bluuebunny/crossref_metadata_2025 huggingface dataset:
An effect of “scattering by absorption” observed in near-infrared properties of nanoporous silica
Authors: Dombrovsky Leonid , Lallich Sylvain , Enguehard Franck , Baillis Dominique
Published: April 2010

The obtained spectroscopic data for absorption and scattering characteristics of nanoporous silica in the wavelength range from 0.25 to 7 μm are analyzed on the basis of the Mie theory. It is shown that aggregates of primary nanoparticles are responsible for relatively high scattering in the short-wave range from 0.25 to 1.4 μm. But the presence of the aggregates and micron-size cracks in the samples cannot explain unusual behavior of scattering in the long-wave part of the spectral range. The attention of the authors is focused on understanding of strong scattering peaks observed at exactly the same wavelengths as the infrared absorption peaks of bulk silica: at λ=2.9, 5.3, and 6.1 μm. The known physical effect of “scattering by absorption” is considered as a source of these scattering peaks. It means that absorption centers are assumed to be not uniformly distributed in the nanoporous matrix but collected in some micron-size regions. The estimates based on this hypothesis are supported by the fact that near-infrared absorption peaks are produced by silanol groups which may be nonuniformly distributed in the hydroxylated nanoporous silica.
Non-Fickian particle diffusion in confined plasmas and the transition from diffusive transport to density waves propagation
Authors: Vázquez Federico , Márkus Ferenc
Published: April 2010

Transport and dissipation phenomena determine the quality of confinement in fusion plasmas devices. Turbulence, fluctuations, and instabilities are mechanisms which make them very complex dynamical processes. Two fluctuating regimes have been identified, which are related with the diffusive and wave propagation of mass in the system. The presence of one or another of these regimes in the plasma dynamics depends on several parameters as size of the container, inhomogeneities, etc. In this paper, we investigate the effects of inhomogeneous diffusion on the mass transport regime in hot plasmas. Small spatial gradients of the diffusion coefficient change the transport from diffusive to mass density waves propagation.
Phase formation and thermal stability of ultrathin nickel-silicides on Si(100)
Authors: De Keyser K. , Van Bockstael C. , Van Meirhaeghe R. L. , Detavernier C. , Verleysen E. , Bender H. , Vandervorst W. , Jordan-Sweet J. , Lavoie C.
Published: April 2010

The solid-state reaction and agglomeration of thin nickel-silicide films was investigated from sputter deposited nickel films (1–10 nm) on silicon-on-insulator (100) substrates. For typical anneals at a ramp rate of 3 °C/s, 5–10 nm Ni films react with silicon and form NiSi, which agglomerates at 550–650 °C, whereas films with a thickness of 3.7 nm of less were found to form an epitaxylike nickel-silicide layer. The resulting films show an increased thermal stability with a low electrical resistivity up to 800 °C.
Simulation of nanowire tunneling transistors: From the Wentzel–Kramers–Brillouin approximation to full-band phonon-assisted tunneling
Authors: Luisier Mathieu , Klimeck Gerhard
Published: April 2010

Nanowire band-to-band tunneling field-effect transistors (TFETs) are simulated using the Wentzel–Kramers–Brillouin (WKB) approximation and an atomistic, full-band quantum transport solver including direct and phonon-assisted tunneling (PAT). It is found that the WKB approximation properly works if one single imaginary path connecting the valence band (VB) and the conduction band (CB) dominates the tunneling process as in direct band gap semiconductors. However, PAT is essential in Si and Ge nanowire TFETs where multiple, tightly-coupled, imaginary paths exist between the VB and the CB.
Hydrogen and deuterium diffusion in lithium hydride
Authors: Dologlou Elisabeth
Published: April 2010

Hydrogen is considered a promising candidate to achieve an alternative source to overcome future energy supply problems. Very recently, an ab initio molecular dynamics study of the hydrogen diffusion in sodium and lithium hydrides appeared by Ramzan and Ahuja [J. Appl. Phys. 106, 016104 (2009)]. Here, we alternatively report the calculation of the temperature dependence of the diffusion coefficients of hydrogen and deuterium in LiH in terms of a thermodynamical model. The resulting values agree fairly well with experimental data.
Ultrafine hollow needle formation on silicon
Authors: Sanaee Z. , Mohajerzadeh S.
Published: April 2010

A method for the formation of ultrafine hollow needles, microcylindrical and nano-wall structures on silicon substrates is reported. The fabrication of these ultrafine structures is possible through a combination of high-precision high aspect ratio vertical etching of silicon with a small angle vacuum deposition technique where nanometric walls are feasible. These structures can be used as the media to transfer gas and liquid through their tiny holes. In addition, the structure has been used to realize cavity-based capacitance inclination sensor suitable for small angle detection. A capacitance variation of 0.6 pF/degree of inclination has been obtained.
Random pn-junctions for physical cryptography
Authors: Jaeger C. , Algasinger M. , Rührmair U. , Csaba G. , Stutzmann M.
Published: April 2010

In this paper, we report on high-rectification pn-diodes (rectification ratios up to 2×107) prepared by aluminum-induced crystallization on crystalline Si-wafers, which exhibit highly random I(V) characteristics. We argue that arrays of such diodes can be employed as physical uncloneable functions for cryptography. To resolve the structure of the active diode area, focused-ion beam imaging was used. The I(V) curves of the diodes reveal that both a smaller polycrystalline silicon film thickness and a smaller diode size lead to increasing randomness due to the increasing inhomogeneity of thinner films and due to more pronounced grain boundary effects for smaller diodes.
Crystallographic orientation dependence of compositional transition and valence band offset at SiO2/Si interface formed using oxygen radicals
Authors: Suwa T. , Teramoto A. , Kumagai Y. , Abe K. , Li X. , Nakao Y. , Yamamoto M. , Kato Y. , Muro T. , Kinoshita T. , Ohmi T. , Hattori T.
Published: April 2010

The chemical and electronic-band structures of SiO2/Si interfaces formed utilizing oxygen radicals were investigated by measuring angle-resolved photoelectron spectra arising from Si 2p and O 1s core levels and a valence band with the same probing depth. We clarified that (1) the SiO2/Si interfaces formed exhibited an almost abrupt compositional transition, (2) the valence band offsets at the Si(111)/Si, Si(110)/Si, and Si(551)/Si interfaces are almost the same and are 0.07 eV smaller than that at the SiO2/Si(100) interface.
Electron energy band alignment at the NiO/SiO2 interface
Authors: Afanas’ev V. V. , Badylevich M. , Houssa M. , Stesmans A. , Aggrawal Gagan , Campbell S. A.
Published: April 2010

Study of the NiO/SiO2 interface band diagram using optical absorption, photoconductivity, and internal photoemission measurements reveals that deposited Ni oxides have a band gap of 3.2±0.1 eV, with the top of the valence band at 5.3±0.1 eV below the conduction band of SiO2 and showing no measurable sensitivity to the oxygen surplus in the layer up to 20%. Annealing in a reducing ambient (forming gas) at 400 °C results in narrowing of the band gap and an up shift in the occupied electron state edge by ≈1 eV, which is tentatively associated with partial reduction in the NiO layer.
Extended orientational correlation study for molecular liquids containing distorted tetrahedral molecules: Application to methylene halides
Authors: Pothoczki Szilvia , Temleitner László , Pusztai László
Published: April 2010

The method of Rey [Rey, J. Chem. Phys. 126, 164506 (2007)] for describing how molecules orient toward each other in systems with perfect tetrahedral molecules is extended to the case of distorted tetrahedral molecules of c2v symmetry by means of introducing 28 subgroups. Additionally, the original analysis developed for perfect tetrahedral molecules, based on six groups, is adapted for molecules with imperfect tetrahedral shape. Deriving orientational correlation functions have been complemented with detailed analyses of dipole-dipole correlations. This way, (up to now) the most complete structure determination can be carried out for such molecular systems. In the present work, these calculations have been applied for particle configurations resulting from reverse Monte Carlo computer modeling. These particle arrangements are fully consistent with structure factors from neutron and x-ray diffraction measurements. Here we present a complex structural study for methylene halide (chloride, bromide, and iodide) molecular liquids, as possibly the best representative examples. It has been found that the most frequent orientations of molecules are of the 2:2 type over the entire distance range in these liquids. Focusing on the short range orientation, neighboring molecules turn toward each other with there “H,Y”–“H,Y” (Y: Cl, Br, I) edges, apart from CH2Cl2 where the H,H–H,Cl arrangement is the most frequent. In general, the structure of methylene chloride appears to be different from the structure of the other two liquids.
Communications: Wall free capillarity and pendant drop removal
Authors: Hong Siang-Jie , Chang Feng-Ming , Chan Seong Heng , Sheng Yu-Jane , Tsao Heng-Kwong
Published: April 2010

When a sessile drop encounters a pendant drop through a hole, it is generally anticipated that they will coalesce and flow downward due to gravity. However, like “wall-free” capillarity, we show that the pendant drop may be sucked up by a sliding drop instantaneously if the radius of the curvature of the former is smaller than that of the later. This phenomenon can be explained by Laplace–Young equation and convective Ostwald ripening. Our results indicate that superhydrophilic perforated surface can be used as an effective way for the removal of small droplets adhering to the inner walls of microchannel systems.
Northern Australia, whither the mercury?
Authors: Jardine Timothy D. , Bunn Stuart E.
Published: April 2010

Biomagnification of mercury (Hg) leads to high concentrations in fish and subsequent health risks for fish-eaters. Despite the global concern afforded to Hg over the past 40 years, little attention has been paid to this toxic heavy metal in Australia in general, and tropical northern Australia in particular. This review examines past Hg research in Australia and explores seven hypotheses as to why so little research and monitoring has been conducted in northern rivers and estuaries. We rule out the possibility that fishing intensity (an indicator of potential Hg exposure in humans) is lower in Australia than in other countries with more intensive Hg research programs. Instead, we hypothesise that low atmospheric deposition, owing to prevailing wind direction and few local point sources, coupled with highly productive waterbodies, contributes to low Hg bioaccumulation and hence the reduced interest in measuring Hg. Outstanding questions regarding Hg in northern Australia include the assessment of atmospheric deposition rates of Hg, the trophic level and growth and food consumption rates of consumers such as large-bodied fishes, linkages between fire regimes and Hg availability, and the capacity for in situ Hg methylation in tropical systems.
Genome-wide association identifies candidate genes that influence the human electroencephalogram
Authors: Hodgkinson Colin A. , Enoch Mary-Anne , Srivastava Vibhuti , Cummins-Oman Justine S. , Ferrier Cherisse , Iarikova Polina , Sankararaman Sriram , Yamini Goli , Yuan Qiaoping , Zhou Zhifeng , Albaugh Bernard , White Kenneth V. , Shen Pei-Hong , Goldman David
Published: April 2010

Complex psychiatric disorders are resistant to whole-genome analysis due to genetic and etiological heterogeneity. Variation in resting electroencephalogram (EEG) is associated with common, complex psychiatric diseases including alcoholism, schizophrenia, and anxiety disorders, although not diagnostic for any of them. EEG traits for an individual are stable, variable between individuals, and moderately to highly heritable. Such intermediate phenotypes appear to be closer to underlying molecular processes than are clinical symptoms, and represent an alternative approach for the identification of genetic variation that underlies complex psychiatric disorders. We performed a whole-genome association study on alpha (α), beta (β), and theta (θ) EEG power in a Native American cohort of 322 individuals to take advantage of the genetic and environmental homogeneity of this population isolate. We identified three genes (
SGIP1
,
ST6GALNAC3
, and
UGDH
) with nominal association to variability of θ or α power. SGIP1 was estimated to account for 8.8% of variance in θ power, and this association was replicated in US Caucasians, where it accounted for 3.5% of the variance. Bayesian analysis of prior probability of association based upon earlier linkage to chromosome 1 and enrichment for vesicle-related transport proteins indicates that the association of
SGIP1
with θ power is genuine. We also found association of
SGIP1
with alcoholism, an effect that may be mediated via the same brain mechanisms accessed by θ EEG, and which also provides validation of the use of EEG as an endophenotype for alcoholism.
A randomized, double-blind, placebo-controlled study of an RNAi-based therapy directed against respiratory syncytial virus
Authors: DeVincenzo John , Lambkin-Williams Robert , Wilkinson Tom , Cehelsky Jeffrey , Nochur Sara , Walsh Edward , Meyers Rachel , Gollob Jared , Vaishnaw Akshay
Published: April 2010

RNA interference (RNAi) is a natural mechanism regulating protein expression that is mediated by small interfering RNAs (siRNA). Harnessing RNAi has potential to treat human disease; however, clinical evidence for the effectiveness of this therapeutic approach is lacking. ALN-RSV01 is an siRNA directed against the mRNA of the respiratory syncytial virus (RSV) nucleocapsid (N) protein and has substantial antiviral activity in a murine model of RSV infection. We tested the antiviral activity of ALN-RSV01 in adults experimentally infected with wild-type RSV. Eighty-eight healthy subjects were enrolled into a randomized, double-blind, placebo-controlled trial. A nasal spray of ALN-RSV01 or saline placebo was administered daily for 2 days before and for 3 days after RSV inoculation. RSV was measured serially in nasal washes using several different viral assays. Intranasal ALN-RSV01 was well tolerated, exhibiting a safety profile similar to saline placebo. The proportion of culture-defined RSV infections was 71.4 and 44.2% in placebo and ALN-RSV01 recipients, respectively (
P
= 0.009), representing a 38% decrease in the number of infected and a 95% increase in the number of uninfected subjects. The acquisition of infection over time was significantly lower in ALN-RSV01 recipients (
P
= 0.007 and
P
= 0.03, viral culture and PCR, respectively). Multiple logistic regression analysis showed that the ALN-RSV01 antiviral effect was independent of other factors, including preexisting RSV antibody and intranasal proinflammatory cytokine concentrations. ALN-RSV01 has significant antiviral activity against human RSV infection, thus establishing a unique proof-of-concept for an RNAi therapeutic in humans and providing the basis for further evaluation in naturally infected children and adults.
Decreased winter severity increases viability of a montane frog population
Authors: McCaffery Rebecca M. , Maxell Bryce A.
Published: April 2010

Many proximate causes of global amphibian declines have been well documented, but the role that climate change has played and will play in this crisis remains ambiguous for many species. Breeding phenology and disease outbreaks have been associated with warming temperatures, but, to date, few studies have evaluated effects of climate change on individual vital rates and subsequent population dynamics of amphibians. We evaluated relationships among local climate variables, annual survival and fecundity, and population growth rates from a 9-year demographic study of Columbia spotted frogs (Rana luteiventris) in the Bitterroot Mountains of Montana. We documented an increase in survival and breeding probability as severity of winter decreased. Therefore, a warming climate with less severe winters is likely to promote population viability in this montane frog population. More generally, amphibians and other ectotherms inhabiting alpine or boreal habitats at or near their thermal ecological limits may benefit from the milder winters provided by a warming climate as long as suitable habitats remain intact. A more thorough understanding of how climate change is expected to benefit or harm amphibian populations at different latitudes and elevations is essential for determining the best strategies to conserve viable populations and allow for gene flow and shifts in geographic range.
Nitrosopumilus maritimus
genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea
Authors: Walker C. B. , de la Torre J. R. , Klotz M. G. , Urakawa H. , Pinel N. , Arp D. J. , Brochier-Armanet C. , Chain P. S. G. , Chan P. P. , Gollabgir A. , Hemp J. , Hügler M. , Karr E. A. , Könneke M. , Shin M. , Lawton T. J. , Lowe T. , Martens-Habbena W. , Sayavedra-Soto L. A. , Lang D. , Sievert S. M. , Rosenzweig A. C. , Manning G. , Stahl D. A.
Published: April 2010

Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of
Candidatus
“
Nitrosopumilus maritimus
” strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates
N. maritimus
grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of
N. maritimus
gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen.
Enigmatic, ultrasmall, uncultivated Archaea
Authors: Baker Brett J. , Comolli Luis R. , Dick Gregory J. , Hauser Loren J. , Hyatt Doug , Dill Brian D. , Land Miriam L. , VerBerkmoes Nathan C. , Hettich Robert L. , Banfield Jillian F.
Published: April 2010

Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge—particularly for Archaea—that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete ~1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher coding density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in
Crenarchaeota
than
Euryarchaeota
, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order
Thermoplasmatales
. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009)
ISME J
3:159–167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that
Cren
- and
Euryarchaeotal
lineages diverged.
Dichotomy in duration and severity of acute inflammatory responses in humans arising from differentially expressed proresolution pathways
Authors: Morris Thea , Stables Melanie , Colville-Nash Paul , Newson Justine , Bellingan Geoffrey , de Souza Patricia M. , Gilroy Derek W.
Published: April 2010

Lipoxins (Lxs) and aspirin-triggered epi-Lxs (15-epi-LxA
4
) act through the ALX/FPRL1 receptor to block leukocyte trafficking, dampen cytokine/chemokine synthesis, and enhance phagocytic clearance of apoptotic leukocytes—key requisites for inflammatory resolution. Although studies using primarily inbred rodents have highlighted resolution as an active event, little is known about the role resolution pathways play in controlling the duration/profile of inflammatory responses in humans. To examine this, we found two types of responders to cantharidin-induced skin blisters in male healthy volunteers: those with immediate leukocyte accumulation and cytokine/chemokine synthesis followed by early resolution and a second group whose inflammation increased gradually over time followed by delayed resolution. In early resolvers, blister 15-epi-LxA
4
and leukocyte ALX were low, but increased as inflammation abated. In contrast, in delayed resolvers, 15-epi-LxA
4
and ALX were high early in the response but waned as inflammation progressed. Elevating 15-epi-LxA
4
in early resolvers using aspirin increased blister leukocyte ALX but reduced cytokines/chemokines as well as polymorphonuclear leukocyte and macrophage numbers. These findings show that two phenotypes exist in humans with respect to inflammation severity/longevity controlled by proresolution mediators, namely 15-epi-LxA
4
. These data have implications for understanding the etiology of chronic inflammation and future directions in antiinflammatory therapy.
Auxins reverse plant male sterility caused by high temperatures
Authors: Sakata Tadashi , Oshino Takeshi , Miura Shinya , Tomabechi Mari , Tsunaga Yuta , Higashitani Nahoko , Miyazawa Yutaka , Takahashi Hideyuki , Watanabe Masao , Higashitani Atsushi
Published: April 2010

With global warming, plant high temperature injury is becoming an increasingly serious problem. In wheat, barley, and various other commercially important crops, the early phase of anther development is especially susceptible to high temperatures. Activation of auxin biosynthesis with increased temperatures has been reported in certain plant tissues. In contrast, we here found that under high temperature conditions, endogenous auxin levels specifically decreased in the developing anthers of barley and
Arabidopsis
. In addition, expression of the
YUCCA
auxin biosynthesis genes was repressed by increasing temperatures. Application of auxin completely reversed male sterility in both plant species. These findings suggest that tissue-specific auxin reduction is the primary cause of high temperature injury, which leads to the abortion of pollen development. Thus, the application of auxin may help sustain steady yields of crops despite future climate change.
Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems
Authors: Chen Yvonne Y. , Jensen Michael C. , Smolke Christina D.
Published: April 2010

RNA molecules perform diverse regulatory functions in natural biological systems, and numerous synthetic RNA-based control devices that integrate sensing and gene-regulatory functions have been demonstrated, predominantly in bacteria and yeast. Despite potential advantages of RNA-based genetic control strategies in clinical applications, there has been limited success in extending engineered RNA devices to mammalian gene-expression control and no example of their application to functional response regulation in mammalian systems. Here we describe a synthetic RNA-based regulatory system and its application in advancing cellular therapies by linking rationally designed, drug-responsive, ribozyme-based regulatory devices to growth cytokine targets to control mouse and primary human T-cell proliferation. We further demonstrate the ability of our synthetic controllers to effectively modulate T-cell growth rate in response to drug input in vivo. Our RNA-based regulatory system exhibits unique properties critical for translation to therapeutic applications, including adaptability to diverse ligand inputs and regulatory targets, tunable regulatory stringency, and rapid response to input availability. By providing tight gene-expression control with customizable ligand inputs, RNA-based regulatory systems can greatly improve cellular therapies and advance broad applications in health and medicine.
Structural insight into the regulatory mechanisms of interactions of the flagellar type III chaperone FliT with its binding partners
Authors: Imada Katsumi , Minamino Tohru , Kinoshita Miki , Furukawa Yukio , Namba Keiichi
Published: April 2010

For self-assembly of the bacterial flagellum, most of the flagellar component proteins synthesized in the cytoplasm are exported by the flagellar type III export apparatus to the growing, distal end. Flagellar protein export is highly organized and well controlled in every step of the flagellar assembly process. Flagellar-specific chaperones not only facilitate the export of their cognate proteins, as well as prevent their premature aggregation in the cytoplasm, but also play a role in fine-tuning flagellar gene expression to be coupled with the flagellar assembly process. FliT is a flagellar-specific chaperone responsible for the export of the filament-capping protein FliD and for negative control of flagellar gene expression by binding to the FlhDC complex. Here we report the crystal structure of
Salmonella
FliT at 3.2-Å resolution. The structural and biochemical analyses clearly reveal that the C-terminal segment of FliT regulates its interactions with the FlhDC complex, FliI ATPase, and FliJ (subunits of the export apparatus), and that its conformational change is responsible for the switch in its binding partners during flagellar protein export.
Magnetic resonance imaging of oscillating electrical currents
Authors: Halpern-Manners Nicholas W. , Bajaj Vikram S. , Teisseyre Thomas Z. , Pines Alexander
Published: April 2010

Functional MRI has become an important tool of researchers and clinicians who seek to understand patterns of neuronal activation that accompany sensory and cognitive processes. However, the interpretation of fMRI images rests on assumptions about the relationship between neuronal firing and hemodynamic response that are not firmly grounded in rigorous theory or experimental evidence. Further, the blood-oxygen-level-dependent effect, which correlates an MRI observable to neuronal firing, evolves over a period that is 2 orders of magnitude longer than the underlying processes that are thought to cause it. Here, we instead demonstrate experiments to directly image oscillating currents by MRI. The approach rests on a resonant interaction between an applied rf field and an oscillating magnetic field in the sample and, as such, permits quantitative, frequency-selective measurements of current density without spatial or temporal cancellation. We apply this method in a current loop phantom, mapping its magnetic field and achieving a detection sensitivity near the threshold required for the detection of neuronal currents. Because the contrast mechanism is under spectroscopic control, we are able to demonstrate how ramped and phase-modulated spin-lock radiation can enhance the sensitivity and robustness of the experiment. We further demonstrate the combination of these methods with remote detection, a technique in which the encoding and detection of an MRI experiment are separated by sample flow or translation. We illustrate that remotely detected MRI permits the measurement of currents in small volumes of flowing water with high sensitivity and spatial resolution.
Alternate protein kinase A activity identifies a unique population of stromal cells in adult bone
Authors: Tsang Kit Man , Starost Matthew F. , Nesterova Maria , Boikos Sosipatros A. , Watkins Tonya , Almeida Madson Q. , Harran Michelle , Li Andrew , Collins Michael T. , Cheadle Christopher , Mertz Edward L. , Leikin Sergey , Kirschner Lawrence S. , Robey Pamela , Stratakis Constantine A.
Published: April 2010

A population of stromal cells that retains osteogenic capacity in adult bone (adult bone stromal cells or aBSCs) exists and is under intense investigation. Mice heterozygous for a null allele of
prkar1a
(
Prkar1a
+/−
), the primary receptor for cyclic adenosine monophosphate (cAMP) and regulator of protein kinase A (PKA) activity, developed bone lesions that were derived from cAMP-responsive osteogenic cells and resembled fibrous dysplasia (FD).
Prkar1a
+/−
mice were crossed with mice that were heterozygous for catalytic subunit Cα (

Prkaca
+/−

), the main PKA activity-mediating molecule, to generate a mouse model with double heterozygosity for
prkar1a
and
prkaca
(
Prkar1a
+/−
Prkaca
+/−
). Unexpectedly,
Prkar1a
+/−
Prkaca
+/−
mice developed a greater number of osseous lesions starting at 3 months of age that varied from the rare chondromas in the long bones and the ubiquitous osteochondrodysplasia of vertebral bodies to the occasional sarcoma in older animals. Cells from these lesions originated from an area proximal to the growth plate, expressed osteogenic cell markers, and showed higher PKA activity that was mostly type II (PKA-II) mediated by an alternate pattern of catalytic subunit expression. Gene expression profiling confirmed a preosteoblastic nature for these cells but also showed a signature that was indicative of mesenchymal-to-epithelial transition and increased
Wnt
signaling. These studies show that a specific subpopulation of aBSCs can be stimulated in adult bone by alternate PKA and catalytic subunit activity; abnormal proliferation of these cells leads to skeletal lesions that have similarities to human FD and bone tumors.
Prion induction involves an ancient system for the sequestration of aggregated proteins and heritable changes in prion fragmentation
Authors: Tyedmers Jens , Treusch Sebastian , Dong Jijun , McCaffery J. Michael , Bevis Brooke , Lindquist Susan
Published: April 2010

When the translation termination factor Sup35 adopts the prion state, [
PSI
+
], the read-through of stop codons increases, uncovering hidden genetic variation and giving rise to new, often beneficial, phenotypes. Evidence suggests that prion induction involves a process of maturation, but this has never been studied in detail. To do so, we used a visually tractable prion model consisting of the Sup35 prion domain fused to GFP (PrD-GFP) and overexpressed it to achieve induction in many cells simultaneously. PrD-GFP first assembled into Rings as previously described. Rings propagated for many generations before the protein transitioned into a Dot structure. Dots transmitted the [
PSI
+
] phenotype through mating and meiosis, but Rings did not. Surprisingly, the underlying amyloid conformation of PrD-GFP was identical in Rings and Dots. However, by electron microscopy, Rings consisted of very long uninterrupted bundles of fibers, whereas Dot fibers were highly fragmented. Both forms were deposited at the IPOD, a biologically ancient compartment for the deposition of irreversibly aggregated proteins that we propose is the site of de novo prion induction. We find that oxidatively damaged proteins are also localized there, helping to explain how proteotoxic stresses increase the rate of prion induction. Curing PrD-GFP prions, by inhibiting Hsp104’s fragmentation activity, reversed the induction process: Dot cells produced Rings before PrD-GFP reverted to the soluble state. Thus, formation of the genetically transmissible prion state is a two-step process that involves an ancient system for the asymmetric inheritance of damaged proteins and heritable changes in the extent of prion fragmentation.
DendroPy: a Python library for phylogenetic computing
Authors: Sukumaran Jeet , Holder Mark T.
Published: April 2010

Summary: DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines.

Availability: The stable release of the library is available for download and automated installation through the Python Package Index site (http://pypi.python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy).

Contact:  jeet@ku.edu
Dentate gyrus is necessary for disambiguating similar object-place representations
Authors: Lee Inah , Solivan Frances
Published: April 2010

Objects are often remembered with their locations, which is an important aspect of event memory. Despite the well-known involvement of the hippocampus in event memory, detailed intrahippocampal mechanisms are poorly understood. In particular, no experimental evidence has been provided in support of the role of the dentate gyrus (DG) in disambiguating such events, even though computational models suggest otherwise. In the current study, rats encountered multiple objects in different locations and were required to discriminate the object-place paired associates for reward. Specifically, two different objects appeared in one of two locations (arms in a radial maze) that were relatively close to each other. Different objects were rewarded depending on the arm in which the objects appeared. The rats with colchicine-based, dorsal DG (dDG) lesions showed severe and sustained impairment in disambiguating the objects compared with controls (Experiment 1). The dDG-lesioned rats were normal, however, in discriminating four different objects presented (Experiment 2) in the same locations as in Experiment 1. Finally, when the two different objects used in Experiment 1 were presented at two remote locations (Experiment 3) involving less overlap between arm-associated contextual cues, the dDG-lesioned animals showed initial deficits in discriminating the objects, but gradually relearned the task, in contrast to the sustained deficits observed in Experiment 1. These results collectively suggest that the DG is necessary when the similarity is maximal between object-place paired associates due to overlapping object and/or spatial information, whereas its role becomes minimal as the overlap in either object or spatial information decreases.
The Sterol Methyltransferases SMT1, SMT2, and SMT3 Influence Arabidopsis Development through Nonbrassinosteroid Products
Authors: Carland Francine , Fujioka Shozo , Nelson Timothy
Published: April 2010

Plant sterols are structural components of cell membranes that provide rigidity, permeability, and regional identity to membranes. Sterols are also the precursors to the brassinosteroid signaling molecules. Evidence is accumulating that specific sterols have roles in pattern formation during development. COTYLEDON VASCULAR PATTERNING1 (CVP1) encodes C-24 STEROL METHYLTRANSFERASE2 (SMT2), one of three SMTs in Arabidopsis (Arabidopsis thaliana). SMT2 and SMT3, which also encodes a C-24 SMT, catalyze the reaction that distinguishes the synthesis of structural sterols from signaling brassinosteroid derivatives and are highly regulated. The deficiency of SMT2 in the cvp1 mutant results in moderate developmental defects, including aberrant cotyledon vein patterning, serrated floral organs, and reduced stature, but plants are viable, suggesting that SMT3 activity can substitute for the loss of SMT2. To test the distinct developmental roles of SMT2 and SMT3, we identified a transcript null smt3 mutant. Although smt3 single mutants appear wild type, cvp1 smt3 double mutants show enhanced defects relative to cvp1 mutants, such as discontinuous cotyledon vein pattern, and produce novel phenotypes, including defective root growth, loss of apical dominance, sterility, and homeotic floral transformations. These phenotypes are correlated with major alterations in the profiles of specific sterols but without significant alterations to brassinosteroid profiles. The alterations to sterol profiles in cvp1 mutants affect auxin response, demonstrated by weak auxin insensitivity, enhanced axr1 auxin resistance, ectopically expressed DR5:β-glucuronidase in developing embryos, and defective response to auxin-inhibited PIN2-green fluorescent protein endocytosis. We discuss the developmental roles of sterols implied by these results.
Acute exercise reduces hepatic glucose production through inhibition of the Foxo1/HNF‐4α pathway in insulin resistant mice
Authors: De Souza Cláudio T. , Frederico Marisa J. S. , Da Luz Gabrielle , Cintra Dennys E. , Ropelle Eduardo R. , Pauli José R. , Velloso Lício A.
Published: April 2010

Protein hepatocyte nuclear factor 4α (HNF‐4α) is atypically activated in the liver of diabetic rodents and contributes to hepatic glucose production. HNF‐4α and Foxo1 can physically interact with each other and represent an important signal transduction pathway that regulates the synthesis of glucose in the liver. Foxo1 and HNF‐4α interact with their own binding sites in the phosphoenolpyruvate carboxykinase (PEPCK) and glucose‐6‐phosphatase (G6Pase) promoters, and this binding is required for their effects on those promoters. However, the effect of physical activity on the HNF‐4α/Foxo1 pathway is currently unknown. Here, we investigate the protein levels of HNF‐4α and the HNF‐4α/Foxo1 pathway in the liver of leptin‐deficient (ob/ob) and diet‐induced obese Swiss (DIO) mice after acute exercise. The ob/ob and DIO mice swam for four 30 min periods, with 5 min rest intervals for a total swimming time of 2 h. Eight hours after the acute exercise protocol, the mice were submitted to an insulin tolerance test (ITT) and determination of biochemical and molecular parameters. Acute exercise improved insulin signalling, increasing insulin‐stimulated Akt and Foxo1 phosphorylation and decreasing HNF‐4α protein levels in the liver of DIO and ob/ob mice under fasting conditions. These phenomena were accompanied by a reduction in the expression of gluconeogenesis genes, such as PEPCK and G6Pase. Importantly, the PI3K inhibitor LY292004 reversed the acute effect of exercise on fasting hyperglycaemia, confirming the involvement of the PI3K pathway. The present study shows that exercise acutely improves the action of insulin in the liver of animal models of obesity and diabetes, resulting in increased phosphorylation and nuclear exclusion of Foxo1, and a reduction in the Foxo1/HNF‐4α pathway. Since nuclear localization and the association of these proteins is involved in the activation of PEPCK and G6Pase, we believe that the regulation of Foxo1 and HNF‐4α activities are important mechanisms involved in exercise‐induced improvement of glucose homeostasis in insulin resistant states.
Differences in subthreshold resonance of hippocampal pyramidal cells and interneurons: the role of h‐current and passive membrane characteristics
Authors: Zemankovics Rita , Káli Szabolcs , Paulsen Ole , Freund Tamás F. , Hájos Norbert
Published: April 2010

The intrinsic properties of distinct types of neuron play important roles in cortical network dynamics. One crucial determinant of neuronal behaviour is the cell's response to rhythmic subthreshold input, characterised by the input impedance, which can be determined by measuring the amplitude and phase of the membrane potential response to sinusoidal currents as a function of input frequency. In this study, we determined the impedance profiles of anatomically identified neurons in the CA1 region of the rat hippocampus (pyramidal cells as well as interneurons located in the stratum oriens, including OLM cells, fast‐spiking perisomatic region‐targeting interneurons and cells with axonal arbour in strata oriens and radiatum). The basic features of the impedance profiles, as well as the passive membrane characteristics and the properties of the sag in the voltage response to negative current steps, were cell‐type specific. With the exception of fast‐spiking interneurons, all cell types showed subthreshold resonance, albeit with distinct features. The HCN channel blocker ZD7288 (10 μm) eliminated the resonance and changed the shape of the impedance curves, indicating the involvement of the hyperpolarisation‐activated cation current Ih. Whole‐cell voltage‐clamp recordings uncovered differences in the voltage‐dependent activation and kinetics of Ih between different cell types. Biophysical modelling demonstrated that the cell‐type specificity of the impedance profiles can be largely explained by the properties of Ih in combination with the passive membrane characteristics. We conclude that differences in Ih and passive membrane properties result in a cell‐type‐specific response to inputs at given frequencies, and may explain, at least in part, the differential involvement of distinct types of neuron in various network oscillations.
Postnatal development of baroreflex sensitivity in infancy
Authors: Yiallourou Stephanie R. , Sands Scott A. , Walker Adrian M. , Horne Rosemary S. C.
Published: April 2010

Baroreflex sensitivity (BRS) using spontaneous sequence analysis in the time domain is not fully applicable in infancy, as the time delay for heart period to change (heart period delay, HPD) after an arterial pressure change is unknown. We estimated and compared HPD and BRS in the frequency (BRSsp, HPDsp) and time domains (BRSseq, HPDseq) from systolic blood pressure (SBP) and heart period fluctuations. Continuous SBP, using photoplethysmography, and heart period measurements were performed on 30 term infants at 2–4 weeks, 2–3 months and 5–6 months postnatal age. Cross‐spectral analysis between SBP and heart period fluctuations was used to estimate BRSspand HPDsp. Spontaneous sequence analysis was used to estimate BRS using a fixed beat delay of 1–12 beats (BRSseq) or a variable delay identified by a novel method accounting for epoch–epoch variability in HPD (BRSseqvar). HPDspaveraged 3.4 s (∼7 beats); BRSspaveraged 11.4 ms mmHg−1. BRSseqand BRSseqvarwere consistently lower than BRSsp(P< 0.05), but the three BRS estimates were strongly correlated using a HPD of ∼5–6 beats. BRSseqvarresulted in the average estimate (8.9 ms mmHg−1) closest to BRSspand overall had the strongest correlation with BRSsp(R2= 0.61;P< 0.001). All three BRS estimates increased progressively with postnatal age, with BRSspaveraging 6.4, 10.5 and 16.0 ms mmHg−1at 2–4 weeks, 2–3 months and 5–6 months, respectively (P< 0.05). Accounting for the HPD of infancy provides estimates of BRS in the time domain that closely parallel spectral estimates, and provides a novel analytical tool to assess normal development and dysfunction of the baroreflex in infants.
A Method to Determine Fuel Transport Dynamics Model Parameters in Port Fuel Injected Gasoline Engines During Cold Start and Warm-Up Conditions
Authors: Shahbakhti M. , Ghafuri M. , Aslani A. R. , Sahraeian A. , Jazayeri S. A. , Azadi S.
Published: April 2010

In order to meet stringent emission standards, it is essential to have a precise control of air-fuel ratio (AFR) under cold start and warm-up conditions. This requires an understanding of the fuel transport dynamics in the intake system during these conditions. This study centers on estimating the parameters of a fuel transport dynamics model during engine operation at different thermal conditions ranging from cold start to fully warmed-up conditions. A method of system identification based on perturbing fuel injection rate is used to find fuel dynamics parameters in a port fuel injected (PFI) spark ignition engine. Since there was no cold chamber available to prepare cold start conditions, a new method was utilized to simulate cold start conditions. The new method can be applied on PFI engines, which use closed valve injection timing. A four-cylinder PFI engine is tested for different thermal conditions from −15°C to 82°C at a range of engine speeds and intake manifold pressures. A good agreement is observed between simulated and experimental AFR for 52 different transient operating conditions presented in this study. Results indicate that both fuel film deposit factor (X) and fuel film evaporation time constant (τf) decrease with increasing coolant temperature or engine speed. In addition, an increase in the intake manifold pressure results in an increase in X while causes a decrease in τf.
A Continuous Multicomponent Fuel Flame Propagation and Chemical Kinetics Model
Authors: Yang Shiyou , Reitz Rolf D.
Published: April 2010

A continuous multicomponent fuel flame propagation and chemical kinetics model has been developed. In the multicomponent fuel model, the theory of continuous thermodynamics was used to model the properties and composition of fuels such as gasoline. The difference between the current continuous multicomponent fuel model and previous similar models in the literature is that the source terms contributed by chemistry in the mean and the second moment transport equations have been considered. This new model was validated using results from a discrete multicomponent fuel model. In the flame propagation and chemical kinetics model, five improved combustion submodels were also integrated with the new continuous multicomponent fuel model. To consider the change in local fuel vapor mixture composition, a “primary reference fuel (PRF) adaptive” method is proposed that formulates a relationship between the fuel vapor mixture PRF number (or research octane number) and the fuel vapor mixture composition based on the mean molecular weight and/or variance of the fuel vapor mixture composition in each cell. Simulations of single droplet vaporization with a single-component fuel (iso-octane) were compared with multicomponent fuel cases.
Modeling and Model Updating of Torsional Behavior of an Industrial Steam Turbo Generator
Authors: Ricci Roberto , Pennacchi Paolo , Pesatori Emanuel , Turozzi Giorgio
Published: April 2010

The methods employed to perform rotordynamics calculations of industrial machines are rather standard and usually allow forecasting the dynamic behavior of the considered machines. Anyhow, in some cases, in order to obtain high level of accuracy, the model has to be updated to fit experimental results, and standard modeling methods have to be improved. In this paper, the updating of the torsional model of a steam turbogenerator is presented. In order to fit the eigenfrequencies calculated using the standard model and the natural frequencies measured on-field, a modeling improvement is proposed, considering partially the dynamics of the components usually modeled as rigid disks. The proposed method has also the aim to preserve the physical meaning of the model. Finally, the new model is updated, and a very good fitting is obtained between eigenfrequencies and experimental natural frequencies.