bluuebunny/crossref_metadata_2025 huggingface dataset:
Occurrence and properties of substorms associated with pseudobreakups
Authors: Kullen A. , Karlsson T. , Cumnock J. A. , Sundberg T.
Published: December 2010

We investigate how substorms with and without growth‐phase pseudobreakups are affected by solar wind and ionospheric conditions. The study is based on 874 events identified with Polar UVI. An AE index analysis shows that substorms with growth‐phase pseudobreakups are typically weak and appear as isolated events after hours of low geomagnetic activity. During the hours before onset the average solar wind merging field Em is weaker, and the length of time with enhanced values shorter than for regular substorms. Integrating Em over the last southward IMF period before onset shows an upper limit above which these substorms do not occur. To estimate how much Em reaches the ionosphere, polar cap potential drop and unified PC indices are examined. It is found that substorms with growth‐phase pseudobreakups have on average lower PC index values than regular substorms. The temporal evolution of the PC indices is similar for both substorm groups; the summer index correlates better with Em, the winter index with AE. Also the average polar cap potential drop curves for both types of substorms resemble one other; the dayside and nightside curves are mainly influenced by Em and AE, respectively. Comparing growth‐phase, isolated and recovery pseudobreakups shows that solar wind and ionospheric conditions around the first substorm after a pseudobreakup are similar, independent of whether the last pseudobreakup appeared hours (recovery and isolated pseudobreakups) or minutes before substorm onset (growth‐phase pseudobreakups). Isolated and recovery pseudobreakups are less often associated with a northward IMF rotation than growth‐phase pseudobreakups or substorms.
Finding their niche: chemokines directing cell migration in the thymus
Authors: Bunting Mark D , Comerford Iain , McColl Shaun R
Published: December 2010

T lymphocytes are generated throughout life, arising from bone marrow‐derived progenitors that complete an essential developmental process in the thymus. Thymic T cell education leads to the generation of a self‐restricted and largely self‐tolerant peripheral T‐cell pool and is facilitated by interactions with thymic stromal cells residing in distinct supportive niches. The signals governing thymocyte precursor migration into the thymus, directing thymocyte navigation through thymic microenvironments and mature T‐cell egress into circulation were, until recently, largely unknown, but presumed to be mediated to a large extent by chemokine signalling. Recent studies have now uncovered various specific functions for members of the chemokine superfamily in the thymus. These studies have not only revealed distinct but also in some cases overlapping roles for several chemokine family members in various thymocyte migration events and have also shown that homing and positioning of other cells in the thymus, such as dendritic cells and natural killer T cells is also chemokine‐dependent. Here, we discuss current understanding of the role of chemokines in the thymus and highlight key future avenues for investigation in this field.
Nanoscale size dependence on pulsed laser sintering of hydroxyapatite/titanium particles on metal implants
Authors: Zhang Martin Yi , Cheng Gary J.
Published: December 2010

Nanoscale size effects on pulsed laser coating of hydroxyapatite/titanium nanoparticles (nanoTi) on metal substrate is discussed in this article. Laser coating method has recently been developed to coat bioceramics material on Ti–6Al–4V substrate. Laser-coated bioceramics implants have several advantages due to the use of nanosized materials: strong interfacial bonding strength, good biocompatibility and potentially longer lifetime cycle. These advantages benefit from intrinsic properties of nanoparticles. Size effects on melting point, heat capacity, thermal, and electrical conductivities have been discussed. Multiphysics model is built to reveal the mechanism of laser coating process. Two submodules are included in the model: electromagnetic module to represent the laser-nanoparticle interactions and heat transfer module to simulate the heat conduction. Both simulation and experimental results showed that nanoTi, functioning as nanoheaters, effectively enhances the laser coating sinterability. For large nanoTi (>100 nm), sinterability enhancement mainly attributes to the stronger laser-particle interactions due to higher plasmon resonance; for small nanoparticles (<100 nm), not only stronger laser-nanoparticle interactions, reduction on melting point also contributes to sinterability enhancement.
The effect of dust charge fluctuations on collisional drift waves in a magnetized plasma cylinder
Authors: Sharma Suresh C. , Gahlot Ajay
Published: December 2010

The nonlinear coupling between collisional drift waves and a lower-hybrid pump wave is studied in a magnetized dusty plasma cylinder. A dispersion relation for the collisional drift wave and growth rate is derived incorporating both pondermotive and Ohmic heating effects. The growth rate and mode frequencies were evaluated based on existing dusty plasma parameters. It is found that the unstable collisional drift mode frequency increases and the growth rate decreases sharply with the relative density of negatively charged dust grains. Moreover, the collisional frequency has no effect on the unstable drift mode frequency. However, the increases in collisional frequency and electron temperature are playing an important role in the damping effect.
Dual energy phase contrast x-ray imaging with Talbot-Lau interferometer
Authors: Kottler Christian , Revol Vincent , Kaufmann Rolf , Urban Claus
Published: December 2010

In weakly absorbing materials such as polymers and soft tissue, x-ray phase sensitive imaging methods can provide substantially enhanced contrast compared to classical, absorption based radiography. For specific applications, the latter can be applied in a dual energy scheme that helps to identify, discriminate and/or quantify materials. In this paper, we report on a new method that combines the idea of dual energy with x-ray phase contrast imaging and thus provides material sensitivity among poor absorbers. The dual energy modality cannot be applied in common phase contrast imaging schemes because of their demand for limited bandwidth or even monochromatic x-ray sources. Our new interferometric method based on diffraction gratings can overcome this shortcoming and thus simultaneously deliver x-ray phase contrast images for two distinct x-ray energy intervals. It has been shown that high quality images can be obtained with the dual energy phase setup. Energy spectra with 40 kV and 70 kV were applied to obtain low- and high-energy images, respectively. Furthermore, an estimation of the effective energy in the image formation process for absorption and phase contrast was experimentally determined. Examples are shown for which the dual energy phase contrast modality delivers complementary information on material composition when compared with the conventional dual energy scheme.
Transmission loss and dynamic response of membrane-type locally resonant acoustic metamaterials
Authors: Naify Christina J. , Chang Chia-Ming , McKnight Geoffrey , Nutt Steven
Published: December 2010

Membrane-type acoustic metamaterials were fabricated, characterized, and analyzed to understand their acoustic response. Thin plates which obey the acoustic mass law have low transmission loss (TL) at low frequencies. Acoustic metamaterials with negative dynamic mass density have been shown to demonstrate a significant (5×) increase in TL over mass law predictions for a narrow band (100 Hz) at low frequencies (100–1000 Hz). The peak TL frequency can be tuned to specific values by varying the membrane and mass properties. In this work, TL magnitude as a function of frequency was measured for variations in the mass magnitude and membrane tension using an impedance tube setup. The dynamic properties of membranes constructed from different materials were measured and compared to the results of coupled field acoustic-structural finite element analysis modeling to understand the role of tension and element quality factor. To better comprehend the mechanism(s) responsible for the TL peak, a laser vibrometer was used to map the out-of-plane dynamic response of the structure under acoustic loading at discrete frequencies. Negative dynamic mass was experimentally demonstrated at the peak TL frequency.
Bessel spatial profile of a soft x-ray laser beam
Authors: Tissandier F. , Sebban S. , Ribière M. , Gautier J. , Zeitoun Ph. , Lambert G. , Goddet J.-Ph. , Burgy F. , Valentin C. , Rousse A. , Nejdl J. , Mocek T. , Maynard G.
Published: December 2010

We report far-field profile measurements of an optical-field-ionized high-order harmonic-seeded soft x-ray laser. We show that the beam transverse profile can be controlled between a regular Gaussian shape and a Bessel profile exhibiting several rings via the infrared laser pump intensity. These experimental data are supported by a complete numerical modeling including a two-dimensional plasma amplifier simulation and a two-level soft x-ray amplification using a Maxwell–Bloch treatment. This model takes into account the experimental high-order harmonic wavefront and intensity before it is numerically amplified.
Electrostatic ion waves in non-Maxwellian pair-ion plasmas
Authors: Arshad Kashif , Mahmood S.
Published: December 2010

The electrostatic ion waves are studied for non-Maxwellian or Lorentzian distributed unmagnetized pair-ion plasmas. The Vlasov equation is solved and damping rates are calculated for electrostatic waves in Lorentzian pair-ion plasmas. The damping rates of the electrostatic ion waves are studied for the equal and different ion temperatures of pair-ion species. It is found that the Landau damping rate of the ion plasma wave is increased in Lorentzian plasmas in comparison with Maxwellian pair-ion plasmas. The numerical results are also presented for illustration by taking into account the parameters reported in fullerene pair-ion plasma experiments.
Mixing of passive tracers in the decay Batchelor regime of a channel flow
Authors: Jun Yonggun , Steinberg Victor
Published: December 2010

We report detailed quantitative studies of passive scalar mixing in a curvilinear channel flow, where elastic turbulence in a dilute polymer solution of high molecular weight polyacrylamide in a high viscosity water-sugar solvent was achieved. For quantitative investigation of mixing, a detailed study of the profiles of mean longitudinal and radial components of the velocity in the channel as a function of Wi was carried out. Besides, a maximum of the average value as well as a rms of the longitudinal velocity was used to determine the threshold of the elastic instability in the channel flow. The rms of the radial derivatives of the longitudinal and radial velocity components was utilized to define the control parameters of the problem, the Weissenberg Wiloc and the Péclet Pe numbers. The main result of these studies is the quantitative test of the theoretical prediction about the value of the mixing length in the decay Batchelor regime. The experiment shows large quantitative discrepancy, more than 200 times in the value of the coefficient C, which appears in the theoretical expression for the mixing length, but with the predicted scaling relation. There are two possible reasons to this discrepancy. First is the assumption made in the theory about the δ-correlated velocity field, which is in odds with the experimental observations. Second, and probably a more relevant suggestion for the significantly increased mixing length and thus reduced mixing efficiency, is the observed jets, the rare, localized, and vigorous ejection of the scalar trapped near the wall, which protrudes into the peripheral region as well as the bulk. They are first found in the recent numerical calculations and then observed in the experiment reported. The jets definitely strongly reduce the mixing efficiency in particular in the peripheral region and so can lead to considerable increase of the mixing length. We hope that this result will initiate further numerical calculations of the mixing length. Finally, we analyze statistical properties of the mixing in the decay Batchelor regime by studying the power spectra, the decay exponents scaling, the structure functions of a tracer and moments of PDF of passive scalar increments, and the temporal and spatial correlation functions and find rather satisfactory agreement with theory.
Effects of toroidal rotation shear on toroidicity-induced Alfvén eigenmodes in the National Spherical Torus Experiment
Authors: Podestà M. , Bell R. E. , Fredrickson E. D. , Gorelenkov N. N. , LeBlanc B. P. , Heidbrink W. W. , Crocker N. A. , Kubota S. , Yuh H.
Published: December 2010

The effects of a sheared toroidal rotation on the dynamics of bursting toroidicity-induced Alfvén eigenmodes are investigated in neutral beam heated plasmas on the National Spherical Torus Experiment (NSTX) [M. Ono et al., Nucl. Fusion 40, 557 (2000)]. The modes have a global character, extending over most of the minor radius. A toroidal rotation shear layer is measured at the location of maximum drive for the modes. Contrary to results from other devices, no clear evidence of decorrelation of the modes by the sheared rotation is found. Instead, experiments with simultaneous neutral beam and radio-frequency auxiliary heating show a strong correlation between the dynamics of the modes and the instability drive. It is argued that kinetic effects involving changes in the mode drive and damping mechanisms other than rotation shear, such as continuum damping, are mostly responsible for the bursting dynamics of the modes on NSTX.
Frost formation and ice adhesion on superhydrophobic surfaces
Authors: Varanasi Kripa K. , Deng Tao , Smith J. David , Hsu Ming , Bhate Nitin
Published: December 2010

We study frost formation and its impact on icephobic properties of superhydrophobic surfaces. Using an environmental scanning electron microscope, we show that frost nucleation occurs indiscriminately on superhydrophobic textures without any particular spatial preference. Ice adhesion measurements on superhydrophobic surfaces susceptible to frost formation show increased adhesion over smooth surfaces with a strong linear trend with the total surface area. These studies indicate that frost formation significantly compromises the icephobic properties of superhydrophobic surfaces and poses serious limitations to the use of superhydrophobic surfaces as icephobic surface treatments for both on-ground and in-flight applications.
Dissection of SNARE-driven membrane fusion and neuroexocytosis by wedging small hydrophobic molecules into the SNARE zipper
Authors: Yang Yoosoo , Shin Jae Yoon , Oh Jung-Mi , Jung Chang Hwa , Hwang Yunha , Kim Sehyun , Kim Jun-Seob , Yoon Kee-Jung , Ryu Ji-Young , Shin Jaeil , Hwang Jae Sung , Yoon Tae-Young , Shin Yeon-Kyun , Kweon Dae-Hyuk
Published: December 2010

Neuronal SNARE proteins mediate neurotransmitter release at the synapse by facilitating the fusion of vesicles to the presynaptic plasma membrane. Cognate v-SNAREs and t-SNAREs from the vesicle and the plasma membrane, respectively, zip up and bring about the apposition of two membranes attached at the C-terminal ends. Here, we demonstrate that SNARE zippering can be modulated in the midways by wedging with small hydrophobic molecules. Myricetin, which intercalated into the hydrophobic inner core near the middle of the SNARE complex, stopped SNARE zippering in motion and accumulated the
trans
-complex, where the N-terminal region of v-SNARE VAMP2 is in the coiled coil with the frayed C-terminal region. Delphinidin and cyanidin inhibited N-terminal nucleation of SNARE zippering. Neuronal SNARE complex in PC12 cells showed the same pattern of vulnerability to small hydrophobic molecules. We propose that the half-zipped
trans
-SNARE complex is a crucial intermediate waiting for a calcium trigger that leads to fusion pore opening.
Non–cell-autonomous factor induces the transition from excitatory to inhibitory GABA signaling in retina independent of activity
Authors: Barkis William B. , Ford Kevin J. , Feller Marla B.
Published: December 2010

During development, the effect of activating GABA
A
receptors switches from depolarizing to hyperpolarizing. Several environmental factors have been implicated in the timing of this GABA switch, including neural activity, although these observations remain controversial. By using acutely isolated retinas from KO mice and pharmacological manipulations in retinal explants, we demonstrate that the timing of the GABA switch in retinal ganglion cells (RGCs) is unaffected by blockade of specific neurotransmitter receptors or global activity. In contrast to RGCs in the intact retina, purified RGCs remain depolarized by GABA, indicating that the GABA switch is not cell-autonomous. Indeed, purified RGCs cocultured with dissociated cells from the superior colliculus or cultured in media conditioned by superior collicular cells undergo a normal switch. Thus, a diffusible signal that acts independent of local circuit activity regulates the maturation of GABAergic inhibition in mouse RGCs.
Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome
Authors: Sarma Kavitha , Levasseur Pierre , Aristarkhov Alexander , Lee Jeannie T.
Published: December 2010

A large fraction of the mammalian genome is transcribed into long noncoding RNAs. The RNAs remain largely uncharacterized as the field awaits new technologies to aid functional analysis. Here, we describe a unique use of locked nucleic acids (LNAs) for studying nuclear long noncoding RNA, an RNA subclass that has been less amenable to traditional knockdown techniques. We target LNAs at Xist RNA and show displacement from the X chromosome with fast kinetics. Xist transcript stability is not affected. By targeting different Xist regions, we identify a localization domain and show that polycomb repressive complex 2 (PRC2) is displaced together with Xist. Thus, PRC2 depends on RNA for both initial targeting to and stable association with chromatin. H3K27-trimethyl marks and gene silencing remain stable. Time-course analysis of RNA relocalization suggests that Xist and PRC2 bind to different regions of the X at the same time but do not reach saturating levels immediately. Thus, LNAs provide a tool for studying an emerging class of regulatory RNA and offer a window of opportunity to target epigenetic modifications with possible therapeutic applications.
Herbaria are a major frontier for species discovery
Authors: Bebber Daniel P. , Carine Mark A. , Wood John R. I. , Wortley Alexandra H. , Harris David J. , Prance Ghillean T. , Davidse Gerrit , Paige Jay , Pennington Terry D. , Robson Norman K. B. , Scotland Robert W.
Published: December 2010

Despite the importance of species discovery, the processes including collecting, recognizing, and describing new species are poorly understood. Data are presented for flowering plants, measuring quantitatively the lag between the date a specimen of a new species was collected for the first time and when it was subsequently described and published. The data from our sample of new species published between 1970 and 2010 show that only 16% were described within five years of being collected for the first time. The description of the remaining 84% involved much older specimens, with nearly one-quarter of new species descriptions involving specimens >50 y old. Extrapolation of these results suggest that, of the estimated 70,000 species still to be described, more than half already have been collected and are stored in herbaria. Effort, funding, and research focus should, therefore, be directed as much to examining extant herbarium material as collecting new material in the field.
Impaired induction of DNA lesions during immunoglobulin class-switch recombination in humans influences end-joining repair
Authors: Kracker Sven , Imai Kohsuke , Gardès Pauline , Ochs Hans D. , Fischer Alain , Durandy Anne H.
Published: December 2010

Ig class-switch recombination (CSR) is a region-specific process that exchanges the constant Ig heavy-chain region and thus modifies an antibody's effector function. DNA lesions in switch (S) regions are induced by activation-induced cytidine deaminase (AID) and uracil-DNA glycosylase 2 (UNG2), subsequently processed to DNA breaks, and resolved by either the classical nonhomologous end-joining pathway or the alternative end-joining pathway (XRCC4/DNA ligase 4– and/or Ku70/Ku80-independent and prone to increased microhomology usage). We examined whether the induction of DNA lesions influences DNA end-joining during CSR by analyzing Sμ–Sα recombination junctions in various human Ig CSR defects of DNA lesion induction. We observed a progressive trend toward the usage of microhomology in Sμ–Sα recombination junctions from AID-heterozygous to AID–autosomal dominant to UNG2-deficient B lymphocytes. We thus hypothesize that impaired induction of DNA lesions in S regions during CSR leads to unusual end-processing of the DNA breaks, resulting in microhomology-mediated end-joining, which could be an indication for preferential processing by alternative end-joining rather than by classical nonhomologous end-joining.
The gametic central cell of
Arabidopsis
determines the lifespan of adjacent accessory cells
Authors: Kägi Christina , Baumann Nadine , Nielsen Nicola , Stierhof York-Dieter , Groß-Hardt Rita
Published: December 2010

Plant germ cells develop in specialized haploid structures, termed gametophytes. The female gametophyte patterns of flowering plants are diverse, with often unknown adaptive value. Here we present the
Arabidopsis fiona
mutant, which forms a female gametophyte that is structurally and functionally reminiscent of a phylogenetic distant female gametophyte. The respective changes include a modified reproductive behavior of one of the female germ cells (central cell) and an extended lifespan of three adjacent accessory cells (antipodals).
FIONA
encodes the cysteinyl t-RNA synthetase SYCO ARATH (SYCO), which is expressed and required in the central cell but not in the antipodals, suggesting that antipodal lifespan is controlled by the adjacent gamete. SYCO localizes to the mitochondria, and ultrastructural analysis of mutant central cells revealed that the protein is necessary for mitochondrial cristae integrity. Furthermore, a dominant ATP/ADP translocator caused mitochondrial cristae degeneration and extended antipodal lifespan when expressed in the central cell of wild-type plants. Notably, this construct did not affect antipodal lifespan when expressed in antipodals. Our results thus identify an unexpected noncell autonomous role for mitochondria in the regulation of cellular lifespan and provide a basis for the coordinated development of gametic and nongametic cells.
Gravity-induced PIN transcytosis for polarization of auxin fluxes in gravity-sensing root cells
Authors: Kleine-Vehn Jürgen , Ding Zhaojun , Jones Angharad R. , Tasaka Masao , Morita Miyo T. , Friml Jiří
Published: December 2010

Auxin is an essential plant-specific regulator of patterning processes that also controls directional growth of roots and shoots. In response to gravity stimulation, the PIN3 auxin transporter polarizes to the bottom side of gravity-sensing root cells, presumably redirecting the auxin flux toward the lower side of the root and triggering gravitropic bending. By combining live-cell imaging techniques with pharmacological and genetic approaches, we demonstrate that PIN3 polarization does not require secretion of de novo synthesized proteins or protein degradation, but instead involves rapid, transient stimulation of PIN endocytosis, presumably via a clathrin-dependent pathway. Moreover, gravity-induced PIN3 polarization requires the activity of the guanine nucleotide exchange factors for ARF GTPases (ARF-GEF) GNOM-dependent polar-targeting pathways and might involve endosome-based PIN3 translocation from one cell side to another. Our data suggest that gravity perception acts at several instances of PIN3 trafficking, ultimately leading to the polarization of PIN3, which presumably aligns auxin fluxes with gravity vector and mediates downstream root gravitropic response.
Discovery of a minimal form of RNase P in
Pyrobaculum
Authors: Lai Lien B. , Chan Patricia P. , Cozen Aaron E. , Bernick David L. , Brown James W. , Gopalan Venkat , Lowe Todd M.
Published: December 2010

RNase P RNA is an ancient, nearly universal feature of life. As part of the ribonucleoprotein RNase P complex, the RNA component catalyzes essential removal of 5′ leaders in pre-tRNAs. In 2004, Li and Altman computationally identified the RNase P RNA gene in all but three sequenced microbes:
Nanoarchaeum equitans
,
Pyrobaculum aerophilum
, and
Aquifex aeolicus
(all hyperthermophiles) [Li Y, Altman S (2004)
RNA
10:1533–1540]. A recent study concluded that
N. equitans
does not have or require RNase P activity because it lacks 5′ tRNA leaders. The “missing” RNase P RNAs in the other two species is perplexing given evidence or predictions that tRNAs are trimmed in both, prompting speculation that they may have developed novel alternatives to 5′ pre-tRNA processing. Using comparative genomics and improved computational methods, we have now identified a radically minimized form of the RNase P RNA in five
Pyrobaculum
species and the related crenarchaea
Caldivirga maquilingensis
and
Vulcanisaeta distributa
, all retaining a conventional catalytic domain, but lacking a recognizable specificity domain. We confirmed 5′ tRNA processing activity by high-throughput RNA sequencing and in vitro biochemical assays. The
Pyrobaculum
and
Caldivirga
RNase P RNAs are the smallest naturally occurring form yet discovered to function as
trans
-acting precursor tRNA-processing ribozymes. Loss of the specificity domain in these RNAs suggests altered substrate specificity and could be a useful model for finding other potential roles of RNase P. This study illustrates an effective combination of next-generation RNA sequencing, computational genomics, and biochemistry to identify a divergent, formerly undetectable variant of an essential noncoding RNA gene.
Genetic immunization in the lung induces potent local and systemic immune responses
Authors: Song Kaimei , Bolton Diane L. , Wei Chih-Jen , Wilson Robert L. , Camp Jeremy V. , Bao Saran , Mattapallil Joseph J. , Herzenberg Leonore A. , Herzenberg Leonard A. , Andrews Charla A. , Sadoff Jerald C. , Goudsmit Jaap , Pau Maria Grazia , Seder Robert A. , Kozlowski Pamela A. , Nabel Gary J. , Roederer Mario , Rao Srinivas S.
Published: December 2010

Successful vaccination against respiratory infections requires elicitation of high levels of potent and durable humoral and cellular responses in the lower airways. To accomplish this goal, we used a fine aerosol that targets the entire lung surface through normal respiration to deliver replication-incompetent recombinant adenoviral vectors expressing gene products from several infectious pathogens. We show that this regimen induced remarkably high and stable lung T-cell responses in nonhuman primates and that it also generated systemic and respiratory tract humoral responses of both IgA and IgG isotypes. Moreover, strong immunogenicity was achieved even in animals with preexisting antiadenoviral immunity, overcoming a critical hurdle to the use of these vectors in humans, who commonly are immune to adenoviruses. The immunogenicity profile elicited with this regimen, which is distinct from either intramuscular or intranasal delivery, has highly desirable properties for protection against respiratory pathogens. We show that it can be used repeatedly to generate mucosal humoral, CD4, and CD8 T-cell responses and as such may be applicable to other mucosally transmitted pathogens such as HIV. Indeed, in a lethal challenge model, we show that aerosolized recombinant adenoviral immunization completely protects ferrets against H5N1 highly pathogenic avian influenza virus. Thus, genetic immunization in the lung offers a powerful platform approach to generating protective immune responses against respiratory pathogens.
All-DNA finite-state automata with finite memory
Authors: Wang Zhen-Gang , Elbaz Johann , Remacle F. , Levine R. D. , Willner Itamar
Published: December 2010

Biomolecular logic devices can be applied for sensing and nano-medicine. We built three DNA tweezers that are activated by the inputs H
+
/OH
-
;

; nucleic acid linker/complementary antilinker to yield a 16-states finite-state automaton. The outputs of the automata are the configuration of the respective tweezers (opened or closed) determined by observing fluorescence from a fluorophore/quencher pair at the end of the arms of the tweezers. The system exhibits a memory because each current state and output depend not only on the source configuration but also on past states and inputs.
Calcineurin increases glucose activation of ERK1/2 by reversing negative feedback
Authors: Duan Lingling , Cobb Melanie H.
Published: December 2010

In pancreatic β cells, ERK1 and ERK2 participate in nutrient sensing, and their activities rise and fall as a function of glucose concentration over the physiologic range. Glucose metabolism triggers calcium influx and release of calcium from intracellular stores to activate ERK1/2. Calcium influx also activates the calcium-dependent phosphatase calcineurin, which is required for maximal ERK1/2 activation by glucose. Calcineurin controls insulin gene expression by ERK1/2-dependent and -independent mechanisms. Here, we show that, in β cells, glucose activates the ERK1/2 cascade primarily through B-Raf. Glucose activation of B-Raf, like that of ERK1/2, is calcineurin-sensitive. Calcineurin binds to B-Raf in both unstimulated and stimulated cells. We show that B-Raf is a calcineurin substrate; among calcineurin target residues on B-Raf is T401, a site of negative feedback phosphorylation by ERK1/2. Blocking calcineurin activity in β cells prevents dephosphorylation of B-Raf T401 and decreases B-Raf and ERK1/2 activities. We conclude that the major calcineurin-dependent event in glucose sensing by ERK1/2 is the activation of B-Raf.
Food Intake Increases Resting Muscle Oxygen Consumption As Measured By Near‐infrared Spectroscopy
Authors: Ueda Chihoko , Hamaoka Takafumi , Murase Norio , Sako Takayuki , Murakami Motohide , Kime Ryotaro , Homma Toshiyuki , Nagasawa Takeshi , Samejima Mitsuhiro , Ichimura Shiro , Moriguchi Tetsushi , Katsumura Toshihito
Published: December 2010

The purpose of this study was to quantitatively examine the changes in muscle oxygen consumption (VO2mus) after food intake as measured by near‐infrared continuous wave spectroscopy (NIRcws). Six healthy male subjects were given a meal with a calculated total energy content of 10 kcal/kg body. VO2mus was measured from 15 min to 150 min after they finished eating. VO2mus in the finger flexor muscles was estimated by the rate of deoxygenation during arterial occlusion using NIRcws. The absolute value of VO2mus was calculated using each subject's resting metabolic rate measured by 31Phosphorus‐magnetic resonance spectroscopy (31P‐MRS). Deep tissue temperature (TD) was also monitored in the forearm same area. The control experiment followed the same protocol but without meal. There was a significant increase in VO2mus: pre‐meal value was 1.47 ± 0.17 μM O2/s, post‐meal peak value (post 120 min) was 2.31 ± 0.38 μM O2/s (p <. 05 vs. pre). In contrast, the control experiment did not show any increase. There was no significant difference in TD between the two experiments. The results indicate that food intake induced a significant increase in VO2mus. NIRcws can be used to provide specific information about changes in localized muscle metabolism elicited by food intake.
AUTOMATIC DETERMINATION OF STELLAR PARAMETERS VIA ASTEROSEISMOLOGY OF STOCHASTICALLY OSCILLATING STARS: COMPARISON WITH DIRECT MEASUREMENTS
Authors: Quirion Pierre-Olivier , Christensen-Dalsgaard Jørgen , Arentoft Torben
Published: December 2010

Space-based projects are providing a wealth of high-quality asteroseismic data, including frequencies for a large number of stars showing solar-like oscillations. These data open the prospect for precise determinations of key stellar parameters, of particular value to the study of extra-solar planetary systems. Given the quantity of the available and expected data, it is important to develop efficient and reliable techniques for analyzing them, including the determination of stellar parameters from the observed frequencies. Here we present the SEEK package developed for the analysis of asteroseismic data from the Kepler mission. A central goal of the package is to obtain a fast and automatic determination of the stellar radius and other parameters in a form that is statistically well defined. The algorithms are tested by comparing the results of the analysis with independent measurements of stellar radius and mass for a sample of well-observed stars. We conclude that the SEEK package fixes stellar parameters with accuracy and precision.
RNA–RNA interaction prediction based on multiple sequence alignments
Authors: Li Andrew X. , Marz Manja , Qin Jing , Reidys Christian M.
Published: December 2010

Motivation: Many computerized methods for RNA–RNA interaction structure prediction have been developed. Recently, O(N6) time and O(N4) space dynamic programming algorithms have become available that compute the partition function of RNA–RNA interaction complexes. However, few of these methods incorporate the knowledge concerning related sequences, thus relevant evolutionary information is often neglected from the structure determination. Therefore, it is of considerable practical interest to introduce a method taking into consideration both: thermodynamic stability as well as sequence/structure covariation.

Results: We present the a priori folding algorithm ripalign, whose input consists of two (given) multiple sequence alignments (MSA). ripalign outputs (i) the partition function, (ii) base pairing probabilities, (iii) hybrid probabilities and (iv) a set of Boltzmann-sampled suboptimal structures consisting of canonical joint structures that are compatible to the alignments. Compared to the single sequence-pair folding algorithm rip, ripalign requires negligible additional memory resource but offers much better sensitivity and specificity, once alignments of suitable quality are given. ripalign additionally allows to incorporate structure constraints as input parameters.

Availability: The algorithm described here is implemented in C as part of the rip package. The supplemental material, source code and input/output files can freely be downloaded from http://www.combinatorics.cn/cbpc/ripalign.html.

Contact:  duck@santafe.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Algorithms for sorting unsigned linear genomes by the DCJ operations
Authors: Jiang Haitao , Zhu Binhai , Zhu Daming
Published: December 2010

Motivation: The double cut and join operation (abbreviated as DCJ) has been extensively used for genomic rearrangement. Although the DCJ distance between signed genomes with both linear and circular (uni- and multi-) chromosomes is well studied, the only known result for the NP-complete unsigned DCJ distance problem is an approximation algorithm for unsigned linear unichromosomal genomes. In this article, we study the problem of computing the DCJ distance on two unsigned linear multichromosomal genomes (abbreviated as UDCJ).

Results: We devise a 1.5-approximation algorithm for UDCJ by exploiting the distance formula for signed genomes. In addition, we show that UDCJ admits a weak kernel of size 2k and hence an FPT algorithm running in O(22kn) time.

Contact:  bhz@cs.montana.edu
Effects of an Industrial Milling Process on Change of Headspace Volatiles in Yihchuan Aromatic Rice
Authors: Liu Tai‐Ti , Yang Tsung‐Shi
Published: December 2010

Headspace volatiles of Yihchuan aromatic rice, a japonica rice cultivar, were extracted by a solid‐phase microextraction (SPME) method and analyzed by GC and GC‐MS. Effects of fiber types and an industrial milling process on the change of headspace volatiles were studied. Of the fiber types, divinylbenzene/carboxen/polydimethylsiloxane (DVB/CAR/PDMS), polydimethylsiloxane/divinylbenzene (PDMS/DVB), and carboxen/polydimethylsiloxane (CAR/PDMS) were suggested for use in the analysis headspace volatiles in terms of absorption or adsorption ability. Regarding the milling effect, the amount of total headspace volatiles from brown rice to white rice decreased ≈30%, and that of aldehydes and alcohols, the two largest groups of volatiles, decreased ≈20 and 15%, respectively. Comparatively, rice bran contained higher amounts of total headspace volatiles than milled rice grains.
Co‐Occurring Alcohol and Cocaine Dependence: Recent Findings From Clinical and Field Studies
Authors: Flannery B. A. , Morgenstern Jon , McKay James , Wechsberg Wendee M. , Litten R. Z.
Published: December 2010

This article represents the proceedings of a symposium held at the 2003 annual meeting of the Research Society on Alcoholism in Ft. Lauderdale, FL. The organizer and chair was Barbara A. Flannery, and the discussant was Raye Z. Litten. The presentations were (1) Examining treatment trajectories of alcohol and cocaine dependent patients, by Jon Morgenstern; (2) Outcomes of alcoholics with and without cocaine dependence in a continuing care study, by James R. McKay; (3) Characteristics of non–treatment seeking cocaine and alcohol dependent African Americans, by Barbara A. Flannery; and (4) Cocaine and alcohol use among sex workers in South Africa, by Wendee M. Wechsberg.
Study of Energy Metabolism of Skeletal Muscles in Alcoholic Liver Disease—Expired Gas Analysis During Exercise
Authors: Shiraishi Koichi , Motegi Shigeyuki , Nagaoka Reiko , Ogasawara Fusao , Saito Tetsuro , Watanabe Mitsuyuki , Matsuzaki Shohei
Published: December 2010

Abstract: Background: The effects of chronic alcohol intake on skeletal muscle are clinically observed as muscle cramps with decrease in the amount of muscle. It was clarified by expired gas analysis that acute alcohol load affects disturbed energy metabolism of skeletal muscle. We studied abnormal energy metabolism of skeletal muscles in alcoholic liver diseases using expired gas analysis.

Methods: Subjects of the study were five inpatients with alcoholic liver disease (fatty liver: one case, hepatic fibrosis: one case, liver cirrhosis: three case). Expired gas analysis during exercise was performed using AEROMONITOR. Minute ventilation, oxygen consumption and carbon dioxide output were monitored, and anaerobic threshold (AT) and respiratory compensation point (RCP) were calculated.

Results: The anaerobic threshold, which is the limit of the aerobic exercise, was significantly reduced in patients with alcoholic disease (p < 0.01). The respiratory compensation point, which is the limit of the metabolic compensation of intracellular lactic acidosis, was decreased (p < 0.01).

Conclusions: The results of expired gas analysis during exercise indicate that the aerobic energy metabolism of skeletal muscle had been disturbed in alcoholic liver disease. The reduced RCP suggests that the lactate metabolism in skeletal muscle is also disturbed in alcoholic liver disease. Expired gas analysis during exercise allows determination of the amount of exercise required to treat liver diseases through analysis of AT.
Relationship Between Ethanol Consumption Level and Lifestyle Status: Excessive Ethanol Consumption Can Account for the Prevalence of Lifestyle‐Related Diseases
Authors: Yokoyama Hirokazu
Published: December 2010

Abstract:Background:Diseases caused by unhealthful lifestyles, namely lifestyle‐related diseases demands prompt solutions including preventive measures and effective treatment, especially in the developed countries. To that effect, clear understandings of such syndromes are required. Our recent observations have indicated that insulin resistance could, at least in part, account for the pathogenesis of lifestyle‐related diseases. The aim of this study was to clarify whether excessive ethanol consumption could also be another cause of such diseases.

Method:Lifestyle status was assessed based on Breslow's questionnaires of lifestyle index in 519 Japanese males aged 30 to 65 years. Averaged ethanol consumption level was determined by additional questionnaires and insulin resistance level was estimated by homeostasis model assessment.

Results:Ethanol consumption level was inversely associated with the total score on Breslow's lifestyle index. Improper drinking manner was associated with improper habit of smoking and proper habit of eating snacks among six lifestyle factors induced in Breslow's index.

Conclusion:Subjects with more unhealthful lifestyles consumed greater amount of ethanol, suggesting that excessive ethanol consumption could be one of causes of lifestyle‐related diseases. In addition to insulin resistance syndrome, alcohol‐related diseases should be cared to address the issues of lifestyle‐related diseases.
Effect of Bromhexine Hydrochloride Therapy for Alcoholic Chronic Pancreatitis
Authors: Tsujimoto Tatsuhiro , Tsuruzono Takuya , Hoppo Kazushige , Matsumura Yoshinobu , Yamao Jyunichi , Fukui Hiroshi
Published: December 2010

Abstract: Background: Abstinence is a prerequisite for the treatment of alcoholic chronic pancreatitis, but there are patients who have repeated attacks because of their inability to abstain and the consequent congestive effects of the continued alcohol intake on pancreatic juice. Bromhexine hydrochloride, a bronchial mucolytic, has an affinity for acinar cells and causes them to secrete pancreatic juice of low viscosity.

Methods: Twelve patients with alcoholic chronic pancreatitis, who were unable to abstain from drinking, were administered bromhexine hydrochloride for 6 months to assess its therapeutic efficacy.

Results: Of 12 patients administered bromhexine, 8 (67%) reported symptomatic improvement, and all patients showed improvement in the levels of pancreatic enzymes. Pancreatic exocrine function also tended to improve, but no improvement of pancreatic endocrine function was detected. Although none of the pancreatic stones present in some patients disappeared, a protein plug present in one patient disappeared, accompanied by improvement in the irregular outline of the lumen of the main pancreatic duct.

Conclusion: Bromhexine hydrochloride may be a new for the morbidity of chronic pancreatitis, in which there is increased viscosity of the pancreatic juice and formation of a protein plug.
Enhancing collaborative learning through dynamic forms of support: the impact of an adaptive domain‐specific support strategy
Authors: Karakostas A. , Demetriadis S.
Published: December 2010

Research on computer‐supported collaborative learning (CSCL) has strongly emphasized the value of providing student support of either fixed (e.g. collaboration scripts) or dynamic form (e.g. adaptive supportive interventions). Currently, however, there is not sufficient evidence corroborating the potential of adaptive support methods to improve domain‐knowledge acquisition in collaborative activities. Furthermore, available adaptive CSCL systems are difficult to integrate in everyday instruction because most of them are research prototypes. This study investigates the capacity of an adaptive support strategy [implemented in the open source Learning Activity Management System (LAMS) environment] to further improve learning outcomes in the context of a scripted collaborative activity. Thirty‐six students collaborated remotely in dyads on a task structured by a collaboration script. Control group dyads worked without any additional support. Treatment dyads were supported by a domain‐specific adaptive intervention in the form of reminding prompts. Treatment students outperformed those in the control group in domain knowledge acquisition. Overall, this study provides evidence that (1) adaptive forms of domain‐specific support can substantially improve learning in the context of a scripted collaborative activity; and (2) implementing simple forms of adaptive support is feasible and can be easily implemented by instructors in a freely available collaboration support system (such as LAMS).
Suppressors of DnaAATP imposed overinitiation in Escherichia coli
Authors: Charbon Godefroid , Riber Leise , Cohen Malene , Skovgaard Ole , Fujimitsu Kazuyuki , Katayama Tsutomu , Løbner‐Olesen Anders
Published: December 2010

Chromosome replication in Escherichia coli is limited by the supply of DnaA associated with ATP. Cells deficient in RIDA (Regulatory Inactivation of DnaA) due to a deletion of the hda gene accumulate suppressor mutations (hsm) to counteract the overinitiation caused by an elevated DnaAATP level. Eight spontaneous hda suppressor mutations were identified by whole‐genome sequencing, and three of these were analysed further. Two mutations (hsm‐2 and hsm‐4) mapped in the dnaA gene and led to a reduced ability to initiate replication from oriC. One mutation (hsm‐1) mapped to the seqA promoter and increased the SeqA protein level in the cell. hsm‐1 cells had prolonged origin sequestration, reduced DnaA protein level and reduced DnaA‐Reactivating Sequence (DARS)‐mediated rejuvenation of DnaAADP to DnaAATP, all of which could contribute to the suppression of RIDA deficiency. Despite of these defects hsm‐1 cells were quite similar to wild type with respect to cell cycle parameters. We speculate that since SeqA binding sites might overlap with DnaA binding sites spread throughout the chromosome, excess SeqA could interfere with DnaA titration and thereby increase free DnaA level. Thus, in spite of reduction in total DnaA, the amount of DnaA molecules available for initiation may not be reduced.
Prevalence of nucleic acid sequences specific for human parvoviruses, hepatitis A and hepatitis E viruses in coagulation factor concentrates
Authors: Modrow S. , Wenzel J. J. , Schimanski S. , Schwarzbeck J. , Rothe U. , Oldenburg J. , Jilg W. , Eis‐Hübinger A. M.
Published: December 2010

Background and Objectives  Due to their high resistance to inactivation procedures, nonenveloped viruses such as parvovirus B19, human bocavirus (HBoV), human parvovirus 4 (PARV4), hepatitis A (HAV) and hepatitis E virus (HEV) pose a particular threat to blood products. Virus transmission to patients treated with blood products presents an additional burden to disease. We determined the frequency and the amount of nucleic acid specific for nonenveloped viruses in recently manufactured preparations of commercial coagulation factor concentrates.

Materials and Methods  At least three different batches of each of 13 different plasma‐derived and recombinant coagulation factor products were tested for the presence and the amount of nucleic acid for parvovirus B19, HBoV, human parvovirus 4, hepatitis A virus and HEV by using quantitative polymerase chain reaction.

Results  Whereas none of the recombinant products tested positive for any of these viruses, parvovirus B19 DNA with amounts ranging between 2 × 101 and 1.3 × 103 genome equivalents/ml was detected in five plasma‐derived products. In addition to parvovirus B19 genotype 1, genotypes 2 and 3 were observed in two batches of a factor VIII/von‐Willebrand factor product. In two products (one factor VIII concentrate and one activated prothrombin complex concentrate), a combination of both genotypes 1 and 2 of parvovirus B19 was detected.

Conclusion  The data show that nucleic acids from several relevant nonenveloped viruses are not found at detectable levels in coagulation factor concentrates. In some cases, parvovirus B19 DNA was detectable at low levels. Testing of the plasma pools for the full range of parvovirus genotypes is advocated for ensuring product safety.