficiently described. Here, we present the identification and characterization of the membrane protein Siliques Are Red1 (SIAR1) from Arabidopsis (Arabidopsis thaliana) that is able to translocate amino acids bidirectionally into as well as out of the cell. Analyses in yeast and oocytes suggest a SIAR1-mediated export of amino acids. In Arabidopsis, SIAR1 localizes to the plasma membrane and is expressed in the vascular tissue, in the pericycle, in stamen, and in the chalazal seed coat of ovules and developing seeds. Mutant alleles of SIAR1 accumulate anthocyanins as a symptom of reduced amino acid content in the early stages of silique development. Our data demonstrate that the SIAR1-mediated export of amino acids plays an important role in organic nitrogen allocation and particularly in amino acid homeostasis in developing siliques.
Cell and molecular biology of the spiny dogfish Squalus acanthias and little skate Leucoraja erinacea: insights from in vitro cultured cells
Authors: Barnes D. W.
Published: February 2012

Two of the most commonly used elasmobranch experimental model species are the spiny dogfish Squalus acanthias and the little skate Leucoraja erinacea. Comparative biology and genomics with these species have provided useful information in physiology, pharmacology, toxicology, immunology, evolutionary developmental biology and genetics. A wealth of information has been obtained using in vitro approaches to study isolated cells and tissues from these organisms under circumstances in which the extracellular environment can be controlled. In addition to classical work with primary cell cultures, continuously proliferating cell lines have been derived recently, representing the first cell lines from cartilaginous fishes. These lines have proved to be valuable tools with which to explore functional genomic and biological questions and to test hypotheses at the molecular level. In genomic experiments, complementary (c)DNA libraries have been constructed, and c. 8000 unique transcripts identified, with over 3000 representing previously unknown gene sequences. A sub‐set of messenger (m)RNAs has been detected for which the 3′ untranslated regions show elements that are remarkably well conserved evolutionarily, representing novel, potentially regulatory gene sequences. The cell culture systems provide physiologically valid tools to study functional roles of these sequences and other aspects of elasmobranch molecular cell biology and physiology. Information derived from the use of in vitro cell cultures is valuable in revealing gene diversity and information for genomic sequence assembly, as well as for identification of new genes and molecular markers, construction of gene‐array probes and acquisition of full‐length cDNA sequences.
Surplus suffering: the search for help when a child has mental‐health issues
Authors: Clarke Juanne N.
Published: February 2012

Social theorists have demonstrated the growth in dominance of two central discourses for understanding the ways that children's mental‐health issues are understood today –medicalization and intensive mothering. In this context, this paper reports on a qualitative interview‐based study of 16 mothers whose children had received a diagnosis with one or more mental‐health or developmental issues such as Tourette's, bipolar, anxiety, depression, autism or attention deficit hyperactivity disorder. It is based on the retrospective accounts of mothers given during interviews, from the time when they noticed what they thought to be unusual behaviours and decided to try to normalize and accommodate to their children's behaviours and then to the various steps they took to seek help. The paper begins with a description of the sorts of problems that mothers noticed. It then moves to the strategies mothers then took to cope, manage and socialize their children. When these failed, mothers sought professional assistance with understanding, remediation and/or a diagnosis for the child(ren). Mothers described uncertainty, confusion and contradictions as they unremittingly sought help. This process may be called surplus suffering. The relevance of the theoretical issues is then reconsidered along with the substantive and practical consequences of the findings.
Genetic analysis of the CYP21A2 gene in neonatal dried blood spots from children with transiently elevated 17‐hydroxyprogesterone
Authors: Malikova Jana , Votava Felix , Vrzalova Zuzana , Lebl Jan , Cinek Ondrej
Published: February 2012

Background

Neonatal screening for congenital adrenal hyperplasia (CAH) identifies a certain proportion of newborns with transient moderate elevation of 17‐hydroxyprogesterone (17‐OHP). These children require regular follow‐up until normalization of their 17‐OHP levels. We investigated the possibility of reducing the individuals' recall rates by using genetic methods on their original neonatal dried blood spots.

Patients and Methods

We analysed neonatal dried blood spots from 753 subjects with transiently elevated levels of 17‐OHP. The
CYP21A2
gene was sequenced to detect point mutations, and the presence of
CYP21A2
was further confirmed by two methods utilizing the difference between
CYP21A2
and its
CYP21A1P
pseudogene in the sequence of exon 3 (8‐bp deletion). The accuracy of the methods was verified using samples from 70 subjects with known
CYP21A2
mutations and 181 healthy children.

Result

Among the 701 successfully sequenced samples from subjects with transiently elevated 17‐OHP, 670 (95%) had no point mutations or novel variants in the
CYP21A2
gene. We found no individuals carrying genotypes consistent with the diagnosis of CAH (i.e. homozygotes or compound heterozygotes for point mutations, large deletions or rearrangements). However, 21 heterozygous carriers of known point mutations that cause the classic and nonclassic forms of CAH were identified. Additionally, we detected eight heterozygous and two homozygous point variants with unknown functional significance.

Conclusion

Although CAH caused by 21‐hydroxylase deficiency could be genetically excluded with a reasonable degree of confidence in 95% of the genotyped subjects that had transiently elevated 17‐OHP, the performance of the tests was suboptimal when performed using dried blood spots and time‐consuming in comparison with the current practice of repeated measurements of 17‐OHP. The introduction of this method into clinical practice seems to be impractical at this stage.
Sleep problems and heart rate variability over the working day
Authors: JACKOWSKA MARTA , DOCKRAY SAMANTHA , ENDRIGHI ROMANO , HENDRICKX HILDE , STEPTOE ANDREW
Published: February 2012

The purpose of this study was to discover whether greater sleep problems are associated with reduced heart rate variability during working hours and at night, and to determine whether this association is in part mediated by experienced affective states. This study involved 199 working women with a mean age of 33.8 years. Sleep problems were assessed with the Jenkins Sleep Problems Scale, and the Day Reconstruction Method was used to measure positive affect and stress on the evening before and during the working day. Heart rate variability was indexed by the mean square root of the successive standard difference in heart period. Disturbed sleep was inversely related to heart rate variability during the working day (P = 0.022), independently of demographic and behavioural confounders. Additional adjustment for positive affect and stress did not lead to further reductions in the association between sleep problems and reduced heart rate variability over the work day. Sleep problems were not predictive of reduced night‐time heart rate variability. This report extends the findings from experimental studies and clinical samples, and suggests that disturbed sleep might impair heart rate variability in real life settings, in particular during working hours. Reduced heart rate variability might be a potential pathway linking sleep problems with cardiovascular disease. Based on the current data there was little evidence that the inverse associations between sleep problems and heart rate variability were mediated by experienced affective states.