bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a lead oxide photopatternable organic-inorganic film
Authors: Han Huilan , Sutherland Alexander M. , Yaghmaie Frank , Davis Cristina E.
Published: April 2009

We have developed a simple method to synthesize organic-inorganic films containing a Pb(II) acrylate precursor in a silicon-methacrylate solution in the presence of a photoactive compound. Film deposition is achieved by simple spin coating, and the presence of a photoactive compound enables rapid polymerization when the film is subjected to UV irradiation. This creates a patternable film that acts as both an imaging layer and also as a functional metal-containing layer for the final device. We also investigated the chemical composition of the film by energy dispersive x-ray spectroscopy.
Interpolating moving least-squares methods for fitting potential energy surfaces: Using classical trajectories to explore configuration space
Authors: Dawes Richard , Passalacqua Alessio , Wagner Albert F. , Sewell Thomas D. , Minkoff Michael , Thompson Donald L.
Published: April 2009

We develop two approaches for growing a fitted potential energy surface (PES) by the interpolating moving least-squares (IMLS) technique using classical trajectories. We illustrate both approaches by calculating nitrous acid (HONO) cis→trans isomerization trajectories under the control of ab initio forces from low-level HF/cc-pVDZ electronic structure calculations. In this illustrative example, as few as 300 ab initio energy/gradient calculations are required to converge the isomerization rate constant at a fixed energy to ∼10%. Neither approach requires any preliminary electronic structure calculations or initial approximate representation of the PES (beyond information required for trajectory initial conditions). Hessians are not required. Both approaches rely on the fitting error estimation properties of IMLS fits. The first approach, called IMLS-accelerated direct dynamics, propagates individual trajectories directly with no preliminary exploratory trajectories. The PES is grown “on the fly” with the computation of new ab initio data only when a fitting error estimate exceeds a prescribed tight tolerance. The second approach, called dynamics-driven IMLS fitting, uses relatively inexpensive exploratory trajectories to both determine and fit the dynamically accessible configuration space. Once exploratory trajectories no longer find configurations with fitting error estimates higher than the designated accuracy, the IMLS fit is considered to be complete and usable in classical trajectory calculations or other applications.
Analytical calculation of the Smith lifetime Q matrix using a Magnus propagator: Applications to the study of resonances occurring in ultracold inelastic collisions with and without an applied magnetic field
Authors: Guillon G. , Stoecklin T.
Published: April 2009

We take advantage of the simple expression of the sector adiabatic wave functions of the Magnus propagator to obtain accurate values of the energy derivative of the S matrix which, in turn, is used to get the Smith lifetime Q matrix. The procedure involves the simultaneous generation of both the R matrix and its energy derivative dR/dE which are propagated along the scattering coordinate. We present a few examples of application to the field free He–N2+ inelastic collisions which we previously studied. This method is then applied to the calculation of the lifetime of tuned zero energy Feshbach resonances using a magnetic field. We give and discuss the law of variation as a function of the magnetic field of the Q matrix eigenvalues across such resonance. Some examples of application are given for the He–N2+ collisions in a magnetic field.
Analytical solution for Stokes flow inside an evaporating sessile drop: Spherical and cylindrical cap shapes
Authors: Masoud Hassan , Felske James D.
Published: April 2009

Exact analytical solutions are derived for the Stokes flows within evaporating sessile drops of spherical and cylindrical cap shapes. The results are valid for all contact angles. Solutions are obtained for arbitrary evaporative flux distributions along the free surface as long as the flux is bounded at the contact line. Specific results and computations are presented for evaporation corresponding to uniform flux and to purely diffusive gas phase transport into an infinite ambient. Wetting and nonwetting contact angles are considered with the flow patterns in each case being illustrated. For the spherical cap with evaporation controlled by vapor phase diffusion, when the contact angle lies in the range 0≤θc<π/2, the mass flux of vapor becomes singular at the contact line. This condition requires modification when solving for the liquid-phase transport. Droplets in all of the above categories are considered for the following two cases: the contact lines are either pinned or free to move during evaporation. The present viscous flow behavior is compared to the inviscid flow behavior previously reported. It is seen that the streamlines for viscous flow lie farther from the substrate than the corresponding inviscid ones.
Ferromagnetic behavior of CdMnCrTe quaternary system
Authors: Shen S. , Liu X. , Cho Y. J. , Furdyna J. K. , Dobrowolska M. , Hwang Y. H. , Um Y. H.
Published: April 2009

We describe magneto-optical and magnetic properties of quaternary Cd1−x−yMnxCryTe crystals (x=0.37, 0≤y≤0.03) grown by the Bridgman method. The presence of Cr in this alloy is observed to induce ferromagnetic behavior and to enhance magneto-optical effects. Using magnetic circular dichroism and magnetization measurements, we describe the dependence of this behavior on the Cr concentration, and we discuss possible mechanisms for the observed effects.
Effects of capping on GaN quantum dots deposited on Al0.5Ga0.5N by molecular beam epitaxy
Authors: Korytov M. , Benaissa M. , Brault J. , Huault T. , Neisius T. , Vennéguès P.
Published: April 2009

The impact of the capping process on the structural and morphological properties of GaN quantum dots (QDs) grown on fully relaxed Al0.5Ga0.5N templates was studied by transmission electron microscopy. A morphological transition between the surface QDs, which have a pyramidal shape, and the buried ones, which have a truncated pyramid shape, is evidenced. This shape evolution is accompanied by a volume change: buried QDs are bigger than surface ones. Furthermore a phase separation into Al0.5Ga0.5N barriers was observed in the close vicinity of buried QDs. As a result, the buried QDs were found to be connected with the nearest neighbors by thin Ga-rich zones, whereas Al-rich zones are situated above the QDs.
DyScO
3
buffer layer for a performing metal-ferroelectric-insulator-semiconductor structure with multiferroic BiFeO3 thin film
Authors: Murari N. M. , Thomas R. , Pavunny S. P. , Calzada J. R. , Katiyar R. S.
Published: April 2009

Metal-ferroelectric-insulator-semiconductor structures with a BiFeO3 ferroelectric layer and DyScO3 insulating buffer layer were fabricated and characterized. BiFeO3 film was polycrystalline with rhombohedral structure and DyScO3 film was amorphous. The size of the capacitance-voltage memory window (ΔVFB) was investigated as a function of voltage sweep and frequency; ΔVFB increased to a saturation value of 1.7 V with the sweep voltage and it almost remained constant over a frequency range of 1 kHz to 1 MHz.
SiGe nanorings by ultrahigh vacuum chemical vapor deposition
Authors: Lee C.-H. , Shen Y.-Y. , Liu C. W. , Lee S. W. , Lin B.-H. , Hsu C.-H.
Published: April 2009

Formation of SiGe nanorings from Si capped Si0.1Ge0.9 quantum dots (QDs) grown at 500 °C by ultrahigh vacuum chemical vapor deposition was investigated. SiGe nanorings have average diameter, width, and depth of 185, 30, and 9 nm, respectively. Based on both Raman and x-ray diffraction results, the formation of SiGe nanorings can be attributed to Ge outdiffusion from central SiGe QDs during in situ annealing. Moreover, the depth of SiGe nanorings can be controlled by Si cap thickness. The Si cap is essential for nanorings formation.
On the influence of elastic strain on the accommodation of carbon atoms into substitutional sites in strained Si:C layers grown on Si substrates
Authors: Cherkashin N. , Hÿtch M. J. , Houdellier F. , Hüe F. , Paillard V , Claverie A. , Gouyé A. , Kermarrec O. , Rouchon D. , Burdin M. , Holliger P.
Published: April 2009

Measurements of strain and composition are reported in tensile strained 10- and 30-nm-thick Si:C layers grown by chemical vapor deposition on a Si (001) substrate. Total carbon concentration varies from 0.62% to 1.97%. Strain measurements were realized by high-resolution x-ray diffraction, convergent-beam electron diffraction, and geometric phase analysis of high-resolution transmission electron microscopy cross-sectional images. Raman spectroscopy was used for the deduction of the substitutional concentration. We demonstrate that in addition to the growth conditions, strain accumulating during deposition, thus depending on a layer thickness, has an influence on the final substitutional carbon composition within a strained Si:C layer.
Spin relaxation and dephasing mechanism in (Ga,Mn)As studied by time-resolved Kerr rotation
Authors: Zhu Yonggang , Zhang Xinhui , Li Tao , Chen Lin , Lu Jun , Zhao Jianhua
Published: April 2009

Spin dynamics in (Ga,Mn)As films grown on GaAs(001) was investigated by Time-resolved magneto-optical Kerr effect. The Kerr signal decay time of (Ga,Mn)As without external magnetic field applied was found to be several hundreds picoseconds, which suggested that photogenerated polarized holes and magnetic ions are coupled as a ferromagnetic system. Nonmonotonic temperature dependence of relaxation and dephasing (R&D) time and Larmor frequency manifests that Bir–Aronov–Pikus mechanism dominates the spin R&D time at low temperature, while D’yakonov–Perel mechanism dominates the spin R&D time at high temperature, and the crossover between the two regimes is Curie temperature.
DNA-quantum dot sensing platform with combined Förster resonance energy transfer and photovoltaic effect
Authors: Qi Huijie , Wang Lixiang , Wong Ka-wai , Du Zuliang
Published: April 2009

A special DNA sensing platform based on a network of hybrid DNA-quantum dot system was designed and fabricated. Upon attachment of hybridized complementary DNA sequences, the molecular switch system can exhibit both photoinduced Förster resonance energy transfer (FRET) and photovoltaic (PV) effects simultaneously, but will give much weakened or no effect for the capture of hybridized products from “mismatched” DNA sequences. This dual sensing scheme based on combined FRET and PV effects can safeguard the accuracy of sensing, as FRET and PV can be singly induced even in the case of mismatch.
Photonic crystal heteroslab-edge microcavity with high quality factor surface mode for index sensing
Authors: Lu Tsan-Wen , Hsiao Yi-Hua , Ho Wei-De , Lee Po-Tsung
Published: April 2009

In this report, we propose a photonic crystal heteroslab-edge microcavity design for optical index sensing, where the high quality (Q) surface mode is confined by mode-gap effect. By optimizing the barrier region of the microcavity, high Q factor of 6.6×105 is obtained in simulations. Lasing actions with high Q factor and low threshold of 6400 and 0.55 mW are obtained from the real devices. High index sensing response and small detectable index variation of 625 nm per refractive index unit and 3.6×10−6 are obtained in simulations.
Surface effects on buckling of nanowires under uniaxial compression
Authors: Wang Gang-Feng , Feng Xi-Qiao
Published: April 2009

Based on the conventional Euler buckling model, uniaxial compression tests have been utilized recently to measure the mechanical properties of nanowires. However, owing to the increasing ratio of surface area to bulk at nanoscale, the influence of surface energy becomes prominent and should be taken into consideration. In this letter, an analytical relation is given for the critical force of axial buckling of a nanowire by accounting for both the effects of surface elasticity and residual surface tension. This study might be helpful to characterize the mechanical properties of nanowires or design nanobeam-based devices in a wide range of applications.
Flow serration and shear-band propagation in bulk metallic glasses
Authors: Chen H. M. , Huang J. C. , Song S. X. , Nieh T. G. , Jang J. S. C.
Published: April 2009

Flow serration in bulk metallic glasses (BMGs) was analyzed using high-sensitivity strain gauges. Based on the displacement-time profile for one serration, shear-band propagating speed was determined and found to be insensitive to the applied strain rates. The disappearance of serration at high strain rates is a result that the signal of displacement burst was overwhelmed by the applied strain rate. In comparison with the ductile Pd-based and brittle Mg-based BMGs, the ductility of BMGs appears to be closely related to the dynamics during shear-band propagation.
On a new topology in the phase diagram of biaxial nematic liquid crystals
Authors: Mukherjee Prabir K. , Sen Kallol
Published: April 2009

We describe new topologies in the phase diagrams involving biaxial nematic liquid crystals. We find that a direct isotropic-biaxial nematic phase transition is possible. Our results show that three different biaxial nematic phases can occur. We outline how the novel phase diagrams could be detected experimentally.
The effect of layer absorbance for complex surface enhanced Raman scattering substrates
Authors: Zhang Z.-Y. , Liu Y.-J. , Zhao Q. , Zhao Y.-P.
Published: April 2009

The “hot spots” mechanism is a common wisdom for surface enhanced Raman scattering (SERS). We argue that this is true when the hot spots are directly exposed to the detector. For complex SERS substrates with layered structures such as nanorod arrays, the structure and the layer absorbance both play important roles, which make the effect of hot spots less significant. Using a numerical calculation of the local electric field distribution of an Ag nanorod array substrate, we demonstrate that the layer absorbance must be considered in order to obtain polarization-dependent SERS intensity that is consistent with experimental data.
Low-voltage InGaZnO thin-film transistors with Al2O3 gate insulator grown by atomic layer deposition
Authors: Kim J. B. , Fuentes-Hernandez C. , Potscavage W. J. , Zhang X.-H. , Kippelen B.
Published: April 2009

We report on low-voltage, high-performance amorphous indium gallium zinc oxide n-channel thin-film transistors fabricated using 100-nm-thick Al2O3 grown by atomic layer deposition as the gate dielectric layer. The Al2O3 gate dielectric shows very small current densities and has a capacitance density of 81±1 nF/cm2. Due to a very small contact resistance, transistors with channel lengths ranging from 100 μm down to 5 μm yield a channel-independent, field-effect mobility of 8±1 cm2/V s, subthreshold slopes of 0.1±0.01 V/decade, low threshold voltages of 0.4±0.1 V, and high on-off current ratios up to 6×107 (W/L=400/5 μm) at 5 V.
Converging biconcave metallic lens by double-negative extraordinary transmission metamaterial
Authors: Navarro-Cía M. , Beruete M. , Sorolla M. , Campillo I.
Published: April 2009

In this letter we present simulation and experimental results of a left-handed converging biconcave metallic lens made of stacked subwavelength hole arrays (SSHAs) working in the millimeter wave range with additional features of polarizer and frequency filter. The converging behavior of the biconcave metallic lens, in contrast with focusing biconvex dielectric lenses, comes as a result of the negative index of refraction that characterizes double-negative metamaterials made of SSHAs. The presented results may find application in the design of lenses and devices both in the microwave, infrared and optical ranges.
Predicting spatial similarity of freshwater fish biodiversity
Authors: Azaele Sandro , Muneepeerakul Rachata , Maritan Amos , Rinaldo Andrea , Rodriguez-Iturbe Ignacio
Published: April 2009

A major issue in modern ecology is to understand how ecological complexity at broad scales is regulated by mechanisms operating at the organismic level. What specific underlying processes are essential for a macroecological pattern to emerge? Here, we analyze the analytical predictions of a general model suitable for describing the spatial biodiversity similarity in river ecosystems, and benchmark them against the empirical occurrence data of freshwater fish species collected in the Mississippi–Missouri river system. Encapsulating immigration, emigration, and stochastic noise, and without resorting to species abundance data, the model is able to reproduce the observed probability distribution of the Jaccard similarity index at any given distance. In addition to providing an excellent agreement with the empirical data, this approach accounts for heterogeneities of different subbasins, suggesting a strong dependence of biodiversity similarity on their respective climates. Strikingly, the model can also predict the actual probability distribution of the Jaccard similarity index for any distance when considering just a relatively small sample. The proposed framework supports the notion that simplified macroecological models are capable of predicting fundamental patterns—a theme at the heart of modern community ecology.
WIP is critical for T cell responsiveness to IL-2
Authors: Le Bras Severine , Massaad Michel , Koduru Suresh , Kumar Lalit , Oyoshi Michiko K. , Hartwig John , Geha Raif S.
Published: April 2009

The Wiskott-Aldrich syndrome (WAS) interacting protein (WIP) stabilizes the WAS protein (WASP), the product of the gene mutated in WAS. WIP-deficient T cells have low WASP levels, limiting the usefulness of WIP KO mice in defining the role of WIP in T cell function. To define this role, we compared WIP/WASP double KO (DKO) mice to WASP KO mice on DO11.10 background. T cell development was normal in both strains, but peripheral T cell numbers were significantly decreased in DKO mice. WASP KO T cells proliferated and secreted IL-2 normally in response to OVA peptide (OVAp). In contrast, T cells from DKO mice proliferated poorly in response to OVAp in vitro, and cutaneous hapten hypersensitivity was deficient in these mice. DKO T cells up-regulated CD25 expression and secreted normal amounts of IL-2 after antigen stimulation, but had defective response to IL-2, evidenced by failure to further up-regulate CD25 expression, phosphorylate STAT5, and induce expression of STAT5-dependent genes. DKO, but not WASP KO, T cells had a disrupted subcortical actin cytoskeleton and impaired actin polymerization after T cell antigen receptor (TCR) ligation. These results indicate that WIP is essential for IL-2 signaling and responsiveness in T cells, possibly because of its critical role in TCR-triggered actin cytoskeletal reorganization.
The protein disulfide isomerase AGR2 is essential for production of intestinal mucus
Authors: Park Sung-Woo , Zhen Guohua , Verhaeghe Catherine , Nakagami Yasuhiro , Nguyenvu Louis T. , Barczak Andrea J. , Killeen Nigel , Erle David J.
Published: April 2009

Protein disulfide isomerases (PDIs) aid protein folding and assembly by catalyzing formation and shuffling of cysteine disulfide bonds in the endoplasmic reticulum (ER). Many members of the PDI family are expressed in mammals, but the roles of specific PDIs in vivo are poorly understood. A recent homology-based search for additional PDI family members identified anterior gradient homolog 2 (AGR2), a protein originally presumed to be secreted by intestinal epithelial cells. Here, we show that AGR2 is present within the ER of intestinal secretory epithelial cells and is essential for in vivo production of the intestinal mucin MUC2, a large, cysteine-rich glycoprotein that forms the protective mucus gel lining the intestine. A cysteine residue within the AGR2 thioredoxin-like domain forms mixed disulfide bonds with MUC2, indicating a direct role for AGR2 in mucin processing. Mice lacking AGR2 were viable but were highly susceptible to colitis, indicating a critical role for AGR2 in protection from disease. We conclude that AGR2 is a unique member of the PDI family, with a specialized and nonredundant role in intestinal mucus production.
Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes
Authors: Hitomi Kenichi , DiTacchio Luciano , Arvai Andrew S. , Yamamoto Junpei , Kim Sang-Tae , Todo Takeshi , Tainer John A. , Iwai Shigenori , Panda Satchidananda , Getzoff Elizabeth D.
Published: April 2009

Homologous flavoproteins from the photolyase (PHR)/cryptochrome (CRY) family use the FAD cofactor in PHRs to catalyze DNA repair and in CRYs to tune the circadian clock and control development. To help address how PHR/CRY members achieve these diverse functions, we determined the crystallographic structure of
Arabidopsis thaliana
(6-4) PHR (UVR3), which is strikingly (>65%) similar in sequence to human circadian clock CRYs. The structure reveals a substrate-binding cavity specific for the UV-induced DNA lesion, (6-4) photoproduct, and cofactor binding sites different from those of bacterial PHRs and consistent with distinct mechanisms for activities and regulation. Mutational analyses were combined with this prototypic structure for the (6-4) PHR/clock CRY cluster to identify structural and functional motifs: phosphate-binding and Pro-Lys-Leu protrusion motifs constricting access to the substrate-binding cavity above FAD, sulfur loop near the external end of the Trp electron-transfer pathway, and previously undefined C-terminal helix. Our results provide a detailed, unified framework for investigations of (6-4) PHRs and the mammalian CRYs. Conservation of key residues and motifs controlling FAD access and activities suggests that regulation of FAD redox properties and radical stability is essential not only for (6-4) photoproduct DNA repair, but also for circadian clock-regulating CRY functions. The structural and functional results reported here elucidate archetypal relationships within this flavoprotein family and suggest how PHRs and CRYs use local residue and cofactor tuning, rather than larger structural modifications, to achieve their diverse functions encompassing DNA repair, plant growth and development, and circadian clock regulation.
Propagule supply controls grazer community structure and primary production in a benthic marine ecosystem
Authors: Lee Sarah C. , Bruno John F.
Published: April 2009

Early theories of species diversity proposed that communities at equilibrium are saturated with species. However, experiments in plant communities suggest that many communities are unsaturated and species richness can be increased by adding propagules of new species. We experimentally tested for community saturation and measured the effects of propagule supply on community structure in a benthic marine system. We manipulated propagule supply (arrival of individuals of numerous species) of mobile grazers in experimental mesocosms over multiple generations and, unlike previous tests, we examined the cascading effects of propagule supply on prey (macroalgae) biomass. We found little evidence for saturation, despite the absence of processes such as disturbance and predation that are thought to alleviate saturation in nature. Increasing propagule supply increased the total number of species and made rare species more abundant. Perhaps surprisingly, given the strong effect of propagule supply on species richness, supply-related changes in body size and composition suggest that competitive interactions remained important. Grazer supply also had strong cascading effects on primary production, possibly because of dietary complementarity modified by territorial behavior. Our results indicate that propagule supply can directly influence the diversity and composition of communities of mobile animals. Furthermore, the supply of consumer propagules can have strong indirect effects on prey and fundamental ecosystem properties.
Signatures of natural selection are not uniform across genes of innate immune system, but purifying selection is the dominant signature
Authors: Mukherjee Souvik , Sarkar-Roy Neeta , Wagener Diane K. , Majumder Partha P.
Published: April 2009

We tested the opposing views concerning evolution of genes of the innate immune system that (
i
) being evolutionary ancient, the system may have been highly optimized by natural selection and therefore should be under purifying selection, and (
ii
) the system may be plastic and continuing to evolve under balancing selection. We have resequenced 12 important innate-immunity genes (
CAMP
,
DEFA4
,
DEFA5
,
DEFA6
,
DEFB1
,
MBL2
, and
TLR
s
1
,
2
,
4
,
5
,
6
, and
9
) in healthy volunteers (
n
= 171) recruited from a region of India with high microbial load. We have compared these data with those of European-Americans (EUR) and African-Americans (AFR). We have found that most of the human haplotypes are many mutational steps away from the ancestral (chimpanzee) haplotypes, indicating that humans may have had to adapt to new pathogens. The haplotype structures in India are significantly different from those of EUR and AFR populations, indicating local adaptation to pathogens. In these genes, there is (
i
) generally an excess of rare variants, (
ii
) high, but variable, degrees of extended haplotype homozygosity, (
iii
) low tolerance to nonsynonymous changes, (
iv
) essentially one or a few high-frequency haplotypes, with star-like phylogenies of other infrequent haplotypes radiating from the modal haplotypes. Purifying selection is the most parsimonious explanation operating on these innate immunity genes. This genetic surveillance system recognizes motifs in pathogens that are perhaps conserved across a broad range of pathogens. Hence, functional constraints are imposed on mutations that diminish the ablility of these proteins to detect pathogens.
Distinct patterns of brain activity in young carriers of the
APOE
-ε4 allele
Authors: Filippini Nicola , MacIntosh Bradley J. , Hough Morgan G. , Goodwin Guy M. , Frisoni Giovanni B. , Smith Stephen M. , Matthews Paul M. , Beckmann Christian F. , Mackay Clare E.
Published: April 2009

The
APOE
ε4 allele is a risk factor for late-life pathological changes that is also associated with anatomical and functional brain changes in middle-aged and elderly healthy subjects. We investigated structural and functional effects of the
APOE
polymorphism in 18 young healthy
APOE
ε4-carriers and 18 matched noncarriers (age range: 20–35 years). Brain activity was studied both at rest and during an encoding memory paradigm using blood oxygen level-dependent fMRI. Resting fMRI revealed increased “default mode network” (involving retrosplenial, medial temporal, and medial-prefrontal cortical areas) coactivation in ε4-carriers relative to noncarriers. The encoding task produced greater hippocampal activation in ε4-carriers relative to noncarriers. Neither result could be explained by differences in memory performance, brain morphology, or resting cerebral blood flow. The
APOE
ε4 allele modulates brain function decades before any clinical or neurophysiological expression of neurodegenerative processes.
Changes in biogenic carbon flow in response to sea surface warming
Authors: Wohlers Julia , Engel Anja , Zöllner Eckart , Breithaupt Petra , Jürgens Klaus , Hoppe Hans-Georg , Sommer Ulrich , Riebesell Ulf
Published: April 2009

The pelagic ocean harbors one of the largest ecosystems on Earth. It is responsible for approximately half of global primary production, sustains worldwide fisheries, and plays an important role in the global carbon cycle. Ocean warming caused by anthropogenic climate change is already starting to impact the marine biota, with possible consequences for ocean productivity and ecosystem services. Because temperature sensitivities of marine autotrophic and heterotrophic processes differ greatly, ocean warming is expected to cause major shifts in the flow of carbon and energy through the pelagic system. Attempts to integrate such biological responses into marine ecosystem and biogeochemical models suffer from a lack of empirical data. Here, we show, using an indoor-mesocosm approach, that rising temperature accelerates respiratory consumption of organic carbon relative to autotrophic production in a natural plankton community. Increasing temperature by 2–6 °C hence decreased the biological drawdown of dissolved inorganic carbon in the surface layer by up to 31%. Moreover, warming shifted the partitioning between particulate and dissolved organic carbon toward an enhanced accumulation of dissolved compounds. In line with these findings, the loss of organic carbon through sinking was significantly reduced at elevated temperatures. The observed changes in biogenic carbon flow have the potential to reduce the transfer of primary produced organic matter to higher trophic levels, weaken the ocean's biological carbon pump, and hence provide a positive feedback to rising atmospheric CO
2
.
Experimentally observed phenomena on cardiac energetics in heart failure emerge from simulations of cardiac metabolism
Authors: Wu Fan , Zhang Jianyi , Beard Daniel A.
Published: April 2009

The failing heart is hypothesized to suffer from energy supply inadequate for supporting normal cardiac function. We analyzed data from a canine left ventricular hypertrophy model to determine how the energy state evolves because of changes in key metabolic pools. Our findings—confirmed by in vivo
31
P-magnetic resonance spectroscopy—indicate that the transition between the clinically observed early compensatory phase and heart failure and the critical point at which the transition occurs are emergent properties of cardiac energy metabolism. Specifically, analysis reveals a phenomenon in which low and moderate reductions in metabolite pools have no major negative impact on oxidative capacity, whereas reductions beyond a critical tipping point lead to a severely compromised energy state. The transition point corresponds to reductions in the total adenine nucleotide pool (TAN) of ≈30%, corresponding to the reduction observed in humans in heart failure [Ingwall JS, Weiss RG (2004) Is the failing heart energy starved? On using chemical energy to support cardiac function.
Circ Res
95(
2
):135–145]. At given values of TAN and the total exchangeable phosphate pool during hypertrophic remodeling, the creatine pool attains a value that is associated with optimal ATP hydrolysis potential. Thus, both increases and decreases to the creatine pool are predicted to result in diminished energetic state unless accompanied by appropriate simultaneous changes in the other pools.
Structural basis for cAMP-mediated allosteric control of the catabolite activator protein
Authors: Popovych Nataliya , Tzeng Shiou-Ru , Tonelli Marco , Ebright Richard H. , Kalodimos Charalampos G.
Published: April 2009

The cAMP-mediated allosteric transition in the catabolite activator protein (CAP; also known as the cAMP receptor protein, CRP) is a textbook example of modulation of DNA-binding activity by small-molecule binding. Here we report the structure of CAP in the absence of cAMP, which, together with structures of CAP in the presence of cAMP, defines atomic details of the cAMP-mediated allosteric transition. The structural changes, and their relationship to cAMP binding and DNA binding, are remarkably clear and simple. Binding of cAMP results in a coil-to-helix transition that extends the coiled-coil dimerization interface of CAP by 3 turns of helix and concomitantly causes rotation, by ≈60°, and translation, by ≈7 Å, of the DNA-binding domains (DBDs) of CAP, positioning the recognition helices in the DBDs in the correct orientation to interact with DNA. The allosteric transition is stabilized further by expulsion of an aromatic residue from the cAMP-binding pocket upon cAMP binding. The results define the structural mechanisms that underlie allosteric control of this prototypic transcriptional regulatory factor and provide an illustrative example of how effector-mediated structural changes can control the activity of regulatory proteins.
A single amino acid change converts Aurora-A into Aurora-B-like kinase in terms of partner specificity and cellular function
Authors: Fu Jingyan , Bian Minglei , Liu Junjun , Jiang Qing , Zhang Chuanmao
Published: April 2009

Aurora kinase-A and -B are key regulators of the cell cycle and tumorigenesis. It has remained a mystery why these 2 Aurora kinases, although highly similar in protein sequence and structure, are distinct in subcellular localization and function. Here, we report the striking finding that a single amino acid residue is responsible for these differences. We replaced the Gly-198 of Aurora-A with the equivalent residue Asn-142 of Aurora-B and found that in HeLa cells, Aurora-A
G198N
was recruited to the inner centromere in metaphase and the midzone in anaphase, reminiscent of the Aurora-B localization. Moreover, Aurora-A
G198N
compensated for the loss of Aurora-B in chromosome misalignment and cell premature exit from mitosis. Furthermore, Aurora-A
G198N
formed a complex with the Aurora-B partners, INCENP and Survivin, and its localization depended on this interaction. Aurora-A
G198N
phosphorylated the Aurora-B substrates INCENP and Survivin in vitro. Therefore, we propose that the presence of Gly or Asn at a single site assigns Aurora-A and -B to their respective partners and thus to their distinctive subcellular localizations and functions.
Impact of clock-associated
Arabidopsis
pseudo-response regulators in metabolic coordination
Authors: Fukushima Atsushi , Kusano Miyako , Nakamichi Norihito , Kobayashi Makoto , Hayashi Naomi , Sakakibara Hitoshi , Mizuno Takeshi , Saito Kazuki
Published: April 2009

In higher plants, the circadian clock controls a wide range of cellular processes such as photosynthesis and stress responses. Understanding metabolic changes in arrhythmic plants and determining output-related function of clock genes would help in elucidating circadian-clock mechanisms underlying plant growth and development. In this work, we investigated physiological relevance of PSEUDO-RESPONSE REGULATORS (PRR 9, 7, and 5) in
Arabidopsis thaliana
by transcriptomic and metabolomic analyses. Metabolite profiling using gas chromatography–time-of-flight mass spectrometry demonstrated well-differentiated metabolite phenotypes of seven mutants, including two arrhythmic plants with similar morphology, a
PRR 9
,
7
, and
5
triple mutant and a
CIRCADIAN CLOCK-ASSOCIATED 1
(
CCA1
)-overexpressor line. Despite different light and time conditions, the triple mutant exhibited a dramatic increase in intermediates in the tricarboxylic acid cycle. This suggests that proteins PRR 9, 7, and 5 are involved in maintaining mitochondrial homeostasis. Integrated analysis of transcriptomics and metabolomics revealed that PRR 9, 7, and 5 negatively regulate the biosynthetic pathways of chlorophyll, carotenoid and abscisic acid, and α-tocopherol, highlighting them as additional outputs of pseudo-response regulators. These findings indicated that mitochondrial functions are coupled with the circadian system in plants.
Microbial translocation, the innate cytokine response, and HIV-1 disease progression in Africa
Authors: Redd Andrew D. , Dabitao Djeneba , Bream Jay H. , Charvat Blake , Laeyendecker Oliver , Kiwanuka Noah , Lutalo Tom , Kigozi Godfrey , Tobian Aaron A. R. , Gamiel Jordyn , Neal Jessica D. , Oliver Amy E. , Margolick Joseph B. , Sewankambo Nelson , Reynolds Steven J. , Wawer Maria J. , Serwadda David , Gray Ronald H. , Quinn Thomas C.
Published: April 2009

Reports from the United States have demonstrated that elevated markers of microbial translocation from the gut may be found in chronic and advanced HIV-1 infection and are associated with an increase in immune activation. However, this phenomenon's role in HIV-1 disease in Africa is unknown. This study examined the longitudinal relationship between microbial translocation and circulating inflammatory cytokine responses in a cohort of people with varying rates of HIV-1 disease progression in Rakai, Uganda. Multiple markers for microbial translocation (lipopolysaccharide, endotoxin antibody, and sCD14) did not change significantly during HIV-1 disease progression. Moreover, circulating immunoreactive cytokine levels either decreased or remained virtually unchanged throughout disease progression. These data suggest that microbial translocation and its subsequent inflammatory immune response do not have a causal relationship with HIV-1 disease progression in Africa.
Association of survival and disease progression with chromosomal instability: A genomic exploration of colorectal cancer
Authors: Sheffer Michal , Bacolod Manny D. , Zuk Or , Giardina Sarah F. , Pincas Hanna , Barany Francis , Paty Philip B. , Gerald William L. , Notterman Daniel A. , Domany Eytan
Published: April 2009

During disease progression the cells that comprise solid malignancies undergo significant changes in gene copy number and chromosome structure. Colorectal cancer provides an excellent model to study this process. To indentify and characterize chromosomal abnormalities in colorectal cancer, we performed a statistical analysis of 299 expression and 130 SNP arrays profiled at different stages of the disease, including normal tissue, adenoma, stages 1–4 adenocarcinoma, and metastasis. We identified broad (> 1/2 chromosomal arm) and focal (< 1/2 chromosomal arm) events. Broad amplifications were noted on chromosomes 7, 8q, 13q, 20, and X and broad deletions on chromosomes 4, 8p, 14q, 15q, 17p, 18, 20p, and 22q. Focal events (gains or losses) were identified in regions containing known cancer pathway genes, such as
VEGFA
,
MYC
,
MET
,
FGF6
,
FGF23
,
LYN
,
MMP9
,
MYBL2
,
AURKA
,
UBE2C
, and
PTEN
. Other focal events encompassed potential new candidate tumor suppressors (losses) and oncogenes (gains), including
CCDC68
,
CSMD1
,
POLR1D
, and
PMEPA1
. From the expression data, we identified genes whose expression levels reflected their copy number changes and used this relationship to impute copy number changes to samples without accompanying SNP data. This analysis provided the statistical power to show that deletions of 8p, 4p, and 15q are associated with survival and disease progression, and that samples with simultaneous deletions in 18q, 8p, 4p, and 15q have a particularly poor prognosis. Annotation analysis reveals that the oxidative phosphorylation pathway shows a strong tendency for decreased expression in the samples characterized by poor prognosis.
Müllerian inhibiting substance contributes to sex-linked biases in the brain and behavior
Authors: Wang Pei-Yu , Protheroe Anna , Clarkson Andrew N. , Imhoff Floriane , Koishi Kyoko , McLennan Ian S.
Published: April 2009

Many behavioral traits and most brain disorders are common to males and females but are more evident in one sex than the other. The control of these subtle sex-linked biases is largely unstudied and has been presumed to mirror that of the highly dimorphic reproductive nuclei. Sexual dimorphism in the reproductive tract is a product of Müllerian inhibiting substance (MIS), as well as the sex steroids. Males with a genetic deficiency in MIS signaling are sexually males, leading to the presumption that MIS is not a neural regulator. We challenge this presumption by reporting that most immature neurons in mice express the MIS-specific receptor (MISRII) and that male
Mis
−/−
and
Misrii
−/−
mice exhibit subtle feminization of their spinal motor neurons and of their exploratory behavior. Consequently, MIS may be a broad regulator of the subtle sex-linked biases in the nervous system.
Inositol phosphatase SHIP1 is a primary target of miR-155
Authors: O'Connell Ryan M. , Chaudhuri Aadel A. , Rao Dinesh S. , Baltimore David
Published: April 2009

MicroRNA-155 (miR-155) has emerged as a critical regulator of immune cell development, function, and disease. However, the mechanistic basis for its impact on the hematopoietic system remains largely unresolved. Because miRNAs function by repressing specific mRNAs through direct 3′UTR interactions, we have searched for targets of miR-155 implicated in the regulation of hematopoiesis. In the present study, we identify Src homology-2 domain-containing inositol 5-phosphatase 1 (SHIP1) as a direct target of miR-155, and, using gain and loss of function approaches, show that miR-155 represses SHIP1 through direct 3′UTR interactions that have been highly conserved throughout evolution. Repression of endogenous SHIP1 by miR-155 occurred following sustained over-expression of miR-155 in hematopoietic cells both in vitro and in vivo, and resulted in increased activation of the kinase Akt during the cellular response to LPS. Furthermore, SHIP1 was also repressed by physiologically regulated miR-155, which was observed in LPS-treated WT versus miR-155
−/−
primary macrophages. In mice, specific knockdown of SHIP1 in the hematopoietic system following retroviral delivery of a miR-155-formatted siRNA against SHIP1 resulted in a myeloproliferative disorder, with striking similarities to that observed in miR-155-expressing mice. Our study unveils a molecular link between miR-155 and SHIP1 and provides evidence that repression of SHIP1 is an important component of miR-155 biology.
IL-1 acts directly on CD4 T cells to enhance their antigen-driven expansion and differentiation
Authors: Ben-Sasson Shlomo Z. , Hu-Li Jane , Quiel Juan , Cauchetaux Stephane , Ratner Maya , Shapira Ilana , Dinarello Charles A. , Paul William E.
Published: April 2009

IL-1 causes a marked increase in the degree of expansion of naïve and memory CD4 T cells in response to challenge with their cognate antigen. The response occurs when only specific CD4 T cells can respond to IL-1β, is not induced by a series of other cytokines and does not depend on IL-6 or CD-28. When WT cells are primed in IL-1R1−/−recipients, IL-1 increases the proportion of cytokine-producing transgenic CD4 T cells, especially IL-17- and IL-4-producing cells, strikingly increases serum IgE levels and serum IgG1 levels. IL-1β enhances antigen-mediated expansion of in vitro primed Th1, Th2, and Th17 cells transferred to IL-1R1−/−recipients. The IL-1 receptor antagonist diminished responses to antigen plus lipopolysaccharide (LPS) by ≈55%. These results indicate that IL-1β signaling in T cells markedly induces robust and durable primary and secondary CD4 responses.
Seem and evidentiality
Authors: Aijmer Karin
Published: April 2009

The paper is an empirical, corpus-based analysis of the functions of seem with different complementation structures and in impersonal constructions as well as in combinations with an experiencer. The focus is on describing how evidentiality (e.g. inferencing/observation or hearsay evidence) interacts with degrees of certainty or factivity of the construction. Other features are subjectivity and intersubjectivity (shared or non-shared information). Translations from English into Swedish have been used to get a more fine-grained picture of the degree of certainty expressed by seem and its relationship to the type of evidence. The different constructions with seem and their functions are explained in a grammaticalization perspective. Seem conforms to a number of principles such as layering and divergence (Hopper). Seem to is the most grammaticalized form and can be regarded as an evidential marker which is similar to the modal auxiliaries.
Fluoroscopically guided percutaneous vertebroplasty: Assessment of radiation doses and implementation of procedural routines to reduce operator exposure
Authors: von Wrangel A. , Cederblad Å. , Rodriguez-Catarino M.
Published: April 2009

Background: Percutaneous vertebroplasty (PVP) is a fluoroscopically guided procedure for the treatment of painful vertebral compression fractures and metastases. Routine legal personal dosimetry repeatedly showed dosimeter doses exceeding 1 mSv/month for the only radiologist performing PVP at our hospital. Based on the nature of the procedure, this raised concern about potentially high doses to the eyes and fingers.

Purpose: To assess radiation doses to the operator, and to evaluate possibilities for dose reduction.

Material and Methods: Measurements of scattered radiation in simulated thoracic and lumbar PVP procedures were performed using two anatomical phantoms—thorax and lower trunk—and a radiation survey meter. The standard position of the operator was determined as being 50 cm from the irradiated area of the phantom. The protection ability of lead-free gloves was evaluated during the simulations. Operator doses to fingers and eyes during 10 clinical PVP procedures performed by a single operator were measured, and the annual dose was calculated. Routine personal dosimetry was performed using thermoluminescent dosimeter (TLD) badges beneath the lead apron, and doses to fingers and eyes were measured with small TLD tablets.

Results: During simulations, the measured operator dose rate arising from lateral fluoroscopy at the thorax and lumbar level was reduced by a factor of 4–5 when the X-ray tube was moved from the operator's side of the patient to the opposite side. Wearing protective gloves reduced radiation dose to the hands by 30–40%. The mean doses arising from the 10 clinical PVP procedures to the right and left hands, using protection gloves, were 2.0 mSv and 4.8 mSv, respectively. The mean dose to the eyes was 0.23 mSv. The mean effective dose to the patients was 12 mSv.

Conclusion: Placing the X-ray tube on the side of the patient opposite to the operator and the use of radiation protection gloves significantly reduces radiation exposure to the operator. In phantom simulations, the dose was reduced by a factor of 4–5. Knowledge of fluoroscopy equipment, radiation physics, and protection is essential in order to reduce exposure.
Study of turbulent fluctuations driven by the electron temperature gradient in the National Spherical Torus Experiment
Authors: Mazzucato E. , Bell R.E. , Ethier S. , Hosea J.C. , Kaye S.M. , LeBlanc B.P. , Lee W.W. , Ryan P.M. , Smith D.R. , Wang W.X. , Wilson J.R. , Yuh H.
Published: April 2009

Various theories and numerical simulations support the conjecture that the ubiquitous problem of anomalous electron transport in tokamaks may arise from a short-scale turbulence driven by the electron temperature gradient. To check whether this turbulence is present in plasmas of the National Spherical Torus Experiment, measurements of turbulent fluctuations were performed with coherent scattering of electromagnetic waves. Results from plasmas heated by high harmonic fast waves show the existence of density fluctuations in the range of wave numbers k
⊥ρe = 0.1–0.4, corresponding to a turbulence scale length of the order of the collisionless skin depth. Experimental observations and agreement with numerical results from the linear gyro-kinetic GS2 code indicate that the observed turbulence is driven by the electron temperature gradient. These turbulent fluctuations were not observed at the location of an internal transport barrier driven by a negative magnetic shear.