bluuebunny/crossref_metadata_2025 huggingface dataset:
Normal Modes and Density of States of Disordered Colloidal Solids
Authors: Kaya D. , Green N. L. , Maloney C. E. , Islam M. F.
Published: August 2010

Measuring Motion

Within a solid, atoms vibrate about their mean position in a series of frequencies known as the normal modes, which relate to the thermal and mechanical transport properties of the material.

D. Kaya
et al.

(p.
656
) used video microscopy to observe the motion of colloidal crystals made from microgel particles. The colloidal particles varied slightly in their properties, allowing the behavior of disordered materials to be probed. Long-wavelength plane-wave modes were observed, characteristic of perfect crystals, and a conventional elastic behavior, modified by short-wavelength features, was also observed, in spite of the disorder of the colloidal crystals. The analysis method will allow studies on the effects of different types of disorder on the structure of the normal modes and the elasticity in a range of material systems.
Quantum Correlations in Optical Angle–Orbital Angular Momentum Variables
Authors: Leach Jonathan , Jack Barry , Romero Jacqui , Jha Anand K. , Yao Alison M. , Franke-Arnold Sonja , Ireland David G. , Boyd Robert W. , Barnett Stephen M. , Padgett Miles J.
Published: August 2010

Entanglement in a Twist

The strong correlations observed in quantum mechanically entangled particles, such as photons, offer potential for secure communication and quantum information processing.

Leach
et al.

(p.
662
) now show such strong quantum correlations between the complementary variables—angular position and orbital angular momentum—of two photons created during the parametric down-conversion process in a nonlinear crystal. This demonstration of entanglement in an angular basis establishes that angles are genuine quantum observables and can therefore be considered a resource for quantum information processing, capable of secure, high-dimension, key distribution.
When UV Meets Fresh Water
Authors: Williamson Craig E. , Rose Kevin C.
Published: August 2010

Ultraviolet radiation has detrimental and beneficial effects in freshwater ecosystems.
Toward an Economy of Well-Being
Happiness Around the World
The Paradox of Happy Peasants and Miserable Millionaires

by Carol Graham

Oxford University Press, Oxford, 2009. 267 pp. $24.95, £14.99. ISBN 9780199549054.
Authors: Ak Prashanth
Published: August 2010

Drawing on survey findings from around the world, Graham explores the relation between happiness and income and considers its implications for social policy.
Nonlinear Elasticity and an 8-nm Working Stroke of Single Myosin Molecules in Myofilaments
Authors: Kaya Motoshi , Higuchi Hideo
Published: August 2010

Measuring Single Myosins at Work

In the past 15 years, the molecular mechanism of muscle contraction has been investigated at the single-molecule level; however, results have varied between laboratories because of the nonprocessive properties of skeletal myosin. Now,
Kaya and Higuchi
(p.
686
) have measured the nonlinear elasticity and working stroke size of single skeletal myosins by combining optical trapping and fluorescence imaging with subnanometer accuracy. The data suggest that it is important to relate myosin's internal structural changes to physiological force generation and filament sliding.
The Give and Take of Alcohol Activation
Authors: Watson Andrew J. A. , Williams Jonathan M. J.
Published: August 2010

Catalysts make alcohols more reactive by taking away hydrogen to create carbonyl compounds and then returning the hydrogen to the final products.
Which Parental Gene Gets the Upper Hand?
Authors: Wilkinson Lawrence S.
Published: August 2010

Maternal and paternal influences on gene expression play a surprisingly large role in the epigenetic regulation of mammalian brain function.
Beta Cell Culture on Synthetic Capillaries: an Artificial Endocrine Pancreas
Authors: Chick William L. , Like Arthur A. , Lauris Vilma
Published: August 2010

Beta cells from neonatal rats were cultured on bundles of artificial capillaries perfused with tissue culture medium. Cells continued to release insulin and remained responsive to changes in glucose concentration. The quantity of insulin released was similar to that of conventional flask cultures.
New Map Illustrates Risk From the 'Other' Malaria
Authors: Vogel Gretchen
Published: August 2010

Nearly 3 billion people are at risk of infection with the malaria parasite
Plasmodium vivax
, according to a new analysis published this week in
PLoS Neglected Tropical Diseases
. Although long considered the milder, less-dangerous cousin of
P. falciparum
, recent studies have made it clear that
P. vivax
can also cause deadly complications in infected people.
A Shot at Cancer Prevention
Authors: Cheng Elaine
Published: August 2010

Vaccination with α-lactalbumin provides prophylaxis against breast cancer in tumor-prone mouse models.
False-Positive Rate of a “Fourth-Generation” HIV Antigen/Antibody Combination Assay in an Area of Low HIV Prevalence
Authors: Kim Sinyoung , Lee Jong-Han , Choi Jun Yong , Kim June Myung , Kim Hyon-Suk
Published: August 2010

We retrospectively analyzed the performance of the Architect HIV antigen/antibody (Ag/Ab) combination assay in a tertiary health care center with a situation of low HIV prevalence. The specificity and positive predictive value (PPV) were 99.78% and 31.21%, respectively. However, the specificity and PPV could increase to 99.99% and 89.70% using an arbitrary cutoff value.
Microevolution ofMycobacterium tuberculosisin a Tuberculosis Patient
Authors: Al-Hajoj Sahal A. M. , Akkerman Onno , Parwati Ida , al-Gamdi Saad , Rahim Zeaur , van Soolingen Dick , van Ingen Jakko , Supply Philip , van der Zanden Adri G. M.
Published: August 2010

FiveMycobacterium tuberculosisisolates were obtained from three body sites from a Dutch patient. The isolates displayed a single genotype by 24-locus MIRU-VNTR typing (except for a single locus not amplified from one isolate) but were differentiated by small variations in IS6110fingerprints, spoligotypes, 6 hypervariable MIRU-VNTR loci, and/or DiversiLab profiles, revealing patterns of microevolution in a clonal infection.
Low Frequency of CXCR4-Using Viruses in Patients at the Time of Primary Non-Subtype-B HIV-1 Infection
Authors: Frange Pierre , Chaix Marie-Laure , Raymond Stéphanie , Galimand Julie , Deveau Christiane , Meyer Laurence , Goujard Cécile , Rouzioux Christine , Izopet Jacques
Published: August 2010

We used genotypic and phenotypic assays to estimate the frequency of X4/DM viruses in 131 patients infected with non-subtype-B viruses at the time of primary HIV-1 infection (PHI). All patients were enrolled in the French PRIMO Cohort from 1996 to 2007. Most strains belonged to CRF02_AG (51.1%) and subtype A (14.5%). Sixteen viruses (12.2%) were classified as CXCR4 tropic (“X4 strains”) by the combined criteria of amino acids 11 and 25 of the V3 loop (11/25) and net charge rules and/or the SVMgeno2pheno
10%
algorithm: 6 strains by the combined genotypic rule, 7 by the SVMgeno2pheno
10%
algorithm, and 3, clustering in subtype D, by both algorithms. However, only one strain (0.8%), belonging to subtype A, was defined as a dual-tropic (DM) virus by the phenotypic assay. The 67 CRF02_AG strains included 2 classified as X4 strains by the combined genotypic rule (3%) and 2 others classified as X4 strains by SVMgeno2pheno
10%
(3%), but none of these 4 strains was an X4 or DM strain according to the phenotypic assay. These results suggest that the cellular virus reservoir was established with X4 strains in very few non-subtype-B-infected patients at the time of PHI. Genotypic predictions can overestimate the proportion of non-subtype-B X4 viruses at PHI.
Incidence, Risk Factors, and Outcomes of Panton-Valentine Leukocidin-Positive Methicillin-Susceptible
Staphylococcus aureus
Infections in Auckland, New Zealand
Authors: Muttaiyah S. , Coombs G. , Pandey S. , Reed P. , Ritchie S. , Lennon D. , Roberts S.
Published: August 2010

Panton-Valentine leukocidin (PVL) has been linked to invasive community-acquired methicillin-resistant
Staphylococcus aureus
infections. However, the association between disease and PVL-positive methicillin-susceptible
Staphylococcus aureus
(MSSA) has not been widely reported. We aimed to examine the epidemiology of PVL in clinical MSSA isolates from patients presenting to Auckland City Hospital. Four hundred eleven MSSA clinical isolates and 93 nasal carriage isolates were collected and tested for the presence of the
lukSF-PV
genes using PCR. The results were examined in light of host and disease factors. Multilocus sequence typing (MLST) was performed on a random subset of isolates to ensure that there was no single PVL-positive MSSA clone responsible for disease in Auckland. The prevalence of the
lukSF-PV
genes in MSSA isolates associated with disease (124/335; 37%) was not significantly different from the prevalence of the
lukSF-PV
genes in MSSA nasal carriage isolates (29/93; 31% [
P
= 0.33]). PVL-positive MSSA isolates in Auckland are genetically diverse and come from a number of different clonal complexes. PVL-positive infections peaked at between 10 and 20 years of age, with a subsequent decline. Pacific ethnicity, age, diagnosis of skin and soft tissue infection (SSTI), community-onset infection, and the need for surgical intervention were found by multivariate analysis to be independently associated with PVL-positive MSSA infection. More than one-third of MSSA infections in our patient population are caused by PVL-positive strains. Those patients with PVL-positive MSSA infection were more likely to be of Pacific ethnicity, be younger in age, have community-onset infection, have SSTI, and need surgical intervention.
Persistence of Genital Tract T Cell Responses in HIV-Infected Women on Highly Active Antiretroviral Therapy
Authors: Mkhize Nonhlanhla N. , Gumbi Pamela P. , Liebenberg Lenine J. , Ren Yuan , Smith Peter , Denny Lynette , Passmore Jo-Ann S.
Published: August 2010

Initiation of highly active antiretroviral therapy (HAART) for HIV-infected individuals is associated with control of viremia, improved CD4 counts, and declining systemic HIV-specific immune responses. While HAART effectively reduces plasma viremia, it remains unclear how effectively antiretroviral drugs reach mucosal surfaces, such as those of the genital tract. The aim of this study was to determine the effect of HAART on genital tract CD4 T cell reconstitution, HIV shedding, and HIV-specific T cell responses. Cervical cytobrush and blood specimens were obtained from 35 HIV-infected, HAART-naïve women and 27 women on HAART in order to investigate HIV Gag-specific T cell responses by intracellular gamma interferon (IFN-γ) staining. Interleukin 1β (IL-1β), IL-6, and IL-8 concentrations were measured by enzyme-linked immunosorbent assays (ELISA). We show that for HIV-infected women, HAART is associated with significantly improved CD4 T cell counts both in blood and at the cervix. While HAART effectively suppressed both blood and cervical viremia, HIV-specific CD8 T cell responses in blood were lost, while those at the cervix were preserved.
The Viral Latency-Associated Nuclear Antigen Augments the B-Cell Response to AntigenIn Vivo
Authors: Sin Sang-Hoon , Fakhari Farnaz D. , Dittmer Dirk P.
Published: August 2010

Gammaherpesviruses, including Kaposi sarcoma-associated herpesvirus (KSHV), establish latency in B cells. We hypothesized that the KSHV latency-associated nuclear antigen (LANA/orf73) provides a selective advantage to infected B cells by driving proliferation in response to antigen. To test this, we used LANA B-cell transgenic mice. Eight days after immunization with antigen without adjuvant, LANA mice had significantly more activated germinal center (GC) B cells (CD19+PNA+CD71+) than controls. This was dependent upon B-cell receptor since LANA did not restore the GC defect of CD19 knockout mice. However, LANA was able to restore the marginal zone defect in CD19 knockout mice.
A gC1qR Prevents White Spot Syndrome Virus Replication in the Freshwater CrayfishPacifastacus leniusculus
Authors: Watthanasurorot Apiruck , Jiravanichpaisal Pikul , Söderhäll Irene , Söderhäll Kenneth
Published: August 2010

The gC1qR/p32 protein is a multiple receptor for several proteins and pathogens. We cloned a gC1qR homologue in a crustacean,Pacifastacus leniusculus, and analyzed the expression ofP. leniusculusC1qR (PlgC1qR) in various tissues. The gC1qR/p32 transcript was significantly enhanced by white spot syndrome virus (WSSV) infection 6 h after viral infection bothin vitroin a hematopoietic tissue cell culture (Hpt) andin vivocompared to appropriate controls. Moreover,PlgC1qRsilencing in both the Hpt cell culture and live crayfish enhanced the WSSV replication. In addition, by making a recombinantPlgC1qR protein we could show that if this recombinant protein was injected in a crayfish,Pacifastacus leniusculus, followed by injection of WSSV, this significantly reduced viral replicationin vivo. Furthermore, if the recombinantPlgC1qR was incubated with Hpt cells and then WSSV was added, this also reduced viral replication. These experiments clearly demonstrate that recombinantPlgC1qR reduce WSSV replication bothin vivoandin vitro. The results from a far-Western overlay and glutathioneS-transferase pull-down assays showed thatPlgC1qRcould bind to VP15, VP26, and VP28. Altogether, these results demonstrate a role forPlgC1qR in antiviral activity against WSSV.
Inactivation and Disassembly of the Anaphase-Promoting Complex during Human Cytomegalovirus Infection Is Associated with Degradation of the APC5 and APC4 Subunits and Does Not Require UL97-Mediated Phosphorylation of Cdh1
Authors: Tran Karen , Kamil Jeremy P. , Coen Donald M. , Spector Deborah H.
Published: August 2010

Infection of quiescent cells by human cytomegalovirus (HCMV) elicits severe cell cycle deregulation, resulting in a G
1
/S arrest, which can be partly attributed to the inactivation of the anaphase-promoting complex (APC). As we previously reported, the premature phosphorylation of its coactivator Cdh1 and/or the dissociation of the core complex can account for the inactivation. We have expanded on these results and further delineated the key components required for disabling the APC during HCMV infection. The viral protein kinase UL97 was hypothesized to phosphorylate Cdh1, and consistent with this, phosphatase assays utilizing a virus with a UL97 deletion mutation (ΔUL97 virus) indicated that Cdh1 is hypophosphorylated at early times in the infection. Mass spectrometry analysis demonstrated that UL97 can phosphorylate Cdh1
in vitro
, and the majority of the sites identified correlated with previously characterized cyclin-dependent kinase (Cdk) consensus sites. Analysis of the APC core complex during ΔUL97 virus infection showed APC dissociation occurring at the same time as during infection with wild-type virus, suggesting that the UL97-mediated phosphorylation of Cdh1 is not required for this to occur. Further investigation of the APC subunits showed a proteasome-dependent loss of the APC5 and APC4 subunits that was temporally associated with the disassembly of the APC. Immediate early viral gene expression was not sufficient for the degradation of APC4 and APC5, indicating that a viral early gene product(s), possibly in association with a
de novo
-synthesized cellular protein(s), is involved.
Simian Immunodeficiency Virus-Specific CD8+T Cells Recognize Vpr- and Rev-Derived Epitopes Early after Infection
Authors: Sacha Jonah B. , Buechler Matthew B. , Newman Laura P. , Reed Jason , Wallace Lyle T. , Loffredo John T. , Wilson Nancy A. , Watkins David I.
Published: August 2010

The kinetics of CD8+T cell epitope presentation contribute to the antiviral efficacy of these cells yet remain poorly defined. Here, we demonstrate presentation of virion-derived Vpr peptide epitopes early after viral penetration and prior to presentation of Vif-derived epitopes, which requiredde novoVif synthesis. Two Rev epitopes exhibited differential presentation kinetics, with one Rev epitope presented within 1 h of infection. We also demonstrate that cytolytic activity mirrors the recognition kinetics of infected cells. These studies show for the first time that Vpr- and Rev-specific CD8+T cells recognize and kill simian immunodeficiency virus (SIV)-infected CD4+T cells early after SIV infection.
AN ACUTE FRACTURE OF THE FEMORAL NECK COMPLICATING BONE MARROW EDEMA IN OSTEONECROSIS OF THE FEMORAL HEAD, TREATED WITH TOTAL HIP REPLACEMENT
Authors: Fenichel Itay , Salai Moshe , Velkes Steven
Published: August 2010

Bone marrow edema is a sign that can be accompanied with osteonecrosis of the femoral head. There is still controversy as to whether it is a reversible form of avascular necrosis or it is a disease entity of its own. The probability and extent of the edema correlate well with the pain and stage of the necrosis. Unlike transient osteoporosis of the hip and regional migratory osteoporosis which are spontaneously resolving conditions, osteonecrosis can cause significant changes in the hip joint. We present a case of a displaced fracture of the femoral neck complicating bone marrow edema in osteonecrosis of the femoral head, in a 42-year-old man, treated with a cementless total hip replacement. This case emphasizes a potential complication associated with the state of diffuse bone marrow edema of the hip.
IMPACT OF PAIN ON SHOULDER ELEVATION VELOCITY IN PATIENTS WITH ROTATOR CUFF TEARS
Authors: Scibek Jason S. , Mell Amy G. , Downie Brian K. , Palmieri-Smith Riann , Hughes Richard E.
Published: August 2010

Pain is routinely implicated as a factor when considering impaired movement in injured populations. Movement velocity is often considered during the rehabilitation process; unfortunately our understanding of pain's impact on shoulder movement velocity in rotator cuff tear patients is less understood. Therefore, the purpose of this study was to test the hypothesis that there would be an increase in peak and mean shoulder elevation velocities following the decrease of shoulder pain in rotator cuff tear patients, regardless of tear size. Fifteen subjects with full-thickness rotator cuff tears (RCT) performed humeral elevation and lowering in three planes before and after receiving a lidocaine injection to relieve pain. Pain was assessed using a visual analog scale. Humeral elevation velocity data were collected using an electromagnetic tracking system. A significant reduction in pain (pre-injection 3.53 ± 1.99; post-injection 1.23 ± 1.43) resulted in significant increases in maximum and mean humeral elevation velocities. Mean shoulder elevation and lowering velocities increased 15.10 ± 2.45% while maximum shoulder movement velocities increased 12.77 ± 3.93%. Furthermore, no significant relationships were noted between tear size and movement velocity. These significant increases in movement velocity provide evidence to further support the notion that human motion can be inhibited by injury-associated pain, and that by reducing that pain through clinical interventions, human movement can be impacted in a positive fashion.
Process Conditions for Improvement of Electrical Properties of Al2O3/n-GaN Structures Prepared by Atomic Layer Deposition
Authors: Hori Yujin , Mizue Chihoko , Hashizume Tamotsu
Published: August 2010

The effects of fabrication processes on the electrical properties of Al2O3/GaN structures prepared by atomic layer deposition were investigated. The annealing process at 800 °C for the formation of ohmic electrodes brought a large number of microcrystallization regions into the Al2O3 layer, causing a marked leakage in the current–voltage characteristics of the Al2O3/GaN structure. The “ohmic-first” process with a SiN protection layer was thus applied to the GaN surface. In this process, the amorphous phase in the atomic configuration of Al2O3 was maintained, leading to the sufficient suppression of leakage current at the Al2O3/GaN interface. In addition, the Al2O3/GaN structures showed good capacitance–voltage characteristics, resulting in low interface state densities of less than 1×1012 cm-2 eV-1.
High Power and High Efficiency Blue InGaN Light Emitting Diodes on Free-Standing Semipolar (3031) Bulk GaN Substrate
Authors: Koslow Ingrid L. , Sonoda Junichi , Chung Roy B. , Pan Chih-Chien , Brinkley Stuart , Ohta Hiroaki , Nakamura Shuji , DenBaars Steven P.
Published: August 2010

High power and high efficiency semipolar (3031) nitride light emitting diodes (LEDs), fabricated on low extended defect bulk GaN substrates, are reported for the first time. The LEDs were grown by metal organic chemical vapor deposition (MOCVD) at atmospheric pressure. The peak wavelength was 452 nm, and a minimal redshift of <1 nm was observed between 5–100 mA, in comparison to large blueshifts in c-plane LEDs. The output power and external quantum efficiency (EQE) of the packaged 200 ×500 µm2 was 14.48 mW and 26.5%, respectively, at 20 mA.
Growth Orientation Control of Semipolar InN Films Using Yttria-Stabilized Zirconia Substrates
Authors: Fujii Tomoaki , Kobayashi Atsushi , Shimomoto Kazuma , Ohta Jitsuo , Oshima Masaharu , Fujioka Hiroshi
Published: August 2010

We have investigated the epitaxial growth of InN films on yttria-stabilized zirconia (YSZ) substrates with various surface orientations. Through systematic crystallographic investigations, we have found that the epitaxial relationship of InN[1120] ∥YSZ [110] and InN[0001] ∥YSZ [111] holds in the InN/YSZ system. This enables us to grow semipolar InN films with arbitrary orientations.
Effect of Oxygen Precipitation in Nitrogen-Doped Annealed Silicon Wafers on Thermal Strain Induced by Rapid Thermal Processing
Authors: Araki Koji , Sudo Haruo , Aoki Tatsuhiko , Senda Takeshi , Isogai Hiromichi , Tsubota Hiroyuki , Miyashita Moriya , Matsumura Hisashi , Saito Hiroyuki , Maeda Susumu , Kashima Kazuhiko , Izunome Koji
Published: August 2010

We have studied the effect of oxygen precipitation in annealed silicon wafers on the thermal strain induced during rapid thermal processing (RTP), focusing on the density of oxygen precipitates. It was found that the strain decreased with an increase in the precipitate density. Furthermore, the strain was drastically suppressed when the density of oxygen precipitates (average size: 80 nm) was greater than 1.5 ×1010 cm-3. This is interpreted as “precipitation hardening” against dislocation movements during RTP.
Theoretical Investigation of the Crystal Structure and Electronic and Dielectric Properties of the Potential Multiferroic (C2H5NH3)2FeCl4
Authors: Baettig Pio , Oguchi Tamio
Published: August 2010

The results of first-principles calculations of the antiferromagnetic potential multiferroic material (C2H5NH3)2FeCl4, ethyl ammonium tetrachloroferrate(II), are presented. Its crystal structure has been optimized using X-ray diffraction data as an initial guess for the atomic positions. The spontaneous polarization is predicted to be approximately 20% of that of the perovskite ferroelectrics.
Surface Relief Formation in Photo-Cross-Linkable Polymer/Benzophenone Composite Films Using 325 nm Laser
Authors: Kawatsuki Nobuhiro , Kondo Mizuho , Okada Makoto , Matsui Shinji , Ono Hiroshi , Emoto Akira
Published: August 2010

We achieved facile surface relief (SR) formation with symmetrical and asymmetrical structure in photoreactive polymer/benzophenone (BP) monomer composite films by holographic exposure to 325-nm He–Cd laser beams. Under holographic exposure, photo-excited BP molecules induced photo-crosslinking of the composite film, incorporating BP molecules into the polymer and generating molecular motion, resulting in SR formation. The height of the SR depended on the polymer/BP ratio, and reached 550 nm. Furthermore, slantwise exposure resulted in asymmetrical SR formation. The resultant SR gratings were transparent to visible light and thermally stable up to 95 °C.
Effects of Pulse Rate and Temperature on Nonlinear Absorption of Pulsed 262-nm Laser Light in β-BaB2O4
Authors: Takahashi Masakuni , Osada Akira , Dergachev Alex , Moulton Peter F. , Cadatal-Raduban Marilou , Shimizu Toshihiko , Sarukura Nobuhiko
Published: August 2010

The efficiency of multi-watt ultraviolet radiation generation by harmonics processes in β-BaB2O4 (BBO) can be improved by reducing thermal dephasing. The dephasing arises from local heating of BBO by the linear absorption of green (second harmonic) and ultraviolet (fourth harmonic) radiation by crystal defects that are induced by two-photon absorption of high peak power ultraviolet radiation. Such absorption can be reduced by decreasing the repetition rate to ∼1 kHz to allow the defects to decay between the laser pulses and/or heating BBO crystal to 150–200 °C to increase the decay rate of the induced defects.
Growth of Single-Walled Carbon Nanotubes below 450 °C Using Cobalt Catalyst
Authors: Ishikawa Yutaka , Fukuda Kazuhiro , Miura Takuya , Yamamoto Takuji
Published: August 2010

The growth of single-walled carbon nanotubes (SWCNTs) by chemical vapor deposition using a carbon-rod filament was performed at low temperatures of below 450 °C. Ethanol vapor was used as the carbon source. By heating a cobalt film used as a catalyst at 450 °C in a gaseous mixture of argon and 3% hydrogen beforehand, it was possible to grow SWCNTs even below 400 °C. The proportion of metallic SWCNTs increased with decreasing growth temperature below 400 °C. This may be because SWCNTs grow from cobalt nanoparticles in the solid phase at such low temperatures.
Transparent Conductor: TiOxNy
Authors: Akazawa Housei
Published: August 2010

We propose the feasibility of using TiO
x
N
y
films as transparent conductors. The TiO
x
N
y
films deposited by electron cyclotron resonance plasma sputtering from a Ti target in the metal mode had a face-centered cubic crystal structure. As deposited films incorporated larger numbers of O and N atoms, their crystallinity approached an amorphous state and optical transparency improved, reflecting the decrease in carrier concentration. Our TiO
x
N
y
films extended the controllable range of resistivity and optical transmittance more than that with TiO
x
and TiN
x
films and outperformed those produced by conventional magnetron sputtering.
Plasma Characteristics of 450 mm Diameter Ferrite-Enhanced Inductively Coupled Plasma Source
Authors: Hong Seung Pyo , Lim Jong Hyeuk , Gweon Gwang Ho , Yeom Geun Young
Published: August 2010

The effect of C-shaped ferrite modules installed above a spiral-type inductively coupled plasma (ICP) antenna coil and the plasma characteristics of an ICP source operated at 2 MHz were investigated in order to realize 450 mm wafer processing. The application of an appropriate amount of Ni–Zn ferrite modules to the antenna increased the plasma density slightly and decreased the plasma potential, while the application of the ferrite modules all over the antenna line decreased the plasma density and increased the plasma potential. In particular, by installing the ferrite modules locally in a low-plasma-density region, plasma uniformity was improved effectively.
Vertically Aligned Liquid Crystal Molecules on TiO2 Film Treated by Ion-Beam Irradiation
Authors: Kim Iee-Gon , Na Hyun-Jae , Park Hong-Gyu , Kim Young-Hwan , Kim Byoung-Yong , Han Jeong-Min , Park Tae-Kyu , Seo Dae-Shik , Yoon Hong-Il
Published: August 2010

In this paper, we describe the formation of vertically aligned liquid crystal molecules on TiO2 films treated by ion-beam (IB) irradiation. Regular or irregular pretilt angles were achieved as a function of IB incident angle. Uniform alignment was obtained only at an incident angle of 45°. The contact angle, which is related to the surface energy, was measured to confirm the tendency of variation in the pretilt angle. In addition, the weak anchoring energy of LC molecules on IB-irradiated TiO2 was ascertained by the thermal stability at low temperature.
Playing the “Harp”: Evolution of Our Understanding of hrp/hrc Genes
Authors: Tampakaki Anastasia P. , Skandalis Nicholas , Gazi Anastasia D. , Bastaki Marina N. , Panagiotis F. Sarris , Charova Spyridoula N. , Kokkinidis Michael , Panopoulos Nickolas J.
Published: August 2010

With the advent of recombinant DNA techniques, the field of molecular plant pathology witnessed dramatic shifts in the 1970s and 1980s. The new and conventional methodologies of bacterial molecular genetics put bacteria center stage. The discovery in the mid-1980s of the hrp/hrc gene cluster and the subsequent demonstration that it encodes a type III secretion system (T3SS) common to Gram negative bacterial phytopathogens, animal pathogens, and plant symbionts was a landmark in molecular plant pathology. Today, T3SS has earned a central role in our understanding of many fundamental aspects of bacterium-plant interactions and has contributed the important concept of interkingdom transfer of effector proteins determining race-cultivar specificity in plant-bacterium pathosystems. Recent developments in genomics, proteomics, and structural biology enable detailed and comprehensive insights into the functional architecture, evolutionary origin, and distribution of T3SS among bacterial pathogens and support current research efforts to discover novel antivirulence drugs.
Ecology of Plant and Free-Living Nematodes in Natural and Agricultural Soil
Authors: Neher Deborah A.
Published: August 2010

Nematodes are aquatic organisms that depend on thin water films to live and move within existing pathways of soil pores of 25–100 μm diameter. Soil nematodes can be a tool for testing ecological hypotheses and understanding biological mechanisms in soil because of their central role in the soil food web and linkage to ecological processes. Ecological succession is one of the most tested community ecology concepts, and a variety of nematode community indices have been proposed for purposes of environmental monitoring. In contrast, theories of biogeography, colonization, optimal foraging, and niche partitioning by nematodes are poorly understood. Ecological hypotheses related to strategies of coexistence of nematode species sharing the same resource have potential uses for more effective biological control and use of organic amendments to foster disease suppression. Essential research is needed on nematodes in natural and agricultural soils to synchronize nutrient release and availability relative to plant needs, to test ecological hypotheses, to apply optimal foraging and niche partitioning strategies for more effective biological control, to blend organic amendments to foster disease suppression, to monitor environmental and restoration status, and to develop better predictive models for land-use decisions.
Induced Systemic Resistance and Plant Responses to Fungal Biocontrol Agents
Authors: Shoresh Michal , Harman Gary E. , Mastouri Fatemeh
Published: August 2010

Biocontrol fungi (BCF) are agents that control plant diseases. These include the well-known Trichoderma spp. and the recently described Sebacinales spp. They have the ability to control numerous foliar, root, and fruit pathogens and even invertebrates such as nematodes. However, this is only a subset of their abilities. We now know that they also have the ability to ameliorate a wide range of abiotic stresses, and some of them can also alleviate physiological stresses such as seed aging. They can also enhance nutrient uptake in plants and can substantially increase nitrogen use efficiency in crops. These abilities may be more important to agriculture than disease control. Some strains also have abilities to improve photosynthetic efficiency and probably respiratory activities of plants. All of these capabilities are a consequence of their abilities to reprogram plant gene expression, probably through activation of a limited number of general plant pathways.
Quantitative Disease Resistance and Quantitative Resistance Loci in Breeding
Authors: St.Clair Dina A.
Published: August 2010

Quantitative disease resistance (QDR) has been observed within many crop plants but is not as well understood as qualitative (monogenic) disease resistance and has not been used as extensively in breeding. Mapping quantitative trait loci (QTLs) is a powerful tool for genetic dissection of QDR. DNA markers tightly linked to quantitative resistance loci (QRLs) controlling QDR can be used for marker-assisted selection (MAS) to incorporate these valuable traits. QDR confers a reduction, rather than lack, of disease and has diverse biological and molecular bases as revealed by cloning of QRLs and identification of the candidate gene(s) underlying QRLs. Increasing our biological knowledge of QDR and QRLs will enhance understanding of how QDR differs from qualitative resistance and provide the necessary information to better deploy these resources in breeding. Application of MAS for QRLs in breeding for QDR to diverse pathogens is illustrated by examples from wheat, barley, common bean, tomato, and pepper. Strategies for optimum deployment of QRLs require research to understand effects of QDR on pathogen populations over time.
Hyaloperonospora arabidopsidis as a Pathogen Model
Authors: Coates Mary E. , Beynon Jim L.
Published: August 2010

Hyaloperonospora arabidopsidis, a downy mildew pathogen of the model plant Arabidopsis, has been very useful in the understanding of the relationship between oomycetes and their host plants. This naturally coevolving pathosystem contains an amazing level of genetic diversity in host resistance and pathogen avirulence proteins. Oomycete effectors identified to date contain a targeting motif, RXLR, enabling effector entry into the host cell. The availability of the H. arabidopsidis genome sequence has enabled bioinformatic analyses to identify at least 130 RXLR effectors, potentially used to quell the host's defense mechanism and manipulate other host cellular processes. Currently, these effectors are being used to reveal their targets in the host cell. Eventually this will result in an understanding of the mechanisms used by a pathogen to sustain a biotrophic relationship with a plant.
Properties of the Arg376 residue of the proton-coupled folate transporter (PCFT-SLC46A1) and a glutamine mutant causing hereditary folate malabsorption
Authors: Mahadeo Kris , Diop-Bove Ndeye , Shin Daniel , Unal Ersin Selcuk , Teo Juliana , Zhao Rongbao , Chang Min-Hwang , Fulterer Andreas , Romero Michael F. , Goldman I. David
Published: August 2010

The proton-coupled folate transporter (PCFT-SLC46A1) is required for intestinal folate absorption and is mutated in the autosomal recessive disorder, hereditary folate malabsorption (HFM). This report characterizes properties and requirements of the R376 residue in PCFT function, including a R376Q mutant associated with HFM. Gln, Cys, and Ala substitutions resulted in markedly impaired transport of 5-formyltetrahydrofolate (5-FTHF) and 5-methyltetrahydrofolate (5-MTHF) due to an increase in Km and decrease in Vmax in HeLa R1–11 transfectants lacking endogenous folate transport function. In contrast, although the influx Km for pemetrexed was increased, transport was fully preserved at saturating concentrations and enhanced for the like-charged R376K- and R376H-PCFT. Pemetrexed and 5-FTHF influx mediated by R376Q-PCFT was markedly decreased at pH 5.5 compared with wild-type PCFT. However, while pemetrexed transport was substantially preserved at low pH (4.5–5.0), 5-FTHF transport remained very low. Electrophysiological studies in Xenopus oocytes demonstrated that 1) the R376Q mutant, like wild-type PCFT, transports protons in the absence of folate substrate, and in this respect has channel-like properties; and 2) the influx Km mediated by R376Q-PCFT is increased for 5-MTHF, 5-FTHF, and pemetrexed. The data suggest that mutation of the R376 residue to Gln impairs proton binding which, in turn, modulates the folate-binding pocket and depresses the rate of conformational alteration of the carrier, a change that appears to be, in part, substrate dependent.
Protein tyrosine phosphatase PTPεM negatively regulates PDGF β-receptor signaling induced by high glucose and PDGF in vascular smooth muscle cells
Authors: Shimizu Hidehisa , Nakagawa Yoshimi , Murakami Chie , Aoki Naohito , Kim-Mitsuyama Shokei , Miyazaki Hitoshi
Published: August 2010

Vascular smooth muscle cell (VSMC) proliferation and migration and vascular endothelial cell (VEC) dysfunction are closely associated with the development of atherosclerosis. We previously demonstrated that protein tyrosine phosphatase ε M (PTPεM) promotes VEC survival and migration. The present study investigates the biological functions of PTPεM in VSMCs and determines whether PTPεM is implicated in diabetes-accelerated atherosclerosis. We overexpressed wild-type and inactive PTPεM and an small interfering RNA (siRNA) of PTPεM by using an adenovirus vector to investigate the effects of PTPεM upon platelet-derived growth factor (PDGF)- and high glucose (HG)-induced responses of rat VSMCs in vitro. We found that PTPεM decreased PDGF-induced DNA synthesis and migration by reducing the phosphorylation level of the PDGF β-receptor (PDGFRβ) with subsequently suppressed H2O2 generation. The HG content in the medium generated H2O2, upregulated PDGFRβ expression and its tyrosine-phosphorylation, and elevated NADPH oxidase 1 (Nox1) expression even without exogenous PDGF, all of which were downregulated by PTPεM. The PDGFR inhibitor AG1296 also blocked HG-induced Nox1 expression and H2O2 production. Moreover, HG suppressed PTPεM expression itself, which was blocked by the antioxidant N-acetyl-l-cysteine. The effects of PTPεM siRNA were the opposite of those of wild-type PTPεM. Therefore, PTPεM negatively regulates PDGFRβ-mediated signaling pathways that are crucial for the pathogenesis of atherosclerosis, and PTPεM may be involved in diabetes-accelerated atherosclerosis.
Impaired glomerular and tubular antioxidative defense mechanisms in nephrotic syndrome
Authors: Granqvist Anna , Nilsson Ulf A. , Ebefors Kerstin , Haraldsson Börje , Nyström Jenny
Published: August 2010

The molecular mechanisms behind acquired nephrotic syndrome (NS) are still largely unknown. One possible explanation for the development of proteinuria is oxidative damage to the glomerular cells. Our hypothesis was that the oxidative defense is weakened in NS, and we focused on measurements of the oxidative-antioxidative status in the glomerular and tubular parts of the nephron. Gene expression was analyzed in renal biopsies from patients with NS. In addition, to compare the acute and chronic phases of the disease, we studied puromycin-treated rats. In the biopsy material, the expression of enzymes involved in the antioxidative defense was higher in the tubulointerstitial compartment than in the glomerular cells. Real-time PCR analysis revealed a decreased glomerular expression in nephrotic kidneys for the antioxidant enzymes catalase and glutathione peroxidase-3, and -4. The tubular gene expression was downregulated for catalase, glutathione peroxidase-3, and thioredoxin reductase-1 and -2. The altered gene expression was accompanied by increased lipid peroxidation in urine. In rats, serum concentrations of ascorbyl-free radicals, measured with electron spin resonance, were elevated in the acute phase of the disease, suggesting increased oxidative stress in the circulation. In addition, we saw an increase in the plasma antioxidant capacity combined with a decreased oxidation of proteins in sera from nephrotic rats, but not from humans. In conclusion, there is a marked downregulation of several antioxidative enzymes in nephrotic kidneys, especially in glomerular structures. Our data suggest that oxidative damage to glomerular cells may contribute significantly to the course and prognosis of nephrotic syndrome.
TRPC6 channels and their binding partners in podocytes: role in glomerular filtration and pathophysiology
Authors: Dryer Stuart E. , Reiser Jochen
Published: August 2010

Loss or dysfunction of podocytes is a major cause of glomerular kidney disease. Several genetic forms of glomerular disease are caused by mutations in genes that encode structural elements of the slit diaphragm or the underlying cytoskeleton of podocyte foot processes. The recent discovery that gain-of-function mutations in Ca2+-permeable canonical transient receptor potential-6 channels (TRPC6) underlie a subset of familial forms of focal segmental glomerulosclerosis (FSGS) has focused attention on the basic cellular physiology of podocytes. Several recent studies have examined the role of Ca2+dynamics in normal podocyte function and their possible contributions to glomerular disease. This review summarizes the properties of TRPC6 and related channels, focusing on their permeation and gating properties, the nature of mutations associated with familial FSGS, and the role of TRPC channels in podocyte cell biology as well as in glomerular pathophysiology. TRPC6 interacts with several proteins in podocytes, including essential slit diaphragm proteins and mechanosensitive large-conductance Ca2+-activated K+channels. The signaling dynamics controlling ion channel function and localization in podocytes appear to be quite complex.
Multiple Ca2+-Dependent Mechanisms Regulate L-Type Ca2+Current in Retinal Amacrine Cells
Authors: Tekmen Merve , Gleason Evanna
Published: August 2010

Understanding the regulation of L-type voltage-gated Ca2+current is an important component of elucidating the signaling capabilities of retinal amacrine cells. Here we ask how the cytosolic Ca2+environment and the balance of Ca2+-dependent effectors shape native L-type Ca2+channel function in these cells. To achieve this, whole cell voltage clamp recordings were made from cultured amacrine cells under conditions that address the contribution of mitochondrial Ca2+uptake (MCU), Ca2+/calmodulin (CaM)-dependent channel inactivation (CDI), protein kinase A (PKA), and Ca2+-induced Ca2+release (CICR). Under control conditions, repeated activation of the L-type channels produces a progressive enhancement of the current. Inhibition of MCU causes a reduction in the Ca2+current amplitude that is dependent on Ca2+influx as well as cytosolic Ca2+buffering, consistent with CDI. Including the Ca2+buffer bis-( o-aminophenoxy)- N,N,N',N'-tetraacetic acid (BAPTA) internally can shift the balance between enhancement and inhibition such that inhibition of MCU can enhance the current. Inhibition of PKA can remove the enhancing effect of BAPTA suggesting that cyclic AMP-dependent phosphorylation is involved. Inhibition of CaM suppresses CDI but spares the enhancement, consistent with the substantially higher sensitivity of the Ca2+-sensitive adenylate cyclase 1 (AC1) to Ca2+/CaM. Inhibition of the ryanodine receptor reduces the current amplitude, suggesting that CICR might normally amplify the activation of AC1 and stimulation of PKA activity. These experiments reveal that the amplitude of L-type Ca2+currents in retinal amacrine cells are both positively and negatively regulated by Ca2+-dependent mechanisms.
Distinct AMPA-Type Glutamatergic Synapses in Developing Rat CA1 Hippocampus
Authors: Stubblefield Elizabeth A. , Benke Tim A.
Published: August 2010

We assessed synaptic α-amino-3-hydroxy-5-methyl-4-isoxazole propionate receptor (AMPAR) properties during synaptogenesis to describe the development of individual glutamatergic synapses on rat hippocampal CA1 principal neurons. Pharmacologically isolated AMPAR-mediated glutamatergic synaptic currents [evoked by stimulation of the Schaffer Collateral pathway, excitatory postsynaptic currents (EPSCs)], had significantly greater inward-rectification at ages P5–7 compared with P8–18. These inward rectifying EPSCs demonstrated paired-pulse dependent unblocking at positive holding potentials, consistent with voltage-dependent internal polyamine block. Measurements of paired-pulse facilitation did not support altered presynaptic properties associated with inward rectification. Using asynchronous EPSCs (aEPSCs) to analyze populations of individual synapses, we found that quantal amplitudes ( Q) increased across early postnatal development (P5-P18) and were directly modulated by increases in the number of activated receptors. Quantal AMPAR decay kinetics (aEPSC τdecays) exhibited the highest coefficient of variation (CV) from P5 to 7 and became markedly less variable at P8–18. At P5–7, faster quantal kinetics coexisted with much slower kinetics; only slower quantal kinetics were found at P8–18. This supports diverse quantal synaptic properties limited to P5–7. Multivariate cluster analysis of Q, CVτdecay, and median τdecaysupported a segregation of neurons into two distinct age groups of P5–7 and P8–18, similar to the age-related segregation suggested by inward rectification. Taken together, these findings support synaptic, calcium permeable AMPARs at a subset of synapses onto CA1 pyramidal neurons exclusively at P5–7. These distinct synapses coexist with those sharing the properties of more mature synapses. These synapses disappear after P7 as activated receptor numbers increase with age.
Regulation of AMPA Receptor Currents by Mitochondrial ATP-Sensitive K+Channels in Anoxic Turtle Neurons
Authors: Zivkovic George , Buck Leslie Thomas
Published: August 2010

Mammalian neurons rapidly undergo excitotoxic cell death during anoxia, whereas neurons from the anoxia-tolerant painted turtle survive without oxygen for hours and offer a unique model to study mechanisms to reduce the severity of cerebral stroke. An anoxia-mediated decrease in whole cell N-methyl-d-aspartate receptor and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) currents are an important part of the turtle's natural defense. Here we investigate the role of mitochondrial ATP-sensitive K+(mKATP) channels in the regulation of AMPAR. Whole cell AMPAR currents were stable over 90 min of normoxic recording; however, anoxia resulted in a 52% decrease in AMPAR currents. Pharmacological activation of mKATPchannels with diazoxide or levcromakalim resulted in a 46% decrease in normoxic AMPAR currents and the decrease was abolished with application of the antagonists 5-hydroxydecanoic acid and glibenclamide, whereas mKATPantagonists blocked the anoxia-mediated decrease. Mitochondrial KCachannel modulators responded similarly. The Ca2+-uniporter antagonist ruthenium red reduced AMPAR currents by 38% and was blocked with the agonist spermine. The calcium chelator BAPTA in the recording electrode during anoxia or diazoxide perfusion also abolished the reduction in AMPAR currents. We conclude that the mKATPchannel is involved in the anoxia-mediated down-regulation of AMPAR activity during anoxia and that it is a common mechanism to reduce glutamatergic excitability.
Linear and Nonlinear Contributions to the Visual Sensitivity of Neurons in Primate Lateral Geniculate Nucleus
Authors: Solomon Samuel G. , Tailby Chris , Cheong Soon K. , Camp Aaron J.
Published: August 2010

Several parallel pathways convey retinal signals to the visual cortex of primates. The signals of the parvocellular (P) and magnocellular (M) pathways are well characterized; the properties of other rarely encountered cell types are distinctive in many ways, but it is not clear that they can provide signals with the same fidelity. Here we study this by characterizing the temporal receptive field of neurons in the lateral geniculate nucleus of anesthetized marmosets. For each neuron, we measured the response to a flickering uniform field, and, from this, estimated the linear and nonlinear receptive fields using spike-triggered average (STA) and spike-triggered covariance (STC) analyses. As expected the response of most P-cells was dominated by the STA, but the response of most M-cells required additional nonlinear components, and these usually acted to suppress cell responses. The STC analysis showed stronger suppressive axes in suppressed-by-contrast cells, and both suppressive and excitatory axes in on-off cells. Together, the STA and the STC analyses form a model of the temporal response to a large uniform field: under this model, the information that was provided by suppressed-by-contrast cells or on-off cells approached that provided by the P- and M-cells. However, whereas P- and M-cells provided more information about luminance, the nonlinear cells provided more information about the contrast energy. This suggests that the nonlinear cells provide complimentary signals to those of P- and M-cells, with reasonably high fidelity, and may play an important role in normal visual processing.