bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced luminescence efficiency due to carrier localization in InGaN∕GaN heterostructures grown on nanoporous GaN templates
Authors: Soh C. B. , Chow S. Y. , Tan L. Y. , Hartono H. , Liu W. , Chua S. J.
Published: October 2008

Low defect density GaN was achieved through dislocation annihilation by regrowing GaN on strain relaxed nanoporous GaN template formed by UV-enhanced electrochemical etching. The InGaN∕GaN single and multiple quantum wells grown on this nanoporous GaN template show enhanced indium incorporation due to strain relaxation. The step edges of regrown GaN on these nanoporous GaN act as effective nucleation sites for impinging indium atoms during growth. Evidence shows fluctuation in the quantum well width caused by indium segregation leading to carrier localization. A higher luminescence efficiency of InGaN∕GaN quantum wells is achieved through a combination of excitons localization, higher energy barrier for nonradiative recombination of carriers with dislocations and the reduction in defect density of the materials grown on the nanoporous GaN template.
Surface force confinement cell for neutron reflectometry studies of complex fluids under nanoconfinement
Authors: Cho Jae-Hie J. , Smith Gregory S. , Hamilton William A. , Mulder Dennis J. , Kuhl Tonya L. , Mays Jimmy
Published: October 2008

In this paper, we describe the construction of a new neutron surface force confinement cell (NSFCC). The NSFCC is equipped with hydraulically powered in situ, temporally stable, force control system for simultaneous neutron reflectometry studies of nanoconfined complex fluid systems. Test measurements with deuterated toluene confined between two opposing diblock copolymer (polystyrene+poly 2-vinylpyridine) coated quartz substrates demonstrate the capabilities of the NSFCC. With increasing hydraulically applied force, a series of well-defined decreasing separations were observed from neutron reflectivity measurements. No noticeable changes in the hydraulic pressure used for controlling the surface separation were observed during the measurements, demonstrating the high stability of the apparatus. This newly designed NSFCC introduces a higher level of control for studies of confinement and consequent finite size effects on nanoscale structure in a variety of complex fluid and soft condensed matter systems.
Piezoelectric actuation of (GaN/)AlGaN/GaN heterostructures
Authors: Tonisch K. , Buchheim C. , Niebelschütz F. , Schober A. , Gobsch G. , Cimalla V. , Ambacher O. , Goldhahn R.
Published: October 2008

A detailed analysis of the piezoelectric response of (GaN/)AlGaN/GaN heterostructures is reported. The electromechanical properties of two types of heterostructures with an Al content of 31% are compared. Only a single two-dimensional electron gas (2DEG) is formed for samples with thin GaN cap layers, while both a 2DEG and a two-dimensional hole gas coexist in the case of thick GaN caps. The lower GaN layer represents the mechanically supporting layer, while the AlGaN film, and in some cases an additional GaN cap layer, serves as the piezoelectrically active layers for actuation. The 2DEG (at the lower AlGaN/GaN interface) provides the conducting channel which was used as back electrode for the applied external voltage. Electroreflectance spectroscopy is applied in order to determine the electric field distribution across the whole structure as a function of the applied voltage. It is found that only a part of the modulation voltage drops across the active region. Piezoelectric force microscopy yields the field (voltage)-dependent actuation of the layers. By correlating the results of the two experimental techniques we are able to determine the piezoelectric modulus d33 with considerably improved reliability. A value for Al0.31Ga0.69N of 5 pm/V is found which is higher than an estimation based on previously reported data for GaN and AlN.
Electric-field-induced resonant tunneling lifetime in semiconductor multibarrier systems
Authors: Panchadhyayee P. , Biswas R. , Khan Arif , Mahapatra P. K.
Published: October 2008

A study on the variation in resonant tunneling lifetime (RTL) with the applied electric field is presented for the GaAs/AlxGa1−xAs periodic multibarrier systems (MBSs). The variation shows a contrasting behavior of lifetime for quasiresonant states situated at the miniband edge and those for well inside the miniband. For fields larger than 500 kV/m, the RTL corresponding to the midband state increases with the increase in electric field, whereas it decreases with the increase in field for the states near the miniband edges. The existence of the characteristic field and the characteristic lifetime that represent the synchronization of carrier velocity associated with all the quasiresonant states is an interesting outcome of the present theoretical investigation in ballistic transport of carriers through a MBS. This synchronization results in the maximum average escape rate through the system. It has also been shown that the characteristic field corresponds to the formation of localized partial Wannier–Stark ladder states in the miniband.
Enhanced ferroelectric and dielectric properties of highly (100)-oriented 0.67Pb(Mg1/3Nb2/3)O3–0.33PbTiO3 thin films with a special Pb(Zr0.2,Ti0.8)O3/PbOx bilayered buffer layer
Authors: Zhu Jiliang , Zhu Xiaohong , Jiang Meng , Li Xuhai , Zhu Jianguo , Xiao Dingquan
Published: October 2008

0.67 Pb ( Mg 1 / 3 Nb 2 / 3 ) O 3 – 0.33 PbTiO 3 (PMN-PT) thin films with a special Pb(Zr0.2,Ti0.8)O3 (PZT)/PbOx bilayered buffer layer have been grown on Pt/Ti/SiO2/Si(100) substrates by rf magnetron sputtering technique. Pure perovskite crystalline phase with highly (100)-preferred orientation, determined by x-ray diffraction, was formed in the PMN-PT thin films. The highly (100)-oriented PMN-PT thin films prepared by using this method possess very good ferroelectric properties with a high remanent polarization Pr (Pr=32 μC/cm2) and a low coercive field Ec (Ec=62 kV/cm). Moreover, the relative dielectric constant as high as 1595 is obtained in the PMN-PT thin films at 1 kHz. The experimental results indicate that the PZT/PbOx buffer layer plays an important role in the crystal orientation, phase purity, and electrical properties of the PMN-PT thin films.
Columnar quantum dashes for an active region in polarization independent semiconductor optical amplifiers at 1.55μm
Authors: Podemski P. , Sęk G. , Ryczko K. , Misiewicz J. , Hein S. , Höfling S. , Forchel A. , Patriarche G.
Published: October 2008

Here comes a report on the optical properties of InP based InAs columnar quantum dashes, which are proposed as an alternative for columnar quantum dots in semiconductor optical amplifiers construction since they offer convenient spectral tuning over 1.55μm together with a very broad and high gain. Electronic structure details are investigated by photoreflectance and photoluminescence and analyzed by comparison with effective mass calculations. Columnar quantum dash emission from the cleaved edge is examined by polarization resolved photoluminescence showing a transition of the dominant polarization from transverse electric to transverse magnetic with an increase in the quantum dash vertical dimension.
Gate-field-induced phase transitions in VO2: Monoclinic metal phase separation and switchable infrared reflections
Authors: Chen Changhong , Wang Renfan , Shang Lang , Guo Chongfeng
Published: October 2008

In a metal-oxide-semiconductor VO2 active layer under uniaxial stress, gate-field-induced phase transitions are revealed by strongly field-dependent Raman scattering and infrared reflections. A metal-insulator transition (MIT) is demonstrated by a strongly correlated monoclinic metal phase separation that percolates, thereby making the reflections switchable. In addition, the MIT occurs at a gate voltage around 3.36V, much lower than the threshold of a structural phase transition (SPT). Hence, the MIT is easily controlled by the gate field to avoid the SPT-caused fatigue and breakdown in high-speed operation.
Photovoltaic effect in micrometer-thick perovskite-type oxide multilayers on Si substrates
Authors: Liu Hao , Zhao Kun , Zhou Na , Lu Huibin , He Meng , Huang Yanhong , Jin Kui-Juan , Zhou Yueliang , Yang Guozhen , Zhao Songqing , Wang Aijun , Leng Wenxiu
Published: October 2008

Micrometer-thick perovskite-type multilayer heterostructures with ten thousands of unit cells, [SrNb0.05Ti0.95O3∕La0.9Sr0.1MnO3]3, have been fabricated on Si substrates. The structure exhibited nonlinear and rectifying current-voltage characteristics. Stable and temporal photovoltaic effects in the multilayer have been experimentally studied by using different wavelength light sources from ultraviolet to infrared, respectively. The photovoltage and photocurrent responsivities as a function of wavelength displayed that two cutoff wavelengths occurred corresponding to the band gaps of SrNb0.05Ti0.95O3 and Si and La0.9Sr0.1MnO3. Under the pulsed laser illumination the nanosecond response characterization of the present multilayer structure was obtained. Based on the band structure of the multilayers, a possible mechanism of photovoltaic process was proposed.
Thermal expansion behavior study of Co nanowire array with in situ x-ray diffraction and x-ray absorption fine structure techniques
Authors: Mo Guang , Cai Quan , Jiang Longsheng , Wang Wei , Zhang Kunhao , Cheng Weidong , Xing Xueqing , Chen Zhongjun , Wu Zhonghua
Published: October 2008

In situ x-ray diffraction and x-ray absorption fine structure techniques were used to study the structural change of ordered Co nanowire array with temperature. The results show that the Co nanowires are polycrystalline with hexagonal close packed structure without phase change up until 700 °C. A nonlinear thermal expansion behavior has been found and can be well described by a quadratic equation with the first-order thermal expansion coefficient of 4.3×10−6/°C and the second-order thermal expansion coefficient of 5.9×10−9/°C. The mechanism of this nonlinear thermal expansion behavior is discussed.
Indirect-to-direct band gap transitions in phosphorus adsorbed ⟨112⟩ silicon nanowires
Authors: Yang X. B. , Zhang R. Q.
Published: October 2008

Using first-principles calculations, we investigated the modification of the band structures of ⟨112⟩ silicon nanowires (SiNWs) that were adsorbed with phosphorus atoms. We found that the phosphorus atom adsorption on the (110) and (111) facets causes considerable modifications in the conduction bands. Interestingly, the modifications result in the indirect band gap characteristic enhancement for the adsorption on the (110) facet and induce an indirect-to-direct band gap transition for the adsorption on the (111) facet due to the distribution of the local density of states that are parallel to the (110) facet. The finding has significant implications for SiNWs in optoelectronic applications.
Experimental demonstration of a structured material with extreme effective parameters at microwaves
Authors: Silveirinha Mário G. , Fernandes Carlos A. , Costa Jorge R. , Medeiros Carla R.
Published: October 2008

Following our recent theoretical studies [M. G. Silveirinha and C. A. Fernandes, Phys. Rev. B 78, 033108 (2008)], it is experimentally verified that an array of crossed metallic wires may behave as a nonresonant material with extremely large index of refraction at microwaves and may enable the realization of ultrasubwavelength waveguides.
Copper and zinc spiking of biosolids: effect of incubation period on metal fractionation and speciation and microbial activity
Authors: Jeyakumar Paramsothy , Loganathan Paripurnanda , Sivakumaran Sivalingam , Anderson Christopher W. N. , McLaren Ronald G.
Published: October 2008

Environmental context. Global sewage sludge (biosolids) production is increasing as a result of rapidly growing human population and ensuing industrial activities. Disposal of this waste is becoming a serious environmental issue because the high levels of heavy metals in biosolids can upset soil microbial activity and nutrient balance when the waste is added to forest or agricultural lands. In the present study, a biosolid matrix was spiked with copper and zinc as a model for an environmental scenario. The findings of the present study are applicable to environmental regulations that seek to protect agriculture land, human and animal health, and soil and drinking water quality, in scenarios where biosolids are applied to soil.
Abstract. Biosolids were amended separately with three levels of copper and zinc sulfate, and anaerobically incubated for 117 days. Copper in the unamended-biosolids solid phase was mainly found in the organic and residual fractions (85–95%). Copper addition decreased the percentage of Cu in these fractions and increased the percentage of Cu in the oxide and specifically adsorbed fractions. Zinc in the solid phase was mainly associated with the oxide (35–65%), specifically adsorbed (25–30%), and the exchangeable fractions (10–40%). Relatively, all Cu in the solution phase was complexed with organic matter; Zn was present mainly as Zn2+ and as an electrically neutral ion pair, ZnSO40. Metals were almost completely incorporated into the biosolids matrix by Day 55. Dehydrogenase activity was reduced by 50% (EC50, effective concentration for 50% activity reduction) at the total solution-phase Cu and Zn concentrations of 0.1 and 20 mg L–1, respectively, and solid-phase exchangeable Cu and Zn concentrations of 410 and 670 mg kg–1, respectively.
CrIII binding by surface polymers in natural biomass: the role of carboxylic groups
Authors: Lodeiro Pablo , Fuentes Adrian , Herrero Roberto , Sastre de Vicente Manuel E.
Published: October 2008

Environmental context. Large quantities of chromium are discharged into the environment as a result of its widespread use in modern industries, and consequently, chromium could constitute a serious pollution problem. Adsorption onto natural biomass offers real potential as a way of removing chromium from the environment, because such adsorbents contain biopolymers with particular chemical stability and selectivity towards metals. In addition, natural biomass constitutes an eco-friendly and cost-effective alternative to the existing methods. Here, specific interactions between chromium and the biomass are investigated.
Abstract. The chromium(III)-binding capacity of several biomaterials has been described under fixed conditions of pH (4.5) and initial metal concentration (100 mg L–1). Three of these materials (Sargassum muticum, orange peel and bracken fern) have been selected and subjected to different studies. Fourier transform infrared and scanning electron microscopy techniques were used to describe the structure of the biomaterials, supporting the hypothesis of a mechanism of metal complexation via carboxylic groups. Potentiometric titrations revealed the quantity of carboxyl groups present in S. muticum, orange peel and bracken fern: 1.78, 0.49 and 0.67 mmol g–1, respectively. Moreover, a model considering different types of binding sites was used to simulate the process and determine the apparent pK values of the main functionalities. The number of carboxylic groups was clearly correlated with the maximum amount of CrIII binding by the materials. A Langmuir competitive model was used to determine the complexation constants for chromium, log KCr, which are very close (~3), supporting the idea of the implication of essentially one acid functionality. Desorption studies were conducted for different times employing H2SO4 and sodium citrate.
Concentration and biotransformation of arsenic by Prosopis sp. grown in soil treated with chelating agents and phytohormones
Authors: López Martha Laura , Peralta-Videa José R. , Parsons Jason G. , Duarte-Gardea Maria , Gardea-Torresdey Jorge L.
Published: October 2008

Environmental context. Arsenic (As) is a metalloid found throughout the environment. Although As can be released from natural phenomena, anthropogenic activities account for most As contamination worldwide. The toxicity of As depends on the form (inorganic or organic) and species (AsIII or AsV), among others. Plants have the ability to absorb and bioreduce As, cleaning the soil and reducing the toxicity of As to some extent. The aim of the present research was to study the effects of cysteine, the chelating agents cyclohexylenedinitrotetraacetic acid and nitrilotriacetic acid, and the phytohormone kinetin on the As concentration and speciation in mesquite (Prosopis sp.). The results give an insight about how a desert plant absorbs, bioreduces, distributes and stores this toxic metalloid.
Abstract. The aim of the present research was to study the effects of cysteine (Cys), cyclohexylenedinitrotetraacetic acid (CDTA), nitrilotriacetic acid (NTA), and kinetin (KN) on the arsenic (As) concentration and speciation in mesquite (Prosopis sp.) grown in soil containing 30 ppm (parts per million) of AsIII or 50 ppm of AsV. Inductively coupled plasma–optical emission spectroscopy (ICP-OES) determinations revealed that, compared with As alone, roots of plants treated with 2.5 mM CDTA or 0.5 mM of Cys + 100 μM KN increased total As concentration from AsIII by ~20 and 36% and from AsV by 100 and 65%, respectively. Liquid chromatography–inductively coupled plasma–mass spectrometry (LC-ICP-MS) studies revealed that in roots, AsIII remained without change, whereas both AsIII and AsV were found in plants grown with AsV. X-ray absorption spectroscopy (XAS) studies revealed that As within plants was mainly coordinated to three sulfur atoms, with interatomic distances of 2.26 Å. Results suggests that Cys + KN increased the mesquite tolerance to AsV, because plants grown in AsV had roots of similar size to plants grown without As.
Changes in sediment microbial community structure within a large water-storage reservoir during an extreme drawdown event
Authors: Boulding A. N. , Rees G. N. , Baldwin D. S. , Suter P. J. , Watson G. O.
Published: October 2008

Although drought and drying of waters occur globally, the effect of drying on sediment microbial communities underpinning aquatic biogeochemical processes is poorly understood. We used the molecular method of terminal-restriction fragment length polymorphism (T-RFLP) to assess changes in the microbial community structure of sediments undergoing different levels of inundation and drying within a reservoir during drawdown in a drought. Sediments with three hydrological conditions were investigated: dry sediments (no overlying water), littoral sediments (covered with 1–2 mm water) and inundated sediments (covered with >1 m water). Sampling was done in winter 2006 (August) and summer 2007 (January) in Lake Hume, Australia. The microbial communities differed significantly between the different levels of inundation at each sampling time. Community structure also changed significantly within each site between winter 2006 and summer 2007, possibly influenced by the change of season or protracted drying. Sites that were ‘littoral’ in winter 2006 became ‘dry’ in summer 2007, and became more similar to communities that were ‘dry’ at both sampling times. This suggested that the hydrological history of specific sites did not heavily influence the response of microbial communities to severe drying, and all communities undergoing ‘dry’ conditions within the summer 2007 sampling responded similarly.
Characterisation of post-larval to juvenile stages, metamorphosis and recruitment of an amphidromous goby, Sicyopterus lagocephalus (Pallas) (Teleostei : Gobiidae : Sicydiinae)
Authors: Keith P. , Hoareau T. B. , Lord C. , Ah-Yane O. , Gimonneau G. , Robinet T. , Valade P.
Published: October 2008

Sicyopterus lagocephalus post-larvae migrating in Mascarene Archipelago rivers, La Réunion Island, provide an important food source to local populations and fishing activity has a socioeconomic impact. Improved knowledge of the life traits and the characterisation of post-larval stages should enable a better understanding of physiological changes triggering migratory behaviour. It would also help to explain the recruitment processes to managers and to implement conservation measures for stock management. Sicyopterus lagocephalus is an amphidromous fish: adults live in rivers, but larvae are carried to the sea after hatching. The present study characterised the metamorphosis and post-larval stages of Sicyopterus lagocephalus during river recolonisation on La Réunion Island. The results show that cranium reorganisation and pectoral fins transformation are part of the first and major transformations and are completed less than 2 weeks after freshwater colonisation (post-larval stages PL1 and PL2). These transformations, mobilising all the available calcium, seem to be critical for survival in their new environment. Individuals then progressively acquire pigmentation, complete scalation and the fork at the end of the caudal fin disappears (juvenile stages J1 and J2). The end of the recruitment phase takes place 21 to 28 days after entering the river mouth, when territorial behaviour appears.
Australian rainfall patterns and the southern oscillation. 2. A regional perspective in relation to Luni-solar (Mn) and Solar-cycle (Sc) signals
Authors: Vines R. G.
Published: October 2008

This investigation is an extension of earlier work on rainfall patterns in eastern Australia. Using district averages rather than rainfall data for individual cities or towns, further evidence is provided for cyclic variations in precipitation with periods of 18–19, 10–11 and 6–7 years. Results from various regional areas in western Queensland and western New South Wales differ from those found further south in Victoria, and connections are suggested between El Niño/southern oscillation events and the incidence of drought in these two separate areas. Such findings are consistent with ecological aspects of the quasi-periodic occurrence of bushfire seasons as observed in both Victorian eucalypt forests after prolonged drought, or after intermittent widespread rains in the semi-arid Mallee rangelands of western New South Wales. The ~19-year cycles may be at least partly a reflection of solar and lunar tidal components and the ~11-year cycles (connected with the Sunspot cycle) could be the result of absorption of short wavelength solar emissions in the stratosphere and resultant photochemical events magnified to produce sea surface temperature changes. The ~19-year cycles are apparently associated with either increased or decreased rainfall, and such connections appear to reverse in parts of Australia about every 100 years. These reversals have been associated with major droughts at the end of the 19th and 20th centuries.
A zinc knuckle protein that negatively controls morning-specific growth in
Arabidopsis thaliana
Authors: Loudet Olivier , Michael Todd P. , Burger Brian T. , Le Metté Claire , Mockler Todd C. , Weigel Detlef , Chory Joanne
Published: October 2008

Growth in plants is modulated by a complex interplay between internal signals and external cues. Although traditional mutagenesis has been a successful approach for the identification of growth regulatory genes, it is likely that many genes involved in growth control remain to be discovered. In this study, we used the phenotypic variation between Bay-0 and Shahdara, two natural strains (accessions) of
Arabidopsis thaliana
, to map quantitative trait loci (QTL) affecting light- and temperature-regulated growth of the embryonic stem (hypocotyl). Using heterogeneous inbred families (HIFs), the gene underlying one QTL,
LIGHT5
, was identified as a tandem zinc knuckle/PLU3 domain encoding gene (At5g43630;
TZP
), which carries a premature stop codon in Bay-0. Hypocotyl growth assays in monochromatic light and microarray analysis demonstrate that
TZP
controls blue light associated growth in a time-of-day fashion by regulating genes involved in growth, such as peroxidase and cell wall synthesis genes.
TZP
expression is phased by the circadian clock and light/dark cycles to the beginning of the day, the time of maximal growth in
A. thaliana
in short-day conditions. Based on its domain structure and localization in the nucleus, we propose that TZP acts downstream of the circadian clock and photoreceptor signaling pathways to directly control genes responsible for growth. The identification of TZP thus provides new insight into how daily synchronization of growth pathways plays a critical role in growth regulation.
Predicting and understanding forest dynamics using a simple tractable model
Authors: Purves Drew W. , Lichstein Jeremy W. , Strigul Nikolay , Pacala Stephen W.
Published: October 2008

The perfect-plasticity approximation (PPA) is an analytically tractable model of forest dynamics, defined in terms of parameters for individual trees, including allometry, growth, and mortality. We estimated these parameters for the eight most common species on each of four soil types in the US Lake states (Michigan, Wisconsin, and Minnesota) by using short-term (≤15-year) inventory data from individual trees. We implemented 100-year PPA simulations given these parameters and compared these predictions to chronosequences of stand development. Predictions for the timing and magnitude of basal area dynamics and ecological succession on each soil were accurate, and predictions for the diameter distribution of 100-year-old stands were correct in form and slope. For a given species, the PPA provides analytical metrics for early-successional performance (
H
20
, height of a 20-year-old open-grown tree) and late-successional performance (
Ẑ
*, equilibrium canopy height in monoculture). These metrics predicted which species were early or late successional on each soil type. Decomposing
Ẑ
* showed that (
i
) succession is driven both by superior understory performance and superior canopy performance of late-successional species, and (
ii
) performance differences primarily reflect differences in mortality rather than growth. The predicted late-successional dominants matched chronosequences on xeromesic (
Quercus rubra
) and mesic (codominance by
Acer rubrum
and
Acer saccharum
) soil. On hydromesic and hydric soils, the literature reports that the current dominant species in old stands (
Thuja occidentalis
) is now failing to regenerate. Consistent with this, the PPA predicted that, on these soils, stands are now succeeding to dominance by other late-successional species (e.g.,
Fraxinus nigra
,
A. rubrum
).
Escape from X chromosome inactivation is an intrinsic property of the
Jarid1c
locus
Authors: Li Nan , Carrel Laura
Published: October 2008

Although most genes on one X chromosome in mammalian females are silenced by X inactivation, some “escape” X inactivation and are expressed from both active and inactive Xs. How these escape genes are transcribed from a largely inactivated chromosome is not fully understood, but underlying genomic sequences are likely involved. We developed a transgene approach to ask whether an escape locus is autonomous or is instead influenced by X chromosome location. Two BACs carrying the mouse
Jarid1c
gene and adjacent X-inactivated transcripts were randomly integrated into mouse XX embryonic stem cells. Four lines with single-copy, X-linked transgenes were identified, and each was inserted into regions that are normally X-inactivated. As expected for genes that are normally subject to X inactivation, transgene transcripts
Tspyl2
and
Iqsec2
were X-inactivated. However, allelic expression and RNA/DNA FISH indicate that transgenic
Jarid1c
escapes X inactivation. Therefore, transgenes at 4 different X locations recapitulate endogenous inactive X expression patterns. We conclude that escape from X inactivation is an intrinsic feature of the
Jarid1c
locus and functionally delimit this escape domain to the 112-kb maximum overlap of the BACs tested. Additionally, although extensive chromatin differences normally distinguish active and inactive loci, unmodified BACs direct proper inactive X expression patterns, establishing that primary DNA sequence alone, in a chromosome position-independent manner, is sufficient to determine X chromosome inactivation status. This transgene approach will enable further dissection of key elements of escape domains and allow rigorous testing of specific genomic sequences on inactive X expression.
Contribution of the Myosin Binding Protein C Motif to Functional Effects in Permeabilized Rat Trabeculae
Authors: Razumova Maria V. , Bezold Kristina L. , Tu An-Yue , Regnier Michael , Harris Samantha P.
Published: October 2008

Myosin binding protein C (MyBP-C) is a thick-filament protein that limits cross-bridge cycling rates and reduces myocyte power output. To investigate mechanisms by which MyBP-C affects contraction, we assessed effects of recombinant N-terminal domains of cardiac MyBP-C (cMyBP-C) on contractile properties of permeabilized rat cardiac trabeculae. Here, we show that N-terminal fragments of cMyBP-C that contained the first three immunoglobulin domains of cMyBP-C (i.e., C0, C1, and C2) plus the unique linker sequence termed the MyBP-C “motif” or “m-domain” increased Ca2+ sensitivity of tension and increased rates of tension redevelopment (i.e., ktr) at submaximal levels of Ca2+. At concentrations ≥20 μM, recombinant proteins also activated force in the absence of Ca2+ and inhibited maximum Ca2+-activated force. Recombinant proteins that lacked the combination of C1 and the motif did not affect contractile properties. These results suggest that the C1 domain plus the motif constitute a functional unit of MyBP-C that can activate the thin filament.
Interleukin-6 and Neural Stem Cells: More Than Gliogenesis
Authors: Islam Omedul , Gong Xiandi , Rose-John Stefan , Heese Klaus
Published: October 2008

Besides its wide range of action as a proinflammatory cytokine in the immune system, interleukin-6 (IL-6) has also attracted much attention due to its influence on the nervous system. In the present study we show that the designer fusion protein H-IL-6, consisting of IL-6 and its specific receptor IL-6R-α, but not IL-6 alone, mediates both neuro- as well as gliogenesis. Using immunocytochemistry, Western blot, and patch-clamp recording, we demonstrate that H-IL-6 induces the differentiation of neural stem cells (NSCs) specifically into glutamate-responsive neurons and two morphological distinctive astroglia cell types. H-IL-6–activated neurogenesis seems to be induced by the MAPK/CREB (mitogen-activated protein kinase/cAMP response element-binding protein) cascade, whereas gliogenesis is mediated via the STAT-3 (signal transducers and activators of transcription protein-3) signaling pathway. Our finding that IL-6 mediates both processes depending on its specific soluble receptor sIL-6R-α has implications for the potential treatment of neurodegenerative diseases.
Conditional random pattern algorithm for LOH inference and segmentation
Authors: Wu Ling-Yun , Zhou Xiaobo , Li Fuhai , Yang Xiaorong , Chang Chung-Che , Wong Stephen T. C.
Published: October 2008

Motivation: Loss of heterozygosity (LOH) is one of the most important mechanisms in the tumor evolution. LOH can be detected from the genotypes of the tumor samples with or without paired normal samples. In paired sample cases, LOH detection for informative single nucleotide polymorphisms (SNPs) is straightforward if there is no genotyping error. But genotyping errors are always unavoidable, and there are about 70% non-informative SNPs whose LOH status can only be inferred from the neighboring informative SNPs.

Results: This article presents a novel LOH inference and segmentation algorithm based on the conditional random pattern (CRP) model. The new model explicitly considers the distance between two neighboring SNPs, as well as the genotyping error rate and the heterozygous rate. This new method is tested on the simulated and real data of the Affymetrix Human Mapping 500K SNP arrays. The experimental results show that the CRP method outperforms the conventional methods based on the hidden Markov model (HMM).

Availability: Software is available upon request.

Contact:  xzhou@tmhs.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Challenges facing a network of representative marine protected areas in the Mediterranean: prioritizing the protection of underrepresented habitats
Authors: Abdulla Ameer , Gomei Marina , Hyrenbach David , Notarbartolo-di-Sciara Giuseppe , Agardy Tundi
Published: October 2008

Abdulla, A., Gomei, M., Hyrenbach, D., Notarbartolo-di-Sciara, G., and Agardy, T. 2009. Challenges facing a network of representative marine protected areas in the Mediterranean: prioritizing the protection of underrepresented habitats. – ICES Journal of Marine Science, 66: 22–28. The high endemism of the Mediterranean Sea provides strong motivation to develop a comprehensive plan for the conservation of its biodiversity and the management of its marine resources. Increasingly, this ecosystem-level approach calls for a comprehensive network of marine protected areas (MPAs) representative of the richness and diversity of this shared basin. Today, Mediterranean MPAs do not represent the diverse geography and habitats in the region. Despite a recent declaration on trawling restrictions in deep waters (>1000 m), there are no true deep-sea Mediterranean MPAs. All but one (98.9%) of the 94 marine areas currently under some type of protection or management are coastal. Moreover, 69 (73.4%) are located along the basin's northern shore, highlighting the lack of MPAs in the south and east coasts. Yet, these underrepresented regions and habitats are ecologically distinctive by virtue of their particular oceanographic and biogeographic conditions. We identify several obstacles to Mediterranean MPA implementation and discuss how they can be overcome through strategic MPA network planning, contending that regional disparities in governance, institutional structures, wealth distribution, social capital, and availability of ecological data are responsible for discrepancies in the establishment and effectiveness of MPAs in this region.
Targeted screening of cis-regulatory variation in human haplotypes
Authors: Verlaan Dominique J. , Ge Bing , Grundberg Elin , Hoberman Rose , Lam Kevin C.L. , Koka Vonda , Dias Joana , Gurd Scott , Martin Nicolas W. , Mallmin Hans , Nilsson Olof , Harmsen Eef , Dewar Ken , Kwan Tony , Pastinen Tomi
Published: October 2008

Regulatory cis-acting variants account for a large proportion of gene expression variability in populations. Cis-acting differences can be specifically measured by comparing relative levels of allelic transcripts within a sample. Allelic expression (AE) mapping for cis-regulatory variant discovery has been hindered by the requirements of having informative or heterozygous single nucleotide polymorphisms (SNPs) within genes in order to assign the allelic origin of each transcript. In this study we have developed an approach to systematically screen for heritable cis-variants in common human haplotypes across >1000 genes. In order to achieve the highest level of information per haplotype studied, we carried out allelic expression measurements by using both intronic and exonic SNPs in primary transcripts. We used a novel RNA pooling strategy in immortalized lymphoblastoid cell lines (LCLs) and primary human osteoblast cell lines (HObs) to allow for high-throughput AE. Screening hits from RNA pools were further validated by performing allelic expression mapping in individual samples. Our results indicate that >10% of expressed genes in human LCLs show genotype-linked AE. In addition, we have validated cis-acting variants in over 20 genes linked with common disease susceptibility in recent genome-wide studies. More generally, our results indicate that RNA pooling coupled with AE read-out by second generation sequencing or by other methods provides a high-throughput tool for cataloging the impact of common noncoding variants in the human genome.
Arabidopsis CLP1-SIMILAR PROTEIN3, an Ortholog of Human Polyadenylation Factor CLP1, Functions in Gametophyte, Embryo, and Postembryonic Development
Authors: Xing Denghui , Zhao Hongwei , Li Qingshun Quinn
Published: October 2008

Polyadenylation factor CLP1 is essential for mRNA 3′-end processing in yeast and mammals. The Arabidopsis (Arabidopsis thaliana) CLP1-SIMILAR PROTEIN3 (CLPS3) is an ortholog of human hCLP1. CLPS3 was previously found to be a subunit in the affinity-purified PCFS4-TAP (tandem affinity purification) complex involved in the alternative polyadenylation of FCA and flowering time control in Arabidopsis. In this article, we further explored the components in the affinity-purified CLPS3-TAP complex, from which Arabidopsis cleavage and polyadenylation specificity factor (CPSF) subunits AtCPSF100 and AtCPSF160 were found. This result implies that CLPS3 may bridge CPSF to the PCFS4 complex. Characterization of the CLPS3 mutant revealed that CLPS3 was essential for embryo development and important for female gametophyte transmission. Overexpression of CLPS3-TAP fusion caused a range of postembryonic development abnormalities, including early flowering time, altered phyllotaxy, and abnormal numbers and shapes of flower organs. These phenotypes are associated with the altered gene expression levels of FCA, WUS, and CUC1. The decreased ratio of FCA-β to FCA-γ in the overexpression plants suggests that CLPS3 favored the usage of FCA regular poly(A) site over the alternative site. These observations indicate that Arabidopsis CLPS3 might be involved in the processing of pre-mRNAs encoded by a distinct subset of genes that are important in plant development.
Managerial Risk‐Taking Incentives and Executive Stock Option Repricing: A Study of US Casino Executives
Authors: Rogers Daniel A.
Published: October 2008

I examine the relation between managerial incentives from holdings of company stock and options and stock option repricing. Because options provide incentives to increase both risk and stock price, firms must realize that as options go underwater, executives might face incentives to invest in risky, negative NPV projects. Repricing may alleviate such incentives. I examine repricing activity by firms in the US gaming industry and find that risk‐taking incentives from options are positively related to the incidence of executive option repricing. The results support the hypothesis that repricing assists firms in alleviating excessive risk‐taking incentives of senior management.
Structural Insights into a Circadian Oscillator
Authors: Johnson Carl Hirschie , Egli Martin , Stewart Phoebe L.
Published: October 2008

An endogenous circadian system in cyanobacteria exerts pervasive control over cellular processes, including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topological changes and compaction. The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC. These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation. The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally. This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo. The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping.
Peptides Enhance Magnesium Signature in Calcite: Insights into Origins of Vital Effects
Authors: Stephenson A. E. , DeYoreo J. J. , Wu L. , Wu K. J. , Hoyer J. , Dove P. M.
Published: October 2008

Studies relating the magnesium (Mg) content of calcified skeletons to temperature often report unexplained deviations from the signature expected for inorganically grown calcite. These “vital effects” are believed to have biological origins, but mechanistic bases for measured offsets remain unclear. We show that a simple hydrophilic peptide, with the same carboxyl-rich character as that of macromolecules isolated from sites of calcification, increases calcite Mg content by up to 3 mole percent. Comparisons to previous studies correlating Mg content of carbonate minerals with temperature show that the Mg enhancement due to peptides results in offsets equivalent to 7° to 14°C. The insights also provide a physical basis for anecdotal evidence that organic chemistry modulates the mineralization of inorganic carbonates and suggest an approach to tuning impurity levels in controlled materials synthesis.
Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome
Authors: Zhao Jing , Sun Bryan K. , Erwin Jennifer A. , Song Ji-Joon , Lee Jeannie T.
Published: October 2008

To equalize X-chromosome dosages between the sexes, the female mammal inactivates one of her two X chromosomes. X-chromosome inactivation (XCI) is initiated by expression of
Xist
, a 17-kb noncoding RNA (ncRNA) that accumulates on the X in cis. Because interacting factors have not been isolated, the mechanism by which
Xist
induces silencing remains unknown. We discovered a 1.6-kilobase ncRNA (RepA) within
Xist
and identified the Polycomb complex, PRC2, as its direct target. PRC2 is initially recruited to the X by RepA RNA, with Ezh2 serving as the RNA binding subunit. The antisense
Tsix
RNA inhibits this interaction. RepA depletion abolishes full-length
Xist
induction and trimethylation on lysine 27 of histone H3 of the X. Likewise, PRC2 deficiency compromises
Xist
up-regulation. Therefore, RepA, together with PRC2, is required for the initiation and spread of XCI. We conclude that a ncRNA cofactor recruits Polycomb complexes to their target locus.
Trampoline Effect in Extreme Ground Motion
Authors: Aoi Shin , Kunugi Takashi , Fujiwara Hiroyuki
Published: October 2008

In earthquake hazard assessment studies, the focus is usually on horizontal ground motion. However, records from the 14 June 2008 Iwate-Miyagi earthquake in Japan, a crustal event with a moment magnitude of 6.9, revealed an unprecedented vertical surface acceleration of nearly four times gravity, more than twice its horizontal counterpart. The vertical acceleration was distinctly asymmetric; the waveform envelope was about 1.6 times as large in the upward direction as in the downward direction, which is not explained by existing models of the soil response. We present a simple model of a mass bouncing on a trampoline to account for this asymmetry and the large vertical amplitude. The finding of a hitherto-unknown mode of strong ground motion may prompt major progress in near-source shaking assessments.
The Power of Cross Pressures
Authors: Peterson David A. M.
Published: October 2008

The Persuadable Voter
. Wedge Issues in Presidential Campaigns.
By D. Sunshine Hillygus and Todd G. Shields
. Princeton University Press, Princeton, NJ, 2008. 267 pp. $29.95, £17.95. ISBN 9780691133416.

Hillygus and Shields explore survey data, experimental results, campaign ads, archives, and interview responses to discuss why wedge issues are used, who they persuade, and how they may affect political equality and democratic governance.
Seroprevalence of Turkey Coronavirus in North American Turkeys Determined by a Newly Developed Enzyme-Linked Immunosorbent Assay Based on Recombinant Antigen
Authors: Gomaa Maged H. , Yoo Dongwan , Ojkic Davor , Barta John R.
Published: October 2008

Turkey coronavirus (TCoV) causes diarrhea in young turkey poults, but little is known about its prevalence in the field. To address this, the complete nucleocapsid gene was cloned and expressed inEscherichia coli. Expressed nucleocapsid gene produced two distinct proteins (52 and 43 kDa); their specificity was confirmed by Western blotting using two different monoclonal antibodies. Recombinant N protein was purified and used as an antigen to develop an enzyme-linked immunosorbent assay (ELISA) for the serological detection of TCoV that was then validated using experimentally derived turkey serum. The N-based ELISA showed (97%) sensitivity and (93%) specificity for TCoV, which was significantly higher than an infectious bronchitis coronavirus-based commercial test for TCoV. To assess the utility of this recombinant ELISA, 360 serum samples from turkey farms in Ontario, Canada, and 81 serum samples from farms in Arkansas were tested for TCoV-specific antibodies. A high seroprevalence of TCoV was found in turkeys from the Ontario farms with 73.9% of breeders and 60.0% of meat turkeys testing seropositive using the N-based ELISA. Similarly, a high field prevalence was found in the turkeys from Arkansas, for which 64.2% of the serum samples tested seropositive.
Carriage of Methicillin-Resistant Staphylococci and Their SCC
mec
Types in a Long-Term-Care Facility
Authors: Ibrahem Salha , Salmenlinna Saara , Virolainen Anni , Kerttula Anne-Marie , Lyytikäinen Outi , Jägerroos Henrik , Broas Markku , Vuopio-Varkila Jaana
Published: October 2008

Following an outbreak caused by staphylococcal cassette chromosome
mec
(SCC
mec
) type V methicillin (meticillin)-resistant
Staphylococcus aureus
(MRSA), a point-prevalence survey of the nasal carriage of staphylococci was conducted in a long-term-care facility in northern Finland in 2004. The focus was directed at methicillin-resistant coagulase-negative staphylococci (MR-CNS) and their SCC
mec
elements. A nasal swab was taken from 76 of the 80 residents 6 months after the onset of the outbreak. Staphylococcal isolates were identified by conventional methods and the GenoType
Staphylococcus
test, and their SCC
mec
elements were analyzed. Of the 76 individuals, 24 (32%) carried
S. aureus
and 67 (88%) CNS in their nostrils. Of the CNS carriers, 41 (61%) had at least one
mecA
-positive MR-CNS, and two individuals (3%) had both MRSA and methicillin-resistant
Staphylococcus epidermidis
(MRSE). Among the 61 MR-CNS isolates identified, 49 (80%) were MRSE. The distribution of the SCC
mec
types was diverse: 20 (33%) were of type IV, 11 (18%) of type V, 4 (6%) of type I or IA, 3 (4%) of type II, and 23 (38%) of new types (with six different combinations of
ccr
and other
mec
genes or only
mecA
). Both of the individuals with MRSA and MRSE shared SCC
mec
type V among their isolates. Nasal MR-CNS carriage was common among the residents of this long-term-care facility. A variety of SCC
mec
types, including many new types, were identified among the MR-CNS strains. The horizontal transfer of SCC
mec
elements is speculated based on the sharing of SCC
mec
type V between MRSA and MRSE.