bluuebunny/crossref_metadata_2025 huggingface dataset:
A plasma signature of human mitochondrial disease revealed through metabolic profiling of spent media from cultured muscle cells
Authors: Shaham Oded , Slate Nancy G. , Goldberger Olga , Xu Qiuwei , Ramanathan Arvind , Souza Amanda L. , Clish Clary B. , Sims Katherine B. , Mootha Vamsi K.
Published: January 2010

Mutations in either the mitochondrial or nuclear genomes can give rise to respiratory chain disease (RCD), a large class of devastating metabolic disorders. Their clinical management is challenging, in part because we lack facile and accurate biomarkers to aid in diagnosis and in the monitoring of disease progression. Here we introduce a sequential strategy that combines biochemical analysis of spent media from cell culture with analysis of patient plasma to identify disease biomarkers. First, we applied global metabolic profiling to spotlight 32 metabolites whose uptake or secretion kinetics were altered by chemical inhibition of the respiratory chain in cultured muscle . These metabolites span a wide range of pathways and include lactate and alanine, which are used clinically as biomarkers of RCD. We next measured the cell culture-defined metabolites in human plasma to discover that creatine is reproducibly elevated in two independent cohorts of RCD patients, exceeding lactate and alanine in magnitude of elevation and statistical significance. In cell culture extracellular creatine was inversely related to the intracellular phosphocreatine:creatine ratio suggesting that the elevation of plasma creatine in RCD patients signals a low energetic state of tissues using the phosphocreatine shuttle. Our study identifies plasma creatine as a potential biomarker of human mitochondrial dysfunction that could be clinically useful. More generally, we illustrate how spent media from cellular models of disease may provide a window into the biochemical derangements in human plasma, an approach that could, in principle, be extended to a range of complex diseases.
A mutation in the first intracellular loop of CACNA1A prevents P/Q channel modulation by SNARE proteins and lowers exocytosis
Authors: Serra Selma A. , Cuenca-León Ester , Llobet Artur , Rubio-Moscardo Francisca , Plata Cristina , Carreño Oriel , Fernàndez-Castillo Noèlia , Corominas Roser , Valverde Miguel A. , Macaya Alfons , Cormand Bru , Fernández-Fernández José M.
Published: January 2010

Familial hemiplegic migraine (FHM)-causing mutations in the gene encoding the P/Q Ca
2+
channel α
1A
subunit (
CACNA1A
) locate to the pore and voltage sensor regions and normally involve gain-of-channel function. We now report on a mutation identified in the first intracellular loop of CACNA1A (α
1A(A454T)
) that does not cause FHM but is associated with the absence of sensorimotor symptoms in a migraine with aura pedigree. α
1A(A454T)
channels showed weakened regulation of voltage-dependent steady-state inactivation by Ca
V
β subunits. More interestingy, A454T mutation suppressed P/Q channel modulation by syntaxin 1A or SNAP-25 and decreased exocytosis. Our findings reveal the importance of I-II loop structural integrity in the functional interaction between P/Q channel and proteins of the vesicle-docking/fusion machinery, and that genetic variation in
CACNA1A
may be not only a cause but also a modifier of migraine phenotype.
Inhibition of the K+channel KCa3.1 ameliorates T cell–mediated colitis
Authors: Di Lie , Srivastava Shekhar , Zhdanova Olga , Ding Yi , Li Zhai , Wulff Heike , Lafaille Maria , Skolnik Edward Y.
Published: January 2010

The calcium-activated K+channel KCa3.1 plays an important role in T lymphocyte Ca2+signaling by helping to maintain a negative membrane potential, which provides an electrochemical gradient to drive Ca2+influx. To assess the role of KCa3.1 channels in lymphocyte activation in vivo, we studied T cell function inKCa3.1−/−mice. CD4 T helper (i.e., Th0) cells isolated fromKCa3.1−/−mice lacked KCa3.1 channel activity, which resulted in decreased T cell receptor–stimulated Ca2+influx and IL-2 production. Although loss of KCa3.1 did not interfere with CD4 T cell differentiation, both Ca2+influx and cytokine production were impaired in KCa3.1−/−Th1 and Th2 CD4 T cells, whereas T-regulatory and Th17 function were normal. We found that inhibition of KCa3.1−/−protected mice from developing severe colitis in two mouse models of inflammatory bowel disease, which were induced by (i) the adoptive transfer of mouse naïve CD4 T cells intorag2−/−recipients and (ii) trinitrobenzene sulfonic acid. Pharmacologic inhibitors of KCa3.1 have already been shown to be safe in humans. Thus, if these preclinical studies continue to show efficacy, it may be possible to rapidly test whether KCa3.1 inhibitors are efficacious in patients with inflammatory bowel diseases such as Crohn’s disease and ulcerative colitis.
Sex, mixability, and modularity
Authors: Livnat Adi , Papadimitriou Christos , Pippenger Nicholas , Feldman Marcus W.
Published: January 2010

The assumption that different genetic elements can make separate contributions to the same quantitative trait was originally made in order to reconcile biometry and Mendelism and ever since has been used in population genetics, specifically for the trait of fitness. Here we show that sex is responsible for the existence of separate genetic effects on fitness and, more generally, for the existence of a hierarchy of genetic evolutionary modules. Using the tools developed in the process, we also demonstrate that in terms of their fitness effects, separation and fusion of genes are associated with the increase and decrease of the recombination rate between them, respectively. Implications for sex and evolution theory are discussed.
Mammalian Mst1 and Mst2 kinases play essential roles in organ size control and tumor suppression
Authors: Song Hai , Mak Kinglun Kingston , Topol Lilia , Yun Kangsun , Hu Jianxin , Garrett Lisa , Chen Yongbin , Park Ogyi , Chang Jia , Simpson R. Mark , Wang Cun-Yu , Gao Bin , Jiang Jin , Yang Yingzi
Published: January 2010

Control of organ size by cell proliferation and survival is a fundamental developmental process, and its deregulation leads to cancer. However, the molecular mechanism underlying organ size control remains elusive in vertebrates. In
Drosophila
, the Hippo (Hpo) signaling pathway controls organ size by both restricting cell growth and proliferation and promoting cell death. Here we investigated whether mammals also require the Hpo pathway to control organ size and adult tissue homeostasis. We found that
Mst1
and
Mst2
, the two mouse homologs of the
Drosophila Hpo
, control the sizes of some, but not all organs, in mice, and
Mst1
and
Mst2
act as tumor suppressors by restricting cell proliferation and survival. We show that
Mst1
and
Mst2
play redundant roles, and removal of both resulted in early lethality in mouse embryos. Importantly, tumors developed in the liver with a substantial increase of the stem/progenitor cells by 6 months after removing
Mst1
and
Mst2
postnatally. We show that Mst1 and Mst2 were required in vivo to control Yap phosphorylation and activity. Interestingly, apoptosis induced by TNFα was blocked in the
Mst1
and
Mst2
double-mutant cells both in vivo and in vitro. As TNFα is a pleiotropic inflammatory cytokine affecting most organs by regulating cell proliferation and cell death, resistance to TNFα-induced cell death may also contribute significantly to tumor formation in the absence of
Mst1
and
Mst2
.
Presynaptic m1 muscarinic receptors are necessary for mGluR long-term depression in the hippocampus
Authors: Kamsler Ariel , McHugh Thomas J. , Gerber David , Huang Shu Ying , Tonegawa Susumu
Published: January 2010

To investigate the role of M1 muscarininc acetylcholine receptors (m1 receptors) in metabotropic glutamate receptor (mGluR)-mediated long-term depression (LTD), we produced mouse lines in which deletion of the m1 gene is restricted to the forebrain (FB–m1KO) or hippocampal CA3 pyramidal neurons (CA3–m1KO). Stimulation in FB–m1KO hippocampal slices resulted in excitatory postsynaptic potentials and long-term synaptic plasticity (long-term potentiation and LTD) similar to controls. The mice were deficient in (
S
)-3,5-dihydroxyphenylglycine hydrate (DHPG)-induced mGluR LTD, which correlated with a presynaptic increase in the release of neurotransmitters. Protein kinase C (PKC) activity, which is downstream from both mGluRs and m1 receptors, was reduced in CA3 but not in CA1. The presynaptic requirement of m1 receptors was confirmed by the lack of DHPG-induced mGluR LTD in the CA1 of slices from CA3–m1KO mice. mGluR LTD was rescued by stimulating PKC activity pharmacologically in CA3–m1KO mice. These data confirm a role for PKC activation in presynaptic induction of mGluR LTD and distinguish between the roles of mGluRs and m1 receptors.
Effect of hydrogen bond cooperativity on the behavior of water
Authors: Stokely Kevin , Mazza Marco G. , Stanley H. Eugene , Franzese Giancarlo
Published: January 2010

Four scenarios have been proposed for the low-temperature phase behavior of liquid water, each predicting different thermodynamics. The physical mechanism that leads to each is debated. Moreover, it is still unclear which of the scenarios best describes water, because there is no definitive experimental test. Here we address both open issues within the framework of a microscopic cell model by performing a study combining mean-field calculations and Monte Carlo simulations. We show that a common physical mechanism underlies each of the four scenarios, and that two key physical quantities determine which of the four scenarios describes water: (
i
) the strength of the directional component of the hydrogen bond and (
ii
) the strength of the cooperative component of the hydrogen bond. The four scenarios may be mapped in the space of these two quantities. We argue that our conclusions are model independent. Using estimates from experimental data for H-bond properties the model predicts that the low-temperature phase diagram of water exhibits a liquid–liquid critical point at positive pressure.
LGP2 is a positive regulator of RIG-I– and MDA5-mediated antiviral responses
Authors: Satoh Takashi , Kato Hiroki , Kumagai Yutaro , Yoneyama Mitsutoshi , Sato Shintaro , Matsushita Kazufumi , Tsujimura Tohru , Fujita Takashi , Akira Shizuo , Takeuchi Osamu
Published: January 2010

RNA virus infection is recognized by retinoic acid-inducible gene (RIG)-I–like receptors (RLRs), RIG-I, and melanoma differentiation–associated gene 5 (MDA5) in the cytoplasm. RLRs are comprised of N-terminal caspase-recruitment domains (CARDs) and a DExD/H-box helicase domain. The third member of the RLR family, LGP2, lacks any CARDs and was originally identified as a negative regulator of RLR signaling. In the present study, we generated mice lacking LGP2 and found that LGP2 was required for RIG-I– and MDA5-mediated antiviral responses. In particular, LGP2 was essential for type I IFN production in response to picornaviridae infection. Overexpression of the CARDs from RIG-I and MDA5 in
Lgp2
−/−
fibroblasts activated the IFN-β promoter, suggesting that LGP2 acts upstream of RIG-I and MDA5. We further examined the role of the LGP2 helicase domain by generating mice harboring a point mutation of Lys-30 to Ala (
Lgp2
K30A/K30A
) that abrogated the LGP2 ATPase activity.
Lgp2
K30A/K30A
dendritic cells showed impaired IFN-β productions in response to various RNA viruses to extents similar to those of
Lgp2
−/−
cells.
Lgp2
−/−
and
Lgp2
K30A/K30A
mice were highly susceptible to encephalomyocarditis virus infection. Nevertheless, LGP2 and its ATPase activity were dispensable for the responses to synthetic RNA ligands for MDA5 and RIG-I. Taken together, the present data suggest that LGP2 facilitates viral RNA recognition by RIG-I and MDA5 through its ATPase domain.
Plant Elongator regulates auxin-related genes during RNA polymerase II transcription elongation
Authors: Nelissen Hilde , De Groeve Steven , Fleury Delphine , Neyt Pia , Bruno Leonardo , Bitonti Maria Beatrice , Vandenbussche Filip , Van Der Straeten Dominique , Yamaguchi Takahiro , Tsukaya Hirokazu , Witters Erwin , De Jaeger Geert , Houben Andreas , Van Lijsebettens Mieke
Published: January 2010

In eukaryotes, transcription of protein-encoding genes is strongly regulated by posttranslational modifications of histones that affect the accessibility of the DNA by RNA polymerase II (RNAPII). The Elongator complex was originally identified in yeast as a histone acetyltransferase (HAT) complex that activates RNAPII-mediated transcription. In
Arabidopsis thaliana
, the Elongator mutants
elo1
,
elo2
, and
elo3
with decreased leaf and primary root growth due to reduced cell proliferation identified homologs of components of the yeast Elongator complex, Elp4, Elp1, and Elp3, respectively. Here we show that the Elongator complex was purified from plant cell cultures as a six-component complex. The role of plant Elongator in transcription elongation was supported by colocalization of the HAT enzyme, ELO3, with euchromatin and the phosphorylated form of RNAPII, and reduced histone H3 lysine 14 acetylation at the coding region of the
SHORT HYPOCOTYL 2
auxin repressor and the
LAX2
auxin influx carrier gene with reduced expression levels in the
elo3
mutant. Additional auxin-related genes were down-regulated in the transcriptome of
elo
mutants but not targeted by the Elongator HAT activity showing specificity in target gene selection. Biological relevance was apparent by auxin-related phenotypes and marker gene analysis. Ethylene and jasmonic acid signaling and abiotic stress responses were up-regulated in the
elo
transcriptome and might contribute to the pleiotropic
elo
phenotype. Thus, although the structure of Elongator and its substrate are conserved, target gene selection has diverged, showing that auxin signaling and influx are under chromatin control.
Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes
Authors: Gresham David , Curry Bo , Ward Alexandra , Gordon D. Benjamin , Brizuela Leonardo , Kruglyak Leonid , Botstein David
Published: January 2010

The use of DNA microarrays to identify nucleotide variation is almost 20 years old. A variety of improvements in probe design and experimental conditions have brought this technology to the point that single-nucleotide differences can be efficiently detected in unmixed samples, although developing reliable methods for detection of mixed sequences (e.g., heterozygotes) remains challenging. Surprisingly, a comprehensive study of the probe design parameters and experimental conditions that optimize discrimination of single-nucleotide polymorphisms (SNPs) has yet to be reported, so the limits of this technology remain uncertain. By targeting 24,549 SNPs that differ between two
Saccharomyces cerevisiae
strains, we studied the effect of SNPs on hybridization efficiency to DNA microarray probes of different lengths under different hybridization conditions. We found that the critical parameter for optimization of sequence discrimination is the relationship between probe melting temperature (T
m
) and the temperature at which the hybridization reaction is performed. This relationship can be exploited through the design of microarrays containing probes of equal T
m
by varying the length of probes. We demonstrate using such a microarray that we detect >90% homozygous SNPs and >80% heterozygous SNPs using the SNPScanner algorithm. The optimized design and experimental parameters determined in this study should guide DNA microarray designs for applications that require sequence discrimination such as mutation detection, genotyping of unmixed and mixed samples, and allele-specific gene expression. Moreover, designing microarray probes with optimized sensitivity to mismatches should increase the accuracy of standard microarray applications such as copy-number variation detection and gene expression analysis.
Relevant use of Klotho in FGF19 subfamily signaling system in vivo
Authors: Tomiyama Ken-ichi , Maeda Ryota , Urakawa Itaru , Yamazaki Yuji , Tanaka Tomohiro , Ito Shinji , Nabeshima Yoko , Tomita Tsutomu , Odori Shinji , Hosoda Kiminori , Nakao Kazuwa , Imura Akihiro , Nabeshima Yo-ichi
Published: January 2010

α-Klotho (α-Kl) and its homolog, β-Klotho (β-Kl) are key regulators of mineral homeostasis and bile acid/cholesterol metabolism, respectively. FGF15/ humanFGF19, FGF21, and FGF23, members of the FGF19 subfamily, are believed to act as circulating metabolic regulators. Analyses of functional interactions between α- and β-Kl and FGF19 factors in wild-type,
α-kl
−/−
, and
β-kl
−/−
mice revealed a comprehensive regulatory scheme of mineral homeostasis involving the mutually regulated positive/negative feedback actions of α-Kl, FGF23, and 1,25(OH)
2
D and an analogous regulatory network composed of β-Kl, FGF15/humanFGF19, and bile acids that regulate bile acid/cholesterol metabolism. Contrary to in vitro data, β-Kl is not essential for FGF21 signaling in adipose tissues in vivo, because (
i
) FGF21 signals are transduced in the absence of β-Kl, (
ii
) FGF21 could not be precipitated by β-Kl, and (
iii
) essential phenotypes in
Fgf21
−/−
mice (decreased expressions of
Hsl
and
Atgl
in WAT) were not replicated in
β-kl
−/−
mice. These findings suggest the existence of Klotho-independent FGF21 signaling pathway(s) where undefined cofactors are involved. One-to-one functional interactions such as α-Klotho/FGF23, β-Klotho/FGF15 (humanFGF19), and undefined cofactor/FGF21 would result in tissue-specific signal transduction of the FGF19 subfamily.
Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands
Authors: Boehr David D. , McElheny Dan , Dyson H. Jane , Wright Peter E.
Published: January 2010

Enzyme catalysis can be described as progress over a multi-dimensional energy landscape where ensembles of interconverting conformational substates channel the enzyme through its catalytic cycle. We applied NMR relaxation dispersion to investigate the role of bound ligands in modulating the dynamics and energy landscape of
Escherichia coli
dihydrofolate reductase to obtain insights into the mechanism by which the enzyme efficiently samples functional conformations as it traverses its reaction pathway. Although the structural differences between the occluded substrate binary complexes and product ternary complexes are very small, there are substantial differences in protein dynamics. Backbone fluctuations on the μs-ms timescale in the cofactor binding cleft are similar for the substrate and product binary complexes, but fluctuations on this timescale in the active site loops are observed only for complexes with substrate or substrate analog and are not observed for the binary product complex. The dynamics in the substrate and product binary complexes are governed by quite different kinetic and thermodynamic parameters. Analogous dynamic differences in the E:THF:NADPH and E:THF:NADP
+
product ternary complexes are difficult to rationalize from ground-state structures. For both of these complexes, the nicotinamide ring resides outside the active site pocket in the ground state. However, they differ in the structure, energetics, and dynamics of accessible higher energy substates where the nicotinamide ring transiently occupies the active site. Overall, our results suggest that dynamics in dihydrofolate reductase are exquisitely “tuned” for every intermediate in the catalytic cycle; structural fluctuations efficiently channel the enzyme through functionally relevant conformational space.
Differential effects and rates of normal aging in cerebellum and hippocampus
Authors: Woodruff-Pak Diana S. , Foy Michael R. , Akopian Garnik G. , Lee Ka Hung , Zach Jordan , Nguyen Kim Phuong Thi , Comalli David M. , Kennard John A. , Agelan Alexis , Thompson Richard F.
Published: January 2010

Cognitive functions show many alternative outcomes and great individual variation during normal aging. We examined learning over the adult life span in CBA mice, along with morphological and electrophysiological substrates. Our aim was to compare cerebellum-dependent delay eyeblink classical conditioning and hippocampus-dependent contextual fear conditioning in the same animals using the same conditioned and unconditioned stimuli for eyeblink and fear conditioning. In a subset of the behaviorally tested mice, we used unbiased stereology to estimate the total number of Purkinje neurons in cerebellar cortex and pyramidal neurons in the hippocampus. Several forms of synaptic plasticity were assessed at different ages in CBA mice: long-term depression (LTD) in both cerebellum and hippocampus and NMDA-mediated long-term potentiation (LTP) and voltage-dependent calcium channel LTP in hippocampus. Forty-four CBA mice tested at one of five ages (4, 8, 12, 18, or 24 months) demonstrated statistically significant age differences in cerebellum-dependent delay eyeblink conditioning, with 24-month mice showing impairment in comparison with younger mice. These same CBA mice showed no significant differences in contextual or cued fear conditioning. Stereology indicated significant loss of Purkinje neurons in the 18- and 24-month groups, whereas pyramidal neuron numbers were stable across age. Slice electrophysiology recorded from an additional 48 CBA mice indicated significant deficits in LTD appearing in cerebellum between 4 and 8 months, whereas 4- to 12-month mice demonstrated similar hippocampal LTD and LTP values. Our results demonstrate that processes of aging impact brain structures and associated behaviors differentially, with cerebellum showing earlier senescence than hippocampus.
Web‐StrabNet: A Web‐Based Expert System for the Differential Diagnosis of Vertical Strabismus (Squint)
Authors: Fisher A. C. , Lake S. P. , Cunningham I. P. , Chandna A.
Published: January 2010

A squint, also known as strabismus, is a condition where the eyes are misaligned because of incorrect balance in the controlling eye muscles. This may result from muscular, neuromuscular or purely mechanical factors. An affected eye will have either predominating vertical or horizontal deviation. Vertical deviations are usually classified into eight classes (diagnoses) and horizontal into 10. The present work considers only the former but extension to the latter is straightforward.

The differential diagnosis of strabismus is usually achieved in the prism cover test (PCT). A range of test prisms is presented to the eye and the resulting deviation in a particular direction of gaze is observed. In the full PCT, 10 positions of gaze are considered: in each position there are, say, 40 prisms of plus and minus power to investigate. The problem can be expressed as the inference 1‐of‐8 diagnoses in the output space from an input space of 10 parameters each with a resolution of 1‐in‐80. However, in the majority of clinical examinations, the corner‐most positions of gaze are difficult to assess, particularly in children. Therefore, frequently the 6‐position subset is reported requiring a corresponding reduction in the input space dimensions of 10 to 6. Web‐StrabNet© is an expert system for the differential diagnosis of strabismus based on parallel instances of multi‐layer perceptrons trained on exemplar data generated in consensus by two clinical experts. This machine expert is programmed in MatLab™ and is freely available as an Internet website (www.strabnet.com) which uses MatSOAP©, an XML/SOAP accessible automation server running a number of simultaneous MatLab instances.

StrabNet achieves diagnostic accuracies of 100 and >94% with artificial data and typically ∼99 and ∼99% in clinical data‐sets for the 10‐position and 6‐position subset PCT′s, respectively.
Neuropilin-2 mediates VEGF-C–induced lymphatic sprouting together with VEGFR3
Authors: Xu Yunling , Yuan Li , Mak Judy , Pardanaud Luc , Caunt Maresa , Kasman Ian , Larrivée Bruno , del Toro Raquel , Suchting Steven , Medvinsky Alexander , Silva Jillian , Yang Jian , Thomas Jean-Léon , Koch Alexander W. , Alitalo Kari , Eichmann Anne , Bagri Anil
Published: January 2010

Vascular sprouting is a key process-driving development of the vascular system. In this study, we show that neuropilin-2 (Nrp2), a transmembrane receptor for the lymphangiogenic vascular endothelial growth factor C (VEGF-C), plays an important role in lymphatic vessel sprouting. Blocking VEGF-C binding to Nrp2 using antibodies specifically inhibits sprouting of developing lymphatic endothelial tip cells in vivo. In vitro analyses show that Nrp2 modulates lymphatic endothelial tip cell extension and prevents tip cell stalling and retraction during vascular sprout formation. Genetic deletion of Nrp2 reproduces the sprouting defects seen after antibody treatment. To investigate whether this defect depends on Nrp2 interaction with VEGF receptor 2 (VEGFR2) and/or 3, we intercrossed heterozygous mice lacking one allele of these receptors. Double-heterozygous nrp2vegfr2 mice develop normally without detectable lymphatic sprouting defects. In contrast, double-heterozygote nrp2vegfr3 mice show a reduction of lymphatic vessel sprouting and decreased lymph vessel branching in adult organs. Thus, interaction between Nrp2 and VEGFR3 mediates proper lymphatic vessel sprouting in response to VEGF-C.
Drosophila Kelch functions with Cullin-3 to organize the ring canal actin cytoskeleton
Authors: Hudson Andrew M. , Cooley Lynn
Published: January 2010

Drosophila melanogaster Kelch (KEL) is the founding member of a diverse protein family defined by a repeated sequence motif known as the KEL repeat (KREP). Several KREP proteins, including Drosophila KEL, bind filamentous actin (F-actin) and contribute to its organization. Recently, a subset of KREP proteins has been shown to function as substrate adaptor proteins for cullin-RING (really interesting new gene) ubiquitin E3 ligases. In this study, we demonstrate that association of Drosophila KEL with Cullin-3, likely in a cullin-RING ligase, is essential for the growth of Drosophila female germline ring canals. These results suggest a role for protein ubiquitylation in the remodeling of a complex F-actin cytoskeletal structure.
Contrasting characteristics of sub-microsecond pulsed atmospheric air and atmospheric pressure helium–oxygen glow discharges
Authors: Walsh J L , Liu D X , Iza F , Rong M Z , Kong M G
Published: January 2010

Glow discharges in air are often considered to be the ultimate low-temperature atmospheric pressure plasmas for numerous chamber-free applications. This is due to the ubiquitous presence of air and the perceived abundance of reactive oxygen and nitrogen species in air plasmas. In this paper, sub-microsecond pulsed atmospheric air plasmas are shown to produce a low concentration of excited oxygen atoms but an abundance of excited nitrogen species, UV photons and ozone molecules. This contrasts sharply with the efficient production of excited oxygen atoms in comparable helium–oxygen discharges. Relevant reaction chemistry analysed with a global model suggests that collisional excitation of O2 by helium metastables is significantly more efficient than electron dissociative excitation of O2, electron excitation of O and ion–ion recombination. These results suggest different practical uses of the two oxygen-containing atmospheric discharges, with air plasmas being well suited for nitrogen and UV based chemistry and He–O2 plasmas for excited atomic oxygen based chemistry.
Direct and indirect electrocaloric measurements using multilayer capacitors
Authors: Kar-Narayan S , Mathur N D
Published: January 2010

We report the discovery of serendipitous electrocaloric (EC) effects in commercial multilayer capacitors based on ferroelectric BaTiO3. Direct thermometry records ∼0.5 K changes due to 300 kV cm−1, over a wide range of temperatures near and above room temperature. Similar results are obtained indirectly, via thermodynamic analysis of ferroelectric hysteresis loops. We compare and contrast these two results. Optimized EC multilayer capacitors could find applications in future cooling technologies.
Quantum dot micropillars
Authors: Reitzenstein S , Forchel A
Published: January 2010

This topical review provides an overview of quantum dot micropillars and their application in cavity quantum electrodynamics (cQED) experiments. The development of quantum dot micropillars is motivated by the study of fundamental cQED effects in solid state and their exploitation in novel light sources. In general, light–matter interaction occurs when the dipole of an emitter couples to the ambient light field. The corresponding coupling strength is strongly enhanced in the framework of cQED when the emitter is located inside a low mode volume microcavity providing three-dimensional photon confinement on a length scale of the photon wavelength. In addition, coherent coupling between light and matter, which is essential for applications in quantum information processing, can be achieved when dissipative losses, predominantly due to photon leakage out of the cavity, are strongly reduced. In this paper, we will demonstrate that high-quality, low mode volume quantum dot micropillars represent an excellent system for the observation of cQED effects. In the first part the fabrication and the technological aspects of quantum dot micropillars will be discussed with a focus on the AlGaAs material system. The discussion involves the epitaxial growth and the processing of optically as well as electrically driven micropillar structures. Moreover, micropillars realized in alternative material systems and other resonator geometries will be addressed briefly. The second part will focus on the optical characterization of micropillar cavities with respect to their mode structure and the quality (Q) factor for different device geometries and resonator layouts. In the final part, we will present cQED experiments with quantum dot micropillars. Here, weak and strong coupling effects in the framework of cQED will be presented. These effects are strongly related to possible applications of quantum dot micropillars, such as single photon sources and low threshold microlasers, which will also be discussed. The paper will close with an outlook on current and future developments and a summary.
Thermal effects induced lateral head shift of thermal flying height control perpendicular magnetic recording head
Authors: Chen Y J , Leong S H , Huang T L , Ho H W , Ng V , Phang J C H
Published: January 2010

In this paper, we report a lateral shift of the read/write head due to thermal actuated protrusion by heating currents as well as writing currents as experimentally observed by atomic force microscopy. It was found that the shift amplitude is approximately proportional to the heating power within working range before saturation, which is consistent with the relationship between reduction of flying height and heating power. Scanning thermal microscopy (SThM) was further used to measure the magnitude of temperature change before and after thermal activation as well as the localized temperature distribution around the active region. The measured temperature change as large as ∼66 K by SThM gave a reasonable explanation for the observed significant lateral shift for non-flying conditions (as large as ∼758 nm along the down-track direction and ∼347 nm along the cross-track direction for heater power ∼16 mW). The asymmetry in fabricated head structures/heating profiles of the working head is proposed to be the cause of the observed lateral shift. The thermal activation induced off-track and down-track effect and the asymmetry may need to be considered in the design of thermal actuated flying height control and in accurate positioning control as areal density of disks increases.
Effect of Zn interstitials on the magnetic and transport properties of bulk Co-doped ZnO
Authors: Shah Lubna R , Zhu Hao , Wang W G , Ali Bakhtyar , Zhu Tao , Fan Xin , Song Y Q , Wen Q Y , Zhang H W , Shah S Ismat , Xiao John Q
Published: January 2010

We have demonstrated that the bound magnetic polaron model is responsible for ferromagnetism in Co–ZnO semiconductors, where the carriers are provided by the interstitial zinc (Zn
i
). Our experiment is unique since by changing the temperature, we are able to cross the carrier concentration threshold above which a long-range ferromagnetic order is established. Consequently, the ferromagnetic order is observed at room temperature but is weakened at temperatures below 100 K. To support our conclusion we have performed a systematic investigation on the structural, magnetic and transport properties which all give consistent results in the context of our proposed two-region model, i.e. (a) a Zn
i
layer where carriers are sufficient to couple Co ions ferromagnetically and (b) a region with little carriers that remain in a paramagnetic state.
Dependence of the organic nonvolatile memory performance on the location of ultra-thin Ag film
Authors: Jiao Bo , Wu Zhaoxin , He Qiang , Tian Yuan , Mao Guilin , Hou Xun
Published: January 2010

We demonstrated organic nonvolatile memory devices based on 4,4′,4″-tris[N-(3-methylphenyl)-N-phenylamino] triphenylamine (m-MTDATA) inserted by an ultra-thin Ag film. The memory devices with different locations of ultra-thin Ag film in m-MTDATA were investigated, and it was found that the location of the Ag film could affect the performance of the organic memory, such as ON/OFF ratio, retention time and cycling endurance. When the Ag film was located at the ITO/m-MTDATA interface, the largest ON/OFF ratio (about 105) could be achieved, but the cycling endurance was poor. When the Ag film was located in the middle region of the m-MTDATA layer, the ON/OFF ratios came down by about 103, but better performance of cycling endurance was exhibited. When the Ag film was located close to the Al electrode, the ON/OFF ratios and the retention time of this device decreased sharply and the bistable phenomenon almost disappeared. Our works show a simple approach to improve the performance of organic memory by adjusting the location of the metal film.
Effect of ionic liquid-templated mesoporous anatase TiO2 on performance of dye-sensitized solar cell
Authors: Han C C , Lin Y P , Ho S Y , Lai Y C , Chen S Y , Huang J , Chen-Yang Y W
Published: January 2010

In this study, the mesoporous anatase TiO2, TBF4, is synthesized by sol–gel polymerization using 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4] as the template. The 450 °C-calcined TBF4 is found maintaining a mesoporous structure with a morphology that benefits dye adsorption and electrolyte diffusion. A series of dye-sensitized electrodes are prepared with a combination of the as-prepared TBF4 and P25, a commercial TiO2. It is found that the short-circuit photocurrent (J
sc) and open-circuit photovoltage (V
oc) of the TBF4-containing electrodes are remarkably increased with the content of TBF4. The improvement is ascribed to an increase in the amount of dye molecules adsorbed and prolongation of the electron lifetimes (τeff). The highest light-to-electricity conversion efficiency (η) of the dye-sensitized solar cell is obtained from that prepared with the pure TBF4 electrode and is about 60% higher than that prepared with the pure P25 electrode under the same condition.
Rubbing effects on the structural and optical properties of poly(3-hexylthiophene) films
Authors: Abbas M , D'Amico F , Ali M , Mencarelli I , Setti L , Bontempi E , Gunnella R
Published: January 2010

Steady state photoconductivity and x-ray diffraction combined with optical and electronic spectroscopies were applied to study spin coated poly(3-hexylthiophene) (P3HT) films mechanically rubbed using a teflon bar. As expected, photoconductivity evidenced a strong increase in the photo-response along the rubbing direction. But, while rubbing during annealing at a temperature of 70 °C resulted in a sizeable photocurrent anisotropy along the direction parallel or perpendicular to the rubbing, the samples rubbed at room temperature (RT) showed an isotropic and comparatively stronger enhancement of absorption and photoconductivity spectral features. According to these observations, rubbing at RT resulted in a significant increase in local order and macroscopic alignment of the film, while a higher degree of global order but with a relaxed local structure was obtained after rubbing at 70 °C.
Flux of multiple charged metal ions of high energy from plasma produced by a moderate energy laser pulse
Authors: Romanov I V , Brantov A V , Rupasov A A , Shikanov A S , Paperny V L , Moorti A , Bhat R K , Naik P A , Gupta P D
Published: January 2010

Studies of the energy spectrum and charge state distribution of ions produced from an Al target irradiated with a laser pulse of moderate energy (90 mJ) and light intensity (4.2 × 1012 W cm−2) and of 27 ps pulse duration are presented. It is established that highly charged ions of the target material up to Al11+ are emitted from the laser produced plasma and evidence of the presence of Al12+ ions is also established. The maximum of the bulk of ion energy distributions approaches 7 keV/Z, which exceeds the values typically observed earlier in plasma produced by laser radiation of the intensity mentioned above. Theoretical examination of the experimental results reveals that the relatively high ion energies can be explained by the specific conditions of the experiments, namely the relatively large diameter of focal spot of the laser beam, appropriate length of the laser pulse, and so on.
Preparation and properties of vanadium-doped TiO2 photocatalysts
Authors: Zhou Wenfang , Liu Qingju , Zhu Zhongqi , Zhang Ji
Published: January 2010

The vanadium-doped TiO2 nanoparticles were prepared by a sol–gel method with Ti(OBu)4 as a precursor. The powders were characterized by XRD, FT-IR, TEM, XPS and UV–Vis absorption spectrum. The photocatalytic activity of the powders for methyl orange degradation was investigated under a fluorescent lamp. The results show that the doping V presents mainly in the form of V5+, and vanadium doping can restrain the crystal growth and promote the phase transfer from anatase to rutile. Vanadium doping can widen the light absorption range of TiO2, and the absorption threshold wavelength is red shifted from 380 nm to about 650 nm. As a result, the photocatalytic activity of the V–TiO2 nanoparticles is higher than that of P25 under the fluorescent lamp.
Hydrolysis and ion exchange of titania nanoparticles towards large-scale titania and titanate nanobelts for gas sensing applications
Authors: Bela Somaiah , Wong Andrew See Weng , Ho Ghim Wei
Published: January 2010

One-dimensional titanate and titania nanostructures are prepared by hydrothermal method from titania nanoparticles precursor via hydrolysis and ion exchange processes. The formation mechanism and the reaction process of the nanobelts are elucidated. The effects of the NaOH concentration, HCl leaching duration and the calcination temperature on the morphology and chemical composition of the produced nanobelts are investigated. Na+ ions of the titanate nanobelts can be effectively removed by longer acid leaching and neutralization process and transformed into metastable hydrogen titanate compound. A hybrid hydrogen titanate and anatase titania nanobelts can be obtained under dehydration process of 500 °C. The nanobelts are produced in gram quantities and easily made into nanostructure paper for the bulk study on their electrical and sensing properties. The sensing properties of the nanobelts sheet are tested and exhibited response to H2 gas.
Thickness dependence of structure, tunable and pyroelectric properties of laser-ablated Ba(Zr0.25Ti0.75)O3 thin films
Authors: Doan T M , Lu L , Lai M O
Published: January 2010

Ba(Zr0.25Ti0.75)O3 thin films are grown on LaNiO3-coated SiO2/Si substrates with thicknesses varying from 100 to 700 nm. The films show (0 0 l)-preferred orientation which gradually decreases with an increase in (0 1 1) orientation due to competitions between interfacial energies and lattice constraint from LaNiO3 template. The out-of-plane lattice parameter d increases or relaxes towards the bulk value, causing a reduction in the in-plane tensile strain and a shift in the ferroelectric–paraelectric phase transition region to room temperature. Orientation, lattice strain and particularly the film/electrode interface are the reasons for the increased dielectric constant εr(0) with thickness. The reduction in tensile strain in combination with enhancement in εr(0) has resulted in an increase in tunability n
r, while the shift of phase transition region in combination with enhancement of εr(0) in this region has resulted in an increase in pyroelectric coefficient p.
Transparent and conductive oxide films of the perovskite LaxSr1−xSnO3 (x ⩽ 0.15): epitaxial growth and application for transparent heterostructures
Authors: Wang Haifeng , Jiao Xingli , Liu Qinzhuang , Xuan Xiaofeng , Chen Feng , Wu Wenbin
Published: January 2010

Transparent and conductive oxide (TCO) films with a cubic perovskite structure, lanthanum-doped strontium stannate La
x
Sr1−x
SnO3 (x = 0–0.15) (LSSO), have been grown epitaxially on SrTiO3(0 0 1) substrates by the pulsed laser deposition method. The doping concentration and growth parameters were optimized based on the high-resolution x-ray diffraction and electric transport measurements. We found that the optimum doping level is around x = 0.07, and the epitaxial films can be grown at temperatures as low as 600 °C and in atmospheres compatible with many other perovskite oxide films. They are n-type TCO films, showing high optical transmittance in the visible range with a direct allowed band gap of 4.65 eV, and a weak metallic transport behaviour with a low resistivity of ∼4.0 mΩ cm within 10–300 K. Due to a very close lattice match with the ferroelectric Pb(Zr0.52Ti0.48)O3 (PZT) and multiferroic BiFeO3 (BFO), all-perovskite LSSO(Pt)PZT(BFO)/LSSO capacitors and p-PZT(⩽20 nm)/n-LSSO [p-BFO (100 nm)/n-LSSO] p–n junctions have also been fabricated and characterized. The square polarization versus electric-field hysteresis loops, good rectifying characteristics, high optical transmittance, as well as the epitaxial growth exhibited by the heterostructures, strongly suggest that the LSSO films are potential candidates for use in transparent thin-film devices.
Deformation distribution maps of β-HMX molecular crystals
Authors: Zamiri Amir Reza , De Suvranu
Published: January 2010

β-HMX, extensively used as an energetic material, exists as monoclinic molecular crystals which exhibit highly nonlinear anisotropic mechanical behaviour. To explain the unique features of the deformation behaviour of β-HMX, we have developed the so-called ‘deformation distribution maps’ (DDMs) based on a single crystal plasticity model based on empirical data. These DDMs reveal that under uniaxial compression there are ten deformation fibres along which β-HMX exhibits maximum plastic deformation and six other deformation fibres along which the deformation response is mostly elastic. These DDMs are applicable to a wider class of molecular crystals for not only understanding their complex mechanical response, but also to serve as important design tools.
Thermal and electrical transport properties of VA-element doped Pb9.6M0.2Te10−xSex (M = Sb, Bi) thermoelectric materials
Authors: Chen Y , Zhu T J , Yang S H , Yu C , Zhao X B
Published: January 2010

The VA-element doped Pb9.6
M
0.2Te10−x
Se
x
(M = Sb, Bi, x = 6, 7, 8) alloys have been synthesized and their thermoelectric (TE) properties were systematically investigated. The power factors of Sb- and Bi-doped samples reached ∼1.4 mW m−1 K−2 and 0.8–1.0 mW m−1 K−2, respectively, while the thermal conductivities decreased to 0.75 W m−1 K−1 and 0.8 W m−1 K−1 as the temperature was increased to 700 K. Due to the rather low thermal conductivity, a highest ZT of ∼1.05 has been attained for the Sb-doped sample, indicating that the VA element is another effective dopant besides the classical dopant iodine. The results show that the introduction of VA element is beneficial to improve TE performance of PbTe-based materials.
Photocatalytic, optical and electrical properties of copper-doped zinc sulfide thin films
Authors: Mohamed S H
Published: January 2010

Thin films of ZnS : Cu nanoparticles were prepared by electron beam evaporation on glass substrates. The Cu content was varied from 0 to 9 at%. XRD examination of the as-prepared films revealed the presence of polycrystalline hexagonal ZnS with preferred orientation depending on the Cu content. As annealing was carried out, grain growth was observed and a new orthorhombic copper sulfate phase emerged. The photocatalytic behaviour of ZnS : Cu was mainly evaluated by measuring the decomposition of methylene blue. The photocatalytic activities were found to decrease with increasing Cu content as well as with increasing annealing temperature. The optical transmittance and reflectance measurements were performed using a spectrophotometer. The spectral transmittance was decreased and the band gap energy was shifted from 3.45 to 3.20 eV with increasing Cu content. The refractive index was determined from transmittance using the Swanepoel method. The refractive index was found to depend on Cu content as well as annealing temperature. A strong decrease in room temperature resistivity was obtained with increasing Cu content. The obtained results are interesting and may find applications in photodegradation of pollutants and future display devices.
Thermally stable hyperbranched polyether-based polymer electrolyte for lithium-ion batteries
Authors: Wu Feng , Feng Ting , Wu Chuan , Bai Ying , Ye Lin , Chen Junzheng
Published: January 2010

A thermally stable polymer matrix, comprising hyperbranched polyether PHEMO (poly(3-{2-[2-(2-hydroxyethoxy) ethoxy] ethoxy}methyl-3′-methyloxetane)) and PVDF-HFP (poly(vinylidene fluoride-hexafluoropropylene)), has been successfully prepared for applications in lithium-ion batteries. This type of polymer electrolyte has been made by adding different amounts of lithium bis(oxalate)borate (LiBOB) to the polymer matrix. Its thermal and structural properties were measured using differential scanning calorimetry and x-ray diffraction. Experimental results show that the polymer electrolyte system possesses good thermal stability, with a decomposition temperature above 420 °C. The ionic conductivity of the polymer electrolyte system is dependent on the lithium salt content, reaching a maximum of 1.1 × 10−5 S cm−1 at 30 °C and 2.3 × 10−4 S cm−1 at 80 °C when doped with 10 wt% LiBOB.