bluuebunny/crossref_metadata_2025 huggingface dataset:
A rational approach to noise discrimination in video microscopy particle tracking
Authors: Savin Thierry , Spicer Patrick T. , Doyle Patrick S.
Published: July 2008

The authors describe a rational approach to an important step in video microscopy particle tracking called noise discrimination. Using the morphology of the brightness profiles produced by the particles, false and dubious detections are eliminated from the valid tracking data. This selection process is found to affect the spatial resolution ε and the depth zb of the tracking. Accordingly, it is shown that a stringent selection of the particles closest to the focal plane improves the spatial resolution (i.e., decreases ε) but also diminishes zb. The authors further demonstrate that the statistical accuracy is worsened by lower zb. Noise discrimination thus has a critical influence on the overall performance of the particle tracking technique.
Optical study of lateral carrier transfer in (In,Ga)As∕GaAs quantum-dot chains
Authors: Wang B. R. , Sun B. Q. , Ji Y. , Dou X. M. , Xu Z. Y. , Wang Zh. M. , Salamo G. J.
Published: July 2008

We have studied the lateral carrier transfer in a specially designed quantum dot chain structure by means of time-resolved photoluminescence (PL) and polarization PL. The PL decay time increases with temperature, following the T1∕2 law for the typical one-dimensional quantum system. The decay time depends strongly on the emission energy: it decreases as the photon energy increases. Moreover, a strong polarization anisotropy is observed. These results are attributed to the efficient lateral transfer of carriers along the chain direction.
Minority carrier lifetime in polycrystalline silicon solar cells studied by photoassisted Kelvin probe force microscopy
Authors: Takihara Masaki , Takahashi Takuji , Ujihara Toru
Published: July 2008

We have proposed a method to evaluate minority carrier lifetime through photovoltage measurements by photoassisted Kelvin probe force microscopy and have applied it to characterize a polycrystalline silicon solar cell. The results indicate that the lifetime significantly decreases in the vicinity of a grain boundary of the polycrystalline material. The photovoltage distribution around the grain boundary is also discussed by considering a contribution of both the intrinsic surface potential and the lifetime.
Room temperature Si δ-growth on Ge incorporating high-K dielectric for metal oxide semiconductor applications
Authors: Hong Augustin J. , Ogawa Masaaki , Wang Kang L. , Wang Yong , Zou Jin , Xu Zheng , Yang Yang
Published: July 2008

A low temperature Al2O3∕4 monolayer amorphous Si gate stack process was demonstrated on p-type Ge wafers using atomic layer deposition and molecular beam epitaxy. Multifrequency capacitance-voltage (C-V) and current-voltage (I-V) characteristics showed excellent electrical properties of the Pt∕Al2O3∕4 ML Si∕Ge metal oxide semiconductor capacitor. No kinks from 1MHzto4kHz and a leakage current density of 2.6×10−6A∕cm2 at 1V with an equivalent oxide thickness of 2.5nm. The interface characterization using a conductance method showed that interface trap density at the near midgap was 8×1012eV−1cm−2 and a mean capture cross section of holes was extracted to be 10−16cm2.
Improved and excellent humidity sensitivities based on KCl-doped TiO2 electrospun nanofibers
Authors: Qi Qi , Zhang Tong , Wang Lijie
Published: July 2008

Pure and KCl-doped TiO2 nanofibers have been synthesized by electrospinning and calcination technique. The measurement results by the sensors fabricated from these fibers at the working electrodes show that KCl-doped TiO2 nanofibers hold the improved humidity sensing properties with the resistance varying more than four orders of magnitude in the range of 11%–95% relative humidity, while the resistance of pure TiO2 nanofibers changes only about two orders of magnitude. An ion-controlled model has been established to explain the results further. Additionally, excellent sensing characteristics (rapid response and recovery behavior and good stability) have been also found based on KCl-doped TiO2 nanofibers, which endows our product with the potentials for humidity sensors.
Dynamic properties of InAs∕InP (311)B quantum dot Fabry–Perot lasers emitting at 1.52μm
Authors: Martinez A. , Merghem K. , Bouchoule S. , Moreau G. , Ramdane A. , Provost J.-G. , Alexandre F. , Grillot F. , Dehaese O. , Piron R. , Loualiche S.
Published: July 2008

Dynamic properties of truly three-dimensional-confined InAs∕InP quantum dot (QD) lasers obtained by molecular beam epitaxy growth on a (311)B oriented substrate are reported. The relative intensity noise and small signal modulation bandwidth experiments evidence maximum relaxation frequency of 3.8GHz with a clear relaxation oscillation peak, indicating less damping than InAs∕GaAs QD lasers. The Henry factor amounts to ∼1.8 below threshold and increases to ∼6 above threshold, which is attributed to band filling of the thick wetting layer.
Suppression of martensitic phase transition at the Ni2MnGa film surface
Authors: Pörsch P. , Kallmayer M. , Eichhorn T. , Jakob G. , Elmers H. J. , Jenkins C. A. , Felser C. , Ramesh R. , Huth M.
Published: July 2008

We investigated magnetic and structural properties at the surface of epitaxial Ni2MnGa(110) Heusler films using x-ray absorption spectroscopy and x-ray magnetic circular dichroism both in transmission and total electron yield mode. The magnetic shape memory films were prepared by dc sputtering from a stoichiometric target onto sapphire substrates at an optimized substrate temperature of 773K. X-ray diffraction confirms a (110) oriented growth on Al2O3(112¯0) and an austenite to martensite transition at 270–280K. At the surface the martensitic phase transition and the magnetization are strongly suppressed. The deviation in the surface properties is caused by a Mn deficiency near the surface.
Influence of oxygen concentration in sputtering gas on piezoelectric response of aluminum nitride thin films
Authors: Akiyama Morito , Kamohara Toshihiro , Kano Kazuhiko , Teshigahara Akihiko , Kawahara Nobuaki
Published: July 2008

The authors have investigated the influence of oxygen concentration in sputtering gas on the piezoelectric response of aluminum nitride (AlN) thin films prepared on silicon substrates. The piezoelectric response strongly depends on the oxygen concentration, and changes from +6.8to−7.0pC∕N with increasing oxygen concentration from 0% to 1.2%. The polar direction drastically inverts from the Al polarity to N polarity. When the oxygen concentration in sputtering gas was 1.2%, the oxygen concentration in the AlN films was 7at.%. Furthermore, the growth rate of the AlN films gradually decreases with increasing oxygen concentration in sputtering gas.
A nanoscale analysis of the leakage current in SiO2 breakdown
Authors: Zhang Gang , Li Xiang , Tung Chih-Hang , Pey Kin-Leong , Lo Guo-Qiang
Published: July 2008

In this work, we provide a nanoscale scheme of the leakage current in SiO2 breakdown. In combination with first-principles calculation, the leakage current is explored with the Landauer–Büttiker transport formula. Large leakage current is generated from the band gap states. The effect of oxygen vacancy is remarkable in the conduction band while almost negligible in the valence band. Our results predict that in a nanoscale metal oxide semiconductor (MOS) field-effect transistor, the leakage current in p-MOS devices is much smaller than that in n-MOS devices.
Barrier effect on hole transport and carrier distribution in InGaN∕GaN multiple quantum well visible light-emitting diodes
Authors: Liu J. P. , Ryou J.-H. , Dupuis R. D. , Han J. , Shen G. D. , Wang H. B.
Published: July 2008

Carrier distributions governed by hole transport in InGaN∕GaN multiple quantum well (MQW) visible light-emitting diodes (LEDs) were investigated using conventional blue LEDs and dual-wavelength blue-green LEDs. It was found that holes were dominantly distributed in the QW close to the p-GaN layer in LEDs with conventional MQW active regions at a current of 20mA. A decrease in the thickness or the height of the quantum-well potential barrier enhanced hole injection into the MQWs located near the n-GaN layer. Reducing the thickness of a GaN quantum-well barrier between the blue QW and green QW did not degrade the electroluminescence (EL) intensity of the LED. In contrast, reducing the potential height of the barrier with material of possibly compromised quality resulted in a degradation of the EL intensity of the LED.
Impact of oxygen incorporation at the Si3N4∕Al2O3 interface on retention characteristics for nonvolatile memory applications
Authors: Chang Man , Ju Yongkyu , Lee Joonmyoung , Jung Seungjae , Choi Hyejung , Jo Minseok , Jeon Sanghun , Hwang Hyunsang
Published: July 2008

The correlation between properties of the Si3N4∕Al2O3 interface and retention degradation was investigated for metal-alumina-nitride-oxide-silicon-type flash memory devices. The intermixed region near the Si3N4∕Al2O3 interface showed an oxygen deficiency, which was confirmed by the binding energy of Al and Si peaks from x-ray photoelectron spectroscopy analysis. This oxygen deficiency led to the enhancement of trap-assisted tunneling current. Additional ambient oxygen annealing can eliminate the oxygen deficiency at the intermixed region, which in turn can significantly reduce charge loss through the blocking oxide. With the aim of better memory characteristics, oxygen incorporation shows promise for future nonvolatile memory applications.
Pattern level assembly of Ge quantum dots on Si with focused ion beam templating
Authors: Gherasimova M. , Hull R. , Reuter M. C. , Ross F. M.
Published: July 2008

Array level assembly mechanisms are described for controlled nucleation of Ge quantum dots (QDs) on Si(100) surfaces templated by low dose focused ion beam pulses. The registration rates of QD positions with the target sites approach 100% for site separations of 100nm and above, but incomplete occupancy is observed at closer distances. We investigate the dependence of the QD array perfection on the site separation, and identify the competition between the intended nucleation sites for the supply of Ge adatoms as a key factor limiting the large area registration fidelity.
Gain and continuous-wave laser oscillation on the 1315nm atomic iodine transition pumped by an air-helium electric discharge
Authors: Woodard B. S. , Zimmerman J. W. , Benavides G. F. , Carroll D. L. , Verdeyen J. T. , Palla A. D. , Field T. H. , Solomon W. C. , Davis S. J. , Rawlins W. T. , Lee S.
Published: July 2008

Herein the authors report on the demonstration of gain and a continuous-wave laser on the 1315nm transition of atomic iodine using the energy transferred to I(P1∕22) from O2(aΔ1) produced by a radio-frequency-excited electric discharge sustained in a dry air-He–NO gas mixture. Active oxygen and nitrogen species were observed downstream of the discharge region. Downstream of the discharge, cold gas injection was employed to raise the gas density and lower the temperature of the continuous gas flow. Gain of 0.0062%cm−1 was obtained and the laser output power was 32mW in a supersonic flow cavity.
Absolute density and temperature of O(D21) in highly Ar or Kr diluted O2 plasma
Authors: Takeda Keigo , Takashima Seigo , Ito Masafumi , Hori Masaru
Published: July 2008

The absolute density and translational temperature of excited O atoms [O(D21)] in O2 surface-wave-excited plasmas (SWPs) with high Kr or Ar dilution were measured by using vacuum ultraviolet laser absorption spectroscopy. It was observed that the absolute density of O(D21) in Kr∕O2 SWP was lower than that in Ar∕O2 SWP above a pressure of 90Pa, and the O(D21) had an elevated temperature of around 2000K in the SWPs. Furthermore, the O(D21) flux was identified as a key parameter in the oxidation process. These results are very important knowledge relevant to plasma oxidation.
Synthesis and Properties of Novel Chiral Ionic Liquids from L-Proline
Authors: Gao Hong-Shuai , Hu Zhi-Guo , Wang Jian-Ji , Qiu Zhao-Fa , Fan Feng-Qiu
Published: July 2008

A novel class of chiral ionic liquids with chiral cations directly derived from natural l-proline has been synthesized and their physical properties such as melting point, thermal degradation, and specific rotation have been characterized. Further, their potential use in chiral recognition was demonstrated by studying interactions with racemic Mosher’s acid salt.
Synthesis and Structure of the Potassium Salt with Monodeprotonated 1,2,3-Tri(ethoxycarbonylpropyl)-p-t-butylcalix[6]arene
Authors: Zheng Ze-Bao , Wu Ren-Tao , Li Ji-Kun , Sun Yi-Feng
Published: July 2008

Alkylation of p-t-butylcalix[6]arene with ethyl 4-bromobutanoate in the presence of K2CO3 results in a potassium salt of the monodeprotonated 1,2,3-tri(ethoxycarbonylpropyl)-p-t-butylcalix[6]arene in high yield. X-Ray crystallographic analysis shows that this compound exists as a double partial cone conformation. The potassium ion is positioned near the centre of the cavity of the macrocycle and binds to four phenolic oxygens. Close contacts between the potassium ion and phenyl rings observed in this compound are indicative of the presence of the cation–π interaction. The molecules are connected via intermolecular K+···O interactions into infinite chains.
Synthesis and Antineoplastic Activity of Quinoline Derivatives
Authors: Zhou Qiang , Hou Jing , Li Huamin , Cui Li , Jia Han , Gong Bing , He Lan
Published: July 2008

Designed as a new series of molecules that contain the quinoline substructure, several 11H-indolo[3.2-c]quinoline derivatives were synthesized and subjected to biological evaluation. Several compounds were found to exhibit cytotoxic activity against the growth of colon (HTC-8), liver (BEL-7402), gastric (BCG-823), pulmonary gland (A549), and ovary (A2780) cancer cell lines. The structure–activity relationship of these compounds is discussed.
A Novel and Efficient Synthesis of 3,3′-Benzylidenebis(4-hydroxy-6-methylpyridin-2(1H)-one) Derivatives Through a Multi-Component Reaction Catalyzed by L-Proline
Authors: Shi Chun-Ling , Shi Da-Qing , Kim Sung Hong , Huang Zhi-Bin , Ji Min
Published: July 2008

N-Substituted pyridinone derivatives are well known for their variety of physiological activities. A series of new 3,3′-benzylidenebis(4-hydroxy-6-methylpyridin-2(1H)-one) derivatives were synthesized by a three-component reaction of an aldehyde, an aniline, and 6-methyl-4-hydroxypyran-2-one in EtOH catalyzed by l-proline. This method is novel and has the advantages of environmental friendliness, high yield, and ease of operation.
Male-derived butterfly anti-aphrodisiac mediates induced indirect plant defense
Authors: Fatouros Nina E. , Broekgaarden Colette , Bukovinszkine'Kiss Gabriella , van Loon Joop J. A. , Mumm Roland , Huigens Martinus E. , Dicke Marcel , Hilker Monika
Published: July 2008

Plants can recruit parasitic wasps in response to egg deposition by herbivorous insects–a sophisticated indirect plant defense mechanism. Oviposition by the Large Cabbage White butterfly
Pieris brassicae
on Brussels sprout plants induces phytochemical changes that arrest the egg parasitoid
Trichogramma brassicae
. Here, we report the identification of an elicitor of such an oviposition-induced plant response. Eliciting activity was present in accessory gland secretions released by mated female butterflies during egg deposition. In contrast, gland secretions from virgin female butterflies were inactive. In the male ejaculate,
P. brassicae
females receive the anti-aphrodisiac benzyl cyanide (BC) that reduces the females' attractiveness for subsequent mating. We detected this pheromone in the accessory gland secretion released by mated female butterflies. When applied onto leaves, BC alone induced phytochemical changes that arrested females of the egg parasitoid. Microarray analyses revealed a similarity in induced plant responses that may explain the arrest of
T. brassicae
to egg-laden and BC-treated plants. Thus, a male-derived compound endangers the offspring of the butterfly by inducing plant defense. Recently, BC was shown to play a role in foraging behavior of
T. brassicae
, by acting as a cue to facilitate phoretic transport by mated female butterflies to oviposition sites. Our results suggest that the anti-aphrodisiac pheromone incurs fitness costs for the butterfly by both mediating phoretic behavior and inducing plant defense.
RNA binding activity of the recessive parkinsonism protein DJ-1 supports involvement in multiple cellular pathways
Authors: van der Brug Marcel P. , Blackinton Jeff , Chandran Jayanth , Hao Ling-Yang , Lal Ashish , Mazan-Mamczarz Krystyna , Martindale Jennifer , Xie Chengsong , Ahmad Rili , Thomas Kelly J. , Beilina Alexandra , Gibbs J. Raphael , Ding Jinhui , Myers Amanda J. , Zhan Ming , Cai Huaibin , Bonini Nancy M. , Gorospe Myriam , Cookson Mark R.
Published: July 2008

Parkinson's disease (PD) is a major neurodegenerative condition with several rare Mendelian forms. Oxidative stress and mitochondrial function have been implicated in the pathogenesis of PD but the molecular mechanisms involved in the degeneration of neurons remain unclear. DJ-1 mutations are one cause of recessive parkinsonism, but this gene is also reported to be involved in cancer by promoting Ras signaling and suppressing PTEN-induced apoptosis. The specific function of DJ-1 is unknown, although it is responsive to oxidative stress and may play a role in the maintenance of mitochondria. Here, we show, using four independent methods, that DJ-1 associates with RNA targets in cells and the brain, including mitochondrial genes, genes involved in glutathione metabolism, and members of the PTEN/PI3K cascade. Pathogenic recessive mutants are deficient in this activity. We show that DJ-1 is sufficient for RNA binding at nanomolar concentrations. Further, we show that DJ-1 binds RNA but dissociates after oxidative stress. These data implicate a single mechanism for the pleiotropic effects of DJ-1 in different model systems, namely that the protein binds multiple RNA targets in an oxidation-dependent manner.
Climate-related increase in the prevalence of urolithiasis in the United States
Authors: Brikowski Tom H. , Lotan Yair , Pearle Margaret S.
Published: July 2008

An unanticipated result of global warming is the likely northward expansion of the present-day southeastern U.S. kidney stone “belt.” The fraction of the U.S. population living in high-risk zones for nephrolithiasis will grow from 40% in 2000 to 56% by 2050, and to 70% by 2095. Predictions based on a climate model of intermediate severity warming (SRESa1b) indicate a climate-related increase of 1.6–2.2 million lifetime cases of nephrolithiasis by 2050, representing up to a 30% increase in some climate divisions. Nationwide, the cost increase associated with this rise in nephrolithiasis would be $0.9–1.3 billion annually (year-2000 dollars), representing a 25% increase over current expenditures. The impact of these changes will be geographically concentrated, depending on the precise relationship between temperature and stone risk. Stone risk may abruptly increase at a threshold temperature (nonlinear model) or increase steadily with temperature change (linear model) or some combination thereof. The linear model predicts increases by 2050 that are concentrated in California, Texas, Florida, and the Eastern Seaboard; the nonlinear model predicts concentration in a geographic band stretching from Kansas to Kentucky and Northern California, immediately south of the threshold isotherm.
Life-history change in disease-ravaged Tasmanian devil populations
Authors: Jones Menna E. , Cockburn Andrew , Hamede Rodrigo , Hawkins Clare , Hesterman Heather , Lachish Shelly , Mann Diana , McCallum Hamish , Pemberton David
Published: July 2008

Changes in life history are expected when new sources of extrinsic mortality impact on natural populations. We report a new disease, devil facial tumor disease, causing an abrupt transition from iteroparity toward single breeding in the largest extant carnivorous marsupial, the Tasmanian devil (
Sarcophilus harrisii
), in which males can weigh as much as 14 kg and females 9 kg. This change in life history is associated with almost complete mortality of individuals from this infectious cancer past their first year of adult life. Devils have shown their capacity to respond to this disease-induced increased adult mortality with a 16-fold increase in the proportion of individuals exhibiting precocious sexual maturity. These patterns are documented in five populations where there are data from before and after disease arrival and subsequent population impacts. To our knowledge, this is the first known case of infectious disease leading to increased early reproduction in a mammal. The persistence of both this disease and the associated life-history changes pose questions about longer-term evolutionary responses and conservation prospects for this iconic species.
The role of microtubule movement in bidirectional organelle transport
Authors: Kulić Igor M. , Brown André E. X. , Kim Hwajin , Kural Comert , Blehm Benjamin , Selvin Paul R. , Nelson Philip C. , Gelfand Vladimir I.
Published: July 2008

We study the role of microtubule movement in bidirectional organelle transport in
Drosophila
S2 cells and show that EGFP-tagged peroxisomes in cells serve as sensitive probes of motor induced, noisy cytoskeletal motions. Multiple peroxisomes move in unison over large time windows and show correlations with microtubule tip positions, indicating rapid microtubule fluctuations in the longitudinal direction. We report the first high-resolution measurement of longitudinal microtubule fluctuations performed by tracing such pairs of co-moving peroxisomes. The resulting picture shows that motor-dependent longitudinal microtubule oscillations contribute significantly to cargo movement along microtubules. Thus, contrary to the conventional view, organelle transport cannot be described solely in terms of cargo movement along stationary microtubule tracks, but instead includes a strong contribution from the movement of the tracks.
Theoretical studies on bimolecular reaction dynamics
Authors: Clary David C.
Published: July 2008

This perspective discusses progress in the theory of bimolecular reaction dynamics in the gas phase. The examples selected show that definitive quantum dynamical computations are providing insights into the detailed mechanisms of chemical reactions.
Deficiency of Aph1B/C-γ-secretase disturbs Nrg1 cleavage and sensorimotor gating that can be reversed with antipsychotic treatment
Authors: Dejaegere T. , Serneels L. , Schäfer M. K. , Van Biervliet J. , Horré K. , Depboylu C. , Alvarez-Fischer D. , Herreman A. , Willem M. , Haass C. , Höglinger G. U. , D'Hooge R. , De Strooper B.
Published: July 2008

Regulated intramembrane proteolysis by γ-secretase cleaves proteins in their transmembrane domain and is involved in important signaling pathways. At least four different γ-secretase complexes have been identified, but little is known about their biological role and specificity. Previous work has demonstrated the involvement of the Aph1A-γ-secretase complex in Notch signaling, but no specific function could be assigned to Aph1B/C-γ-secretase. We demonstrate here that the Aph1B/C-γ-secretase complex is expressed in brain areas relevant to schizophrenia pathogenesis and that Aph1B/C deficiency causes pharmacological and behavioral abnormalities that can be reversed by antipsychotic drugs. At the molecular level we find accumulation of Nrg1 fragments in the brain of
Aph1BC
−/−
mice. Our observations gain clinical relevance by the demonstration that a Val-to-Leu mutation in the Nrg1 transmembrane domain, associated with increased risk for schizophrenia, affects γ-secretase cleavage of Nrg1. This finding suggests that dysregulation of intramembrane proteolysis of Nrg1 could increase risk for schizophrenia and related disorders.
Glucose controls CREB activity in islet cells via regulated phosphorylation of TORC2
Authors: Jansson Deidre , Ng Andy Cheuk-Him , Fu Accalia , Depatie Chantal , Al Azzabi Mufida , Screaton Robert A.
Published: July 2008

CREB is a cAMP- and calcium-responsive transcriptional activator that is required for islet beta cell proliferation and survival. Glucose and incretin hormones elicit beta cell insulin secretion and promote synergistic CREB activity by inducing the nuclear relocalization of TORC2 (also known as Crtc2), a coactivator for CREB. In islet cells under basal conditions when CREB activity is low, TORC2 is phosphorylated and sequestered in the cytoplasm by 14-3-3 proteins. In response to feeding stimuli, TORC2 is dephosphorylated, enters the nucleus, and binds to CREB located at target gene promoters. The dephosphorylation of TORC2 at Ser-171 in response to cAMP is insufficient to account for the dynamics of TORC2 localization and CREB activity in islet cells. Here, we identify Ser-275 of TORC2 as a 14-3-3 binding site that is phosphorylated under low glucose conditions and which becomes dephosphorylated by calcineurin in response to glucose influx. Dephosphorylation of Ser-275 is essential for both glucose and cAMP-mediated activation of CREB in beta cells and islets. Using a cell-based screen of 180 human protein kinases, we identified MARK2, a member of the AMPK family of Ser/Thr kinases, as a Ser-275 kinase that blocks TORC2:CREB activity. Taken together, these data provide the mechanistic underpinning for how cAMP and glucose cooperatively promote a transcriptional program critical for islet cell survival, and identifies MARK2 as a potential target for diabetes treatment.
Microsatellites as EWS/FLI response elements in Ewing's sarcoma
Authors: Gangwal Kunal , Sankar Savita , Hollenhorst Peter C. , Kinsey Michelle , Haroldsen Stephen C. , Shah Atul A. , Boucher Kenneth M. , Watkins W. Scott , Jorde Lynn B. , Graves Barbara J. , Lessnick Stephen L.
Published: July 2008

The ETS gene family is frequently involved in chromosome translocations that cause human cancer, including prostate cancer, leukemia, and sarcoma. However, the mechanisms by which oncogenic ETS proteins, which are DNA-binding transcription factors, target genes necessary for tumorigenesis is not well understood. Ewing's sarcoma serves as a paradigm for the entire class of ETS-associated tumors because nearly all cases harbor recurrent chromosomal translocations involving ETS genes. The most common translocation in Ewing's sarcoma encodes the EWS/FLI oncogenic transcription factor. We used whole genome localization (ChIP-chip) to identify target genes that are directly bound by EWS/FLI. Analysis of the promoters of these genes demonstrated a significant over-representation of highly repetitive GGAA-containing elements (microsatellites). In a parallel approach, we found that EWS/FLI uses GGAA microsatellites to regulate the expression of some of its target genes including
NR0B1
, a gene required for Ewing's sarcoma oncogenesis. The microsatellite in the
NR0B1
promoter bound EWS/FLI
in vitro
and
in vivo
and was both necessary and sufficient to confer EWS/FLI regulation to a reporter gene. Genome wide computational studies demonstrated that GGAA microsatellites were enriched close to EWS/FLI-up-regulated genes but not down-regulated genes. Mechanistic studies demonstrated that the ability of EWS/FLI to bind DNA and modulate gene expression through these repetitive elements depended on the number of consecutive GGAA motifs. These findings illustrate an unprecedented route to specificity for ETS proteins and use of microsatellites in tumorigenesis.
uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs
Authors: Ivanov Ivaylo P. , Loughran Gary , Atkins John F.
Published: July 2008

In a minority of eukaryotic mRNAs, a small functional upstream ORF (uORF), often performing a regulatory role, precedes the translation start site for the main product(s). Here, conserved uORFs in numerous ornithine decarboxylase homologs are identified from yeast to mammals. Most have noncanonical evolutionarily conserved start codons, the main one being AUU, which has not been known as an initiator for eukaryotic chromosomal genes. The AUG-less uORF present in mouse antizyme inhibitor, one of the ornithine decarboxylase homologs in mammals, mediates polyamine-induced repression of the downstream main ORF. This repression is part of an autoregulatory circuit, and one of its sensors is the AUU codon, which suggests that translation initiation codon identity is likely used for regulation in eukaryotes.
Conserved T cell receptor α-chain induces insulin autoantibodies
Authors: Kobayashi Masakazu , Jasinski Jean , Liu Edwin , Li Marcella , Miao Dongmei , Zhang Li , Yu Liping , Nakayama Maki , Eisenbarth George S.
Published: July 2008

A fundamental question is what are the molecular determinants that lead to spontaneous preferential targeting of specific autoantigens in autoimmune diseases, such as the insulin B:9–23 peptide sequence in type 1 diabetes. Anti-insulin B:9–23 T cell clones isolated from prediabetic NOD islets have a conserved Vα-segment/Jα-segment, but no conservation of the α-chain N region and no conservation of the Vβ-chain. Here, we show that the conserved T cell receptor α-chain generates insulin autoantibodies when transgenically or retrogenically introduced into mice without its corresponding Vβ. We suggest that a major part of the mystery as to why islet autoimmunity develops relates to recognition of a primary insulin peptide by a conserved α chain T cell receptor.
Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding
Authors: Zarrine-Afsar Arash , Wallin Stefan , Neculai A. Mirela , Neudecker Philipp , Howell P. Lynne , Davidson Alan R. , Chan Hue Sun
Published: July 2008

Many experimental and theoretical studies have suggested a significant role for nonnative interactions in protein folding pathways, but the energetic contributions of these interactions are not well understood. We have addressed the energetics and the position specificity of nonnative hydrophobic interactions by developing a continuum coarse-grained chain model with a native-centric potential augmented by sequence-dependent hydrophobic interactions. By modeling the effect of different hydrophobicity values at various positions in the Fyn SH3 domain, we predicted energetically significant nonnative interactions that led to acceleration or deceleration of the folding rate depending on whether they were more populated in the transition state or unfolded state. These nonnative contacts were centered on position 53 in the Fyn SH3 domain, which lies in an exposed position in a 3
10
-helix. The energetic importance of the predicted nonnative interactions was confirmed experimentally by folding kinetics studies combined with double mutant thermodynamic cycles. By attaining agreement of theoretical and experimental investigations, this study provides a compelling demonstration that specific nonnative interactions can significantly influence folding energetics. Moreover, we show that a coarse-grained model with a simple consideration of hydrophobicity is sufficient for the accurate prediction of kinetically important nonnative interactions.
Quantification of the infectious dose ofLeishmania majortransmitted to the skin by single sand flies
Authors: Kimblin Nicola , Peters Nathan , Debrabant Alain , Secundino Nagila , Egen Jackson , Lawyer Phillip , Fay Michael P. , Kamhawi Shaden , Sacks David
Published: July 2008

Leishmaniasis is transmitted between mammalian hosts by the bites of bloodsucking vector sand flies. The dose of parasites transmitted to the mammalian host has never been directly determined. We developed a real-time PCR-based method to determine the number ofLeishmania majorparasites inoculated into the ears of living mice during feeding by individual infected flies (Phlebotomus duboscqi). The number of parasites transmitted varied over a wide range in the 58 ears in whichLeishmaniawere detected and demonstrated a clear bimodal distribution. Most of the infected mice were inoculated with a low dose of <600 parasites. One in four received a higher dose of >1,000 and up to 100,000 cells. High-dose transmission was associated with a heavy midgut infection of >30,000 parasites, incomplete blood feeding, and transmission of a high percentage of the parasite load in the fly. To test the impact of inoculum size on infection outcome, we compared representative high- (5,000) and low- (100) dose intradermal needle infections in the ears of C57BL/6 mice. To mimic natural transmission, we used sand fly-derived metacyclic forms ofL. majorand preexposed the injection site to the bites of uninfected flies. Large lesions developed rapidly in the ears of mice receiving the high-dose inoculum. The low dose resulted in only minor pathology but a higher parasite titer in the chronic phase, and it established the host as an efficient long-term reservoir of infection back to vector sand flies.
Transporters of arsenite in rice and their role in arsenic accumulation in rice grain
Authors: Ma Jian Feng , Yamaji Naoki , Mitani Namiki , Xu Xiao-Yan , Su Yu-Hong , McGrath Steve P. , Zhao Fang-Jie
Published: July 2008

Arsenic poisoning affects millions of people worldwide. Human arsenic intake from rice consumption can be substantial because rice is particularly efficient in assimilating arsenic from paddy soils, although the mechanism has not been elucidated. Here we report that two different types of transporters mediate transport of arsenite, the predominant form of arsenic in paddy soil, from the external medium to the xylem. Transporters belonging to the NIP subfamily of aquaporins in rice are permeable to arsenite but not to arsenate. Mutation in OsNIP2;1 (Lsi1, a silicon influx transporter) significantly decreases arsenite uptake. Furthermore, in the rice mutants defective in the silicon efflux transporter Lsi2, arsenite transport to the xylem and accumulation in shoots and grain decreased greatly. Mutation in Lsi2 had a much greater impact on arsenic accumulation in shoots and grain in field-grown rice than Lsi1. Arsenite transport in rice roots therefore shares the same highly efficient pathway as silicon, which explains why rice is efficient in arsenic accumulation. Our results provide insight into the uptake mechanism of arsenite in rice and strategies for reducing arsenic accumulation in grain for enhanced food safety.
Preprocalcitonin signal peptide generates a cytotoxic T lymphocyte-defined tumor epitope processed by a proteasome-independent pathway
Authors: El Hage Faten , Stroobant Vincent , Vergnon Isabelle , Baurain Jean-François , Echchakir Hamid , Lazar Vladimir , Chouaib Salem , Coulie Pierre G. , Mami-Chouaib Fathia
Published: July 2008

We identified an antigen recognized on a human non-small-cell lung carcinoma by a cytotoxic T lymphocyte clone derived from autologous tumor-infiltrating lymphocytes. The antigenic peptide is presented by HLA-A2 and is encoded by the
CALCA
gene, which codes for calcitonin and for the α-calcitonin gene-related peptide. The peptide is derived from the carboxy-terminal region of the preprocalcitonin signal peptide and is processed independently of proteasomes and the transporter associated with antigen processing. Processing occurs within the endoplasmic reticulum of all tumoral and normal cells tested, including dendritic cells, and it involves signal peptidase and the aspartic protease, signal peptide peptidase. The
CALCA
gene is overexpressed in medullary thyroid carcinomas and in several lung carcinomas compared with normal tissues, leading to recognition by the T cell clone. This new epitope is, therefore, a promising candidate for cancer immunotherapy.
Quantum percolation in cuprate high-temperature superconductors
Authors: Phillips J. C.
Published: July 2008

Although it is now generally acknowledged that electron–phonon interactions cause cuprate superconductivity with
T
c
values ≈100 K, the complexities of atomic arrangements in these marginally stable multilayer materials have frustrated both experimental analysis and theoretical modeling of the remarkably rich data obtained both by angle-resolved photoemission (ARPES) and high-resolution, large-area scanning tunneling microscopy (STM). Here, we analyze the theoretical background in terms of our original (1989) model of dopant-assisted quantum percolation (DAQP), as developed further in some two dozen articles, and apply these ideas to recent STM data. We conclude that despite all of the many difficulties, with improved data analysis it may yet be possible to identify quantum percolative paths.
Carbon dioxide sequestration in deep-sea basalt
Authors: Goldberg David S. , Takahashi Taro , Slagle Angela L.
Published: July 2008

Developing a method for secure sequestration of anthropogenic carbon dioxide in geological formations is one of our most pressing global scientific problems. Injection into deep-sea basalt formations provides unique and significant advantages over other potential geological storage options, including (i) vast reservoir capacities sufficient to accommodate centuries-long U.S. production of fossil fuel CO2at locations within pipeline distances to populated areas and CO2sources along the U.S. west coast; (ii) sufficiently closed water-rock circulation pathways for the chemical reaction of CO2with basalt to produce stable and nontoxic (Ca2+, Mg2+, Fe2+)CO3infilling minerals, and (iii) significant risk reduction for post-injection leakage by geological, gravitational, and hydrate-trapping mechanisms. CO2sequestration in established sediment-covered basalt aquifers on the Juan de Fuca plate offer promising locations to securely accommodate more than a century of future U.S. emissions, warranting energized scientific research, technological assessment, and economic evaluation to establish a viable pilot injection program in the future.
Pupils' perspectives on racism and differential treatment by teachers: On stragglers, the ill and being deviant
Authors: Stevens Peter A. J.
Published: July 2008

While British educational researchers have given considerable attention to issues of racism, little attention has been given to how pupils themselves perceive differential teacher treatment and how such views relate to pupils' claims of teacher racism and racial discrimination. This article employs ethnographic data gathered from one English and two Flemish (Belgian) secondary schools to investigate pupils' perceptions of teachers' differential treatment of pupils. All schools were multi‐ethnic in character and located in inner‐city areas. The analysis of the data suggests that three ideal types of pupils were perceived as legitimate recipients of a less or more favourable teacher treatment: the ill, stragglers and deviants. This study illustrates how pupils' claims about teacher racism and racial discrimination relate to conflicts between particular pupils and their teachers over the appropriateness of their status as ill, stragglers or deviants and related role expectations. The final section discusses implications of this study for future research on processes of racism and racial discrimination in educational settings.
Sustainable Communities: a Conceited Metaphor or an Achievable Aim?
Authors: Morad Munir
Published: July 2008

The obvious problem with our modern lifestyles is that we have seemingly grown accustomed to living beyond our ecological and socio-economic means. This ‘excess’ has manifested itself in a variety of forms, ranging from environmental disasters and ‘credit crunch’ to breakdown in community cohesion.
Mixed Communities as a Means of Achieving Sustainable Communities: A Comparison Between US Experiences and UK Policy Intentions
Authors: Gullino Silvia
Published: July 2008

Current British urban policy reflects the importance of the concept of mixed communities as a means of achieving sustainable communities. This paper will argue that the relationship expressed in UK policies between ‘mixed’ and ‘sustainable’ communities tends to refer to the final stage of the (re)development process of a community (the product), with far less consideration of all the in-between phases (the process). By comparing actual experiences in two US cities with the UK's policy intentions, this paper suggests that one of the implications of the emphasis on ‘product’ rather than ‘process’ is that the aims of sustainable communities may not be realised because they may be diverted during the process and because the in-between phases themselves could be intrinsically unsustainable.
Democratic Deficit, Decentralisation and the Quest for Sustainable Communities: A Case Study of Peckham Community Council
Authors: Murat T. , Morad Munir
Published: July 2008

This study explores the impact of decentralisation and the concept of democratic deficit. The focus of the research is Peckham Community Council which is an area committee set up under the provisions of the 2000 Local Government Act (2000). The central question of this study is: can decentralisation address the democratic deficit and the quest for sustainable communities? As will be discussed, a democratic deficit is often assumed where the local community has little direct influence on local policy decisions and where regeneration is unresponsive to the community's needs, thus fostering a sense of alienation from the political system. More specifically, this research aims to examine (1) whether Peckham Community Council signifies a high level of community power and political participation (and thus a low level of alienation) and (2) plays a significant role in militating against democratic deficit by steering a regeneration agenda which responds to community needs.
The Significance of Sustainability Practices by the Malaysian Property Sector
Authors: Newell Graeme , Manaf Zaharah
Published: July 2008

Sustainability has taken on increased significance in recent years, with ‘green buildings’ becoming increasingly important to tenants, owners and property developers. The purpose of this paper is to assess the implementation of sustainable property practices by property companies in Malaysia. This will be assessed by reviewing the annual reports and websites of the listed property companies in Malaysia to assess a range of sustainability criteria to determine the significance of sustainability practices in their property development activities. Some of Malaysian property companies are seen to be leading the sustainable property agenda, although the overall property company sector in Malaysia has room for improvement to align more fully with international best practice in sustainability.
Social Housing Regeneration and the Creation of Sustainable Communities in Dublin
Authors: Redmond Declan , Russell Paula
Published: July 2008

In the past decade many social housing flat (apartment) complexes in Dublin have undergone some form of regeneration, from minor refurbishment to complete demolition and redevelopment. The context and impetus for such widespread regeneration has been the political articulation that social housing in Ireland, and especially in Dublin, is dysfunctional and unsustainable. It is contended, primarily on the basis of tenure mix arguments, that regeneration will lead to longterm social and environmental sustainability. Consequently, a number of inner city social housing complexes are currently subject to regeneration that involves their demolition and redevelopment as mixed-tenure estates through Public-Private Partnership (PPP) methods. This represents a new social and economic model of regeneration, albeit one which has generated considerable controversy. The process of regeneration has, for example, been criticised as lacking any meaningful community participation, with the mechanisms of the redevelopment process making it difficult for the community to influence the process. More generally, the creation of mixed tenure estates has been criticised as leading to a diminution of social housing in Dublin, as the social housing component in these estates has been significantly reduced. On the positive side, however, it has been argued that this model of social mixing will lead to sustainable regeneration. This paper, which is partly based on ongoing research of some case study estates in Dublin, examines and reflects on the issues of sustainable regeneration and the creation of sustainable communities.
Development and Evaluation of the Transport to Employment (T2E) Service: Overcoming Transport Barriers to Job Opportunities Leading to More Sustainable Rural Communities in Highland Scotland
Authors: Wright Steve , Nelson John D. , Cooper James M.
Published: July 2008

We highlight the specific problem of lack of transport as a significant barrier to local job seekers finding work in rural areas with a focus on the Sutherland and Easter Ross area of Highland Scotland. The paper describes the Transport to Employment (T2E) scheme: a novel solution to overcoming transport barriers to job opportunities. Evaluation of the scheme has revealed an effective, reliable and popular transport service for job seekers in rural areas that produces an excellent return on investment for funding bodies, healthy economic benefits to individuals, employers and the State. The scheme also contributes to sustainable community development, by reductions in depopulation amongst young local job seekers.
Carbon Reduction: Obligation and Opportunity at Regional and Local Levels
Authors: White Geoff , Gardner Nick , Swift Jenny
Published: July 2008

The UK government has set out a clear framework for tackling climate change which establishes a carbon reduction pathway to 2050. If, as is claimed, this is the first of its kind anywhere in the world, can the obligation it brings be converted into ‘first mover’ opportunities for businesses and the economy as a whole? This question will be of heightened importance to the English Regional Development Agencies and local authorities following the government's recently strengthened endorsement of their responsibility for economic growth and efficiency at regional and local levels. This paper considers the policy levers that can help turn the obligation into opportunity and the role that regional and local agencies can play in this through spatial planning, innovation, procurement, skills development and enterprise. It summarises and updates a previous SQW Viewpoint which can be found at www.sqw.co.uk.
Gin and Tonic or Oil and Water: The Entrepreneurial City and Sustainable Managerial Regeneration in Manchester
Authors: Leary Michael E.
Published: July 2008

This paper explores the notion of local urban policy hybridity in Manchester, England. It presents the findings of qualitative research set in the context of the parallel entrepreneurial city and sustainable regeneration debates. The research objective was to examine the extent of Manchester's conversion to the politics of the entrepreneurial city on the assumption that this signals a departure from efforts towards the city's achievement of sustainable regeneration and social equity goals. Manchester was selected because it has been held up as an iconic entrepreneurial city. The continuing entrepreneurial city debate, instigated by David Harvey in the 1980s, runs alongside that of sustainable regeneration in ways that are seen as sometimes complementary but usually contradictory. The software package NVivo 7 was used to assist with data analysis. The methodological approach was based loosely on the grounded theory approach of Strauss and Corbin: the approach of the analysis mainly followed the qualitative interpretive approach of discourse analysis. Key community strategy documents are found to interweave elements of the entrepreneurial and managerial governance discourses and also incorporate conceptual elements that have emerged recently such as a concern with crime, sustainability and community involvement. The paper provides valuable insights into the hybrid nature of Manchester's actually existing local community strategies which feature a robust adherence to the managerial mode of local urban policy.