bluuebunny/crossref_metadata_2025 huggingface dataset:
Aircraft measurements of spectral surface albedo and its consistency with ground‐based and space‐borne observations
Authors: Coddington Odele , Schmidt K. Sebastian , Pilewskie Peter , Gore Warren J. , Bergstrom Robert W. , Román Miguel , Redemann Jens , Russell Philip B. , Liu Jicheng , Schaaf Crystal C.
Published: September 2008

Spectral surface albedo, a boundary condition which needs to be accurately known for aerosol remote sensing, surface aerosol forcing, and radiative transfer calculations, also strongly affects Earth's radiation balance. The difficulty in deriving surface albedo from space and aircraft observations lies mainly in the atmospheric correction, especially in aerosol‐burdened regions. Because of the different scales, comparing satellite retrievals with airborne or ground‐based observations is not straightforward. We use Solar Spectral Flux Radiometer (SSFR) measurements of upward and downward irradiance from aircraft altitude during Megacity Initiative: Local and Global Research Observations (MILAGRO) to determine spectral surface albedo at ground stations and along the flight track (over the wavelength range 350 to 2100 nm), thereby linking flight‐level retrieved measurements to larger‐scale satellite observations in the polluted Mexico City environment. Our approach involves iteratively adjusting the surface albedo input of a SSFR specific radiative transfer model until the modeled upward irradiance matches the SSFR measurements at flight level. A sensitivity analysis of surface albedo to aerosol optical properties provides a retrieval uncertainty, which can outweigh the SSFR instrument uncertainty under highly variable conditions (or uncertain measurements) of aerosol optical depth and asymmetry parameter. Comparisons between spectral surface albedo derived from the SSFR, Multi‐Filter Rotating Shadowband Radiometer, and the Moderate Resolution Imaging Spectroradiometer (MODIS) instrument onboard the NASA‐EOS Terra and Aqua satellites are shown with differences of 6–10% and 0.025–0.05 units, respectively. Along‐track comparisons between the SSFR and MODIS show that two instruments (aircraft and satellite) can capture inhomogeneous surface albedo scene changes.
Contrasting Changes in Cortical Activation Induced by Acute High-Frequency Stimulation within the Globus Pallidus in Parkinson's Disease
Authors: Payoux Pierre , Remy Philippe , Miloudi Malika , Houeto Jean-Luc , Stadler Claudio , Bejjani Boulos-Paul , Yelnik Jérome , Samson Yves , Rascol Olivier , Agid Yves , Damier Philippe
Published: September 2008

Continuous stimulation of the globus pallidus (GP) has been shown to be an effective treatment for Parkinson's disease (PD). We used the fact that the implanted quadripolar leads contain electrodes within the GPi and GPe to investigate the clinical effects of acute high-frequency stimulation applied in these nuclei and changes in regional cerebral blood flow (rCBF) as an index of synaptic activity. In five patients treated by chronic GP stimulation, we compared the effects on PD symptoms and the changes in rCBF at rest and during paced right-hand movements, with and without left GPe or GPi stimulation. Although improving contralateral rigidity and akinesia, left GPe stimulation decreased rCBF in the left cerebellum and lateral premotor cortex at rest and significantly increased it in the left primary sensorimotor cortex (SM1) during movement. In contrast, left ventral GPi stimulation, which improved rigidity and worsened akinesia, decreased rCBF in the left SM1, premotor area, anterior cingulum, and supplementary motor area but did not modify the movement-related activation. GPe stimulation seems to result in a reduced activity of motor-related areas and the facilitation of motor cortex activation during movement, the latter component being absent during GPi stimulation, and this may explain the observed worsening of akinesia.
New Insights into Central Roles of Cerebral Oxygen Metabolism in the Resting and Stimulus-Evoked Brain
Authors: Zhu Xiao-Hong , Zhang Nanyin , Zhang Yi , Uğurbil Kâmil , Chen Wei
Published: September 2008

The possible role of oxygen metabolism in supporting brain activation remains elusive. We have used a newly developed neuroimaging approach based on high-field in vivo17O magnetic resonance spectroscopic (MRS) imaging to noninvasively image cerebral metabolic rate of oxygen (CMRO2) consumption in cats at rest and during visual stimulation. It was found that CMRO2 increases significantly (32.3% ± 10.8%, n = 6) in the activated visual cortical region as depicted in blood oxygenation level dependence functional maps; this increase is also accompanied by a CMRO2 decrease in surrounding cortical regions, resulting a smaller increase (9.7% ± 1.9%) of total CMRO2 change over a larger cortical region displaying either a positive or negative CMRO2 alteration. Moreover, a negative correlation between stimulus-evoked percent CMRO2 increase and resting CMRO2 was observed, indicating an essential impact of resting brain metabolic activity level on stimulus-evoked percent CMRO2 change and neuroimaging signals. These findings provide new insights into the critical roles of oxidative metabolism in supporting brain activation and function. They also suggest that in vivo17O MRS imaging should provide a sensitive neuroimaging modality for mapping CMRO2 and its change induced by brain physiology and/or pathologic alteration.
Margarine products quality monitoring using reflectance UV-VIS-SWNIR spectroscopy
Authors: Martins Rui , Lopes Vitor , Vicente António
Published: September 2008

Margarine is a term that can indicate any of a wide range of butter substitutes. Due to the great diversity of the raw material, margarine end-product quality characteristics are expected to be highly diversified. This article proposes the use of reflectance UV-VIS-SWNIR spectroscopy to monitor the margarine end-product quality properties. The main effort in this work was the development of a fast monitoring procedure to assess the quality of the manufactured margarines. The study was performed on two margarine products: regular margarine (less than 80% fat) and reduced-fat margarine (less than 60% fat). The nine product samples were collected during the production line normal operating conditions on different days. The samples had the surface cleaned in order to remove any sign of oxidized material. Then, spectra were collected by a reflectance probe normal to the sample surface. The samples temperature was recorded (10.0± 2.0ºC) and the probe-sample distance was kept constant for all the samples. The integration time was set to 40s for the collection of the five UV/VIS spectra per samples; the three VIS/NIR spectra per sample were collected using a 10s integration time.The data analysis was performed on each product and for each spectral range independently. The spectra were normalized by its maximum intensity and the corrected for using a robust multiplicative scatter correction algorithm. A principal component analysis was performed to the pre-process spectra and the multivariate statistical process control limits were determined with bootstrap for each product/spectral range.Results show that UV-VIS-SWNIR reflectance spectroscopy provides a quick and fast assessment of these products characteristics and thus it can be used as an indication of the overall product variability.
Organophosphorus Chemistry
Authors: Loakes David , Migaud M , Skowronska Aleksandra , Van De Grampel J C , Keglevich Gyorgy , Hewson Alan T
Published: September 2008

Organophosphorus Chemistry provides a comprehensive annual review of the literature. Coverage includes phosphines and their chalcogenides, phosphonium salts, low coordination number phosphorus compounds, penta- and hexa-coordinated compounds, tervalent phosphorus acids, nucleotides and nucleic acids, ylides and related compounds, and phosphazenes. The series will be of value to research workers in universities, government and industrial research organisations, whose work involves the use of organophosphorus compounds. It provides a concise but comprehensive survey of a vast field of study with a wide variety of applications, enabling the reader to rapidly keep abreast of the latest developments in their specialist areas.
Unsaturated fatty acid regulation of cytochrome P450 expression via a CAR-dependent pathway
Authors: Finn Robert D. , Henderson Colin J. , Scott Claire L. , Wolf C. Roland
Published: September 2008

The liver is responsible for key metabolic functions, including control of normal homoeostasis in response to diet and xenobiotic metabolism/detoxification. We have shown previously that inactivation of the hepatic cytochrome P450 system through conditional deletion of POR (P450 oxidoreductase) induces hepatic steatosis, liver growth and P450 expression. We have exploited a new conditional model of POR deletion to investigate the mechanism underlying these changes. We demonstrate that P450 induction, liver growth and hepatic triacylglycerol (triglyceride) homoeostasis are intimately linked and provide evidence that the observed phenotypes result from hepatic accumulation of unsaturated fatty acids, which mediate these phenotypes by activation of the nuclear receptor CAR (constitutive androstane receptor) and, to a lesser degree, PXR (pregnane X receptor). To our knowledge this is the first direct evidence that P450s play a major role in controlling unsaturated fatty acid homoeostasis via CAR. The regulation of P450s involved in xenobiotic metabolism by this mechanism has potentially significant implications for individual responses to drugs and environmental chemicals.
Glucose regulation of insulin gene expression in pancreatic β-cells
Authors: Andrali Sreenath S. , Sampley Megan L. , Vanderford Nathan L. , Özcan Sabire
Published: September 2008

Production and secretion of insulin from the β-cells of the pancreas is very crucial in maintaining normoglycaemia. This is achieved by tight regulation of insulin synthesis and exocytosis from the β-cells in response to changes in blood glucose levels. The synthesis of insulin is regulated by blood glucose levels at the transcriptional and post-transcriptional levels. Although many transcription factors have been implicated in the regulation of insulin gene transcription, three β-cell-specific transcriptional regulators, Pdx-1 (pancreatic and duodenal homeobox-1), NeuroD1 (neurogenic differentiation 1) and MafA (V-maf musculoaponeurotic fibrosarcoma oncogene homologue A), have been demonstrated to play a crucial role in glucose induction of insulin gene transcription and pancreatic β-cell function. These three transcription factors activate insulin gene expression in a co-ordinated and synergistic manner in response to increasing glucose levels. It has been shown that changes in glucose concentrations modulate the function of these β-cell transcription factors at multiple levels. These include changes in expression levels, subcellular localization, DNA-binding activity, transactivation capability and interaction with other proteins. Furthermore, all three transcription factors are able to induce insulin gene expression when expressed in non-β-cells, including liver and intestinal cells. The present review summarizes the recent findings on how glucose modulates the function of the β-cell transcription factors Pdx-1, NeuroD1 and MafA, and thereby tightly regulates insulin synthesis in accordance with blood glucose levels.
Structural requirements of KTS-disintegrins for inhibition of α1β1 integrin
Authors: Brown Meghan C. , Eble Johannes A. , Calvete Juan J. , Marcinkiewicz Cezary
Published: September 2008

Obtustatin and viperistatin represent the shortest known snake venom monomeric disintegrins. In the present study, we have produced recombinant full-length wild-type and site-directed mutants of obtustatin to assess the role of the K21TS23 tripeptide and C-terminal residues for specific inhibition of the α1β1 integrin. Thr22 appeared to be the most critical residue for disintegrin activity, whereas substitution of the flanking lysine or serine residues for alanine resulted in a less pronounced decrease in the anti-α1β1 integrin activity of the disintegrin. The triple mutant A21AA23 was devoid of blocking activity towards α1β1 integrin-mediated cell adhesion. The potency of recombinant KTS-disintegrins also depended on the residue C-terminally adjacent to the active motif. Substitution of Leu24 of wild-type obtustatin for an alanine residue slightly decreased the inhibitory activity of the mutant, whereas an arginine residue in this position enhanced the potency of the mutant over wild-type obtustatin by 6-fold. In addition, the replacements L38V and P40Q may account for a further 25-fold increase in α1β1 inhibitory potency of viperistatin over KTSR-obtustatin.
Hf
O
2
-based InP n-channel metal-oxide-semiconductor field-effect transistors and metal-oxide-semiconductor capacitors using a germanium interfacial passivation layer
Authors: Kim Hyoung-Sub , Ok I. , Zhang M. , Zhu F. , Park S. , Yum J. , Zhao H. , Lee Jack C. , Majhi Prashant
Published: September 2008

In this letter, we present our experimental results of HfO2-based n-channel metal-oxide-semiconductor field-effect transistors (MOSFETs) and metal-oxide-semiconductor capacitors (MOSCAPs) on indium phosphide (InP) substrates using a thin germanium (Ge) interfacial passivation layer (IPL). We found that MOSCAPs on n-InP substrates showed good C-V characteristics such as a small capacitance equivalent thickness (14Å), a small frequency dispersion (<10% and <200mV), and a low dielectric leakage current (∼5×10−4A∕cm2 at Vg=1.5V), whereas MOSCAPs on p-InP exhibited poor characteristics, implying severe Fermi level pinning. It was also found that InP was more vulnerable to a high temperature process such that C-V curves showed a characteristic “bump” and inversion capacitance at relatively high frequencies. From n-channel MOSFETs on a semi-insulating InP substrate using Ge IPL, HfO2, and TaN gate electrodes, excellent electrical characteristics such as a large transconductance (9.3mS∕mm) and large drain currents (12.3mA∕mm at Vd=2V and Vg=Vth+2V) were achieved, which are comparable to other works.
Chaotic scattering of two identical point vortex pairs revisited
Authors: Tophøj Laust , Aref Hassan
Published: September 2008

A new numerical exploration suggests that the motion of two vortex pairs, with constituent vortices all of the same absolute circulation, displays chaotic scattering regimes. The mechanisms leading to chaotic scattering are different from the “slingshot effect” identified by Price [Phys. Fluids A 5, 2479 (1993)] and occur in a different region of the four-vortex phase space. They may, in many cases, be understood by appealing to the solutions of the three-vortex problem obtained by merging two like-signed vortices into one of twice the strength and by assuming that the four-vortex problem has unstable periodic solutions similar to those seen in the thereby associated three-vortex problems. The integrals of motion, linear impulse and Hamiltonian are recast in a form appropriate for vortex pair scattering interactions that provides constraints on the parameters characterizing the outgoing vortex pairs in terms of the initial conditions.
A simple cell for the analysis of nanoelectromechanical systems under gas pressure
Authors: Svitelskiy Oleksiy , Liu Ning , Sauer Vince , Cheng Kar-Mun , Finley Eric , Belov Miro , Freeman Mark R. , Hiebert Wayne K.
Published: September 2008

A simple yet versatile apparatus for optical microscopy investigations of solid-state devices under high gas pressures is presented. Interchangeable high-grade sapphire windows with different thicknesses allow variable choice of trade-off between the maximum operating pressure and maximum spatial resolution. The capabilities of this compact chamber were tested by performing stroboscopic optical interferometry on nanoelectromechanical systems (NEMSs) under capacitive excitation. With a 1.7 mm thick sapphire window, the cell is safe to operate at pressures ranging from vacuum to 5 MPa. Minimal optical wavefront distortion allows NEMSs with linear dimensions of 0.1×1.6 μm2 to be explored. For a sapphire window with a maximum thickness of 6 mm, the safe operating pressure increases up to an estimated 60 MPa; however, the increasing distortions inhibit signal from NEMSs smaller than ∼0.5×1 μm2. The cell can be used for confocal microscopy, microphotoluminescence and electroluminescence, light scattering spectroscopy, and reflectivity. The light weight and compact design of the chamber allow mounting on a precision piezomotion control stage or inside a volume tight apparatus such as cryostats.
Demonstration of a ZnO/MgZnO-based one-dimensional photonic crystal multiquantum well laser
Authors: Hofstetter Daniel , Théron Ricardo , El-Shaer Abdel-Hamid , Bakin Andrey , Waag Andreas
Published: September 2008

A ZnO/MgZnO-based one-dimensional photonic crystal multiquantum well laser operating at an emission wavelength of 360.7 nm is demonstrated. The photonic crystal providing optical feedback was fabricated in the form of parallel grooves with a period of 277.3 nm and a depth of 100 nm in a Si3N4 layer deposited directly on the epitaxial material. At a temperature of 11 K, 16 mW peak power is emitted from the laser surface, and the threshold intensity amounts to 0.33 MW/cm2. From temperature-dependent output power versus pump intensity curves, we deduced a T0 of 60 K and a maximal operating temperature of 135 K.
Electrokinetic flows over inhomogeneously slipping surfaces
Authors: Squires Todd M.
Published: September 2008

Recent measurements and theory suggest that some solid/liquid surfaces can exhibit slip, at times to a surprising degree. Proposed mechanisms for slip include both intrinsic molecular slip as well as “effective” slip over complex and multiphase interfaces (i.e., covered with “lubricating” nanobubbles or trapped gas pockets). Electrokinetic flow velocities can be significantly enhanced over slipping surfaces as the high shear rates within the double layer drive high slip velocities at the interface. It is not clear, however, that surfaces whose effective slip results from a macroscale average of microscopically inhomogeneous slip will exhibit the same effective slip in an electrokinetically driven system. As well, since the surface charge density is generally set by surface chemistry, one might reasonably expect the ζ potential over “slipping” regions to be different than that over nonslip surfaces. Here, we consider electrokinetic flows over inhomogeneously slipping and inhomogeneously charged surfaces that exhibit a macroscopic effective slip. Using the Lorentz reciprocal theorem for the Stokes flow, we derive general relations for the electrokinetic slip velocity and flow rates over effectively slipping surfaces in the thin double-layer limit. We place particular emphasis on surfaces that consist of discrete slip and no-slip regions, which are meant to model either geometrically rough superhydrophobic surfaces or surfaces with nanobubbles. We derive several surprising results: (i) electro-osmotic flows with uniformly charged (i.e., constant ζ) liquids over an arbitrarily slipping surface are enhanced by precisely the same amount as would be found by naively assuming the (macroscopic) effective slip length to apply homogeneously; (ii) surfaces whose “slip” regions are uncharged (as one might expect should be the case) show no enhancement due to slip, instead giving precisely the same electro-osmotic flow as though the surface were nonslip and homogeneously charged. Our results have clear implications for the practical implementation of electrokinetic effects over effective slip surfaces and give an additional “handle” to probe the properties of surfaces that exhibit effective slip. We briefly discuss the effects of inhomogeneous slip upon electrokinetic pumps, surface conduction, and streaming currents.
Nature of heterointerfaces in GaAs/InAs and InAs/GaAs axial nanowire heterostructures
Authors: Paladugu Mohanchand , Zou Jin , Guo Ya-Nan , Zhang Xin , Kim Yong , Joyce Hannah J. , Gao Qiang , Tan H. Hoe , Jagadish C.
Published: September 2008

The structural and compositional characteristics of heterointerfaces of Au-catalyzed GaAs/InAs and InAs/GaAs axial nanowire heterostructures were comprehensively investigated by transmission electron microscopy. It has been found that the GaAs/InAs interface is not sharp and contains an InGaAs transition segment, and in contrast, the InAs/GaAs interface is atomically sharp. This difference in the nature of heterointerfaces can be attributed to the difference in the affinity of the group III elements with the catalyst material.
Kinetic Monte Carlo study of metal organic chemical vapor deposition growth mechanism of GaSb quantum dots
Authors: Fu K. , Fu Y.
Published: September 2008

The growth dynamics of self-assembled GaSb quantum dots (QDs) on GaAs substrate in the strain-induced Stranski–Krastanov mode was investigated using kinetic Monte Carlo method. The strain induced by the lattice mismatch between the epitaxial material and the substrate was shown to be directly responsible for the QD formation and the transition of growth mode from two dimensional to three dimensional.
Molecular imaging of proteins in tissues by mass spectrometry
Authors: Seeley Erin H. , Caprioli Richard M.
Published: September 2008

Imaging MS (IMS) is an emerging technology that permits the direct analysis and determination of the distribution of molecules in tissue sections. Biological molecules such as proteins, peptides, lipids, xenobiotics, and metabolites can be analyzed in a high-throughput manner with molecular specificity not readily achievable through other means. Tissues are analyzed intact and thus spatial localization of molecules within a tissue is preserved. Several studies are presented that focus on the unique types of information obtainable by IMS, such as Aβ isoform distributions in Alzheimer's plaques, protein maps in mouse brain, and spatial protein distributions in human breast carcinoma. The analysis of a biopsy taken 100 years ago from a patient with amyloidosis illustrates the use of IMS with formalin-fixed tissues. Finally, the registration and correlation of IMS with MRI is presented.
The hearing gene
Prestin
reunites echolocating bats
Authors: Li Gang , Wang Jinhong , Rossiter Stephen J. , Jones Gareth , Cotton James A. , Zhang Shuyi
Published: September 2008

The remarkable high-frequency sensitivity and selectivity of the mammalian auditory system has been attributed to the evolution of mechanical amplification, in which sound waves are amplified by outer hair cells in the cochlea. This process is driven by the recently discovered protein prestin, encoded by the gene
Prestin
. Echolocating bats use ultrasound for orientation and hunting and possess the highest frequency hearing of all mammals. To test for the involvement of
Prestin
in the evolution of bat echolocation, we sequenced the coding region in echolocating and nonecholocating species. The resulting putative gene tree showed strong support for a monophyletic assemblage of echolocating species, conflicting with the species phylogeny in which echolocators are paraphyletic. We reject the possibilities that this conflict arises from either gene duplication and loss or relaxed selection in nonecholocating fruit bats. Instead, we hypothesize that the putative gene tree reflects convergence at stretches of functional importance. Convergence is supported by the recovery of the species tree from alignments of hydrophobic transmembrane domains, and the putative gene tree from the intra- and extracellular domains. We also found evidence that
Prestin
has undergone Darwinian selection associated with the evolution of specialized constant-frequency echolocation, which is characterized by sharp auditory tuning. Our study of a hearing gene in bats strongly implicates
Prestin
in the evolution of echolocation, and suggests independent evolution of high-frequency hearing in bats. These results highlight the potential problems of extracting phylogenetic signals from functional genes that may be prone to convergence.
Resistance to RevM10 inhibition reflects a conformational switch in the HIV-1 Rev response element
Authors: Legiewicz Michal , Badorrek Christopher S. , Turner Kevin B. , Fabris Daniele , Hamm Tiffany E. , Rekosh David , Hammarskjöld Marie-Louise , Le Grice Stuart F. J.
Published: September 2008

Nuclear export of certain HIV-1 mRNAs requires an interaction between the viral Rev protein and the Rev response element (RRE), a structured element located in the Env region of its RNA genome. This interaction is an attractive target for both drug design and gene therapy, exemplified by RevM10, a transdominant negative protein that, when introduced into host cells, disrupts viral mRNA export. However, two silent G->A mutations in the RRE (RRE61) confer RevM10 resistance, which prompted us to examine RRE structure using a novel chemical probing strategy. Variations in region III/IV/V of mutant RNAs suggest a stepwise rearrangement to RevM10 resistance. Mass spectrometry was used to directly assess Rev “loading” onto RRE and its variants, indicating that this is unaffected by RNA structural changes. Similarity in chemical footprints with mutant protein implicates additional host factors in RevM10 resistance.
Cell type-specific DNA methylation patterns in the human breast
Authors: Bloushtain-Qimron Noga , Yao Jun , Snyder Eric L. , Shipitsin Michail , Campbell Lauren L. , Mani Sendurai A. , Hu Min , Chen Haiyan , Ustyansky Vadim , Antosiewicz Jessica E. , Argani Pedram , Halushka Marc K. , Thomson James A. , Pharoah Paul , Porgador Angel , Sukumar Saraswati , Parsons Ramon , Richardson Andrea L. , Stampfer Martha R. , Gelman Rebecca S. , Nikolskaya Tatiana , Nikolsky Yuri , Polyak Kornelia
Published: September 2008

Cellular identity and differentiation are determined by epigenetic programs. The characteristics of these programs in normal human mammary epithelium and their similarity to those in stem cells are unknown. To begin investigating these issues, we analyzed the DNA methylation and gene expression profiles of distinct subpopulations of mammary epithelial cells by using MSDK (methylation-specific digital karyotyping) and SAGE (serial analysis of gene expression). We identified discrete cell-type and differentiation state-specific DNA methylation and gene expression patterns that were maintained in a subset of breast carcinomas and correlated with clinically relevant tumor subtypes. CD44+ cells were the most hypomethylated and highly expressed several transcription factors with known stem cell function including HOXA10 and TCF3. Many of these genes were also hypomethylated in BMP4-treated compared with undifferentiated human embryonic stem (ES) cells that we analyzed by MSDK for comparison. Further highlighting the similarity of epigenetic programs of embryonic and mammary epithelial cells, genes highly expressed in CD44+ relative to more differentiated CD24+ cells were significantly enriched for Suz12 targets in ES cells. The expression of FOXC1, one of the transcription factors hypomethylated and highly expressed in CD44+ cells, induced a progenitor-like phenotype in differentiated mammary epithelial cells. These data suggest that epigenetically controlled transcription factors play a key role in regulating mammary epithelial cell phenotypes and imply similarities among epigenetic programs that define progenitor cell characteristics.
Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles ofEGFRandKRAS
Authors: Guha Udayan , Chaerkady Raghothama , Marimuthu Arivusudar , Patterson A. Scott , Kashyap Manoj K. , Harsha H. C. , Sato Mitsuo , Bader Joel S. , Lash Alex E. , Minna John D. , Pandey Akhilesh , Varmus Harold E.
Published: September 2008

We have used unbiased phosphoproteomic approaches, based on quantitative mass spectrometry using stable isotope labeling with amino acids in cell culture (SILAC), to identify tyrosine phosphorylated proteins in isogenic human bronchial epithelial cells (HBECs) and human lung adenocarcinoma cell lines, expressing either of the two mutant alleles ofEGFR(L858RandDel E746-A750), or a mutantKRASallele, which are common in human lung adenocarcinomas. Tyrosine phosphorylation of signaling molecules was greater in HBECs expressing the mutant EGFRs than in cells expressing WT EGFR or mutant KRAS. Receptor tyrosine kinases (such as EGFR, ERBB2, MET, and IGF1R), and Mig-6, an inhibitor of EGFR signaling, were more phosphorylated in HBECs expressing mutant EGFR than in cells expressing WT EGFR or mutant RAS. Phosphorylation of some proteins differed in the two EGFR mutant-expressing cells; for example, some cell junction proteins (β-catenin, plakoglobin, and E-cadherin) were more phosphorylated in HBECs expressing L858R EGFR than in cells expressing Del EGFR. There were also differences in degree of phosphorylation at individual tyrosine sites within a protein; for example, a previously uncharacterized phosphorylation site in the nucleotide-binding loop of the kinase domains of EGFR (Y727), ERBB2 (Y735), or ERBB4 (Y733), is phosphorylated significantly more in HBECs expressing the deletion mutant than in cells expressing the wild type or L858R EGFR. Signaling molecules not previously implicated in ERBB signaling, such as polymerase transcript release factor (PTRF), were also phosphorylated in cells expressing mutant EGFR. Bayesian network analysis of these and other datasets revealed that PTRF might be a potentially important component of the ERBB signaling network.
The guanylate kinase domain of the β-subunit of voltage-gated calcium channels suffices to modulate gating
Authors: Gonzalez-Gutierrez Giovanni , Miranda-Laferte Erick , Nothmann Doreen , Schmidt Silke , Neely Alan , Hidalgo Patricia
Published: September 2008

Inactivation of voltage-gated calcium channels is crucial for the spatiotemporal coordination of calcium signals and prevention of toxic calcium buildup. Only one member of the highly conserved family of calcium channel β-subunits—Ca
V
β—inhibits inactivation. This unique property has been attributed to short variable regions of the protein; however, here we report that this inhibition actually is conferred by a conserved guanylate kinase (GK) domain and, moreover, that this domain alone recapitulates Ca
V
β-mediated modulation of channel activation. We expressed and refolded the GK domain of Ca
V
β
2a
, the unique variant that inhibits inactivation, and of Ca
V
β
1b
, an isoform that facilitates it. The refolded domains of both Ca
V
β variants were found to inhibit inactivation of Ca
V
2.3 channels expressed in
Xenopus laevis
oocytes. These findings suggest that the GK domain endows calcium channels with a brake restraining voltage-dependent inactivation, and thus facilitation of inactivation by full-length Ca
V
β requires additional structural determinants to antagonize the GK effect. We found that Ca
V
β can switch the inactivation phenotype conferred to Ca
V
2.3 from slow to fast after posttranslational modifications during channel biogenesis. Our findings provide a framework within which to understand the modulation of inactivation and a new functional map of Ca
V
β in which the GK domain regulates channel gating and the other conserved domain (Src homology 3) may couple calcium channels to other signaling pathways.
Quantum chemical
13
C
α
chemical shift calculations for protein NMR structure determination, refinement, and validation
Authors: Vila Jorge A. , Aramini James M. , Rossi Paolo , Kuzin Alexandre , Su Min , Seetharaman Jayaraman , Xiao Rong , Tong Liang , Montelione Gaetano T. , Scheraga Harold A.
Published: September 2008

A recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code
2JVD
), is validated here by comparing the observed
13
C
α
chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed
13
C
α
chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed
13
C
α
chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed
13
C
α
chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-Å resolution (PDB ID code
3BHP
) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed
13
C
α
chemical shifts in solution than the 3BHP crystal structure. In addition, the
13
C
α
-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures.
Superconductivity in the PbO-type structure α-FeSe
Authors: Hsu Fong-Chi , Luo Jiu-Yong , Yeh Kuo-Wei , Chen Ta-Kun , Huang Tzu-Wen , Wu Phillip M. , Lee Yong-Chi , Huang Yi-Lin , Chu Yan-Yi , Yan Der-Chung , Wu Maw-Kuen
Published: September 2008

The recent discovery of superconductivity with relatively high transition temperature (Tc) in the layered iron-based quaternary oxypnictides La[O

1−
x

F

x

] FeAs by Kamihara
et al.
[Kamihara Y, Watanabe T, Hirano M, Hosono H (2008) Iron-based layered superconductor La[O1-xFx] FeAs (x = 0.05–0.12) with Tc = 26 K.
J Am Chem Soc
130:3296–3297.] was a real surprise and has generated tremendous interest. Although superconductivity exists in alloy that contains the element Fe, LaOMPn (with M = Fe, Ni; and Pn = P and As) is the first system where Fe plays the key role to the occurrence of superconductivity. LaOMPn has a layered crystal structure with an Fe-based plane. It is quite natural to search whether there exists other Fe based planar compounds that exhibit superconductivity. Here, we report the observation of superconductivity with zero-resistance transition temperature at 8 K in the PbO-type α-FeSe compound. A key observation is that the clean superconducting phase exists only in those samples prepared with intentional Se deficiency. FeSe, compared with LaOFeAs, is less toxic and much easier to handle. What is truly striking is that this compound has the same, perhaps simpler, planar crystal sublattice as the layered oxypnictides. Therefore, this result provides an opportunity to better understand the underlying mechanism of superconductivity in this class of unconventional superconductors.
Hemiplasy and homoplasy in the karyotypic phylogenies of mammals
Authors: Robinson Terence J. , Ruiz-Herrera Aurora , Avise John C.
Published: September 2008

Phylogenetic reconstructions are often plagued by difficulties in distinguishing phylogenetic signal (due to shared ancestry) from phylogenetic noise or homoplasy (due to character-state convergences or reversals). We use a new interpretive hypothesis, termed hemiplasy, to show how random lineage sorting might account for specific instances of seeming “phylogenetic discordance” among different chromosomal traits, or between karyotypic features and probable species phylogenies. We posit that hemiplasy is generally less likely for underdominant chromosomal polymorphisms (i.e., those with heterozygous disadvantage) than for neutral polymorphisms or especially for overdominant rearrangements (which should tend to be longer-lived), and we illustrate this concept by using examples from chiropterans and afrotherians. Chromosomal states are especially powerful in phylogenetic reconstructions because they offer strong signatures of common ancestry, but their evolutionary interpretations remain fully subject to the principles of cladistics and the potential complications of hemiplasy.
The Naqīb of Ray Alids and His Support of Scientists
Authors: Manzoor al-Adjdad Sayyed Mohammad Hossein
Published: September 2008

The contributions of Shī‘a scholars and noblemen to the advancement of knowledge is well documented. These contributions culminated in the institution of dār al-‘ilm during the Buyids (334–447/945–1055). While the advent of the Saljūqs signaled the disappearance of the dār al-‘ilm, the Shī‘a minority continued to serve in the production of both religious and secular knowledge, despite the increasingly strict social policies under the Saljūqs. This article examines the remarkable role of Abu al-assan Muahhar, the naqīb of Ray Alids, who provided protection as well as immense support for scholars of his time. It further elucidates the sectarian tensions that affected the institutionalization of the sciences, hence a greater need for the opportune support afforded by the naqīb Muahhar.
Sharaf al-Dīn ‘Alī Yazdī: Historian and Mathematician
Authors: Monfared Mahdi Farhani
Published: September 2008

The present article aims to shed light on the professional activities of the historian and mathematician Sharaf al-Dīn ‘Alī Yazdī and his afar-nāmah. In so doing, two questions are addressed: (1) Did Yazdī’s expertise in mathematics influence his historical narrative? (2) Did Yazdī simply expand on Niām al-Dīn Shāmī's afar-nāmah, composed some twenty years earlier? Comparing the frequency of quantitative and qualitative data in Yazdī's and Shāmī's afar-nāmahs, the article finds that although Yazdī made an effort to incorporate quantitative data in his history, his narrative is not particularly informed by his expertise in arithmetic. This seems, at first glance, a byproduct of a predominant tradition in the Islamic-Iranian historiography, which makes extensive use of literary techniques. The comparison between the two afar-nāmahs, however, suggests that both Yazdī and Shāmī subscribed to a notion of “accuracy” which bore little resemblance to its modern counterpart manifested in quantitative precision. Finally, the article concludes that the allegation of plagiarism against Yazdī is unfounded.
A single-shot measurement of the energy of product states in a translation invariant spin chain can replace any quantum computation
Authors: Janzing Dominik , Wocjan Pawel , Zhang Shengyu
Published: September 2008

In measurement-based quantum computation, quantum algorithms are implemented viasequencesof measurements. We describe a translationally invariant finite-range interaction on a one-dimensional qudit chain and prove that asingle-shotmeasurement of theenergyof an appropriate computational basis state with respect to this Hamiltonian provides the output of any quantum circuit. The required measurement accuracy scales inverse polynomially with the size of the simulated quantum circuit. This shows that the implementation of energy measurements on generic qudit chains is as hard as the realization of quantum computation. Here, a ‘measurement’ is any procedure that samples from the spectral measurement induced by the observable and the state under consideration. As opposed to measurement-based quantum computation, the post-measurement state is irrelevant.
An Immunofluorescence Assay to Detect Urediniospores of Phakopsora pachyrhizi
Authors: Baysal-Gurel Fulya , Ivey Melanie L. Lewis , Dorrance Anne , Luster Douglas , Frederick Reid , Czarnecki Jill , Boehm Michael , Miller Sally A.
Published: September 2008

An indirect immunofluorescence spore assay (IFSA) was developed to detect urediniospores of Phakopsora pachyrhizi, utilizing rabbit polyclonal antisera produced in response to intact nongerminated (SBR1A) or germinated (SBR2) urediniospores of P. pachyrhizi. Both antisera were specific to Phakopsora spp. and did not react with other common soybean pathogens or healthy soybean leaf tissue in enzyme-linked immunosorbent assay (ELISA). SBR1A and SBR2 bound to P. pachyrhizi and P. meibomiae urediniospores were detected with goat anti-rabbit Alexa Fluor 488-tagged antiserum using a Leica DM IRB epifluorescent microscope with an I3 blue filter (excitation 450 to 490 nm, emission 515 nm). The assay was performed on standard glass microscope slides; double-sided tape was superior to a thin coating of petroleum jelly both in retaining spores and in immunofluorescence. The IFSA was used to confirm the identity of P. pachyrhizi urediniospores captured on glass slides from passive air samplers from Georgia, Kentucky, and Ohio during 2006.
Baseline Sensitivity of Botrytis cinerea to Pyraclostrobin and Boscalid and Control of Anilinopyrimidine- and Benzimidazole-Resistant Strains by These Fungicides
Authors: Myresiotis C. K. , Bardas G. A. , Karaoglanidis G. S.
Published: September 2008

Fifty-five isolates of Botrytis cinerea collected from vegetable crops were used to determine the pathogen's baseline sensitivity to two new fungicides: boscalid, which inhibits the enzyme succinate dehydrogenase in the electron transport chain, and pyraclostrobin, which blocks electron transport between cytochrome b and cytochrome c1. Measurement of sensitivity to boscalid was based on both inhibition of mycelial growth and spore germination, while measurement of sensitivity to pyraclostrobin was based only on inhibition of spore germination. For both fungicides, the sensitivity distribution was a unimodal curve, with a mean EC50 value (effective concentration that reduces mycelial growth or spore germination by 50%) of 0.033 μg ml-1 for pyraclostrobin and 2.09 and 2.14 μg ml-1 for boscalid based on the inhibition of mycelial growth and spore germination, respectively. No cross-sensitivity relationship was observed between the two fungicides (r = 0.09). In addition, no cross-resistance relationship was observed between these two fungicides with other botryticides: cyprodinil, pyrimethanil, fenhexamid, fludioxonil, and iprodione. Moreover, the control efficacy of the two fungicides was tested against two anilinopyrimidine-resistant and two benzimidazole-resistant isolates, and two of wild-type sensitivity. Both pyraclostrobin and boscalid provided satisfactory control of all six isolates that was independent of the isolate sensitivity to benzimidazoles and anilinopyrimidines. In contrast, carbendazim failed to control sufficiently the benzimidazole-resistant isolates, while cyprodinil failed to provide satisfactory control of the anilinopyrimidine-resistant isolates.
First Report of Citrus leaf blotch virus in New Zealand
Authors: Harper S. J. , Chooi K. M. , Pearson M. N.
Published: September 2008

Despite a high incidence of Citrus tristeza virus (CTV) in citrus in New Zealand, viral diseases have had only a minor impact on the New Zealand citrus industry, largely because of the use of Poncirus trifoliata and hybrid rootstocks derived from this. In August of 2007, a PCR-based survey for seven citrus viruses was conducted on 104 commercial orchard trees that represented a range of Citrus scion species, as well as P. trifoliata and P. trifoliata × Citrus sinensis rootstock, grown from imported and local budwood or from seed in the case of rootstocks, from the citrus-growing regions of Kerikeri, Tauranga, and Gisborne. Total RNA was extracted from young, green bark and leaf tissue from each source. Using a primer pair amplifying a 425-bp region of the Citrus leaf blotch virus (CLBV) coat protein gene (sense: 5′-AGCCATAGTTGAACCATTCCTC-3′ and antisense: 5′-GCAGATCATTCACCACATGC-3′), 26 (25%) of the plant samples yielded a DNA fragment of the size expected for CLBV, including 6 of 21 C. sinensis, 1 of 2 C. limon, 3 of 10 C. unshiu, and 5 of 7 C. paradisi scion samples and 5 of 9 P. trifoliata and 6 of 9 P. trifoliata × C. sinensis rootstock samples. Identification of CLBV (an unclassified member of the family Flexiviridae) was confirmed by amplification of a second region of the genome of 1,045 bp spanning the ORF2/ORF3 domains (sense: 5′-ATGAAAAGCCAGTTATGCACCA-3′ and antisense: 5′-CTCAGCATTCCCAGGAATAACC-3′). A subset of the PCR products for the CP and ORF2/ORF3 fragments were sequenced for analysis (GenBank Accession nos. EU670243–EU670251 and EU862284–EU862288). Sequences from all CLBV isolates showed 97 to 99% nucleotide identity with the CLBV reference isolate SRA-153 (GenBank Accession No. AF318061) (1) in the coat protein fragment and 98 to 99% nucleotide identity for the partial ORF2/ORF3 fragment. The bud-union crease symptom reported to be caused by CLBV was observed only on one C. paradisi scion on P. trifoliata rootstock, while the remaining samples were either asymptomatic or symptoms were attributed to co-infection with CTV. Since CLBV-infected plants were found from all major growing regions, it is apparent that CLBV is widespread in New Zealand, although it is not known where in this country it may have originated.

Reference: (1) M. C. Vives et al. Virology 287:225, 2000.
First Report of Alternanthera mosaic virus Infection in Angelonia in the United States
Authors: Lockhart B. E. , Daughtrey M. L.
Published: September 2008

Stunting, chlorosis, and light yellow mottling resembling symptoms of nutrient deficiency were observed in angelonia (Angelonia angustifolia) in commercial production in New York. Numerous, filamentous particles 520 to 540 nm long and spherical virus particles 30 nm in diameter were observed by transmission electron microscopy (TEM) in negatively stained partially purified extracts of symptomatic Angelonia leaf tissue. Two viruses, the filamentous potexvirus Alternanthera mosaic virus (AltMV) and the spherical carmovirus Angelonia flower break virus (AnFBV) were subsequently identified on the basis of nucleotide sequence analysis of amplicons generated by reverse transcription (RT)-PCR using total RNA isolated from infected leaf tissue. A 584-bp portion of the replicase-encoding region of the AltMV genome was obtained with the degenerate primers Potex 2RC (5′-AGC ATR GNN SCR TCY TG-3′) and Potex 5 (5′-CAY CAR CAR GCM AAR GAT GA-3′) (3). Forward (AnFBV CP 1F-5′-AGC CTG GCA ATC TGC GTA CTG ATA-3′) and reverse (AnFBV CP 1R-5′-AAT ACC GCC CTC CTG TTT GGA AGT-3′) primers based on the published AnFBV genomic sequence (GenBank Accession No. NC_007733) were used to amplify a portion of the viral coat protein (CP) gene. The nucleotide sequence of the amplicon generated using the potexvirus-specific primers (GenBank Accession No. EU679362) was 99% identical to the published AltMV (GenBank Accession No. NC_007731) sequence and the nucleotide sequence of the amplicon obtained using the AnFBV CP primers was 99% identical to the published AnFBV genomic sequence (GenBank Accession No. EU679363). AnFBV occurs widely in angelonia (1) and AltMV has been identified in phlox (2). These data confirm the presence of AltMV and AnFBV in diseased angelonia plants showing stunting and nutrient deficiency-like symptoms and substantiates, to our knowledge, this first report of AltMV in angelonia in the United States.

References: (1) S. Adkins et al. Phytopathology 96:460, 2006. (2) J. Hammond et al. Arch. Virol. 151:477, 2006. (3) R. A. A. van der Vlugt and M. Berendeson. Eur. J. Plant Pathol. 108:367, 2002.