bluuebunny/crossref_metadata_2025 huggingface dataset:
Vibrational sum-frequency spectroscopy of the liquid/vapor interface for dilute HOD in D2O
Authors: Auer B. M. , Skinner J. L.
Published: December 2008

An electronic structure/molecular dynamics approach, originally developed to describe the vibrational spectroscopy of the OH stretch of dilute HOD in liquid D2O, is applied to the vibrational sum-frequency spectroscopy of the liquid/vapor interface of this system. In both cases the OH stretch is effectively decoupled from the OD stretches, allowing it to act as a local probe of structure and dynamics. A mixed quantum/classical expression for the vibrational sum-frequency response that includes the effect of motional narrowing is used to calculate the resonant susceptibility. Despite being developed for the bulk liquid, our method works well for the surface in that the real and imaginary parts of the resonant susceptibility are in good agreement with experiment. We explore the nature of hydrogen bonding at the interface as well as its impact on the sum-frequency spectrum. It is found that the spectrum is dominated by single-donor molecules with a total of two or three hydrogen bonds.
Reaction coordinates for electron transfer reactions
Authors: Rasaiah Jayendran C. , Zhu Jianjun
Published: December 2008

The polarization fluctuation and energy gap formulations of the reaction coordinate for outer sphere electron transfer are linearly related to the constant energy constraint Lagrangian multiplier m in Marcus’ theory of electron transfer. The quadratic dependence of the free energies of the reactant and product intermediates on m and m+1, respectively, leads to similar dependence of the free energies on the reaction coordinates and to the same dependence of the activation energy on the reorganization energy and the standard reaction free energy. Within the approximations of a continuum model of the solvent and linear response of the longitudinal polarization to the electric field in Marcus’ theory, both formulations of the reaction coordinate are expected to lead to the same results.
Efficient vibrational and translational excitations of a solid metal surface: State-to-state time-of-flight measurements of HCl(v=2,J=1) scattering from Au(111)
Authors: Rahinov Igor , Cooper Russell , Yuan Cheng , Yang Xueming , Auerbach Daniel J. , Wodtke Alec M.
Published: December 2008

We report high resolution state-to-state time-of-flight (TOF) measurements for scattering of HCl(v=2, J=1) from a Au(111) single crystal surface for both vibrationally elastic (v=2→2) as well as inelastic (v=2→1) channels at seven incidence energies between 0.28 and 1.27 eV. The dependences of the TOF results on final HCl rotational state and surface temperature are also reported. The translational energy transferred to the surface depends linearly on incidence energy and is close to the single surface-atom impulse (Baule) limit over the entire range of incidence energies studied. The probability of vibrational relaxation is also large. For molecules that relax from v=2 to v=1, the fraction of vibrational energy that is transferred to the surface is approximately 74%. We discuss these observations in terms of an impulse approximation as well as the possible role of translational and vibrational excitations of electron-hole pairs in the solid.
Packing of poly(tetrafluoroethylene) in the liquid state: Molecular dynamics simulation and theory
Authors: Tsige Mesfin , Curro John G. , Grest Gary S.
Published: December 2008

Molecular dynamics simulations and polymer reference interaction site model theory calculations were carried out on the C48F98 oligomer of poly(tetrafluoroethylene) (PTFE) at 500 and 600 K. The exp-6 force field of Borodin, Smith, and Bedrov, was used in both the simulation and theory. The agreement between theory and simulation was equivalent to earlier studies on polyolefin melts. The intermolecular pair correlation functions of PTFE were shifted to larger distances relative to polyethylene (PE) due to the difference in the van der Waals radii of F and H atoms. A similar shift to lower wave vectors was found in the structure factor of PTFE relative to PE.
Imaging piezospectroscopy
Authors: Abbiss John B. , Heeg Bauke
Published: December 2008

A novel instrument is described for obtaining accurate high-resolution residual stress images of aluminum oxide materials, based on the piezospectroscopy of Cr3+ dopant ions. The instrument employs a charge coupled device camera, a narrow bandpass tunable filter and the use of Tikhonov regularization for reconstruction of the raw spectral data. The experimental accuracy and spectral shift resolution of this method were analyzed with two calibration light sources and with independently measured spectra, and were found to be approximately ±0.01 nm across the pixel array. This is close to the theoretically obtainable accuracy for the particular filter used, a solid etalon Fabry–Pérot filter with a passband of 0.25 nm, based on an analysis with simulated data. The spectral resolution corresponds to a stress resolution, under biaxial stress conditions, of ±40 MPa.
Impedance spectroscopy and optical characterization of polymethyl methacrylate/indium tin oxide nanocomposites with three-dimensional Voronoi microstructures
Authors: Capozzi Charles J. , Li Zhi , Samuels Robert J. , Gerhardt Rosario A.
Published: December 2008

This study describes the optical and ac electrical characterization of polymethyl methacrylate (PMMA)/indium tin oxide (ITO) nanocomposites containing a Voronoi-type segregated network microstructure. Optical transmission microscopy, scanning electron microscopy (SEM), and impedance spectroscopy were used to investigate the microstructure and electrical properties of the composites. The complex refractive index values of the composites were measured by using a modified version of the internal reflection intensity analysis (IRIA) method. SEM images of the composites reveal that the microstructure consists of polyhedral-shaped PMMA particles, where the ITO nanoparticles become concentrated along the edges of the PMMA to form a percolated network. Electrical measurements as a function of filler content indicate that the percolation threshold is <0.50 vol % ITO. The in-plane and through-plane refractive indices obtained by the modified IRIA method suggest that the microstructure is isotropic. The estimated extinction coefficients increase with higher ITO content, which is expected for a percolating system. A microstructural model, which takes into account the accumulation of the ITO nanoparticles at the edges of the polyhedron-shaped PMMA particles, is proposed that can predict the percolation threshold in composites that have Voronoi-type segregated network microstructures.
Experimental determination of the third derivative of G. I. Enthalpic interaction
Authors: Westh Peter , Inaba Akira , Koga Yoshikata
Published: December 2008

The solute (i)—solute interaction in terms of enthalpy, Hi−iE=N(∂2HE/∂ni2)=(1−xi)(∂2HE/∂ni∂xi), the third derivative of G, was experimentally determined using a Thermal Activity Monitor isothermal titration calorimeter for aqueous solutions of 2-butoxyethanol (BE) and 1-propanol (1P). This was done using both calorimetric reference and sample vessels actively. We simultaneously titrate small and exactly equal amounts of solute i (=BE or 1P) into both cells which contain the binary mixtures at an average mole fraction, xi, which differs by a small amount Δxi. The appropriate amount of titrant δni was chosen so that the quotient (δHE/δni) can be approximated as (∂HE/∂ni), and so that the scatter of the results is reasonable. δHE is the thermal response from an individual cell on titration, and we measure directly the difference in the thermal response between the two cells, Δ(δHE). The resulting quotient, Δ(δHE)/δni/Δxi, can be approximated as (∂2HE/∂ni∂xi) and hence provides a direct experimental avenue for the enthalpy interaction function. We varied the value of Δxi to seek its appropriate size. Since HE contains the first derivative of G with respect to T, the result is the third derivative quantity. Thus we present here a third derivative quantity directly determined experimentally for the first time.
Indentation-induced tin whiskers on electroplated tin coatings
Authors: Yang Fuqian , Li Yan
Published: December 2008

The indentation-induced growth of tin whiskers/hillocks was observed for the tin coatings over copper substrate. There existed multiple tin whiskers/hillocks surrounding the indents in contrast to only a few whiskers/hillocks in the nonindented area. The number of the tin whiskers surrounding the indents increased with the increase in the indentation load and decreased with the increase in the thickness of the tin coatings. The formation and growth of the tin whiskers were due to the pressure gradient at the contact edge, which is qualitatively in accord with the analysis for the indentation of thin coatings with a power-law flow behavior.
A focused view of the behavior of granular flows down a confined inclined chute into the horizontal run-out zone
Authors: Tai Yih-Chin , Lin Yang-Chen
Published: December 2008

In this paper a detailed approach is proposed for the behavior of two-dimensional cohesionless granular materials moving down a confined inclined plane chute into the horizontal run-out zone, where the upslope propagating bore is treated as a growing deposition heap. It deals with the theoretical-numerical and experimental treatments. The depth-averaged field equations of balance of mass and linear momentum are described in moving coordinates for general topography as prescribed by Tai and Kuo [Acta Mech. 199, 71 (2008)]. A most simplistic approach to the erosion/deposition parameterization is proposed and the spatial coordinate coincides with the arc length of the variable basal surface. These equations describe the temporal evolution of the depth and velocity of the granular mass, especially the locations and shapes of the growing deposition heaps beneath the flowing layer. Experiments were carried out with different material supply rates and in two types of chutes, which differed by the bottom surface of the chute. In these experiments the sequential motions of the granular mass were recorded by a high-speed digital camera. The outlines of the deposition heap and flowing layers were obtained by successive images differences. Comparison of the experimental findings with the computational results proved to lead to good correspondence between experiment and theory. Even the development of the detailed geometry of the deposition heap is satisfactorily reproduced.
The roles of thermally evaporated cesium carbonate to enhance the electron injection in organic light emitting devices
Authors: Chen Mei-Hsin , Wu Chih-I
Published: December 2008

The properties of thermally evaporated cesium carbonate (Cs2CO3) and its role as electron injection layers in organic light emitting diodes were investigated. According to the ultraviolet photoemission spectra (UPS), the Fermi level of tris-(8-hydroxyquinoline)-aluminum (Alq3) after being doped with Cs2CO3 shifts toward or into the lowest unoccupied molecular orbital as a result of chemical reaction and charge transfer between Cs2CO3 and Alq3, which lowers the electron injection barrier and improves the current efficiency. As for whether Cs2CO3 being decomposed during the evaporation, we found that Cs2CO3 molecules were deposited on the substrates without decomposition, regardless of the evaporation rates, based on the signature features of carbonate groups and ionization energies measured in UPS spectra and the binding energy shifts of core level electrons. The reaction mechanisms between Cs2CO3 and Alq3 are also proposed. Since Cs2CO3 is not only used in the electron injection layer but also in converting high work function materials to cathodes, we further quantitatively investigated the work function modification of indium tin oxide (ITO) with deposition of Cs2CO3 at the surfaces. We found that while 0.5 Å thick Cs2CO3 is sufficient to reduce the electron injection barrier of Alq3, the thickness needed to convert ITO surface to low work function cathode is about 10 Å.
Observation of persistent photoconductivity in bulk gallium arsenide and gallium phosphide samples at cryogenic temperatures using the whispering gallery mode method
Authors: Hartnett John G. , Mouneyrac David , Le Floch Jean-Michel , Krupka Jerzy , Tobar Michael E. , Cros D.
Published: December 2008

Whispering gallery modes in bulk cylindrical gallium arsenide and gallium phosphide samples have been examined both in darkness and under white light at cryogenics temperatures ≤50 K. In both cases persistent photoconductivity was observed after initially exposing semiconductors to white light from a halogen lamp. Photoconductance decay time constants for GaP and GaAs were determined to be 0.900±0.081 and 1.098±0.063 ns, respectively, using this method.
Magnetocaloric effect and Griffiths-like phase in La0.67Sr0.33MnO3 nanoparticles
Authors: Lu W. J. , Luo X. , Hao C. Y. , Song W. H. , Sun Y. P.
Published: December 2008

The effect of grain size on electrical and magnetic properties of La0.67Sr0.33MnO3 nanoparticles with average grain size 32–85 nm has been investigated. The metal-insulator transition temperature TP gradually decreases with decreasing grain size, while the ferromagnetic-paramagnetic transition temperature TC remains almost constant. For the 32 nm sample, the larger effective magnetic moments and the deviation of the inverse susceptibility from the Curie–Weiss law are observed, indicating the possible existence of a Griffiths-like cluster phase. The ferromagnetic transition of the samples is further investigated by measuring magnetocaloric effect (MCE). The presence of short-range magnetic order greatly depresses the magnetic entropy of the paramagnetic phase. Moreover, the analysis of the MCE using Landau theory of phase transition confirms the importance of magnetoelastic coupling and electron interaction in magnetocaloric properties of manganites.
Continuous optoelectrowetting for picoliter droplet manipulation
Authors: Chiou P. Y. , Park Sung-Yong , Wu Ming C.
Published: December 2008

We report on a continuous optoelectrowetting mechanism enabling continuous high spatial resolution optical modulation of electrowetting effect on a featureless planar photoconductive amorphous silicon surface. Dynamically patterned “virtual electrode” switches voltage between the amorphous silicon layer and the dielectric layer for contact angle modulation. This device is particularly attractive for manipulating picoliter droplets. We have experimentally demonstrated trapping and moving of 10 and 50 pl droplets at a speed of 1 mm/s using a light beam.
An inverted organic solar cell employing a sol-gel derived ZnO electron selective layer and thermal evaporated MoO3 hole selective layer
Authors: Kyaw A. K. K. , Sun X. W. , Jiang C. Y. , Lo G. Q. , Zhao D. W. , Kwong D. L.
Published: December 2008

We reported an efficient inverted bulk-heterojunction [regioregular of poly(3-hexylthiophene): (6,6)-phenyl C61 butyric acid methyl ester] solar cell with a highly transparent sol-gel derived ZnO film as electron selective layer and MoO3 as hole selective layer. By modifying the precursor concentration of sol from 0.75 to 0.1M, the optical transmittance of ZnO film increases from 75% to 95%. This improvement in transmittance increases the short-circuit density of inverted solar cell from 5.986 to 8.858 mA/cm2 without sacrificing the open-circuit voltage and fill factor of the device. We also demonstrated that the device incorporated with MoO3 has a larger open-circuit voltage and fill factor than the device without MoO3. Power conversion efficiency of 3.09% was achieved under simulated AM 1.5G illumination of 100 mW/cm2.
Nanocrystalline multiferroic BiFeO3 ultrafine fibers by sol-gel based electrospinning
Authors: Xie S. H. , Li J. Y. , Proksch Roger , Liu Y. M. , Zhou Y. C. , Liu Y. Y. , Ou Y. , Lan L. N. , Qiao Y.
Published: December 2008

Novel nanocrystalline BiFeO3 ultrafine fibers have been synthesized by sol-gel based electrospinning, with fiber diameter in the range of 100–300 nm and grain size of around 20 nm. Phase pure perovskite BiFeO3 can be obtained if the fibers are fired in Ar atmosphere, eliminating impurity phases often observed when fired in air or N2 atmosphere. Excellent piezoelectricity and clear ferroelectric domain structure of the ultrafine fibers are characterized by high voltage piezoresponse force microscopy. Enhanced weak ferromagnetism arising from the nanocrystalline structure of ultrafine fibers is also observed.
Tuning the tunnel coupling of quantum dot molecules with longitudinal magnetic fields
Authors: Climente J. I.
Published: December 2008

We show that the energy splitting between the bonding and antibonding molecular states of holes in vertically stacked quantum dots can be tuned using longitudinal magnetic fields. With increasing field, the energy splitting first decreases to zero and then to negative values, which implies a bonding-to-antibonding ground state transition. This effect is a consequence of the enhancement of the valence band spin-orbit interaction induced by the magnetic field; it provides a flexible mechanism to switch the molecular ground state from bonding to antibonding.
Magnetism in Mn doped yttrium nitride: First-principles calculations
Authors: Jia Xingtao , Yang Wei , Qin Minghui
Published: December 2008

The magnetism and aggregation trends in 25% and 12.5% Mn doped yttrium nitride (YN) have been investigated using the first-principles calculations. We demonstrate that the ferromagnetic delta doping is the ground state in higher concentration Mn doped YN, and the ferromagnetic homogeneous half-delta doping is the ground state in lower concentration Mn half-delta-doped YN. The latter shows ferromagnetic stabilization energy of 424.8 meV/Mn–Mn pair, which is substantially higher than many other compound semiconductor based magnetic semiconductors. Finally, we anticipate the potential spintronics application of Mn doped YN.
Elimination of total internal reflection in GaInN light-emitting diodes by graded-refractive-index micropillars
Authors: Kim Jong Kyu , Noemaun Ahmed N. , Mont Frank W. , Meyaard David , Schubert E. Fred , Poxson David J. , Kim Hyunsoo , Sone Cheolsoo , Park Yongjo
Published: December 2008

A method for enhancing the light-extraction efficiency of GaInN light-emitting diodes (LEDs) by complete elimination of total internal reflection is reported. Analytical calculations show that GaInN LEDs with multilayer graded-refractive-index pillars, in which the thickness and refractive index of each layer are optimized, have no total internal reflection. This results in a remarkable improvement in light-extraction efficiency. GaInN LEDs with five-layer graded-refractive-index pillars, fabricated by cosputtering TiO2 and SiO2, show a light-output power enhanced by 73% and a strong side emission, consistent with analytical calculations and ray-tracing simulations.
Infra-familial phylogeny of Urticaceae, using chloroplast sequence data
Authors: Hadiah Julisasi T. , Conn Barry J. , Quinn Christopher J.
Published: December 2008

Recent studies of the phylogeny of the Urticales have suggested that Cecropiaceae, at least in part, should be included within Urticaceae. To evaluate phylogenetic relationship between these two taxa, together with the consequences on tribal concepts (of the Urticaceae) of including any part of Cecropiaceae within Urticaceae, we analysed sequence variation for larger databases of both rbcL and trnL-F sequences. We conclude that the circumscription of Urticaceae needs to be broadened to include taxa of Cecropiaceae, with Urticeae here expanded to include Poikilospermum. The tribal placement of Cecropia and Coussapoa (both Cecropiaceae) remains unclear but their affinities are with the Forsskaoleeae, Parietarieae and Boehmerieae. The circumscription of Boehmerieae should be changed to exclude Myriocarpa, with the latter genus exhibiting a strong relationship with Elatostemeae. The intratribal structure of the Elatostemeae is unclear because of the uncertainty of the position of Myriocarpa, but there is a strong suggestion that the tribe consists of two sister taxa, one of Elatostemeae sensu stricto, including Elatostema and Procris, and the other consisting of Lecanthus and Pilea. It is reconfirmed that Pellionia should not be recognised as a distinct genus and is here regarded as a synonym of Procris, rather than part of the synonymy of Elatostema, as previously suggested. Boehmeria, Cypholophus and Laportea as currently circumscribed are all paraphyletic. There are three evolutionary lineages in the Urticaceae revealed by our study, namely (1) Boehmeriea–Cecropieae–Forsskaoleeae–Parietarieae, (2) Urticeae and (3) Elatostemeae.
The nuclear corepressor, NCoR, regulates thyroid hormone action in vivo
Authors: Astapova Inna , Lee Larissa J. , Morales Crystal , Tauber Stefanie , Bilban Martin , Hollenberg Anthony N.
Published: December 2008

The thyroid hormone receptor (TR) has been proposed to regulate expression of target genes in the absence of triiodothyronine (T
3
) through the recruitment of the corepressors, NCoR and SMRT. Thus, NCoR and SMRT may play an essential role in thyroid hormone action, although this has never been tested in vivo. To accomplish this, we developed mice that express in the liver a mutant NCoR protein (L-NCoRΔID) that cannot interact with the TR. L-NCoRΔID mice appear grossly normal, however, when made hypothyroid the repression of many positively regulated T
3
-target genes is abrogated, demonstrating that NCoR plays a specific and sufficient role in repression by TR in the absence of T
3
. Remarkably, in the euthyroid state, expression of many T
3
-targets is also up-regulated in L-NCoRΔID mice, demonstrating that NCoR also determines the magnitude of the response to T
3
in euthyroid animals. Although positive T
3
targets were up-regulated in L-NCoRΔID mice in the hypo- and euthyroid state, there was little effect seen on negatively regulated T
3
target genes. Thus, NCoR is a specific regulator of T
3
-action in vivo and mediates repression by the unliganded TR in hypothyroidism. Furthermore, NCoR appears to play a key role in determining the tissue-specific responses to similar levels of circulating T
3
. Interestingly, NCoR recruitment to LXR is also impaired in this model, leading to activation of LXR-target genes, further demonstrating that NCoR recruitment regulates multiple nuclear receptor signaling pathways.
In vitro selection of a neutralization-resistant hepatitis C virus escape mutant
Authors: Gal-Tanamy Meital , Keck Zhen-Yong , Yi MinKyung , McKeating Jane A. , Patel Arvind H. , Foung Steven K. H. , Lemon Stanley M.
Published: December 2008

Effective immunization against hepatitis C virus (HCV) infections is likely to require the induction of both robust T and B cell immunity. Although neutralizing antibodies may play an important role in control of infection, there is little understanding of the structure of the HCV envelope glycoproteins and how they interact with such antibodies. An additional challenge for vaccine design is the genetic diversity of HCV and the rapid evolution of viral quasispecies that escape antibody-mediated neutralization. We used a cell culture-infectious, chimeric HCV with the structural proteins of genotype 1a virus to identify envelope residues contributing to the epitope recognized by a broadly neutralizing, murine monoclonal antibody, AP33. By repetitive rounds of neutralization followed by amplification, we selected a population of viral escape mutants that resist stringent neutralization with AP33 and no longer bind the antibody. Two amino acid substitutions, widely separated in the linear sequence of the E2 envelope protein (N415Y and E655G), were identified by sequencing of cloned cDNA and shown by reverse genetics analysis to contribute jointly to the AP33 resistance phenotype. The N415Y mutation substantially lowered virus fitness, most likely because of a defect in viral entry, but did not reduce binding of soluble CD81 to immobilized HCV-pseudotyped retrovirus particles. The in vitro selection of an HCV escape mutant recapitulates the ongoing evolution of antigenic variants that contributes to viral persistence in humans and reveals information concerning the conformational structure of the AP33 epitope, its role in viral replication, and constraints on its molecular evolution.
No evidence for presence of bacteria in modic type I changes
Authors: Wedderkopp N. , Thomsen K. , Manniche C. , Kolmos H. J. , Secher Jensen T. , Leboeuf Yde C.
Published: December 2008

Background: Recent studies suggest an association between sciatica and Propionibacterium acnes. “Modic type I changes” in the vertebrae are closely associated with sciatica and lower back pain, and recent studies have questioned the ability of conventional magnetic resonance imaging (MRI) to differentiate between degenerative Modic type I changes and vertebral abnormalities caused by infection.

Purpose: To test whether bacteria could be cultured from biopsies of Modic type I changes.

Material and Methods: Twenty-four consecutive patients with Modic type I changes in lumbar vertebrae had a biopsy taken from the affected vertebra by a strict aseptic procedure. The biopsy was split into two specimens, which were inoculated into thioglycolate agar tubes in the surgical theatre and transported to the microbiology laboratory. In the laboratory, one specimen was streaked onto plates and analyzed for anaerobic and aerobic culture. The other tube was left unopened and incubated directly. Plates and tubes were incubated for 2 weeks and observed for visible growth.

Results: None of the biopsies yielded growth of anaerobic bacteria. In one patient, both biopsies yielded growth of Staphylococcus epidermidis, and in another patient coagulase-negative staphylococci were isolated from one biopsy. Both patients received oral antibiotics without convincing effect on symptoms.

Conclusion: Our results showed no evidence of bacteria in vertebrae with Modic type I changes. The isolation of staphylococci from two patients probably represented contamination.
Amount drained at ultrasound-guided thoracentesis and risk of pneumothorax
Authors: Josephson T. , Nordenskjold C. A. , Larsson J. , Rosenberg L. U. , Kaijser M.
Published: December 2008

Background: It has been suggested that no upper limit of the fluid amount drained is necessary when performing ultrasound-guided thoracentesis, but the risk of pneumothorax when large amounts of fluid are drained has not been studied in detail.

Purpose: To study the amount of drained fluid at ultrasound-guided thoracentesis and the subsequent risk of pneumothorax.

Material and Methods: Prospectively collected information on all ultrasound-guided thoracenteses performed at a county hospital between 2004 and 2006 was evaluated. In total, 735 thoracenteses in 471 patients were included. Chest radiographs performed within 14 days after thoracentesis were identified to obtain cases of pneumothorax and cases treated with tube thoracostomy. Data were analyzed by logistic regression. The study was approved by the regional research ethics committee.

Results: There was a steep increase in risk for pneumothorax when large amounts of fluid were drained. Compared to a thoracentesis of 0.8–1.2 l, drainage of 1.8–2.2 l was associated with a more than threefold increase in risk for pneumothorax (odds ratio [OR] 3.8, 95% confidence interval [CI] 1.28–11.2), and after drainage of 2.3 l or more, the increase in risk was almost sixfold (OR 5.7, 95% CI 1.30–24.7). The association between the amount drained and the risk of pneumothorax was even more pronounced for pneumothoraces requiring tube thoracostomy ( P for trend <0.0001). Nine of 11 tube thoracostomies occurred after thoracenteses of 1.8 l or more.

Conclusion: Our study suggests that drainage of large amounts of fluid at ultrasound-guided thoracentesis is a risk factor for pneumothorax.
Exploring the forgetting mechanisms in working memory: Evidence from a reasoning span test
Authors: Saito Satoru , Jarrold Christopher , Riby Deborah M.
Published: December 2008

In working memory (WM) span tests participants have to maintain to-be-remembered information while processing other, potentially distracting, information. Previous studies have shown that WM span scores are greater when span lists start with a long processing task and end with a short processing task than when these processing tasks are presented in the reverse order (e.g., Towse, Hitch, & Hutton, 2000). In Experiment 1, we obtained a similar stimulus order effect in a reasoning span test, using reasoning sentences that were equated for length in terms of the number of constituent words, but which differed in processing complexity; span scores were greater when lists began with a complex sentence and ended with a simple sentence than when this stimulus order was reversed. In Experiment 2, the stimulus order effect was not found when processing duration was held constant while sentence complexity was varied using a computer-paced moving window presentation paradigm. These results suggest that duration-based constraints can affect degree of forgetting independently of the load generated during processing phases in WM span performance and therefore imply that time-related forgetting can occur in WM span tests, particularly when the difficulty of the processing component blocks active maintenance of to-be-remembered material.
Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields
Authors: Barutcuoglu Zafer , Airoldi Edoardo M. , Dumeaux Vanessa , Schapire Robert E. , Troyanskaya Olga G.
Published: December 2008

Motivation: The heterogeneity of cancer cannot always be recognized by tumor morphology, but may be reflected by the underlying genetic aberrations. Array comparative genome hybridization (array-CGH) methods provide high-throughput data on genetic copy numbers, but determining the clinically relevant copy number changes remains a challenge. Conventional classification methods for linking recurrent alterations to clinical outcome ignore sequential correlations in selecting relevant features. Conversely, existing sequence classification methods can only model overall copy number instability, without regard to any particular position in the genome.

Results: Here, we present the heterogeneous hidden conditional random field, a new integrated array-CGH analysis method for jointly classifying tumors, inferring copy numbers and identifying clinically relevant positions in recurrent alteration regions. By capturing the sequentiality as well as the locality of changes, our integrated model provides better noise reduction, and achieves more relevant gene retrieval and more accurate classification than existing methods. We provide an efficient L1-regularized discriminative training algorithm, which notably selects a small set of candidate genes most likely to be clinically relevant and driving the recurrent amplicons of importance. Our method thus provides unbiased starting points in deciding which genomic regions and which genes in particular to pursue for further examination. Our experiments on synthetic data and real genomic cancer prediction data show that our method is superior, both in prediction accuracy and relevant feature discovery, to existing methods. We also demonstrate that it can be used to generate novel biological hypotheses for breast cancer.

Contact:  ogt@cs.princeton.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
First Report of Bacterial Leaf Spot of Lettuce (Lactuca sativa) Caused by Xanthomonas campestris pv. vitians in Saudi Arabia
Authors: Al-Saleh M. , Ibrahim Y.
Published: December 2008

In April of 2008, lettuce (Lactuca sativa L. cv. Darkland) plants grown in the Al-Ouunia Region of Saudi Arabia were observed with numerous lesions typical of bacterial leaf spot. Leaf lesions were irregular, small, pale green to black, and 2 to 5 mm in diameter. Bacteria were isolated from diseased leaf tissues by cutting leaves into small pieces (0.5 mm) and soaking them in 2 ml of sterile distilled water. The resulting suspension was streaked onto yeast dextrose calcium carbonate agar (YDC) (1) and plates were incubated at 28°C. Large, round, butyrus, bright yellow colonies typical of Xanthomonas spp. formed after 48 h and five strains were selected for further tests. A yellow, mucoid bacterium was consistently isolated from lettuce samples with typical bacterial leaf spot symptoms. All five strains tested in this study were gram negative, oxidase negative, nitrate reduction negative, catalase and esculin hydrolysis positive, motile, and strictly aerobic. All were slightly pectolytic but not amylolytic. All were identified as Xanthomonas campestris pv. vitians. The bacterium was identified with specific oligonucleotide primers (2). This primer pair directed the amplification of an approximately 700-bp DNA fragment from total genomic DNA of all X. campestris pv. vitians strains tested. Pathogenicity tests were performed by using bacterial cultures grown on YDC for 48 h at 28°C. Each strain was suspended in sterile distilled water and the bacterial concentration was adjusted to 106 CFU/ml. Leaves of 5-week-old lettuce plants (cv. Darkland) were sprayed with the bacterial suspension. The inoculated and sterile-water-sprayed control plants were covered with polyethylene bags for 48 h at 25°C, after which the bags were removed and plants were transferred to a greenhouse at 25 to 28°C (1). All strains were pathogenic on the lettuce cv. Darkland, causing typical bacterial leaf spot symptoms by 2 weeks after inoculation. All inoculated plants showed typical symptoms of bacterial leaf spot and symptoms similar to those observed on the samples collected. No symptoms developed on the control plants. The bacterium was reisolated from inoculated plants and identified as X. campestris pv. vitians by morphological, physiological, and biochemical tests as described above. To our knowledge, this is the first report of bacterial leaf spot of lettuce by X. campestris pv. vitians in Saudi Arabia.

References: (1) F. Sahin and A. Miller. Plant Dis.81:1443, 1997. (2) J. D. Barak. Plant Dis.85:169, 2001.
First Detection of Virulence in Puccinia triticina to Resistance Genes Lr27 + Lr31 Present in Durum Wheat in Mexico
Authors: Huerta-Espino J. , Singh R. P. , Herrera-Foessel S. A. , Pérez-López J. B. , Figueroa-López P.
Published: December 2008

Leaf rust caused by Puccinia triticina Eriks. was observed during the 2007–2008 crop season in the state of Sonora, Mexico on previously resistant durum wheat (Triticum turgidum L.) cvs. Jupare C2001 (Lr27 + 31) and Banamichi C2004. Single uredinial isolates were made from disease samples collected in the field and tested mostly on ‘Thatcher’ differentials at seedling or adult-plant stages (1). The isolates were identified as a new race, BBG/BP, resembling race BBG/BN predominant on durum wheat (2), but with additional virulences to resistance genes Lr27 + Lr31 in Gatcher and adult-plant resistance gene Lr12. The new race was also identified in samples collected from durum wheat in the State of Nuevo Leon during the same season. The avirulence/virulence formula of race BBG/BP is Lr1, 2a, 2b, 2c, 3, 3ka, 3bg, 9, 13, 14a, 15, 16, 17, 18, 19, 21, 22a, 24, 25, 26, 28, 29, 30, 32, 35, 37/Lr10, 11, 12, 14b, 20, 23, 27 + 31, 33. Although virulences to Lr27 + Lr31 and Lr12 is known to occur in P. triticina races predominant on bread wheat (T. aestivum L.) (1), to our knowledge, this is the first report of such virulences in the pathogen population on durum wheat. Pure isolates of race BBG/BP are stored in the CIMMYT leaf rust collection.

References: (1) R. P. Singh. Plant Dis. 75:790, 1991. (2) R. P. Singh et al. Plant Dis. 88:703, 2004.
Response of Sweet Orange (Citrus sinensis) to ‘CandidatusLiberibacter asiaticus’ Infection: Microscopy and Microarray Analyses
Authors: Kim Jeong-Soon , Sagaram Uma Shankar , Burns Jacqueline K. , Li Jian-Liang , Wang Nian
Published: December 2008

Citrus greening or huanglongbing (HLB) is a devastating disease of citrus. HLB is associated with the phloem-limited fastidious prokaryotic α-proteobacterium ‘Candidatus Liberibacter spp.’ In this report, we used sweet orange (Citrus sinensis) leaf tissue infected with ‘Ca. Liberibacter asiaticus’ and compared this with healthy controls. Investigation of the host response was examined with citrus microarray hybridization based on 33,879 expressed sequence tag sequences from several citrus species and hybrids. The microarray analysis indicated that HLB infection significantly affected expression of 624 genes whose encoded proteins were categorized according to function. The categories included genes associated with sugar metabolism, plant defense, phytohormone, and cell wall metabolism, as well as 14 other gene categories. The anatomical analyses indicated that HLB bacterium infection caused phloem disruption, sucrose accumulation, and plugged sieve pores. The up-regulation of three key starch biosynthetic genes including ADP-glucose pyrophosphorylase, starch synthase, granule-bound starch synthase and starch debranching enzyme likely contributed to accumulation of starch in HLB-affected leaves. The HLB-associated phloem blockage resulted from the plugged sieve pores rather than the HLB bacterial aggregates since ‘Ca. Liberibacter asiaticus’ does not form aggregate in citrus. The up-regulation of pp2 gene is related to callose deposition to plug the sieve pores in HLB-affected plants.
A Nested-Polymerase Chain Reaction Protocol for Detection and Population Biology Studies ofPeronospora arborescens, the Downy Mildew Pathogen of Opium Poppy, Using Herbarium Specimens and Asymptomatic, Fresh Plant Tissues
Authors: Montes-Borrego Miguel , Ledesma Francisco J. Muñoz , Jiménez-Díaz Rafael M. , Landa Blanca B.
Published: December 2008

A sensitive nested-polymerase chain reaction (PCR) protocol was developed using either of two primer pairs that improves the in planta detection of Peronospora arborescens DNA. The new protocol represented an increase in sensitivity of 100- to 1,000-fold of detection of the oomycete in opium poppy tissue compared with the detection limit of single PCR using the same primer pairs. The new protocol allowed amplification of 5 to 0.5 fg of Peronospora arborescens DNA mixed with Papaver somniferum DNA. The protocol proved useful for amplifying Peronospora arborescens DNA from 96-year-old herbarium specimens of Papaver spp. and to demonstrate that asymptomatic, systemic infections by Peronospora arborescens can occur in wild Papaver spp. as well as in cultivated opium poppy. Also, the increase in sensitivity of the protocol made possible the detection of seedborne Peronospora arborescens in commercial opium poppy seed stocks in Spain with a high frequency, which poses a threat for pathogen spread. Direct sequencing of purified amplicons allowed alignment of a Peronospora arborescens internal transcribed spacer (ITS) ribosomal DNA (rDNA) sequence up to 730-bp long when combining the sequences obtained with the two primer sets. Maximum parsimony analysis of amplified Peronospora arborescens ITS rDNA sequences from specimens of Papaver dubium, P. hybridum, P. rhoeas, and P. somniferum from different countries indicated for the first time that a degree of host specificity may exist within populations of Peronospora arborescens. The reported protocol will be useful for epidemiological and biogeographical studies of downy mildew diseases as well as to unravel misclassification of Peronospora arborescens and Peronospora cristata, the reported causal agents of the opium poppy downy mildew disease.
Quantification of Fusarium graminearum in Harvested Grain by Real-Time Polymerase Chain Reaction to Assess Efficacies of Fungicides on Fusarium Head Blight, Deoxynivalenol Contamination, and Yield of Winter Wheat
Authors: Zhang Y. J. , Fan P. S. , Zhang X. , Chen C. J. , Zhou M. G.
Published: December 2008

We used a real time polymerase chain reaction-based assay and visual disease assessment to evaluate the efficacies of Js399-19, tebuconazole, a mixture of tebuconazole and thiram, azoxystrobin, carbendazim, and thiram on the development of Fusarium head blight (FHB) and deoxynivalenol (DON) contamination and on the yield of winter wheat (cv. Nannong no. 9918) after artificial inoculation under field conditions with Fusarium graminearum. The incidence of infected spikelets (IIS), amount of F. graminearum DNA (Tri5 DNA), total DON (containing DON, 3-acetyl-deoxynivalenol, and 15-acetyl-deoxynivalenol) concentration, and 1,000-grain weight (TGW) were quantified in 2006 and 2007. A strong positive correlation was found between IIS or Log10Tri5 DNA and total DON concentration in the harvested grain. The Js399-19, tebuconazole, and the mixture of tebuconazole and thiram significantly reduced IIS of FHB, amount of Tri5 DNA, and total DON within the grain and increased TGW. Although azoxystrobin, carbendazim, and thiram can increase TGW, they had no effect on the occurrence of F. graminearum compared with those of the untreated controls. Surprisingly, azoxystrobin and carbendazim significantly increased the total DON content in the harvested grain because they might have stimulated the amount of total DON production per Tri5 DNA. The fungicides Js399-19, tebuconazole, and the mixture of tebuconazole and thiram were the most effective in controlling FHB and reducing DON contamination of the wheat.
Antimicrobial Activity of Pyrrocidines from Acremonium zeae Against Endophytes and Pathogens of Maize
Authors: Wicklow Donald T. , Poling Stephen M.
Published: December 2008

Acremonium zeae produces pyrrocidines A and B, which are polyketide-amino acid-derived antibiotics, and is recognized as a seedborne protective endophyte of maize which augments host defenses against microbial pathogens causing seedling blights and stalk rots. Pyrrocidine A displayed significant in vitro activity against Aspergillus flavus and Fusarium verticillioides in assays performed using conidia as inoculum, with pyrrocidine A being more active than B. In equivalent assays performed with conidia or hyphal cells as inoculum, pyrrocidine A revealed potent activity against major stalk and ear rot pathogens of maize, including F. graminearum, Nigrospora oryzae, Stenocarpella (Diplodia) maydis, and Rhizoctonia zeae. Pyrrocidine A displayed significant activity against seed-rotting saprophytes A. flavus and Eupenicillium ochrosalmoneum, as well as seed-infecting colonists of the phylloplane Alternaria alternata, Cladosporium cladosporioides, and Curvularia lunata, which produces a damaging leaf spot disease. Protective endophytes, including mycoparasites which grow asymptomatically within healthy maize tissues, show little sensitivity to pyrrocidines. Pyrrocidine A also exhibited potent activity against Clavibacter michiganense subsp. nebraskense, causal agent of Goss's bacterial wilt of maize, and Bacillus mojaviense and Pseudomonas fluorescens, maize endophytes applied as biocontrol agents, but were ineffective against the wilt-producing bacterium Pantoea stewartii.
A functional link between Wnt signaling and SKP2-independent p27 turnover in mammary tumors
Authors: Miranda-Carboni Gustavo A. , Krum Susan A. , Yee Kathleen , Nava Miguel , Deng Qiming E. , Pervin Shehla , Collado-Hidalgo Alicia , Galić Zoran , Zack Jerome A. , Nakayama Keiko , Nakayama Keiichi I. , Lane Timothy F.
Published: December 2008

Loss of the CDK inhibitor p27KIP1 is widely linked with poor prognosis in human cancer. In Wnt10b-expressing mammary tumors, levels of p27KIP1 were extremely low; conversely, Wnt10b-null mammary cells expressed high levels of this protein, suggesting Wnt-dependent regulation of p27KIP1. Interestingly we found that Wnt-induced turnover of p27KIP1 was independent from classical SCFSKP2-mediated degradation in both mouse and human cells. Instead, turnover required Cullin 4A and Cullin 4B, components of an alternative E3 ubiquitin ligase induced in response to active Wnt signaling. We found that CUL4A was a novel Wnt target gene in both mouse and human cells and that CUL4A physically interacted with p27KIP1 in Wnt-responding cells. We further demonstrated that both Cul4A and Cul4B were required for Wnt-induced p27KIP1 degradation and S-phase progression. CUL4A and CUL4B are therefore components of a conserved Wnt-induced proteasome targeting (WIPT) complex that regulates p27KIP1 levels and cell cycle progression in mammalian cells.
Initiation of meiotic chromosome synapsis at centromeres in budding yeast
Authors: Tsubouchi Tomomi , MacQueen Amy J. , Roeder G. Shirleen
Published: December 2008

Previous studies of synaptonemal complex assembly in budding yeast have suggested that chromosome synapsis initiates at the sites of crossing over. The data presented here, however, indicate that centromeric regions are preferred sites for synapsis initiation. At early times during meiosis in wild type, the Zip1 protein (a major building block of the synaptonemal complex) localizes specifically to centromeric regions. As synapsis progresses and linear stretches of Zip1 are formed, the majority of stretches are associated with a centromere, as expected if the Zip1 protein present at the centromere polymerized outward along the chromosome arm. In many cases, the centromere is present at one end of a linear stretch, suggesting that synapsis is often unidirectional. Furthermore, the Zip2 protein, a protein that promotes Zip1 polymerization, is often present at the opposite end from the centromere, implying that Zip2 and associated proteins move at the leading edge of Zip1 polymerization. Surprisingly, synapsis initiation at centromeres is independent of the Zip3 protein, which plays a major role in synapsis initiation events at noncentromeric locations. Our data provide evidence for two classes of synapsis initiation events that differ in location, timing, genetic requirements, and relationship to meiotic recombination.
Endocycling cells do not apoptose in response to DNA rereplication genotoxic stress
Authors: Mehrotra Sonam , Maqbool Shahina B. , Kolpakas Alexis , Murnen Katherine , Calvi Brian R.
Published: December 2008

Initiation of DNA replication at origins more than once per cell cycle results in rereplication and has been implicated in cancer. Here we use Drosophila to examine the checkpoint responses to rereplication in a developmental context. We find that increased Double-parked (Dup), the Drosophila ortholog of Cdt1, results in rereplication and DNA damage. In most cells, this rereplication triggers caspase activation and apoptotic cell death mediated by both p53-dependent and -independent pathways. Elevated Dup also caused DNA damage in endocycling cells, which switch to a G/S cycle during normal development, indicating that rereplication and the endocycling DNA reduplication program are distinct processes. Unexpectedly, however, endocycling cells do not apoptose regardless of tissue type. Our combined evidence suggests that endocycling apoptosis is repressed in part because proapoptotic gene promoters are silenced. Normal endocycling cells had DNA lesions near heterochromatin, which increased after rereplication, explaining why endocycling cells must constantly repress the genotoxic apoptotic response. Our results reveal a novel regulation of apoptosis in development and new insights into the little-understood endocycle. Similar mechanisms may operate during vertebrate development, with implications for cancer predisposition in certain tissues.